ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-11-30T15:59:30+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/211Jflow issues2022-11-30T15:59:30+01:00Romain ThervilleJflow issuesLately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.Lately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/210switch_space_id workflow fail2021-06-04T10:39:18+02:00Romain Thervilleswitch_space_id workflow failThe switch_space_id workflow fails on nG6 and via bash commands.
**on NG6:**
Error "bad username/password" when entering the correct ng6 credentials.
**using bash commands:**
`python3.4 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_...The switch_space_id workflow fails on nG6 and via bash commands.
**on NG6:**
Error "bad username/password" when entering the correct ng6 credentials.
**using bash commands:**
`python3.4 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py switch_space_id --project_id "xxx" --space_id "longterm_bioinfo"`
python3.4 not found
`python2.7 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py switch_space_id --project_id "1713" --space_id "longterm_bioinfo"`
Traceback (most recent call last):
File "/usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py", line 27, in <module>
from jflow.workflows_manager import WorkflowsManager
File "/usr/local/bioinfo/src/ng6_sources/nG6/src/jflow/__init__.py", line 23, in <module>
from jflow.config_reader import JFlowConfigReader
File "/usr/local/bioinfo/src/ng6_sources/nG6/src/jflow/config_reader.py", line 24, in <module>
from configparser import RawConfigParser, NoOptionError
ImportError: No module named configparser
The module configparser seems to be missing from the python libs.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/208RunStats image paths are wrong for A2P1b-PlaGe-Caille2021-05-20T13:54:56+02:00Romain ThervilleRunStats image paths are wrong for A2P1b-PlaGe-CailleEven after the migration, the filepaths are still '/data_shortterm/' instead of '/data_seqoccin/'.
**TODO:**
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT an...Even after the migration, the filepaths are still '/data_shortterm/' instead of '/data_seqoccin/'.
**TODO:**
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT analyze_id FROM tx_nG6_run_analyze WHERE run_id IN (
SELECT run_id FROM tx_nG6_project_run WHERE project_id = xxx
)
);
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT analyze_id FROM tx_nG6_project_analyze WHERE project_id = xxx
);
```V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/207Usergroup with deleted = 1 / Error for "tsime-ngando" 's password sync2021-05-27T14:45:34+02:00Romain ThervilleUsergroup with deleted = 1 / Error for "tsime-ngando" 's password syncThe user "tsime-ngando" has its correct password "xxx" on esitoul.
Its password on nG6 is "yyy" instead.
If we set the right password via the nG6 interface or the database, it is automatically set back to the wrong one "yyy".
So, why do...The user "tsime-ngando" has its correct password "xxx" on esitoul.
Its password on nG6 is "yyy" instead.
If we set the right password via the nG6 interface or the database, it is automatically set back to the wrong one "yyy".
So, why does the synch sets a password different than the one from esitoul?
(See also : https://forgemia.inra.fr/get-plage/e-sitoul_adminscripts/-/blob/master/synchronizeUsers.pl)V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/206Login / logout issues2021-05-27T14:45:45+02:00Romain ThervilleLogin / logout issuesAfter a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, ope...After a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, openning a new one allows to connect one user, once.
(Maybe restarting the entire computer works, I haven't tried yet.)V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/144Javascript visual bug on a project's runs list2020-06-11T17:06:27+02:00Romain ThervilleJavascript visual bug on a project's runs listThe mouseover on a cell in the 'Sequencer' column sometimes adds a "end of line" character (on the "-" character).
(This seems to happen on every cell, but is only really visible when the cell contains a long string).
The "visual artef...The mouseover on a cell in the 'Sequencer' column sometimes adds a "end of line" character (on the "-" character).
(This seems to happen on every cell, but is only really visible when the cell contains a long string).
The "visual artefact" can be seen on this project (just mouseover the cells in the Sequencer column) :
https://ng6.toulouse.inra.fr/index.php?id=55&tx_nG6_pi1%5Bproject_id%5D=289
It appears on: Google Chrome
It doesn't appear on: Mozilla Firefox, Internet ExplorerV4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/138Display error in a project view : Table can not be sorted by date if the user...2020-04-03T15:58:05+02:00Audrey GibertDisplay error in a project view : Table can not be sorted by date if the user is not administratorMargot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could ...Margot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could not reproduce her bug because we were logged as CTD and it works perfectly for us...
One lead has been reported with the inspector column of web explorer :
what is sent in member view
![image](/uploads/2d8f69ffb2bbd8d28acc37314637bdeb/image.png)
what is sent in admin view
![image](/uploads/7114492349815c674d45ff5ba62c93f4/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/112[ont-qc] Adding new analysis : Demultiplex Stat for ONT2021-03-25T13:39:09+01:00Maxime Manno[ont-qc] Adding new analysis : Demultiplex Stat for ONT#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqki...#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqkit stats logs for all the samples (included the unmappaed files)
* [x] Add fastq files only for the barcodes added into the pool
* [x] Add Qcat and Seqkit path and oprions into the application.propertiesV4 - MaintenanceMaxime MannoMaxime Manno2019-08-31