debian/0000755000000000000000000000000012014517702007165 5ustar debian/rules0000755000000000000000000000663311767637712010277 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 JAVA_HOME := $(firstword $(wildcard /usr/lib/jvm/java-7-openjdk-$(DEB_HOST_ARCH))) PATH := ${JAVA_HOME}/bin:${PATH} JARS := commons-logging.jar commons-pool.jar gnu-getopt.jar log4j-1.2.jar mysql-connector-java.jar xml-resolver.jar xercesImpl.jar xmlParserAPIs.jar xmlrpc-common.jar build: build-arch build-indep build-arch: build-arch-stamp build-indep: build-indep-stamp build-arch-stamp: dh_testdir # during build we need symlinks to system provided jars (cd share/pegasus/java && \ rm -f *.jar && \ for JAR in $(JARS); do \ ln -s /usr/share/java/$$JAR ; \ done \ ) ant dist rm -f dist/*.tar.gz mv dist/pegasus-* dist/pegasus touch build-arch-stamp build-indep-stamp: dh_testdir # during build we need symlinks to system provided jars (cd share/pegasus/java && \ rm -f *.jar && \ for JAR in $(JARS); do \ ln -s /usr/share/java/$$JAR ; \ done \ ) # build documentation to get updated PDFs ant doc rm -f dist/*.tar.gz mv dist/pegasus-* dist/doc touch build-indep-stamp # Build architecture-independent files here. binary-indep: build-indep dh_testdir dh_testroot dh_prep dh_installdirs # move documentation to the -doc package mkdir -p debian/pegasus-wms-doc/usr/share/doc/pegasus-wms-doc cp doc/*.pdf debian/pegasus-wms-doc/usr/share/doc/pegasus-wms-doc/ cp -r doc/schemas debian/pegasus-wms-doc/usr/share/doc/pegasus-wms-doc/ cp -r dist/doc/share/doc/pegasus/html debian/pegasus-wms-doc/usr/share/doc/pegasus-wms-doc/ rm -f debian/pegasus-wms-doc/usr/share/doc/pegasus-wms-doc/html/*.php dh_installchangelogs dh_installdocs dh_compress dh_fixperms dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -i # Build architecture-dependent files here. binary-arch: build-arch dh_testdir dh_testroot dh_prep dh_installdirs # /etc/pegasus mkdir -p debian/pegasus-wms/etc/pegasus cp -a dist/pegasus/etc/* debian/pegasus-wms/etc/pegasus/ # /usr/bin mkdir -p debian/pegasus-wms/usr cp -a dist/pegasus/bin debian/pegasus-wms/usr/ strip debian/pegasus-wms/usr/bin/pegasus-cluster strip debian/pegasus-wms/usr/bin/pegasus-invoke strip debian/pegasus-wms/usr/bin/pegasus-keg strip debian/pegasus-wms/usr/bin/pegasus-kickstart # /usr/share/ mkdir -p debian/pegasus-wms/usr cp -a dist/pegasus/share debian/pegasus-wms/usr/ # documentation is in the -doc package rm -rf debian/pegasus-wms/usr/share/doc/pegasus # /usr/lib mkdir -p debian/pegasus-wms/usr cp -a dist/pegasus/lib debian/pegasus-wms/usr/ # remove stuff we don't need rm -f debian/pegasus-wms/etc/pegasus/stampede* rm -rf debian/pegasus-wms/usr/lib/pegasus/externals/python/boto/tests # replace jar symlinks with relative symlinks (cd debian/pegasus-wms/usr/share/pegasus/java/ && \ for JAR in $(JARS); do \ rm $$JAR && \ ln -s ../../java/$$JAR ; \ done \ ) dh_installchangelogs dh_installdocs dh_installman dh_compress dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb -a binary: binary-indep binary-arch clean: dh_testdir dh_testroot rm -f build-arch-stamp build-indep-stamp ant clean rm -f src/externals/._boto* rm -f lib/pegasus/python/Pegasus/DAX3.pyc rm -f lib/pegasus/perl/*.tmp rm -rf dist dh_clean %: echo "Unknown make target: $@" exit 1 .PHONY: build build-arch build-indep binary-indep binary-arch binary clean debian/docs0000644000000000000000000000003011757531731010044 0ustar LicenseBlurb.txt README debian/patches/0000755000000000000000000000000012014517663010622 5ustar debian/patches/dep-removal0000644000000000000000000144331111757544422012775 0ustar Index: pegasus-wms_4.0.1+dfsg/etc/advanced.properties =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/etc/advanced.properties 2012-05-24 16:47:52.064156782 -0700 +++ pegasus-wms_4.0.1+dfsg/etc/advanced.properties 2012-05-24 16:47:54.072166747 -0700 @@ -596,12 +596,10 @@ # System : Pegasus # Since : 2.0 # Type : enumeration -# Value[0] : RLS -# Value[1] : LRC -# Value[2] : JDBCRC -# Value[3] : File -# Value[4] : MRC -# Default : RLS +# Value[0] : JDBCRC +# Value[1] : File +# Value[2] : MRC +# Default : File # # Pegasus queries a Replica Catalog to discover the physical filenames # (PFN) for input files specified in the DAX. Pegasus can interface @@ -609,29 +607,6 @@ # which type of Replica Catalog to use during the planning process. # # -# RLS -# RLS (Replica Location Service) is a distributed replica -# catalog, which ships with GT4. There is an index service called -# Replica Location Index (RLI) to which 1 or more Local Replica -# Catalog (LRC) report. Each LRC can contain all or a subset of -# mappings. In this mode, Pegasus queries the central RLI to -# discover in which LRC's the mappings for a LFN reside. It then -# queries the individual LRC's for the PFN's. -# To use RLS, the user additionally needs to set the property -# pegasus.catalog.replica.url to specify the URL for the RLI to -# query. -# Details about RLS can be found at -# http://www.globus.org/toolkit/data/rls/ -# -# LRC -# If the user does not want to query the RLI, but directly a -# single Local Replica Catalog. -# To use LRC, the user additionally needs to set the property -# pegasus.catalog.replica.url to specify the URL for the LRC to -# query. -# Details about RLS can be found at -# http://www.globus.org/toolkit/data/rls/ -# # JDBCRC # In this mode, Pegasus queries a SQL based replica catalog that # is accessed via JDBC. The sql schema's for this catalog can be Index: pegasus-wms_4.0.1+dfsg/etc/basic.properties =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/etc/basic.properties 2012-05-24 16:47:52.064156782 -0700 +++ pegasus-wms_4.0.1+dfsg/etc/basic.properties 2012-05-24 16:47:54.072166747 -0700 @@ -93,12 +93,10 @@ # System : Pegasus # Since : 2.0 # Type : enumeration -# Value[0] : RLS -# Value[1] : LRC -# Value[2] : JDBCRC -# Value[3] : File -# Value[4] : MRC -# Default : RLS +# Value[0] : JDBCRC +# Value[1] : File +# Value[2] : MRC +# Default : File # # Pegasus queries a Replica Catalog to discover the physical filenames # (PFN) for input files specified in the DAX. Pegasus can interface @@ -107,35 +105,6 @@ # # # -# RLS -# -# RLS (Replica Location Service) is a distributed replica -# catalog, which ships with GT4. There is an index service called -# Replica Location Index (RLI) to which 1 or more Local Replica -# Catalog (LRC) report. Each LRC can contain all or a subset of -# mappings. In this mode, Pegasus queries the central RLI to -# discover in which LRC's the mappings for a LFN reside. It then -# queries the individual LRC's for the PFN's. -# To use RLS, the user additionally needs to set the property -# pegasus.catalog.replica.url to specify the URL for the RLI to -# query. -# Details about RLS can be found at -# http://www.globus.org/toolkit/data/rls/ -# -# -# -# LRC -# -# If the user does not want to query the RLI, but directly a -# single Local Replica Catalog. -# To use LRC, the user additionally needs to set the property -# pegasus.catalog.replica.url to specify the URL for the LRC to -# query. -# Details about RLS can be found at -# http://www.globus.org/toolkit/data/rls/ -# -# -# # JDBCRC # # In this mode, Pegasus queries a SQL based replica catalog that Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/catalog/replica/impl/LRC.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/catalog/replica/impl/LRC.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,2922 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package edu.isi.pegasus.planner.catalog.replica.impl; - -import edu.isi.pegasus.planner.catalog.replica.*; -import edu.isi.pegasus.common.logging.LogManagerFactory; -import edu.isi.pegasus.common.logging.LogManager; - -import edu.isi.pegasus.planner.catalog.ReplicaCatalog; -import edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry; -import edu.isi.pegasus.planner.catalog.CatalogException; - -import edu.isi.pegasus.common.util.CommonProperties; - -import org.globus.replica.rls.RLSClient; -import org.globus.replica.rls.RLSException; -import org.globus.replica.rls.RLSAttribute; -import org.globus.replica.rls.RLSAttributeObject; -import org.globus.replica.rls.RLSString2Bulk; -import org.globus.replica.rls.RLSString2; -import org.globus.replica.rls.RLSOffsetLimit; - -import java.util.Collection; -import java.util.Collections; -import java.util.Comparator; -import java.util.Map; -import java.util.HashMap; -import java.util.Set; -import java.util.HashSet; -import java.util.Properties; -import java.util.List; -import java.util.ArrayList; -import java.util.Iterator; - -/** - * This class implements the VDS replica catalog interface on top of the - * LRC. This class implementation ends up talking to a single LRC. - * It is accessed internally from the RLI implementation. - * RLS Exceptions are being caught here. They probably should be thrown - * and caught at the calling class (i.e the RLI implementation). - * - * @author Karan Vahi - * @author Gaurang Mehta - * - * @version $Revision: 2585 $ - */ -public class LRC implements ReplicaCatalog { - - /** - * The number of entries searched in each bulk query to RLS. - */ - public static final int RLS_BULK_QUERY_SIZE = 1000; - - /** - * The default timeout in seconds to be used while querying the LRC. - */ - public static final String DEFAULT_LRC_TIMEOUT = "30"; - - /** - * The key that is used to get hold of the timeout value from the properties - * object. - */ - public static final String RLS_TIMEOUT_KEY = "rls.timeout"; - - - /** - * The key that is used to get hold of the timeout value from the properties - * object. - */ - public static final String LRC_TIMEOUT_KEY = "lrc.timeout"; - - /** - * The properties key that allow us to associate a site with a LRC URL, - * and hence providing a value for the SITE_ATTRIBUTE. - * User will specify lrc.site.isi_viz rls://isi.edu to associate - * site isi_viz with rls://isi.edu - */ - public static final String LRC_SITE_TO_LRC_URL_KEY = "lrc.site."; - - /** - * The attribute in RLS that maps to a site handle. - */ - public static final String SITE_ATTRIBUTE = ReplicaCatalogEntry.RESOURCE_HANDLE; - - /** - * The undefined pool attribute value. The pool attribute is assigned this - * value if the pfn queried does not have a pool associated with it. - */ - public static final String UNDEFINED_SITE = "UNDEFINED_POOL"; - - /** - * The key that is used to get hold of the url from the properties object. - */ - public static final String URL_KEY = "url"; - - /** - * The key that if set, specifies the proxy to be picked up while connecting - * to the RLS. - */ - public static final String PROXY_KEY = "proxy"; - - /** - * The error message for not connected to LRC. - */ - public static final String LRC_NOT_CONNECTED_MSG = "Not connected to LRC "; - - - /** - * The handle to the logging object. Should be log4j soon. - */ - private LogManager mLogger; - - /** - * The string holding the message that is logged in the logger. - */ - private String mLogMsg; - - /** - * The URL pointing to the LRC to which this instance of class talks to. - */ - private String mLRCURL; - - /** - * The handle to the client that allows access to the RLS running at the - * url specified while connecting. - */ - private RLSClient mRLS; - - /** - * The handle to the client that allows access to the LRC running at the - * url specified while connecting. - */ - private RLSClient.LRC mLRC; - - /** - * The batch size while querying the LRC in the bulk mode. - */ - private int mBatchSize; - - /** - * The timeout in seconds while querying to the LRC. - */ - private int mTimeout; - - /** - * The default site attribute to be associated with the results. - */ - private String mDefaultSiteAttribute; - - /** - * The default constructor, that creates an object which is not linked with - * any RLS. Use the connect method to connect to the LRC and use it. - * - * @see #connect(Properties). - */ - public LRC() { - mRLS = null; - mLRC = null; - mLogger = LogManagerFactory.loadSingletonInstance(); - mBatchSize = LRC.RLS_BULK_QUERY_SIZE; - mTimeout = Integer.parseInt(LRC.DEFAULT_LRC_TIMEOUT); - } - - /** - * Establishes a connection to the LRC. - * - * @param props contains all necessary data to establish the link. - * @return true if connected now, or false to indicate a failure. - */ - public boolean connect(Properties props) { - boolean con = false; - Object obj = props.get(URL_KEY); - mLRCURL = (obj == null) ? null : (String) obj; - - if (mLRCURL == null) { - //nothing to connect to. - log("The LRC url is not specified", - LogManager.ERROR_MESSAGE_LEVEL); - return con; - } - - //try to see if a proxy cert has been specified or not - String proxy = props.getProperty(PROXY_KEY); - - //determine timeout - mTimeout = getTimeout(props); - - //set the batch size for querie - setBatchSize(props); - - //stripe out the properties that assoicate site handle to lrc url - Properties site2LRC = CommonProperties.matchingSubset( props, LRC.LRC_SITE_TO_LRC_URL_KEY, false); - //traverse through the properties to figure out - //the default site attribute for the URL - for( Iterator it = site2LRC.entrySet().iterator(); it.hasNext(); ){ - Map.Entry entry = (Map.Entry)it.next(); - if( entry.getValue().equalsIgnoreCase( mLRCURL ) ){ - mDefaultSiteAttribute = entry.getKey(); - } - } - - if( mDefaultSiteAttribute != null ){ - mLogger.log( "Default Site attribute is " + mDefaultSiteAttribute, - LogManager.DEBUG_MESSAGE_LEVEL ); - } - - return connect(mLRCURL, proxy); - } - - /** - * Establishes a connection to the LRC, picking up the proxy from the default - * location usually /tmp/ directory. - * - * @param url the url to lrc to connect to. - * - * @return true if connected now, or false to indicate a failure. - */ - public boolean connect(String url) { - return connect(url,null); - } - - - /** - * Establishes a connection to the LRC. - * - * @param url the url to lrc to connect to. - * @param proxy the path to the proxy file to be picked up. null denotes - * default location. - * - * @return true if connected now, or false to indicate a failure. - * - * @throws ReplicaCatalogException in case of - */ - public boolean connect(String url, String proxy) { - mLRCURL = url; - try { - mRLS = (proxy == null) ? - new RLSClient(url) : //proxy is picked up from default loc /tmp - new RLSClient(url, proxy); - - //set the timeout - mRLS.SetTimeout(mTimeout); - - //connect is only successful if we have - //successfully connected to the LRC - mLRC = mRLS.getLRC(); - - } - catch (RLSException e) { - log("RLS Exception", e,LogManager.ERROR_MESSAGE_LEVEL); - return false; - } - return true; - } - - /** - * Gets a handle to the LRC that is associated with the RLS running at - * url. - * - * @return RLSClient.LRC that points to the RLI that is - * running , or null in case connect method not being called. - * @see #mLRCURL - */ - public RLSClient.LRC getLRC() { - return (isClosed()) ? null : mLRC; - } - - /** - * Retrieves the entry for a given filename and resource handle from - * the LRC. - * - * @param lfn is the logical filename to obtain information for. - * @param handle is the resource handle to obtain entries for. - * @return the (first) matching physical filename, or - * null if no match was found. - * - * @throws ReplicaCatalogException in case of any error that is throw by LRC - * that can't be handled. - */ - public String lookup(String lfn, String handle) { - //sanity check - if (this.isClosed()) { - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - String pfn = null; - String site = null; - - //query the lrc - try { - List l = mLRC.getPFN(lfn); - for (Iterator it = l.iterator(); it.hasNext(); ) { - //query for the pool attribute - pfn = ( (RLSString2) it.next()).s2; - site = getSiteHandle(pfn); - if (site.equalsIgnoreCase(handle)) { - //ok we have the first pfn with for the site and lfn - break; - } - } - } - catch (RLSException ex) { - if(ex.GetRC() == RLSClient.RLS_LFN_NEXIST || - ex.GetRC() == RLSClient.RLS_MAPPING_NEXIST){ - pfn = null; - } - else{ - throw exception("lookup(String,String)", ex); - } - } - - return pfn; - } - - /** - * Retrieves all entries for a given LFN from the LRC. - * Each entry in the result set is a tuple of a PFN and all its - * attributes. - * - * @param lfn is the logical filename to obtain information for. - * @return a collection of replica catalog entries, or null in case of - * unable to connect to RLS or error. - * - * @throws ReplicaCatalogException in case of any error that is throw by LRC - * that can't be handled. - * @see ReplicaCatalogEntry - */ - public Collection lookup(String lfn) throws ReplicaCatalogException { - //sanity check - if (this.isClosed()) { - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - List res = new ArrayList(3); - - //query the lrc - try { - List l = mLRC.getPFN(lfn); - for (Iterator it = l.iterator(); it.hasNext(); ) { - String pfn = ( (RLSString2) it.next()).s2; - //get hold of all attributes - ReplicaCatalogEntry entry = new ReplicaCatalogEntry(pfn, - getAttributes(pfn)); - res.add(entry); - } - } - catch (RLSException ex) { - if(ex.GetRC() == RLSClient.RLS_LFN_NEXIST || - ex.GetRC() == RLSClient.RLS_MAPPING_NEXIST){ - log("Mapping for lfn " + lfn + " does not exist", - LogManager.DEBUG_MESSAGE_LEVEL); - } - else{ - throw exception("lookup(String)", ex); - } - } - - return res; - - } - - /** - * Retrieves all entries for a given LFN from the replica catalog. - * Each entry in the result set is just a PFN string. Duplicates - * are reduced through the set paradigm. - * - * @param lfn is the logical filename to obtain information for. - * @return a set of PFN strings, or null in case of unable to connect - * to RLS. - * - */ - public Set lookupNoAttributes(String lfn) { - //sanity check - if (this.isClosed()) { - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - Set res = new HashSet(3); - - //query the lrc - try { - List l = mLRC.getPFN(lfn); - for (Iterator it = l.iterator(); it.hasNext(); ) { - String pfn = ( (RLSString2) it.next()).s2; - res.add(pfn); - } - } - catch (RLSException ex) { - //am not clear whether to throw the exception or what - log("lookup(String,String):", ex,LogManager.ERROR_MESSAGE_LEVEL); - return null; - } - - return res; - - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It uses the bulk query api to the LRC to query for stuff. - * Bulk query has been in RLS since version 2.0.8. Internally, the bulk - * queries are done is sizes specified by variable mBatchSize. - * - * @param lfns is a set of logical filename strings to look up. - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries for the LFN. - * @see ReplicaCatalogEntry - * @see #getBatchSize() - */ - public Map lookup(Set lfns) throws ReplicaCatalogException { - //one has to do a bulk query in batches - Set s = null; - int size = mBatchSize; - Map map = new HashMap(lfns.size()); - - log("Number of files to query LRC " + lfns.size() + - " in batch sizes of " + size, LogManager.DEBUG_MESSAGE_LEVEL); - - for (Iterator it = lfns.iterator(); it.hasNext(); ) { - s = new HashSet(size); - for (int j = 0; (j < size) && (it.hasNext()); j++) { - s.add(it.next()); - } - if (!s.isEmpty()) { - //there is no conflict, as the keys are unique - //via the set paradigm. Passing null as we want - //to get hold of all attributes. - map.putAll(bulkLookup(s, null)); - } - - } - - return map; - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. - * - * The noAttributes flag is missing on purpose, because - * due to the resource handle, attribute lookups are already required. - * - * @param lfns is a set of logical filename strings to look up. - * @param handle is the resource handle, restricting the LFNs. - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries. - * - * @see ReplicaCatalogEntry - */ - public Map lookup(Set lfns, String handle) { - return lookup(lfns,SITE_ATTRIBUTE,handle); - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It returns the complete RCE for each entry i.e all the - * attributes a pfn is associated with in addition to the one that is - * the key for matching. - * - * @param lfns is a set of logical filename strings to look up. - * @param name is the name of the attribute. - * @param value is the value of the attribute. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries. - * - * @see ReplicaCatalogEntry - */ - public Map lookup(Set lfns, String name, Object value) { - //one has to do a bulk query in batches - Set s = null; - int size = mBatchSize; - Map map = new HashMap(lfns.size()); - - log("Number of files to query LRC " + lfns.size() + - " in batch sizes of " + size, LogManager.DEBUG_MESSAGE_LEVEL); - - for (Iterator it = lfns.iterator(); it.hasNext(); ) { - s = new HashSet(size); - for (int j = 0; (j < size) && (it.hasNext()); j++) { - s.add(it.next()); - } - if (!s.isEmpty()) { - //there is no conflict, as the keys are unique - //via the set paradigm. - //temp contains results indexed by lfn but each value - //is a collection of ReplicaCatalogEntry objects - //we query for all attributes as we are to return - //complete RCE as stipulated by the interface. - Map temp = bulkLookup(s, null); - //iterate thru it - for (Iterator it1 = temp.entrySet().iterator(); it1.hasNext(); ) { - Map.Entry entry = (Map.Entry) it1.next(); - Set pfns = subset( (Collection) entry.getValue(), - name, value); - if (!pfns.isEmpty()) { - map.put(entry.getKey(), pfns); - } - } - } - - } - - return map; - } - - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in an online display or portal. - * - * @param lfns is a set of logical filename strings to look up. - * @return a map indexed by the LFN. Each value is a set - * of PFN strings. - */ - public Map lookupNoAttributes(Set lfns) { - //one has to do a bulk query in batches - Set s = null; - int size = mBatchSize; - size = (size > lfns.size())?lfns.size():size; - Map map = new HashMap(lfns.size()); - - log("Number of files to query LRC " + lfns.size() + - " in batch sizes of " + size,LogManager.DEBUG_MESSAGE_LEVEL); - - for (Iterator it = lfns.iterator(); it.hasNext(); ) { - s = new HashSet(size); - for (int j = 0; (j < size) && (it.hasNext()); j++) { - s.add(it.next()); - } - if (!s.isEmpty()) { - //there is no conflict, as the keys are unique - //via the set paradigm. - map.putAll(bulkLookupNoAttributes(s)); - } - - } - - return map; - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * @param lfns is a set of logical filename strings to look up. - * @param handle is the resource handle, restricting the LFNs. - * - * @return a map indexed by the LFN. Each value is a set of - * physical filenames. - */ - public Map lookupNoAttributes(Set lfns, String handle) { - return lookupNoAttributes(lfns,SITE_ATTRIBUTE,handle); - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * @param lfns is a set of logical filename strings to look up. - * @param name is the PFN attribute name to look for. - * @param value is an exact match of the attribute value to match. - * - * @return a map indexed by the LFN. Each value is a set of - * physical filenames. - */ - public Map lookupNoAttributes(Set lfns, String name, Object value) { - //one has to do a bulk query in batches - Set s = null; - Collection c ; - int size = mBatchSize; - Map map = new HashMap(lfns.size()); - - log("Number of files to query LRC " + lfns.size() + - " in batch sizes of " + size,LogManager.DEBUG_MESSAGE_LEVEL); - - for (Iterator it = lfns.iterator(); it.hasNext(); ) { - s = new HashSet(size); - for (int j = 0; (j < size) && (it.hasNext()); j++) { - s.add(it.next()); - } - if (!s.isEmpty()) { - //there is no conflict, as the keys are unique - //via the set paradigm. - //temp contains results indexed by lfn but each value - //is a collection of ReplicaCatalogEntry objects - Map temp = bulkLookup(s, name,value); - //iterate thru it - for (Iterator it1 = temp.entrySet().iterator(); it1.hasNext(); ) { - Map.Entry entry = (Map.Entry) it1.next(); - c = (Collection) entry.getValue(); - //System.out.println("Entry is " + entry); - Set pfns = new HashSet(c.size()); - for(Iterator cit = c.iterator();cit.hasNext();){ - pfns.add( ((ReplicaCatalogEntry)cit.next()).getPFN()); - } - if (!pfns.isEmpty()) { - map.put(entry.getKey(), pfns); - } - } - } - - } - - return map; - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * At present it DOES NOT SUPPORT ATTRIBUTE MATCHING. - * - * @param constraints is mapping of keys 'lfn', 'pfn', to a string that - * has some meaning to the implementing system. This can be a SQL - * wildcard for queries, or a regular expression for Java-based memory - * collections. Unknown keys are ignored. Using an empty map requests - * the complete catalog. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries. - * - * @see ReplicaCatalogEntry - */ - public Map lookup(Map constraints) throws ReplicaCatalogException{ - return (constraints.isEmpty())? - lookup(list()): - getAttributes(lookupLFNPFN(constraints),null,null); - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal. At present it does not - * support attribute matching. - * - * @param constraints is mapping of keys 'lfn', 'pfn', or any - * attribute name, e.g. the resource handle 'site', to a string that - * has some meaning to the implementing system. This can be a SQL - * wildcard for queries, or a regular expression for Java-based memory - * collections. Unknown keys are ignored. Using an empty map requests - * the complete catalog. - * - * @return A list of MyRLSString2Bulk objects containing - * the lfn in s1 field, and pfn in s2 field. The list is - * grouped by lfns. The set may be empty. - */ - public List lookupLFNPFN(Map constraints) { - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - /* - if(constraints == null || constraints.isEmpty()){ - //return the set of all LFNs in the catalog - return list(); - }*/ - - List result = new ArrayList(); - boolean notFirst = false; - - for (Iterator i = constraints.keySet().iterator(); i.hasNext(); ) { - String key = (String) i.next(); - if ( key.equals("lfn") ) { - if(notFirst){ - //do the AND(intersect)operation - result.retainAll(listLFNPFN((String)constraints.get(key),true)); - } - else{ - result = listLFNPFN( (String) constraints.get(key), true); - } - } - else if ( key.equals("pfn") ) { - if(notFirst){ - //do the AND(intersect)operation - result.retainAll(listLFNPFN((String)constraints.get(key),false)); - } - else{ - result = listLFNPFN( (String) constraints.get(key), false); - } - } - else{ - //just a warning - log("Implementation does not support constraint " + - "matching of type " + key, - LogManager.WARNING_MESSAGE_LEVEL); - } - if(result.isEmpty()){ - //the intersection is already empty. No use matching further - break; - } - notFirst = true; - } - - //sort according to lfn - Collections.sort(result,new RLSString2BulkComparator()); - - return result; - } - - /** - * Lists all logical filenames in the catalog. - * - * @return a set of all logical filenames known to the catalog or null in - * case of not connected to the LRC or error. - */ - public Set list() { - return list("*"); - } - - - /** - * Lists a subset of all logical filenames in the catalog. - * - * @param constraint is a constraint for the logical filename only. It - * is a string that has some meaning to the implementing system. This - * can be a SQL wildcard for queries, or a regular expression for - * Java-based memory collections. - * - * @return A set of logical filenames that match. The set may be empty - */ - public Set list(String constraint) { - List l = listLFNPFN(constraint,true); - Set result = new HashSet(l.size()); - for(Iterator it = l.iterator();it.hasNext();){ - RLSString2Bulk rs = (RLSString2Bulk)it.next(); - result.add(rs.s1); - } - return result; - } - - /** - * Lists a subset of all LFN,PFN pairs in the catalog matching to - * a pfn or a lfn constraint. - * - * @param constraint is a constraint for the logical filename only. It - * is a string that has some meaning to the implementing system. This - * can be a SQL wildcard for queries, or a regular expression for - * Java-based memory collections. - * - * @return A set a list of MyRLSString2Bulk objects containing - * the lfn in s1 field, and pfn in s2 field. The list is - * grouped by lfns. The set may be empty. - * - * @see #getAttributes(List,String,Object) - */ - public List listLFNPFN( String constraint, boolean lfnConstraint ) - throws ReplicaCatalogException{ - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - int size = getBatchSize(); - List l = new ArrayList(); - ArrayList result = new ArrayList(); - int capacity = size; - - //do a wildcard query in batch sizes - RLSOffsetLimit offset = new RLSOffsetLimit(0,size); - while(true){ - try{ - l = (lfnConstraint)? - //do lfn matching - mLRC.getPFNWC(constraint, offset): - //do pfn matching - mLRC.getLFNWC(constraint, offset); - - //we need to group pfns by lfn - Collections.sort(l, new RLSString2Comparator()); - } - catch(RLSException e){ - if(e.GetRC() == RLSClient.RLS_PFN_NEXIST || - e.GetRC() == RLSClient.RLS_LFN_NEXIST || - e.GetRC() == RLSClient.RLS_MAPPING_NEXIST){ - log("listLFNPFN(String, boolean) :Mapping matching constraint " + - constraint + " does not exist",LogManager.ERROR_MESSAGE_LEVEL); - } - else{ - //am not clear whether to throw the exception or what - log("list()", e,LogManager.ERROR_MESSAGE_LEVEL); - } - //return empty list - return new ArrayList(0); - } - //result = new ArrayList(l.size()); - //increment the size of the list - //but first the capacity - capacity += l.size(); - result.ensureCapacity(capacity); - - for(Iterator it = l.iterator();it.hasNext();){ - RLSString2 res = (RLSString2)it.next(); - result.add(convert(res)); - } - if(offset.offset == -1) - break;//offset is set to -1 when no more results - - } - - return result; - - } - - - /** - * Inserts multiple mappings into the replica catalog. The input is a - * map indexed by the LFN. The value for each LFN key is a collection - * of replica catalog entries. Ends up doing a sequential insert for all - * the entries instead of doing a bulk insert. Easier to track failure this - * way. - * - * @param x is a map from logical filename string to list of replica - * catalog entries. - * @return the number of insertions. - * @see ReplicaCatalogEntry - */ - public int insert(Map x) { - int result = 0; - String lfn; - ReplicaCatalogEntry rce = null; - -// Not doing sequential inserts any longer -// Karan April 9, 2006 -// Collection c; -// for(Iterator it = x.entrySet().iterator();it.hasNext();){ -// Map.Entry entry = (Map.Entry)it.next(); -// lfn = (String)entry.getKey(); -// c = (Collection)entry.getValue(); -// log("Inserting entries for lfn " + lfn, -// LogManager.DEBUG_MESSAGE_LEVEL); -// for(Iterator pfnIt = c.iterator();pfnIt.hasNext();){ -// try{ -// rce = (ReplicaCatalogEntry)pfnIt.next(); -// insert(lfn,rce); -// res += 1; -// } -// catch(ReplicaCatalogException e){ -// log("Inserting lfn->pfn " + -// lfn + "->" + rce.getPFN(),e, -// LogManager.ERROR_MESSAGE_LEVEL); -// } -// } -// } -// return res; - - int size = this.getBatchSize(); - int current = 0; - String pfn; - List lfnPfns = new ArrayList(size); - List attrs = new ArrayList(size); - CatalogException exception = new ReplicaCatalogException(); - - //indexed by pfn and values as RLSAttributeObject objects - Map attrMap = new HashMap(size); - - for (Iterator it = x.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - lfn = (String)entry.getKey(); - Collection c = (Collection)entry.getValue(); - - //traverse through the rce's for the pfn's - for(Iterator pfnIt = c.iterator();pfnIt.hasNext();){ - rce = (ReplicaCatalogEntry)pfnIt.next(); - pfn = rce.getPFN(); - lfnPfns.add(new RLSString2(lfn,pfn)); - - //increment current only once per pfn - if(rce.getAttributeCount() == 0)current++; - - //build the attributes list - for(Iterator attrIt = rce.getAttributeIterator(); attrIt.hasNext();current++){ - String key = (String)attrIt.next(); - RLSAttribute attr = new RLSAttribute(key,RLSAttribute.LRC_PFN, - (String)rce.getAttribute(key)); - attrs.add(new RLSAttributeObject(attr,pfn)); - attrMap.put(pfn,new RLSAttributeObject(attr,pfn)); - } - } - //check if diff is more than batch size - if( current >= size){ - //we have the subset of RCE's on which we - //want to do bulk inserts, and the value till - //we want to do bulk inserts - try{ - result += bulkInsert(lfnPfns, attrMap); - } - catch(ReplicaCatalogException e){exception.setNextException(e);} - - //reset data structures - current = 0; - lfnPfns.clear(); - attrs.clear(); - attrMap.clear(); - } - } - //check for the last bunch - if(!lfnPfns.isEmpty()){ - //we have the subset of RCE's on which we - //want to do bulk inserts, and the value till - //we want to do bulk inserts - try{ - result += bulkInsert(lfnPfns, attrMap); - }catch(ReplicaCatalogException e){exception.setNextException(e);} - current = 0; - } - - //throw an exception only if a nested exception - if( (exception = exception.getNextException()) != null) throw exception; - - return result; - } - - /** - * Calls the bulk delete on the mappings. This function can timeout if the - * size of the list passed is too large. - * - * @param lfnPfns list of RLSString2 objects containing the - * lfn pfn mappings to be deleted. - * - * @return the number of items deleted - * - * @throws ReplicaCatalogException in case of error - */ - private int bulkDelete(List lfnPfns) throws ReplicaCatalogException{ - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - //result only tracks successful lfn->pfn mappings - int result = lfnPfns.size(); - Collection failedDeletes; - CatalogException exception = new ReplicaCatalogException(); - - //do a bulk delete - //FIX ME: The deletes should have been done in batches. - try{ - failedDeletes = mLRC.deleteBulk( (ArrayList)lfnPfns); - } - catch(RLSException e){ - mLogger.log("RLS: Bulk Delete " ,e , LogManager.ERROR_MESSAGE_LEVEL); - throw new ReplicaCatalogException("RLS: Bulk Delete " + e.getMessage()); - } - - if(!failedDeletes.isEmpty()){ - result -= failedDeletes.size(); - //FIXME: Do we really care about failed deletes - //and reporting why deletes failed. - // i think we do. - RLSString2Bulk rs; - int error; - for(Iterator it = failedDeletes.iterator();it.hasNext();){ - rs = (RLSString2Bulk)it.next(); - error = rs.rc; - - if(error == RLSClient.RLS_PFN_NEXIST || - error == RLSClient.RLS_LFN_NEXIST || - error == RLSClient.RLS_MAPPING_NEXIST){ - - log("Mapping " + rs.s1 + "->" + rs.s2 + - " does not exist",LogManager.DEBUG_MESSAGE_LEVEL); - } - else{ - exception.setNextException(exception(rs)); - } - } - - } - - //throw an exception only if a nested exception - if( (exception = exception.getNextException()) != null) throw exception; - - return result; - - } - - /** - * Calls the bulk insert on the mappings. This function can timeout if the - * size of the list passed is too large. - * - * @param lfnPfns list of RLSString2 objects containing the - * lfn pfn mappings to be inserted. - * @param attrMap a map indexed by pfn and values as RLSAttributeObject objects. - * - * @return the number of items inserted - * - * @throws ReplicaCatalogException in case of error - */ - private int bulkInsert(List lfnPfns, Map attrMap){ - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - //result only tracks successful lfn->pfn mappings - int result = lfnPfns.size(); - - List failedCreates; - List failedAdds; - CatalogException exception = new ReplicaCatalogException(); - - - try{ - /* bulk insert on mappings starts*/ - failedCreates = mLRC.createBulk( (ArrayList) lfnPfns); - - //try to do a bulkAdd on the failed creates - List bulkAdd = new ArrayList(failedCreates.size()); - for (Iterator it = failedCreates.iterator(); it.hasNext(); ) { - RLSString2Bulk rs = (RLSString2Bulk) it.next(); - if (rs.rc == RLSClient.RLS_LFN_EXIST) { - //s1 is lfn and s2 is pfn - bulkAdd.add(new RLSString2(rs.s1, rs.s2)); - } - else { - exception.setNextException(exception(rs)); - result--; - } - } - - //do a bulk add if list non empty - if (!bulkAdd.isEmpty()) { - failedAdds = mLRC.addBulk( (ArrayList) bulkAdd); - //pipe all the failed adds to the exception - for (Iterator it = failedAdds.iterator(); it.hasNext(); ) { - RLSString2Bulk rs = (RLSString2Bulk) it.next(); - - //just log that mapping already exists - if (rs.rc == RLSClient.RLS_MAPPING_EXIST) { - //we want to log instead of throwning an exception - log("LFN-PFN Mapping alreadys exists in LRC " - + mLRCURL + " for " + rs.s1 + "->" + rs.s2, - LogManager.DEBUG_MESSAGE_LEVEL); - result --; - - } - else { - exception.setNextException(exception(rs)); - result--; - } - } - } - /*bulk insert on mappings ends */ - - /*bulk insert on attributes starts */ - ArrayList failedAttrs;//the failed attributes - - //build the attribute list - ArrayList attrs = new ArrayList(attrMap.size()); - int num = 0; - for(Iterator it = attrMap.values().iterator();it.hasNext();num++){ - attrs.add(it.next()); - } - - //try a bulk add on attributes assuming attrs already exist - failedAttrs = mLRC.attributeAddBulk((ArrayList)attrs); - - //go through the failed attributes and create them - for(Iterator it = failedAttrs.iterator();it.hasNext();){ - RLSString2Bulk s2b = (RLSString2Bulk)it.next(); - /* - RLSAttribute attributeToAdd = - new RLSAttribute(s2b.s2,RLSAttribute.LRC_PFN, - (String)tuple.getAttribute(s2b.s2)); - */ - - - //s1 is the pfn - //s2 is the attribute name - String pfn = s2b.s1; - RLSAttributeObject attrObject = (RLSAttributeObject)attrMap.get(pfn); - RLSAttribute attributeToAdd = - attrObject.attr; - - if(s2b.rc == RLSClient.RLS_ATTR_NEXIST){ - //we need to create the attribute - log("Creating an attribute name " + s2b.s2 + - " for pfn " + pfn, LogManager.DEBUG_MESSAGE_LEVEL); - try{ - //FIXME : should have done a bulkAttributeCreate that doesnt exist - mLRC.attributeCreate(s2b.s2, RLSAttribute.LRC_PFN, - RLSAttribute.STR); - //add the attribute in sequentially instead of bulk - mLRC.attributeAdd(pfn,attributeToAdd); - - } - catch(RLSException e){ - //ignore any attribute already exist error - //case of multiple creates of same attribute - if(e.GetRC() != RLSClient.RLS_ATTR_EXIST){ - exception.setNextException( - new ReplicaCatalogException("Adding attrib to pfn " + - pfn + " " + e.getMessage())); - } - } - } - else if(s2b.rc == RLSClient.RLS_ATTR_EXIST){ - log("Attribute " + s2b.s2 + " for pfn " + pfn + - " already exists", LogManager.DEBUG_MESSAGE_LEVEL); - //get the existing value of attribute - List l = null; - try{ - l = mLRC.attributeValueGet(pfn, s2b.s2, RLSAttribute.LRC_PFN); - } - catch(RLSException e){ - exception.setNextException( - new ReplicaCatalogException("Getting value of existing attrib "+ - e.getMessage())); - } - if(l == null || l.isEmpty() || l.size() > 1){ - log("Contents of list are " + l,LogManager.DEBUG_MESSAGE_LEVEL); - //should never happen - log("Unreachable case.",LogManager.FATAL_MESSAGE_LEVEL); - throw new ReplicaCatalogException( - "Whammy while trying to get value of an exisiting attribute " + - s2b.s2 + " associated with PFN " + pfn); - } - - //try to see if it matches with the existing value - RLSAttribute attribute = (RLSAttribute)l.get(0); - if(!attribute.GetStrVal().equalsIgnoreCase( - attributeToAdd.GetStrVal())){ - - //log a warning saying updating value - mLogMsg = "Existing value for attribute " + s2b.s2 + - " associated with PFN " + pfn + - " updated with new value " + attributeToAdd.GetStrVal(); - - //update the value - try{ - mLRC.attributeModify(pfn, attributeToAdd); - log(mLogMsg,LogManager.WARNING_MESSAGE_LEVEL); - } - catch(RLSException e){ - exception.setNextException( - new ReplicaCatalogException("RLS Exception "+ e.getMessage())); - } - } - } - else { - exception.setNextException(exception(s2b)); - } - } - - /*bulk insert on attributes ends */ - - } - catch(RLSException e){ - exception.setNextException( - new ReplicaCatalogException("RLS Exception "+ e.getMessage())); - } - - - - //throw an exception only if a nested exception - if( (exception = exception.getNextException()) != null) throw exception; - - return result; - } - - /** - * Inserts a new mapping into the replica catalog. The attributes are added - * in bulk assuming the attribute definitions already exist. If an attribute - * definition does not exist, it is created and inserted. Note there is no - * notion of transactions in LRC. It assumes all the attributes are of type - * String. - * - * @param lfn is the logical filename under which to book the entry. - * @param tuple is the physical filename and associated PFN attributes. - * - * @return number of insertions, should always be 1. On failure, - * throws an exception instead of returning zero. - */ - public int insert(String lfn, ReplicaCatalogEntry tuple) { - Map m = new HashMap(1); - List l = new ArrayList(1); l.add(tuple); - m.put(lfn,l); - return insert(m); - -// Just composing the call to insert(Map method) -// Only one code handles inserts. Karan April 12, 2006 -// if(isClosed()){ -// //not connected to LRC -// //throw an exception?? -// throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); -// } -// int res = 0; - -// //we have no notion of transaction at this point. -// String pfn = tuple.getPFN(); -// try{ -// //insert the pfn -// mLRC.add(lfn, pfn); -// } -// catch(RLSException e){ -// if(e.GetRC() == RLSClient.RLS_LFN_NEXIST){ -// //the first instance of the lfn, so we add -// //instead of creating the mapping -// try{ -// mLRC.create(lfn, pfn); -// } -// catch(RLSException ex){ -// throw new ReplicaCatalogException("RLS Exception "+ ex.getMessage()); -// } -// } -// else if(e.GetRC() == RLSClient.RLS_MAPPING_EXIST){ -// log("LFN-PFN Mapping alreadys exists in LRC " -// + mLRCURL + " for " + lfn + "->" + pfn, -// LogManager.ERROR_MESSAGE_LEVEL); -// return res; -// } -// else -// throw new ReplicaCatalogException("RLS Exception "+ e.getMessage()); -// } -// -// //we need to add attributes in bulk -// String key; -// ArrayList failedAttrs;//the failed attributes -// ArrayList attrs = new ArrayList(tuple.getAttributeCount()); -// for(Iterator it = tuple.getAttributeIterator(); it.hasNext();){ -// key = (String)it.next(); -// RLSAttribute attr = new RLSAttribute(key,RLSAttribute.LRC_PFN, -// (String)tuple.getAttribute(key)); -// attrs.add(new RLSAttributeObject(attr,pfn)); -// -// } -// -// try{ -// failedAttrs = mLRC.attributeAddBulk(attrs); -// } -// catch(RLSException e){ -// throw new ReplicaCatalogException("RLS Exception "+ e.getMessage()); -// } -// -// //go through the failed attributes and create them -// for(Iterator it = failedAttrs.iterator();it.hasNext();){ -// RLSString2Bulk s2b = (RLSString2Bulk)it.next(); -// RLSAttribute attributeToAdd = new RLSAttribute(s2b.s2,RLSAttribute.LRC_PFN, -// (String)tuple.getAttribute(s2b.s2)); -// //s1 is the pfn -// //s2 is the attribute name -// if(s2b.rc == RLSClient.RLS_ATTR_NEXIST){ -// //we need to create the attribute -// log("Creating an attribute name " + s2b.s2 + -// " for pfn " + pfn, LogManager.DEBUG_MESSAGE_LEVEL); -// try{ -// mLRC.attributeCreate(s2b.s2, RLSAttribute.LRC_PFN, -// RLSAttribute.STR); -// //add the attribute in sequentially instead of bulk -// mLRC.attributeAdd(pfn,attributeToAdd); -// -// } -// catch(RLSException e){ -// throw new ReplicaCatalogException("RLS Exception "+ e.getMessage()); -// } -// } -// else if(s2b.rc == RLSClient.RLS_ATTR_EXIST){ -// log("Attribute " + s2b.s2 + " for pfn " + pfn + -// " already exists", LogManager.DEBUG_MESSAGE_LEVEL); -// //get the existing value of attribute -// List l = null; -// try{ -// l = mLRC.attributeValueGet(pfn, s2b.s2, RLSAttribute.LRC_PFN); -// } -// catch(RLSException e){ -// throw new ReplicaCatalogException("RLS Exception "+ e.getMessage()); -// } -// if(l == null || l.isEmpty() || l.size() > 1){ -// log("Contents of list are " + l,LogManager.DEBUG_MESSAGE_LEVEL); -// //should never happen -// log("Unreachable case.",LogManager.FATAL_MESSAGE_LEVEL); -// throw new ReplicaCatalogException( -// "Whammy while trying to get value of an exisiting attribute " + -// s2b.s2 + " associated with PFN " + pfn); -// } -// //try to see if it matches with the existing value -// RLSAttribute attribute = (RLSAttribute)l.get(0); -// if(!attribute.GetStrVal().equalsIgnoreCase( -// attributeToAdd.GetStrVal())){ -// -// //log a warning saying updating value -// mLogMsg = "Existing value for attribute " + s2b.s2 + -// " associated with PFN " + pfn + -// " updated with new value " + attributeToAdd.GetStrVal(); -// -// //update the value -// try{ -// mLRC.attributeModify(pfn, attributeToAdd); -// log(mLogMsg,LogManager.WARNING_MESSAGE_LEVEL); -// } -// catch(RLSException e){ -// throw new ReplicaCatalogException("RLS Exception" + -// e.getMessage()); -// } -// } -// } -// else{ -// throw new ReplicaCatalogException( -// "Unknown Error while adding attributes. RLS Error Code " + -// s2b.rc); -// } -// } -// -// return 1; - - } - - /** - * Inserts a new mapping into the replica catalog. This is a - * convenience function exposing the resource handle. Internally, - * the ReplicaCatalogEntry element will be contructed, and passed to - * the appropriate insert function. - * - * @param lfn is the logical filename under which to book the entry. - * @param pfn is the physical filename associated with it. - * @param handle is a resource handle where the PFN resides. - * - * @return number of insertions, should always be 1. On failure, - * throw an exception, don't use zero. - * - * @see #insert( String, ReplicaCatalogEntry ) - * @see ReplicaCatalogEntry - */ - public int insert(String lfn, String pfn, String handle) { - //prepare the appropriate ReplicaCatalogEntry object - ReplicaCatalogEntry rce = new ReplicaCatalogEntry(pfn,handle); - return insert(lfn,rce); - } - - /** - * Deletes multiple mappings into the replica catalog. The input is a - * map indexed by the LFN. The value for each LFN key is a collection - * of replica catalog entries. On setting matchAttributes to false, all entries - * having matching lfn pfn mapping to an entry in the Map are deleted. - * However, upon removal of an entry, all attributes associated with the pfn - * also evaporate (cascaded deletion). - * The deletes are done in batches. - * - * @param x is a map from logical filename string to list of - * replica catalog entries. - * @param matchAttributes whether mapping should be deleted only if all - * attributes match. - * - * @return the number of deletions. - * @see ReplicaCatalogEntry - */ - public int delete( Map x , boolean matchAttributes){ - int result = 0; - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - String lfn,pfn; - ReplicaCatalogEntry rce; - Collection c; - CatalogException exception = new ReplicaCatalogException(); - - if(matchAttributes){ - //do a sequential delete for the time being - for(Iterator it = x.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - lfn = (String)entry.getKey(); - c = (Collection)entry.getValue(); - - //iterate through all RCE's for this lfn and delete - for(Iterator rceIt = c.iterator();rceIt.hasNext();){ - rce = (ReplicaCatalogEntry)it.next(); - result += delete(lfn,rce); - } - } - } - else{ - //we can use bulk delete - int size = this.getBatchSize(); - int current = 0; - List lfnPfns = new ArrayList(size); - for (Iterator it = x.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - lfn = (String)entry.getKey(); - c = (Collection)entry.getValue(); - - //traverse through the rce's for the pfn's - for(Iterator pfnIt = c.iterator();pfnIt.hasNext();){ - rce = (ReplicaCatalogEntry) pfnIt.next(); - pfn = rce.getPFN(); - lfnPfns.add(new RLSString2(lfn, pfn)); - current++; - - //check if diff is more than batch size - if( current >= size){ - //we have the subset of RCE's on which we - //want to do bulk deletes - try{ - result += bulkDelete(lfnPfns); - } - catch(ReplicaCatalogException e){exception.setNextException(e);} - - current = 0; - lfnPfns.clear(); - } - - } - } - //check for the last bunch - if(!lfnPfns.isEmpty()){ - //we have the subset of RCE's on which we - //we want to do bulk deletes - try{ - result += bulkDelete(lfnPfns); - } - catch(ReplicaCatalogException e){exception.setNextException(e);} - - current = 0; - } - } - - //throw an exception only if a nested exception - if( (exception = exception.getNextException()) != null) throw exception; - - return result; - } - - - - /** - * Deletes a specific mapping from the replica catalog. We don't care - * about the resource handle. More than one entry could theoretically - * be removed. Upon removal of an entry, all attributes associated - * with the PFN also evaporate (cascading deletion) automatically at the - * RLS server end. - * - * @param lfn is the logical filename in the tuple. - * @param pfn is the physical filename in the tuple. - * - * @return the number of removed entries. - */ - public int delete(String lfn, String pfn) { - int res = 0; - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - try{ - mLRC.delete(lfn,pfn); - res++; - } - catch(RLSException e){ - if(e.GetRC() == RLSClient.RLS_PFN_NEXIST || - e.GetRC() == RLSClient.RLS_LFN_NEXIST || - e.GetRC() == RLSClient.RLS_MAPPING_NEXIST){ - log("Mapping " + lfn + "->" + pfn + - " does not exist",LogManager.DEBUG_MESSAGE_LEVEL); - } - else{ - throw new ReplicaCatalogException("Error while deleting mapping " + - e.getMessage()); - } - } - return res; - } - - /** - * Deletes a very specific mapping from the replica catalog. The LFN - * must be matches, the PFN, and all PFN attributes specified in the - * replica catalog entry. More than one entry could theoretically be - * removed. Upon removal of an entry, all attributes associated with - * the PFN also evaporate (cascading deletion). - * - * @param lfn is the logical filename in the tuple. - * @param tuple is a description of the PFN and its attributes. - * @return the number of removed entries, either 0 or 1. - */ - public int delete(String lfn, ReplicaCatalogEntry tuple) { - int res = 0; - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - //get hold of all the RCE in this LRC matching to lfn - Collection c = lookup(lfn); - ReplicaCatalogEntry rce; - for(Iterator it = c.iterator();it.hasNext();){ - rce = (ReplicaCatalogEntry)it.next(); - if(rce.equals(tuple)){ - //we need to delete the rce - //cascaded deletes take care of the attribute deletes - delete(lfn,tuple.getPFN()); - res++; - } - } - - return res; - } - - /** - * Deletes all PFN entries for a given LFN from the replica catalog - * where the PFN attribute is found, and matches exactly the object - * value. This method may be useful to remove all replica entries that - * have a certain MD5 sum associated with them. It may also be harmful - * overkill. - * - * @param lfn is the logical filename to look for. - * @param name is the PFN attribute name to look for. - * @param value is an exact match of the attribute value to match. - * - * @return the number of removed entries. - */ - public int delete(String lfn, String name, Object value) { - int result = 0; - Collection c = null; - if(isClosed()){ - //not connected to LRC - //throw an exception?? - throw new ReplicaCatalogException(LRC_NOT_CONNECTED_MSG + this.mLRCURL); - } - - //query lookup for that lfn and delete accordingly. - Set s = new HashSet(1); - s.add(lfn); - Map map = this.lookupNoAttributes(s,name,value); - if(map == null || map.isEmpty()){ - return 0; - } - - //we need to pipe this into a list of RLSString2 objects - ArrayList lfnPfns = new ArrayList(3); - for(Iterator it = map.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry) it.next(); - lfn = (String)entry.getKey(); - - for (Iterator it1 = ( (Set) entry.getValue()).iterator(); - it1.hasNext(); ) { - RLSString2 lfnPfn = new RLSString2(lfn, (String) it1.next()); - lfnPfns.add(lfnPfn); - result++; - } - - } - - try{ - c = mLRC.deleteBulk(lfnPfns); - } - catch(RLSException e){ - log("remove(Set)" ,e,LogManager.ERROR_MESSAGE_LEVEL); - } - - //c should be empty ideally - if(!c.isEmpty()){ - result -= c.size(); - log("Removing lfns remove(Set)" + c, LogManager.ERROR_MESSAGE_LEVEL); - } - return result; - - } - - /** - * Deletes all PFN entries for a given LFN from the replica catalog - * where the resource handle is found. Karan requested this - * convenience method, which can be coded like - * 

-     *  delete( lfn, SITE_ATTRIBUTE, handle )
-     *
- * - * @param lfn is the logical filename to look for. - * @param handle is the resource handle - * - * @return the number of entries removed. - * - * @see #SITE_ATTRIBUTE - */ - public int deleteByResource(String lfn, String handle) { - return delete(lfn,SITE_ATTRIBUTE,handle); - } - - /** - * Removes all mappings for a set of LFNs. - * - * @param lfn is a set of logical filename to remove all mappings for. - * - * @return the number of removed entries. - */ - public int remove(String lfn) { - //first get hold of all the pfn mappings for the lfn - Collection c = this.lookupNoAttributes(lfn); - int result = 0; - if(c == null || c.isEmpty()){ - return 0; - } - - //we need to pipe this into a list of RLSString2Bulk objects - result = c.size(); - ArrayList lfnPfns = new ArrayList(result); - for(Iterator it = c.iterator();it.hasNext();){ - RLSString2 lfnPfn = new RLSString2(lfn,(String)it.next()); - lfnPfns.add(lfnPfn); - } - - //do a bulk delete - try{ - c = mLRC.deleteBulk(lfnPfns); - } - catch(RLSException e){ - log("remove(String)",e,LogManager.ERROR_MESSAGE_LEVEL); - } - - //c should be empty ideally - if(!c.isEmpty()){ - result -= c.size(); - log("remove(String)" + c,LogManager.ERROR_MESSAGE_LEVEL); - } - return result; - } - - /** - * Removes all mappings for a set of LFNs. - * - * @param lfns is a set of logical filename to remove all mappings for. - * - * @return the number of removed entries. - */ - public int remove(Set lfns) { - String lfn = null; - Collection c = null; - int result = 0; - - //first get hold of all the pfn mappings for the lfn - Map map = this.lookupNoAttributes(lfns); - if(map == null || map.isEmpty()){ - return 0; - } - //we need to pipe this into a list of RLSString2 objects - ArrayList lfnPfns = new ArrayList(map.keySet().size()); - for(Iterator it = map.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry) it.next(); - lfn = (String)entry.getKey(); - for (Iterator it1 = ( (Set) entry.getValue()).iterator(); - it1.hasNext(); ) { - RLSString2 lfnPfn = new RLSString2(lfn, (String) it1.next()); - lfnPfns.add(lfnPfn); - result++; - } - } - - //do a bulk delete - //FIX ME: The deletes should have been done in batches. - try{ - c = mLRC.deleteBulk(lfnPfns); - } - catch(RLSException e){ - log("remove(Set)" + e,LogManager.ERROR_MESSAGE_LEVEL); - } - - //c should be empty ideally - if(!c.isEmpty()){ - result -= c.size(); - log("remove(Set)" + c,LogManager.ERROR_MESSAGE_LEVEL); - for(Iterator it = c.iterator();it.hasNext();){ - RLSString2Bulk rs2 = (RLSString2Bulk)it.next(); - System.out.println("(" + rs2.s1 + "->" + rs2.s2 +"," + - rs2.rc + ")"); - } - } - return result; - - } - - /** - * Removes all entries associated with a particular resource handle. - * This is useful, if a site goes offline. It is a convenience method, - * which calls the generic removeByAttribute method. - * - * @param handle is the site handle to remove all entries for. - * - * @return the number of removed entries. - * - * @see #removeByAttribute( String, Object ) - */ - public int removeByAttribute(String handle) { - return removeByAttribute(SITE_ATTRIBUTE,handle); - } - - /** - * Removes all entries from the replica catalog where the PFN attribute - * is found, and matches exactly the object value. - * - * @param name is the PFN attribute name to look for. - * @param value is an exact match of the attribute value to match. - * - * @return the number of removed entries. - */ - public int removeByAttribute(String name, Object value) { - String lfn = null; - String pfn = null; - Collection c = null; - int result = 0; - - //get hold of all the lfns in the lrc - Set s = list(); - - //first get hold of all the pfn mappings for the lfn - Map map = this.lookup(s,name,value); - if(map == null || map.isEmpty()){ - return 0; - } - - //we need to pipe this into a list of RLSString2 objects - ArrayList lfnPfns = new ArrayList(result); - for(Iterator it = map.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry) it.next(); - lfn = (String)entry.getKey(); - //System.out.println(lfn + " ->"); - for (Iterator it1 = ( (Set) entry.getValue()).iterator(); - it1.hasNext(); ) { - pfn = ((ReplicaCatalogEntry)it1.next()).getPFN(); - RLSString2 lfnPfn = new RLSString2(lfn, pfn); - lfnPfns.add(lfnPfn); - result++; - //System.out.print(lfnPfn.s2 + ","); - } - } - - //do a bulk delete - //FIX ME: The deletes should have been done in batches. - try{ - c = mLRC.deleteBulk(lfnPfns); - } - catch(RLSException e){ - throw new ReplicaCatalogException("Bulk Delete: " + e.getMessage()); - } - - //c should be empty ideally - if(!c.isEmpty()){ - result -= c.size(); - log("removeByAttribute(String,Object)" + c, - LogManager.ERROR_MESSAGE_LEVEL); - } - return result; - } - - /** - * Removes everything. Use with caution! - * - * @return the number of removed entries. - */ - public int clear() { - - //do a bulk delete - //FIX ME: The deletes should have been done in batches. - try{ - mLRC.clear(); - } - catch(RLSException e){ - log("clear()",e,LogManager.ERROR_MESSAGE_LEVEL); - } - return 0; - /* - String lfn = null; - String pfn = null; - Collection c = null; - int result = 0; - - //get hold of all the lfns in the lrc - Set s = list(); - - //first get hold of all the pfn mappings for the lfn - Map map = this.lookupNoAttributes(s); - if(map == null || map.isEmpty()){ - return 0; - } - - //we need to pipe this into a list of RLSString2 objects - ArrayList lfnPfns = new ArrayList(result); - for(Iterator it = map.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry) it.next(); - lfn = (String)entry.getKey(); - //System.out.println(lfn + " ->"); - for (Iterator it1 = ( (Set) entry.getValue()).iterator(); - it1.hasNext(); ) { - pfn = ((String)it1.next()); - RLSString2 lfnPfn = new RLSString2(lfn, pfn); - lfnPfns.add(lfnPfn); - result++; - //System.out.print(lfnPfn.s2 + ","); - } - } - - //do a bulk delete - //FIX ME: The deletes should have been done in batches. - try{ - c = mLRC.deleteBulk(lfnPfns); - } - catch(RLSException e){ - log("clear()",e,LogManager.ERROR_MESSAGE_LEVEL); - } - - //c should be empty ideally - if(!c.isEmpty()){ - result -= c.size(); - log("clear()" + c,LogManager.ERROR_MESSAGE_LEVEL); - } - return result; - */ - } - - /** - * Explicitely free resources before the garbage collection hits. - */ - public void close() { - try { - if (mRLS != null) { - mRLS.Close(); - } - } - catch (RLSException e) { - //ignore - } - finally { - mRLS = null; - } - } - - /** - * Returns whether the connection to the RLS with which this instance is - * associated is closed or not. - * - * @return true, if the implementation is disassociated, false otherwise. - * @see #close() - */ - public boolean isClosed() { - return (mRLS == null); - } - - - /** - * It returns the timeout value in seconds after which to timeout in case of - * no activity from the LRC. - * - * Referred to by the "lrc.timeout" property. - * - * @return the timeout value if specified else, - * the value specified by "rls.timeout" property, else - * DEFAULT_LRC_TIMEOUT. - * - * @see #DEFAULT_LRC_TIMEOUT - */ - protected int getTimeout(Properties properties) { - String prop = properties.getProperty( this.LRC_TIMEOUT_KEY); - - //if prop is null get rls timeout, - prop = (prop == null)? properties.getProperty(this.RLS_TIMEOUT_KEY):prop; - - int val = 0; - try { - val = Integer.parseInt( prop ); - } catch ( Exception e ) { - val = Integer.parseInt( DEFAULT_LRC_TIMEOUT ); - } - return val; - - } - - - /** - * Returns the site handle associated with the pfn at the lrc to which - * the instance of this application binds. It returns UNDEFINED_SITE - * even when the pfn is not in the lrc. - * - * @param pfn The pfn with which the attribute is associated. - * - * @return value of the attribute if found - * else UNDEFINED_POOL - */ - private String getSiteHandle(String pfn) { - return getSiteHandle(mLRC, pfn); - } - - /** - * Returns the site handle associated with a pfn at the lrc associated - * with the RLSClient passed. It returns UNDEFINED_SITE - * even when the pfn is not in the lrc. - * - * @param lrc the handle to the lrc , where the attributes are stored. - * @param pfn the pfn with which the attribute is associated. - * - * @return value of the attribute if found - * else UNDEFINED_POOL - * - */ - private String getSiteHandle(RLSClient.LRC lrc, String pfn) { - String poolAttr = getAttribute(lrc, pfn, SITE_ATTRIBUTE); - return (poolAttr == null) ? - defaultResourceHandle() : - poolAttr; - } - - - - /** - * Returns the default value that is to be assigned to site handle - * for a replica catalog entry. - * - * @return default site handle - */ - private String defaultResourceHandle(){ - return ( this.mDefaultSiteAttribute == null ) ? - LRC.UNDEFINED_SITE: - this.mDefaultSiteAttribute; - } - - /** - * Sets the resource handle in an attribute map. - * The resource handle is set to the default site handle if the map - * does not contain the site attribute key. - * - * @param m the attribute map. - * - * @see #defaultResourceHandle() - */ - private void setResourceHandle( Map m ){ - String dflt = defaultResourceHandle(); - //update the site attribute only if the default - //attribute is other than undefined site - if( m.containsKey( LRC.SITE_ATTRIBUTE) && !dflt.equals(LRC.UNDEFINED_SITE ) ){ - //populate the default site handle - m.put( LRC.SITE_ATTRIBUTE, dflt ); - } - else if( !m.containsKey( LRC.SITE_ATTRIBUTE ) ){ - //populate the default site handle - m.put( LRC.SITE_ATTRIBUTE, dflt ); - } - } - - /** - * Sets the resource handle in an attribute map. - * The resource handle is set to the default site handle if the map - * does not contain the site attribute key. - * - * @param rce the ReplicaCatalogEntry - * - * @see #defaultResourceHandle() - */ - private void setResourceHandle( ReplicaCatalogEntry rce ){ - String dflt = defaultResourceHandle(); - //update the site attribute only if the default - //attribute is other than undefined site - if( rce.hasAttribute( LRC.SITE_ATTRIBUTE) && !dflt.equals(LRC.UNDEFINED_SITE ) ){ - //populate the default site handle - rce.setResourceHandle( dflt ); - } - else if( ! rce.hasAttribute( LRC.SITE_ATTRIBUTE ) ){ - //populate the default site handle - rce.setResourceHandle( dflt ); - } - } - - /** - * Retrieves from the lrc, associated with this instance all the - * attributes associated with the pfn in a map. All the - * attribute values are stored as String. - * - * @param pfn the pfn with which the attribute is associated. - * - * @return Mapcontaining the attribute keys and values, - * else an empty Map. - */ - private Map getAttributes(String pfn) { - return getAttributes(mLRC, pfn); - } - - /** - * Retrieves from the lrc associated with this instance, all the - * attributes associated with the lfn-pfns in a map indexed by the lfn. - * The value for each entry is a collection of - * ReplicaCatalogEntry objects. - * All the attribute values are stored as String. - * - * If the attribute value passed is not null, then explicit matching occurs - * on attribute values in addition. - * - * @param lfnPfns a list of RLSString2Bulk objects containing - * the lfn in s1 field, and pfn in s2 field. The list is - * assumed to be grouped by lfns. - * @param attrKey the name of attribute that needs to be queried for each - * pfn. a value of null denotes all attributes. - * @param attrVal the value of the attribute that should be matching. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries for the LFN. - */ - private Map getAttributes(List lfnPfns, String attrKey, Object attrVal) { - Map result = new HashMap(); - String curr = null; - String prev = null; - //loss of information. i should have known the size at this pt! - List l = new ArrayList(); - ArrayList pfns = new ArrayList(lfnPfns.size()); - int size = mBatchSize; - ReplicaCatalogEntry entry = null; - Map temp = new HashMap(); - Map pfnMap = new HashMap(); //contains pfn and their ReplicaCatalogEntry objects - - //sanity check - if(lfnPfns == null || lfnPfns.isEmpty()){ - return result; - } - - //put just the pfns in a list that needs - //to be sent to the RLS API - for (Iterator it = lfnPfns.iterator(); it.hasNext(); ) { - pfns.add( ( (RLSString2Bulk) it.next()).s2); - } - //now query for the attributes in bulk - List attributes = null; - try { - attributes = mLRC.attributeValueGetBulk(pfns, attrKey, - RLSAttribute.LRC_PFN); - } - catch (RLSException e) { - //some other error, but we can live with it. - //just flag as warning - mLogMsg = "getAttributes(List,String,Object)"; - log(mLogMsg, e,LogManager.ERROR_MESSAGE_LEVEL); - return result; - } - - //we need to sort them on the basis of the pfns - //which is the populate the key field - Collections.sort(attributes, new RLSAttributeComparator()); - /* - System.out.println("Sorted attributes are "); - for(Iterator it = attributes.iterator(); it.hasNext();){ - RLSAttributeObject obj = (RLSAttributeObject) it.next(); - if(obj.rc == RLSClient.RLS_ATTR_NEXIST){ - System.out.print("\tAttribute does not exist"); - } - System.out.println("\t" + obj.key + "->rc" + obj.rc); - } - */ - - for (Iterator it = attributes.iterator(); it.hasNext(); ) { - RLSAttributeObject attr = (RLSAttributeObject) it.next(); - Object value = (attr.rc == RLSClient.RLS_ATTR_NEXIST)? - null: //assign an empty value - getAttributeValue(attr.attr);//retrieve the value - - curr = attr.key; - - //push in the attribute into the temp map only - //if prev is null or the prev and current pfn's match - if((prev == null || curr.equalsIgnoreCase(prev)) - && - (value != null)//value being null means no attribute associated - && - ((attrVal == null) - || (attrVal.equals(value)) )){ - temp.put(attr.attr.name,value); - } - else{ - //push it into the map all attributes for a single pfn - //only if the map is not empty or there was no matching - //being done attrVal (i.e it is null) - if(attrVal == null || !temp.isEmpty()){ - entry = new ReplicaCatalogEntry(prev, temp); - //System.out.println("0:Entry being made is " + entry); - //the entry has to be put in a map keyed by the pfn name - pfnMap.put(prev, entry); - temp = new HashMap(); - } - //added June 15,2005 - if(value != null && - ( attrVal == null || attrVal.equals(value))){ - temp.put(attr.attr.name,value); - } - } - //push in the last attribute entry - if(!it.hasNext()){ - //push it into the map all attributes for a single pfn - //only if the map is not empty or there was no matching - //being done attrVal (i.e it is null) - if(attrVal == null || !temp.isEmpty()){ - entry = new ReplicaCatalogEntry(curr, temp); - //System.out.println("1:Entry being made is " + entry); - //the entry has to be put in a map keyed by the pfn name - pfnMap.put(curr, entry); - } - } - prev = curr; - - } - - //the final iteration that groups the pfn and their - //attributes according to the lfn - prev = null; - for (Iterator it = lfnPfns.iterator(); it.hasNext(); ) { - RLSString2Bulk lfnPfn = (RLSString2Bulk) it.next(); - curr = lfnPfn.s1; - - entry = (ReplicaCatalogEntry) pfnMap.get(lfnPfn.s2); - if(entry == null){ - //means no match on attribute or attribute value was found - continue; - } - - if (!curr.equalsIgnoreCase(prev) && (prev != null)) { - //push it into the map - //we have entry for one lfn and all pfns constructed - //System.out.println("Putting in entry for " + prev + " " + l); - result.put(prev, l); - l = new ArrayList(); - } - - //set a site handle if not already set - setResourceHandle( entry ); - - l.add(entry); - //if this was the last one push it in result - if(!it.hasNext()){ - //System.out.println("Putting in entry for " + curr + " " + l); - result.put(curr, l); - } - prev = curr; - } - - return result; - } - - /** - * Retrieves from the lrc, all the attributes associated with the pfn - * in a map. All the attribute values are stored as String. - * - * @param lrc the handle to the lrc , where the attributes are stored. - * @param pfn the pfn with which the attribute is associated. - * @return Mapcontaining the attribute keys and values, - * else an empty Map. - */ - private Map getAttributes(RLSClient.LRC lrc, String pfn) { - String val = null; - List attrList = null; - Map m = new HashMap(); - RLSAttribute att = null; - - try { - //passing null denotes to get - //hold of all attributes - attrList = lrc.attributeValueGet(pfn, null, - RLSAttribute.LRC_PFN); - } - catch (RLSException e) { - //attribute does not exist error means no attributes - //associated, return empty map else just denote a warning - if(e.GetRC() != RLSClient.RLS_ATTR_NEXIST){ - //some other error, but we can live with it. - //just flag as warning - mLogMsg = "getAttributes(RLSClient.LRC,String)"; - log(mLogMsg, e,LogManager.ERROR_MESSAGE_LEVEL); - } - - //associate a default value if required. - setResourceHandle( m ); - - return m; - } - - //iterate throught the list and push all - //the attributes in the map - for (Iterator it = attrList.iterator(); it.hasNext(); ) { - att = (RLSAttribute) it.next(); - //the list can contain a null attribute key - //we dont want that. - if( att.name != null ){ - m.put(att.name, att.GetStrVal()); - } - } - - //populate default site handle if - //site attribute is not specified - setResourceHandle( m ); - - return m; - } - - /** - * Retrieves from the lrc associated with this instance all, the attribute - * value associated with the pfn for a given attribute name. - * - * @param pfn the pfn with which the attribute is associated. - * @param name the name of the attribute for which we want to search. - * - * @return value of the attribute if found - * else null - */ - private String getAttribute(String pfn, String name) { - return getAttribute(mLRC, pfn, name); - } - - /** - * Retrieves from the lrc, the attribute value associated with the pfn - * for a given attribute name. - * - * @param lrc the handle to the lrc , where the attributes are stored. - * @param pfn the pfn with which the attribute is associated. - * @param name the name of the attribute for which we want to search. - * - * @return value of the attribute if found - * else null - */ - private String getAttribute(RLSClient.LRC lrc, String pfn, String name) { - String val = null; - List attrList = null; - - try { - attrList = lrc.attributeValueGet(pfn, name, - RLSAttribute.LRC_PFN); - } - catch (RLSException e) { - if (e.GetRC() == RLSClient.RLS_ATTR_NEXIST) { - //attribute does not exist we return null - } - else { - //some other error, but we can live with it. - //just flag as warning - mLogMsg = "getAttribute(String,String,String):"; - log(mLogMsg, e,LogManager.ERROR_MESSAGE_LEVEL); - } - return null; - } - - return (attrList.isEmpty()) ? - null : - //we return the first attribute value - //Does not make much sense for - //more than one attribute value - //for the same key and pfn - attrList.get(0).toString(); - } - - - /** - * Retrieves the attribute value as an object from the RLSAttribute - * object. Does automatic boxing (i.e converts int to Integer) etc. - * The value is returned of the type as determined from the internal value - * type. - * - * @param attr the RLSAttribute from which to extract the value. - * - * @return Object containing the value. - * - * @throws ReplicaCatalogException if illegal value associated. - */ - private Object getAttributeValue(RLSAttribute attr){ - Object obj = null; - int type = attr.GetValType(); - - switch(type){ - case RLSAttribute.STR: - obj = attr.GetStrVal(); - break; - - case RLSAttribute.DATE: - obj = attr.GetDateVal(); - break; - - case RLSAttribute.DOUBLE: - obj = new Double(attr.GetDoubleVal()); - break; - - case RLSAttribute.INT: - obj = new Integer(attr.GetIntVal()); - break; - - default: - throw new ReplicaCatalogException("Invalid value type associated " + type); - } - - return obj; - } - - /** - * Sets the number of lfns in each batch while querying the lrc in the - * bulk mode. - * - * @param properties the properties passed while connecting. - * - */ - private void setBatchSize(Properties properties) { - String s = properties.getProperty(this.BATCH_KEY); - int size = this.RLS_BULK_QUERY_SIZE; - try{ - size = Integer.parseInt(s); - } - catch(Exception e){} - mBatchSize = size; - } - - - /** - * Returns the number of lfns in each batch while querying the lrc in the - * bulk mode. - * - * @return the batch size. - */ - private int getBatchSize() { - return mBatchSize; - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It uses the bulk query api to the LRC to query for stuff. - * Bulk query has been in RLS since version 2.0.8. All the lfns in set - * are put in one single bulk query to the LRC. There is a risk of seeing - * a timeout error in case of large set of lfns. User should use the - * lookup function that internally does the bulk query in batches. - * Passing a null value for the attribute key results in the querying for all - * attributes. The function returns ReplicaCatalogEntry objects - * that have the attribute identified by attribute key passed. - * - * @param lfns set of logical filename strings to look up. - * @param attrKey the name of attribute that needs to be queried for each - * pfn. a value of null denotes all attributes. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries for the LFN. - * @see ReplicaCatalogEntry - * @see #lookup(Set) - */ - private Map bulkLookup(Set lfns, String attrKey) { - return bulkLookup(lfns,attrKey,null); - } - - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It uses the bulk query api to the LRC to query for stuff. - * Bulk query has been in RLS since version 2.0.8. All the lfns in set - * are put in one single bulk query to the LRC. There is a risk of seeing - * a timeout error in case of large set of lfns. User should use the - * lookup function that internally does the bulk query in batches. - * Passing a null value for the attribute key results in the querying for all - * attributes. A null value for the attribute value, disables attribute matching - * and results in the ReplicaCatalogEntry objects that have - * the attribute identified by attribute key passed. - * - * @param lfns set of logical filename strings to look up. - * @param attrKey the name of attribute that needs to be queried for each - * pfn. a value of null denotes all attributes. - * @param attrVal the value of the attribute that should be matching. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries for the LFN. - * @see ReplicaCatalogEntry - * @see #lookup(Set) - */ - private Map bulkLookup(Set lfns, String attrKey, Object attrVal) { - List list = null; - List lfnsFound = null; - RLSString2Bulk curr = null; - int size = mBatchSize; - Map result = new HashMap(lfns.size()); - - try { - list = mLRC.getPFNBulk( new ArrayList(lfns)); - //we need to group pfns by lfn - Collections.sort(list, new RLSString2BulkComparator()); - /* - System.out.println("Sorted list is "); - for(Iterator it = list.iterator(); it.hasNext();){ - RLSString2Bulk s2b = (RLSString2Bulk) it.next(); - System.out.println("\t" + s2b.s1 + "->" + s2b.s2); - } - */ - size = list.size() <= size ? list.size() :size; - for (Iterator it = list.iterator(); it.hasNext(); ) { - //the pfn themseleves need to be queried - //in batches to avoid timeout errors but the batch size - //should have all the pfns for a lfn!! - List l = new ArrayList(size); - String prev = ""; - if (curr != null) { - //this is the case where the current - //item is not in any of the sublists - l.add(curr); - } - for (int j = 0; (it.hasNext()); ) { - RLSString2Bulk s2b = (RLSString2Bulk) it.next(); - //s1 is the lfn - //s2 denotes the pfn - //rc is the exit status returned by the RLI - if (s2b.rc == RLSClient.RLS_SUCCESS) { - curr = s2b; - if (s2b.s2 != null) { - //query for the pool attribute - //for that pfn to the lrc - //if none is found or you do not - //query for the attribute - //pool is set to UNDEFINED_POOL - if (!curr.s1.equalsIgnoreCase(prev)) { - //do nothing - //check if j > size - if (j >= size) { - //break out of the loop. - //current needs to go into the next list - break; - } - } - - l.add(s2b); - j++; - } - else { - mLogMsg = - "bulkLookup(Set): Unexpected Mapping with no pfn for lfn: " + - s2b.s1; - log(mLogMsg,LogManager.ERROR_MESSAGE_LEVEL); - } - prev = curr.s1; - } - else if (s2b.rc != RLSClient.RLS_LFN_NEXIST) { - mLogMsg = "bulkLookup(Set): " + - mRLS.getErrorMessage(s2b.rc); - log(mLogMsg,LogManager.ERROR_MESSAGE_LEVEL); - } - //prev = curr.s1; - } - //get hold of all attributes for the pfn's - result.putAll(getAttributes(l, attrKey,attrVal)); - - } - - } - catch (Exception e) { - log("bulkLookup(Set)", e,LogManager.FATAL_MESSAGE_LEVEL); - System.exit(1); - } - - return result; - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It uses the bulk query api to the LRC to query for stuff. - * Bulk query has been in RLS since version 2.0.8. All the lfns in set - * are put in one single bulk query to the LRC. There is a risk of seeing - * a timeout error in case of large set of lfns. User should use the - * lookup function that internally does the bulk query in batches. - * - * @param lfns is a set of logical filename strings to look up. - * - * @return a map indexed by the LFN. Each value is a set - * of PFN strings. - * - * @see #lookupNoAttributes(Set) - */ - private Map bulkLookupNoAttributes(Set lfns) { - List list = null; - List lfnsFound = null; - Map result = new HashMap(lfns.size()); - String prev = null; - String curr = null; - Set s = new HashSet(); - - try { - list = mLRC.getPFNBulk( new ArrayList(lfns)); - //we need to group pfns by lfn - Collections.sort(list, new RLSString2BulkComparator()); - - for (Iterator it = list.iterator(); it.hasNext(); ) { - RLSString2Bulk s2b = (RLSString2Bulk) it.next(); - - //s1 is the lfn - //s2 denotes the pfn - //rc is the exit status returned by the RLI - if (s2b.rc == RLSClient.RLS_SUCCESS) { - curr = s2b.s1; - if (s2b.s2 != null) { - if (!curr.equalsIgnoreCase(prev) && (prev != null)) { - //push it into the map - //we have entry for one lfn and all pfns constructed - result.put(prev, s); - s = new HashSet(); - } - s.add(s2b.s2); - //if this was the last one push it in result - if(!it.hasNext()){ - result.put(curr,s); - } - } - else { - mLogMsg = - "bulkLookupNoAttributes(Set): Unexpected Mapping with no pfn for lfn: " + - s2b.s1; - log(mLogMsg,LogManager.ERROR_MESSAGE_LEVEL); - } - prev = curr; - } - else if (s2b.rc != RLSClient.RLS_LFN_NEXIST) { - mLogMsg = "bulkLookupNoAttributes(Set): " + - mRLS.getErrorMessage(s2b.rc); - log(mLogMsg,LogManager.ERROR_MESSAGE_LEVEL); - } - //prev = curr; - } - } - catch (Exception e) { - log("bulkLookupNoAttributes(Set):", e, - LogManager.FATAL_MESSAGE_LEVEL); - System.exit(1); - } - - return result; - } - - /** - * Constructs replica catalog exception out the RLSException that is - * thrown by the API underneath. - * - * @param prefix the prefix that is to be applied to the message - * passed while creating the exception. - * @param e the RLSException that is caught underneath. - * - * @return a ReplicaCatalogException - */ - private ReplicaCatalogException exception(String prefix,RLSException e){ - StringBuffer message = new StringBuffer(32); - message.append("{LRC ").append(mLRCURL).append("} ") - .append(prefix).append(": ").append(e.getMessage()); - return new ReplicaCatalogException(message.toString(),e); - } - - - /** - * Constructs an exception from the RLSString2Bulk object. - * - * @return a ReplicaCatalogException - */ - private ReplicaCatalogException exception(RLSString2Bulk rs){ - StringBuffer sb = new StringBuffer(32); - sb.append("Error (lfn,pfn,ec)").append(" (") - .append(rs.s1).append(',') - .append(rs.s2).append(',') - .append(rs.rc).append(',').append(mRLS.getErrorMessage(rs.rc)) - .append(')'); - return new ReplicaCatalogException(sb.toString()); - - } - - /** - * Returns a subset of a collection of ReplicaCatalogEntry - * objects that have attributes matchin to the attribute identified by - * the parameters passed. - * - * @param collection the collection of ReplicaCatalogEntry - * objects. - * @param name the attribute name to match. - * @param value the attribute value. - * - * @return Set of matching ReplicaCatalogEntry objects. - */ - private Set subset(Collection collection, String name, - Object value) { - return subset(collection,name,value,false); - } - - - /** - * Returns a subset of a collection of ReplicaCatalogEntry - * objects that have attributes matchin to the attribute identified by - * the parameters passed. - * - * @param collection the collection of ReplicaCatalogEntry - * objects. - * @param name the attribute name to match. - * @param value the attribute value. - * @param onlyPFN boolean to denote if we only want the PFN's - * - * @return Set of ReplicaCatalogEntry objects if onlyPfn - * parameter is set to false, else a Set of pfns. - */ - private Set subset(Collection collection, String name, - Object value, boolean onlyPFN) { - Set s = new HashSet(); - ReplicaCatalogEntry rce; - Object attrVal; - for (Iterator it = collection.iterator(); it.hasNext(); ) { - rce = (ReplicaCatalogEntry) it.next(); - //System.out.println("RCE is " + rce); - attrVal = rce.getAttribute(name); - if ( attrVal != null && attrVal.equals(value)) { - //adding to the set only if - //the attribute existed in the rce - s.add(onlyPFN? - (Object)rce.getPFN(): - rce); - } - } - - return s; - } - - /** - * A helper method that converts RLSString2 to MyRLSString2Bulk object. - * - * @param obj the RLSString2 to convert. - * - * @return the converted MyRLSString2 object. - */ - private RLSString2Bulk convert(RLSString2 obj){ - return new MyRLSString2Bulk(0,obj.s1,obj.s2); - } - - /** - * Logs to the logger object. - * - * @param message the message to be logged. - * @param level the logger level at which the message is to be logged. - */ - private void log(String message,int level){ - message = "{LRC " + mLRCURL + "} " + message; - mLogger.log(message,level); - } - - /** - * Logs to the logger object. - * - * @param message the message to be logged. - * @param e the exception that occured. - * @param level the logger level at which the message is to be logged. - */ - private void log(String message,Exception e,int level){ - message = "{LRC " + mLRCURL + "} " + message; - mLogger.log(message,e,level); - } - - - - /** - * The comparator that is used to group the RLSString2 objects by the - * value in the s1 field. This comparator should only be used for grouping - * purposes not in Sets or Maps etc. - */ - private class RLSString2Comparator implements Comparator { - - /** - * Compares this object with the specified object for order. Returns a - * negative integer, zero, or a positive integer if the first argument is - * less than, equal to, or greater than the specified object. The - * RLSString2 are compared by their s1 field. - * - * @param o1 is the first object to be compared. - * @param o2 is the second object to be compared. - * - * @return a negative number, zero, or a positive number, if the - * object compared against is less than, equals or greater than - * this object. - * @exception ClassCastException if the specified object's type - * prevents it from being compared to this Object. - */ - public int compare(Object o1, Object o2) { - if (o1 instanceof RLSString2 && o2 instanceof RLSString2) { - return ( (RLSString2) o1).s1.compareTo( ( (RLSString2) - o2).s1); - } - else { - throw new ClassCastException("object is not RLSString2"); - } - } - - } - - /** - * The comparator that is used to group the RLSString2Bulk objects by the - * value in the s1 field. This comparator should only be used for grouping - * purposes not in Sets or Maps etc. - */ - private class RLSString2BulkComparator implements Comparator { - - /** - * Compares this object with the specified object for order. Returns a - * negative integer, zero, or a positive integer if the first argument is - * less than, equal to, or greater than the specified object. The - * RLSString2Bulk are compared by their s1 field. - * - * @param o1 is the first object to be compared. - * @param o2 is the second object to be compared. - * - * @return a negative number, zero, or a positive number, if the - * object compared against is less than, equals or greater than - * this object. - * @exception ClassCastException if the specified object's type - * prevents it from being compared to this Object. - */ - public int compare(Object o1, Object o2) { - if (o1 instanceof RLSString2Bulk && o2 instanceof RLSString2Bulk) { - return ( (RLSString2Bulk) o1).s1.compareTo( ( (RLSString2Bulk) - o2).s1); - } - else { - throw new ClassCastException("object is not RLSString2Bulk"); - } - } - - } - - /** - * The comparator that is used to group the RLSAttributeObject objects by the - * value in the key field. This comparator should only be used for grouping - * purposes not in Sets or Maps etc. - */ - private class RLSAttributeComparator implements Comparator { - - /** - * Compares this object with the specified object for order. Returns a - * negative integer, zero, or a positive integer if the first argument is - * less than, equal to, or greater than the specified object. The - * RLSAttributeObject are compared by their s1 field. - * - * @param o1 is the first object to be compared. - * @param o2 is the second object to be compared. - * - * @return a negative number, zero, or a positive number, if the - * object compared against is less than, equals or greater than - * this object. - * @exception ClassCastException if the specified object's type - * prevents it from being compared to this Object. - */ - public int compare(Object o1, Object o2) { - if (o1 instanceof RLSAttributeObject && o2 instanceof RLSAttributeObject) { - return ( (RLSAttributeObject) o1).key.compareTo( ( ( - RLSAttributeObject) o2).key); - } - else { - throw new ClassCastException("object is not RLSAttributeObject"); - } - } - - } - - /** - * The class that extends RLSString2Bulk and adds on the equals method, - * that allows me to do the set operations - */ - private class MyRLSString2Bulk extends RLSString2Bulk{ - - - /** - * The overloaded constructor. - * - * @param rca the rls exitcode - * @param s1a the String object usually containing the lfn - */ - public MyRLSString2Bulk(int rca, java.lang.String s1a){ - super(rca,s1a); - } - - - /** - * The overloaded constructor. - * - * @param rca the rls exitcode. - * @param s1a the String object usually containing the lfn. - * @param s2a the String object usually containing the pfn. - */ - public MyRLSString2Bulk(int rca, java.lang.String s1a, java.lang.String s2a){ - super(rca,s1a,s2a); - } - - /** - * Indicates whether some other object is "equal to" this one. - * - * An object is considered equal if it is of the same type and - * all the fields s1 and s2 match. - * - * @return boolean whether the object is equal or not. - */ - public boolean equals(Object obj){ - if(obj instanceof MyRLSString2Bulk){ - MyRLSString2Bulk sec = (MyRLSString2Bulk)obj; - return this.s1.equals(sec.s1) && this.s2.equals(sec.s2); - } - return false; - } - - /** - * Returns a string representation of the object. - * - * @return the String representation. - */ - public String toString(){ - StringBuffer sb = new StringBuffer(10); - sb.append("(").append(s1).append("->").append(s2). - append(",").append(rc).append(")"); - return sb.toString(); - } - } - - /** - * Testing function. - */ - public static void main(String[] args){ - LRC lrc = new LRC(); - lrc.connect("rls://sukhna.isi.edu"); - String lfn = "test"; - LogManagerFactory.loadSingletonInstance().setLevel(LogManager.DEBUG_MESSAGE_LEVEL); - - /* - ReplicaCatalogEntry rce = new ReplicaCatalogEntry("gsiftp://sukhna.isi.edu/tmp/test"); - rce.addAttribute("name","karan"); - lrc.insert("test",rce); - lrc.insert("test","gsiftp://sukhna.isi.edu/tmp/test1","isi"); - lrc.insert("test","gsiftp://sukhna.isi.edu/constraint/testvahi","isi"); - lrc.insert("vahi.f.a","file:///tmp/vahi.f.a","isi"); - lrc.insert("testvahi.f.a","file:///tmp/testvahi.f.a","isi"); - - rce = new ReplicaCatalogEntry("gsiftp://sukhna.isi.edu/tmp/testX"); - rce.addAttribute("name","karan"); - rce.addAttribute("pool","isi"); - lrc.insert("testX",rce); - */ - - /* - System.out.println("Getting list of lfns"); - System.out.println("\t" + lrc.list()); - - - - Set s = new HashSet(); - s.add("test");s.add("vahi.f.a");s.add("testX"); - s.add("unknown"); - - - System.out.println("\nQuerying for complete RCE for site " + s ); - System.out.println(lrc.lookup(s)); - */ - - /* - System.out.println("\n Deleting " + lfn); - System.out.println(lrc.deleteByResource(lfn,"isi")); - - - System.out.println("\nQuerying for PFN for site" + s ); - System.out.println(lrc.lookupNoAttributes(s,"isi")); - - System.out.println("\nRemoving lfns " + s); - //System.out.println(lrc.remove(s)); - System.out.println(lrc.removeByAttribute("isi")); - - - System.out.println("\n\nClearing catalog " + lrc.clear()); - */ - - //System.out.println("Getting list of lfns"); - //System.out.println("\t" + lrc.listLFNPFN("*vahi*",false)); - - /* - System.out.println("Removing lfns in set " + s + " "); - System.out.println(lrc.removeByAttribute("isi")); - - Map m = new HashMap(); - //m.put("pfn","*vahi*"); - m.put("lfn","test*"); - System.out.println("Getting lfns matching constraint"); - System.out.println("\t" + lrc.lookup(m)); - */ - - - //test bulk insert - System.out.println("Clearing the database"); - //lrc.clear(); - Map inserts = new HashMap(); - Collection c1 = new ArrayList(); - c1.add(new ReplicaCatalogEntry("gsiftp://test/f.a","isi")); - Collection c2 = new ArrayList(); - c2.add(new ReplicaCatalogEntry("gsiftp://test/f.b","isi")); - Collection c3 = new ArrayList(); - c3.add(new ReplicaCatalogEntry("gsiftp://test/f.c","isi1")); - inserts.put("f.a",c1); - inserts.put("f.b",c2); - inserts.put("f.c",c3); - System.out.println("Doing bulk inserts"); - try{ - System.out.println("Inserted " + lrc.insert(inserts) + " entries"); - } - catch(ReplicaCatalogException rce){ - do { - System.out.println(rce.getMessage()); - rce = (ReplicaCatalogException) rce.getNextException(); - } while ( rce != null ); - - } - - lrc.close(); - } - - -} //end of class LRC Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/catalog/replica/impl/RLI.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/catalog/replica/impl/RLI.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,1988 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package edu.isi.pegasus.planner.catalog.replica.impl; - -import edu.isi.pegasus.planner.catalog.replica.*; -import edu.isi.pegasus.common.logging.LogManagerFactory; -import edu.isi.pegasus.common.logging.LogManager; - -import edu.isi.pegasus.planner.catalog.ReplicaCatalog; -import edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry; -import edu.isi.pegasus.planner.catalog.CatalogException; - -import edu.isi.pegasus.common.util.Version; -import org.globus.replica.rls.RLSClient; -import org.globus.replica.rls.RLSException; -import org.globus.replica.rls.RLSAttribute; -import org.globus.replica.rls.RLSAttributeObject; -import org.globus.replica.rls.RLSLRCInfo; -import org.globus.replica.rls.RLSString2Bulk; -import org.globus.replica.rls.RLSString2; - -import java.util.Collection; -import java.util.Collections; -import java.util.Comparator; -import java.util.Map; -import java.util.HashMap; -import java.util.Set; -import java.util.HashSet; -import java.util.Properties; -import java.util.List; -import java.util.ArrayList; -import java.util.LinkedHashSet; -import java.util.Iterator; - -/** - * This class implements the VDS replica catalog interface on top of RLI API. - * A thing to take care of is that all delete and remove operations are - * propoagated to all the Local Replica Catalogs (LRCs) reporting to the RLI. - * Hence, - * you should be careful while deleting LFNs, as deletions can cascade to - * multiple LRCs. If you want to delete or remove an LFN from a particular LRC, - * use the LRC implementation to connect to that LRC and call the corresponding - * delete functions on that. - * There is no transaction support in the implementation. The implementation - * is best effort. Inconsistencies can occur if one of the LRCs goes offline, - * or an operation fails for whatsoever reason. - * - * @author Karan Vahi - * @author Gaurang Mehta - * - * @version $Revision: 2079 $ - */ -public class RLI implements ReplicaCatalog { - - /** - * The number of entries searched in each bulk query to RLS. - */ - public static final int RLS_BULK_QUERY_SIZE = 1000; - - /** - * The default timeout in seconds to be used while querying the RLI. - */ - public static final String DEFAULT_RLI_TIMEOUT = "30"; - - /** - * The key that is used to get hold of the timeout value from the properties - * object. - */ - public static final String RLS_TIMEOUT_KEY = "rls.timeout"; - - /** - * The key that is used to get hold of the timeout value from the properties - * object. - */ - public static final String RLI_TIMEOUT_KEY = "rli.timeout"; - - /** - * The key that is used to designate the LRC whose results are to be - * ignored. - */ - public static final String LRC_IGNORE_KEY = "lrc.ignore"; - - /** - * The key that is used to designate the LRC whose results are to be - * restricted. - */ - public static final String LRC_RESTRICT_KEY = "lrc.restrict"; - - /** - * The attribute in RLS that maps to a site handle. - */ - public static final String SITE_ATTRIBUTE = "pool"; - - /** - * The key that is used to get hold of the url from the properties object. - */ - public static final String URL_KEY = "url"; - - /** - * The key that if set, specifies the proxy to be picked up while connecting - * to the RLS. - */ - public static final String PROXY_KEY = "proxy"; - - /** - * The error message for not connected to RLI. - */ - public static final String RLI_NOT_CONNECTED_MSG = "Not connected to RLI "; - - /** - * The error message for not connected to LRC. - */ - public static final String LRC_NOT_CONNECTED_MSG = "Unable to connect to LRC "; - - - /** - * The LRC query state indicating that LRC needs to queried fully. The LRC - * returns all PFNs irrespective of whether they have a site attribute or - * not. - */ - public static final int LRC_QUERY_NORMAL = 0; - - /** - * The LRC query state indicating that LRC has to be restricted query. - * LRC should return only PFNs with site attributes tagged. - */ - public static final int LRC_QUERY_RESTRICT = 1; - - /** - * The LRC query state indicating that LRC has to be ignored. - */ - public static final int LRC_QUERY_IGNORE = 2; - - - /** - * The handle to the client that allows access to both the RLI and the LRC - * running at the url specified while connecting. - */ - private RLSClient mRLS; - - /** - * The handle to the client that allows access to the LRC running at the - * url specified while connecting. - */ - private RLSClient.RLI mRLI; - - /** - * The url to the RLI to which this instance implementation talks to. - */ - private String mRLIURL; - - /** - * A String array contains the LRC URLs that have to be ignored for querying. - */ - private String[] mLRCIgnoreList; - - /** - * A String array contains the LRC URLs that have to be restricted for querying. - * Only those entries are returned that have a site attribute associated - * with them. - */ - private String[] mLRCRestrictList; - - - /** - * The handle to the logging object. Should be log4j soon. - */ - private LogManager mLogger; - - /** - * The string holding the message that is logged in the logger. - */ - private String mLogMsg; - - - /** - * The properties object containing all the properties, that are required - * to connect to a RLS. - */ - private Properties mConnectProps; - - /** - * The batch size while querying the RLI in the bulk mode. - */ - private int mBatchSize; - - /** - * The timeout in seconds to be applied while querying the RLI. - */ - private int mTimeout; - - /** - * The default constructor, that creates an object which is not linked with - * any RLS. Use the connect method to connect to the RLS. - * - * @see #connect(Properties). - */ - public RLI() { - mRLS = null; - mLogger = LogManagerFactory.loadSingletonInstance(); - mConnectProps = new Properties(); - mBatchSize = this.RLS_BULK_QUERY_SIZE; - mTimeout = Integer.parseInt(DEFAULT_RLI_TIMEOUT); - - } - - /** - * Establishes a connection to the RLI, picking up the proxy from the default - * location usually /tmp/ directory. - * - * @param url the url to lrc to connect to. - * - * @return true if connected now, or false to indicate a failure. - */ - public boolean connect(String url) { - return connect(url,null); - } - - - /** - * Establishes a connection to the RLI. - * - * @param props contains all necessary data to establish the link. - * - * @return true if connected now, or false to indicate a failure. - */ - public boolean connect(Properties props) { - boolean con = false; - Object obj = props.remove(URL_KEY); - mRLIURL = (obj == null) ? null : (String) obj; - - if (mRLIURL == null) { - //nothing to connect to. - mLogger.log("The RLI url is not specified", - LogManager.ERROR_MESSAGE_LEVEL); - return con; - } - - //try to see if a proxy cert has been specified or not - String proxy = props.getProperty(PROXY_KEY); - mConnectProps = props;//?? - - mLogger.log( "[RLI-RC] Connection properties passed are " + props, - LogManager.DEBUG_MESSAGE_LEVEL ); - - mLRCIgnoreList = this.getRLSLRCIgnoreURLs( props ); - mLRCRestrictList = this.getRLSLRCRestrictURLs( props ); - - - //determine timeout - mTimeout = getTimeout(props); - - //set the batch size for queries - setBatchSize(props); - - return connect(mRLIURL, proxy); - } - - /** - * Establishes a connection to the RLI. - * - * @param url the url to lrc to connect to. - * @param proxy the path to the proxy file to be picked up. null denotes - * default location. - * - * @return true if connected now, or false to indicate a failure. - */ - public boolean connect(String url, String proxy) { - mRLIURL = url; - //push it into the internal properties object - mConnectProps.setProperty(URL_KEY,url); - if(proxy != null){ - mConnectProps.setProperty(PROXY_KEY, proxy); - } - try { - mRLS = (proxy == null) ? - new RLSClient(url) : //proxy is picked up from default loc /tmp - new RLSClient(url, proxy); - - //set RLI timeout - mRLS.SetTimeout(mTimeout); - - //connect is only successful if we have - //successfully connected to the LRC - mRLI = mRLS.getRLI(); - - } - catch (RLSException e) { - mLogger.log("RLS Exception", e,LogManager.ERROR_MESSAGE_LEVEL); - return false; - } - return true; - } - - - /** - * Gets a handle to the RLI that is associated with the RLS running at - * url. - * - * @return RLSClient.RLI that points to the RLI that is - * running , or null in case connect method not being called. - * @see #mRLIURL - */ - public RLSClient.RLI getRLI() { - return (this.isClosed()) ? null: mRLS.getRLI() ; - } - - /** - * Gets a handle to the LRC that is associated with the RLS running at - * url. - * - * @return RLSClient.LRC that points to the RLI that is - * running , or null in case connect method not being called. - * @see #mRLIURL - */ - public RLSClient.LRC getLRC() { - return (this.isClosed()) ? null : mRLS.getLRC(); - } - - /** - * Retrieves the entry for a given filename and resource handle from - * the RLS. - * - * @param lfn is the logical filename to obtain information for. - * @param handle is the resource handle to obtain entries for. - * - * @return the (first) matching physical filename, or - * null if no match was found. - */ - public String lookup(String lfn, String handle) { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - String pfn = null; - ArrayList lrcList = null; - try { - lrcList = mRLI.getLRC(lfn); - for (Iterator it = lrcList.iterator(); it.hasNext(); ) { - //connect to an lrc - String lrcURL = ( (RLSString2) it.next()).s2; - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,lrcURL); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + lrcURL, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //query the lrc - try{ - pfn = lrc.lookup(lfn,handle); - if(pfn != null) - return pfn; - } - catch(Exception ex){ - mLogger.log("lookup(String,String)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - } - } - catch (RLSException ex) { - mLogger.log("lookup(String,String)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - - return null; - } - - /** - * Retrieves all entries for a given LFN from the replica catalog. - * Each entry in the result set is a tuple of a PFN and all its - * attributes. - * - * @param lfn is the logical filename to obtain information for. - * - * @return a collection of replica catalog entries, or null in case of - * unable to connect to RLS. - * - * @see ReplicaCatalogEntry - */ - public Collection lookup(String lfn) { - Set lfns = new HashSet(); - lfns.add( lfn ); - - Map> result = this.lookup( lfns ); - - if( result == null ){ - return null; - } - else{ - Collection values = result.get( lfn ); - if( values == null ){ - //JIRA PM-74 - values = new ArrayList(); - } - return values; - } - - } - - - - /** - * Retrieves all entries for a given LFN from the replica catalog. - * Each entry in the result set is just a PFN string. Duplicates - * are reduced through the set paradigm. - * - * @param lfn is the logical filename to obtain information for. - * @return a set of PFN strings, or null in case of unable to connect - * to RLS. - * - */ - public Set lookupNoAttributes(String lfn) { - Set lfns = new HashSet(); - lfns.add( lfn ); - - Map> result = this.lookupNoAttributes( lfns ); - - if( result == null ){ - return null; - } - else{ - Set values = result.get( lfn ); - if( values == null ){ - //JIRA PM-74 - values = new HashSet(); - } - return values; - } - - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete LRC. It uses the bulk query api to the LRC to query for stuff. - * Bulk query has been in RLS since version 2.0.8. Internally, the bulk - * queries are done is sizes specified by variable mBatchSize. - * - * @param lfns is a set of logical filename strings to look up. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries for the LFN. - * - * @see ReplicaCatalogEntry - * @see #getBatchSize() - */ - public Map lookup(Set lfns) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Map lrc2lfn = this.getLRC2LFNS(lfns); - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return null; - } - - // now query the LRCs with the LFNs that they are responsible for - // and aggregate stuff. - String key = null; - Map result = new HashMap(lfns.size()); - String message; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Querying LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //query the lrc - try{ - Map m = lrc.lookup((Set)entry.getValue()); - - //figure out if we need to restrict our queries or not. - //restrict means only include results if they have a site - //handle associated - boolean restrict = ( this.determineQueryType(key) == this.LRC_QUERY_RESTRICT ); - - for(Iterator mit = m.entrySet().iterator();mit.hasNext();){ - entry = (Map.Entry)mit.next(); - List pfns = (( List )entry.getValue()); - if ( restrict ){ - //traverse through all the PFN's and check for resource handle - for ( Iterator pfnIterator = pfns.iterator(); pfnIterator.hasNext(); ){ - ReplicaCatalogEntry pfn = (ReplicaCatalogEntry) pfnIterator.next(); - if ( pfn.getResourceHandle() == null ){ - //do not include in the results if the entry does not have - //a pool attribute associated with it. - mLogger.log("Ignoring entry " + entry.getValue() + - " from LRC " + key, - LogManager.DEBUG_MESSAGE_LEVEL); - pfnIterator.remove(); - } - } - - } - - //if pfns are empty which could be due to - //restriction case taking away all pfns - //do not merge in result - if( pfns.isEmpty() ){ continue; } - - //merge the entries into the main result - key = (String)entry.getKey(); //the lfn - if( result.containsKey(key) ){ - //right now no merging of RCE being done on basis - //on them having same pfns. duplicate might occur. - ((List)result.get(key)).addAll( pfns ); - } - else{ - result.put( key, pfns ); - } - } - } - catch(Exception ex){ - mLogger.log("lookup(Set)",ex,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - - - mLogger.log( message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - return result; - } - - /** - * Retrieves all entries for a given LFN from the replica catalog. - * Each entry in the result set is just a PFN string. Duplicates - * are reduced through the set paradigm. - * - * @param lfns is a set of logical filename strings to look up. - * @return a map indexed by the LFN. Each value is a collection - * of PFN's for the LFN. - */ - public Map lookupNoAttributes(Set lfns) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Map lrc2lfn = this.getLRC2LFNS(lfns); - if(lrc2lfn == null){ - //probably RLI is not connected!! - return null; - } - - // now query the LRCs with the LFNs that they are responsible for - // and aggregate stuff. - String key = null; - String message; - Map result = new HashMap(lfns.size()); - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Querying LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //query the lrc - try{ - Map m = lrc.lookupNoAttributes((Set)entry.getValue()); - for(Iterator mit = m.entrySet().iterator();mit.hasNext();){ - entry = (Map.Entry)mit.next(); - //merge the entries into the main result - key = (String)entry.getKey(); //the lfn - if(result.containsKey(key)){ - //right now no merging of RCE being done on basis - //on them having same pfns. duplicate might occur. - ((Set)result.get(key)).addAll((Set)entry.getValue()); - } - else{ - result.put(key,entry.getValue()); - } - } - } - catch(Exception ex){ - mLogger.log("lookup(Set)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - - - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - return result; - - } - - /** - * Retrieves multiple entries for a given logical filenames, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * @param lfns is a set of logical filename strings to look up. - * @param handle is the resource handle, restricting the LFNs. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries (all attributes). - * - * @see ReplicaCatalogEntry - */ - public Map lookup(Set lfns, String handle) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Map lrc2lfn = this.getLRC2LFNS(lfns); - if(lrc2lfn == null){ - //probably RLI is not connected!! - return null; - } - - // now query the LRCs with the LFNs they are responsible for - // and aggregate stuff. - String key = null,message = null; - Map result = new HashMap(lfns.size()); - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Querying LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //query the lrc - try{ - Map m = lrc.lookup((Set)entry.getValue(),handle); - for(Iterator mit = m.entrySet().iterator();mit.hasNext();){ - entry = (Map.Entry)mit.next(); - //merge the entries into the main result - key = (String)entry.getKey(); //the lfn - if(result.containsKey(key)){ - //right now no merging of RCE being done on basis - //on them having same pfns. duplicate might occur. - ((Set)result.get(key)).addAll((Set)entry.getValue()); - } - else{ - result.put(key,entry.getValue()); - } - } - } - catch(Exception ex){ - mLogger.log("lookup(Set,String)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - - - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - return result; - - - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * The noAttributes flag is missing on purpose, because - * due to the resource handle, attribute lookups are already required. - * - * @param lfns is a set of logical filename strings to look up. - * @param handle is the resource handle, restricting the LFNs. - * - * @return a map indexed by the LFN. Each value is a set of - * physical filenames. - */ - public Map lookupNoAttributes( Set lfns, String handle ){ - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Map lrc2lfn = this.getLRC2LFNS(lfns); - if(lrc2lfn == null){ - //probably RLI is not connected!! - return null; - } - - // now query the LRCs with the LFNs that they are responsible for - // and aggregate stuff. - String key = null,message = null; - Map result = new HashMap(lfns.size()); - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Querying LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //query the lrc - try{ - Map m = lrc.lookupNoAttributes((Set)entry.getValue(),handle); - for(Iterator mit = m.entrySet().iterator();mit.hasNext();){ - entry = (Map.Entry)mit.next(); - //merge the entries into the main result - key = (String)entry.getKey(); //the lfn - if(result.containsKey(key)){ - //right now no merging of RCE being done on basis - //on them having same pfns. duplicate might occur. - ((Set)result.get(key)).addAll((Set)entry.getValue()); - } - else{ - result.put(key,entry.getValue()); - } - } - } - catch(Exception ex){ - mLogger.log("lookup(Set,String):",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - - - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - return result; - - } - - /** - * Retrieves multiple entries for a given logical filename, up to the - * complete catalog. Retrieving full catalogs should be harmful, but - * may be helpful in online display or portal.

- * - * - * At present it DOES NOT SUPPORT ATTRIBUTE MATCHING. - * - * @param constraints is mapping of keys 'lfn', 'pfn' to a string that - * has some meaning to the implementing system. This can be a SQL - * wildcard for queries, or a regular expression for Java-based memory - * collections. Unknown keys are ignored. Using an empty map requests - * the complete catalog. - * - * @return a map indexed by the LFN. Each value is a collection - * of replica catalog entries. - * - * @see ReplicaCatalogEntry - */ - public Map lookup(Map constraints) { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - Map result = new HashMap(); - String url = null,message = null; - //we need to get hold of all the LRC - //that report to the RLI and call the - //list() method on each of them - for(Iterator it = this.getReportingLRC().iterator();it.hasNext();){ - url = (String)it.next(); - message = "Querying LRC " + url; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,url); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + url, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - try{ - Map m = lrc.lookup(constraints); - for(Iterator mit = m.entrySet().iterator();mit.hasNext();){ - Map.Entry entry = (Map.Entry)mit.next(); - //merge the entries into the main result - String key = (String)entry.getKey(); //the lfn - if(result.containsKey(key)){ - //right now no merging of RCE being done on basis - //on them having same pfns. duplicate might occur. - ((List)result.get(key)).addAll((List)entry.getValue()); - } - else{ - result.put(key,entry.getValue()); - } - } - - } - catch(Exception e){ - mLogger.log("list(String)",e,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - lrc.close(); - } - } - - return result; - - } - - /** - * Lists all logical filenames in the catalog. - * - * @return A set of all logical filenames known to the catalog. - */ - public Set list() { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - Set result = new HashSet(); - String url = null,message = null; - //we need to get hold of all the LRC - //that report to the RLI and call the - //list() method on each of them - for(Iterator it = this.getReportingLRC().iterator();it.hasNext();){ - url = (String)it.next(); - message = "Querying LRC " + url; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,url); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + url, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - try{ - result.addAll(lrc.list()); - } - catch(Exception e){ - mLogger.log("list()",e,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - } - - /** - * Lists a subset of all logical filenames in the catalog. - * - * @param constraint is a constraint for the logical filename only. It - * is a string that has some meaning to the implementing system. This - * can be a SQL wildcard for queries, or a regular expression for - * Java-based memory collections. - * - * @return A set of logical filenames that match. The set may be empty - */ - public Set list(String constraint) { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - Set result = new HashSet(); - String url = null,message = null; - //we need to get hold of all the LRC - //that report to the RLI and call the - //list() method on each of them - for(Iterator it = this.getReportingLRC().iterator();it.hasNext();){ - url = (String)it.next(); - message = "Querying LRC " + url; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,url); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + url, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - try{ - result.addAll(lrc.list(constraint)); - } - catch(Exception e){ - mLogger.log("list(String)",e,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - } - - /** - * Inserts a new mapping into the LRC running at the URL, where the RLI - * is running. - * - * @param lfn is the logical filename under which to book the entry. - * @param tuple is the physical filename and associated PFN attributes. - * - * @return number of insertions, should always be 1. On failure, - * throws a RuntimeException. - */ - public int insert(String lfn, ReplicaCatalogEntry tuple) { - //get hold of the LRC if that is running - LRC lrc = new LRC(); - int result = 1; - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - throw new RuntimeException(LRC_NOT_CONNECTED_MSG + - mConnectProps.getProperty(URL_KEY)); - } - result = lrc.insert(lfn,tuple); - //better to keep a handle to the running LRC - //as a member variable, and close it in - //RLI.close() - lrc.close(); - return result; - - } - - /** - * Inserts a new mapping into the LRC running at the URL, where the RLI - * is running. - * This is a convenience function exposing the resource handle. Internally, - * the ReplicaCatalogEntry element will be contructed, and passed to - * the appropriate insert function. - * - * @param lfn is the logical filename under which to book the entry. - * @param pfn is the physical filename associated with it. - * @param handle is a resource handle where the PFN resides. - * - * @return number of insertions, should always be 1. On failure, - * throws a RuntimeException. - * - * @see #insert( String, ReplicaCatalogEntry ) - * @see ReplicaCatalogEntry - */ - public int insert(String lfn, String pfn, String handle) { - //get hold of the LRC if that is running - LRC lrc = new LRC(); - int result = 1; - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - throw new RuntimeException(LRC_NOT_CONNECTED_MSG + - mConnectProps.getProperty(URL_KEY)); - } - result = lrc.insert(lfn,pfn,handle); - //better to keep a handle to the running LRC - //as a member variable, and close it in - //RLI.close() - lrc.close(); - return result; - - } - - /** - * Inserts multiple mappings into the replica catalog. The input is a - * map indexed by the LFN. The value for each LFN key is a collection - * of replica catalog entries. - * - * @param x is a map from logical filename string to list of replica - * catalog entries. - * - * @return the number of insertions. - * @see ReplicaCatalogEntry - */ - public int insert(Map x) { - //get hold of the LRC if that is running - LRC lrc = new LRC(); - int result = 1; - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - throw new RuntimeException(LRC_NOT_CONNECTED_MSG + - mConnectProps.getProperty(URL_KEY)); - } - result = lrc.insert(x); - //better to keep a handle to the running LRC - //as a member variable, and close it in - //RLI.close() - lrc.close(); - return result; - - } - - /** - * Deletes a specific mapping from the replica catalog. We don't care - * about the resource handle. More than one entry could theoretically - * be removed. Upon removal of an entry, all attributes associated - * with the PFN also evaporate (cascading deletion). - * - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfn is the logical filename in the tuple. - * @param pfn is the physical filename in the tuple. - * - * @return the number of removed entries. - */ - public int delete(String lfn, String pfn) { - ReplicaCatalogEntry rce = new ReplicaCatalogEntry(pfn); - return delete(lfn,rce); - } - - /** - * Deletes a very specific mapping from the replica catalog. The LFN - * must be matches, the PFN, and all PFN attributes specified in the - * replica catalog entry. More than one entry could theoretically be - * removed. Upon removal of an entry, all attributes associated with - * the PFN also evaporate (cascading deletion). - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfn is the logical filename in the tuple. - * @param tuple is a description of the PFN and its attributes. - * - * @return the number of removed entries, either 0 or 1. - */ - public int delete(String lfn, ReplicaCatalogEntry tuple) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Set lfns = new HashSet(1); - lfns.add(lfn); - Map lrc2lfn = this.getLRC2LFNS(lfns); - int result = 0; - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return 0; - } - - // call the delete function on the individual - // LRCs where the mapping resides - String key = null,message = null; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Querying LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //delete from the LRC - try{ - result += lrc.delete(lfn,tuple); - } - catch(Exception ex){ - mLogger.log("delete(String, ReplicaCatalogEntry)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - - } - - /** - * Deletes all PFN entries for a given LFN from the replica catalog - * where the PFN attribute is found, and matches exactly the object - * value. This method may be useful to remove all replica entries that - * have a certain MD5 sum associated with them. It may also be harmful - * overkill. - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfn is the logical filename to look for. - * @param name is the PFN attribute name to look for. - * @param value is an exact match of the attribute value to match. - * - * @return the number of removed entries. - */ - public int delete(String lfn, String name, Object value) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Set lfns = new HashSet(1); - lfns.add(lfn); - Map lrc2lfn = this.getLRC2LFNS(lfns); - int result = 0; - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return 0; - } - - // call the delete function on the individual - // LRCs where the mapping resides - String key = null,message = null; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Deleting from LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //delete from the LRC - try{ - result += lrc.delete(lfn,name,value); - } - catch(Exception ex){ - mLogger.log("delete(String, String, Object)", - ex,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - - } - - /** - * Deletes all PFN entries for a given LFN from the replica catalog - * where the resource handle is found. Karan requested this - * convenience method, which can be coded like - * 

-      *  delete( lfn, SITE_ATTRIBUTE, handle )
-      *
- * - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfn is the logical filename to look for. - * @param handle is the resource handle - * - * @return the number of entries removed. - */ - public int deleteByResource(String lfn, String handle) { - return delete(lfn,SITE_ATTRIBUTE,handle); - } - - /** - * Deletes multiple mappings into the replica catalog. The input is a - * map indexed by the LFN. The value for each LFN key is a collection - * of replica catalog entries. On setting matchAttributes to false, all entries - * having matching lfn pfn mapping to an entry in the Map are deleted. - * However, upon removal of an entry, all attributes associated with the pfn - * also evaporate (cascaded deletion). - * The deletes are done in batches. - * - * @param x is a map from logical filename string to list of - * replica catalog entries. - * @param matchAttributes whether mapping should be deleted only if all - * attributes match. - * - * @return the number of deletions. - * @see ReplicaCatalogEntry - */ - public int delete( Map x , boolean matchAttributes){ - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Set lfns = new HashSet(x.size()); - for(Iterator it = x.keySet().iterator();it.hasNext();){ - lfns.add( (String)it.next()); - } - Map lrc2lfn = this.getLRC2LFNS(lfns); - int result = 0; - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return 0; - } - - //compose an exception that might need to be thrown - CatalogException exception = new ReplicaCatalogException(); - - // call the delete function on the individual - // LRCs where the mapping resides - String key = null,message = null; - String lfn; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = ( String )entry.getKey(); - lfns = ( Set )entry.getValue(); - message = "Deleting from LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //compose the map to delete for a particular LRC - Map lmap = new HashMap(lfns.size()); - for(Iterator lfnIt = lfns.iterator();lfnIt.hasNext();){ - lfn = (String)lfnIt.next(); - lmap.put(lfn,x.get(lfn)); - } - - //delete from the LRC - try{ - result += lrc.delete(x,matchAttributes); - } - catch(ReplicaCatalogException e){ - exception.setNextException(e); - } - catch(Exception ex){ - mLogger.log("delete(Map,boolean)", - ex,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - - //throw an exception only if a nested exception - if( (exception = exception.getNextException()) != null) throw exception; - - return result; - - } - - /** - * Removes all mappings for an LFN from the replica catalog. - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfn is the logical filename to remove all mappings for. - * - * @return the number of removed entries. - */ - public int remove(String lfn) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Set lfns = new HashSet(1); - lfns.add(lfn); - Map lrc2lfn = this.getLRC2LFNS(lfns); - int result = 0; - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return 0; - } - - // call the delete function on the individual - // LRCs where the mapping resides - String key = null,message = null; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Deleting from LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //delete from the LRC - try{ - result += lrc.remove(lfn); - } - catch(Exception ex){ - mLogger.log("remove(String):",ex, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - - } - - /** - * Removes all mappings for a set of LFNs. - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param lfns is a set of logical filename to remove all mappings for. - * - * @return the number of removed entries. - */ - public int remove(Set lfns) { - //Map indexed by lrc url and each value a collection - //of lfns that the RLI says are present in it. - Map lrc2lfn = this.getLRC2LFNS(lfns); - int result = 0; - Set s = null; - - if(lrc2lfn == null){ - //probably RLI is not connected!! - return 0; - } - - // call the delete function on the individual - // LRCs where the mapping resides - String key = null,message = null; - for(Iterator it = lrc2lfn.entrySet().iterator();it.hasNext();){ - Map.Entry entry = (Map.Entry)it.next(); - key = (String)entry.getKey(); - message = "Deleting from LRC " + key; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,key); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + key, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - - //delete from the LRC - try{ - s = (Set)entry.getValue(); - mLogger.log("\tDeleting the following lfns " + s, - LogManager.DEBUG_MESSAGE_LEVEL); - result += lrc.remove((Set)entry.getValue()); - } - catch(Exception ex){ - mLogger.log("remove(Set)",ex,LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - //disconnect - lrc.close(); - } - mLogger.log(message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - - } - - /** - * Removes all entries from the replica catalog where the PFN attribute - * is found, and matches exactly the object value. - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param name is the PFN attribute name to look for. - * @param value is an exact match of the attribute value to match. - * - * @return the number of removed entries. - */ - public int removeByAttribute(String name, Object value) { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - int result = 0; - String url = null; - //we need to get hold of all the LRC - //that report to the RLI and call the - //list() method on each of them - for(Iterator it = this.getReportingLRC().iterator();it.hasNext();){ - url = (String)it.next(); - - mLogger.log("Removing from LRC " + url,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,url); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + url, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - try{ - result += lrc.removeByAttribute(name,value); - } - catch(Exception e){ - mLogger.log("removeByAttribute(String,Object)",e, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - lrc.close(); - } - mLogger.log( "Removing from LRC " + url + LogManager.MESSAGE_DONE_PREFIX, - LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - - } - - /** - * Removes all entries associated with a particular resource handle. - * This is useful, if a site goes offline. It is a convenience method, - * which calls the generic removeByAttribute method. - * It can result in a deletion of more than one entry, and from more - * than one local replica catalog that might be reporting to the RLI. - * - * @param handle is the site handle to remove all entries for. - * - * @return the number of removed entries. - * @see #removeByAttribute( String, Object ) - */ - public int removeByAttribute(String handle) { - return removeByAttribute(SITE_ATTRIBUTE,handle); - } - - /** - * Removes everything from all the LRCs that report to this RLI. - * Use with caution! - * - * @return the number of removed entries. - */ - public int clear() { - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - int result = 0; - String url = null,message = null; - //we need to get hold of all the LRC - //that report to the RLI and call the - //list() method on each of them - for(Iterator it = this.getReportingLRC().iterator();it.hasNext();){ - url = (String)it.next(); - message = "Querying LRC " + url; - mLogger.log(message,LogManager.DEBUG_MESSAGE_LEVEL); - - //push the lrcURL to the properties object - mConnectProps.setProperty(this.URL_KEY,url); - LRC lrc = new LRC(); - if(!lrc.connect(mConnectProps)){ - //log an error/warning message - mLogger.log("Unable to connect to LRC " + url, - LogManager.ERROR_MESSAGE_LEVEL); - continue; - } - try{ - result += lrc.clear(); - } - catch(Exception e){ - mLogger.log("list(String)",e, - LogManager.ERROR_MESSAGE_LEVEL); - } - finally{ - lrc.close(); - } - mLogger.log( message + LogManager.MESSAGE_DONE_PREFIX,LogManager.DEBUG_MESSAGE_LEVEL); - } - - return result; - } - - /** - * Explicitely free resources before the garbage collection hits. - */ - public void close() { - try{ - if (mRLS != null) - mRLS.Close(); - } - catch(RLSException e){ - //ignore - } - finally{ - mRLS = null; - } - } - - /** - * Returns whether the connection to the RLS with which this instance is - * associated is closed or not. - * - * @return true, if the implementation is disassociated, false otherwise. - * @see #close() - */ - public boolean isClosed() { - return (mRLS == null); - } - - - /** - * It returns the timeout value in seconds after which to timeout in case of - * no activity from the RLI. - * - * Referred to by the "rli.timeout" property. - * - * @param properties the properties passed in the connect method. - * - * @return the timeout value if specified else, - * the value specified by "rls.timeout" property, else - * DEFAULT_RLI_TIMEOUT. - * - * @see #DEFAULT_RLI_TIMEOUT - */ - public int getTimeout(Properties properties) { - String prop = properties.getProperty( this.RLI_TIMEOUT_KEY); - - //if prop is null get rls timeout, - prop = (prop == null)? properties.getProperty(this.RLS_TIMEOUT_KEY):prop; - - int val = 0; - try { - val = Integer.parseInt( prop ); - } catch ( Exception e ) { - val = Integer.parseInt( DEFAULT_RLI_TIMEOUT ); - } - return val; - - } - - - - /** - * Sets the number of lfns in each batch while querying the lrc in the - * bulk mode. - * - * @param properties the properties passed while connecting. - * - */ - protected void setBatchSize(Properties properties) { - String s = properties.getProperty(this.BATCH_KEY); - int size = this.RLS_BULK_QUERY_SIZE; - try{ - size = Integer.parseInt(s); - } - catch(Exception e){} - mBatchSize = size; - } - - - /** - * Returns the number of lfns in each batch while querying the lrc in the - * bulk mode. - * - * @return the batch size. - */ - protected int getBatchSize() { - return mBatchSize; - } - - - /** - * Returns a map indexed by lrc urls. Each value is a set of - * String objects referring to the logical filenames whose mappings reside - * at a particular lrc amongst the set of logical filenames passed. - * - * @param lfns the set of lfns queried to the RLI. - * - * @return Map indexed by lrc urls. Each value is a set of lfn strings. - * null in case the connection to RLI is closed or error. - */ - private Map getLRC2LFNS(Set lfns){ - int batch = lfns.size() > mBatchSize ? mBatchSize:lfns.size(); - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - - Map lrc2lfn = new HashMap();//indexed by lrc url and each value a collection - //of lfns that the RLI says are present init. - //get a handle to the rli - - //we need to query the RLI in batches - for (Iterator it = lfns.iterator(); it.hasNext(); ) { - ArrayList l = new ArrayList(batch); - for (int j = 0; (j < batch) && (it.hasNext()); j++) { - l.add(it.next()); - } - - //query the RLI for one batch - List res = null; - try{ - res = mRLI.getLRCBulk(l); - } - catch(RLSException ex){ - mLogger.log("getLRC2LFNS(Set)",ex, - LogManager.ERROR_MESSAGE_LEVEL); - //or throw a runtime exception - return null; - } - //iterate through the results and put them in the map - String lrc = null; - String lfn = null; - for(Iterator lit = res.iterator();lit.hasNext();){ - RLSString2Bulk s2b = (RLSString2Bulk) lit.next(); - lfn = s2b.s1;//s1 is the lfn - lrc = s2b.s2;//s2 denotes the lrc which contains the mapping - - //rc is the exit status returned by the RLI - if (s2b.rc == RLSClient.RLS_SUCCESS) { - //we are really only concerned with success - //and do not care about other exit codes - Object val = null; - Set s = null; - s = ( (val = lrc2lfn.get(lrc)) == null) ? - new LinkedHashSet(): - (LinkedHashSet)val; - s.add(lfn); - if(val == null) - lrc2lfn.put(lrc,s); - - } - } - } - - //match LRC's just once against ingore and restrict lists - for( Iterator it = lrc2lfn.keySet().iterator(); it.hasNext(); ){ - String lrc = ( String ) it.next(); - int state = this.determineQueryType(lrc); - - //do the query on the basis of the state - if (state == LRC_QUERY_IGNORE) { - mLogger.log("Skipping LRC " + lrc, - LogManager.DEBUG_MESSAGE_LEVEL); - it.remove(); - } - } - - - - return lrc2lfn; - } - - - /** - * Returns a tri state indicating what type of query needs to be done to - * a particular LRC. - * - * @param url the LRC url. - * - * @return tristate - */ - private int determineQueryType(String url){ - int type = RLI.LRC_QUERY_NORMAL; - - if(mLRCRestrictList != null){ - for ( int j = 0; j < mLRCRestrictList.length; j++ ) { - if ( url.indexOf( mLRCRestrictList[ j ] ) != -1 ) { - type = RLI.LRC_QUERY_RESTRICT; - break; - } - } - } - if(mLRCIgnoreList != null){ - for ( int j = 0; j < mLRCIgnoreList.length; j++ ) { - if ( url.indexOf( mLRCIgnoreList[ j ] ) != -1 ) { - type = RLI.LRC_QUERY_IGNORE; - break; - } - } - } - - - return type; - } - - - /** - * Returns the rls LRC urls to ignore for querying (requested by LIGO). - * - * Referred to by the "pegasus.catalog.replica.lrc.ignore" property. - * - * @param properties the properties passed in the connect method. - * - * @return String[] if a comma separated list supplied as the property value, - * else null - */ - protected String[] getRLSLRCIgnoreURLs( Properties properties ) { - String urls = properties.getProperty( this.LRC_IGNORE_KEY, - null ); - if ( urls != null ) { - String[] urllist = urls.split( "," ); - return urllist; - } else { - return null; - } - } - - /** - * Returns the rls LRC urls to restrict for querying (requested by LIGO). - * - * Referred to by the "pegasus.catalog.replica.lrc.restrict" property. - * - * @param properties the properties passed in the connect method. - * - * @return String[] if a comma separated list supplied as the property value, - * else null - */ - protected String[] getRLSLRCRestrictURLs( Properties properties ) { - String urls = properties.getProperty( this.LRC_RESTRICT_KEY, - null ); - if ( urls != null ) { - String[] urllist = urls.split( "," ); - return urllist; - } else { - return null; - } - } - - - /** - * Retrieves the URLs of all the LRCs that report to the RLI. - * - * @return a Set containing the URLs to all the LRCs that report to the - * RLI. - */ - private Set getReportingLRC(){ - //sanity check - if (this.isClosed()) { - //probably an exception should be thrown here!! - throw new RuntimeException(RLI_NOT_CONNECTED_MSG + this.mRLIURL); - } - Set result = new HashSet(); - Collection c = null; - - try{ - c = mRLI.lrcList(); - } - catch(RLSException e){ - mLogger.log("getReportingLRC(Set)",e,LogManager.ERROR_MESSAGE_LEVEL); - } - - for(Iterator it = c.iterator(); it.hasNext();){ - RLSLRCInfo lrc = (RLSLRCInfo)it.next(); - result.add(lrc.url); - } - - return result; - } - - - - - /** - * Populates the mapping table by querying the LRC in the mLRCList. At - * present it searches for all the files in the original DAG. At this point - * it should be all the files in the Reduced Dag but not doing so in order to - * conserve memory. - * - * @param allInCache indicates whether all input file entries were found in - * cache or not. - * - * @return List - */ - /* - private List populateMapTable( boolean allInCache ) { - String lrcURL = null; - List list = null; - RLSQuery client = null; - ReplicaLocation rl = null; - List pfnList = null; - - mTable = new HashMap( mSearchFiles.size() ); - - int size = mLRCMap.size(); - mLogger.log("Number of LRCs that will be queried: "+size, - LogManager.DEBUG_MESSAGE_LEVEL); - for ( Iterator iter = mLRCMap.keySet().iterator(); iter.hasNext(); ) { - lrcURL = ( String ) iter.next(); - int state = this.determineQueryType(lrcURL); - - //do the query on the basis of the state - if ( state == LRC_QUERY_IGNORE ) { - mLogger.log( "Skipping LRC " + lrcURL, - LogManager.DEBUG_MESSAGE_LEVEL); - } - else{ - mLogger.log( "Querying LRC " + lrcURL, - LogManager.DEBUG_MESSAGE_LEVEL); - list = ( ArrayList ) mLRCMap.get( lrcURL ); - try { - client = new RLSQuery( lrcURL ); - boolean restrict = (state == LRC_QUERY_RESTRICT); - client.bulkQueryLRC( list, RLSQuery.RLS_BULK_QUERY_SIZE, - mTable,restrict); - client.close(); - } catch ( Exception e ) { - mLogMsg = - "RLSEngine.java: While getting connection to LRC " + - lrcURL + " " + e; - mLogger.log( mLogMsg, LogManager.ERROR_MESSAGE_LEVEL ); - size--; - - //do a hard fail only if the RLS exitmode is set to error - //or we could not query to all the LRCs - // and we could not find all the entries in the cache - mLogger.log("RLS exit mode is " + mProps.getRLSExitMode(), - LogManager.DEBUG_MESSAGE_LEVEL); - boolean exitOnError = mProps.getRLSExitMode().equalsIgnoreCase( "error" ); - if ( exitOnError || ( size == 0 && !allInCache )) { - mLogMsg = ( exitOnError ) ? - "Unable to access LRC " + lrcURL : - "Unable to query any LRC and not all input files are in cache!"; - throw new RuntimeException( mLogMsg ); - } - } - mLogger.logCompletion("Querying LRC " + lrcURL, - LogManager.DEBUG_MESSAGE_LEVEL); - - } - } - return new ArrayList( mTable.keySet() ); - - } - -*/ - /** - * The main program, for some unit testing. - * - * @param args String[] - */ - public static void main(String[] args) { - //setup the logger for the default streams. - LogManager logger = LogManagerFactory.loadSingletonInstance( ); - logger.logEventStart( "event.pegasus.catalog.replica.RLI", "planner.version", Version.instance().toString() ); - - RLI rli = new RLI(); - Properties props = new Properties(); - props.setProperty( RLI.URL_KEY, "rls://dataserver.phy.syr.edu" ); - props.setProperty( RLI.LRC_IGNORE_KEY, "rls://ldas-cit.ligo.caltech.edu:39281" ); - rli.connect(props); - System.out.println( "Complete Lookup " + rli.lookup("H-H1_RDS_C03_L2-847608132-128.gwf" ) ); - System.out.println( "Lookup without attributes " + rli.lookupNoAttributes("H-H1_RDS_C03_L2-847608132-128.gwf" ) ); - rli.close(); - - - //RLI rli = new RLI(); - String lfn = "test"; - Set s = new HashSet(); - s.add(lfn);s.add("testX");s.add("vahi.f.a"); - System.out.println("Connecting " + rli.connect("rls://sukhna")); - boolean insert = false; - - - if(insert){ - ReplicaCatalogEntry rce = new ReplicaCatalogEntry( - "gsiftp://sukhna.isi.edu/tmp/test"); - rce.addAttribute("name", "karan"); - LRC sukhna = new LRC(); - sukhna.connect("rls://sukhna"); - sukhna.insert("test", rce); - sukhna.insert("test", "gsiftp://sukhna.isi.edu/tmp/test1", "isi"); - sukhna.insert("vahi.f.a", "file:///tmp/vahi.f.a", "isi"); - sukhna.insert("testX", "gsiftp://sukhna.isi.edu/tmp/testX", "isi"); - sukhna.insert("testX", "gsiftp://sukhna.isi.edu/tmp/testXvahi", "isi"); - sukhna.close(); - - LRC smarty = new LRC(); - ReplicaCatalogEntry rce1 = new ReplicaCatalogEntry( - "gsiftp://smarty.isi.edu/tmp/test"); - rce1.addAttribute("name", "gaurang"); - - smarty.connect("rlsn://smarty"); - smarty.insert("test", rce1); - smarty.insert("test", "gsiftp://smarty.isi.edu/tmp/test1", "isi"); - smarty.insert("vahi.f.a", "file:///tmp-smarty/vahi.f.a", "isi"); - smarty.insert("testX", "gsiftp://smarty.isi.edu/tmp/testX", "isi"); - smarty.close(); - } - - System.out.println("\n Searching for lfn " + lfn); - System.out.println(rli.lookup(lfn)); - - System.out.println("\n Searching for lfn w/o attributes " + lfn); - System.out.println(rli.lookupNoAttributes(lfn)); - - System.out.println("\nSearching for a set of lfn " + s); - System.out.println(rli.lookup(s)); - - System.out.println("\nSearching for a set of lfn with handle matching" + s); - System.out.println(rli.lookup(s,"isi")); - - System.out.println("\nSearching for a set of lfn with handle matching "+ - " returning only pfns" + s); - System.out.println(rli.lookupNoAttributes(s,"isi")); - - System.out.println("\nListing all the lfns tracked in RLI"); - System.out.println(rli.list("*").size()); - - //System.out.println("\n Removing entry for lfn " + lfn); - //System.out.println(rli.remove(lfn)); - - //System.out.println("\n Removing entry for lfns " + s); - //System.out.println(rli.remove(s)); - - //System.out.println("\n Removing entry for lfn by handle matching " + lfn); - //System.out.println(rli.deleteByResource(lfn,"isi")); - - //System.out.println("\nSearching for a set of lfn " + s); - //System.out.println(rli.lookup(s)); - Map m = new HashMap(); - m.put("lfn","test*"); - m.put("pfn","*vahi*"); - System.out.println("\nDoing a constraint lookup " + rli.lookup(m)); - rli.close(); - } - - -}//end of main class - Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/catalog/site/impl/old/classes/LRCResult.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/catalog/site/impl/old/classes/LRCResult.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,150 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - - - -package edu.isi.pegasus.planner.catalog.site.impl.old.classes; - -import edu.isi.pegasus.planner.classes.Data; - -import edu.isi.pegasus.common.logging.LogManager; - -import org.globus.replica.rls.RLSClient; -import org.globus.replica.rls.RLSString2Bulk; - - -/** - * A class that stores the results - * of querying an LRC. It includes - * whether the operation was a success - * or not and in addition the value - * of the pool attribute. - * - * @author Gaurang Mehta - * @author Karan Vahi - * @version $Revision: 2572 $ - * - * @see org.globus.replica.rls.RLSString2Bulk - */ - -public class LRCResult extends Data { - - /** - * The lfn for which the LRC - * was queried. - */ - public String lfn; - - /** - * The pfn associated - * with the lfn, if an - * entry found in the LRC. - * Else it can be null. - */ - public String pfn; - - /** - * The pool attribute associated - * with the pfn returned. - * This should be set to null - * if pfn is not found. - */ - public String pool; - - /** - * The status of the operation. - * Whether it was a sucess or not. - * The status are defined in - * RLSClient.java - * - * @see org.globus.replica.rls.RLSClient - */ - public int LRCExitStatus; - - - - /** - * The default constructor - */ - public LRCResult() { - lfn = new String(); - pfn = new String(); - pool= new String(); - LRCExitStatus = 0; - } - - /** - * The overloaded constructor. - * Takes in RLSString2Bulk - * object. - */ - public LRCResult(RLSString2Bulk s2, String poolAtt){ - lfn = s2.s1; - pfn = s2.s2; - LRCExitStatus = s2.rc; - pool = poolAtt; - } - - /** - * Returns a clone of the - * existing object. - */ - public Object clone(){ - LRCResult res = new LRCResult(); - - res.lfn = this.lfn; - res.pfn = this.pfn; - res.pool = this.pool; - res.LRCExitStatus = this.LRCExitStatus; - - return res; - } - - /** - * Returns a textual description - * of the object. - */ - public String toString(){ - String str = "\n lfn: " + lfn + - " exit status: " + getErrorMessage()+ - " pfn: " + pfn + - " pool: " + pool; - return str; - - - } - - /** - * Returns the error/status - * message according to - * the LRCExitStatus. - */ - public String getErrorMessage(){ - RLSClient rls = null; - - try{ - rls = new RLSClient(); - } - catch(Exception e){ - mLogger.log("Exception while initialising to RLS" + e.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - } - String err = rls.getErrorMessage(this.LRCExitStatus); - - return err; - } - -} Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/client/PasoaProvenanceClient.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/client/PasoaProvenanceClient.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,1485 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package edu.isi.pegasus.planner.client; - - -import java.io.BufferedReader; -import java.io.StringReader; -import java.io.FileReader; -import java.net.URL; -import java.util.LinkedList; -import java.io.File; -import java.util.List; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.Map; -import java.util.HashMap; - -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.parsers.DocumentBuilder; - -import org.pasoa.common.Constants; -import org.pasoa.pstructure.Record; -import org.pasoa.pstructure.ActorStatePAssertion; -import org.pasoa.pstructure.GlobalPAssertionKey; -import org.pasoa.pstructure.InteractionKey; -import org.pasoa.pstructure.InteractionPAssertion; -import org.pasoa.pstructure.ObjectID; -import org.pasoa.pstructure.RelationshipPAssertion; -import org.pasoa.storeclient.ClientLib; -import org.pasoa.util.httpsoap.WSAddressEndpoint; -import org.w3c.dom.Document; -import org.w3c.dom.Element; -import org.w3c.dom.NodeList; -import org.w3c.dom.Node; - -import org.xml.sax.InputSource; -import java.io.StringWriter; -import java.io.IOException; -import java.io.Reader; -import edu.isi.pegasus.planner.transfer.Refiner; -import org.xml.sax.InputSource; -public class PasoaProvenanceClient { - - /** change this to connect to the preserv server **/ - public static String URL = "http://localhost:8080/preserv-1.0"; - public static String XMLHEADER =""; - public static String CONDOR= "www.cs.wisc.edu/condor"; - public long filecount=0; - public static String documentationStyle = "http://www.pasoa.org/schemas/pegasus"; - public ClientLib clientLib = null; - public URL provenanceStore = null; - public String jobname=null; - public String wf_label=null; - public String wf_planned_time=null; - public String transformation=null; - public Element docelement=null; - public Element daxelement=null; - // public List input=null; - // public List output=null; - public List parents=null; - public List children=null; - public Map input = null; - public Map output = null; - - - public PasoaProvenanceClient(String url){ - clientLib=new ClientLib(); - try{ - provenanceStore = new URL(url + "/record"); - }catch(Exception e){ - System.err.println("Bad Bad Bad url"); - } - } - - public PasoaProvenanceClient(){ - clientLib=new ClientLib(); - try{ - provenanceStore = new URL(URL + "/record"); - }catch(Exception e){ - System.err.println("Bad Bad Bad url"); - } - - } - - - - public static void main(String[] args) throws Exception { - - PasoaProvenanceClient cle=null; - String jobfile=null; - String daxfile=null; - String dagfile=null; - String url=null; - if(args.length<3){ - System.err.println("Usage: Client daxfile dagfile outfile"); - // System.err.println("Usage: Client daxfile dagfile preservurl"); - System.exit(1); - - }else if(args.length==3){ - jobfile=args[2]; - daxfile=args[0]; - dagfile=args[1]; - cle = new PasoaProvenanceClient(); - - } - /*}else { - jobfile=args[0]; - daxfile=args[0]; - dagfile=args[2]; - url=args[3]; - cle = new PasoaProvenanceClient(url); - - }*/ - try{ - cle.jobname=(new File(jobfile)).getName().split("\\.out")[0]; - System.out.println("Processing job --- "+ cle.jobname); - cle.parseKickstartRecord(jobfile); - cle.parseDag(dagfile); - List newlist=new ArrayList(); - if(cle.parents!=null && !cle.parents.isEmpty()){ - System.out.println("Adding parents "+ cle.parents); - newlist.addAll(cle.parents); - } - if(cle.children!=null && !cle.children.isEmpty()){ - System.out.println("Adding children "+ cle.children); - newlist.addAll(cle.children); - } - System.out.println("Adding job "+ cle.jobname); - - newlist.add(cle.jobname); - System.out.println("Job List is "+ newlist); - cle.parseFiles(newlist); -// cle.parseDaxFile(daxfile,newlist); - // cle.parseInput(); - System.out.println("Inputs == "+cle.input); - System.out.println("Outputs == "+cle.output); - - if(cle.jobname.startsWith( Refiner.STAGE_IN_PREFIX )|| (cle.jobname.startsWith(Refiner.STAGE_OUT_PREFIX))){ - InteractionKey ik = cle.transferInvocationInteraction(); - cle.transferCompletionInteraction(ik); - } else if(cle.jobname.startsWith("new_rc_register")){ - InteractionKey ik = cle.registerInvocationInteraction(); - cle.registerCompletionInteraction(ik); - } else if(cle.jobname.startsWith("create_dir")) { - //write this handler - } else if(cle.jobname.startsWith("clean_up")){ - //write this handler - }else if(cle.jobname.startsWith("pegasus_concat")){ - //write this handler - }else{ - InteractionKey ik = cle.jobInvocationInteraction(); - cle.jobCompletionInteraction(ik); - } - }catch (Exception e){ - e.printStackTrace(); - } - - } - - private void parseDag(String file) throws Exception{ - BufferedReader bf = new BufferedReader(new FileReader(file)); - String line = null; - while((line=bf.readLine())!=null){ - String[] list = null; - if (line.startsWith("PARENT")){ - list = line.split(" "); - } - if(list!=null){ - if(list[1].equalsIgnoreCase(jobname)){ - if(children==null){ - children=new ArrayList(); - } - children.add(list[3]); - } - if(list[3].equalsIgnoreCase(jobname)){ - if(parents==null){ - parents=new ArrayList(); - } - parents.add(list[1]); - } - } - } - bf.close(); - } - - private void parseKickstartRecord(String file) throws Exception{ - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - List records=extractToMemory(new File(file)); - if(records!=null){ - for (Iterator i=records.iterator();i.hasNext();){ - - Document msgDoc = db.parse(new InputSource(new StringReader((String)i.next()))); - docelement = msgDoc.getDocumentElement(); - transformation = docelement.getAttribute("transformation"); - wf_label=docelement.getAttribute("wf-label"); - wf_planned_time=docelement.getAttribute("wf-stamp"); - - } - } - } - - public List extractToMemory( java.io.File input ) - throws Exception - { - List result = new ArrayList(); - StringWriter out = null; - // open the files - int p1, p2, state = 0; - try { - BufferedReader in = new BufferedReader( new FileReader(input) ); - out = new StringWriter(4096); - String line = null; - while ( (line = in.readLine()) != null ) { - if ( (state & 1) == 0 ) { - // try to copy the XML line in any case - if ( (p1 = line.indexOf( " -1 ) - if ( (p2 = line.indexOf( "?>", p1 )) > -1 ) { - // out.write( line, p1, p2+2 ); - System.out.println( "state=" + state + ", seen " ); - } - // start state with the correct root element - if ( (p1 = line.indexOf( " -1 ) { - if ( p1 > 0 ) line = line.substring( p1 ); - System.out.println( "state=" + state + ", seen " ); - out.write(XMLHEADER); - ++state; - } - } - if ( (state & 1) == 1 ) { - out.write( line ); - if ( (p1 = line.indexOf("")) > -1 ) { - System.out.println( "state=" + state + ", seen " ); - ++state; - - out.flush(); - out.close(); - result.add( out.toString() ); - out = new StringWriter(4096); - } - } - } - - in.close(); - out.close(); - } catch ( IOException ioe ) { - throw new Exception( "While copying " + input.getPath() + - " into temp. file: " + ioe.getMessage() ); - } - - - // some sanity checks - if ( state == 0 ) - throw new Exception( "File " + input.getPath() + - " does not contain invocation records," + - " assuming failure"); - if ( (state & 1) == 1 ) - throw new Exception( "File " + input.getPath() + - " contains an incomplete invocation record," + - " assuming failure" ); - - // done - return result; - } - -private void parseFiles(List jobs)throws Exception{ - File infile = null; - File outfile = null; - List ilist = null; - List temp = new ArrayList(jobs); - for (Iterator i = temp.iterator(); i.hasNext(); ) { - String job = (String) i.next(); - if (job.startsWith( Refiner.STAGE_IN_PREFIX )) { - //this is for stagein jobs - outfile = new File(job + ".out.lof"); - if (outfile.exists() && outfile.canRead() && outfile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(outfile)); - String str; - while ( (str = in.readLine()) != null) { - if (output == null) { - output = new HashMap(); - } - if (!output.containsKey(job)) { - output.put(job, new ArrayList()); - } - ilist = (List) output.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - - }else if (job.startsWith( Refiner.STAGE_OUT_PREFIX )) { - //this is for stageout/inter tx jobs - outfile = new File(job + ".out.lof"); - if (outfile.exists() && outfile.canRead() && outfile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(outfile)); - String str; - while ( (str = in.readLine()) != null) { - if (input == null) { - input = new HashMap(); - } - if (!input.containsKey(job)) { - input.put(job, new ArrayList()); - } - ilist = (List) input.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - - }else if(job.startsWith( Refiner.INTER_POOL_PREFIX )){ - outfile = new File(job + ".out.lof"); - if (outfile.exists() && outfile.canRead() && outfile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(outfile)); - String str; - while ( (str = in.readLine()) != null) { - if (output == null) { - output = new HashMap(); - } - if (!output.containsKey(job)) { - output.put(job, new ArrayList()); - } - ilist = (List) output.get(job); - ilist.add(str); - if (input == null) { - input = new HashMap(); - } - if (!input.containsKey(job)) { - input.put(job, new ArrayList()); - } - ilist = (List) input.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - - } else if(job.startsWith("new_rc_register")){ - BufferedReader bf =new BufferedReader(new FileReader(new File(job+".in"))); - String line = null; - while((line=bf.readLine())!=null){ - String lfn=null; - lfn= line.split(" ")[0]; - if(input==null){ - input=new HashMap(); - } - if(!input.containsKey(job)){ - input.put(job, new ArrayList()); - } - ilist=(List)input.get(job); - ilist.add(lfn); - } - bf.close(); - }else if (job.startsWith("cln_")) { - //this is for cleanup jobs - infile = new File(job + ".in.lof"); - if (infile.exists() && infile.canRead() && infile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(infile)); - String str; - while ( (str = in.readLine()) != null) { - - if (input == null) { - input = new HashMap(); - } - if (!input.containsKey(job)) { - input.put(job, new ArrayList()); - } - ilist = (List) input.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - } else if (!job.endsWith("_cdir")) { - //this is a regular job - outfile = new File(job + ".out.lof"); - if (outfile.exists() && outfile.canRead() && outfile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(outfile)); - String str; - while ( (str = in.readLine()) != null) { - if (output == null) { - output = new HashMap(); - } - if (!output.containsKey(job)) { - output.put(job, new ArrayList()); - } - ilist = (List) output.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - - infile = new File(job + ".in.lof"); - if (infile.exists() && infile.canRead() && infile.length() != 0) { - try { - BufferedReader in = new BufferedReader(new FileReader(infile)); - String str; - while ( (str = in.readLine()) != null) { - - if (input == null) { - input = new HashMap(); - } - if (!input.containsKey(job)) { - input.put(job, new ArrayList()); - } - ilist = (List) input.get(job); - ilist.add(str); - } - in.close(); - } - catch (IOException e) { - } - } - } - } -} - - private void parseDaxFile(String file, List jobs)throws Exception { - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new File(file)); - NodeList nlist = msgDoc.getElementsByTagName("job"); - List temp = new ArrayList(jobs); - input = new HashMap(); - output = new HashMap(); - - for (int i =0;i and obtaining the source urls - - BufferedReader bf =new BufferedReader(new FileReader(new File(jobname+".in"))); - String line = null; - StringBuffer message = new StringBuffer(""); - while((bf.readLine())!=null){ - line=bf.readLine(); - filecount++; - if(!jobname.startsWith(Refiner.STAGE_OUT_PREFIX)){ - message.append(""+line+""); - } else { - String lfn= line.split("run\\d{4}/")[1]; - - message.append(""+line+""); - } - bf.readLine(); - bf.readLine(); - } - bf.close(); - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - } - - private InteractionPAssertion createTransferCompletionInteractionPAssertion() - throws Exception { - // Create an interaction p-assertion - // First we make a local p-assertion id and then - // we make a documentationStyle. In this case we - // call it verbatium. - // - // In most cases, you'll be grabing the messageBody from the message - // being sent between parties. So a SOAP message, or a CORBA message. - // With this example we'll just use a hard coded message body. - - String localPAssertionId = "1"; - - // this message content will be obtained by parsing the transfer input files and obtaining the destination urls - - - BufferedReader bf =new BufferedReader(new FileReader(new File(jobname+".in"))); - String line = null; - StringBuffer message = new StringBuffer(""); - while((line=bf.readLine())!=null){ - bf.readLine(); - bf.readLine(); - line = bf.readLine(); - filecount++; - if(jobname.startsWith(Refiner.STAGE_OUT_PREFIX)){ - message.append(""+line+""); - }else { - String lfn= line.split("run\\d{4}/")[1]; - message.append(""+line+""); - } - } - bf.close(); - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - } - - private ActorStatePAssertion createActorStatePAssertion(long count) - throws Exception { - // Create an actor state p-assertion - // Just like the interaction p-assertion this p-assertion - // needs a local p-assertion id. Remember, all the p-assertions - // in one view need a different id. Therefore, we give this assertion - // the id of "2" instead of "1". - // - // Again you'll typically be getting some state from the actor, - // translating it to XML to create the actor state p-assertion - // In this example, we just use a hard coded string. - - String localPAssertionId = "aspa-"+count; - - ActorStatePAssertion asa = new ActorStatePAssertion(localPAssertionId, docelement); - - return asa; - } - - private RelationshipPAssertion createTransferRelationshipPAssertion(InteractionKey invocationik, long index) - throws Exception { - // Create a relationship p-assertion - // Again a different local p-assertion id - // - // We'll create a "usage" relationship between the interaction p-assertion - // and the actor state p-assertion. This relationship says that - // message represented by interaction p-assertion "1" used the actor state - // represented by actor state p-assertion "2". - // There are no data accessors or links so we pass null. - - // Create the information to identify the subject of the relationship - // Remember, parameter names must be identified and they need to be URIs - String localPAssertionId = "rpa"+index; - String subjectLocalPAssertionId = "1"; - String subjectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/outputfile"; - - // Create the information to identify the object of the relationship - - String objectLocalPAssertionId = "1"; // points to the interaction p-assertion of the invocation interaction receiver - - - GlobalPAssertionKey gpak = new GlobalPAssertionKey(invocationik, "receiver", objectLocalPAssertionId); - String objectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/inputfile"; - - Element dataAccessor= createTransferDataAccessor(index); - - ObjectID objId = new ObjectID(gpak, objectParameterName, dataAccessor, null); - - // We add the objId to the list of objects. We only have one objectId here - // but when making another type of relationship more than one objectId may - // be required - LinkedList objectIds = new LinkedList(); - objectIds.add(objId); - - // Create the "use" relation. Again this should be a URI - String relation = "http://pegasus.isi.edu/pasoa/relation/transfer/copy-of"; - dataAccessor= createTransferDataAccessor( index); - // Finally, create the relationship object and return it. - RelationshipPAssertion rel = new RelationshipPAssertion(localPAssertionId, - subjectLocalPAssertionId, - dataAccessor, - subjectParameterName, - relation, - objectIds); - - return rel; - - } - - //will have to do for handling merged jobs correctly. - private InteractionPAssertion createMergedJobInvocationInteractionPAssertion() throws Exception{ - - String localPAssertionId = "1"; - - // this message content will be obtained by parsing the transfer input files and obtaining the source urls - StringBuffer message = new StringBuffer(""); - if(input!=null){ - if(input.containsKey(jobname)){ - List inputs = (List) input.get(jobname); - for (Iterator i = inputs.iterator(); i.hasNext(); ) { - message.append("" + (String) i.next() + - ""); - } - } - } - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - - } - - - private InteractionPAssertion createJobInvocationInteractionPAssertion() throws Exception{ - - String localPAssertionId = "1"; - - // this message content will be obtained by parsing the transfer input files and obtaining the source urls - - StringBuffer message = new StringBuffer(""); - if(input!=null){ - if(input.containsKey(jobname)){ - List inputs = (List) input.get(jobname); - for (Iterator i = inputs.iterator(); i.hasNext(); ) { - message.append("" + (String) i.next() + - ""); - } - } - } - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - - } - - - - private InteractionPAssertion createJobCompletionInteractionPAssertion() throws Exception{ - - String localPAssertionId = "1"; - - // this message content will be obtained by parsing the transfer input files and obtaining the source urls - - StringBuffer message = new StringBuffer(""); - if(output!=null){ - if(output.containsKey(jobname)){ - List outputs = (List) output.get(jobname); - for (Iterator i = outputs.iterator(); i.hasNext(); ) { - message.append("" + (String) i.next() + - ""); - } - } - } - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - } - - private RelationshipPAssertion createJobRelationshipPAssertion(InteractionKey invocationik, String filename, long index) - throws Exception { - String localPAssertionId = "rpa"+index; - String subjectLocalPAssertionId = "1"; - String subjectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/outputfile"; - - // Create the information to identify the object of the relationship - - String objectLocalPAssertionId = "1"; // points to the interaction p-assertion of the invocation interaction receiver - - - GlobalPAssertionKey gpak = new GlobalPAssertionKey(invocationik, "receiver", objectLocalPAssertionId); - String objectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/inputfile"; - LinkedList objectIds = new LinkedList(); - - for(Iterator i=((List)input.get(jobname)).iterator();i.hasNext();){ - Element dataAccessor= createLFNDataAccessor((String)i.next()); - // We add the objId to the list of objects. We only have one objectId here - // but when making another type of relationship more than one objectId may - // be required - objectIds.add(new ObjectID(gpak, objectParameterName, dataAccessor, null)); - } - - // Create the "use" relation. Again this should be a URI - String relation = "http://pegasus.isi.edu/pasoa/relation/transformation/product-of"; - Element dataAccessor= createLFNDataAccessor(filename); - - // Finally, create the relationship object and return it. - RelationshipPAssertion rel = new RelationshipPAssertion(localPAssertionId, - subjectLocalPAssertionId, - dataAccessor, - subjectParameterName, - relation, - objectIds); - - return rel; - - } - private RelationshipPAssertion createJobToTransferRelationshipPAssertion(String filename,String parentjob,int index) throws Exception{ - String localPAssertionId = "rpa"+index; - String subjectLocalPAssertionId = "1"; - String subjectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/inputfile"; - - // Create the information to identify the object of the relationship - - String objectLocalPAssertionId = "1"; // points to the interaction p-assertion of the invocation interaction receiver - // interaction. - - WSAddressEndpoint source = new WSAddressEndpoint(parentjob); - WSAddressEndpoint sink = new WSAddressEndpoint(CONDOR); - - String interactionId = wf_label+wf_planned_time+parentjob; - InteractionKey ik = new InteractionKey(source.getElement(), sink.getElement(), interactionId); - - GlobalPAssertionKey gpak = new GlobalPAssertionKey(ik, "receiver", objectLocalPAssertionId); - String objectParameterName = "http://pegasus.isi.edu/schema/pasoa/type/outputfile"; - - Element dataAccessor= createLFNDataAccessor(filename); - - ObjectID objId = new ObjectID(gpak, objectParameterName, dataAccessor, null); - - // We add the objId to the list of objects. We only have one objectId here - // but when making another type of relationship more than one objectId may - // be required - LinkedList objectIds = new LinkedList(); - objectIds.add(objId); - - // Create the "use" relation. Again this should be a URI - String relation = "http://pegasus.isi.edu/pasoa/relation/transfer/same-as"; - // dataAccessor=createNameValueDataAccessor(filename); - // Finally, create the relationship object and return it. - RelationshipPAssertion rel = new RelationshipPAssertion(localPAssertionId, - subjectLocalPAssertionId, - dataAccessor, - subjectParameterName, - relation, - objectIds); - - return rel; - } - private Element createTransferDataAccessor(long index){ - Map namespaces = new HashMap(); - namespaces.put("tr", "http://pegasus.isi.edu/schema/pasoa/content/transfer"); - return new org.pasoa.accessors.snxpath.SingleNodeXPathManager().createAccessor("/tr:transfer[0]/tr:filename[" + index + "]", - namespaces); - - } - - private Element createLFNDataAccessor(String value){ - return new org.pasoa.accessors.lfn.LFNAccessorManager().createLFNAccessor(value); - } - - private InteractionPAssertion createRegisterInvocationInteractionPAssertion() - throws Exception { - // Create an interaction p-assertion - // First we make a local p-assertion id and then - // we make a documentationStyle. In this case we - // call it verbatium. - // - // In most cases, you'll be grabing the messageBody from the message - // being sent between parties. So a SOAP message, or a CORBA message. - // With this example we'll just use a hard coded message body. - - String localPAssertionId = "1"; - - - BufferedReader bf =new BufferedReader(new FileReader(new File(jobname+".in"))); - String line = null; - StringBuffer message = new StringBuffer(""); - while((line=bf.readLine())!=null){ - filecount++; - String[] lfn= line.split(" "); - message.append(""+lfn[1]+""); - - } - message.append(""); - - // Convert it into a DOM Element - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - DocumentBuilder db = dbf.newDocumentBuilder(); - Document msgDoc = db.parse(new InputSource(new StringReader(message.toString()))); - Element messageBody = msgDoc.getDocumentElement(); - - InteractionPAssertion ipa = new InteractionPAssertion(localPAssertionId, documentationStyle, messageBody); - - return ipa; - } - - public InteractionKey registerInvocationInteraction() throws Exception{ - - System.out.println("We now create the transfer Invocation interaction key"); - - // Create addresses for the source and sink of the - // interaction. - WSAddressEndpoint source = new WSAddressEndpoint(CONDOR); - WSAddressEndpoint sink = new WSAddressEndpoint(jobname); - - - String interactionId = wf_label+wf_planned_time+jobname; - InteractionKey ik = new InteractionKey(source.getElement(), sink.getElement(), interactionId); - - System.out.println("Building p-assertions..."); - - InteractionPAssertion ipa = createRegisterInvocationInteractionPAssertion(); - - List records=new ArrayList(); - //setting sender type - System.out.println("We are the sender/client view of the interaction"); - String vk = Constants.SENDER_VIEW_TYPE; - System.out.println(); - - //set asserter to CONDOR - - WSAddressEndpoint asserter = new WSAddressEndpoint(CONDOR); - - - System.out.println("Creating Record objects for each p-assertion"); - - Record recIpa = new Record(ipa, ik, vk, asserter.getElement()); - records.add(recIpa); - Record recRpa = null; - - String tempparent=null; - if(parents !=null || !parents.isEmpty()){ - tempparent=(String)parents.get(0); - } - for(int i=0; i" + jobID + ""); - } - - /** - * Creates an interaction p-assertion asserting that a given partially - * refined workflow was exchanged between actors. - * - * @param workflow The (XML) content of the partially refined workflow - * @return A JavaBean representation of an interaction p-assertion containing the workflow - */ - public InteractionPAssertion createInteractionPAssertion (String workflow) throws IOException, SAXException { - return new InteractionPAssertion ("1", - BestPractice.VERBATIM_STYLE, - toElement (workflow + _workflowPostfix)); - } - - /** - * Creates an interaction key to identify an interaction between two actors. - * - * @param refinementID The unique identifier for this workflow refinement (run of Pegasus) - * @param refinementAddress The URI of the particular refinement step (site selection, cluster etc.) - * @param preRefinement True if the interaction is pre-refinement, i.e. from Pegasus to a refiner, rather than the other way round - */ - public InteractionKey createInteractionKey (String refinementID, String refinementAddress, boolean preRefinement) { - if (preRefinement) { - return new InteractionKey (addressToElement (PEGASUS), - addressToElement (refinementAddress), refinementID + "Start"); - } else { - return new InteractionKey (addressToElement (refinementAddress), - addressToElement (PEGASUS), refinementID + "End"); - } - } - - /** - * Creates a relationship p-assertion between nodes in two partially refined workflows. - * - * @param count The index of this relationship p-assertion in the interaction (to support the requirement that each p-assertion has a unique ID) - * @param effectJobID The job ID of the subject (effect) of the relationship - * @param effectParameter The role played by the subject of the relationship - * @param relationType The type of the relationship - * @param causeKey The interaction key of the object of the relationship - * @param causeJobID The job ID of the object (cause) of the relationship - * @param causeParameter The role played by the object of the relationship - * @return A RelationshipPAssertion JavaBean representing the relationship p-assertion with the given arguments - */ - public RelationshipPAssertion createRelationship (int count, String effectJobID, - String effectParameter, String relationType, InteractionKey causeKey, - String causeJobID, String causeParameter) throws IOException, SAXException { - List objectIDs = new LinkedList (); - ObjectID objectID = new ObjectID ( - new GlobalPAssertionKey (causeKey, Constants.RECEIVER_VIEW_TYPE, "1"), - effectParameter, - createDataAccessor (causeJobID), - null); - - objectIDs.add (objectID); - - return new RelationshipPAssertion ("RPA" + count, - new SubjectID ("1", createDataAccessor (effectJobID), effectParameter), - relationType, - objectIDs); - } - - public void record (PAssertion passertion, InteractionKey interactionKey, boolean isSender, String asserterURL) throws Exception { - if (isSender) { - _storeProxy.record (new Record (passertion, interactionKey, Constants.SENDER_VIEW_TYPE, addressToElement (asserterURL)), _storeRecordURL); - } else { - _storeProxy.record (new Record (passertion, interactionKey, Constants.RECEIVER_VIEW_TYPE, addressToElement (asserterURL)), _storeRecordURL); - } - } - - public void recordInteraction (InteractionPAssertion passertion, InteractionKey interactionKey, String refinerType, boolean refinementInput) throws Exception { - if (refinementInput) { - record (passertion, interactionKey, true, PEGASUS); - record (passertion, interactionKey, false, refinerType); - } else { - record (passertion, interactionKey, true, refinerType); - record (passertion, interactionKey, false, PEGASUS); - } - } - - public void recordInteraction (String workflow, InteractionKey interactionKey, String refinerType, boolean refinementInput) throws Exception { - recordInteraction (createInteractionPAssertion (workflow), interactionKey, refinerType, refinementInput); - } - - public RelationshipPAssertion recordRelationship (int count, String effectJobID, - String effectParameter, String relationType, InteractionKey causeKey, - String causeJobID, String causeParameter, String asserterURL) throws Exception { - RelationshipPAssertion passertion = createRelationship (count, effectJobID, effectParameter, relationType, - causeKey, causeJobID, causeParameter); - record (passertion, _effectKey, true, asserterURL); - return passertion; - } - - /** - * Convenience method to parse string represented XML into a DOM XML fragment representation - */ - public Element toElement (String xmlAsString) throws IOException, SAXException { - //System.out.println( "XML as string is " + xmlAsString ); - return _builder.parse (new InputSource (new StringReader (xmlAsString))).getDocumentElement (); - } -} Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/refiner/AuthenticateEngine.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/refiner/AuthenticateEngine.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,191 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package edu.isi.pegasus.planner.refiner; - -import edu.isi.pegasus.planner.catalog.site.classes.FileServer; -import edu.isi.pegasus.planner.catalog.site.classes.GridGateway; -import edu.isi.pegasus.planner.classes.AuthenticateRequest; -import edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer; -import edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager; - -import edu.isi.pegasus.common.logging.LogManager; -import edu.isi.pegasus.planner.common.PegasusProperties; - -import java.util.HashSet; -import java.util.Iterator; -import java.util.List; -import java.util.Set; -import edu.isi.pegasus.planner.classes.PegasusBag; - -/** - * It authenticates the user with the sites, that the user specifies at the - * execution time. It spawns out a thread for each pool that authenticates - * against the jobmanager for the vanilla universe as specified in the pool - * configuration file. - * - * @author Karan Vahi - * @version $Revision: 2582 $ - */ -public class AuthenticateEngine extends Engine { - - /** - * The Set of pools that need to be authenticated against. - */ - private Set mExecPools; - - - /** - * The overloaded constructor. - * - * @param props the PegasusProperties to be used. - * @param pools The set of pools against which you want to authenticate the - * user. - */ -/* public AuthenticateEngine( PegasusProperties props, Set pools) { - super( props ); - mExecPools = pools; - - } -*/ - - /** - * The overloaded constructor. - * - * @param bag the PegasusBag to be used. - * @param pools The set of pools against which you want to authenticate the - * user. - */ - public AuthenticateEngine( PegasusBag bag, Set pools) { - super( bag ); - mExecPools = pools; - } - - /** - * It returns a set of pools against which the user can authenticate to. - * - * @return the set of authenticated pools. - */ - public Set authenticate(){ - Iterator it = mExecPools.iterator(); - ThreadPool manager = new ThreadPool( mProps, mExecPools); - String pool; - GridGateway jm; - FileServer gserv; - String contact; - - //we need synchronization to ensure that an threads are started only - //when all the requests have been sent to the threadpool, as this - //failure to authenticate against a pool leads to it's removal from - //this set. - synchronized(mExecPools){ - while(it.hasNext()){ - pool = (String)it.next(); - - // List jmList = mPoolHandle.getJobmanagers(pool); - // Iterator it1 = jmList.iterator(); - for( Iterator it1 = mSiteStore.lookup( pool ).getGridGatewayIterator(); it1.hasNext() ;){ - jm = (GridGateway)it1.next(); -// contact = jm.getInfo(JobManager.URL); - AuthenticateRequest ar = new AuthenticateRequest('j',pool, jm.getContact()); - manager.acceptRequest(ar); - } - -// List gridFtpList = mPoolHandle.getGridFTPServers(pool); -// it1 = gridFtpList.iterator(); -// while(it1.hasNext()){ - for( Iterator it1 = mSiteStore.lookup( pool ).getFileServerIterator(); it1.hasNext();){ - gserv = ( FileServer )it1.next(); -// contact = gserv.getInfo(GridFTPServer.GRIDFTP_URL); - AuthenticateRequest ar = new AuthenticateRequest('g',pool, gserv.getURLPrefix() ); - manager.acceptRequest(ar); - - } - } - } - manager.shutdown(); - purgePools(); - - return mExecPools; - } - - - /** - * It removies from the list of pools the pool that was not authenticated - * against. It queries the soft state of the pool config to see if there - * are at least one jobmanager and gridftp server on the pool. - * Due to the authentication the unauthenticated jobmanagers and servers - * would have been removed from the soft state of the pool config. - */ - private synchronized void purgePools(){ - Iterator it = mExecPools.iterator(); - String pool; - List l; - - while(it.hasNext()){ - pool = (String)it.next(); - l = mSiteStore.lookup( pool ).getFileServers(); - if(l == null || l.isEmpty()){ - mLogger.log("Removing Exec pool " + pool + - " as no authenticated gridftp server", - LogManager.DEBUG_MESSAGE_LEVEL); - it.remove(); - continue; - } - - List l1 = mSiteStore.lookup( pool ).getGridGateways( ); -// List l1 = mPoolHandle.getJobmanagers(pool,"transfer"); - if( (l == null || l.isEmpty()) || - (l1 == null || l1.isEmpty())){ - //we have no jobmanagers for universe vanilla or transfer universe - mLogger.log("Removing Exec pool " + pool + - " as no authenticated jobmanager", - LogManager.DEBUG_MESSAGE_LEVEL); - it.remove(); - continue; - } - - } - - } - - - - - /** - * The main testing method. - * - */ - public static void main(String[] args){ - Set s = new HashSet(); - //s.add("isi_condor"); - s.add("isi_lsf"); -/* - AuthenticateEngine a = new AuthenticateEngine( PegasusProperties.getInstance(),s); - a.mLogger.setLevel(1); - - a.authenticate(); - - System.out.println("Authentication Done!!"); - System.out.println(a.mPoolHandle.getGridFTPServers("isi_lsf")); - a.mLogger.log("Vanilla JMS " + a.mPoolHandle.getJobmanagers("isi_lsf"), - LogManager.DEBUG_MESSAGE_LEVEL); -*/ - - } - - -} Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/refiner/Authenticate.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/refiner/Authenticate.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,508 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - - -package edu.isi.pegasus.planner.refiner; - - -import edu.isi.pegasus.common.logging.LogManagerFactory; -import edu.isi.pegasus.planner.classes.AuthenticateRequest; - -import edu.isi.pegasus.common.logging.LogManager; -import edu.isi.pegasus.planner.common.PegasusProperties; - -import edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider; - -import org.globus.gram.Gram; -import org.globus.gram.GramException; - -import org.ietf.jgss.GSSCredential; -import org.ietf.jgss.GSSException; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.InterruptedIOException; -import java.io.OutputStreamWriter; - -import java.net.ConnectException; -import java.net.InetSocketAddress; -import java.net.Socket; - -import java.util.StringTokenizer; - -/** - * It takes in a authenticate request and authenticates against the resource - * on the basis of the type of the resource against which authentication is - * required. - * - * @author Karan Vahi - * @version $Revision: 2582 $ - */ - -public class Authenticate { - - - /** - * The standard port at which Grid FTP runs. - */ - public static final int GRID_FTP_STANDARD_PORT = 2811; - - /** - * The timeout in seconds. All sockets opened timeout after this period. - */ - public static final int TIMEOUT_VALUE = 120; - - /** - * The timeout value that is to be used in milliseconds - */ - private int mTimeout; - - /** - * The object containing the authenticate request. - */ - private AuthenticateRequest mAuthRequest; - - /** - * The handle to the Pool Info Provider. - */ - private PoolInfoProvider mPoolHandle; - - /** - * The handle to the LogManager object. - */ - private LogManager mLogger; - - /** - * The handle to the PegasusProperties object. - */ - private PegasusProperties mProps; - - /** - * The credential to be used while authentication to jobmanager. - */ - private GSSCredential mCredential; - - - /** - * The overloaded constructor. - * - * @param properties the PegasusProperties to be used. - */ - public Authenticate( PegasusProperties properties, PoolInfoProvider poolHandle ) { - mPoolHandle = poolHandle; - mLogger = LogManagerFactory.loadSingletonInstance( ); - mProps = properties; - mTimeout = (mProps.getGridFTPTimeout() == null)? - this.TIMEOUT_VALUE: - Integer.parseInt(mProps.getGridFTPTimeout()); - mTimeout *= 1000; - } - - /** - * Sets the credential that has to be used for authentication. - * - * @param credential the credential to be set. - */ - public void setCredential(GSSCredential credential){ - mCredential = credential; - } - - - /** - * Authenticates against a resource referred to in the authenticate request - * object. - */ - public boolean authenticate(AuthenticateRequest ar) { - mAuthRequest = ar; - char type = ar.getResourceType(); - boolean alive = false; - - //check if the request is invalid - if (ar.requestInvalid()) { - throw new RuntimeException("Invalid authentication request " + ar); - } - - if (type == AuthenticateRequest.GRIDFTP_RESOURCE) { - //check if the grid ftp server is alive. - HostPort hp = getHostPort(ar.getResourceContact()); - alive = gridFTPAlive(hp.getHost(),hp.getPort()); - - } - if (type == AuthenticateRequest.JOBMANAGER_RESOURCE) { - alive = authenticateJobManager(ar.getResourceContact()); - } - - return alive; - } - - - - - /** - * It tries to remove a resource from the soft state of the pool. This is - * possible only if the underlying pool interface implementation is soft - * state. - * - * @param ar the AuthenticateRequest containing the resource info - * - * @return boolean true removal was successful. - * false unable to remove. - */ - public boolean removeResource(AuthenticateRequest ar){ - char type = ar.getResourceType(); - - if(type == AuthenticateRequest.GRIDFTP_RESOURCE){ - return mPoolHandle.removeGridFtp(ar.getPool(), - ar.getResourceContact()); - } - if(type == AuthenticateRequest.JOBMANAGER_RESOURCE){ - return mPoolHandle.removeJobManager(ar.getPool(),null,ar.getResourceContact()); - } - - return false; - } - - - /** - * It authenticates against the jobmanager specifyied. - * - * @param contact the jobmanager contact. - */ - public boolean authenticateJobManager(String contact){ - boolean val = true; - try{ - mLogger.log( "Authenticating " + contact, LogManager.DEBUG_MESSAGE_LEVEL); - - if(mCredential == null){ - //try authenticating the default credential - Gram.ping(contact); - } - else - Gram.ping(mCredential,contact); - } - catch(GramException gex){ - mLogger.log("Unable authenticate against jobmanager " + - contact + " because " + gex.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - val = false; - } - catch(GSSException gss){ - String message = (gss.getMajor() == GSSException.CREDENTIALS_EXPIRED)? - "Your credentials have expired. You need to do a grid-proxy-init.": - "GssException caught " +gss.getMajorString() - + gss.getMinorString(); - mLogger.log(message,LogManager.ERROR_MESSAGE_LEVEL); - val = false; - } - catch(Exception e){ - //an unknown exception occured. print a message and return false - mLogger.log("Unknown Exception occured " + e.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - val = false; - } - finally{ - mLogger.log("Authenticating completed for " + contact,LogManager.DEBUG_MESSAGE_LEVEL); - } - return val; - } - - /** - * It checks with a grid ftp server running at a particular host - * and port, to see if it is up or not. This is done by opening a - * socket to the specified host at the specified port. If the socket - * timesout (which could be due to excessive load on the server or - * server being hung) false is returned. - * - * @param host the host at which the gridftp server is running . - * @param port the port at which server is running on the host. - * - * @return true the gridftp server is alive and kicking. - * false - the submit host is not connected to the network. - * - the server is not running. - * - we were able to connect but timeout. - * - version is not compatible. - * - */ - public boolean gridFTPAlive(String host, int port) { - Socket s = new Socket(); - String hp = combine(host, port); - boolean alive = false; - - mLogger.log("Checking status of " + hp, LogManager.DEBUG_MESSAGE_LEVEL); - InetSocketAddress addrs = new InetSocketAddress(host, port); - if (addrs.isUnresolved()) { - //either the host on which Pegasus is running is not connected - //to the network, or the hostname is invalid. Either way we return - //false; - mLogger.log("Unresolved address to " + hp, - LogManager.DEBUG_MESSAGE_LEVEL); - return false; - } - - try { - s.connect(addrs,mTimeout); - //set the timeout for the input streams - // gotten from this socket - s.setSoTimeout(mTimeout); - String response; - char type = 'c'; - BufferedReader rd = new BufferedReader(new InputStreamReader( - s.getInputStream())); - - BufferedWriter out = new BufferedWriter(new OutputStreamWriter( - s.getOutputStream())); - - while ( (response = rd.readLine()) != null) { - /*mLogger.logMessage("Response from server " + hp + " " + - response, - 1);*/ - - alive = parseGridFTPResponse(response, type); - - if (type == 'c' && alive) { - //send the quit command to the server - out.write("quit\r\n"); - //do a half close. We just need to wait for the response - //from server now - s.shutdownOutput(); - type = 'q'; - } - else { - //invalid response or the server is stuck. - //break out of the infinite waiting. - break; - } - - } - } - catch(java.net.SocketTimeoutException se){ - //means we experienced a timeout on read - mLogger.log("Timeout experienced while reading from ip" + - " stream of " + hp, LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - catch (InterruptedIOException e) { - //timeout was reached. - mLogger.log("Timeout experienced while contacting " + - hp, LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - catch (ConnectException ce) { - //probably no process running at the port - mLogger.log("GridFtp server on " + host + " not running on port " + - port + " .Exception " + ce.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - catch (IOException ie) { - mLogger.log("Unable to contact " + hp + " due to " + ie.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - catch(Exception e){ - //an unknown exception occured. print a message and return false - mLogger.log("Unknown Exception occured " + e.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - finally{ - try{ - s.close(); - } - catch(IOException e){ - mLogger.log("Unable to close socket to " + hp + " because" + - e.getMessage(),LogManager.ERROR_MESSAGE_LEVEL); - alive = false; - } - } - - - return alive; - } - - /** - * The parses the grid ftp server response and returns if the response - * was valid or not. - * - * @param response the response got from the grid ftp server. - * @param type c response when first connected to server. - * q response when sent the quit command. - * - * @return boolean true if the response was valid - * false invalid response. - */ - private boolean parseGridFTPResponse(String response, char type) { - StringTokenizer st = new StringTokenizer(response); - boolean valid = false; - - switch (type) { - case 'c': - - //valid response should be of type 220 blah - while (st.hasMoreTokens()) { - if (st.nextToken().equals("220")) { - valid = true; - } - break; - } - break; - - case 'q': - - //valid response would be type 221 blah - while (st.hasMoreTokens()) { - if (st.nextToken().equals("221")) { - valid = true; - } - break; - } - break; - - default: - valid = false; - - } - - if(valid == false) - mLogger.log(response,LogManager.ERROR_MESSAGE_LEVEL); - return valid; - - } - - /** - * A small helper method that returns the standard host and port - * combination to be used for logging purposes. - * - * @param host the host. - * @param port the port. - * - * @return combined string. - */ - private String combine(String host, int port) { - String st = host + ":" + port; - return st; - } - - /** - * Determines the hostname from the urlPrefix string in the pool file. - * - * @param urlPrefix the protocol, hostname and port combination. - * - * @return the host name. - */ - private HostPort getHostPort(String urlPrefix) { - StringTokenizer st = new StringTokenizer(urlPrefix); - String hostPort; - String hostName = new String(); - String token = new String(); - int count = 0; - int port = this.GRID_FTP_STANDARD_PORT; - HostPort hp = null; - - while (st.hasMoreTokens()) { - token = st.nextToken("/"); - count++; - if (count == 2) { - hostPort = token.trim(); - StringTokenizer st1 = new StringTokenizer(hostPort,":"); - hostName = st1.nextToken(); - if(st1.hasMoreTokens()){ - //port is specified - try{ - port = Integer.parseInt(st1.nextToken()); - } - catch(NumberFormatException e){ - port = this.GRID_FTP_STANDARD_PORT; - } - } - //System.out.println("Host->" + hostName + " Port->" + port); - hp = new HostPort(hostName,port); - //System.out.println(hp); - return hp; - } - - } - return null; - - } - - - /** - * A convenience inner class that stores the host and the port associated - * with a server. - */ - class HostPort{ - - /** - * The host at which the server is running. - */ - private String mHost; - - /** - * The port at which the server is running. - */ - private int mPort; - - /** - * The overloaded constructor - */ - public HostPort(String host, int port){ - mHost = host; - mPort = port; - } - - /** - * Returns the host associated with this object. - * - * @return String - */ - public String getHost(){ - return mHost; - } - - - /** - * Returns the port associated with this object. - * - * @return int - */ - public int getPort(){ - return mPort; - } - - /** - * Returns the string version of this object. - */ - public String toString(){ - StringBuffer sb = new StringBuffer(); - sb.append("host name ").append(mHost). - append(" port ").append(mPort); - - return sb.toString(); - } - } - - public static void main(String[] args){ - Authenticate a = new Authenticate( PegasusProperties.getInstance(), null ); - String contact = "dc-user2.isi.edu/jobmanager-lsf"; - String contact1 = "dc-n1.isi.edu"; - System.out.println("Authenticating " + contact1); - //a.authenticateJobManager(contact); - a.gridFTPAlive("dc-n1.isi.edu",a.GRID_FTP_STANDARD_PORT); - } -} Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/refiner/MainEngine.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/refiner/MainEngine.java 2012-05-24 16:47:52.064156782 -0700 +++ pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/refiner/MainEngine.java 2012-05-24 16:47:54.088166819 -0700 @@ -115,12 +115,6 @@ private RemoveDirectory mRemoveEng; /** - * The handle to the Authentication Engine that performs the authentication - * with the various sites. - */ - private AuthenticateEngine mAuthEng; - - /** * The handle to the node collapser. */ private NodeCollapser mNodeCollapser; @@ -161,27 +155,7 @@ //refinement process starting mOriginalDag.setWorkflowRefinementStarted( true ); - - //do the authentication against the pools - if (mPOptions.authenticationSet()) { - mAuthEng = new AuthenticateEngine( mBag, - new java.util.HashSet(mPOptions.getExecutionSites())); - - mLogger.logEventStart( LoggingKeys.EVENT_PEGASUS_AUTHENTICATION, LoggingKeys.DAX_ID, mOriginalDag.getAbstractWorkflowName() ); - Set authenticatedSet = mAuthEng.authenticate(); - if (authenticatedSet.isEmpty()) { - StringBuffer error = new StringBuffer( ); - error.append( "Unable to authenticate against any site. "). - append( "Probably your credentials were not generated" ). - append( " or have expired" ); - throw new RuntimeException( error.toString() ); - } - mLogger.log("Sites authenticated are " + - setToString(authenticatedSet, ","), - LogManager.DEBUG_MESSAGE_LEVEL); - mLogger.logEventCompletion(); - mPOptions.setExecutionSites(authenticatedSet); - } + String message = null; mRCBridge = new ReplicaCatalogBridge( mOriginalDag, mBag ); Index: pegasus-wms_4.0.1+dfsg/src/edu/isi/pegasus/planner/refiner/ThreadPool.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/edu/isi/pegasus/planner/refiner/ThreadPool.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,484 +0,0 @@ -/** - * Copyright 2007-2008 University Of Southern California - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - - -package edu.isi.pegasus.planner.refiner; - -import edu.isi.pegasus.common.logging.LogManagerFactory; -import java.io.File; -import java.io.FileInputStream; -import java.util.LinkedList; -import java.util.Set; - -import org.gridforum.jgss.ExtendedGSSCredential; -import org.gridforum.jgss.ExtendedGSSManager; -import edu.isi.pegasus.planner.classes.AuthenticateRequest; -import edu.isi.pegasus.planner.classes.Profile; -import edu.isi.pegasus.common.logging.LogManager; -import edu.isi.pegasus.planner.common.PegasusProperties; -import edu.isi.pegasus.planner.namespace.ENV; -import edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider; -import edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode; -import org.ietf.jgss.GSSCredential; - - -/** - * This maintains a pool of authenticate threads that authenticate against a - * particular resource. - * - * @author Karan Vahi - * @version $Revision: 2582 $ - */ - -public class ThreadPool { - - /** - * The maximum number of authentication threads that are spawned. - */ - public static final int NUMBER_OF_THREADS = 5; - - /** - * The request queue that holds the authenticate requests. The worker - * threads do access this job queue. - */ - private LinkedList mQueue; - - /** - * The handle to the properties object. - */ - private PegasusProperties mProps; - - /** - * The handle to the Pool Info Provider. - */ - private PoolInfoProvider mPoolHandle; - - /** - * The handle to the LogManager object. - */ - private LogManager mLogger; - - /** - * The Set of pools that need to be authenticated against. - */ - private Set mExecPools; - - /** - * The number of pools that one has to authenticate against. - */ - private Integer mNumOfPools; - - /** - * The handle to the pool of threads that this thread pool is reponsible for. - */ - private AuthenticateThread[] mWorkers; - - /** - * The condition variable that is used to synchronize the shutdown. - */ - private ConditionVariable mCurrentNum; - - /** - * The namespace object holding the environment variables for local - * pool. - */ - private ENV mLocalEnv; - - /** - * The credential loaded from the non default location if specified. - */ - private GSSCredential mCredential; - - /** - * The overloaded constructor. - * - * @param properties the PegasusProperties to be used. - * @param pools the set of pools against which the user is authenticating. - */ - public ThreadPool( PegasusProperties properties, Set pools ) { - mQueue = new LinkedList(); - mCurrentNum = new ConditionVariable(); - mProps = properties; - mLogger = LogManagerFactory.loadSingletonInstance( properties ); - String poolClass = PoolMode.getImplementingClass(mProps.getPoolMode()); - mPoolHandle = PoolMode.loadPoolInstance(poolClass,mProps.getPoolFile(), - PoolMode.SINGLETON_LOAD); - mExecPools = pools; - mNumOfPools = new Integer(pools.size()); - - //load the local environment variables - mLocalEnv = loadLocalEnvVariables(); - //load the credential if the user has set the - //corresponding environment variable. - mCredential = (mLocalEnv.containsKey(ENV.X509_USER_PROXY_KEY))? - //load the proxy from the path specified - getGSSCredential((String)mLocalEnv.get(ENV.X509_USER_PROXY_KEY)): - null; - - if(mCredential == null){ - //log message - mLogger.log("Proxy will be picked up from the default location in /tmp", - LogManager.DEBUG_MESSAGE_LEVEL); - } - - //intialise the worker threads - mWorkers = new AuthenticateThread[this.NUMBER_OF_THREADS]; - for(int i = 0; i < NUMBER_OF_THREADS; i++){ - mWorkers[i] = new AuthenticateThread(i); - - //start the threads - mWorkers[i].start(); - } - } - - - /** - * This method is called to ensure the clean shutdown of threads, and - * waits till all the requests have been serviced. - */ - public void shutdown(){ - - //mNumOfPools is the CV on which you do a shutdowm - synchronized(mCurrentNum){ - - int numOfPools = mNumOfPools.intValue(); - for (int i = 0; i < NUMBER_OF_THREADS; i++) { - //send the shutdown signal to the worker threads - mWorkers[i].shutdown(); - } - - //wake up all the threads on this - synchronized(mQueue){ - //mLogger.logMessage("Manager sending notify to all"); - mQueue.notifyAll(); - } - - while(mCurrentNum.getValue() < NUMBER_OF_THREADS){ - try{ - mCurrentNum.wait(); - } - catch(InterruptedException e){ - mLogger.log( - "Manager got interrupted during shutdown" + e.getMessage(), - LogManager.ERROR_MESSAGE_LEVEL); - } - } - } - - } - - - /** - * Accepts an authentication request, that has to be serviced. It is added - * to queue of requests. - */ - public void acceptRequest(Object request){ - - //see if any of the worker threads are available - /*for(int i = 0; i < NUMBER_OF_THREADS; i++){ - if(mWorkers[i].isAvailable()){ - //no need to add to queue. - } - }*/ - - synchronized(mQueue){ - mQueue.addLast(request); - //send a notification to a worker thread - mQueue.notify(); - } - - } - - - /** - * Reads in the environment variables into memory from the properties file - * and the pool catalog. - * - * @return the ENV namespace object holding the environment - * variables. - */ - private ENV loadLocalEnvVariables(){ - //assumes that pool handle, and property handle are initialized. - ENV env = new ENV(); - - //load from the pool.config - env.checkKeyInNS(mPoolHandle.getPoolProfile("local",Profile.ENV)); - //load from property file - env.checkKeyInNS(mProps.getLocalPoolEnvVar()); - - return env; - } - - /** - * Loads a GSSCredential from the proxy file residing at the path specified. - * - * @param file the path to the proxy file. - * - * @return GSSCredential - * null in case the file format is wrong, or file does not exist. - */ - private GSSCredential getGSSCredential(String file){ - File f = new File(file); - GSSCredential gcred = null; - //sanity check first - if(!f.exists()){ - return null; - } - - try{ - byte[] data = new byte[ (int) f.length()]; - FileInputStream in = new FileInputStream(f); - in.read(data); - in.close(); - - ExtendedGSSManager manager = - (ExtendedGSSManager) ExtendedGSSManager.getInstance(); - - gcred = manager.createCredential(data, - ExtendedGSSCredential.IMPEXP_OPAQUE, - GSSCredential.DEFAULT_LIFETIME, - null, - GSSCredential.INITIATE_AND_ACCEPT); - mLogger.log("Loaded the credential from proxy file " + file, - LogManager.DEBUG_MESSAGE_LEVEL); - - } - catch(Exception e){ - mLogger.log( - "Unable to load proxy from file" + file + " " + - e.getMessage(),LogManager.ERROR_MESSAGE_LEVEL); - } - return gcred; - } - - /** - * A thread as an inner class, that authenticates against one particular - * pool. - */ - class AuthenticateThread implements Runnable{ - - /** - * The pool against which to authenticate. - */ - private String mPool; - - /** - * The thread object that is used to launch the thread. - */ - private Thread mThread; - - /** - * Whether the thread is available to do some work or not. - */ - private boolean mAvailable; - - /** - * Whether to shutdown or not. - */ - private boolean mShutdown; - - /** - * The unique identifying id of the thread. - */ - private int mIndex; - - /** - * The overloaded constructor. - * - * - */ - public AuthenticateThread(int index){ - mAvailable = true; - mShutdown = false; - mIndex = index; - } - - /** - * The start method for the thread. It initialises the thread and calls - * it's start method. - */ - public void start(){ - mThread = new Thread(this); - mThread.start(); - } - - - /** - * Returns whether a thread is available to do some work or not. - */ - public boolean isAvailable(){ - return mAvailable; - } - - /** - * Sets the shutdown flag to true. This does not make the thread stop. - * The thread only stops when it's current request is serviced and the - * queue is empty. - */ - public void shutdown(){ - mShutdown = true; - } - - /** - * Calls the corresponding join method of the thread associated with - * this class. - * - * @param millis The time to wait in milliseconds. - */ - public void join(long millis) throws InterruptedException{ - mThread.join(millis); - } - - /** - * The runnable method of the thread, that is called when the thread is - * started. - */ - public void run(){ - AuthenticateRequest ar; - Authenticate a = new Authenticate( mProps, mPoolHandle ); - a.setCredential(mCredential); - boolean authenticated = false; - - for(;;){ - //remain in an infinite loop and wait for a request to be released - //from the queue. - ar = getAuthenticateRequest(); - if(ar == null){ - //no more requests to service and the shutdown signal has - //been received. send the notification to the manager and exit - mLogger.log("Thread [" + mIndex +"] got shutdown signal", - LogManager.DEBUG_MESSAGE_LEVEL); - synchronized(mCurrentNum){ - mCurrentNum.increment(); - mCurrentNum.notify(); - } - - break; - } - - //means worker is busy, processing a request. - mAvailable = false; - //do the processing. - authenticated = a.authenticate(ar); - mLogger.log("Thread [" + mIndex +"] Authentication of " + ar + - " successful:" + authenticated, - LogManager.DEBUG_MESSAGE_LEVEL); - if(!authenticated){ - //we need to remove - boolean removal = a.removeResource(ar); - mLogger.log("Thread [" + mIndex +"] Removal of resource" + ar + - " successful:" + removal,LogManager.DEBUG_MESSAGE_LEVEL); - } - mAvailable = true; - //be nice and sleep - try{ - mThread.sleep(5); - } - catch (InterruptedException ex) { - mLogger.log( - "Authenticate Thread [" + mIndex +"] got interrupted while waiting", - LogManager.DEBUG_MESSAGE_LEVEL); - //go into sleep again - continue; - } - - } - - } - - /** - * Returns an authentication request to the worker thread. - * - * @return the authentication request. - */ - public AuthenticateRequest getAuthenticateRequest(){ - synchronized(mQueue){ - - for(;;){ - if(mQueue.isEmpty() && mShutdown){ - //no more requests to service and the shutdown signal has - //been received. - return null; - } - else if (mQueue.isEmpty()) { - //there is nothing in the queue so wait on it. - try { - mLogger.log("Thread [" + mIndex +"] going to wait", - LogManager.DEBUG_MESSAGE_LEVEL); - mQueue.wait(); - //again check for empty queue and shutdown signal - if(mQueue.isEmpty() && !mShutdown) - //go back to the wait state to receive a new - //request or a AR request - continue; - } - catch (InterruptedException ex) { - mLogger.log( - "Authenticate Thread [" + mIndex +"] got interrupted while waiting " + - ex.getMessage(),LogManager.ERROR_MESSAGE_LEVEL); - //go into sleep again - continue; - } - - } - return (mQueue.isEmpty() && mShutdown)? - //indicates shutdown - null: - (AuthenticateRequest)mQueue.removeFirst(); - - - } - - } - } - - } - - - /** - * A wrapper around an int that acts as a Condition Variable, and is used - * as such. In behaviour it is probably closer to a semaphore. - */ - class ConditionVariable{ - - /** - * The int that is associated with this object. - */ - private int value; - - /** - * The default constructor. - */ - public ConditionVariable(){ - value = 0; - } - - /** - * It increments the value by 1. - */ - public void increment(){ - value++; - } - - /** - * Returns the value. - */ - public int getValue(){ - return value; - } - } - -} Index: pegasus-wms_4.0.1+dfsg/src/org/globus/common/CoGProperties.java =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ pegasus-wms_4.0.1+dfsg/src/org/globus/common/CoGProperties.java 2012-05-24 16:49:26.696626021 -0700 @@ -0,0 +1,693 @@ +/* + * Copyright 1999-2006 University of Chicago + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.globus.common; + +import java.util.Properties; +import java.util.Enumeration; +import java.io.IOException; +import java.io.InputStream; +import java.io.FileInputStream; +import java.io.OutputStream; +import java.io.FileOutputStream; +import java.net.InetAddress; +import java.net.UnknownHostException; + +import org.globus.util.ConfigUtil; + +/** Responsible for managing the properties file + * "~/.globus/cog.properties", which holds information about various properties + * needed by the security classes. These properties include: + *
    + *
  • the location of the user certificate file
    • + *
  • the location of the user key file
    • + *
  • the location of the CA certificates
    • + *
  • the location of the proxy file
    • + *
  • the tcp port range
    • + *
  • the local ip address for DHCP systems
    • + *
  • the socket timeout when connecting to a myproxy host
    • + *
+ */ +public class CoGProperties extends Properties { + + private static final String DEFAULT_RANDOM_PROVIDER = + "cryptix.jce.provider.CryptixRandom"; + + private static final String DEFAULT_RANDOM_ALGORITHM = + "DevRandom"; + + public static final String ENFORCE_SIGNING_POLICY = + "java.security.gsi.signing.policy"; + + public static final String DELEGATION_KEY_CACHE_LIFETIME = + "org.globus.jglobus.delegation.cache.lifetime"; + + public static final String CRL_CACHE_LIFETIME = + "org.globus.jglobus.crl.cache.lifetime"; + + public static final String MDSHOST = "localhost"; + public static final String MDSPORT = "2135"; + public static final String BASEDN = "Mds-Vo-name=local, o=Grid"; + + /** the configuration file properties are read from -- + * located in ~/.globus" */ + public static final String CONFIG_FILE = "cog.properties"; + + /** the default properties file **/ + private static CoGProperties defaultProps = null; + + /** the config file location **/ + public static String configFile = null; + + public CoGProperties() { + } + + public CoGProperties(String file) + throws IOException { + load(file); + } + + public synchronized static CoGProperties getDefault() { + if (defaultProps != null) { + return defaultProps; + } + + defaultProps = new CoGProperties(); + + String file = System.getProperty("org.globus.config.file"); + if (file == null) { + file = ConfigUtil.globus_dir + CONFIG_FILE; + } else if (file.equalsIgnoreCase("none")) { + return defaultProps; + } + + configFile = file; + + try { + defaultProps.load(configFile); + } + catch(Exception e) {} + + return defaultProps; + } + + /** + * Sets default configuration. It can be used + * to set a different configuration dynamically. + */ + public static void setDefault(CoGProperties properties) { + defaultProps = properties; + } + + public void save() + throws IOException { + save(configFile); + } + + public void save(String file) + throws IOException { + OutputStream out = null; + try { + out = new FileOutputStream(file); + store(out, "Java CoG Kit Configuration File"); + } finally { + if (out != null) { + try { out.close(); } catch (Exception e) {} + } + } + } + + public void load(String file) + throws IOException { + FileInputStream in = null; + try { + in = new FileInputStream(file); + load(in); + } finally { + if (in != null) { + try { in.close(); } catch(Exception e) {} + } + } + } + + public void load(InputStream in) + throws IOException { + super.load(in); + fixSpace(this); + } + + public static void fixSpace(Properties p) { + // this will get rid off the trailing spaces + String key, value; + Enumeration e = p.keys(); + while(e.hasMoreElements()) { + key = e.nextElement().toString(); + value = p.getProperty(key); + p.put(key, value.trim()); + } + } + + /** + * Retrieves the location of the user cert file. + * It first checks the X509_USER_CERT system property. If the property + * is not set, it checks next the 'usercert' property in the current + * configuration. If that property is not set, it returns a default + * location of the user cert file. The default value + * is the 'usercert.pem' file in the user's globus directory. For example: + * ${user.home}/.globus/usercert.pem. + * + * @return String the location of the user cert file + */ + public String getUserCertFile() { + String location; + location = System.getProperty("X509_USER_CERT"); + if (location != null) { + return location; + } + location = getProperty("usercert"); + if (location != null) { + return location; + } + return ConfigUtil.discoverUserCertLocation(); + } + + public void setUserCertFile(String userCertFile) { + put("usercert", userCertFile); + } + + public String getPKCS11LibraryName() { + String lib; + lib = System.getProperty("PKCS11_LIB"); + if (lib != null) { + return lib; + } + lib = getProperty("pkcs11lib"); + if (lib != null) { + return lib; + } + return ConfigUtil.discoverPKCS11LibName(); + } + + public String getDefaultPKCS11Handle() { + return getProperty("pkcs11.handle", "Globus User Credentials"); + } + + /** + * Retrieves the location of the user key file. + * It first checks the X509_USER_KEY system property. If the property + * is not set, it checks next the 'userkey' property in the current + * configuration. If that property is not set, it returns a default + * location of the user key file. The default value + * is the 'userkey.pem' file in the user's globus directory. For example: + * ${user.home}/.globus/userkey.pem. + * + * @return String the location of the user key file + */ + public String getUserKeyFile() { + String location; + location = System.getProperty("X509_USER_KEY"); + if (location != null) { + return location; + } + location = getProperty("userkey"); + if (location != null) { + return location; + } + return ConfigUtil.discoverUserKeyLocation(); + } + + /** + * Sets user key file location + * @param userKeyFile user key file location + */ + public void setUserKeyFile(String userKeyFile) { + put("userkey", userKeyFile); + } + + /** + * Returns the user specified hostname. This is used + * for DHCP machines where java is unable to determine the + * right hostname/IP address. + * It first checks the 'GLOBUS_HOSTNAME' system property. If the property + * is not set, it checks the 'host' system property next. If the 'host' + * property is not set in the current configuration, null is returned + * (and default 'localhost' hostname will be used) + * + * @return String the hostname of the machine. + */ + public String getHostName() { + String value = System.getProperty("GLOBUS_HOSTNAME"); + if (value != null) { + return value; + } + return getProperty("hostname", null); + } + + /** + * Sets hostname + * @param host hostname + */ + public void setHostName(String host) { + put("hostname", host); + } + + /** + * Returns the user specified ip address. This is used + * for DHCP machines where java is unable to determine the + * right IP address. + * It first checks the 'org.globus.ip' system property. + * If that property is not set, it checks next the 'ip' property + * in the current configuration. If the 'ip' property is not set in the + * current configuration, the hostname of the machine is looked up + * using the {@link #getHostName() getHostName()} function. If + * getHostName() returns a hostname that hostname is converted + * into an IP address and it is returned. Otherwise, null is returned + * (and default ip address will be used) + * + * @return String the ip address of the machine. + */ + public String getIPAddress() { + String value = System.getProperty("org.globus.ip"); + if (value != null) { + return value; + } + value = getProperty("ip", null); + if (value != null) { + return value; + } + value = getHostName(); + if (value != null) { + try { + return InetAddress.getByName(value).getHostAddress(); + } catch (UnknownHostException e) { + return null; + } + } + return value; + } + + /** + * Sets ip address + * @param ipAddress ip address + */ + public void setIPAddress(String ipAddress) { + put("ip", ipAddress); + } + + /** + * @deprecated Use getCaCertLocations() instead. + * + * @see #getCaCertLocations() getCaCertLocations + * + * @return String the locations of the CA certificates + */ + public String getCaCertFile() { + return getCaCertLocations(); + } + + /** + * @deprecated Use getCaCertLocations() instead. + * + * @see #getCaCertLocations() getCaCertLocations + * + * @return String the locations of the CA certificates + */ + public String getCaCerts() { + return getCaCertLocations(); + } + + /** + * Retrieves the location of the CA certificate files. + * It first checks the X509_CERT_DIR system property. If the property + * is not set, it checks next the 'cacert' property in the current + * configuration. If that property is not set, it tries to find + * the certificates using the following rules:
+ * First the ${user.home}/.globus/certificates directory is checked. + * If the directory does not exist, and on a Unix machine, the + * /etc/grid-security/certificates directory is checked next. + * If that directory does not exist and GLOBUS_LOCATION + * system property is set then the ${GLOBUS_LOCATION}/share/certificates + * directory is checked. Otherwise, null is returned. + * This indicates that the certificates directory could + * not be found. + *
+ * Moreover, this function can return multiple file and directory + * locations. The locations must be comma separated. + * + * @return String the locations of the CA certificates + */ + public String getCaCertLocations() { + String location; + location = System.getProperty("X509_CERT_DIR"); + if (location != null) { + return location; + } + location = getProperty("cacert"); + if (location != null) { + return location; + } + return ConfigUtil.discoverCertDirLocation(); + } + + public void setCaCertLocations(String list) { + put("cacert", list); + } + + /** + * Retrieves the location of the proxy file. + * It first checks the X509_USER_PROXY system property. If the property + * is not set, it checks next the 'proxy' property in the current + * configuration. If that property is not set, then it defaults to a + * value based on the following rules:
+ * If a UID system property is set, and running on a Unix machine it + * returns /tmp/x509up_u${UID}. If any other machine then Unix, it returns + * ${tempdir}/x509up_u${UID}, where tempdir is a platform-specific + * temporary directory as indicated by the java.io.tmpdir system property. + * If a UID system property is not set, the username will be used instead + * of the UID. That is, it returns ${tempdir}/x509up_u_${username} + *
+ * This is done this way because Java is not able to obtain the current + * uid. + * + * @return String the location of the proxy file + */ + public String getProxyFile() { + String location; + location = System.getProperty("X509_USER_PROXY"); + if (location != null) { + return location; + } + location = getProperty("proxy"); + if (location != null) { + return location; + } + return ConfigUtil.discoverProxyLocation(); + } + + public void setProxyFile(String proxyFile) { + put("proxy", proxyFile); + } + + /** + * Returns the tcp port range. + * It first checks the 'GLOBUS_TCP_PORT_RANGE' system property. If that + * system property is not set then 'org.globus.tcp.port.range' system + * property is checked. If that system property is not set then it returns + * the value specified in the configuration file. Returns null if the port + * range is not defined.
+ * The port range is in the following form: , + * + * @return String the port range. + */ + public String getTcpPortRange() { + String value = null; + value = System.getProperty("GLOBUS_TCP_PORT_RANGE"); + if (value != null) { + return value; + } + value = System.getProperty("org.globus.tcp.port.range"); + if (value != null) { + return value; + } + return getProperty("tcp.port.range", null); + } + + /** + * Returns the tcp source port range. + * It first checks the 'GLOBUS_TCP_SOURCE_PORT_RANGE' system property. + * If that system property is not set then + * 'org.globus.source.tcp.port.range' system property is checked. + * If that system property is not set then it returns + * the value specified in the configuration file. Returns null if the port + * range is not defined.
+ * The port range is in the following form: , + * + * @return String the port range. + */ + public String getTcpSourcePortRange() { + String value = null; + value = System.getProperty("GLOBUS_TCP_SOURCE_PORT_RANGE"); + if (value != null) { + return value; + } + value = System.getProperty("org.globus.tcp.source.port.range"); + if (value != null) { + return value; + } + return getProperty("tcp.source.port.range", null); + } + + /** + * Returns the udp source port range. + * It first checks the 'GLOBUS_UDP_SOURCE_PORT_RANGE' system property. + * If that system property is not set then + * 'org.globus.source.udp.port.range' system property is checked. + * If that system property is not set then it returns + * the value specified in the configuration file. Returns null if the port + * range is not defined.
+ * The port range is in the following form: , + * + * @return String the port range. + */ + public String getUdpSourcePortRange() { + String value = null; + value = System.getProperty("GLOBUS_UDP_SOURCE_PORT_RANGE"); + if (value != null) { + return value; + } + value = System.getProperty("org.globus.udp.source.port.range"); + if (value != null) { + return value; + } + return getProperty("udp.source.port.range", null); + } + + /** + * Returns whether to use the /dev/urandom device + * for seed generation. + * + * @return true if the device should be used (if available of course) + * Returns true by default unless specified otherwise by the + * user. + */ + public boolean useDevRandom() { + String value = System.getProperty("org.globus.dev.random"); + if (value != null && value.equalsIgnoreCase("no")) { + return false; + } + return getAsBoolean("org.globus.dev.random", true); + } + + public boolean enforceSigningPolicy() { + + String value = System.getProperty(ENFORCE_SIGNING_POLICY); + if ((value != null) && (value.equalsIgnoreCase("no") + || (value.equalsIgnoreCase("false")))) { + return false; + } + return getAsBoolean(ENFORCE_SIGNING_POLICY, true); + } + + /** + * Returns the delegation key cache lifetime for all delegations from this + * JVM. If this property is not set or set to zero or less, no caching is done. The + * value is the number of milliseconds the key/pair is cached. + * @return + */ + public int getDelegationKeyCacheLifetime() { + + int valueInt = 0; + + String valueStr = System.getProperty(DELEGATION_KEY_CACHE_LIFETIME); + + if (valueStr != null && valueStr.length() > 0) { + int parsedvalueInt = Integer.parseInt(valueStr); + if (parsedvalueInt > 0) { + valueInt = parsedvalueInt; + } + } + + if (valueInt == -1) { // Didn't find a system property + valueStr = getProperty(DELEGATION_KEY_CACHE_LIFETIME); + if (valueStr != null && valueStr.length() > 0) { + int parsedvalueInt = Integer.parseInt(valueStr); + if (parsedvalueInt > 0) { + valueInt = parsedvalueInt; + } + } + } + return valueInt; + } + + + /** + * Returns the CRL cache lifetime. If this property is not set or + * set to zero or less, no caching is done. The value is the + * number of milliseconds the CRLs are cached without checking for + * modifications on disk. + * + * @throws NumberFormatException if the cache lifetime property + * could not be parsed + * @return the CRL cache lifetime in milliseconds + */ + public long getCRLCacheLifetime() + throws NumberFormatException { + + long value = 0; + + String property = getProperty(CRL_CACHE_LIFETIME); + if (property != null && property.length() > 0) { + long parsedValue = Long.parseLong(property); + if (parsedValue > 0) { + value = parsedValue; + } + } + + // System property takes precedence + property = System.getProperty(CRL_CACHE_LIFETIME); + if (property != null && property.length() > 0) { + long parsedValue = Long.parseLong(property); + if (parsedValue > 0) { + value = parsedValue; + } + } + + return value; + } + + public String getSecureRandomProvider() { + String value = System.getProperty("org.globus.random.provider"); + if (value != null) { + return value; + } + return getProperty("random.provider", + DEFAULT_RANDOM_PROVIDER); + } + + public String getSecureRandomAlgorithm() { + String value = System.getProperty("org.globus.random.algorithm"); + if (value != null) { + return value; + } + return getProperty("random.algorithm", + DEFAULT_RANDOM_ALGORITHM); + } + + /** + * Returns the timeout (in seconds) for creating a new socket connection + * to a MyProxy host. The socket timeout property can be set either as + * the Java system property "MYPROXY_SOCKET_TIMEOUT" (i.e. via the '-D' + * command line option or environment variable) or via the + * "sockettimeout" property in the cog.properties file. If no such + * property is found, the default timeout of 10 seconds is returned. + * + * @return The timeout for creating a socket connectino to a MyProxy + * host. Defaults to 10 seconds. + */ + public int getSocketTimeout() { + int timeoutInt = -1; // -1 indicates it hasn't been set yet + String timeoutStr = System.getProperty("MYPROXY_SOCKET_TIMEOUT"); + if (timeoutStr != null && timeoutStr.length() > 0) { + int parsedTimeoutInt = Integer.parseInt(timeoutStr); + if (parsedTimeoutInt >= 0) { + timeoutInt = parsedTimeoutInt; + } + } + if (timeoutInt == -1) { // Didn't find a system property + timeoutStr = getProperty("sockettimeout"); + if (timeoutStr != null && timeoutStr.length() > 0) { + int parsedTimeoutInt = Integer.parseInt(timeoutStr); + if (parsedTimeoutInt >= 0) { + timeoutInt = parsedTimeoutInt; + } + } + } + if (timeoutInt == -1) { // Didn't find any property at all + timeoutInt = 10; + } + return timeoutInt; + } + + public void setSocketTimeout(int socketTimeout) { + put("sockettimeout", String.valueOf(socketTimeout)); + } + + + // ------------------------------------------------------- + + public int getProxyStrength() { + return getAsInt("proxy.strength", 512); + } + + public void setProxyStrength(int strength) { + put("proxy.strength", String.valueOf(strength)); + } + + public int getProxyLifeTime() { + return getAsInt("proxy.lifetime", 12); + } + + public void setProxyLifeTime(int lifeTimeInHours) { + put("proxy.lifetime", String.valueOf(lifeTimeInHours)); + } + + // -------------------------------------------------------- + + // --- Most of these functions are deprecated --- + + public String getRootMDSHost() { + return getProperty("mds.root.host", MDSHOST); + } + + public String getRootMDSPort() { + return getProperty("mds.root.port", MDSPORT); + } + + public String getRootMDSBaseDN() { + return getProperty("mds.root.basedn", BASEDN); + } + + public String getOrgMDSHost() { + return getProperty("mds.org.host", MDSHOST); + } + + public String getOrgMDSPort() { + return getProperty("mds.org.port", MDSPORT); + } + + public String getOrgMDSBaseDN() { + return getProperty("mds.org.basedn", BASEDN); + } + + // ---------------------------------------------------- + + protected boolean getAsBoolean(String key, boolean defaultValue) { + String tmp = getProperty(key); + if (tmp == null) { + return defaultValue; + } + return (tmp.equalsIgnoreCase("yes") || tmp.equalsIgnoreCase("true")); + } + + protected int getAsInt(String label, int defValue) { + String tmp = getProperty(label); + return (isNullOrEmpty(tmp)) ? defValue : Integer.parseInt(tmp); + } + + protected final static boolean isNullOrEmpty(String tmp) { + return (tmp == null || (tmp != null && tmp.length() == 0)); + } + +} Index: pegasus-wms_4.0.1+dfsg/src/org/globus/util/ConfigUtil.java =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ pegasus-wms_4.0.1+dfsg/src/org/globus/util/ConfigUtil.java 2012-05-24 16:47:54.092166841 -0700 @@ -0,0 +1,259 @@ +/* + * Copyright 1999-2006 University of Chicago + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.globus.util; + +import java.io.IOException; +import java.io.File; +import java.io.BufferedReader; +import java.io.InputStreamReader; + +public class ConfigUtil { + + public static final int UNDEFINED_OS = -1; + public static final int WINDOWS_OS = 0; + public static final int UNIX_OS = 1; + public static final int MAC_OS = 2; + public static final int OTHER_OS = 3; + + private static int osType = UNDEFINED_OS; + + private static final String PROXY_NAME = "x509up_u"; + + private static final String SOLARIS_ID_EXEC = + "/usr/xpg4/bin/id"; + + public static String globus_dir = null; + + static { + globus_dir = System.getProperty("user.home") + + File.separator + + ".globus" + + File.separator; + } + + /** Returns default PKCS11 library name */ + public static String discoverPKCS11LibName() { + return "dspkcs"; // use the ibutton library as the default for now + } + + /** Returns default location of user cert file */ + public static String discoverUserCertLocation() { + String location = null; + location = globus_dir + "usercert.pem"; + return location; + } + + /** Returns default location of user key file */ + public static String discoverUserKeyLocation() { + String location = null; + location = globus_dir + "userkey.pem"; + return location; + } + + /** + * Tries to discover user proxy location. + * If a UID system property is set, and running on a Unix machine it + * returns /tmp/x509up_u${UID}. If any other machine then Unix, it returns + * ${tempdir}/x509up_u${UID}, where tempdir is a platform-specific + * temporary directory as indicated by the java.io.tmpdir system property. + * If a UID system property is not set, the username will be used instead + * of the UID. That is, it returns ${tempdir}/x509up_u_${username} + */ + public static String discoverProxyLocation() { + + String dir = null; + + if (getOS() == UNIX_OS) { + dir = "/tmp/"; + } else { + String tmpDir = System.getProperty("java.io.tmpdir"); + dir = (tmpDir == null) ? globus_dir : tmpDir; + } + + String uid = System.getProperty("UID"); + + if (uid != null) { + return getLocation(dir, PROXY_NAME + uid); + } else if (getOS() == UNIX_OS) { + try { + return getLocation(dir, PROXY_NAME + getUID()); + } catch (IOException e) { + } + } + + /* If all else fails use username */ + String suffix = System.getProperty("user.name"); + if (suffix != null) { + suffix = suffix.toLowerCase(); + } else { + suffix = "nousername"; + } + + return getLocation(dir, PROXY_NAME + "_" + suffix); + } + + private static String getLocation(String dir, String file) { + File f = new File(dir, file); + return f.getAbsolutePath(); + } + + /** + * Returns the user id. The user id is obtained by executing 'id -u' + * external program. + *

Note: + * Under some circumstances, this function executes an external program; + * thus, its behavior is influenced by environment variables such as the + * caller's PATH and the environment variables that control dynamic + * loading. Care should be used if calling this function from a program + * that will be run as a Unix setuid program, or in any other manner in + * which the owner of the Unix process does not completely control its + * runtime environment. + * + * + * @throws IOException if unable to determine the user id. + * @return the user id + */ + public static String getUID() throws IOException { + String exec = "id"; + String osname = System.getProperty("os.name"); + if (osname != null) { + osname = osname.toLowerCase(); + if ((osname.indexOf("solaris") != -1) || + (osname.indexOf("sunos") != -1)) { + if ((new File(SOLARIS_ID_EXEC).exists())) { + exec = SOLARIS_ID_EXEC; + } + } else if (osname.indexOf("windows") != -1) { + throw new IOException("Unable to determine the user id"); + } + } + + Runtime runTime = Runtime.getRuntime(); + Process process = null; + BufferedReader buffInReader = null; + String s = null; + StringBuffer output = new StringBuffer(); + int exitValue = -1; + + try { + process = runTime.exec(exec + " -u"); + buffInReader = new BufferedReader + ( new InputStreamReader(process.getInputStream()) ); + while ((s = buffInReader.readLine()) != null) { + output.append(s); + } + exitValue = process.waitFor(); + } catch (Exception e) { + throw new IOException("Unable to execute 'id -u'"); + } finally { + if (buffInReader != null) { + try { + buffInReader.close(); + } catch (IOException e) {} + } + if (process != null) { + try { + process.getErrorStream().close(); + } catch (IOException e) {} + try { + process.getOutputStream().close(); + } catch (IOException e) {} + } + } + if (exitValue != 0) { + throw new IOException("Unable to perform 'id -u'"); + } + return output.toString().trim(); + } + + /** + * Discovers location of CA certificates directory. + * First the ${user.home}/.globus/certificates directory is checked. + * If the directory does not exist, and on a Unix machine, the + * /etc/grid-security/certificates directory is checked next. + * If that directory does not exist and GLOBUS_LOCATION + * system property is set then the ${GLOBUS_LOCATION}/share/certificates + * directory is checked. Otherwise, null is returned. + * This indicates that the certificates directory could + * not be found. + */ + public static String discoverCertDirLocation() { + String location = null; + + location = getDir(globus_dir + "certificates"); + if (location != null) return location; + + if (getOS() == UNIX_OS) { + location = getDir( "/etc/grid-security/certificates"); + if (location != null) return location; + } + + String suffix = File.separator + "share" + File.separator + + "certificates"; + + location = getDir(System.getProperty("GLOBUS_LOCATION") + + suffix); + if (location != null) return location; + + return null; + } + + + public static int getOS() { + if (osType != UNDEFINED_OS) { + return osType; + } + + String osname = System.getProperty("os.name"); + if (osname != null) { + osname = osname.toLowerCase(); + if (osname.indexOf("windows") != -1) { + osType = WINDOWS_OS; + } else if ( (osname.indexOf("solaris") != -1) || + (osname.indexOf("sunos") != -1) || + (osname.indexOf("linux") != -1) || + (osname.indexOf("aix") != -1) || + (osname.indexOf("hp-ux") != -1) || + (osname.indexOf("compaq's digital unix") != -1) || + (osname.indexOf("osf1") != -1) || + (osname.indexOf("mac os x") != -1) || + (osname.indexOf("netbsd") != -1) || + (osname.indexOf("freebsd") != -1) || + (osname.indexOf("irix") != -1) ) { + osType = UNIX_OS; + } else if (osname.indexOf("mac") != -1) { + osType = MAC_OS; + } else { + osType = OTHER_OS; + } + } else { + osType = OTHER_OS; + } + + return osType; + } + + private static String getDir(String directory) { + if (directory == null) return null; + File f = new File(directory); + if (f.isDirectory() && f.canRead()) { + return f.getAbsolutePath(); + } else { + return null; + } + } + +} Index: pegasus-wms_4.0.1+dfsg/src/org/griphyn/vdl/dbschema/NXDInvSchema.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/org/griphyn/vdl/dbschema/NXDInvSchema.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,204 +0,0 @@ -/* - * This file or a portion of this file is licensed under the terms of - * the Globus Toolkit Public License, found in file ../GTPL, or at - * http://www.globus.org/toolkit/download/license.html. This notice must - * appear in redistributions of this file, with or without modification. - * - * Redistributions of this Software, with or without modification, must - * reproduce the GTPL in: (1) the Software, or (2) the Documentation or - * some other similar material which is provided with the Software (if - * any). - * - * Copyright 1999-2004 University of Chicago and The University of - * Southern California. All rights reserved. - */ -package org.griphyn.vdl.dbschema; - -import edu.isi.pegasus.planner.invocation.InvocationRecord; -import java.sql.*; -import java.util.List; -import java.util.ArrayList; -import java.util.Properties; -import java.io.*; -import java.lang.reflect.*; -import java.net.InetAddress; - -import org.xmldb.api.base.*; -import org.xmldb.api.modules.*; -import org.xmldb.api.*; -import javax.xml.transform.OutputKeys; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.parsers.ParserConfigurationException; - -import org.w3c.dom.Document; -import org.w3c.dom.Element; -import org.w3c.dom.DOMException; -import org.xml.sax.SAXException; -import org.xml.sax.SAXParseException; -import org.xml.sax.InputSource; - -import org.griphyn.vdl.util.ChimeraProperties; -import org.griphyn.vdl.util.Logging; -import org.griphyn.vdl.parser.*; - -import edu.isi.pegasus.common.util.Separator; -import org.xml.sax.InputSource; -/** - * This class provides basic functionalities to interact with the - * backend database for invocation records, such as insertion, deletion, - * and search. - * - * @author Jens-S. Vöckler - * @author Yong Zhao - * @version $Revision: 2587 $ - */ -public class NXDInvSchema extends DatabaseSchema - implements PTC -{ - private DocumentBuilderFactory m_factory; - - private DocumentBuilder m_builder; - - protected Collection m_db; - - protected Collection m_ptc; - - protected CollectionManagementService m_dbColService; - - protected CollectionManagementService m_ptcColService; - - protected XPathQueryService m_dbQrySvc; - - protected XPathQueryService m_ptcQrySvc; - - /** - * Default constructor for the provenance tracking. - * - * @param dbDriverName is the database driver name - */ - public NXDInvSchema( String dbDriverName ) - throws ClassNotFoundException, - NoSuchMethodException, InstantiationException, - IllegalAccessException, InvocationTargetException, - SQLException, IOException, ParserConfigurationException - { - // load the driver from the properties - super(); // call minimalistic c'tor, no driver loading! - ChimeraProperties props = ChimeraProperties.instance(); - - m_dbschemaprops = - props.getDatabaseSchemaProperties( PROPERTY_PREFIX ); - - // extract those properties specific to the database driver. - // use default settings. - String driverPrefix = null; - String driverName = props.getDatabaseDriverName(driverPrefix); - Properties driverprops = props.getDatabaseDriverProperties(driverPrefix); - String url = props.getDatabaseURL(driverPrefix); - - try { - m_factory = DocumentBuilderFactory.newInstance(); - m_builder = m_factory.newDocumentBuilder(); - - - Class cl = Class.forName(driverName); - Database database = (Database) cl.newInstance(); - DatabaseManager.registerDatabase(database); - - // get the collection - m_db = DatabaseManager.getCollection(url + "/db"); - m_dbColService = (CollectionManagementService) - m_db.getService("CollectionManagementService", "1.0"); - - m_ptc = m_db.getChildCollection("ptc"); - - if(m_ptc == null) { - // collection does not exist, create - m_ptc = m_dbColService.createCollection("ptc"); - } - m_ptc.setProperty(OutputKeys.INDENT, "no"); - - m_ptcColService = (CollectionManagementService) - m_ptc.getService("CollectionManagementService", "1.0"); - - m_dbQrySvc = (XPathQueryService) m_db.getService("XPathQueryService", "1.0"); - - m_ptcQrySvc = (XPathQueryService) m_ptc.getService("XPathQueryService", "1.0"); - - m_dbQrySvc.setProperty("indent", "no"); - - m_ptcQrySvc.setProperty("indent", "no"); - } catch (XMLDBException e) { - throw new SQLException (e.getMessage()); - } - } - - /** - * Checks the existence of an invocation record in the database. - * The information is based on the (start,host,pid) tuple, although - * with private networks, cases may arise that have this tuple - * identical, yet are different. - * - * @param start is the start time of the grid launcher - * @param host is the address of the host it ran upon - * @param pid is the process id of the grid launcher itself. - * @return the id of the existing record, or -1 - */ - public long - getInvocationID( java.util.Date start, InetAddress host, int pid ) - throws SQLException - { - long result = -1; - Logging.instance().log("xaction", 1, "START select invocation id" ); - - String xquery = "/invocation[@start='" + start + "']"; - xquery += "[@host='" + host.getHostAddress() + "']"; - xquery += "[@pid=" + pid + "]"; - - try { - Logging.instance().log( "nxd", 2, xquery ); - ResourceSet rs = m_dbQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - if (i.hasMoreResources()) { - result = 1; - } else { - result = -1; - } - } catch (XMLDBException e) { - throw new SQLException (e.getMessage()); - } - - Logging.instance().log("xaction", 1, "FINAL select invocation id" ); - return result; - } - - /** - * Inserts an invocation record into the database. - * - * @param ivr is the invocation record to store. - * @return true, if insertion was successful, false otherwise. - */ - public boolean - saveInvocation( InvocationRecord ivr ) - throws SQLException - { - try { - StringWriter sw = new StringWriter(); - - ivr.toXML(sw, "", null); - // create new XMLResource; an id will be assigned to the new resource - XMLResource document = (XMLResource)m_ptc.createResource(null, "XMLResource"); - document.setContent(sw.toString()); - System.out.println(sw.toString()); - m_ptc.storeResource(document); - return true; - } catch (Exception e) { - throw new SQLException (e.getMessage()); - } - } -} - - - - Index: pegasus-wms_4.0.1+dfsg/src/org/griphyn/vdl/dbschema/NXDSchema.java =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/org/griphyn/vdl/dbschema/NXDSchema.java 2012-05-24 16:47:52.064156782 -0700 +++ /dev/null 1970-01-01 00:00:00.000000000 +0000 @@ -1,1656 +0,0 @@ -/* - * This file or a portion of this file is licensed under the terms of - * the Globus Toolkit Public License, found in file ../GTPL, or at - * http://www.globus.org/toolkit/download/license.html. This notice must - * appear in redistributions of this file, with or without modification. - * - * Redistributions of this Software, with or without modification, must - * reproduce the GTPL in: (1) the Software, or (2) the Documentation or - * some other similar material which is provided with the Software (if - * any). - * - * Copyright 1999-2004 University of Chicago and The University of - * Southern California. All rights reserved. - */ -package org.griphyn.vdl.dbschema; - -import java.sql.*; -import java.util.List; -import java.util.ArrayList; -import java.util.Properties; -import java.io.*; -import java.lang.reflect.*; - -import org.xmldb.api.base.*; -import org.xmldb.api.modules.*; -import org.xmldb.api.*; -import javax.xml.transform.OutputKeys; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.parsers.ParserConfigurationException; - -import org.w3c.dom.Document; -import org.w3c.dom.Element; -import org.w3c.dom.DOMException; -import org.xml.sax.SAXException; -import org.xml.sax.SAXParseException; -import org.xml.sax.InputSource; - -import org.griphyn.vdl.util.ChimeraProperties; -import org.griphyn.vdl.classes.*; -import org.griphyn.vdl.util.Logging; -import org.griphyn.vdl.parser.*; -import org.griphyn.vdl.router.Cache; -import org.griphyn.vdl.annotation.*; -import edu.isi.pegasus.common.util.Separator; -import org.xml.sax.InputSource; - -/** - * This class provides basic functionalities to interact with the - * backend database, such as insertion, deletion, and search of - * entities in the VDC. - * - * @author Jens-S. Vöckler - * @author Yong Zhao - * @version $Revision: 2079 $ - */ -public class NXDSchema extends DatabaseSchema implements XDC -{ - /** - * An instance of the VDLx XML parser. - */ - private org.griphyn.vdl.parser.VDLxParser m_parser; - - private DocumentBuilderFactory m_factory; - - private DocumentBuilder m_builder; - - /** - * reference to collection '/db/vdc'; - */ - protected Collection m_db; - - protected Collection m_vdc; - - protected Collection m_meta; - - protected CollectionManagementService m_dbColService; - - protected CollectionManagementService m_vdcColService; - - protected XPathQueryService m_dbQrySvc; - - protected XPathQueryService m_vdcQrySvc; - - protected XPathQueryService m_metaQrySvc; - - protected XUpdateQueryService m_xupdQrySvc; - - /** - * A cache for definitions to avoid reloading from the database. - */ - protected Cache m_cache; - - /** - * Instantiates an XML parser for VDLx on demand. Since XML parsing - * and parser instantiation is an expensive business, the reader will - * only be generated on demand. - * - * @return a valid VDLx parser instance. - */ - private org.griphyn.vdl.parser.VDLxParser parserInstance() - { - if ( this.m_parser == null ) { - // obtain the schema location URL from the schema properties: - // url is a list of strings representing schema locations. The - // content exists in pairs, one of the namespace URI, one of the - // location URL. - String url = null; - try { - ChimeraProperties props = ChimeraProperties.instance(); - url = - m_dbschemaprops.getProperty( "xml.url", props.getVDLSchemaLocation() ); - } catch (IOException e) { - Logging.instance().log("nxd", 0, "ignored " + e); - } - this.m_parser = new org.griphyn.vdl.parser.VDLxParser(url); - } - - // done - return this.m_parser; - } - - /** - * Default constructor for the NXD schema. - */ - public NXDSchema(String dbDriver) - throws ClassNotFoundException, - NoSuchMethodException, InstantiationException, - IllegalAccessException, InvocationTargetException, - SQLException, IOException,ParserConfigurationException - { - // load the driver from the properties - super(); // call minimalistic c'tor, no driver loading! - ChimeraProperties props = ChimeraProperties.instance(); - - m_dbschemaprops = - props.getDatabaseSchemaProperties( PROPERTY_PREFIX ); - - m_cache = null; - m_parser = null; - - // extract those properties specific to the database driver. - // use default settings. - String driverPrefix = null; - String driverName = props.getDatabaseDriverName(driverPrefix); - Properties driverprops = props.getDatabaseDriverProperties(driverPrefix); - String url = props.getDatabaseURL(driverPrefix); - String user = driverprops.getProperty("user", "guest"); - String passwd = driverprops.getProperty("password", "guest"); - - try { - m_factory = DocumentBuilderFactory.newInstance(); - m_builder = m_factory.newDocumentBuilder(); - - - Class cl = Class.forName(driverName); - Database database = (Database) cl.newInstance(); - DatabaseManager.registerDatabase(database); - - // get the collection - m_db = DatabaseManager.getCollection(url + "/db", user, passwd); - m_dbColService = (CollectionManagementService) - m_db.getService("CollectionManagementService", "1.0"); - - m_vdc = m_db.getChildCollection("vdc"); - - if(m_vdc == null) { - // collection does not exist, create - m_vdc = m_dbColService.createCollection("vdc"); - } - m_vdc.setProperty(OutputKeys.INDENT, "no"); - - m_meta = m_db.getChildCollection("metadata"); - - if(m_meta == null) { - // collection does not exist, create - m_meta = m_dbColService.createCollection("metadata"); - } - m_meta.setProperty(OutputKeys.INDENT, "no"); - - m_vdcColService = (CollectionManagementService) - m_vdc.getService("CollectionManagementService", "1.0"); - - m_dbQrySvc = (XPathQueryService) m_db.getService("XPathQueryService", "1.0"); - - m_vdcQrySvc = (XPathQueryService) m_vdc.getService("XPathQueryService", "1.0"); - - m_metaQrySvc = (XPathQueryService) m_meta.getService("XPathQueryService", "1.0"); - - m_dbQrySvc.setProperty("indent", "no"); - - m_vdcQrySvc.setProperty("indent", "no"); - - m_metaQrySvc.setProperty("indent", "no"); - - XUpdateQueryService m_xupdQrySvc = (XUpdateQueryService) m_meta.getService("XUpdateQueryService", "1.0"); - - } catch (XMLDBException e) { - throw new SQLException (e.getMessage()); - } - } - - private String getDefinitionId(Definition def) { - String prefix = (def.getType() == Definition.TRANSFORMATION)?"TR_":"DV_"; - String version = def.getVersion(); - String suffix = ""; - if (version != null) - suffix = "_" + version; - return prefix + def.getName() + suffix; - } - - private String getDefinitionId(String name, - String version, - int type) { - String prefix = (type == Definition.TRANSFORMATION)?"TR_":"DV_"; - String suffix = ""; - if (version != null) - suffix = "_" + version; - return prefix + name + suffix; - } - - // - // lower level methods, working directly on specific definitions - // - - /** - * Loads a single Definition from the backend database into an Java object. - * This method does not allow wildcarding! - * - * @param namespace namespace, null will be converted into empty string - * @param name name, null will be converted into empty string - * @param version version, null will be converted into empty string - * @param type type of the definition (TR or DV), must not be -1. - * @return the Definition as specified, or null if not found. - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - * @see #saveDefinition( Definition, boolean ) - */ - public Definition - loadDefinition( String namespace, - String name, - String version, - int type ) - throws SQLException - { - Definition result = null; - Logging.instance().log("xaction", 1, "START load definition" ); - - try { - Collection col; - if (namespace != null) - col = m_vdc.getChildCollection(namespace); - else - col = m_vdc; - String id = getDefinitionId(name, version, type); - //Logging.instance().log( "nxd", 0, "Definition id " + id ); - XMLResource res = (XMLResource)col.getResource(id); - if(res != null) { - MyCallbackHandler cb = new MyCallbackHandler(); - - parserInstance().parse( new org.xml.sax.InputSource(new StringReader((String)res.getContent())), cb ); - result = cb.getDefinition(); - - } else { - Logging.instance().log( "nxd", 0, "Definition not found" ); - } - } catch (Exception e) { - throw new SQLException(e.getMessage()); - } - Logging.instance().log("xaction", 1, "FINAL load definition" ); - return result; - } - - /** - * Saves a Definition, that is either a Transformation or Derivation, - * into the backend database. This method, of course, does not allow - * wildcarding. The definition has to be completely specified and - * valid. - * - * @param definition is the new Definition to store. - * @param overwrite true, if existing defitions will be overwritten by - * new ones with the same primary (or secondary) key (-set), or false, - * if a new definition will be rejected on key matches. - * - * @return true, if the backend database was changed, or - * false, if the definition was not accepted into the backend. - * - * @see org.griphyn.vdl.classes.Definition - * @see org.griphyn.vdl.classes.Transformation - * @see org.griphyn.vdl.classes.Derivation - * @see #loadDefinition( String, String, String, int ) - */ - public boolean - saveDefinition( Definition definition, - boolean overwrite ) - throws SQLException - { - Logging.instance().log( "nxd", 2, "START save definition"); - - try { - String namespace = definition.getNamespace(); - Collection col; - if (namespace != null) - col = m_vdc.getChildCollection(namespace); - else - col = m_vdc; - String id = getDefinitionId(definition); - - if (col == null) { - // collection does not exist, create - col = m_vdcColService.createCollection(namespace); - } else if (!overwrite) { - if (col.getResource(id) != null){ - Logging.instance().log( "app", 0, definition.shortID() + - " already exists, ignoring" ); - return false; - } - } - - // create new XMLResource; an id will be assigned to the new resource - XMLResource document = (XMLResource)col.createResource(id, "XMLResource"); - document.setContent(definition.toXML("", null)); - col.storeResource(document); - - // add to cache - //if ( m_cache != null ) m_cache.set( new Long(id), definition ); - - } catch (Exception e) { - throw new SQLException(e.getMessage()); - } - // done - Logging.instance().log( "nxd", 2, "FINAL save definition"); - return true; - } - - /** - * Search the database for the existence of a definition. - * - * @param definition the definition object to search for - * @return true, if the definition exists, false if not found - */ - public boolean containsDefinition( Definition definition ) - throws SQLException - { - boolean result = false; - try { - String namespace = definition.getNamespace(); - Collection col; - if (namespace != null) - col = m_vdc.getChildCollection(namespace); - else - col = m_vdc; - String id = getDefinitionId(definition); - - if(col != null) { - if (col.getResource(id) != null){ - result = true; - } - } - } catch ( Exception e ) { - throw new SQLException(e.getMessage()); - } - return result; - } - - /** - * Delete a specific Definition objects from the database. No wildcard - * matching will be done. "Fake" definitions are permissable, meaning - * it just has the secondary key triple. - * - * @param definition is the definition specification to delete - * @return true is something was deleted, false if non existent. - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public boolean deleteDefinition( Definition definition ) - throws SQLException - { - boolean result = false; - - Logging.instance().log("xaction", 1, "START delete definition" ); - - try { - String namespace = definition.getNamespace(); - Collection col; - if (namespace != null) - col = m_vdc.getChildCollection(namespace); - else - col = m_vdc; - String id = getDefinitionId(definition); - - if(col != null) { - XMLResource res = (XMLResource)col.getResource(id); - if (res != null){ - col.removeResource(res); - result = true; - } - } - } catch ( Exception e ) { - // ignore - } - - Logging.instance().log("xaction", 1, "FINAL delete definition" ); - return result; - } - - /** - * Delete Definition objects from the database. This method allows for - * wildcards in the usual fashion. Use null for strings as wildcards, - * and -1 for the type wildcard. - * - * @param namespace namespace, null to match any namespace - * @param name name, null to match any name - * @param version version, null to match any version - * @param type definition type (TR or DV) - * @return a list containing all Definitions that were deleted - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public java.util.List deleteDefinition( String namespace, - String name, - String version, - int type ) - throws SQLException - { - Logging.instance().log("xaction", 1, "START delete definitions" ); - - java.util.List result = searchDefinition(namespace, name, version, type); - for (int i=0; i < result.size(); i++) - deleteDefinition((Definition)result.get(i)); - - Logging.instance().log("xaction", 1, "FINAL delete definitions" ); - return result; - } - - /** - * Search the database for definitions by ns::name:version triple - * and by type (either Transformation or Derivation). This version - * of the search allows for jokers expressed as null value - * - * @param namespace namespace, null to match any namespace - * @param name name, null to match any name - * @param version version, null to match any version - * @param type type of definition (TR/DV, or both) - * @return a list of definitions - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public java.util.List searchDefinition( String namespace, - String name, - String version, - int type ) - throws SQLException - { - String xquery = ""; //"declare namespace vdl='http://www.griphyn.org/chimera/VDL';" - - String triple = ""; - if (namespace != null) - triple += "[@namespace='" + namespace + "']"; - - if (name != null) - triple += "[@name='" + name + "']"; - - if (version != null) - triple += "[@version='" + version + "']"; - - if (type != -1) { - if (type == Definition.TRANSFORMATION) - xquery = "//transformation" + triple; - else - xquery += "//derivation" + triple; - } else - xquery = "//derivation" + triple + "|//transformation" + triple; - - return searchDefinition(xquery); - } - - /** - * Searches the database for all derivations that satisfies a certain query. - * - * @param xquery the query statement - * @return a list of definitions - */ - public java.util.List searchDefinition( String xquery ) - throws SQLException - { - if ( xquery == null ) - throw new NullPointerException("You must specify a query!"); - - java.util.List result = new ArrayList(); - - try { - Logging.instance().log("xaction", 1, "query: " + xquery ); - - ResourceSet rs = m_dbQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - while(i.hasMoreResources()) { - Resource res = i.nextResource(); - - MyCallbackHandler cb = new MyCallbackHandler(); - - parserInstance().parse( new org.xml.sax.InputSource(new StringReader((String)res.getContent())), cb ); - result.add(cb.getDefinition()); - } - - } catch ( Exception e ) { - throw new SQLException(e.getMessage()); - } - - return result; - } - - /** - * Searches the database for elements that satisfies a certain query. - * - * @param xquery the query statement - * @return a list of string - */ - public java.util.List searchElements( String xquery ) - throws SQLException - { - if ( xquery == null ) - throw new NullPointerException("You must specify a query!"); - - java.util.List result = new ArrayList(); - - try { - Logging.instance().log("nxd", 1, "query: " + xquery ); - - ResourceSet rs = m_dbQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - while(i.hasMoreResources()) { - Resource res = i.nextResource(); - result.add((String)res.getContent()); - } - } catch ( Exception e ) { - throw new SQLException(e.getMessage()); - } - return result; - } - - /** - * Searches the database for annotations that satisfies a certain query. - * - * @param xquery the query statement - * @return true if found, false otherwise - */ - public XMLResource findAnnotation( String xquery ) - throws SQLException - { - if ( xquery == null ) - return null; - - try { - Logging.instance().log("nxd", 1, "query: " + xquery ); - - ResourceSet rs = m_metaQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - if (i.hasMoreResources()) { - XMLResource res = (XMLResource)i.nextResource(); - return res; - } else - return null; - } catch ( Exception e ) { - throw new SQLException(e.getMessage()); - } - } - - public java.util.List searchFilename( String lfn, int link ) - throws SQLException - { - if ( lfn == null ) - throw new NullPointerException("You must query for a filename"); - - String linkQuery = ""; - String type = LFN.toString(link); - if (type != null) - linkQuery = "[@link = '" + type + "']"; - - String xquery = - "//derivation[.//lfn[@file = '" + lfn + "']" + linkQuery + "]"; - java.util.List result = searchDefinition(xquery); - - Logging.instance().log("xaction", 1, "FINAL select LFNs" ); - return result; - } - - - /** - * Delete one or more definitions from the backend database. The key - * triple parameters may be wildcards. Wildcards are expressed as - * null value, or have regular expression. - * - * @param namespace namespace - * @param name name - * @param version version - * @param type definition type (TR or DV) - * @return a list of definitions that were deleted. - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public java.util.List - deleteDefinitionEx( String namespace, - String name, - String version, - int type ) - throws SQLException { - Logging.instance().log("xaction", 1, "START delete definitions ex" ); - - java.util.List result = searchDefinitionEx(namespace, name, version, type); - for (int i=0; i < result.size(); i++) - deleteDefinition((Definition)result.get(i)); - - Logging.instance().log("xaction", 1, "FINAL delete definitions ex" ); - return result; - } - - /** - * Searches the database for definitions by ns::name:version triple - * and by type (either Transformation or Derivation). This version of - * the search allows for jokers expressed as null value - * - * @param namespace namespace, null to match any namespace - * @param name name, null to match any name - * @param version version, null to match any version - * @param type type of definition, see below, or -1 as wildcard - * @return a list of Definition items, which may be empty - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - * @see #loadDefinition( String, String, String, int ) - */ - public java.util.List - searchDefinitionEx( String namespace, - String name, - String version, - int type ) - throws SQLException { - String xquery = ""; - - String triple = ""; - if (namespace != null) - triple += "[matches(@namespace, '" + namespace + "')]"; - - if (name != null) - triple += "[matches(@name, '" + name + "')]"; - - if (version != null) - triple += "[matches(@version, '" + version + "')]"; - - if (type != -1) { - if (type == Definition.TRANSFORMATION) - xquery = "//transformation" + triple; - else - xquery += "//derivation" + triple; - } else - xquery = "//derivation" + triple + "|//transformation" + triple; - return searchDefinition(xquery); - } - - /** - * Searches the database for all LFNs that match a certain pattern. - * The linkage is an additional constraint. This method allows - * regular expression - * - * @param lfn the LFN name - * @param link the linkage type of the LFN - * @return a list of filenames that match the criterion. - * - * @see org.griphyn.vdl.classes.LFN#NONE - * @see org.griphyn.vdl.classes.LFN#INPUT - * @see org.griphyn.vdl.classes.LFN#OUTPUT - * @see org.griphyn.vdl.classes.LFN#INOUT - */ - public java.util.List - searchLFN( String lfn, int link ) - throws SQLException { - if ( lfn == null ) - throw new NullPointerException("You must query for a filename"); - - String linkQuery = ""; - String type = LFN.toString(link); - if (type != null) - linkQuery = "[@link = '" + type + "')]"; - - String xquery = - // "//lfn[matches(@file, '" + lfn + "')]" + linkQuery + "/@file"; - "//lfn" + linkQuery + "/@file[matches(., '" + lfn + "')]"; - java.util.List result = searchElements(xquery); - - Logging.instance().log("xaction", 1, "FINAL select LFNs" ); - return result; - } - - /** - * Searches the database for a list of namespaces of the definitions - * Sorted in ascending order. - * - * @param type type of definition, see below, or -1 for both - * @return a list of namespaces - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public java.util.List - getNamespaceList( int type ) - throws SQLException { - - String xquery = ""; - if (type == Definition.TRANSFORMATION) - xquery = "for $n in distinct-values(//transformation/@namespace) order by $n return $n"; - else if (type == Definition.DERIVATION) - xquery = "for $n in distinct-values(//derivation/@namespace) order by $n return $n"; - else - xquery = "for $n in distinct-values(//derivation/@namespace|//transformation/@namespace) order by $n return $n"; - - java.util.List result = searchElements(xquery); - - Logging.instance().log("xaction", 1, "FINAL select LFNs" ); - return result; - } - - /** - * Searches the database for a list of fully-qualified names of - * the definitions sorted in ascending order. - * - * @param type type of definition, see below, or -1 for both. - * @return a list of FQDNs - * - * @see org.griphyn.vdl.classes.Definition#TRANSFORMATION - * @see org.griphyn.vdl.classes.Definition#DERIVATION - */ - public java.util.List - getFQDNList( int type ) - throws SQLException { - String xquery = ""; - - if (type == Definition.TRANSFORMATION) - xquery = "for $d in //transformation order by $d/@namespace empty least, $d/@name, $d/@version return string-join((string-join(($d/@namespace, $d/@name), '::'), $d/@version), ':')"; - else if (type == Definition.DERIVATION) - xquery = "for $d in //derivation order by $d/@namespace empty least, $d/@name, $d/@version return string-join((string-join(($d/@namespace, $d/@name), '::'), $d/@version), ':')"; - else - xquery = "for $d in (//transformation|//derivation) order by $d/@namespace empty least, $d/@name, $d/@version return string-join((string-join(($d/@namespace, $d/@name), '::'), $d/@version), ':')"; - - java.util.List result = searchElements(xquery); - - Logging.instance().log("xaction", 1, "FINAL select LFNs" ); - return result; - } - - /** - * Deletes an annotation with the specified key. - * - * @param primary is the primary object specifier for the class. - * According to the type, this is either the FQDI, or the filename. - * @param secondary is a helper argument for annotations to calls - * and formal arguments, and should be null for all other classes. - * For calls, the argument must be packed into {@link java.lang.Integer}. - * @param kind defines the kind/class of object to annotate. - * @param key is the annotation key. - * @return true, if the database was modified, false otherwise. - * @exception SQLException, if something went wrong during database - * access. - */ - public boolean deleteAnnotation( String primary, Object secondary, - int kind, String key ) - throws SQLException, IllegalArgumentException - { - String subject = ""; - String select = null; - - switch ( kind ) { - case CLASS_TRANSFORMATION: - subject = "tr"; - break; - case CLASS_DERIVATION: - subject = "dv"; - break; - case CLASS_CALL: - // may throw ClassCastException - subject = "tr"; - select = "call[" + ((Integer) secondary).intValue() + "]"; - break; - case CLASS_DECLARE: - subject = "tr"; - // may throw ClassCastException - //select = "declare[@name='" + (String)secondary + "']"; - select = (String)secondary; - break; - case CLASS_FILENAME: - subject = "lfn"; - break; - default: - throw new IllegalArgumentException( "The class kind=" + kind + " cannot be annotated" ); - } - - try { - XMLResource res = null; - String xquery = "/annotation/metadata[@subject=\"" + subject + "\"][@name=\"" + - primary + "\"]"; - if (select == null) { - if (kind != CLASS_FILENAME) { - xquery += "[empty(@select)]"; - } - } else { - xquery += "[@select=\"" + select + "\"]"; - } - - xquery += "/attribute[@name=\"" + key + "\"]"; - - if ((res = findAnnotation(xquery)) != null) { - String id = res.getDocumentId(); - - // get the document - XMLResource document = (XMLResource)m_meta.getResource(id); - m_meta.removeResource(document); - return true; - } - return false; - } catch (XMLDBException e) { - throw new SQLException(e.getMessage()); - } - } - - /** - * Deletes a specific key in an annotated transformation. - * - * @param fqdi is the FQDI of the transformation - * @param key is the key to search for - * @return true, if the database was modified, false otherwise. - * @see org.griphyn.vdl.classes.Transformation - */ - public boolean deleteAnnotationTransformation( String fqdi, String key ) - throws SQLException, IllegalArgumentException - { - return deleteAnnotation(fqdi, null, CLASS_TRANSFORMATION, key); - } - - /** - * Deletes a specific key in an annotated derivation. - * - * @param fqdi is the FQDI of the derivation - * @param key is the key to search for - * @return true, if the database was modified, false otherwise. - * @see org.griphyn.vdl.classes.Derivation - */ - public boolean deleteAnnotationDerivation( String fqdi, String key ) - throws SQLException, IllegalArgumentException - { - return deleteAnnotation(fqdi, null, CLASS_DERIVATION, key); - } - - /** - * Deletes a specific key in an annotated formal argument. - * - * @param fqdi is the FQDI of the transformation - * @param farg is the name of the formal argument - * @param key is the key to search for - * @return true, if the database was modified, false otherwise. - * @see org.griphyn.vdl.classes.Declare - */ - public boolean deleteAnnotationDeclare( String fqdi, String farg, - String key ) - throws SQLException, IllegalArgumentException - { - return deleteAnnotation(fqdi, farg, CLASS_DECLARE, key); - } - - /** - * Deletes a specific key for a call statement. - * - * @param fqdi is the FQDI of the transformation - * @param index is the number of the call to annotate. - * @param key is the key to search for - * @return true, if the database was modified, false otherwise. - * @see org.griphyn.vdl.classes.Call - */ - public boolean deleteAnnotationCall( String fqdi, int index, - String key ) - throws SQLException, IllegalArgumentException - { - return deleteAnnotation(fqdi, new Integer(index), CLASS_CALL, key); - } - - /** - * Deletes a specific key in an annotated filename. - * - * @param filename is the name of the file that was annotated. - * @param key is the key to search for - * @return true, if the database was modified, false otherwise. - * @see org.griphyn.vdl.classes.LFN - */ - public boolean deleteAnnotationFilename( String filename, String key ) - throws SQLException, IllegalArgumentException - { - return deleteAnnotation(filename, null, CLASS_FILENAME, key); - } - - /** - * Annotates a transformation with a tuple. - * - * @param fqdi is the FQDI to annotate - * @param annotation is the value to place - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see org.griphyn.vdl.classes.Transformation - */ - public long saveAnnotationTransformation( String fqdi, - Tuple annotation, - boolean overwrite ) - throws SQLException, IllegalArgumentException - { - /* - try { - String key = annotation.getKey(); - String type = annotation.getTypeString(); - Object value = annotation.getValue(); - - Logging.instance().log( "nxd", 2, "INSERT INTO anno_tr" ); - - String id = null; - XMLResource res = null; - - String xupdate = - ""; - String xquery = "//annotation/metadata[@subject='tr'][@name='" + - fqdi + "']"; - if ((res = findAnnotation(xquery)) != null) { - //annotation for tr exists - id = res.getDocumentId(); - String xquery_attr = xquery + "/attribute[@name='" + key + "']/text()"; - if (findAnnotation(xquery_attr)!=null) { - //attribute already exists - Logging.instance().log( "nxd", 2, "Attribute already exists." ); - - if (!overwrite) - return -1; - xupdate += "" + - value + ""; - //xupdate += "" + - //type + ""; - } else { - //attribute does not exist - Logging.instance().log( "nxd", 2, "Attribute does not exist." ); - - xupdate += "" + - "" + - "" + key + "" + - "" + type + "" + - value + "" + - ""; - } - xupdate += ""; - System.out.println(xupdate); - long l = m_xupdQrySvc.update(xupdate); - } else { - //create the annotation - String anno = "" + - "" + value + "" + - ""; - - // create new XMLResource; an id will be assigned to the new resource - XMLResource document = (XMLResource)m_meta.createResource(null, "XMLResource"); - document.setContent(anno); - m_meta.storeResource(document); - } - return 0; - } catch (XMLDBException e) { - throw new SQLException(e.getMessage()); - } - */ - return saveAnnotation(fqdi, null, CLASS_TRANSFORMATION, annotation, overwrite); - } - - /** - * Annotates a derivation with a tuple. - * - * @param fqdi is the FQDI to annotate - * @param annotation is the value to place - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see org.griphyn.vdl.classes.Derivation - */ - public long saveAnnotationDerivation( String fqdi, - Tuple annotation, - boolean overwrite ) - throws SQLException, IllegalArgumentException - { - return saveAnnotation(fqdi, null, CLASS_DERIVATION, annotation, overwrite); - } - - /** - * Annotates a transformation argument with a tuple. - * - * @param fqdi is the FQDI to annotate - * @param formalname is the name of the formal argument to annotoate. - * @param annotation is the value to place - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see org.griphyn.vdl.classes.Declare - */ - public long saveAnnotationDeclare( String fqdi, - String formalname, - Tuple annotation, - boolean overwrite ) - throws SQLException, IllegalArgumentException - { - return saveAnnotation(fqdi, formalname, CLASS_DECLARE, annotation, overwrite); - } - - /** - * Annotates a transformation call with a tuple. - * - * @param fqdi is the FQDI to annotate - * @param index is the number of the call to annotate. - * @param annotation is the value to place - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see org.griphyn.vdl.classes.Call - */ - public long saveAnnotationCall( String fqdi, - int index, - Tuple annotation, - boolean overwrite ) - throws SQLException, IllegalArgumentException - { - return saveAnnotation(fqdi, new Integer(index), CLASS_CALL, annotation, overwrite); - } - - /** - * Annotates a logical filename with a tuple. - * - * @param filename is the FQDI to annotate - * @param annotation is the value to place - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see org.griphyn.vdl.classes.LFN - */ - public long saveAnnotationFilename( String filename, - Tuple annotation, - boolean overwrite ) - throws SQLException, IllegalArgumentException - { - return saveAnnotation(filename, null, CLASS_FILENAME, annotation, overwrite); - } - - /** - * Annotates any of the annotatable classes with the specified tuple. - * This is an interface method to the various class-specific methods. - * - * @param primary is the primary object specifier for the class. - * According to the type, this is either the FQDI, or the filename. - * @param secondary is a helper argument for annotations to calls - * and formal arguments, and should be null for all other classes. - * For calls, the argument must be packed into {@link java.lang.Integer}. - * @param kind defines the kind/class of object to annotate. - * @param annotation is the value to place into the class. - * @param overwrite is a predicate on replace or maintain. - * @return the insertion id, or -1, if the database was untouched - * @see #saveAnnotationTransformation( String, Tuple, boolean ) - * @see #saveAnnotationDerivation( String, Tuple, boolean ) - * @see #saveAnnotationCall( String, int, Tuple, boolean ) - * @see #saveAnnotationDeclare( String, String, Tuple, boolean ) - * @see #saveAnnotationFilename( String, Tuple, boolean ) - */ - public long saveAnnotation( String primary, Object secondary, - int kind, Tuple annotation, boolean overwrite ) - throws SQLException, IllegalArgumentException - { - long result = -1; - String subject = ""; - String select = null; - String q_sec = null; - String defn = "transformation"; - - switch ( kind ) { - case CLASS_TRANSFORMATION: - subject = "tr"; - break; - case CLASS_DERIVATION: - subject = "dv"; - defn = "derivation"; - break; - case CLASS_CALL: - // may throw ClassCastException - subject = "tr"; - select = "call[" + ((Integer) secondary).intValue() + "]"; - q_sec = select; - break; - case CLASS_DECLARE: - subject = "tr"; - // may throw ClassCastException - q_sec = "declare[@name='" + (String)secondary + "']"; - select = (String)secondary; - break; - case CLASS_FILENAME: - subject = "lfn"; - break; - default: - throw new IllegalArgumentException( "The class kind=" + kind + " cannot be annotated" ); - } - - try { - - if (kind != CLASS_FILENAME) { - String[] names = Separator.split(primary); - String q_ns, q_name, q_ver; - - if (names[0] == null) - q_ns = "[empty(@namespace)]"; - else - q_ns = "[@namespace='" + names[0] + "']"; - - if (names[1] == null) - q_name = "[empty(@name)]"; - else - q_name = "[@name='" + names[1] + "']"; - - if (names[2] == null) - q_ver = "[empty(@version)]"; - else - q_ver = "[@version='" + names[2] + "']"; - - //check if tr/dv is valid - String xquery = "//" + defn + q_ns + q_name + q_ver; - if (q_sec != null ) - xquery += "/" + q_sec; - Logging.instance().log("nxd", 0, "query: " + xquery); - ResourceSet rs = m_vdcQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - if (!i.hasMoreResources()) { - Logging.instance().log("app", 0, "definition not found!"); - return -1; - } - } - - String key = annotation.getKey(); - String type = annotation.getTypeString(); - Object value = annotation.getValue(); - - String id = null; - XMLResource res = null; - String xquery = "/annotation/metadata[@subject=\"" + subject + "\"][@name=\"" + - primary + "\"]"; - if (select == null) { - if (kind != CLASS_FILENAME) { - xquery += "[empty(@select)]"; - } - } else { - xquery += "[@select=\"" + select + "\"]"; - } - - xquery += "/attribute[@name=\"" + key + "\"]"; - - if ((res = findAnnotation(xquery)) != null) { - if (!overwrite) { - System.err.println("key " + key + " already defined!"); - return -1; - } - id = res.getDocumentId(); - } - - //create the annotation - String anno = "" + value + "" + - ""; - - // create new XMLResource; an id will be assigned to the new resource - XMLResource document = (XMLResource)m_meta.createResource(id, "XMLResource"); - - document.setContent(anno); - m_meta.storeResource(document); - - return 0; - } catch (XMLDBException e) { - throw new SQLException(e.getMessage()); - } - } - - /** - * Obtains the value to a specific key in an annotated transformation. - * - * @param fqdi is the FQDI of the transformation - * @param key is the key to search for - * @return the annotated value, or null if not found. - * @see org.griphyn.vdl.classes.Transformation - */ - public Tuple loadAnnotationTransformation( String fqdi, String key ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, null, CLASS_TRANSFORMATION, key); - } - - /** - * Obtains the value to a specific key in an annotated derivation. - * - * @param fqdi is the FQDI of the derivation - * @param key is the key to search for - * @return the annotated value, or null if not found. - * @see org.griphyn.vdl.classes.Derivation - */ - public Tuple loadAnnotationDerivation( String fqdi, String key ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, null, CLASS_DERIVATION, key); - } - - /** - * Obtains the value to a specific key in an annotated formal argument. - * - * @param fqdi is the FQDI of the transformation - * @param farg is the name of the formal argument - * @param key is the key to search for - * @return the annotated value, or null if not found - * @see org.griphyn.vdl.classes.Declare - */ - public Tuple loadAnnotationDeclare( String fqdi, String farg, - String key ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, farg, CLASS_DECLARE, key); - } - - /** - * Obtains the value to a specific key for a call statement. - * - * @param fqdi is the FQDI of the transformation - * @param index is the number of the call to annotate. - * @param key is the key to search for - * @return the annotated value, or null if not found - * @see org.griphyn.vdl.classes.Call - */ - public Tuple loadAnnotationCall( String fqdi, int index, - String key ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, new Integer(index), CLASS_CALL, key); - } - - /** - * Obtains the value to a specific key in an annotated filename. - * - * @param filename is the name of the file that was annotated. - * @param key is the key to search for - * @return the annotated value, or null if not found. - * @see org.griphyn.vdl.classes.LFN - */ - public Tuple loadAnnotationFilename( String filename, String key ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(filename, null, CLASS_FILENAME, key); - } - - /** - * Retrieves a specific annotation from an annotatable classes with - * the specified tuple. This is an interface method to the various - * class-specific methods. - * - * @param primary is the primary object specifier for the class. - * According to the type, this is either the FQDI, or the filename. - * @param secondary is a helper argument for annotations to calls - * and formal arguments, and should be null for all other classes. - * For calls, the argument must be packed into {@link java.lang.Integer}. - * @param kind defines the kind/class of object to annotate. - * @param key is the key to look for. - * @return null if not found, otherwise the annotation tuple. - * @see #loadAnnotationTransformation( String, String ) - * @see #loadAnnotationDerivation( String, String ) - * @see #loadAnnotationCall( String, int, String ) - * @see #loadAnnotationDeclare( String, String, String ) - * @see #loadAnnotationFilename( String, String ) - */ - public Tuple loadAnnotation( String primary, Object secondary, - int kind, String key ) - throws SQLException, IllegalArgumentException - { - Tuple result = null; - String subject = ""; - String select = null; - - switch ( kind ) { - case CLASS_TRANSFORMATION: - subject = "tr"; - break; - case CLASS_DERIVATION: - subject = "dv"; - break; - case CLASS_CALL: - // may throw ClassCastException - subject = "tr"; - select = "call[" + ((Integer) secondary).intValue() + "]"; - break; - case CLASS_DECLARE: - subject = "tr"; - // may throw ClassCastException - //select = "declare[@name='" + (String)secondary + "']"; - select = (String)secondary; - break; - case CLASS_FILENAME: - subject = "lfn"; - break; - default: - throw new IllegalArgumentException( "The class kind=" + kind + " cannot be annotated" ); - } - - try { - String id = null; - String xquery = "/annotation/metadata[@subject=\"" + subject + "\"][@name=\"" + - primary + "\"]"; - if (select == null) { - if (kind != CLASS_FILENAME) { - xquery += "[empty(@select)]"; - } - } else { - xquery += "[@select=\"" + select + "\"]"; - } - - xquery += "/attribute[@name=\"" + key + "\"]"; - - XMLResource res = null; - if ((res = findAnnotation(xquery)) != null) { - result = loadAnnotationResource(res); - } - return result; - } catch (Exception e) { - throw new SQLException(e.getMessage()); - } - } - - /** - * get the annotation from a XML resource - */ - protected Tuple loadAnnotationResource(XMLResource res) - throws SQLException - { - Tuple result = null; - - if (res == null) - return result; - - Element elem; - try { - elem = (Element)res.getContentAsDOM(); - } catch (Exception e) { - throw new SQLException( e.getMessage()); - } - if (elem != null) { - String key = elem.getAttribute("name"); - String type = elem.getAttributeNS("http://www.w3.org/2001/XMLSchema-instance","type"); - String value = elem.getFirstChild().getNodeValue(); - if (key == null || type == null || value == null) - return result; - if (type.equals("xs:string")) { - result = new TupleString(key, null); - result.setValue(value); - return result; - } - if (type.equals("xs:float")){ - result = new TupleFloat(key, 0); - result.setValue(value); - return result; - } - if (type.equals("xs:int")){ - result = new TupleInteger(key, 0); - result.setValue(value); - return result; - } - if (type.equals("xs:boolean")) { - result = new TupleBoolean(key, false); - result.setValue(value); - return result; - } - if (type.equals("xs:date")) { - result = new TupleDate(key, null); - result.setValue(value); - return result; - } - } - return result; - } - - /** - * Lists all annotations for a transformation. - * - * @param fqdi is the FQDI of the transformation - * @return a list of tuples, which may be empty. - * @see org.griphyn.vdl.classes.Transformation - */ - public java.util.List loadAnnotationTransformation( String fqdi ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, null, CLASS_TRANSFORMATION); - } - - /** - * Lists all annotations for a derivation. - * - * @param fqdi is the FQDI of the derivation - * @return a list of tuples, which may be empty. - * @see org.griphyn.vdl.classes.Derivation - */ - public java.util.List loadAnnotationDerivation( String fqdi ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, null, CLASS_DERIVATION); - } - - - /** - * Lists all annotations for a formal argument. - * - * @param fqdi is the FQDI of the transformation - * @param farg is the name of the formal argument - * @return a list of tuples, which may be empty. - * @see org.griphyn.vdl.classes.Declare - */ - public java.util.List loadAnnotationDeclare( String fqdi, String farg ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, farg, CLASS_DECLARE); - } - - /** - * Lists all annotations for a call statement. - * - * @param fqdi is the FQDI of the transformation - * @param index is the number of the call to annotate. - * @return a list of tuples, which may be empty. - * @see org.griphyn.vdl.classes.Call - */ - public java.util.List loadAnnotationCall( String fqdi, int index ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(fqdi, new Integer(index), CLASS_CALL); - } - - /** - * Lists all annotations for a logical filename. - * - * @param filename is the logical filename. - * @return a list of tuples, which may be empty. - * @see org.griphyn.vdl.classes.LFN - */ - public java.util.List loadAnnotationFilename( String filename ) - throws SQLException, IllegalArgumentException - { - return loadAnnotation(filename, null, CLASS_FILENAME); - } - - /** - * Retrieves all annotations from an annotatable classes with - * the specified tuple. This is an interface method to the various - * class-specific methods. - * - * @param primary is the primary object specifier for the class. - * According to the type, this is either the FQDI, or the filename. - * @param secondary is a helper argument for annotations to calls - * and formal arguments, and should be null for all other classes. - * For calls, the argument must be packed into {@link java.lang.Integer}. - * @param kind defines the kind/class of object to annotate. - * - * @return null if not found, otherwise the annotation tuple. - * @see #loadAnnotationTransformation( String ) - * @see #loadAnnotationDerivation( String ) - * @see #loadAnnotationCall( String, int ) - * @see #loadAnnotationDeclare( String, String ) - * @see #loadAnnotationFilename( String ) - */ - public java.util.List loadAnnotation( String primary, - Object secondary, - int kind ) - throws SQLException, IllegalArgumentException - { - java.util.List result = new java.util.ArrayList(); - String subject = ""; - String select = null; - - switch ( kind ) { - case CLASS_TRANSFORMATION: - subject = "tr"; - break; - case CLASS_DERIVATION: - subject = "dv"; - break; - case CLASS_CALL: - // may throw ClassCastException - subject = "tr"; - select = "call[" + ((Integer) secondary).intValue() + "]"; - break; - case CLASS_DECLARE: - subject = "tr"; - // may throw ClassCastException - //select = "declare[@name='" + (String)secondary + "']"; - select = (String)secondary; - break; - case CLASS_FILENAME: - subject = "lfn"; - break; - default: - throw new IllegalArgumentException( "The class kind=" + kind + " cannot be annotated" ); - } - - try { - String id = null; - String xquery = "/annotation/metadata[@subject=\"" + subject + "\"][@name=\"" + - primary + "\"]"; - if (select == null) { - if (kind != CLASS_FILENAME) { - xquery += "[empty(@select)]"; - } - } else { - xquery += "[@select=\"" + select + "\"]"; - } - - xquery += "/attribute"; - Logging.instance().log("nxd", 1, "query: " + xquery ); - - ResourceSet rs = m_metaQrySvc.query(xquery); - ResourceIterator i = rs.getIterator(); - while (i.hasMoreResources()) { - XMLResource res = (XMLResource)i.nextResource(); - Tuple tuple = loadAnnotationResource(res); - if (tuple != null) { - result.add(tuple); - } - } - return result; - } catch (Exception e) { - throw new SQLException(e.getMessage()); - } - } - - - /** - * Search for LFNs or Definitions that has certain annotations - * - * @param kind defines the kind/class of object annotated. - * @param arg is used only for TR ARG and TR CALL. For the former - * it is the name of the argument (String), for the latter the position of - * the call (Integer). - * @param tree stores the query tree to query the annotation - * @return a list of LFNs if search for filenames, otherwise a list of - * definitions. - * @exception SQLException if something goes wrong with the database. - * @see org.griphyn.vdl.annotation.QueryTree - */ - public java.util.List searchAnnotation( int kind, - Object arg, - QueryTree tree) - throws SQLException - { - java.util.List result = new java.util.ArrayList(); - - if ( tree == null) - return result; - - String subject = ""; - String defn = "transformation"; - String select = null; - - switch ( kind ) { - case CLASS_TRANSFORMATION: - subject = "tr"; - break; - case CLASS_DERIVATION: - subject = "dv"; - defn = "derivation"; - break; - case CLASS_CALL: - // may throw ClassCastException - subject = "tr"; - select = "call[" + ((Integer) arg).intValue() + "]"; - break; - case CLASS_DECLARE: - subject = "tr"; - // may throw ClassCastException - //select = "declare[@name='" + (String)arg + "']"; - select = (String)arg; - break; - case CLASS_FILENAME: - subject = "lfn"; - break; - default: - throw new IllegalArgumentException( "The class kind=" + kind + " cannot be annotated" ); - } - - try { - String id = null; - String cond = "[@subject=\"" + subject + "\"]"; - if (select == null) { - if (kind != CLASS_FILENAME) { - cond += "[empty(@select)]"; - } - } else { - cond += "[@select=\"" + select + "\"]"; - } - String xquery = "for $mn in distinct-values(//annotation/metadata" + cond + "/@name) " + - "let $m := //annotation/metadata[@name=$mn]" + cond; - - String where = " where "; - where += tree.toXQuery("$m/attribute"); - - if (kind == CLASS_FILENAME) { - xquery += ", $r := $m"; - xquery += where; - xquery += " return $mn"; - - return searchElements(xquery); - } else { - xquery += ", $n := substring-before($mn, '::'), $na := substring-after($mn, '::'), $iv := if ($na) then $na else $mn, $v := substring-after($iv, ':'), $ib := substring-before($iv, ':'), $i := if ($ib) then $ib else $iv,"; - xquery += " $t := if ($n) then if ($v) then //" + defn + "[@namespace=$n][@name=$i][@version=$v] else //" + defn + "[@namespace=$n][@name=$i][empty(@version)] else if ($v) then //" + defn + "[empty(@namespace)][@name=$i][@version=$v] else //" + defn + "[empty(@namespace)][@name=$i][empty(@version)]"; - - xquery += where; - if (kind == CLASS_DECLARE) - xquery += " return $t[" + "declare[@name='" + select + "']" + "]"; - else - xquery += " return $t"; - return searchDefinition(xquery); - } - - } catch (Exception e) { - throw new SQLException(e.getMessage()); - } - } - - - /** - * pass-thru to driver. - * @return true, if it is feasible to cache results from the driver - * false, if requerying the driver is sufficiently fast (e.g. driver - * is in main memory, or driver does caching itself). - */ - public boolean cachingMakesSense() - { - return true; - } - - public void close() - throws SQLException - { - try { - //m_vdc.close(); - //m_db.close(); - } catch (Exception e){ - throw new SQLException(e.getMessage()); - } - } -} Index: pegasus-wms_4.0.1+dfsg/build.xml =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/build.xml 2012-05-24 16:47:52.064156782 -0700 +++ pegasus-wms_4.0.1+dfsg/build.xml 2012-05-24 16:47:54.096166867 -0700 @@ -117,7 +117,7 @@ @@ -148,7 +148,7 @@ description="Create the PEGASUS JAR files excluding tests"> debian/patches/portability0000644000000000000000000000505711761174534013122 0ustar Index: pegasus-wms_4.0.1+dfsg/release-tools/getsystem/getsystem =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/release-tools/getsystem/getsystem 2012-05-24 15:12:47.023867019 -0700 +++ pegasus-wms_4.0.1+dfsg/release-tools/getsystem/getsystem 2012-05-29 09:29:12.044630165 -0700 @@ -42,7 +42,9 @@ "x86_64", "x86_64", "X86-based PC", "x86", "HP-UX", "hppa", - "arm", "arm" + "arm", "arm", + "s390", "s390", + "s390x", "s390x" ); # Override the flags based on a system @@ -113,8 +115,11 @@ if ( lc($os) eq "linux") { my %distro = &get_linux_distro(); - - return($short_arch{$arch},$distro{'short'},$distro{'version'}); + my $s_arch = $arch; + if (defined $short_arch{$arch}) { + $s_arch = $short_arch{$arch}; + } + return($s_arch,$distro{'short'},$distro{'version'}); } elsif($short_os{$os} eq "macos") { # need something like 'ppc_macos_10.3' # find if processor is 64 bit. Index: pegasus-wms_4.0.1+dfsg/src/tools/pegasus-cluster/Makefile =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/tools/pegasus-cluster/Makefile 2012-05-24 15:12:47.155867670 -0700 +++ pegasus-wms_4.0.1+dfsg/src/tools/pegasus-cluster/Makefile 2012-05-29 08:35:40.224703954 -0700 @@ -57,12 +57,6 @@ else ifeq (armv7l, ${MARCH}) # nothing to do -else -# -# Linux IA32 -# -CFLAGS += -march=i686 -# LDFLAGS += -static endif endif endif Index: pegasus-wms_4.0.1+dfsg/src/tools/pegasus-invoke/Makefile =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/tools/pegasus-invoke/Makefile 2012-05-24 15:12:47.147867638 -0700 +++ pegasus-wms_4.0.1+dfsg/src/tools/pegasus-invoke/Makefile 2012-05-29 08:34:24.784329862 -0700 @@ -63,9 +63,9 @@ CFLAGS = -Wall -O2 -ggdb -m64 else ifeq (armv7l,${MARCH}) -CFLAGS = -Wall -02 -ggdb +CFLAGS = -Wall -O2 -ggdb else -CFLAGS = -Wall -O2 -march=i686 -ggdb +CFLAGS = -Wall -O2 -ggdb #EXTRA_LDFLAGS += -static endif endif Index: pegasus-wms_4.0.1+dfsg/src/tools/pegasus-keg/Makefile =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/src/tools/pegasus-keg/Makefile 2012-05-24 15:12:47.147867638 -0700 +++ pegasus-wms_4.0.1+dfsg/src/tools/pegasus-keg/Makefile 2012-05-29 08:36:28.156941640 -0700 @@ -99,7 +99,7 @@ ifeq (armv7l, ${MARCH}) CXXFLAGS = -Wall -O2 -ggdb else -CXXFLAGS = -Wall -O2 -march=i686 -ggdb +CXXFLAGS = -Wall -O2 -ggdb #LDFLAGS += -static endif endif debian/patches/python_2_7_3_urlparse_fix.patch0000644000000000000000000000221712014517663016642 0ustar Description: Fix crash with python2.7 2.7.3 due to urlparse.uses_query . pegasus-wms (4.0.1+dfsg-7) UNRELEASED; urgency=low . * In lib/pegasus/python/netlogger/nlapi.py add try/except around use of urlparse.uses_query to avoid crash when run with python (2.7.3) that does not have it (Closes: #682148) Author: Scott Kitterman Bug-Debian: http://bugs.debian.org/682148 Origin: Forwarded: Last-Update: <2012-07-24> Index: pegasus-wms_4.0.1+dfsg/lib/pegasus/python/netlogger/nlapi.py =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/lib/pegasus/python/netlogger/nlapi.py 2012-05-24 15:12:47.067867242 -0700 +++ pegasus-wms_4.0.1+dfsg/lib/pegasus/python/netlogger/nlapi.py 2012-08-13 07:51:54.000000000 -0700 @@ -415,7 +415,10 @@ # set up urlparse to recognize x-netlog schemes for scheme in 'x-netlog','x-netlog-udp': urlparse.uses_netloc.append(scheme) - urlparse.uses_query.append(scheme) + try: + urlparse.uses_query.append(scheme) + except AttributeError as errorstring: + pass def urlfile(url): """urlfile(url:str) -> file debian/patches/classpath0000644000000000000000000000415111757737041012537 0ustar Index: pegasus-wms_4.0.1+dfsg/build.xml =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/build.xml 2012-05-24 19:21:06.225748167 -0700 +++ pegasus-wms_4.0.1+dfsg/build.xml 2012-05-25 10:14:58.185108598 -0700 @@ -149,7 +149,11 @@ + excludes="*.class,edu/isi/pegasus/**/*Test.class,org/griphyn/**/*Test.class,org/griphyn/**/*.class"> + + + + @@ -158,7 +162,11 @@ + excludes="*.class,org/griphyn/vdl/**/*Test.class,org/griphyn/vdl/*Test.class,edu/isi/pegasus/**/*.jar"> + + + + debian/patches/series0000644000000000000000000000020212012212160012007 0ustar disable-externals dep-removal doc-build classpath portability python_2_7_3_urlparse_fix.patch fix-build-with-new-subversion.patch debian/patches/disable-externals0000644000000000000000000000265411757531731014167 0ustar Index: pegasus-source-4.0.0/build.xml =================================================================== --- pegasus-source-4.0.0.orig/build.xml 2012-03-01 07:46:25.000000000 -0800 +++ pegasus-source-4.0.0/build.xml 2012-05-21 11:17:39.305907895 -0700 @@ -362,7 +362,7 @@ - @@ -439,9 +439,6 @@ - - - @@ -512,9 +509,9 @@ - - + debian/patches/fix-build-with-new-subversion.patch0000644000000000000000000000254312012212425017451 0ustar Description: fix build with new subversion Recent versions of subversion return "Unversioned directory" in response to svnversion . in a non-svn directory, this breaks the build process due to an inability to handle spaces in this field, the attached patch fixes this by not defining -DHAS_SVNVERSION if svnversion . reutrns "Unversioned directory" Author: Peter Michael Green --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: --- pegasus-wms-4.0.1+dfsg.orig/src/tools/pegasus-keg/Makefile +++ pegasus-wms-4.0.1+dfsg/src/tools/pegasus-keg/Makefile @@ -129,8 +129,10 @@ CONDOR_CXX = $(CONDOR) $(CXX) SVNVERSION = $(shell svnversion . 2>> /dev/null) ifneq (,${SVNVERSION}) +ifneq (Unversioned directory,${SVNVERSION}) CXXFLAGS += -DHAS_SVNVERSION=\"${SVNVERSION}\" endif +endif # add large file support ifneq (,${LFS_CFLAGS}) debian/patches/doc-build0000644000000000000000000000424311757571475012430 0ustar Index: pegasus-wms_4.0.1+dfsg/doc/manpages/Makefile =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/doc/manpages/Makefile 2012-05-24 19:21:06.225748167 -0700 +++ pegasus-wms_4.0.1+dfsg/doc/manpages/Makefile 2012-05-24 19:21:20.845820668 -0700 @@ -4,7 +4,7 @@ endif ASCIIDOC = asciidoc -d manpage -b docbook -XSLTPROC = xsltproc -xinclude +XSLTPROC = xsltproc --nonet -xinclude FOP = fop DOCBOOK2FO = $(XSLTPROC) $(DOCBOOK_XSL)/fo/docbook.xsl @@ -55,6 +55,7 @@ BASENAME=`echo $< | sed 's/.txt//'`; \ sed -E "s/id=\"(_[^\"]+)\"/id=\"$$BASENAME\1\"/" -i"" $@; \ sed -E "s//" -i"" $@ + sed -E "s/http:\/\/www\.oasis-open\.org\/docbook\/xml\/4\.5\/docbookx\.dtd/\/usr\/share\/xml\/docbook\/schema\/dtd\/4.5\/docbookx.dtd/" -i"" $@ clean: rm -f pegasus-*.xml *.fo *.pdf *.1 *.html Index: pegasus-wms_4.0.1+dfsg/doc/docbook/pegasus-pdf-style.xsl =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/doc/docbook/pegasus-pdf-style.xsl 2012-05-24 19:45:33.225022631 -0700 +++ pegasus-wms_4.0.1+dfsg/doc/docbook/pegasus-pdf-style.xsl 2012-05-24 19:46:09.629203149 -0700 @@ -2,7 +2,7 @@ - + 9 Index: pegasus-wms_4.0.1+dfsg/doc/docbook/pegasus-style.xsl =================================================================== --- pegasus-wms_4.0.1+dfsg.orig/doc/docbook/pegasus-style.xsl 2012-05-24 15:12:47.387868828 -0700 +++ pegasus-wms_4.0.1+dfsg/doc/docbook/pegasus-style.xsl 2012-05-24 19:49:24.438169148 -0700 @@ -2,7 +2,7 @@ - + debian/changelog0000644000000000000000000000364012014517614011044 0ustar pegasus-wms (4.0.1+dfsg-8) unstable; urgency=low * Improved the fix for a Python 2.7.3 problem where urlparse does not have an attribute named uses_query anymore. The problem was reported in bug #682148. The previously applied fix still printed a one line debugging message, which with this upload, is now removed. -- Mats Rynge Mon, 20 Aug 2012 13:30:44 -0700 pegasus-wms (4.0.1+dfsg-7) unstable; urgency=low * Fixed FTBFS problem with Subversion 1.7 (closes: #679561) * Fixed Python 2.7.3 problem with uses_query - this affected several Pegasus command line tools (closes: #682148) -- Mats Rynge Mon, 13 Aug 2012 07:38:33 -0700 pegasus-wms (4.0.1+dfsg-6) unstable; urgency=low * Fixed pegasus-wms-doc misspelling in Suggests: * Moved to JDK 7 for better doc generation -- Mats Rynge Mon, 18 Jun 2012 07:45:53 -0700 pegasus-wms (4.0.1+dfsg-5) unstable; urgency=low * Included missing changelog in the -doc package -- Mats Rynge Tue, 05 Jun 2012 11:08:37 -0700 pegasus-wms (4.0.1+dfsg-4) unstable; urgency=low * Split up the build into the build-arch and build-indep targets -- Mats Rynge Sat, 02 Jun 2012 22:59:55 -0700 pegasus-wms (4.0.1+dfsg-3) unstable; urgency=low * Portability improvements for Arm and s390 -- Mats Rynge Tue, 29 May 2012 08:43:12 -0700 pegasus-wms (4.0.1+dfsg-2) unstable; urgency=low * Added build-arch and build-indep to debian/rules (closes: #674725)) -- Mats Rynge Sun, 27 May 2012 23:45:57 -0700 pegasus-wms (4.0.1+dfsg-1) unstable; urgency=low * Initial upload (closes: #673893) * Worked with upstream on a DFSG source tarball * Removed included jars and replaced with dependencies on existing Debian packages. * PDFs are now regenerated during build -- Mats Rynge Thu, 24 May 2012 15:20:50 -0700 debian/source/0000755000000000000000000000000011757550422010476 5ustar debian/source/format0000644000000000000000000000001411757531731011706 0ustar 3.0 (quilt) debian/source/options0000644000000000000000000000014511757550422012114 0ustar extend-diff-ignore = "(Version.java|\.jar|doc/docbook/.*|doc/manpages/.*|share/man/man1/.*|\.pdf)$" debian/copyright0000644000000000000000000001443411757733633011146 0ustar The package was downloaded from: http://pegasus.isi.edu Upstream Author: Pegasus Development Team Copyright and license: ## # Copyright 2007-2011 University Of Southern California # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, # software distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. ## On Debian systems, the complete Apache version 2.0 license can be found in "/usr/share/common-licenses/Apache-2.0" Source under src/org/griphyn/ and a few other files are under Globus Toolkit Public License: Globus Toolkit Public License Version 2, July 31, 2003 Copyright 1999-2003 University of Chicago and The University of Southern California. All rights reserved. This software referred to as the Globus Toolkit software ("Software") includes voluntary contributions made to the Globus Project collaboration. Persons and entities that have made voluntary contributions are hereinafter referred to as "Contributors." This Globus Toolkit Public License is referred to herein as "the GTPL." For more information on the Globus Project, please see http://www.globus.org/. Permission is granted for the installation, use, reproduction, modification, display, performance and redistribution of this Software, with or without modification, in source and binary forms. Permission is granted for the installation, use, reproduction, modification, display, performance and redistribution of user files, manuals, and training and demonstration slides ("Documentation") distributed with or specifically designated as distributed under the GTPL. Any exercise of rights under the GTPL is subject to the following conditions: 1. 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Globus Toolkit Public License 7-31-03 The Debian packaging is: Copyright 2007-2012 University Of Southern California and is licenced under the Apache version 2.0 debian/compat0000644000000000000000000000000211757531731010376 0ustar 9 debian/control0000644000000000000000000000513011767637661010614 0ustar Source: pegasus-wms Section: science Priority: optional Maintainer: Mats Rynge Build-Depends: debhelper (>= 9), openjdk-7-jdk, ant, docbook-xsl, docbook-xml, asciidoc, xsltproc, fop, perl, python, python-dev, libcommons-logging-java, libcommons-pool-java, libgetopt-java, liblog4j1.2-java, libmysql-java, libxml-commons-resolver1.1-java, libxerces2-java, libxmlrpc3-common-java Standards-Version: 3.9.3 Homepage: http://pegasus.isi.edu Package: pegasus-wms Section: science Priority: optional Architecture: any Depends: java7-runtime | java6-runtime, perl, python, python-boto, python-sqlalchemy, libcommons-logging-java, libcommons-pool-java, libgetopt-java, liblog4j1.2-java, libmysql-java, libxml-commons-resolver1.1-java, libxerces2-java, libxmlrpc3-common-java, ${shlibs:Depends}, ${misc:Depends} Recommends: condor Suggests: pegasus-wms-doc Description: Scientific workflow management system for Condor The Pegasus project encompasses a set of technologies the help workflow-based applications execute in a number of different environments including desktops, campus clusters, grids, and now clouds. Scientific workflows allow users to easily express multi-step computations, for example retrieve data from a database, reformat the data, and run an analysis. Once an application is formalized as a workflow the Pegasus Workflow Management Service can map it onto available compute resources and execute the steps in appropriate order. Package: pegasus-wms-doc Section: doc Priority: optional Architecture: all Depends: ${misc:Depends} Recommends: pegasus-wms Description: Scientific workflow management system for Condor - data files The Pegasus project encompasses a set of technologies the help workflow-based applications execute in a number of different environments including desktops, campus clusters, grids, and now clouds. Scientific workflows allow users to easily express multi-step computations, for example retrieve data from a database, reformat the data, and run an analysis. Once an application is formalized as a workflow the Pegasus Workflow Management Service can map it onto available compute resources and execute the steps in appropriate order. . This package contains the user documentation.