ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-10-07T17:07:41+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/233add support to typo3 v112022-10-07T17:07:41+02:00Gerald Salingerald.salin@inra.fradd support to typo3 v11typo3 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 V11typo3 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 V11V3.4Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/232download symlink finished without error, but no data is available2022-10-06T21:29:54+02:00Gerald Salingerald.salin@inra.frdownload symlink finished without error, but no data is availablein case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outp...in case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outputFolder/file.xml;
avoid these characters in the names of run/analysis/projects or replace them when creating the symlinksV3.4https://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/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/227[ont_qc] Change end of sequencing report file2022-05-11T10:29:03+02:00Jules Sabban[ont_qc] Change end of sequencing report fileNanopore has change the end of sequencing report file format from PDF to HTMLNanopore has change the end of sequencing report file format from PDF to HTMLV3.3Jules SabbanJules Sabbanhttps://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/225[Purge] Do not purge the hidden runs and analyses2022-04-26T14:00:23+02:00Romain Therville[Purge] Do not purge the hidden runs and analysesHidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)Hidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/224Project page : Remove the "Raw data and analysis results use xxx"2022-04-26T14:00:49+02:00Romain ThervilleProject page : Remove the "Raw data and analysis results use xxx"This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.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/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/214add a link to the reinit password interface2021-10-12T08:47:06+02:00Gerald Salingerald.salin@inra.fradd a link to the reinit password interfaceV3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/213upgrade to typo3 v102021-10-12T08:47:15+02:00Gerald Salingerald.salin@inra.frupgrade to typo3 v10V3.3Gerald 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/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/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 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 - Maintenance