GitLab

- 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

- 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

- 2 useless prints removed.

issue#129

- The type ng6space has been debugged.
- The workflow now generates a .stdout trace file.
- The synthax has changed: python3.4
/save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py switchspaceid
--project-id 1293 --space-id seqoccin --admin-login CTD

issue #129

("/work/ng6-test/jflow_rtherville/ng6_python.log") -> has to be updated.


Issue  #219

[demultiplexont.py]

See merge request !62

Merge branch issue#126.2 with master

See merge request !59

#134 : debug ng6workflow.py and sample.py

See merge request !58

Little display correction #132

Logs are retrieved from the path of fastq files, and not on the working
directory

Script was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process part

merge branche issue#119 with master

See merge request !61

issue #119

Merge branch issue#121 with master

See merge request !60

limit.

issue#119

The purge mails 'Errors-To:' field has been set to the 'email_from'
value, instead of 'email_copy'.

Issue#121

Superadmin users are now allowed to update any user (and their
password), from any project.

issue #126

Merge branch issue#126 with master

See merge request !57

Merge branch issue#129 with master

See merge request !56

I have moved the DB updates down in the code, to only register
migrations that went well.

issue #129

merge branch issue#95 with master

See merge request !55

merge branch issue#129 with master

See merge request !54

Merge branch issue#120 with master

See merge request !53

The displayed date (when the retention is a fixed date) was wrong.

Issue #120

The workflow has been re-writed to put most of the BD treatments in the
corresponding classes (Run, Analysis, Project).

issue#129

Resolves the addanalysis bug

issue#95, issue#85

index files in casava directory who isn't 10X data.

Issue#129

See merge request !52

I removed a few logging calls that a used for debugging.

issue #129

There was a problem with file's paths. Fixed.

Ng6 slurm 10 x

See merge request !50

Issue#120

See merge request !51

N g6 ont demultiplex

See merge request !48

# Conflicts:
#   ui/nG6/pi6/class.tx_nG6_pi6.php

The conflict only concerned php comments. I would have prefered to remove them, but the resulting script seemed really fishy on the git file compare display.
Anyway, we'll be able to remove those comments later.

Issue#129

See merge request !49

issue #120

The srcipt had to be reworked, the retention period was relative to
"today", we wanted it relative to "the run or analysis's creation date".
Also, a message is raised and the process is stopped if the project
already belongs to the given space_id.

issue #129

The new workflow allows to migrate a project to a space_id defined in
application.properties.
Every run and analyse gets a new retention and new path, the directories
and files are moved, the old directories are removed.

Use:
python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py
switchprojectspaceid --project-id 1292 --space-id default --admin-login
CTD

issue #129

Merge branch Issue#127 with master

See merge request !45