ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-10-07T17:07:32+02:00https://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/124Analysis added to a run have no space_id2019-09-27T14:50:59+02:00Romain ThervilleAnalysis added to a run have no space_idError:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --ana...Error:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --analysis-software-version "GATK:3.7
Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 -
Bcftools:1.3.1" --admin-login sigenae --project-id 1144
**Error: 'NoneType' object has no attribute 'space_id'**
Origin:
Issue#114
src/ng6/ng6workflow.py
```
if addto == "project": cmpt_object.project = self.project
elif addto == "run": cmpt_object.run = self.runobj
#We replace the default space_id
if cmpt_object.space_id == "default" and cmpt_object.space_id != cmpt_object.run.space_id:
cmpt_object.space_id = cmpt_object.run.space_id
```
We should set the space_id according to the project containing the run, not the run itself.V3.2.5.2Romain 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/105sort order not numeric in contaminationsearch table2019-10-28T15:44:50+01:00Gerald Salingerald.salin@inra.frsort order not numeric in contaminationsearch table![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/104loadin icon go on display while an error is raised2019-08-30T13:22:58+02:00Roxane Boyerloadin icon go on display while an error is raisedwhile downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)while downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/95Ajout d'analyse à un projet2019-10-21T11:52:25+02:00Philippe BardouAjout d'analyse à un projetImpossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)Impossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)V3.2.5.2Romain 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 Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/31add link and name to runs and analyses and projects in the purge email2019-09-10T11:58:20+02:00Gerald Salingerald.salin@inra.fradd link and name to runs and analyses and projects in the purge emaile.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,585...e.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,5855,5845,6309,6310,6311,6313,6314,6320,6321,6382,6381,6380,6379,6378,6383,6758,6757,6759,6763,8532,8539,8544,8547,8559,8568,8571,8582,158V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/27Project view : hidden run and analyses are counted2019-09-18T17:27:36+02:00Celine NoirotProject view : hidden run and analyses are countedIn data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)In data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/9Regenerate a password for users added by the project manager2020-01-22T16:22:03+01:00Audrey GibertRegenerate a password for users added by the project managerFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedRomain ThervilleRomain Thervillehttps://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 Therville