ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2023-05-02T11:07:22+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/244Purge management - In the "mail obsolete project" tab, the "nb run stored" an...2023-05-02T11:07:22+02:00Romain ThervillePurge management - In the "mail obsolete project" tab, the "nb run stored" and "project category" columns are wrongTo test, select the space "longterm_get".
- nb run stored = 1 instead of 2 for BETAGALL
- "project category" should be "finished" only when all data from the project has already been purgedTo test, select the space "longterm_get".
- nb run stored = 1 instead of 2 for BETAGALL
- "project category" should be "finished" only when all data from the project has already been purgedV3.4.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/242Infinite loading when deleting a run2022-12-16T16:20:51+01:00Romain ThervilleInfinite loading when deleting a runTests ongoing for the following:
Project SATI-1 (id 2017), Run SATI-1 (id 20284)
Project -> Select a run -> Delete -> ng6 credentialsTests ongoing for the following:
Project SATI-1 (id 2017), Run SATI-1 (id 20284)
Project -> Select a run -> Delete -> ng6 credentialsRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/241Jflow and SSL error2022-11-18T16:26:19+01:00Romain ThervilleJflow and SSL errorhttps://ng6.toulouse.inra.fr/jflow -> Code 500
```
Proxy Error
The proxy server could not handle the request GET /jflow.
Reason: Error during SSL Handshake with remote server
```https://ng6.toulouse.inra.fr/jflow -> Code 500
```
Proxy Error
The proxy server could not handle the request GET /jflow.
Reason: Error during SSL Handshake with remote server
```Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/240Purge process, some errors and suspected problems2023-10-04T11:13:50+02:00Romain ThervillePurge process, some errors and suspected problemsSure problem:
- Some projects with an active demand still appear in the "purgeable" list.
Maybe a problem:
- Make sure we don't check ".log.gz" files when looking for purgeable analyzes.
- Make sure the "purgeable" projects really do ha...Sure problem:
- Some projects with an active demand still appear in the "purgeable" list.
Maybe a problem:
- Make sure we don't check ".log.gz" files when looking for purgeable analyzes.
- Make sure the "purgeable" projects really do have expired files in their runs/analyzes.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/238add user not working2022-10-14T15:36:00+02:00Gerald Salingerald.salin@inra.fradd user not workingthe user receives an email telling him he can access a project, but it is not right.
the record is not stored in database.
due to the ng6 extension install in typo3 which asks for a primary key > uid was selected, but it is not auto in...the user receives an email telling him he can access a project, but it is not right.
the record is not stored in database.
due to the ng6 extension install in typo3 which asks for a primary key > uid was selected, but it is not auto incremented
Apply solved the problem : ALTER TABLE `fe_rights`MODIFY `uid` int(11) NOT NULL AUTO_INCREMENT;V3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/237readstat image visualization not displayed when samples are compared2022-10-11T13:27:10+02:00Gerald Salingerald.salin@inra.frreadstat image visualization not displayed when samples are comparedV3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/236structure of ng6 extension tables changes at each new deployment2022-10-10T11:15:44+02:00Gerald Salingerald.salin@inra.frstructure of ng6 extension tables changes at each new deploymentdescription field of tx_ng6_run chnages from text to VARCHAR(255) as well as primary(uid) of table fe_rights.
it seems ext_tables.php fil is executed when deplying a new version. This file was never updatedescription field of tx_ng6_run chnages from text to VARCHAR(255) as well as primary(uid) of table fe_rights.
it seems ext_tables.php fil is executed when deplying a new version. This file was never updateV3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/231The "addfiles" workflow changes the rights to the target directory to root:root2022-09-27T14:58:40+02:00Romain ThervilleThe "addfiles" workflow changes the rights to the target directory to root:rootThis happened on august 26th, 2022 (09:18 am)
**Target directory :** /data_seqoccin/analyze/99200b167
```
ng6@genologin1 /save/ng6/data_seqoccin/analyze $ stat 99200b167
File: ‘99200b167’
Size: 4096 Blocks: 1 IO ...This happened on august 26th, 2022 (09:18 am)
**Target directory :** /data_seqoccin/analyze/99200b167
```
ng6@genologin1 /save/ng6/data_seqoccin/analyze $ stat 99200b167
File: ‘99200b167’
Size: 4096 Blocks: 1 IO Block: 262144 directory
Device: 3ah/58d Inode: 297274441 Links: 2
Access: (0751/drwxr-x--x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2022-08-29 00:31:23.219591326 +0200
Modify: 2022-08-26 09:18:24.227200000 +0200
Change: 2022-08-26 09:18:52.285248179 +0200
Birth: -
```
**Logs :** /work/ng6/jflow/ng6.log
```
08-26 09:18 Analysis.sync DEBUG Synchronizing analysis id=80043 from /work/ng6/jflow/work/data_seqoccin/analyze/99200b167 to /save/ng6//data_seqoccin/analyze/99200b167
08-26 09:18 Analysis.sync DEBUG rsync -avh --remove-sent-files /work/ng6/jflow/work/data_seqoccin/analyze/99200b167/ /save/ng6//data_seqoccin/analyze/99200b167
08-26 09:18 Analysis.sync DEBUG Synchronization done for analysis id=80043(retcode=0)
```
**Workflow :** /work/ng6/jflow/work/addfiles/wf005296
**Tests :**
I tried launching addfiles from the ng6 website, the jflow directory AND the file transfered where both "root:root". It seems the workflow is launched by the user root from the web interface...V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/230[contaminationSearch] Bwa mem configuration causes some misunderstandings in ...2022-12-16T16:21:27+01:00Claire Kuchly[contaminationSearch] Bwa mem configuration causes some misunderstandings in the calculation of the contamination and explodes the CPU quotat of ng6After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng...After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng6 cPU quota due to the parameters used for launched bwa mem analyzis.Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/229The project name 'xxx' does not exists ->Erreur de handshake SSL lors de la c...2022-10-06T18:55:47+02:00Romain ThervilleThe project name 'xxx' does not exists ->Erreur de handshake SSL lors de la connexion à la BDDPlus d'informations dans le mantis:
https://genomique.genotoul.fr/Mantis/view.php?id=5221#c18361Plus d'informations dans le mantis:
https://genomique.genotoul.fr/Mantis/view.php?id=5221#c18361V3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/228Using addanalysis on a run unhides it.2022-06-16T16:54:26+02:00Romain ThervilleUsing addanalysis on a run unhides it.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/226The form to delete projects and runs bugs : there is a '&' in the ng6's password2022-05-10T13:53:23+02:00Romain ThervilleThe form to delete projects and runs bugs : there is a '&' in the ng6's passwordIf there is a '&' in the ng6 user's password, many forms bug on nG6.
The password should be changed again, but an additionnal password is needed:
```
LDAP administrator password:
passwd: Authentication token manipulation error
```If there is a '&' in the ng6 user's password, many forms bug on nG6.
The password should be changed again, but an additionnal password is needed:
```
LDAP administrator password:
passwd: Authentication token manipulation error
```V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/223Cannot create a new user on TROCADERO2022-04-14T11:10:12+02:00Romain ThervilleCannot create a new user on TROCADEROAdding a new user to the TROCADERO project bugs.
-> No new user in the database.
-> No linking to the project.
![bug_ng6](/uploads/c76ffa23f9410333ffb056359f26e5a1/bug_ng6.png)Adding a new user to the TROCADERO project bugs.
-> No new user in the database.
-> No linking to the project.
![bug_ng6](/uploads/c76ffa23f9410333ffb056359f26e5a1/bug_ng6.png)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/220The reset password mail sent to the users is bugged2023-08-31T14:55:13+02:00Romain ThervilleThe reset password mail sent to the users is bugged"Hi Jerome,
Found the mail with the username and password in the Junk mailbox (happens a lot in our mail system).
I'm a little confused on how to decipher the info about the password. It is something like some ## and a word in-between.
I..."Hi Jerome,
Found the mail with the username and password in the Junk mailbox (happens a lot in our mail system).
I'm a little confused on how to decipher the info about the password. It is something like some ## and a word in-between.
If I copy this into the login page I get an error. "Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/218Warning : In Run -> Analysis -> Download, every ".png" file is excluded from ...2022-04-26T14:02:29+02:00Romain ThervilleWarning : In Run -> Analysis -> Download, every ".png" file is excluded from the listIs it normal? (It's the case for every analysis on nG6.)
See the following :
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/blob/master/ui/nG6/pi1/analyzes/AnalysisTemplate.tpl#L145
@edarnige needs to upload .png images to an analysis...Is it normal? (It's the case for every analysis on nG6.)
See the following :
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/blob/master/ui/nG6/pi1/analyzes/AnalysisTemplate.tpl#L145
@edarnige needs to upload .png images to an analysis, can we remove this constraint?V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/215SQL error in ./nG6/src/pymysql/cursors.py2022-12-16T16:21:27+01:00Jules SabbanSQL error in ./nG6/src/pymysql/cursors.pyNew error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 ...New error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 updates ?Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/212switchspaceid doesn't work right now (project colocation is supposed to be se...2021-07-09T15:21:39+02:00Romain Thervilleswitchspaceid doesn't work right now (project colocation is supposed to be sent to longterm_get)How to find the error?
-> Try to migrate any project.
What's the error?
```
Traceback (most recent call last):
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 95, in <module>
out...How to find the error?
-> Try to migrate any project.
What's the error?
```
Traceback (most recent call last):
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 95, in <module>
outputs = migrate_project(*new_args)
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 71, in migrate_project
run_analyzes = run.get_analysis()
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/run.py", line 194, in get_analysis
analysis.append(Analysis.get_from_id(analysis_id))
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/analysis.py", line 680, in get_from_id
[name, date, description, software, options, version] = t3mysql.select_analysis(id)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/t3MySQLdb.py", line 802, in select_analysis
res = qresult.rows[0]
IndexError: tuple index out of range
```
See the following files:
ng6\src\ng6\t3MySQLdb.py
ng6\src\ng6\analysis.py
(They were not updated recently.)V3.3Romain ThervilleRomain Therville2021-07-16https://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/209Download failed for files with .log extension2021-10-11T18:30:36+02:00Claire KuchlyDownload failed for files with .log extension[Mantis associated](https://genomique.genotoul.fr/Mantis/view.php?id=5158)
Team wants to download the .log files of a Pacbio run but they get an error. After investigation, it seems to be an error due to the security set up after the ha...[Mantis associated](https://genomique.genotoul.fr/Mantis/view.php?id=5158)
Team wants to download the .log files of a Pacbio run but they get an error. After investigation, it seems to be an error due to the security set up after the hacking.
The same file with .txt extension can be downloaded.V3.3Claire KuchlyClaire Kuchlyhttps://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 Therville