ng6 merge requestshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests2020-01-08T17:30:39+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/78#155 convert bool to int to avaoid warning2020-01-08T17:30:39+01:00Celine Noirot#155 convert bool to int to avaoid warningcorrect warningcorrect warningV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/68WIP: Resolve "illumina_10X debug due to test"2020-01-08T09:36:49+01:00Claire KuchlyWIP: Resolve "illumina_10X debug due to test"Closes #143Closes #143V3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/74Merge branch issue#150 with master2020-01-06T11:29:35+01:00Romain ThervilleMerge branch issue#150 with masterThe expired projects table's design has been fixed.
issue #150The expired projects table's design has been fixed.
issue #150V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/75Merge branch issue#153 with master2020-01-06T11:28:58+01:00Romain ThervilleMerge branch issue#153 with masterUtils.py update
The get_directories_structure_and_content() function has been reworked
to make the projects, runs and analyzes names normalization way more
consistent. This will solve the differences between sources and
destinations in ...Utils.py update
The get_directories_structure_and_content() function has been reworked
to make the projects, runs and analyzes names normalization way more
consistent. This will solve the differences between sources and
destinations in this function.
issue #153V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/73Merge test (isue 126 with master)2019-12-11T14:25:59+01:00Romain ThervilleMerge test (isue 126 with master)This is a test.This is a test.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/72Merge issue#129 with master2019-12-09T13:23:18+01:00Romain ThervilleMerge issue#129 with master- I have removed the "local = True" parameter to execute the workflow on
the computing cluster instead of ng6's host.
(It was a test parameter, only meant for testing.)
issue #129- I have removed the "local = True" parameter to execute the workflow on
the computing cluster instead of ng6's host.
(It was a test parameter, only meant for testing.)
issue #129V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/69Merge branch issue#129 with master2019-11-29T14:02:56+01:00Romain ThervilleMerge branch issue#129 with masterHuge update for the new migration workflow:
- New name : switch_space_id.
- The given space id is checked in application.properties.
- Most of the treatments have been moved to a "components" folder,
allowing us to create easily a new "...Huge update for the new migration workflow:
- New name : switch_space_id.
- The given space id is checked in application.properties.
- Most of the treatments have been moved to a "components" folder,
allowing us to create easily a new "migrate_several_projects" (or
"bulk_project_migration") later.
- The workflow can be launched from the single project view on the nG6
website, when logged a superadmin user.
- The project's space_id is visible to everyone on the single project
view.
- A warning indicating that the migration updates the retention has been
added to the workflow's form in single project view.
- More logs in ng6.log, and the new log file MoveProject.stdout. (path
exemple : [...]/jflow/work/switchspaceid/wf000452/MoveProject_default/MoveProject.stdout)
- CSS updates for the project views.
- For new space_ids, the <space_id>/run and <space_id>/analyze
directories will be created if missing.
Issue #129
Commit db1b75b8db3b4e2379c570c9de77061a40d8cc6eV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/71Merge branch issue#119 with master2019-11-28T17:37:57+01:00Romain ThervilleMerge branch issue#119 with masterMinor visual update for the retention display in the single run and single analysis views.
issue #119Minor visual update for the retention display in the single run and single analysis views.
issue #119V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/70Merge branch Issue#119 with master2019-11-28T17:23:00+01:00Romain ThervilleMerge branch Issue#119 with masterMinor visual fixes. More infos in this commit: 5928040b25307b2c61450eb14a4247f4510ad207Minor visual fixes. More infos in this commit: 5928040b25307b2c61450eb14a4247f4510ad207V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/67Merge branch issue#119.2 with master2019-11-21T15:47:34+01:00Romain ThervilleMerge branch issue#119.2 with master- Display fixed when the analysis or run's data state is 'extended'
- New line in the analysis and run single element display, indicating
the purge date when the element has been purged.
issue#119- Display fixed when the analysis or run's data state is 'extended'
- New line in the analysis and run single element display, indicating
the purge date when the element has been purged.
issue#119V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/66Merge branch Issue#129 with master2019-11-19T09:32:54+01:00Romain ThervilleMerge branch Issue#129 with masterV3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/65#141 change REGEX to display pictures from FASTQC analysis from new2019-11-13T15:26:01+01:00Claire Kuchly#141 change REGEX to display pictures from FASTQC analysis from newstorage spacesstorage spacesV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/63#139 debug2019-11-13T15:25:44+01:00Claire Kuchly#139 debugDebug number of reads add to saved files for illumina ng6 workflow.Debug number of reads add to saved files for illumina ng6 workflow.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/64Merge branch issue#120 with master2019-11-12T13:39:32+01:00Romain ThervilleMerge branch issue#120 with masterfile_put_contents() php logs have been removed.
(Refactoring only commit)
issue #120file_put_contents() php logs have been removed.
(Refactoring only commit)
issue #120V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/62[demultiplexont.py]2019-10-28T13:22:00+01:00Audrey Gibert[demultiplexont.py]Script was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partScript was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/59Merge branch issue#126.2 with master2019-10-28T10:29:29+01:00Romain ThervilleMerge branch issue#126.2 with masterSuperadmin users are now allowed to update any user (and their
password), from any project.
issue #126Superadmin users are now allowed to update any user (and their
password), from any project.
issue #126V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/58#134 : debug ng6workflow.py and sample.py2019-10-28T10:29:18+01:00Claire Kuchly#134 : debug ng6workflow.py and sample.pyindex files in casava directory who isn't 10X data.index files in casava directory who isn't 10X data.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/61merge branche issue#119 with master2019-10-24T09:50:03+02:00Romain Thervillemerge branche issue#119 with masterUpdate the run and analysis display to add the data state, and retention limit.
commit 20f6a237798424ef1b82cb236ff21fbbaaba03be
issue #119Update the run and analysis display to add the data state, and retention limit.
commit 20f6a237798424ef1b82cb236ff21fbbaaba03be
issue #119V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/60Merge branch issue#121 with master2019-10-24T09:39:03+02:00Romain ThervilleMerge branch issue#121 with masterThe purge mails 'Errors-To:' field has been set to the 'email_from'
value, instead of 'email_copy'.
Issue#121The purge mails 'Errors-To:' field has been set to the 'email_from'
value, instead of 'email_copy'.
Issue#121V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/57Merge branch issue#126 with master2019-10-17T14:40:49+02:00Romain ThervilleMerge branch issue#126 with masterIssue#126
* The superadmin group allows to navigate every project, run and analysis on nG6, hidden or not, with admin rights.
* There is a new table in the admin section ( Administration > Admin management ) that allow superadmins to ad...Issue#126
* The superadmin group allows to navigate every project, run and analysis on nG6, hidden or not, with admin rights.
* There is a new table in the admin section ( Administration > Admin management ) that allow superadmins to add and remove users to and from the superadmin group.
* The group's key is NEVER written directly in the source code, allowing an easier deployment for production use.
* The only requirement outside of the source deployment is to create a group with title = 'ng6_superadmin'. For additional informations, check the SQL file.V3.2.6Romain ThervilleRomain Therville