ng6 issues
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues
2020-02-11T14:32:56+01:00
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/169
FAQ style is ugly
2020-02-11T14:32:56+01:00
Celine Noirot
FAQ style is ugly
Do it less ugly
Do it less ugly
V3.2.6
Celine Noirot
Celine Noirot
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/156
Style error
2020-04-03T14:00:13+02:00
Celine Noirot
Style error
- Cadre pour les projets chevauchant et n'utilise pas tout l'espace
- foooter non centré
- Cadre pour les projets chevauchant et n'utilise pas tout l'espace
- foooter non centré
V3.2.6
Celine Noirot
Celine Noirot
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/151
Add a space id column in Administration > Mail obsolete project
2020-01-16T17:33:08+01:00
Romain Therville
Add a space id column in Administration > Mail obsolete project
- New space_id column
- Replace the "size greater than" filter with a "space_id" selection
- New space_id column
- Replace the "size greater than" filter with a "space_id" selection
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137
The static retention period given in the purge mail has to be computed
2020-01-27T17:01:35+01:00
Romain Therville
The 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.
V3.2.6
Romain Therville
Romain Therville
2019-11-21
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/128
Discard some email adress from purge email.
2019-09-20T10:27:40+02:00
Celine Noirot
Discard 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 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 email
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/127
Purge email should be send to all the users of the project.
2019-09-20T11:37:40+02:00
Celine Noirot
Purge 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.
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/126
Add a new group superadmin
2019-10-29T09:36:55+01:00
Celine Noirot
Add a new group superadmin
During purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interest...
During purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interesting to have a new group "superadmin" which give access to all the projects.
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/122
changes to NG6's database structure should appear in a .sql file
2019-10-14T16:19:52+02:00
Romain Therville
changes to NG6's database structure should appear in a .sql file
We should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).
We should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).
V3.2.6
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/120
add the retention policy to project view
2020-01-22T11:28:03+01:00
Gerald Salin
gerald.salin@inra.fr
add the retention policy to project view
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/39
Purge : Set Email From, in ng6 conf pi6 comme pour pi1
2019-08-30T10:09:24+02:00
Celine Noirot
Purge : Set Email From, in ng6 conf pi6 comme pour pi1
![image](/uploads/59f957cf14964106c3b4e51914488f29/image.png)
![image](/uploads/59f957cf14964106c3b4e51914488f29/image.png)
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/31
add link and name to runs and analyses and projects in the purge email
2019-09-10T11:58:20+02:00
Gerald Salin
gerald.salin@inra.fr
add link and name to runs and analyses and projects in the purge email
e.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,585...
e.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,5855,5845,6309,6310,6311,6313,6314,6320,6321,6382,6381,6380,6379,6378,6383,6758,6757,6759,6763,8532,8539,8544,8547,8559,8568,8571,8582,158
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/117
Add duplication stat to alignmentStat analyze
2019-08-30T13:23:44+02:00
Claire Kuchly
Add duplication stat to alignmentStat analyze
V3.2.5
Natacha Faivre
Natacha Faivre
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/116
Custom message for purged data
2019-08-30T13:23:46+02:00
Romain Therville
Custom message for purged data
We 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.
V3.2.5
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/107
handle limit storage period/date depending on storage space parameter
2019-08-30T17:25:07+02:00
Celine Noirot
handle limit storage period/date depending on storage space parameter
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 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
V3.2.5
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/106
Configuring different storage space
2019-09-06T17:11:30+02:00
Celine Noirot
Configuring different storage space
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 ...
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 space
V3.2.5
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/246
allow to create symlinks on genobioinfo
2023-11-14T05:38:23+01:00
Gerald Salin
gerald.salin@inra.fr
allow to create symlinks on genobioinfo
allow to choose the server where to create the cymbolic links (genologin pr genobioinfo)
allow to choose the server where to create the cymbolic links (genologin pr genobioinfo)
V3.4.3
Gerald Salin
gerald.salin@inra.fr
Gerald Salin
gerald.salin@inra.fr
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/245
store ngl-bi analysis code in ng6 run
2024-03-11T10:40:45+01:00
Gerald Salin
gerald.salin@inra.fr
store ngl-bi analysis code in ng6 run
to allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflow
to allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflow
V3.4.5
Gerald Salin
gerald.salin@inra.fr
Gerald Salin
gerald.salin@inra.fr
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/239
error displaying workflow status if too much runs present
2022-11-07T16:33:55+01:00
Gerald Salin
gerald.salin@inra.fr
error displaying workflow status if too much runs present
error in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.
error in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.
V3.4.1
Gerald Salin
gerald.salin@inra.fr
Gerald Salin
gerald.salin@inra.fr
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/235
Hide and unhide a run
2022-10-07T17:07:32+02:00
Jules Sabban
Hide and unhide a run
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' ...
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 !
V3.4
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/233
add support to typo3 v11
2022-10-07T17:07:41+02:00
Gerald Salin
gerald.salin@inra.fr
add support to typo3 v11
typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11
typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11
V3.4
Gerald Salin
gerald.salin@inra.fr
Gerald Salin
gerald.salin@inra.fr