October 2016 - Echobase-commits - mailman.cloud.codelutin.com

annotated tag echobase-4.0 created (now f264989)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to annotated tag echobase-4.0 in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git at f264989 (tag) tagging bf4bec08c17d8f9c25cc838ccd224750733cdb10 (commit) replaces echobase-4.0-alpha-7 tagged by Maven Release on Thu Oct 27 17:51:12 2016 +0200 - Log ----------------------------------------------------------------- [jgitflow-maven-plugin]tagging release 4.0 ----------------------------------------------------------------------- No new revisions were added by this update. -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch develop updated (d33fd4a -> 1c34736)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from d33fd4a [jgitflow-maven-plugin]updating poms for 4.1-SNAPSHOT development new 235562e [jgitflow-maven-plugin]updating develop poms to master versions to avoid merge conflicts new 99a4263 Fix license headers new 1fbab04 [jgitflow-maven-plugin]updating poms for branch'release/4.0' with non-snapshot versions new bf4bec0 [jgitflow-maven-plugin]merging 'release/4.0' into 'master' new 0df326d [jgitflow-maven-plugin]merging 'master' into 'develop' new 1c34736 [jgitflow-maven-plugin]Updating develop poms back to pre merge state The 6 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Detailed log of new commits: commit 1c3473601efb1fd861cf4b57263203d436c088ee Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:51:23 2016 +0200 [jgitflow-maven-plugin]Updating develop poms back to pre merge state commit 0df326d7a961d596f89de13cd8e78a090f17986b Merge: 235562e bf4bec0 Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:51:22 2016 +0200 [jgitflow-maven-plugin]merging 'master' into 'develop' commit 235562ef65dd5cceffd13a6b1019e03d2ba5876e Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:51:21 2016 +0200 [jgitflow-maven-plugin]updating develop poms to master versions to avoid merge conflicts commit bf4bec08c17d8f9c25cc838ccd224750733cdb10 Merge: 6f26a64 1fbab04 Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:51:12 2016 +0200 [jgitflow-maven-plugin]merging 'release/4.0' into 'master' commit 1fbab04dae95ef83ef467c0107010493f218e5c3 Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:47:19 2016 +0200 [jgitflow-maven-plugin]updating poms for branch'release/4.0' with non-snapshot versions commit 99a4263a725973d16865d9ecf07c6084baeedf88 Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:47:05 2016 +0200 Fix license headers Summary of changes: .../echobase/entities/references/MissionImpl.java | 21 +++++++++++++++++++++ .../service/atlantos/xml/VocabularyExport.java | 21 +++++++++++++++++++++ 2 files changed, 42 insertions(+) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch release/4.0 updated (4c5074d -> 1fbab04)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch release/4.0 in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 4c5074d #8173 Fix SubsamplingFactor adds 99a4263 Fix license headers adds 1fbab04 [jgitflow-maven-plugin]updating poms for branch'release/4.0' with non-snapshot versions No new revisions were added by this update. Summary of changes: echobase-domain/pom.xml | 2 +- .../echobase/entities/references/MissionImpl.java | 21 +++++++++++++++++++++ echobase-services/pom.xml | 2 +- .../service/atlantos/xml/VocabularyExport.java | 21 +++++++++++++++++++++ echobase-ui/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 46 insertions(+), 4 deletions(-) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch master updated (6f26a64 -> bf4bec0)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch master in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 6f26a64 [jgitflow-maven-plugin]merging 'release/4.0-alpha-7' into 'master' adds a175b26 Update docuementation adds ab7c146 [jgitflow-maven-plugin]updating develop poms to master versions to avoid merge conflicts adds bd56f3d [jgitflow-maven-plugin]merging 'master' into 'develop' adds 4f7be5d [jgitflow-maven-plugin]Updating develop poms back to pre merge state adds fe76025 Merge branch 'develop' of gitlab.nuiton.org:codelutin/echobase into develop adds 66fc6f0 Fix function for spacial data for mooring adds eaffa46 ref #8007, create double legend for pelagic trawl catch adds c7d4927 ref #8173, create the first basic export for the cruise adds 7478779 ref #8173, continue export models adds 5699c79 ref #8173, continue export models adds 526aa06 ref #8173, create all data structures adds a7f7032 ref #8173, plug export with concatenation adds 828df0a ref #8173, begin export to xml instead of csv adds eddc84e ref #8173, add export biotic adds cdf5d7a Complete acoustic xml export adds 20110c7 Add missing for atlantos export adds c584b14 #8669 Fix conversion for the pagination adds 6b64d24 #8173 Add vocabulary table adds afab4f6 Export biotic export for atlantos adds 85315cc Handle vocabulary in xml adds 1a3f794 Concat files adds f25dc92 Translate adds dcb135a Modify redirection after create mission adds 735993d Put the length to mm adds b1253ac Complete doc for GearCharacteristicValues adds 36198f0 Fix unit tests adds 1d11422 Export altantos on a vessel adds e71351b Fix dependency adds f63aac7 Create UI for atlantos export adds 52303b8 Complete i18n adds de0f765 Complete i18n adds 8d1d613 #8677 Force refresh import file adds 0498112 Add translates adds 791d7a8 Add translates adds 05fb0af Migrate databases for tests adds 4c5074d #8173 Fix SubsamplingFactor adds 99a4263 Fix license headers adds 1fbab04 [jgitflow-maven-plugin]updating poms for branch'release/4.0' with non-snapshot versions adds bf4bec0 [jgitflow-maven-plugin]merging 'release/4.0' into 'master' No new revisions were added by this update. Summary of changes: echobase-domain/pom.xml | 2 +- .../ifremer/echobase/entities/data/VoyageImpl.java | 6 +- .../references/MissionImpl.java} | 23 +- .../echobase/persistence/EchoBaseDbMeta.java | 4 +- ...WorkingDbMigrationCallBackForVersion3_910.java} | 12 +- ...WorkingDbMigrationCallBackForVersion3_911.java} | 9 +- .../workingDb/h2/3.905-0-update-model.sql | 4 - .../workingDb/h2/3.905-2-migrate-voyage-ports.sql | 3 - .../migration/workingDb/h2/3.911-0-atlantos.sql | 57 +++ .../workingDb/pg/3.905-0-update-model.sql | 4 - .../workingDb/pg/3.905-2-migrate-voyage-ports.sql | 3 - .../workingDb/pg/3.910-0-update-procedure.sql | 187 ++++++++++ .../migration/workingDb/pg/3.911-0-atlantos.sql | 57 +++ .../src/main/resources/postgis-structure.sql | 8 +- echobase-domain/src/main/xmi/echobase.properties | 2 +- echobase-domain/src/main/xmi/echobase.zargo | Bin 99798 -> 100339 bytes echobase-services/pom.xml | 2 +- .../echobase/services/csv/EchoBaseCsvUtil.java | 4 + .../services/service/DecoratorService.java | 4 + .../services/service/UserDbPersistenceService.java | 33 +- .../echobase/services/service/UserService.java | 2 +- .../ExportAtlantosConfiguration.java} | 72 ++-- .../service/atlantos/ExportAtlantosService.java | 157 ++++++++ .../service/atlantos/xml/VocabularyExport.java | 144 ++++++++ .../service/atlantos/xml/XmlAccousticExport.java | 411 +++++++++++++++++++++ .../service/atlantos/xml/XmlBioticExport.java | 388 +++++++++++++++++++ .../services/service/atlantos/xml/XmlWriter.java | 98 +++++ .../actions/ImportAcousticsActionSupport.java | 8 +- .../actions/ImportDataActionSupport.java | 2 +- .../ImportAcousticsConfiguration.java | 30 ++ .../gis/templates/EchoBaseLizmapTemplate.qgs.cfg | 2 +- .../gis/templates/EchoBaseQGisTemplate.qgs | 159 ++++++-- .../echobase/services/ImportDataFixtures.java | 11 + .../services/MigrateImportDataDatabasesIT.java | 6 + .../atlantos/ExportAtlantosServiceTest.java | 63 ++++ .../resources/echobase-importDb-referentiel.zip | Bin 50514 -> 51131 bytes .../import-data/echobase-atlantos.h2.db.gz | Bin 0 -> 1234109 bytes .../echobase-catches-and-voyage-result.h2.db.gz | Bin 991130 -> 998860 bytes .../import-data/echobase-catches.h2.db.gz | Bin 924955 -> 932467 bytes .../import-data/echobase-commonData.h2.db.gz | Bin 370149 -> 373494 bytes .../import-data/echobase-mooring-results.h2.db.gz | Bin 930474 -> 937442 bytes .../import-data/echobase-mooring.h2.db.gz | Bin 925371 -> 932719 bytes .../resources/import-data/echobase-nodata.h2.db.gz | Bin 318631 -> 326412 bytes .../echobase-operation-total-samples.h2.db.gz | Bin 785190 -> 793954 bytes .../import-data/echobase-operation.h2.db.gz | Bin 508067 -> 515535 bytes echobase-ui/pom.xml | 2 +- .../{exportDb => exportAtlantos}/Configure.java | 76 ++-- .../{exportCoser => exportAtlantos}/Download.java | 14 +- .../{exportDb => exportAtlantos}/Export.java | 41 +- .../actions/importData/AbstractLaunchImport.java | 9 +- ...ruts-exportDb.xml => struts-exportAtlantos.xml} | 26 +- .../main/resources/config/struts-importData.xml | 2 +- .../resources/i18n/echobase-ui_en_GB.properties | 18 +- .../resources/i18n/echobase-ui_fr_FR.properties | 22 +- echobase-ui/src/main/resources/struts.xml | 1 + echobase-ui/src/main/webapp/WEB-INF/decorators.xml | 1 + .../src/main/webapp/WEB-INF/includes/header.jsp | 9 +- .../configure.jsp} | 40 +- .../{exportCoser => exportAtlantos}/progress.jsp | 4 +- .../jsp/{exportCoser => exportAtlantos}/result.jsp | 6 +- .../jsp/importData/configureAcousticImport.jsp | 12 + .../importData/configureMooringAcousticImport.jsp | 12 + .../WEB-INF/jsp/importData/createMission.jsp | 3 + pom.xml | 2 +- src/site/en/rst/importData.rst | 86 +++-- src/site/rst/importData.rst | 74 +++- 66 files changed, 2148 insertions(+), 289 deletions(-) copy echobase-domain/src/main/java/fr/ifremer/echobase/{I18nAble.java => entities/references/MissionImpl.java} (69%) copy echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/{WorkingDbMigrationCallBackForVersion3_906.java => WorkingDbMigrationCallBackForVersion3_910.java} (84%) copy echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/{WorkingDbMigrationCallBackForVersion3_906.java => WorkingDbMigrationCallBackForVersion3_911.java} (88%) create mode 100644 echobase-domain/src/main/resources/migration/workingDb/h2/3.911-0-atlantos.sql create mode 100644 echobase-domain/src/main/resources/migration/workingDb/pg/3.910-0-update-procedure.sql create mode 100644 echobase-domain/src/main/resources/migration/workingDb/pg/3.911-0-atlantos.sql copy echobase-services/src/main/java/fr/ifremer/echobase/services/service/{exportdb/ExportDbConfiguration.java => atlantos/ExportAtlantosConfiguration.java} (55%) create mode 100644 echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/ExportAtlantosService.java create mode 100644 echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/VocabularyExport.java create mode 100644 echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlAccousticExport.java create mode 100644 echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlBioticExport.java create mode 100644 echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlWriter.java create mode 100644 echobase-services/src/test/java/fr/ifremer/echobase/services/service/atlantos/ExportAtlantosServiceTest.java create mode 100644 echobase-services/src/test/resources/import-data/echobase-atlantos.h2.db.gz copy echobase-ui/src/main/java/fr/ifremer/echobase/ui/actions/{exportDb => exportAtlantos}/Configure.java (51%) copy echobase-ui/src/main/java/fr/ifremer/echobase/ui/actions/{exportCoser => exportAtlantos}/Download.java (84%) copy echobase-ui/src/main/java/fr/ifremer/echobase/ui/actions/{exportDb => exportAtlantos}/Export.java (58%) copy echobase-ui/src/main/resources/config/{struts-exportDb.xml => struts-exportAtlantos.xml} (68%) copy echobase-ui/src/main/webapp/WEB-INF/jsp/{importData/configureMooringCommonsImport.jsp => exportAtlantos/configure.jsp} (54%) copy echobase-ui/src/main/webapp/WEB-INF/jsp/{exportCoser => exportAtlantos}/progress.jsp (91%) copy echobase-ui/src/main/webapp/WEB-INF/jsp/{exportCoser => exportAtlantos}/result.jsp (86%) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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[ANN] - EchoBase 4.0 released
by codelutin.com Release Notification Oct. 27, 2016

Oct. 27, 2016

The EchoBase team is pleased to announce the echobase-4.0 release! The French Institute for the Exploitation of the Sea (Ifremer) has designed an open software suite for storing fisheries acoustic data and computing acoustic indicators for survey-based ecosystem monitoring. It comprises a postgreSQL database designed to store acoustic, navigation and fishing data from ecosystemic surveys (EchoBase) and a suite of R codes (EchoR) for computing fish population indicators based on Echobase data. Documentation of the project can be found here: http://echobase.codelutin.com Changes ------- Changes in this version include: New features: o Export au format Atlantos Issue: 8173. Resolved by jruchaud. o Valider les imports au format Coser Issue: 8174. Resolved by jruchaud. o Bloquer les imports si des doublons sont détectés Issue: 2246. Thanks to Mathieu Doray. Resolved by jruchaud. Fixed Bugs: o Les utilisateurs n'apparaissent plus dans le menu gestion des utilisateurs Issue: 8669. Thanks to Mathieu Doray. Resolved by jruchaud. o Ajouter champ dans menu import données acoustiques pour saisir le "softwareName" et "processingSoftwareVersion" de la table dataprocessing Issue: 8667. Thanks to Mathieu Doray. Resolved by jruchaud. o Après avoir créé une mission, on arrive sur un menu d'import de données V/T/T : pas approprié pour bouées Issue: 8676. Thanks to Mathieu Doray. Resolved by jruchaud. o Modifications liées à compatibilité mission/voyage avec base CIEM Issue: 8668. Thanks to Mathieu Doray. Resolved by jruchaud. o Mettre dans la doc en ligne le format du fichier d'import des caractéristiques d'engins Issue: 8680. Thanks to Mathieu Doray. Resolved by jruchaud. o Traductions manquantes Issue: 8681. Thanks to Mathieu Doray. Resolved by jruchaud. o Ajout d'une colonne "wormsCode" dans la table de référence "Species" Issue: 8682. Thanks to Mathieu Doray. Resolved by jruchaud. o Plantage quand export d'un fichier d'export (ex check-PELGAS2015_Voyage4Echobase.csv) dans tableau de bord Issue: 8677. Thanks to Mathieu Doray. Resolved by jruchaud. o A l'import du voyage, EB va cherche le compare la valeur du champ "startPort" du fichier d'import avec le champ "code" de la table 'port', alors qu'il faudrait la comparer avec le champ "name" Issue: 8713. Thanks to Mathieu Doray. Resolved by jruchaud. o Les couleurs des camemberts des captures ne s'affichent pas dans la légende dans la visualisation spatiale Issue: 8007. Thanks to Mathieu Doray. Resolved by sbavencoff. Downloads --------- For a manual installation, you can download files here: https://forge.codelutin.com/projects/echobase/files * echobase-embedded-4.0.zip - https://forge.codelutin.com/attachments/download/4176 * echobase-referentiel-4.0.echobase - https://forge.codelutin.com/attachments/download/4177 * echobase-ui-4.0-full.war - https://forge.codelutin.com/attachments/download/4178 * echobase-ui-4.0-lizmap.zip - https://forge.codelutin.com/attachments/download/4179 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -EchoBase team

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branch release/4.0 created (now 4c5074d)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch release/4.0 in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git at 4c5074d #8173 Fix SubsamplingFactor No new revisions were added by this update. -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch develop updated (4c5074d -> d33fd4a)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 4c5074d #8173 Fix SubsamplingFactor new d33fd4a [jgitflow-maven-plugin]updating poms for 4.1-SNAPSHOT development The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Detailed log of new commits: commit d33fd4a2fff8ec7089726f7e33f8542f77f5ec46 Author: Maven Release <maven-release(a)codelutin.com> Date: Thu Oct 27 17:40:29 2016 +0200 [jgitflow-maven-plugin]updating poms for 4.1-SNAPSHOT development Summary of changes: echobase-domain/pom.xml | 2 +- echobase-services/pom.xml | 2 +- echobase-ui/pom.xml | 2 +- pom.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch develop updated (05fb0af -> 4c5074d)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 05fb0af Migrate databases for tests new 4c5074d #8173 Fix SubsamplingFactor The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Detailed log of new commits: commit 4c5074d84f8f527deb6d8b2064e3ac70bc7dc628 Author: Julien Ruchaud <julien.ruchaud(a)debux.org> Date: Thu Oct 27 17:37:00 2016 +0200 #8173 Fix SubsamplingFactor Summary of changes: .../service/atlantos/xml/XmlBioticExport.java | 32 +++++++++++++++------- 1 file changed, 22 insertions(+), 10 deletions(-) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch develop updated (791d7a8 -> 05fb0af)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 791d7a8 Add translates new 05fb0af Migrate databases for tests The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Detailed log of new commits: commit 05fb0af070b90bcc4a3aab7df99c810d32c97705 Author: Julien Ruchaud <julien.ruchaud(a)debux.org> Date: Thu Oct 27 09:56:59 2016 +0200 Migrate databases for tests Summary of changes: .../services/MigrateImportDataDatabasesIT.java | 6 ++++++ .../import-data/echobase-atlantos.h2.db.gz | Bin 1236305 -> 1234109 bytes .../echobase-catches-and-voyage-result.h2.db.gz | Bin 991130 -> 998860 bytes .../import-data/echobase-catches.h2.db.gz | Bin 924956 -> 932467 bytes .../import-data/echobase-commonData.h2.db.gz | Bin 370150 -> 373494 bytes .../import-data/echobase-mooring-results.h2.db.gz | Bin 930474 -> 937442 bytes .../import-data/echobase-mooring.h2.db.gz | Bin 925373 -> 932719 bytes .../resources/import-data/echobase-nodata.h2.db.gz | Bin 318632 -> 326412 bytes .../echobase-operation-total-samples.h2.db.gz | Bin 785188 -> 793954 bytes .../import-data/echobase-operation.h2.db.gz | Bin 508066 -> 515535 bytes 10 files changed, 6 insertions(+) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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branch develop updated (0498112 -> 791d7a8)
by codelutin.com scm Oct. 27, 2016

Oct. 27, 2016

This is an automated email from the git hooks/post-receive script. New change to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git from 0498112 Add translates new 791d7a8 Add translates The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Detailed log of new commits: commit 791d7a8db9f696e6a4eba6b713d29fed3c649dfe Author: Julien Ruchaud <julien.ruchaud(a)debux.org> Date: Thu Oct 27 09:26:05 2016 +0200 Add translates Summary of changes: echobase-ui/src/main/resources/i18n/echobase-ui_en_GB.properties | 2 +- echobase-ui/src/main/resources/i18n/echobase-ui_fr_FR.properties | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm(a)codelutin.com>.

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