ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-06-20T16:49:27+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/19Bug project view nb run / analyse / size2018-06-20T16:49:27+02:00Celine NoirotBug project view nb run / analyse / size![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)V3.1 - Purge2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/17Add project extention2018-07-18T15:48:10+02:00Celine NoirotAdd project extentionIf a project has a obsolete run (not all), all its run or analysis can be extentedIf a project has a obsolete run (not all), all its run or analysis can be extentedV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/11Correct list of id analyse and run stored in db for a purge demand2018-08-02T14:55:49+02:00Celine NoirotCorrect list of id analyse and run stored in db for a purge demandWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsV3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/8Metacharacter "&" in password creates a bug2019-09-12T09:27:13+02:00Audrey GibertMetacharacter "&" in password creates a bugWhen "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"When "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/5Bug ng6_cli status --all and on the interface2018-08-28T14:15:51+02:00Maxime MannoBug ng6_cli status --all and on the interfaceAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workV3.2 - SlurmClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/4ONT_QC analysis : Fast5archive component bug with multiple runs2018-03-30T10:38:47+02:00Maxime MannoONT_QC analysis : Fast5archive component bug with multiple runsIf a run has been launch many times, it has multiple subdirectory of raw data that we have to tar with différents namesIf a run has been launch many times, it has multiple subdirectory of raw data that we have to tar with différents namesV3.3 - ONT_QC analysisMaxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/2Purge : somme par projet incoherente2018-06-19T15:08:13+02:00Celine NoirotPurge : somme par projet incoherenteLa somme des données "purgeables" n'est pas coherente dans le table de puge.La somme des données "purgeables" n'est pas coherente dans le table de puge.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-04-18https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137The static retention period given in the purge mail has to be computed2020-01-27T17:01:35+01:00Romain ThervilleThe static retention period given in the purge mail has to be computed"Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention..."Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention period.V3.2.6Romain ThervilleRomain Therville2019-11-21https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/130In run view, the blue retention limit message should be hidden for now2019-09-12T13:12:08+02:00Romain ThervilleIn run view, the blue retention limit message should be hidden for nowThis message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")This message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")V3.2.5.3Romain ThervilleRomain Therville2019-09-12https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/235Hide and unhide a run2022-10-07T17:07:32+02:00Jules SabbanHide and unhide a runWhen I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' ...When I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' analysis.
The behavouir we want when I hide a run : nothing at analysis level OR same as now (to be discuss).
---
At analysis level, everything works well.
When I hide an analysis : the run above is no hidden : OK !
When I unhide an analysis : the run above is not unhidden : OK !V3.4Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/193The purge process should ignore hidden runs and analyses2021-03-25T14:28:42+01:00Romain ThervilleThe purge process should ignore hidden runs and analysesWe don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.We don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.V3.2.7.5Romain ThervilleRomain Therville2021-03-05https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/133[10X] Add index files to the files return by ng6workflow.py2019-10-09T14:36:00+02:00Claire Kuchly[10X] Add index files to the files return by ng6workflow.pyIl faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqi...Il faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, filtered_index_files, saved_files, concatenatefastq`Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/128Discard some email adress from purge email.2019-09-20T10:27:40+02:00Celine NoirotDiscard some email adress from purge email.Add a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailAdd a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/127Purge email should be send to all the users of the project.2019-09-20T11:37:40+02:00Celine NoirotPurge email should be send to all the users of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/116Custom message for purged data2019-08-30T13:23:46+02:00Romain ThervilleCustom message for purged dataWe need another message, replacing "Results folder not synchronized yet... " when the data has been purged.We need another message, replacing "Results folder not synchronized yet... " when the data has been purged.V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/110handle several data space2019-09-06T17:11:30+02:00Celine Noirothandle several data spaceFor seqOccIn project need to handle several project space.
To do:
* [x] handle different space when add run/analyse/project ...
* [x] handle different retention date thanks to space_id
* [x] handle spaces in download plugin
Validatio...For seqOccIn project need to handle several project space.
To do:
* [x] handle different space when add run/analyse/project ...
* [x] handle different retention date thanks to space_id
* [x] handle spaces in download plugin
Validation to be checked :
* [x] addproject with default space
* [x] addproject with specific space
* [x] addrun to a project with a specific space -> run data are in space ?
* [x] addanalysis to a project with a specific space -> analysis data are in space ?
* [x] addanalysis to a run with a specific space -> analysis data are in space ?V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/107handle limit storage period/date depending on storage space parameter2019-08-30T17:25:07+02:00Celine Noirothandle limit storage period/date depending on storage space parameterData storage period depend on kind of project (eg seqoccin), this should be a workflow parameter.
To ensure the user do not set period value, the period has to be set in application.properties.
- For rented space validate how to set en...Data storage period depend on kind of project (eg seqoccin), this should be a workflow parameter.
To ensure the user do not set period value, the period has to be set in application.properties.
- For rented space validate how to set end of storage date
![image](/uploads/dcb383c6dea62c2d9ededd61a85fe433/image.png)
- end of storage date could depend on a date or a period depending on storage space name
```
[space_default]
retention_period = 3m
path=/ng6
[space_default_old]
retention_period = 2y
path=/ng6
[space_seqoc]
# pour un espace donnee : deux parametre exclusif retention_date != retention_period
retention_date=12/03/2021
#retention_period = 2year
path=/seqoc
```
- Add retention_time parameter in application.properties.example
V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/106Configuring different storage space2019-09-06T17:11:30+02:00Celine NoirotConfiguring different storage spaceAdd a workflow parameter to store raw data and processed results in different storage space depending on project (ng6 or seqoccin or labs ?)
Warn:
- Quality control must be keep even if storage space is deleted, must be store in in ng6 ...Add a workflow parameter to store raw data and processed results in different storage space depending on project (ng6 or seqoccin or labs ?)
Warn:
- Quality control must be keep even if storage space is deleted, must be store in in ng6 space ?
- Think to handle data purge (do not delete if it's in rented space), check administration purge.
Code :
- web interface:
- storage info is stored in application.properties and db
- file eg: run_view.tmpl use relative path : `{$link=(('fileadmin'|cat:$runs[key($runs)].directory)|cat:'/')|cat:$file}`
- statistics storage space: check and define how to handle those spaces
- jflow code :
- application.properties will contain new section for storage space defined py project/lab name
- the storage space name is linked to a project
- functions get_save_directory() ... has to be adapted
- db must contain storage space name
- filesystem
- web interface: create symbolic link in fileadmin directory on different spaces
- adding new storage space, create symbolic link (look at how is done in jflow for [storage] section
- only project table has new attribute storage spaceV3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/86downloadsymlink, special characters2019-09-27T09:11:39+02:00Gerald Salingerald.salin@inra.frdownloadsymlink, special characterssome special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)some special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)V3.2.5Romain ThervilleRomain Therville