debian/0000755000000000000000000000000012246070047007170 5ustar debian/source/0000755000000000000000000000000012246070047010470 5ustar debian/source/format0000644000000000000000000000001411657164767011720 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000013212512146131107011121 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: BioMAJ Source: svn://scm.gforge.inria.fr/svn/biomaj/ Files: debian/* Copyright: 2011 Olivier Sallou License: GPL-3 On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. Files: usr/share/biomaj/workflows/mirror.xml usr/share/biomaj/src/org/gmod/biomaj/ant/conditions/DirectoryHasFilesCondition.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/SymlinkList.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FileCheck.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FtpListingParser.java usr/share/biomaj/src/org/gmod/ant/selectors/FilenamePatternSelector.java usr/share/biomaj/build.xml Copyright: 2004 Indiana University License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: * Copyright: 2011 GenOuest Platform License: CeCILL Notice . This Agreement is a Free Software license agreement that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting: . * firstly, compliance with the principles governing the distribution of Free Software: access to source code, broad rights granted to users, * secondly, the election of a governing law, French law, with which it is conformant, both as regards the law of torts and intellectual property law, and the protection that it offers to both authors and holders of the economic rights over software. . The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) license are: . Commissariat à l'Energie Atomique - CEA, a public scientific, technical and industrial research establishment, having its principal place of business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. . Centre National de la Recherche Scientifique - CNRS, a public scientific and technological establishment, having its principal place of business at 3 rue Michel-Ange, 75794 Paris cedex 16, France. . Institut National de Recherche en Informatique et en Automatique - INRIA, a public scientific and technological establishment, having its principal place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le Chesnay cedex, France. . . Preamble . The purpose of this Free Software license agreement is to grant users the right to modify and redistribute the software governed by this license within the framework of an open source distribution model. . The exercising of these rights is conditional upon certain obligations for users so as to preserve this status for all subsequent redistributions. . In consideration of access to the source code and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. . In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its Free Software status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the suitability of the software as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom. . This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions. . . Article 1 - DEFINITIONS . For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning: . Agreement: means this license agreement, and its possible subsequent versions and annexes. . Software: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. . Initial Software: means the Software in its Source Code and possibly its Object Code form and, where applicable, its documentation, "as is" when it is first distributed under the terms and conditions of the Agreement. . Modified Software: means the Software modified by at least one Contribution. . Source Code: means all the Software's instructions and program lines to which access is required so as to modify the Software. . Object Code: means the binary files originating from the compilation of the Source Code. . Holder: means the holder(s) of the economic rights over the Initial Software. . Licensee: means the Software user(s) having accepted the Agreement. . Contributor: means a Licensee having made at least one Contribution. . Licensor: means the Holder, or any other individual or legal entity, who distributes the Software under the Agreement. . Contribution: means any or all modifications, corrections, translations, adaptations and/or new functions integrated into the Software by any or all Contributors, as well as any or all Internal Modules. . Module: means a set of sources files including their documentation that enables supplementary functions or services in addition to those offered by the Software. . External Module: means any or all Modules, not derived from the Software, so that this Module and the Software run in separate address spaces, with one calling the other when they are run. . Internal Module: means any or all Module, connected to the Software so that they both execute in the same address space. . GNU GPL: means the GNU General Public License version 2 or any subsequent version, as published by the Free Software Foundation Inc. . Parties: mean both the Licensee and the Licensor. . These expressions may be used both in singular and plural form. . . Article 2 - PURPOSE . The purpose of the Agreement is the grant by the Licensor to the Licensee of a non-exclusive, transferable and worldwide license for the Software as set forth in Article 5 hereinafter for the whole term of the protection granted by the rights over said Software. . . Article 3 - ACCEPTANCE . 3.1 The Licensee shall be deemed as having accepted the terms and conditions of this Agreement upon the occurrence of the first of the following events: . * (i) loading the Software by any or all means, notably, by downloading from a remote server, or by loading from a physical medium; * (ii) the first time the Licensee exercises any of the rights granted hereunder. . 3.2 One copy of the Agreement, containing a notice relating to the characteristics of the Software, to the limited warranty, and to the fact that its use is restricted to experienced users has been provided to the Licensee prior to its acceptance as set forth in Article 3.1 hereinabove, and the Licensee hereby acknowledges that it has read and understood it. . . Article 4 - EFFECTIVE DATE AND TERM . . 4.1 EFFECTIVE DATE . The Agreement shall become effective on the date when it is accepted by the Licensee as set forth in Article 3.1. . . 4.2 TERM . The Agreement shall remain in force for the entire legal term of protection of the economic rights over the Software. . . Article 5 - SCOPE OF RIGHTS GRANTED . The Licensor hereby grants to the Licensee, who accepts, the following rights over the Software for any or all use, and for the term of the Agreement, on the basis of the terms and conditions set forth hereinafter. . Besides, if the Licensor owns or comes to own one or more patents protecting all or part of the functions of the Software or of its components, the Licensor undertakes not to enforce the rights granted by these patents against successive Licensees using, exploiting or modifying the Software. If these patents are transferred, the Licensor undertakes to have the transferees subscribe to the obligations set forth in this paragraph. . . 5.1 RIGHT OF USE . The Licensee is authorized to use the Software, without any limitation as to its fields of application, with it being hereinafter specified that this comprises: . 1. permanent or temporary reproduction of all or part of the Software by any or all means and in any or all form. . 2. loading, displaying, running, or storing the Software on any or all medium. . 3. entitlement to observe, study or test its operation so as to determine the ideas and principles behind any or all constituent elements of said Software. This shall apply when the Licensee carries out any or all loading, displaying, running, transmission or storage operation as regards the Software, that it is entitled to carry out hereunder. . . 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS . The right to make Contributions includes the right to translate, adapt, arrange, or make any or all modifications to the Software, and the right to reproduce the resulting software. . The Licensee is authorized to make any or all Contributions to the Software provided that it includes an explicit notice that it is the author of said Contribution and indicates the date of the creation thereof. . . 5.3 RIGHT OF DISTRIBUTION . In particular, the right of distribution includes the right to publish, transmit and communicate the Software to the general public on any or all medium, and by any or all means, and the right to market, either in consideration of a fee, or free of charge, one or more copies of the Software by any means. . The Licensee is further authorized to distribute copies of the modified or unmodified Software to third parties according to the terms and conditions set forth hereinafter. . . 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION . The Licensee is authorized to distribute true copies of the Software in Source Code or Object Code form, provided that said distribution complies with all the provisions of the Agreement and is accompanied by: . 1. a copy of the Agreement, . 2. a notice relating to the limitation of both the Licensor's warranty and liability as set forth in Articles 8 and 9, . and that, in the event that only the Object Code of the Software is redistributed, the Licensee allows future Licensees unhindered access to the full Source Code of the Software by indicating how to access it, it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data. . . 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE . When the Licensee makes a Contribution to the Software, the terms and conditions for the distribution of the resulting Modified Software become subject to all the provisions of this Agreement. . The Licensee is authorized to distribute the Modified Software, in source code or object code form, provided that said distribution complies with all the provisions of the Agreement and is accompanied by: . 1. a copy of the Agreement, . 2. a notice relating to the limitation of both the Licensor's warranty and liability as set forth in Articles 8 and 9, . and that, in the event that only the object code of the Modified Software is redistributed, the Licensee allows future Licensees unhindered access to the full source code of the Modified Software by indicating how to access it, it being understood that the additional cost of acquiring the source code shall not exceed the cost of transferring the data. . . 5.3.3 DISTRIBUTION OF EXTERNAL MODULES . When the Licensee has developed an External Module, the terms and conditions of this Agreement do not apply to said External Module, that may be distributed under a separate license agreement. . . 5.3.4 COMPATIBILITY WITH THE GNU GPL . The Licensee can include a code that is subject to the provisions of one of the versions of the GNU GPL in the Modified or unmodified Software, and distribute that entire code under the terms of the same version of the GNU GPL. . The Licensee can include the Modified or unmodified Software in a code that is subject to the provisions of one of the versions of the GNU GPL, and distribute that entire code under the terms of the same version of the GNU GPL. . . Article 6 - INTELLECTUAL PROPERTY . . 6.1 OVER THE INITIAL SOFTWARE . The Holder owns the economic rights over the Initial Software. Any or all use of the Initial Software is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to modify the terms and conditions for the distribution of said Initial Software. . The Holder undertakes that the Initial Software will remain ruled at least by this Agreement, for the duration set forth in Article 4.2. . . 6.2 OVER THE CONTRIBUTIONS . The Licensee who develops a Contribution is the owner of the intellectual property rights over this Contribution as defined by applicable law. . . 6.3 OVER THE EXTERNAL MODULES . The Licensee who develops an External Module is the owner of the intellectual property rights over this External Module as defined by applicable law and is free to choose the type of agreement that shall govern its distribution. . . 6.4 JOINT PROVISIONS . The Licensee expressly undertakes: . 1. not to remove, or modify, in any manner, the intellectual property notices attached to the Software; . 2. to reproduce said notices, in an identical manner, in the copies of the Software modified or not. . The Licensee undertakes not to directly or indirectly infringe the intellectual property rights of the Holder and/or Contributors on the Software and to take, where applicable, vis-à-vis its staff, any and all measures required to ensure respect of said intellectual property rights of the Holder and/or Contributors. . . Article 7 - RELATED SERVICES . 7.1 Under no circumstances shall the Agreement oblige the Licensor to provide technical assistance or maintenance services for the Software. . However, the Licensor is entitled to offer this type of services. The terms and conditions of such technical assistance, and/or such maintenance, shall be set forth in a separate instrument. Only the Licensor offering said maintenance and/or technical assistance services shall incur liability therefor. . 7.2 Similarly, any Licensor is entitled to offer to its licensees, under its sole responsibility, a warranty, that shall only be binding upon itself, for the redistribution of the Software and/or the Modified Software, under terms and conditions that it is free to decide. Said warranty, and the financial terms and conditions of its application, shall be subject of a separate instrument executed between the Licensor and the Licensee. . . Article 8 - LIABILITY . 8.1 Subject to the provisions of Article 8.2, the Licensee shall be entitled to claim compensation for any direct loss it may have suffered from the Software as a result of a fault on the part of the relevant Licensor, subject to providing evidence thereof. . 8.2 The Licensor's liability is limited to the commitments made under this Agreement and shall not be incurred as a result of in particular: (i) loss due the Licensee's total or partial failure to fulfill its obligations, (ii) direct or consequential loss that is suffered by the Licensee due to the use or performance of the Software, and (iii) more generally, any consequential loss. In particular the Parties expressly agree that any or all pecuniary or business loss (i.e. loss of data, loss of profits, operating loss, loss of customers or orders, opportunity cost, any disturbance to business activities) or any or all legal proceedings instituted against the Licensee by a third party, shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor. . . Article 9 - WARRANTY . 9.1 The Licensee acknowledges that the scientific and technical state-of-the-art when the Software was distributed did not enable all possible uses to be tested and verified, nor for the presence of possible defects to be detected. In this respect, the Licensee's attention has been drawn to the risks associated with loading, using, modifying and/or developing and reproducing the Software which are reserved for experienced users. . The Licensee shall be responsible for verifying, by any or all means, the suitability of the product for its requirements, its good working order, and for ensuring that it shall not cause damage to either persons or properties. . 9.2 The Licensor hereby represents, in good faith, that it is entitled to grant all the rights over the Software (including in particular the rights set forth in Article 5). . 9.3 The Licensee acknowledges that the Software is supplied "as is" by the Licensor without any other express or tacit warranty, other than that provided for in Article 9.2 and, in particular, without any warranty as to its commercial value, its secured, safe, innovative or relevant nature. . Specifically, the Licensor does not warrant that the Software is free from any error, that it will operate without interruption, that it will be compatible with the Licensee's own equipment and software configuration, nor that it will meet the Licensee's requirements. . 9.4 The Licensor does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent, software or any other property right. Therefore, the Licensor disclaims any and all liability towards the Licensee arising out of any or all proceedings for infringement that may be instituted in respect of the use, modification and redistribution of the Software. Nevertheless, should such proceedings be instituted against the Licensee, the Licensor shall provide it with technical and legal assistance for its defense. Such technical and legal assistance shall be decided on a case-by-case basis between the relevant Licensor and the Licensee pursuant to a memorandum of understanding. The Licensor disclaims any and all liability as regards the Licensee's use of the name of the Software. No warranty is given as regards the existence of prior rights over the name of the Software or as regards the existence of a trademark. . . Article 10 - TERMINATION . 10.1 In the event of a breach by the Licensee of its obligations hereunder, the Licensor may automatically terminate this Agreement thirty (30) days after notice has been sent to the Licensee and has remained ineffective. . 10.2 A Licensee whose Agreement is terminated shall no longer be authorized to use, modify or distribute the Software. However, any licenses that it may have granted prior to termination of the Agreement shall remain valid subject to their having been granted in compliance with the terms and conditions hereof. . . Article 11 - MISCELLANEOUS . . 11.1 EXCUSABLE EVENTS . Neither Party shall be liable for any or all delay, or failure to perform the Agreement, that may be attributable to an event of force majeure, an act of God or an outside cause, such as defective functioning or interruptions of the electricity or telecommunications networks, network paralysis following a virus attack, intervention by government authorities, natural disasters, water damage, earthquakes, fire, explosions, strikes and labor unrest, war, etc. . 11.2 Any failure by either Party, on one or more occasions, to invoke one or more of the provisions hereof, shall under no circumstances be interpreted as being a waiver by the interested Party of its right to invoke said provision(s) subsequently. . 11.3 The Agreement cancels and replaces any or all previous agreements, whether written or oral, between the Parties and having the same purpose, and constitutes the entirety of the agreement between said Parties concerning said purpose. No supplement or modification to the terms and conditions hereof shall be effective as between the Parties unless it is made in writing and signed by their duly authorized representatives. . 11.4 In the event that one or more of the provisions hereof were to conflict with a current or future applicable act or legislative text, said act or legislative text shall prevail, and the Parties shall make the necessary amendments so as to comply with said act or legislative text. All other provisions shall remain effective. Similarly, invalidity of a provision of the Agreement, for any reason whatsoever, shall not cause the Agreement as a whole to be invalid. . . 11.5 LANGUAGE . The Agreement is drafted in both French and English and both versions are deemed authentic. . . Article 12 - NEW VERSIONS OF THE AGREEMENT . 12.1 Any person is authorized to duplicate and distribute copies of this Agreement. . 12.2 So as to ensure coherence, the wording of this Agreement is protected and may only be modified by the authors of the License, who reserve the right to periodically publish updates or new versions of the Agreement, each with a separate number. These subsequent versions may address new issues encountered by Free Software. . 12.3 Any Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version, subject to the provisions of Article 5.3.4. . . Article 13 - GOVERNING LAW AND JURISDICTION . 13.1 The Agreement is governed by French law. The Parties agree to endeavor to seek an amicable solution to any disagreements or disputes that may arise during the performance of the Agreement. . 13.2 Failing an amicable solution within two (2) months as from their occurrence, and unless emergency proceedings are necessary, the disagreements or disputes shall be referred to the Paris Courts having jurisdiction, by the more diligent Party. . . Version 2.0 dated 2006-09-05. Files: usr/share/biomaj/workflows/* Copyright: 2011 INRIA/INRA License: CeCILL-B Notice . This Agreement is a Free Software license agreement that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting: . * firstly, compliance with the principles governing the distribution of Free Software: access to source code, broad rights granted to users, * secondly, the election of a governing law, French law, with which it is conformant, both as regards the law of torts and intellectual property law, and the protection that it offers to both authors and holders of the economic rights over software. . The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) license are: . Commissariat à l'Energie Atomique - CEA, a public scientific, technical and industrial research establishment, having its principal place of business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. . Centre National de la Recherche Scientifique - CNRS, a public scientific and technological establishment, having its principal place of business at 3 rue Michel-Ange, 75794 Paris cedex 16, France. . Institut National de Recherche en Informatique et en Automatique - INRIA, a public scientific and technological establishment, having its principal place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le Chesnay cedex, France. . . Preamble . This Agreement is an open source software license intended to give users significant freedom to modify and redistribute the software licensed hereunder. . The exercising of this freedom is conditional upon a strong obligation of giving credits for everybody that distributes a software incorporating a software ruled by the current license so as all contributions to be properly identified and acknowledged. . In consideration of access to the source code and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. . In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its Free Software status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the suitability of the software as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom. . This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions. . . Article 1 - DEFINITIONS . For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning: . Agreement: means this license agreement, and its possible subsequent versions and annexes. . Software: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. . Initial Software: means the Software in its Source Code and possibly its Object Code form and, where applicable, its documentation, "as is" when it is first distributed under the terms and conditions of the Agreement. . Modified Software: means the Software modified by at least one Contribution. . Source Code: means all the Software's instructions and program lines to which access is required so as to modify the Software. . Object Code: means the binary files originating from the compilation of the Source Code. . Holder: means the holder(s) of the economic rights over the Initial Software. . Licensee: means the Software user(s) having accepted the Agreement. . Contributor: means a Licensee having made at least one Contribution. . Licensor: means the Holder, or any other individual or legal entity, who distributes the Software under the Agreement. . Contribution: means any or all modifications, corrections, translations, adaptations and/or new functions integrated into the Software by any or all Contributors, as well as any or all Internal Modules. . Module: means a set of sources files including their documentation that enables supplementary functions or services in addition to those offered by the Software. . External Module: means any or all Modules, not derived from the Software, so that this Module and the Software run in separate address spaces, with one calling the other when they are run. . Internal Module: means any or all Module, connected to the Software so that they both execute in the same address space. . Parties: mean both the Licensee and the Licensor. . These expressions may be used both in singular and plural form. . . Article 2 - PURPOSE . The purpose of the Agreement is the grant by the Licensor to the Licensee of a non-exclusive, transferable and worldwide license for the Software as set forth in Article 5 hereinafter for the whole term of the protection granted by the rights over said Software. . . Article 3 - ACCEPTANCE . 3.1 The Licensee shall be deemed as having accepted the terms and conditions of this Agreement upon the occurrence of the first of the following events: . * (i) loading the Software by any or all means, notably, by downloading from a remote server, or by loading from a physical medium; * (ii) the first time the Licensee exercises any of the rights granted hereunder. . 3.2 One copy of the Agreement, containing a notice relating to the characteristics of the Software, to the limited warranty, and to the fact that its use is restricted to experienced users has been provided to the Licensee prior to its acceptance as set forth in Article 3.1 hereinabove, and the Licensee hereby acknowledges that it has read and understood it. . . Article 4 - EFFECTIVE DATE AND TERM . . 4.1 EFFECTIVE DATE . The Agreement shall become effective on the date when it is accepted by the Licensee as set forth in Article 3.1. . . 4.2 TERM . The Agreement shall remain in force for the entire legal term of protection of the economic rights over the Software. . . Article 5 - SCOPE OF RIGHTS GRANTED . The Licensor hereby grants to the Licensee, who accepts, the following rights over the Software for any or all use, and for the term of the Agreement, on the basis of the terms and conditions set forth hereinafter. . Besides, if the Licensor owns or comes to own one or more patents protecting all or part of the functions of the Software or of its components, the Licensor undertakes not to enforce the rights granted by these patents against successive Licensees using, exploiting or modifying the Software. If these patents are transferred, the Licensor undertakes to have the transferees subscribe to the obligations set forth in this paragraph. . . 5.1 RIGHT OF USE . The Licensee is authorized to use the Software, without any limitation as to its fields of application, with it being hereinafter specified that this comprises: . 1. permanent or temporary reproduction of all or part of the Software by any or all means and in any or all form. . 2. loading, displaying, running, or storing the Software on any or all medium. . 3. entitlement to observe, study or test its operation so as to determine the ideas and principles behind any or all constituent elements of said Software. This shall apply when the Licensee carries out any or all loading, displaying, running, transmission or storage operation as regards the Software, that it is entitled to carry out hereunder. . . 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS . The right to make Contributions includes the right to translate, adapt, arrange, or make any or all modifications to the Software, and the right to reproduce the resulting software. . The Licensee is authorized to make any or all Contributions to the Software provided that it includes an explicit notice that it is the author of said Contribution and indicates the date of the creation thereof. . . 5.3 RIGHT OF DISTRIBUTION . In particular, the right of distribution includes the right to publish, transmit and communicate the Software to the general public on any or all medium, and by any or all means, and the right to market, either in consideration of a fee, or free of charge, one or more copies of the Software by any means. . The Licensee is further authorized to distribute copies of the modified or unmodified Software to third parties according to the terms and conditions set forth hereinafter. . . 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION . The Licensee is authorized to distribute true copies of the Software in Source Code or Object Code form, provided that said distribution complies with all the provisions of the Agreement and is accompanied by: . 1. a copy of the Agreement, . 2. a notice relating to the limitation of both the Licensor's warranty and liability as set forth in Articles 8 and 9, . and that, in the event that only the Object Code of the Software is redistributed, the Licensee allows effective access to the full Source Code of the Software at a minimum during the entire period of its distribution of the Software, it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data. . . 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE . If the Licensee makes any Contribution to the Software, the resulting Modified Software may be distributed under a license agreement other than this Agreement subject to compliance with the provisions of Article 5.3.4. . . 5.3.3 DISTRIBUTION OF EXTERNAL MODULES . When the Licensee has developed an External Module, the terms and conditions of this Agreement do not apply to said External Module, that may be distributed under a separate license agreement. . . 5.3.4 CREDITS . Any Licensee who may distribute a Modified Software hereby expressly agrees to: . 1. indicate in the related documentation that it is based on the Software licensed hereunder, and reproduce the intellectual property notice for the Software, . 2. ensure that written indications of the Software intended use, intellectual property notice and license hereunder are included in easily accessible format from the Modified Software interface, . 3. mention, on a freely accessible website describing the Modified Software, at least throughout the distribution term thereof, that it is based on the Software licensed hereunder, and reproduce the Software intellectual property notice, . 4. where it is distributed to a third party that may distribute a Modified Software without having to make its source code available, make its best efforts to ensure that said third party agrees to comply with the obligations set forth in this Article . . If the Software, whether or not modified, is distributed with an External Module designed for use in connection with the Software, the Licensee shall submit said External Module to the foregoing obligations. . . 5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES . Where a Modified Software contains a Contribution subject to the CeCILL license, the provisions set forth in Article 5.3.4 shall be optional. . A Modified Software may be distributed under the CeCILL-C license. In such a case the provisions set forth in Article 5.3.4 shall be optional. . . Article 6 - INTELLECTUAL PROPERTY . . 6.1 OVER THE INITIAL SOFTWARE . The Holder owns the economic rights over the Initial Software. Any or all use of the Initial Software is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to modify the terms and conditions for the distribution of said Initial Software. . The Holder undertakes that the Initial Software will remain ruled at least by this Agreement, for the duration set forth in Article 4.2. . . 6.2 OVER THE CONTRIBUTIONS . The Licensee who develops a Contribution is the owner of the intellectual property rights over this Contribution as defined by applicable law. . . 6.3 OVER THE EXTERNAL MODULES . The Licensee who develops an External Module is the owner of the intellectual property rights over this External Module as defined by applicable law and is free to choose the type of agreement that shall govern its distribution. . . 6.4 JOINT PROVISIONS . The Licensee expressly undertakes: . 1. not to remove, or modify, in any manner, the intellectual property notices attached to the Software; . 2. to reproduce said notices, in an identical manner, in the copies of the Software modified or not. . The Licensee undertakes not to directly or indirectly infringe the intellectual property rights of the Holder and/or Contributors on the Software and to take, where applicable, vis-à-vis its staff, any and all measures required to ensure respect of said intellectual property rights of the Holder and/or Contributors. . . Article 7 - RELATED SERVICES . 7.1 Under no circumstances shall the Agreement oblige the Licensor to provide technical assistance or maintenance services for the Software. . However, the Licensor is entitled to offer this type of services. The terms and conditions of such technical assistance, and/or such maintenance, shall be set forth in a separate instrument. Only the Licensor offering said maintenance and/or technical assistance services shall incur liability therefor. . 7.2 Similarly, any Licensor is entitled to offer to its licensees, under its sole responsibility, a warranty, that shall only be binding upon itself, for the redistribution of the Software and/or the Modified Software, under terms and conditions that it is free to decide. Said warranty, and the financial terms and conditions of its application, shall be subject of a separate instrument executed between the Licensor and the Licensee. . . Article 8 - LIABILITY . 8.1 Subject to the provisions of Article 8.2, the Licensee shall be entitled to claim compensation for any direct loss it may have suffered from the Software as a result of a fault on the part of the relevant Licensor, subject to providing evidence thereof. . 8.2 The Licensor's liability is limited to the commitments made under this Agreement and shall not be incurred as a result of in particular: (i) loss due the Licensee's total or partial failure to fulfill its obligations, (ii) direct or consequential loss that is suffered by the Licensee due to the use or performance of the Software, and (iii) more generally, any consequential loss. In particular the Parties expressly agree that any or all pecuniary or business loss (i.e. loss of data, loss of profits, operating loss, loss of customers or orders, opportunity cost, any disturbance to business activities) or any or all legal proceedings instituted against the Licensee by a third party, shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor. . . Article 9 - WARRANTY . 9.1 The Licensee acknowledges that the scientific and technical state-of-the-art when the Software was distributed did not enable all possible uses to be tested and verified, nor for the presence of possible defects to be detected. In this respect, the Licensee's attention has been drawn to the risks associated with loading, using, modifying and/or developing and reproducing the Software which are reserved for experienced users. . The Licensee shall be responsible for verifying, by any or all means, the suitability of the product for its requirements, its good working order, and for ensuring that it shall not cause damage to either persons or properties. . 9.2 The Licensor hereby represents, in good faith, that it is entitled to grant all the rights over the Software (including in particular the rights set forth in Article 5). . 9.3 The Licensee acknowledges that the Software is supplied "as is" by the Licensor without any other express or tacit warranty, other than that provided for in Article 9.2 and, in particular, without any warranty as to its commercial value, its secured, safe, innovative or relevant nature. . Specifically, the Licensor does not warrant that the Software is free from any error, that it will operate without interruption, that it will be compatible with the Licensee's own equipment and software configuration, nor that it will meet the Licensee's requirements. . 9.4 The Licensor does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent, software or any other property right. Therefore, the Licensor disclaims any and all liability towards the Licensee arising out of any or all proceedings for infringement that may be instituted in respect of the use, modification and redistribution of the Software. Nevertheless, should such proceedings be instituted against the Licensee, the Licensor shall provide it with technical and legal assistance for its defense. Such technical and legal assistance shall be decided on a case-by-case basis between the relevant Licensor and the Licensee pursuant to a memorandum of understanding. The Licensor disclaims any and all liability as regards the Licensee's use of the name of the Software. No warranty is given as regards the existence of prior rights over the name of the Software or as regards the existence of a trademark. . . Article 10 - TERMINATION . 10.1 In the event of a breach by the Licensee of its obligations hereunder, the Licensor may automatically terminate this Agreement thirty (30) days after notice has been sent to the Licensee and has remained ineffective. . 10.2 A Licensee whose Agreement is terminated shall no longer be authorized to use, modify or distribute the Software. However, any licenses that it may have granted prior to termination of the Agreement shall remain valid subject to their having been granted in compliance with the terms and conditions hereof. . . Article 11 - MISCELLANEOUS . . 11.1 EXCUSABLE EVENTS . Neither Party shall be liable for any or all delay, or failure to perform the Agreement, that may be attributable to an event of force majeure, an act of God or an outside cause, such as defective functioning or interruptions of the electricity or telecommunications networks, network paralysis following a virus attack, intervention by government authorities, natural disasters, water damage, earthquakes, fire, explosions, strikes and labor unrest, war, etc. . 11.2 Any failure by either Party, on one or more occasions, to invoke one or more of the provisions hereof, shall under no circumstances be interpreted as being a waiver by the interested Party of its right to invoke said provision(s) subsequently. . 11.3 The Agreement cancels and replaces any or all previous agreements, whether written or oral, between the Parties and having the same purpose, and constitutes the entirety of the agreement between said Parties concerning said purpose. No supplement or modification to the terms and conditions hereof shall be effective as between the Parties unless it is made in writing and signed by their duly authorized representatives. . 11.4 In the event that one or more of the provisions hereof were to conflict with a current or future applicable act or legislative text, said act or legislative text shall prevail, and the Parties shall make the necessary amendments so as to comply with said act or legislative text. All other provisions shall remain effective. Similarly, invalidity of a provision of the Agreement, for any reason whatsoever, shall not cause the Agreement as a whole to be invalid. . . 11.5 LANGUAGE . The Agreement is drafted in both French and English and both versions are deemed authentic. . . Article 12 - NEW VERSIONS OF THE AGREEMENT . 12.1 Any person is authorized to duplicate and distribute copies of this Agreement. . 12.2 So as to ensure coherence, the wording of this Agreement is protected and may only be modified by the authors of the License, who reserve the right to periodically publish updates or new versions of the Agreement, each with a separate number. These subsequent versions may address new issues encountered by Free Software. . 12.3 Any Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version. . . Article 13 - GOVERNING LAW AND JURISDICTION . 13.1 The Agreement is governed by French law. The Parties agree to endeavor to seek an amicable solution to any disagreements or disputes that may arise during the performance of the Agreement. . 13.2 Failing an amicable solution within two (2) months as from their occurrence, and unless emergency proceedings are necessary, the disagreements or disputes shall be referred to the Paris Courts having jurisdiction, by the more diligent Party. . . Version 1.0 dated 2006-09-05. debian/config0000755000000000000000000000073712237635715010403 0ustar #!/bin/sh set -e # Source debconf library. . /usr/share/debconf/confmodule # jdk_home #db_input low biomaj/jdk_home || true #db_go # Configure mysql ? db_input critical biomaj/mysql || true db_go db_get biomaj/mysql if [ "$RET" = "true" ]; then # MySQL server db_input critical biomaj/mysql_host || true db_go # MySQL login db_input critical biomaj/mysql_login || true db_go # MySQL password db_input critical biomaj/mysql_passwd || true db_go fi debian/biomaj.links0000644000000000000000000000021711657164770011507 0ustar etc/biomaj/general.conf usr/share/biomaj/general.conf etc/biomaj/unix_command_system.cfg usr/share/biomaj/conf/process/unix_command_system.cfg debian/po/0000755000000000000000000000000012246070047007606 5ustar debian/po/es.po0000644000000000000000000000676411712456370010576 0ustar # biomaj po-debconf translation to Spanish # Copyright (C) 2010 Software in the Public Interest # This file is distributed under the same license as the biomaj package. # # Changes: # - Initial translation # Camaleón , 2011 # # - Updates # # # Traductores, si no conocen el formato PO, merece la pena leer la # documentación de gettext, especialmente las secciones dedicadas a este # formato, por ejemplo ejecutando: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Equipo de traducción al español, por favor lean antes de traducir # los siguientes documentos: # # - El proyecto de traducción de Debian al español # http://www.debian.org/intl/spanish/ # especialmente las notas y normas de traducción en # http://www.debian.org/intl/spanish/notas # # - La guía de traducción de po's de debconf: # /usr/share/doc/po-debconf/README-trans # o http://www.debian.org/intl/l10n/po-debconf/README-trans # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0.4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-16 15:28+0100\n" "Last-Translator: Camaleón \n" "Language-Team: Debian Spanish \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "¿Desea configurar la conexión MySQL ahora?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Una vez que se haya creado y configurado la base de datos para BioMAJ, ésta " "se puede poblar automáticamente en lugar de tener que actualizarla de forma " "manual." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Por favor, especifique si se debe configurar ahora la conexión de la base de " "datos." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Servidor MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Por favor, introduzca el nombre del equipo y la dirección IP del servidor " "MySQL que desea utilizar." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Nombre del usuario para la base de datos BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Por favor, introduzca el nombre del usuario que desea utilizar para " "conectarse al servidor MySQL y acceder a la base de datos biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Contraseña del usuario para la base de datos BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Por favor, introduzca la contraseña que desea utilizar para conectarse al " "servidor MySQL y acceder a la base de datos biomaj_log." #~ msgid "The JDK home directory:" #~ msgstr "Directorio raíz de JDK:" debian/po/ja.po0000644000000000000000000000521112146131107010531 0ustar # Japanese translation. # Copyright (C) 2012 # This file is distributed under the same license as the biomaj package. # victory , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2012-10-11 14:27+0000\n" "PO-Revision-Date: 2012-10-11 23:27+0900\n" "Last-Translator: victory \n" "Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "MySQL をここで設定しますか?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "BioMAJ 用の MySQL データベースの作成と設定が終わると、手作業で更新させる必要は" "なく、自動的に更新させることができます。" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "データベース接続をここで設定するかどうかを選択してください。" #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL サーバ:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "使用する MySQL サーバのホスト名か IP アドレスを入力してください。" #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "BioMAJ データベース用の MySQL ID:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "biomaj_log データベースにアクセスする際 MySQL データベースサーバに接続するの" "に使う ID を入力してください。" #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "BioMAJ データベース用の MySQL パスワード:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "biomaj_log データベースにアクセスする際 MySQL データベースサーバに接続するの" "に使うパスワードを入力してください。" debian/po/da.po0000644000000000000000000000511711712456370010542 0ustar # Danish translation biomaj. # Copyright (C) 2011 biomaj & nedenstående oversættere. # This file is distributed under the same license as the biomaj package. # Joe Hansen , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-25 17:30+01:00\n" "Last-Translator: Joe Hansen \n" "Language-Team: Danish \n" "Language: da\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Konfigurer MySQL-forbindelsen nu?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Når først MySQL-databasen for BioMAJ er blevet oprettet og konfigureret, så " "kan den befolke sig selv automatisk i stedet for at skulle opdateres manuelt." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Angiv venligst om databaseforbindelsen skal konfigureres nu." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL-server:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Indtast venligst værtsnavnet eller IP-adressen for MySQL-serveren du ønsker " "at bruge." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "MySQL-logind for BioMAJ-database:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Indtast venligst logindet der skal bruges, når der forbindes til MySQL-" "databaseserveren, for at tilgå biomaj_log-databasen." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "MySQL-adgangskode for BioMAJ-databasen:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Indtast venligst adgangskoden der skal bruges, når der forbindes til MySQL-" "databaseserveren, for at tilgå biomaj_log-databasen." debian/po/pl.po0000644000000000000000000000527011712456370010571 0ustar # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # # Michał Kułach , 2012. msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-26 19:18+0100\n" "Last-Translator: Michał Kułach \n" "Language-Team: Polish \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Lokalize 1.2\n" "Plural-Forms: nplurals=3; plural=(n==1 ? 0 : n%10>=2 && n%10<=4 && (n%100<10 " "|| n%100>=20) ? 1 : 2);\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Skonfigurować teraz połączenie z MySQL?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Po skonfigurowaniu bazy danych MySQL do BioMAJ, może być ona uzupełniana " "automatycznie; nie będzie wtedy konieczności ręcznych uaktualnień." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Proszę określić, czy połączenie z bazą danych powinno być teraz " "skonfigurowane." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Serwer MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Proszę wprowadzić nazwę hosta lub adres IP serwera, który ma zostać użyty." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Login MySQL do bazy danych BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Proszę wprowadzić login używany do połączenia z serwerem bazy danych MySQL, " "do dostępu do bazy danych biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Hasło MySQL do bazy danych BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Proszę wprowadzić hasło do połączenia z bazą danych MySQL, do dostępu do " "bazy danych biomaj_log." debian/po/sv.po0000644000000000000000000000534611712456370010612 0ustar # Translation of biomaj debconf template to Swedish # Copyright (C) 2012 Martin Bagge # This file is distributed under the same license as the biomaj package. # # Martin Bagge , 2012 msgid "" msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-26 23:21+0100\n" "Last-Translator: Martin Bagge / brother \n" "Language-Team: Swedish \n" "Language: sv\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Swedish\n" "X-Poedit-Country: Sweden\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Ska inställningar för MySQL-anslutning göras nu?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "När MySQL-databasen för BioMAJ har skapats och inställningarna är klara kan " "den populera sig själv automatisk istället för att uppdateringarna ska göras " "manuellt." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Ange om databasanslutningen ska konfigureras nu." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL-server:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "Ange värdnamn eller IP-adress för MySQL-servern du vill använda." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "MySQL-användarnamn för BioMAJ-databasen:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Ange användarnamnet som ska användas vid anslutning till MySQL-" "databasservern för att komma åt databasen biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "MySQL-lösenord för BioMAJ-databasen:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Ange lösenordet som ska användas vid anslutning till MySQL-databasservern " "för att komma åt databasen biomaj_log." #~ msgid "The JDK home directory:" #~ msgstr "Hemkatalog för JDK:" debian/po/templates.pot0000644000000000000000000000356111712456370012341 0ustar # SOME DESCRIPTIVE TITLE. # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # FIRST AUTHOR , YEAR. # #, fuzzy msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=CHARSET\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" debian/po/pt.po0000644000000000000000000000544711712456370010607 0ustar # Portuguese translation for biomaj debconf's messages # Copyright (C) 2011 THE biomaj'S COPYRIGHT HOLDER # This file is distributed under the same license as the biomaj package. # Pedro Ribeiro , 2011 # Miguel Figueiredo , 2012 # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-2\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-27 19:44+0000\n" "Last-Translator: Miguel Figueiredo \n" "Language-Team: Portuguese \n" "Language: Portuguese\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Configurar a ligação ao MySQL agora?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Assim que a base de dados para o BioMAJ tiver sido criada e configurada, " "pode ser automaticamente preenchida em vez de ter de a actualizar " "manualmente." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Por favor especifique se a ligação à base de dados deve ser configurada " "agora." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Servidor MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Por favor introduza o nome da máquina ou endereço IP do servidor MySQL que " "deseja utilizar." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Login de MySQL para a base de dados BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Por favor introduza o login a utilizar ao ligar ao servidor de bases de " "dados MySQL para aceder à base de dados biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Palavra-passe de MySQL para a base de dados BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Por favor introduza a palavra-passe a utilizar ao ligar ao servidor de bases " "de dados MySQL para aceder à base-de-dados biomaj_log." #~ msgid "The JDK home directory:" #~ msgstr "Directório home do JDK:" debian/po/cs.po0000644000000000000000000000524711712456370010567 0ustar # Czech PO debconf template translation of biomaj. # Copyright (C) 2012 Michal Simunek # This file is distributed under the same license as the biomaj package. # Michal Simunek , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-20 17:31+0100\n" "Last-Translator: Michal Simunek \n" "Language-Team: Czech \n" "Language: cs\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Nastavit nyní připojení k MySQL?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Jakmile byla MySQL databáze pro BioMAJ vytvořena a nastavena, je možné ji, " "namísto nutnosti ruční aktualizace, automaticky naplnit." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Určete prosím, zda se má nyní vytvořit připojení k databázi." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL server:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Zadejte prosím název hostitele nebo IP adresu MySQL serveru, který chcete " "použít." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "MySQL uživatel pro databázi BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Zadejte prosím uživatele, který se má použít při připojování k databázovému " "serveru MySQL při přístupu k databázi biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Heslo MySQL uživatele pro databázi BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Zadejte prosím heslo pro uživatele, které se má použít při připojování k " "databázovému serveru MySQL při přístupu k databázi biomaj_log." debian/po/nl.po0000644000000000000000000000534011710563462010564 0ustar # Dutch translation of biomaj debconf templates. # Copyright (C) 2012 THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the biomaj package. # Jeroen Schot , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-19 14:35+0100\n" "Last-Translator: Jeroen Schot \n" "Language-Team: Debian l10n Dutch \n" "Language: nl\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "De MySQL-verbinding nu instellen?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Zodra de MySQL-database voor BioMAJ is aangemaakt en ingesteld kan deze " "zichzelf automatisch vullen, in plaats van handmatig te moeten worden " "bijwerkt." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Geef aan of de databaseverbinding nu moet worden ingesteld." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL-server:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Wat is de computernaam of het IP-adres van de MySQL-server die u wilt " "gebruiken?" #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "MySQL-login voor de BioMAJ-database:" # Type: password # Description #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Welke loginnaam moet worden gebruikt bij het verbinden met de MySQL-database-" "server om toegang te krijgen tot de database biomaj_log?" # Type: password # Description #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "MySQL-wachtwoord voor de BioMAJ-database:" # Type: password # Description #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Welk wachtwoord moet worden gebruikt bij het verbinden met de MySQL-database-" "server om toegang te krijgen tot de database biomaj_log?" debian/po/POTFILES.in0000644000000000000000000000004411657164770011375 0ustar [type: gettext/rfc822deb] templates debian/po/ru.po0000644000000000000000000000610611712456370010603 0ustar # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the biomaj package. # # Yuri Kozlov , 2011, 2012. msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-16 20:35+0400\n" "Last-Translator: Yuri Kozlov \n" "Language-Team: Russian \n" "Language: ru\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Lokalize 1.0\n" "Plural-Forms: nplurals=3; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && n" "%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2);\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Настроить подключение к MySQL прямо сейчас?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "После того, как база данных MySQL для BioMAJ будет создана и настроена, её " "можно заполнять автоматически, а не вручную." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Укажите, настраивать ли подключение к базе данных прямо сейчас." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Сервер MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Введите имя машины или IP-адрес сервера MySQL, который нужно использовать." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Учётная запись в MySQL для базы данных BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Введите имя пользователя для подключения к базе данных biomaj_log на сервере " "MySQL." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Пароль к учётной записи в MySQL для базы данных BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Введите пароль для подключения к базе данных biomaj_log на сервере MySQL." #~ msgid "The JDK home directory:" #~ msgstr "Домашний каталог JDK:" debian/po/id.po0000644000000000000000000000517511712456370010556 0ustar # SOME DESCRIPTIVE TITLE. # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # FIRST AUTHOR , YEAR. # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-26 19:20+0700\n" "Last-Translator: Mahyuddin Susanto \n" "Language-Team: Debian Indonesia Translator \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Indonesian\n" "X-Poedit-Country: INDONESIA\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Mengatur koneksi MySQL sekarang?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Setelah basisdata MySQL untuk BioMAJ telah dibuat dan diatur, dapat mengisi " "sendirisecara otomatis daripada memperbarui secara manual." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "Silakan tentukan apakah koneksi basisdata akan diatur sekarang." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Server MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Silakan masukkan nama host atau alamat IP dari server MySQL yang akan anda " "gunakan." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Login MySQL untuk basisdata BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Silakan masukkan login yang digunakan untuk koneksi ke server basisdata " "MySQLuntuk mengakses basisdata biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Kata sandi untuk basisdata BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Silakan masukkan kata sandi untuk digunakan ketika koneksi ke server " "basisdata MySQL untuk mengakses basisdata biomaj_log" debian/po/it.po0000644000000000000000000000511511712456370010570 0ustar # Italian translation for biomaj # Copyright (C) 2012 the biomaj copyright holder # This file is distributed under the same license as the biomaj package. # Francesca Ciceri , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-17 20:17+0100\n" "Last-Translator: Francesca Ciceri \n" "Language-Team: Italian \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Si desidera configurare la connessione MySQL adesso?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Una volta creato e configurato, il database MySQL per BioMAJ si popolerà " "automaticamente senza bisogno di aggiornamenti manuali." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Specificare se si desidera configurare adesso la connessione al database." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Server MySQL:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Inserire l'hostname o l'indirizzo IP del server MySQL che si desidera " "utilizzare." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Login MySQL per il database BioMAJ:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Inserire il login da utilizzare quando ci si connette al server del database " "MySQL per accedere al database biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Password MySQL per il database BioMAJ:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Inserire la password da utilizzare quando ci si connette al server del " "database MySQL per accedere al database biomaj_log." debian/po/fr.po0000644000000000000000000000525212006223757010563 0ustar # French translation for biomaj # Copyright (C) 2012 the biomaj copyright holder # This file is distributed under the same license as the biomaj package. # Olivier Sallou , 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 10:16+0100\n" "PO-Revision-Date: 2012-01-18 11:00+0100\n" "Last-Translator: Olivier Sallou \n" "Language-Team: French \n" "Language: fr\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "Souhaitez-vous configurer MySQL maintenant ?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Une fois la base de données pour BioMAJ créée et configurée, il est possible " "de la faire remplir automatiquement plutôt que d'avoir à la peupler vous-" "même." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Veuillez indiquer si vous souhaitez configurer l'accès à la base de données " "maintenant." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "Serveur MySQL :" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Veuillez indiquer le nom ou l'adresse IP du serveur MySQL que vous souhaitez " "utiliser." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "Identifiant de connexion à la base de données de BioMAJ :" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Veuillez indiquer l'identifiant à utiliser pour la connexion au serveur " "MySQL et l'accès à la base biomaj_log." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "Mot de passe de connexion à la base de données de BioMAJ :" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Veuillez indiquer le mot de passe à utiliser pour la connexion au serveur " "MySQL et l'accès à la base biomaj_log." debian/po/de.po0000644000000000000000000000544411712456370010551 0ustar # German translation of biomaj. # Copyright 2011 Olivier Sallou. # This file is distributed under the same license as the biomaj package. # Translation by Chris Leick , 2011, 2012. # msgid "" msgstr "" "Project-Id-Version: biomaj 1.2.0-4\n" "Report-Msgid-Bugs-To: biomaj@packages.debian.org\n" "POT-Creation-Date: 2012-01-16 07:17+0100\n" "PO-Revision-Date: 2012-01-18 10:09+0100\n" "Last-Translator: Chris Leick \n" "Language-Team: German \n" "Language: de\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" #. Type: boolean #. Description #: ../templates:2001 msgid "Configure MySQL connection now?" msgstr "MySQL-Verbindung jetzt konfigurieren?" #. Type: boolean #. Description #: ../templates:2001 msgid "" "Once the MySQL database for BioMAJ has been created and configured, it can " "populate itself automatically instead of needing to be updated manually." msgstr "" "Sobald die MySQL-Datenbank für BioMAJ erstellt und konfiguriert wurde, kann " "Sie selbstständig automatisch befüllt werden, ohne dass eine manuelle " "Aktualisierung notwendig wird." #. Type: boolean #. Description #: ../templates:2001 msgid "" "Please specify whether the database connection should be configured now." msgstr "" "Bitte geben Sie an, ob die Datenbankverbindung jetzt konfiguriert werden " "soll." #. Type: string #. Description #: ../templates:3001 msgid "MySQL server:" msgstr "MySQL-Server:" #. Type: string #. Description #: ../templates:3001 msgid "" "Please enter the hostname or IP address of the MySQL server you want to use." msgstr "" "Bitte geben Sie den Rechnernamen oder die IP-Adresse des MySQL-Servers an, " "den Sie verwenden wollen." #. Type: string #. Description #: ../templates:4001 msgid "MySQL login for BioMAJ database:" msgstr "MySQL-Anmeldename für BioMAJ-Datenbank:" #. Type: string #. Description #: ../templates:4001 msgid "" "Please enter the login to use when connecting to the MySQL database server " "to access the biomaj_log database." msgstr "" "Bitte geben Sie den Anmeldenamen an, der benutzt wird, wenn die Verbindung " "mit dem MySQL-Datenbankserver hergestellt wird, um auf die Datenbank " "»biomaj_log« zuzugreifen." #. Type: password #. Description #: ../templates:5001 msgid "MySQL password for BioMAJ database:" msgstr "MySQL-Passwort für BioMAJ-Datenbank:" #. Type: password #. Description #: ../templates:5001 msgid "" "Please enter the password to use when connecting to the MySQL database " "server to access the biomaj_log database." msgstr "" "Bitte geben Sie das Passwort an, das benutzt wird, wenn die Verbindung mit " "dem MySQL-Datenbankserver hergestellt wird, um auf die Datenbank " "»biomaj_log« zuzugreifen." debian/compat0000644000000000000000000000000211657164770010402 0ustar 7 debian/README.source0000644000000000000000000000076411657164770011372 0ustar Biomaj configuration file has been adapted to Debian file structure. The script debian/get-orig-source downloads biomaj source code and builds the orig.tar.gz tarball. Biomaj makes use of the Apache commons-cli2 library. As project is not maintained anymore, it includes the source code of the library and compile the library in biomaj package. Next version expects to remove this dependency to make use of commons-cli. -- Olivier Sallou Wed, 05 Jan 2011 10:39:00 +0100 debian/watch0000644000000000000000000000016011657164770010232 0ustar version=3 http://biomaj.gforge.inria.fr/download.php .*/biomaj_(\d[\d.-]+)\.orig.(?:tar(?:\.gz|\.bz2)?|tgz|zip) debian/biomaj.lintian-overrides0000644000000000000000000000013212146131107013777 0ustar biomaj binary: non-standard-file-perm usr/share/biomaj/global.properties.tpl 0600 != 0644 debian/links0000644000000000000000000000006611657164770010251 0ustar etc/biomaj/general.conf usr/share/biomaj/general.conf debian/biomaj.manpages0000644000000000000000000000003611657164770012161 0ustar usr/share/doc/biomaj/biomaj.1 debian/biomaj-properties.install0000644000000000000000000000005011657164770014222 0ustar usr/share/biomaj/examples/db_properties debian/postrm0000644000000000000000000000140412146131107010430 0ustar #!/bin/sh set -e # Source debconf library. . /usr/share/debconf/confmodule case "$1" in purge) # Remove generated data and migration info if [ -e /var/lib/biomaj ]; then rm -rf /var/lib/biomaj fi # Remove all if [ -e /usr/share/biomaj ]; then rm -rf /usr/share/biomaj fi # Remove generated conf file rm -f /etc/biomaj/db_properties/global.properties echo "Warning, BioMAJ database for MySQL is not deleted by process removal." ;; remove|upgrade|failed-upgrade|abort-install|disappear) echo "Warning, BioMAJ database for MySQL is not deleted by process removal." ;; abort-upgrade) ;; *) echo "postrm called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# debian/patches/0000755000000000000000000000000012246070047010617 5ustar debian/patches/set_env_file_for_debian0000644000000000000000000000161212146131107015346 0ustar Subject: Prevent shipped file modification Description: Program updates a shipped file at install and upgrades. Patch sets the file once and prevent program update. Forwarded: not-needed Author: Olivier Sallou Last-Updated: 2012-10-04 Bug: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=688433 --- a/usr/share/biomaj/bin/Configurator.java +++ b/usr/share/biomaj/bin/Configurator.java @@ -117,7 +117,7 @@ /* * Creer env.sh */ - createEnv(params.get("ant_home"), params.get("java_home")); + //createEnv(params.get("ant_home"), params.get("java_home")); log("Configuration complete"); --- a/usr/share/biomaj/bin/env.sh +++ b/usr/share/biomaj/bin/env.sh @@ -1 +1,4 @@ -#!/bin/sh \ No newline at end of file +#!/bin/sh +export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:bin/javac::") +export ANT_HOME=/usr/share/ant +export BIOMAJ_ROOT=/usr/share/biomaj debian/patches/series0000644000000000000000000000011312211552346012026 0ustar removeSqlToolDependency set_env_file_for_debian useFormSpecs_from_jgoodies debian/patches/fix623558_remove_pid0000644000000000000000000000200311657164767014253 0ustar From: Anthony Boureux Applied-Upstream: 1.2 Last-Update: 2011-04-25 --- a/usr/share/biomaj/bin/biomaj.sh +++ b/usr/share/biomaj/bin/biomaj.sh @@ -91,21 +91,6 @@ fi done } -# creates one file per bank that contains the pid of this process -create_pid() -{ - ok="false"; - for arg in $@; do - regex=`echo $arg | egrep '^\-+[[:alnum:]]+'` - if [ $arg = "--update" ] || [ $arg = "-d" ]; then - ok="true" - elif [ -z $regex ] && [ $ok = "true" ]; then - echo $$>$BIOMAJ_ROOT/tmp/.bmajpid_$arg - elif [ -w $regex ] && [ $ok = "true" ]; then - ok="false" - fi - done -} #echo "Loading variables environment" SCRIPT_PATH="${BASH_SOURCE[0]}"; @@ -129,7 +114,6 @@ #echo "Verifying Pre-requisists" test_ant_version test_java_version -create_pid $@ #echo "Executing biomaj ..." debian/patches/useFormSpecs_from_jgoodies0000644000000000000000000001057112146133725016074 0ustar Subject: replace FormFactory by FormSpecs Description: jgoodies-form >1.3 has changed its API, changed FormFactory to FormSpecs Author: Olivier Sallou Last-Updated: 2013-05-19 Forwarded: No --- a/usr/share/biomaj/src/org/inria/biomaj/exe/options/BioMAJLogger.java +++ b/usr/share/biomaj/src/org/inria/biomaj/exe/options/BioMAJLogger.java @@ -714,12 +714,12 @@ setLayout(new FormLayout( ColumnSpec.decodeSpecs("default:grow"), new RowSpec[] { - FormFactory.DEFAULT_ROWSPEC, - FormFactory.LINE_GAP_ROWSPEC, - FormFactory.DEFAULT_ROWSPEC, - FormFactory.LINE_GAP_ROWSPEC, - FormFactory.DEFAULT_ROWSPEC, - FormFactory.LINE_GAP_ROWSPEC, + FormSpecs.DEFAULT_ROWSPEC, + FormSpecs.LINE_GAP_ROWSPEC, + FormSpecs.DEFAULT_ROWSPEC, + FormSpecs.LINE_GAP_ROWSPEC, + FormSpecs.DEFAULT_ROWSPEC, + FormSpecs.LINE_GAP_ROWSPEC, new RowSpec(RowSpec.CENTER, Sizes.dluY(171), FormSpec.DEFAULT_GROW) })); @@ -732,25 +732,25 @@ panel1.setLayout(new FormLayout( new ColumnSpec[] { new ColumnSpec(Sizes.dluX(64)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(203)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(19)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(44)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(75)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(57)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(87)) }, new RowSpec[] { - FormFactory.DEFAULT_ROWSPEC, - FormFactory.LINE_GAP_ROWSPEC, - FormFactory.DEFAULT_ROWSPEC, - FormFactory.LINE_GAP_ROWSPEC, - FormFactory.DEFAULT_ROWSPEC + FormSpecs.DEFAULT_ROWSPEC, + FormSpecs.LINE_GAP_ROWSPEC, + FormSpecs.DEFAULT_ROWSPEC, + FormSpecs.LINE_GAP_ROWSPEC, + FormSpecs.DEFAULT_ROWSPEC })); //---- label13 ---- @@ -912,11 +912,11 @@ panel2.setLayout(new FormLayout( new ColumnSpec[] { new ColumnSpec(Sizes.dluX(64)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(198)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, - FormFactory.DEFAULT_COLSPEC, - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.DEFAULT_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(195)) }, RowSpec.decodeSpecs("default, default, default, default, default"))); @@ -976,19 +976,19 @@ panel3.setLayout(new FormLayout( new ColumnSpec[] { new ColumnSpec(Sizes.dluX(66)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(197)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(50)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(34)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(44)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(30)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(42)), - FormFactory.LABEL_COMPONENT_GAP_COLSPEC, + FormSpecs.LABEL_COMPONENT_GAP_COLSPEC, new ColumnSpec(Sizes.dluX(43)) }, RowSpec.decodeSpecs("default"))); debian/patches/removeSqlToolDependency0000644000000000000000000002541311657164767015403 0ustar Author: Olivier Sallou Subject: remove usage of hsqld2 Description: remote sqltool references, not used in debian packaging as hsqldb2 is not packaged. Last-Update: 2011-08 --- a/usr/share/biomaj/src/org/inria/biomaj/exe/migration/CoreMigrationFrom1_1To1_2.java +++ b/usr/share/biomaj/src/org/inria/biomaj/exe/migration/CoreMigrationFrom1_1To1_2.java @@ -14,8 +14,8 @@ import java.util.List; import java.util.UUID; -import org.hsqldb.cmdline.SqlFile; -import org.hsqldb.cmdline.SqlToolError; +//import org.hsqldb.cmdline.SqlFile; +//import org.hsqldb.cmdline.SqlToolError; import org.inria.biomaj.singleton.BiomajInformation; import org.inria.biomaj.sql.SQLConnection; import org.inria.biomaj.sql.SQLConnectionFactory; @@ -210,19 +210,6 @@ } private static void createNewHSQLTables(Statement stat) { - File file = new File(biomajRoot + "/sql/hsql-to_1.2.sql"); - try { - SqlFile sqlFile = new SqlFile(file); - sqlFile.setConnection(stat.getConnection()); - - sqlFile.execute(); - } catch (IOException e) { - e.printStackTrace(); - } catch (SQLException e) { - e.printStackTrace(); - } catch (SqlToolError e) { - e.printStackTrace(); - } } private static boolean createNewMySQLTables(SQLConnection connection, Statement stat) { --- a/usr/share/biomaj/src/org/inria/biomaj/sql/HSQLDBConnection.java +++ b/usr/share/biomaj/src/org/inria/biomaj/sql/HSQLDBConnection.java @@ -21,8 +21,6 @@ import java.util.UUID; import org.apache.commons.dbcp.BasicDataSource; -import org.hsqldb.cmdline.SqlFile; -import org.hsqldb.cmdline.SqlToolError; import org.inria.biomaj.singleton.BiomajLogger; import org.inria.biomaj.utils.BiomajConst; import org.inria.biomaj.utils.BiomajUtils; @@ -130,156 +128,6 @@ */ @Override public boolean createDB(String adminLogin, String adminPasswd, String adminMail) { - - Statement statement = getStatement(); - try { - - TreeSet versions = new TreeSet(); - File[] filz = new File(dbPath).listFiles(new FilenameFilter() { - - @Override - public boolean accept(File dir, String name) { - return name.startsWith("hsql-to"); - } - }); - - for (File fl : filz) { - versions.add(fl.getName()); // sort versions - } - - List runFiles = new ArrayList(); - Collections.addAll(runFiles, new File(dbPath + "/migration").list()); - - if (!runFiles.contains("hsql.sql")) { // Run all - System.out.println("Run all sql scripts..."); - /* - * Base file - */ - File file = new File(dbPath + "/hsql.sql"); - SqlFile sqlFile = new SqlFile(file); - sqlFile.setConnection(statement.getConnection()); - - sqlFile.execute(); - - System.out.println("hsql.sql run."); - writeFileVersion("hsql.sql"); - - /* - * New versions - */ - for (String name : versions) { - File nf = new File(dbPath + "/" + name); - sqlFile = new SqlFile(nf); - sqlFile.setConnection(statement.getConnection()); - sqlFile.execute(); - - System.out.println(name + " run."); - writeFileVersion(name); - } - - } else { - System.out.println("Run new sql scripts..."); - /* - * New versions only - */ - for (String name : versions) { - if (!runFiles.contains(name)) { - File file = new File(dbPath + "/" + name); - SqlFile sqlFile = new SqlFile(file); - sqlFile.setConnection(statement.getConnection()); - - sqlFile.execute(); - - System.out.println(name + " run."); - writeFileVersion(name); - } - } - } - - /* - * Insert admin records - */ - - // Generates admin auth_key - String key = UUID.randomUUID().toString(); - String hash = ""; - - // Generates password hash - MessageDigest digest; - try { - digest = MessageDigest.getInstance("SHA1"); - digest.update(adminPasswd.getBytes()); - byte[] hashedPasswd = digest.digest(); - hash = BiomajUtils.getHexString(hashedPasswd); - } catch (NoSuchAlgorithmException e) { - e.printStackTrace(); - } - - String testUser = "SELECT * FROM bw_user WHERE login='" + adminLogin + "'"; - ResultSet rs = executeQuery(testUser, statement); - if (!rs.next()) { - - String insertUser = "INSERT INTO bw_user(login, password, auth_type, auth_key, mail_address) " + - "VALUES('" + adminLogin + "','" + hash + "','local','" + key + "','" + adminMail + "')"; - int userId = executeUpdateAndGetGeneratedKey(insertUser, statement); - - String testGroup = "SELECT idgroup FROM bw_group WHERE name='admin'"; - rs = executeQuery(testGroup, statement); - int groupId; - if (rs.next()) { - System.out.println("Adding " + adminLogin + " to current admin group"); - groupId = rs.getInt(1); - } else { - String createGroup = "INSERT INTO bw_group(name) VALUES('admin')"; - groupId = executeUpdateAndGetGeneratedKey(createGroup, statement); - } - - String userToGroup = "INSERT INTO bw_user_has_group(ref_iduser, ref_idgroup) VALUES(" + userId + "," + groupId + ")"; - executeUpdate(userToGroup, statement); - - - boolean updated = false; - try { - String testTable = "SELECT visibility FROM bank"; - statement.executeQuery(testTable); - updated = true; // No error, column already added - } catch (SQLException e) { - updated = false; - } - - if (!updated) { // Not yet updated - - String hsql_addColumnToBank = "ALTER TABLE bank ADD COLUMN ref_iduser INT DEFAULT " + userId; - executeUpdate(hsql_addColumnToBank, statement); - - hsql_addColumnToBank = "ALTER TABLE bank ADD COLUMN visibility BOOLEAN DEFAULT false"; - executeUpdate(hsql_addColumnToBank, statement); - - String hsql_addConstraint = "ALTER TABLE bank ADD CONSTRAINT fk_bank_to_user FOREIGN KEY (ref_iduser) REFERENCES bw_user(iduser)"; - executeUpdate(hsql_addConstraint, statement); - } - - } else { - System.err.println("User " + adminLogin + " already exists"); - } - - - - SQLConnectionFactory.closeConnection(statement); -// statement.executeBatch(); - } catch (SQLException e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } catch (IOException e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } catch (SqlToolError e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } return true; } --- a/usr/share/biomaj/src/org/inria/biomaj/sql/TestConnection.java +++ b/usr/share/biomaj/src/org/inria/biomaj/sql/TestConnection.java @@ -16,8 +16,6 @@ import java.util.UUID; import org.apache.commons.dbcp.BasicDataSource; -import org.hsqldb.cmdline.SqlFile; -import org.hsqldb.cmdline.SqlToolError; import org.inria.biomaj.singleton.BiomajLogger; import org.inria.biomaj.utils.BiomajUtils; @@ -60,132 +58,6 @@ */ @Override public boolean createDB(String adminLogin, String adminPasswd, String adminMail) { - - Statement statement = getStatement(); - try { - - TreeSet versions = new TreeSet(); - File[] filz = new File(dbPath).listFiles(new FilenameFilter() { - - @Override - public boolean accept(File dir, String name) { - return name.startsWith("hsql-to"); - } - }); - - for (File fl : filz) { - versions.add(fl.getName()); // sort versions - } - - - /* - * Base file - */ - File file = new File(dbPath + "/hsql.sql"); - SqlFile sqlFile = new SqlFile(file); - sqlFile.setConnection(statement.getConnection()); - - sqlFile.execute(); - - System.out.println("hsql.sql run."); - - /* - * New versions - */ - for (String name : versions) { - File nf = new File(dbPath + "/" + name); - sqlFile = new SqlFile(nf); - sqlFile.setConnection(statement.getConnection()); - sqlFile.execute(); - - System.out.println(name + " run."); - } - - - - /* - * Insert admin records - */ - - // Generates admin auth_key - String key = UUID.randomUUID().toString(); - String hash = ""; - - // Generates password hash - MessageDigest digest; - try { - digest = MessageDigest.getInstance("SHA1"); - digest.update(adminPasswd.getBytes()); - byte[] hashedPasswd = digest.digest(); - hash = BiomajUtils.getHexString(hashedPasswd); - } catch (NoSuchAlgorithmException e) { - e.printStackTrace(); - } - - String testUser = "SELECT * FROM bw_user WHERE login='" + adminLogin + "'"; - ResultSet rs = executeQuery(testUser, statement); - if (!rs.next()) { - - String insertUser = "INSERT INTO bw_user(login, password, auth_type, auth_key, mail_address) " + - "VALUES('" + adminLogin + "','" + hash + "','local','" + key + "','" + adminMail + "')"; - int userId = executeUpdateAndGetGeneratedKey(insertUser, statement); - - String testGroup = "SELECT idgroup FROM bw_group WHERE name='admin'"; - rs = executeQuery(testGroup, statement); - int groupId; - if (rs.next()) { - System.out.println("Adding " + adminLogin + " to current admin group"); - groupId = rs.getInt(1); - } else { - String createGroup = "INSERT INTO bw_group(name) VALUES('admin')"; - groupId = executeUpdateAndGetGeneratedKey(createGroup, statement); - } - - String userToGroup = "INSERT INTO bw_user_has_group(ref_iduser, ref_idgroup) VALUES(" + userId + "," + groupId + ")"; - executeUpdate(userToGroup, statement); - - boolean updated = false; - try { - String testTable = "SELECT visibility FROM bank"; - statement.executeQuery(testTable); - updated = true; // No error, column already added - } catch (SQLException e) { - updated = false; - } - - if (!updated) { // Not yet updated - - String hsql_addColumnToBank = "ALTER TABLE bank ADD COLUMN ref_iduser INT DEFAULT " + userId; - executeUpdate(hsql_addColumnToBank, statement); - - hsql_addColumnToBank = "ALTER TABLE bank ADD COLUMN visibility BOOLEAN DEFAULT false"; - executeUpdate(hsql_addColumnToBank, statement); - - String hsql_addConstraint = "ALTER TABLE bank ADD CONSTRAINT fk_bank_to_user FOREIGN KEY (ref_iduser) REFERENCES bw_user(iduser)"; - executeUpdate(hsql_addConstraint, statement); - } - - } else { - System.err.println("User " + adminLogin + " already exists"); - } - - - - SQLConnectionFactory.closeConnection(statement); -// statement.executeBatch(); - } catch (SQLException e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } catch (IOException e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } catch (SqlToolError e) { - SQLConnectionFactory.closeConnection(statement); - e.printStackTrace(); - return false; - } return true; } debian/postinst0000755000000000000000000000300612211552544010777 0ustar #!/bin/sh set -e # Source debconf library. . /usr/share/debconf/confmodule case "$1" in configure) ant_home="/usr/share/ant" biomaj_root="/usr/share/biomaj" jdk_home=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::") db_type="MySQL" db_get biomaj/mysql_host db_host="$RET" db_url="jdbc:mysql://$RET/biomaj_log" db_get biomaj/mysql_login db_login="$RET" db_get biomaj/mysql_passwd db_passwd="$RET" tomcat_port="0" cd $biomaj_root if [ ! -e /etc/biomaj/db_properties/global.properties ]; then # If no configuration file exits, create one with template and debconf configuration cp /usr/share/biomaj/global.properties.tpl /etc/biomaj/db_properties/global.properties fi java -cp $biomaj_root/bin Configurator java_home:=$jdk_home ant_home:=$ant_home biomaj_root:=$biomaj_root db_type:=$db_type db_url:=$db_url db_login:=$db_login db_passwd:=$db_passwd if [ ! -e /usr/share/biomaj/sql/migration ]; then ln -s /var/lib/biomaj/migration /usr/share/biomaj/sql/migration fi # Database and scripts install and upgrades if [ "$DEBIAN_FRONTEND" != "noninteractive" ]; then perl /var/lib/biomaj/migration/update.pl -dbuser $db_login -dbpwd $db_passwd -db mysql -dbhost $db_host fi ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# debian/preinst0000644000000000000000000000063611657164770010620 0ustar #!/bin/sh set -e case "$1" in install) ;; upgrade) if [ $2 = "1.1.0-1" ]; then echo "There is an issue in version 1.1.0-1, you need to first remove the package, then to install it. There is no impact on data." exit 1 fi ;; abort-upgrade) ;; *) echo "preinst called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# debian/control0000644000000000000000000000457312246067771010616 0ustar Source: biomaj Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biomaj/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biomaj/trunk/ Homepage: http://biomaj.genouest.org Build-Depends: debhelper (>= 7.1) Build-Depends-Indep: debconf, po-debconf, default-jdk, ant, libhsqldb-java, ant-contrib, liblog4j1.2-java, libcommons-net2-java, libcommons-dbcp-java, libgnumail-java, libcommons-pool-java, libgnujaf-java, libjgoodies-forms-java (>= 1.3), liboro-java, libregexp-java, libjcommon-java, libjsch-java, libjdom1-java, junit4, libsaxonb-java, libjdepend-java, javahelper (>=0.25), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java, libjets3t-java Standards-Version: 3.9.4 Package: biomaj Architecture: all Depends: ${misc:Depends}, ${java:Depends}, default-jre | java6-runtime, ant (>= 1.9.1), libmysql-java, debconf, libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>= 2.2),libcommons-dbcp-java (>= 1.2), libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.3), liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>= 1.0),libjsch-java (>= 0.1.42), libjdom1-java (>= 1.1),junit4,libsaxonb-java (>= 0.9), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, mysql-client Suggests: ncbi-tools-bin, blast2, mysql-server Description: biological data-bank updater BioMAJ downloads remote data banks, checks their status and applies transformation workflows, with consistent state, to provide ready-to-use data for biologists and bioinformaticians. For example, it can transform original FASTA files into BLAST indexes. It is very flexible and its post-processing facilities can be extended very easily. Package: biomaj-properties Architecture: all Depends: ${misc:Depends} Description: biological data-bank updater - example properties files This package contains a set of data bank properties files that can be used as examples for BioMAJ. It contains descriptions for many existing data banks with or without workflows to transform data. Some files may require additional programs (such as BLAST) for post-processing. debian/templates0000755000000000000000000000224711712456371011126 0ustar # These templates have been reviewed by the debian-l10n-english # team # # If modifications/additions/rewording are needed, please ask # debian-l10n-english@lists.debian.org for advice. # # Even minor modifications require translation updates and such # changes should be coordinated with translators and reviewers. Template: biomaj/mysql Type: boolean _Description: Configure MySQL connection now? Once the MySQL database for BioMAJ has been created and configured, it can populate itself automatically instead of needing to be updated manually. . Please specify whether the database connection should be configured now. Template: biomaj/mysql_host Type: string _Description: MySQL server: Please enter the hostname or IP address of the MySQL server you want to use. Template: biomaj/mysql_login Type: string _Description: MySQL login for BioMAJ database: Please enter the login to use when connecting to the MySQL database server to access the biomaj_log database. Template: biomaj/mysql_passwd Type: password _Description: MySQL password for BioMAJ database: Please enter the password to use when connecting to the MySQL database server to access the biomaj_log database. debian/biomaj.install0000644000000000000000000000035312146131107012014 0ustar usr/share/biomaj/sql usr/share/biomaj/bin usr/share/biomaj/conf usr/share/biomaj/workflows usr/share/biomaj/lib usr/share/doc/biomaj var/lib/biomaj var/log/biomaj etc/biomaj usr/bin usr/share/biomaj/console_help.txt usr/share/biomaj/ debian/rules0000755000000000000000000000207312146131107010244 0ustar #!/usr/bin/make -f # debian/rules for biomaj # Author: Olivier Sallou # License: CeCILL # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # This has to be exported to make some magic below work. export DH_OPTIONS export ANT_HOME=/usr/share/ant export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::") %: dh $@ --with javahelper override_dh_auto_build: echo ${JAVA_HOME} ant -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 -f usr/share/biomaj/build.xml javac -source 1.5 -target 1.5 -d usr/share/biomaj/bin usr/share/biomaj/bin/Configurator.java override_dh_install: dh_install mv debian/biomaj/etc/biomaj/db_properties/global.properties debian/biomaj/usr/share/biomaj/global.properties.tpl override_dh_clean: dh_clean rm -rf usr/share/biomaj/build rm -rf usr/share/biomaj/dist rm -f usr/share/biomaj/lib/biomaj.jar rm -f usr/share/biomaj/bin/*.class override_dh_fixperms: dh_fixperms chmod 600 debian/biomaj/usr/share/biomaj/global.properties.tpl chmod 644 debian/biomaj/usr/share/biomaj/sql/*.sql debian/biomaj.doc-base0000644000000000000000000000033011657164770012040 0ustar Document: biomaj Title: BioMAJ User Manual Author: Romaric Sabas Abstract: Usage instructions for BioMAJ and BMajWatcher Section: Science/Biology Format: PDF Files: /usr/share/doc/biomaj/UsersGuide_BioMAJ_EN.pdf.gz debian/upstream0000644000000000000000000000135212006223757010756 0ustar Homepage: http://biomaj.genouest.org Reference: Author: Olivier Filangi and Yoann Beausse and Anthony Assi and Ludovic Legrand and Jean-Marc Larré and Véronique Martin and Olivier Collin and Christophe Caron and Hugues Leroy and David Allouche Title: > BioMAJ: a flexible framework for databanks synchronization and processing Journal: Oxford Journals Bioinformatics Year: 2008 Volume: 24 Number: 16 Pages: 1823-1825 PMID: 18593718 DOI: 10.1093/bioinformatics/btn325 URL: http://bioinformatics.oxfordjournals.org/content/24/16/1823.abstract eprint: http://bioinformatics.oxfordjournals.org/content/24/16/1823.full.pdf+html Repository: https://gforge.inria.fr/scm/?group_id=369 Screenshots: http://biomaj.genouest.org/?page_id=449 debian/prerm0000644000000000000000000000133711657164770010260 0ustar #!/bin/sh set -e # Source debconf library. . /usr/share/debconf/confmodule case "$1" in upgrade) ;; remove|deconfigure) # Remove post installation created files # Remove admin credentials if [ -e /usr/share/biomaj/.bmajwatcherpasswd ]; then rm /usr/share/biomaj/.bmajwatcherpasswd fi # Installation logs if [ -e /usr/share/biomaj/install_log.log ]; then rm /usr/share/biomaj/install_log.log fi # Configurator if [ -e /usr/share/biomaj/bin/Configurator.class ]; then rm /usr/share/biomaj/bin/Configurator.class fi ;; failed-upgrade) ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# debian/changelog0000644000000000000000000001446312246067720011056 0ustar biomaj (1.2.3-3) unstable; urgency=low * d/control: remove dependency on mysql-server but rather set it to mysql-client as server can be remote. -- Olivier Sallou Sun, 10 Nov 2013 09:00:17 +0100 biomaj (1.2.3-2) unstable; urgency=low * d/control: Fix browse url for svn d/config: Fix test for non-interactive mode -- Olivier Sallou Wed, 06 Nov 2013 09:51:55 +0100 biomaj (1.2.3-1) unstable; urgency=low * New upstream release (fixes on local storage and stage option). -- Olivier Sallou Wed, 30 Oct 2013 15:34:34 +0100 biomaj (1.2.2-2) unstable; urgency=low * d/postinst: Fix install in noninteractive mode (Closes: #721773). -- Olivier Sallou Fri, 30 Aug 2013 12:11:50 +0200 biomaj (1.2.2-1) unstable; urgency=low * New upstream release with minor fixes d/patches/series: upstream bug 15914 fixed. -- Olivier Sallou Tue, 18 Jun 2013 14:30:28 +0200 biomaj (1.2.1-3) unstable; urgency=low * Add patch to manage ant properties api change (Closes: #712328). -- Olivier Sallou Tue, 18 Jun 2013 11:39:36 +0200 biomaj (1.2.1-2) unstable; urgency=low * Add patch to match libjgoodies-form-java >1.3, FormFactory replaced by FormSpecs (Closes: #708454) d/control: Depends on libjgoodies-form-java > 1.3 -- Olivier Sallou Sun, 19 May 2013 13:21:55 +0200 biomaj (1.2.1-1) unstable; urgency=low * New usptream release * Add Japanase debconf translation (Closes: #690698) Thanks to victory -- Olivier Sallou Fri, 19 Oct 2012 17:04:19 +0200 biomaj (1.2.0-10) unstable; urgency=low * debian/rules, debian/postinst: fix permissions on properties file. -- Olivier Sallou Thu, 04 Oct 2012 18:34:01 +0200 biomaj (1.2.0-9) unstable; urgency=low * debian/patches/set_env_file_for_debian: Prevent env.sh file update by program at install (Closes: #688433) -- Olivier Sallou Wed, 03 Oct 2012 13:54:44 +0200 biomaj (1.2.0-8) unstable; urgency=low [ Olivier Sallou ] * debian/copyright: Fix copyright URL * debian/control: Switch to Standards 3.9.4 * debian/rules, debian/postinst, debian/postrm: fix conffile update conflicting with Debian Policy (Closes: #688433). -- Olivier Sallou Wed, 01 Aug 2012 15:59:55 +0200 biomaj (1.2.0-7) unstable; urgency=low [ Olivier Sallou ] Patch from James Page (Closes: #683517) * Transition package to use default java implementation: - d/rules: Specify source/target = 1.5 to ensure bytecode is backwards compatible. - d/control: BD on default-jdk only. Switch runtime dependency to default-jre | java6-runtime. -- Olivier Sallou Wed, 01 Aug 2012 14:58:41 +0200 biomaj (1.2.0-6) unstable; urgency=low [ Olivier Sallou ] * Clean files for purge (Closes: #678490). [ Andreas Tille ] * debian/upstream: Enhance upstream information (authors format, missing fields) [Debconf translation updates] * French (Olivier Sallou, proofread by the French l10n team). -- Olivier Sallou Tue, 08 May 2012 22:46:34 +0200 biomaj (1.2.0-5) unstable; urgency=low * Add missing file to package to get the console help (Closes: #658833) - biomaj.install -- Olivier Sallou Wed, 01 Feb 2012 10:00:03 +0100 biomaj (1.2.0-4) unstable; urgency=low * [Olivier Sallou] * config: remove biomaj/jdk_home, not needed anymore * Debconf templates and debian/control reviewed by the debian-l10n- english team as part of the Smith review project. Closes: #653408 * [Debconf translation updates] * Russian (Yuri Kozlov). Closes: #656111 * Italian (Francesca Ciceri). Closes: #656254 * French (Olivier Sallou). Closes: #656066 * Czech (Michal Simunek). Closes: #656670 * Dutch; (Jeroen Schot). Closes: #657009 * German (Chris Leick). Closes: #657024 * Danish (Joe Hansen). Closes: #657341 * Indonesian (Mahyuddin Susanto). Closes: #657463 * Spanish; (Camaleón). Closes: #657491 * Polish (Michał Kułach). Closes: #657512 * Swedish (Martin Bagge / brother). Closes: #657548 * Portuguese (Miguel Figueiredo). Closes: #657664 -- Olivier Sallou Fri, 16 Dec 2011 15:53:10 +0100 biomaj (1.2.0-3) unstable; urgency=low * Add Portuguese translation for debconf (Closes: #651680) - Thanks to Pedro Ribeiro -- Olivier Sallou Fri, 16 Dec 2011 09:25:22 +0100 biomaj (1.2.0-2) unstable; urgency=low * Fix Mysql dependency name. -- Olivier Sallou Fri, 11 Nov 2011 10:25:39 +0100 biomaj (1.2.0-1) unstable; urgency=low * New upstream release with new features and bug fixes. * Change in database model, migration script ran at install * New post processes added in default install (emboss) -- Olivier Sallou Thu, 18 Aug 2011 09:55:23 +0200 biomaj (1.1.0-3) unstable; urgency=low * Change priority in debconf message for jdk home * Add spanish translation of debconf: Thanks to Camaleón Closes: #632952 * Add sweden translation of debconf: Thanks to Martin Bagge Closes: #628927 * Add german translation of debconf: Thanks to Chris Leick Closes: #629455 * Change openjdk dependency to add default-jdk and sun jdk possible depends Closes: #633523 -- Olivier Sallou Thu, 11 Jul 2011 09:55:23 +0200 biomaj (1.1.0-2) unstable; urgency=low * Add russian translation of debconf: Thanks to Yuri Kozlov Closes: #623807 * debian/patches/fix623558_remove_pid: Remove unnecessary pid file creation Closes: #623558 * debian/postrm,debian/preinst: Issue for smooth upgrade, require old package removal then new package install Closes: #624284 -- Olivier Sallou Fri, 22 Apr 2011 16:27:11 +0200 biomaj (1.1.0-1) unstable; urgency=low * Initial release (Closes: #609038) First Debian package, fixed copyright file to list all licenses -- Olivier Sallou Wed, 05 Jan 2011 10:39:00 +0100