ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-06-11T17:02:37+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/158On nG6, trying a project space migration results in a wf that stays "started"2020-06-11T17:02:37+02:00Romain ThervilleOn nG6, trying a project space migration results in a wf that stays "started"Since the last update, I have tried validating the migration feature in production environment, and a bug occured.
* The workflow stays started:
![Sans_titre](/uploads/607ad112d43bc1d57610f4308af1fda2/Sans_titre.png)
* The directorie...Since the last update, I have tried validating the migration feature in production environment, and a bug occured.
* The workflow stays started:
![Sans_titre](/uploads/607ad112d43bc1d57610f4308af1fda2/Sans_titre.png)
* The directories generated by Makeflow have "root" as Owner and group:
```
[root@ng6-slurm switchspaceid]# pwd
/work/ng6/jflow/work/switchspaceid
[root@ng6-slurm switchspaceid]# ls -lt
total 6
drwxr-x--x 4 root root 4096 17 janv. 09:05 wf004643
drwxr-x--x 4 root root 4096 16 janv. 16:11 wf004638
drwxr-x--x 4 ng6 ng6 4096 15 janv. 17:28 wf004616
drwxr-x--x 4 ng6 ng6 4096 10 janv. 14:48 wf004542
drwxr-x--x 4 ng6 ng6 4096 24 déc. 13:48 wf004448
drwxr-x--x 4 ng6 ng6 4096 24 déc. 13:39 wf004447
drwxr-x--x 4 ng6 ng6 4096 24 déc. 13:35 wf004446
drwxr-x--x 4 ng6 ng6 4096 24 déc. 13:22 wf004445
drwxr-x--x 4 ng6 ng6 4096 23 déc. 15:57 wf004440
drwxr-x--x 4 ng6 ng6 4096 11 déc. 16:45 wf004238
drwxr-x--x 4 ng6 ng6 4096 11 déc. 16:38 wf004237
```
* No ".stdout" log file, and not much more infos in ng6.log:
```
01-17 09:05 MoveProject.process DEBUG Begin MoveProject Component.
01-17 09:05 MoveProject.process DEBUG self.space_id=seqoccin
01-17 09:05 MoveProject.process DEBUG self.project_id=1518
01-17 09:05 MoveProject.process DEBUG stdout = /work/ng6/jflow/work/switchspaceid/wf004643/MoveProject_default/MoveProject.stdout
```V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/157Workflow addproject introuvable2020-06-11T17:12:34+02:00Romain ThervilleWorkflow addproject introuvableManque 1 import dans /workflows/addproject/__init__.py
Chargement infini en tentant addproject depuis l'interface web, et addproject est le seul workflow qui n'apparait pas dans get_available_workflows.
Plus d'infos dans le commit à sui...Manque 1 import dans /workflows/addproject/__init__.py
Chargement infini en tentant addproject depuis l'interface web, et addproject est le seul workflow qui n'apparait pas dans get_available_workflows.
Plus d'infos dans le commit à suivre.V3.2.6Romain ThervilleRomain Therville2020-01-16https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/150The "send mail" footer covers 10 columns instead of 11.2020-06-11T17:05:13+02:00Romain ThervilleThe "send mail" footer covers 10 columns instead of 11.In Administration > Mail obsolete project, the last table line has a bad display.
`<th colspan="10"> should be replaced with <th colspan="11">.`In Administration > Mail obsolete project, the last table line has a bad display.
`<th colspan="10"> should be replaced with <th colspan="11">.`V3.2.6Romain 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/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/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/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/203Download by URL gives wrong URLs2021-04-30T20:45:23+02:00Gerald Salingerald.salin@inra.frDownload by URL gives wrong URLs![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gz![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gzV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/202ng6 interface slow2021-04-30T20:13:17+02:00Gerald Salingerald.salin@inra.frng6 interface slowNG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom...NG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom configuration [Active] : BE=1, FE=1, devIPMask=*, displayErrors=1, systemLogLevel=0
refreshing the view displays the error :
Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
Increasing memory_limit in php.ini solved for some time, but Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
I did not found a way to display sql queries, so I added file_put_contents("/var/www/html/ng6/typo3temp/sql.log", $query."\n",FILE_APPEND);
in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php > query function
while refreshing the page, output SQL log :
> nG6_project_analyze.analyze_id WHERE tx_nG6_project.uid=1700
> SELECT * FROM tx_nG6_view_project_run WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_analyze WHERE project_id = 1700
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT * FROM tx_nG6_view_project_user
in phpMyAdmin :
SELECT count(*) FROM tx_nG6_view_project_user > 13619506!!!!!!!!!!!!
SELECT * FROM `fe_rights_levels` > 8911!!! whereas we should only have 3 records
refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > 2 more records in fe_rights_levels
DELETE FROM `fe_rights_levels` where uid > 3 : refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > the page loading is fast
but 2 more records inserted in fe_rights_levels
![image](/uploads/88e304647f722386078feb20ed52b912/image.png)V3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/201[View Reads Stat compare] Images do not appear in the "compare" view2021-05-03T10:06:27+02:00Claire Kuchly[View Reads Stat compare] Images do not appear in the "compare" viewWhen we want to compare all the images from READSTATS analysis, we have acces to the status " FAIl, PASS" but not the image.
The status is a url link to image.
![failToViewImage](/uploads/15aaab0e7a4c7d8bd44b2545e31d13b3/failToViewIm...When we want to compare all the images from READSTATS analysis, we have acces to the status " FAIl, PASS" but not the image.
The status is a url link to image.
![failToViewImage](/uploads/15aaab0e7a4c7d8bd44b2545e31d13b3/failToViewImage.PNG)V3.2.8https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/195multiple CC in purge emails2021-03-25T14:28:31+01:00Gerald Salingerald.salin@inra.frmultiple CC in purge emails![image](/uploads/c6e10d7c41b8932e146e5218aab123fe/image.png)
the headers array given to the sent email is populated in each loop of the foreach block![image](/uploads/c6e10d7c41b8932e146e5218aab123fe/image.png)
the headers array given to the sent email is populated in each loop of the foreach blockV3.2.7.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/194The Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase2021-05-04T11:49:20+02:00Romain ThervilleThe Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/j...**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 86, in <module>
outputs = create_symbolik_link(*new_args)
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 79, in create_symbolik_link
s.cmd('bash %s'%user_script)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 568, in cmd
return self.ssh_results(pid, f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 561, in ssh_results
got = self._read(f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 538, in _read
x = os.read(f, 1024)
**Cause of the problem:**
When lauching an SSH connection with the ng6 user (Python : s = SSH(username, password, server_params[0]) ), a passphrase defined in /home/ng6/.ssh/id_rsa is asked.V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/190[Purge] not include md5sum.txt file in purge process2020-11-30T11:30:20+01:00Claire Kuchly[Purge] not include md5sum.txt file in purge processThe purge process deleted all the files in the raw data directory. Or we want to keep the md5sum.txt file which is a metadata file.The purge process deleted all the files in the raw data directory. Or we want to keep the md5sum.txt file which is a metadata file.V3.2.7.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/176Design error in single project view2020-06-11T16:59:48+02:00Romain ThervilleDesign error in single project viewThe .ng6-content-header-left is not long enough.
A solution given by Philippe B below:
![screen_css_prob_ng6](/uploads/38818f2932fea8c9a9aa1ec7ecee4fd8/screen_css_prob_ng6.png)
(Replace "height" with "min-height".)The .ng6-content-header-left is not long enough.
A solution given by Philippe B below:
![screen_css_prob_ng6](/uploads/38818f2932fea8c9a9aa1ec7ecee4fd8/screen_css_prob_ng6.png)
(Replace "height" with "min-height".)V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/175In the web interface, the addAnalysis "Run" button doesn't do anything2020-06-11T16:51:47+02:00Romain ThervilleIn the web interface, the addAnalysis "Run" button doesn't do anythingThis happens on nG6 and nG6-test.
Nothing in the the browser's "network" and "console" debug tabs.This happens on nG6 and nG6-test.
Nothing in the the browser's "network" and "console" debug tabs.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/174In administration, the "workflow Monitoring" doesn't work2021-04-23T15:33:42+02:00Romain ThervilleIn administration, the "workflow Monitoring" doesn't work![2020-03-10_153035](/uploads/1bda9cc3373a2b156896e5abfee2f0ba/2020-03-10_153035.png)![2020-03-10_153035](/uploads/1bda9cc3373a2b156896e5abfee2f0ba/2020-03-10_153035.png)V3.2.8Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/172When creating a project, the 'space' is not a select field2020-06-11T16:58:50+02:00Romain ThervilleWhen creating a project, the 'space' is not a select fieldThere must be a problem with the add_project form, or the 'ng6space' data type.There must be a problem with the add_project form, or the 'ng6space' data type.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/171Unable to add an analysis on web interface2020-06-11T16:58:26+02:00Celine NoirotUnable to add an analysis on web interfacewith a server file, on a project, run button on form addanalysis do nothing !with a server file, on a project, run button on form addanalysis do nothing !V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/163Broken links in adminstration pages2020-06-11T17:01:15+02:00Romain ThervilleBroken links in adminstration pagesThere are broken links in the administration page:
- In the "Mail obsolete" tab, the project links.
- In the "Process mail demands" tab, the project links.
For more information on how to resolve this, check the issue #146.There are broken links in the administration page:
- In the "Mail obsolete" tab, the project links.
- In the "Process mail demands" tab, the project links.
For more information on how to resolve this, check the issue #146.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/160Error when updating a user's email on nG62021-05-04T11:18:53+02:00Romain ThervilleError when updating a user's email on nG6When logged as CTD, on the project "HOLISTIC", I tried to update MAJJ's email, and the new email has been set for CTD instead of MAJJ.
![2020-01-21_113722](/uploads/33afb05071f8d7d0382a0a7743fd2fd8/2020-01-21_113722.png)
Was it because...When logged as CTD, on the project "HOLISTIC", I tried to update MAJJ's email, and the new email has been set for CTD instead of MAJJ.
![2020-01-21_113722](/uploads/33afb05071f8d7d0382a0a7743fd2fd8/2020-01-21_113722.png)
Was it because CTD was on top of the list, or because the logged user was CTD?
Anyway, it's an issue.V3.2.8.1Romain ThervilleRomain Therville