ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2021-03-25T14:29:06+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/192Project 'Mutua16s' always appears in the obsolete project list2021-03-25T14:29:06+01:00Romain ThervilleProject 'Mutua16s' always appears in the obsolete project listDuring the purge process, the alert mail for the Mutua16s project has been sent 19 times.
There should be only one mail per project.During the purge process, the alert mail for the Mutua16s project has been sent 19 times.
There should be only one mail per project.V3.2.7.5Romain ThervilleRomain Therville2021-02-08https://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/178[purge] do ont include hidden analyzes (nor runs) in the email sent to resear...2021-03-25T14:28:54+01:00Gerald Salingerald.salin@inra.fr[purge] do ont include hidden analyzes (nor runs) in the email sent to research teams> Files impacted of:
> • Runs : NemaTools-1 (12035), NemaTools-1 (12336)
> • Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)...> Files impacted of:
> • Runs : NemaTools-1 (12035), NemaTools-1 (12336)
> • Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)
IlluminaFilter is not accessible to users.V3.2.7.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/177No error message if login failed2020-06-11T16:56:51+02:00Celine NoirotNo error message if login failedSince last upgrade no error message :/Since last upgrade no error message :/V3.2.7Romain ThervilleRomain Therville2020-04-03https://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/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/170No more error msg while delete analysis with wrong user/login2020-06-11T17:12:05+02:00Celine NoirotNo more error msg while delete analysis with wrong user/loginwheel still present even when get return from server !
Error message is not printed.
![image](/uploads/4a5b432288244f8bf24dfe55fd511e62/image.png)wheel still present even when get return from server !
Error message is not printed.
![image](/uploads/4a5b432288244f8bf24dfe55fd511e62/image.png)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 Thervillehttps://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/155Warning on hidden column while create a run, analyse or projet2020-01-10T10:24:43+01:00Celine NoirotWarning on hidden column while create a run, analyse or projet`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "A...`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "Analyse de run" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1"
parsing Makeflow...
checking Makeflow for consistency...
Makeflow has 1 rules.
starting workflow....
submitting job: /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/.working/153171b866/_Stash/0/0/0/w0000000 none /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/BasicAnalysis_default/analysis.cfg /work/ng6-test/jflow_rtherville/tmp/tmp22_7y9dk.dump
submitted job 16508
**/save/ng6-test/src/ng6-git-rtherville/src/weaver/../pymysql/cursors.py:146: Warning: Incorrect integer value: 'True' for column 'hidden' at row 1
result = self._query(query)
**
job 16508 completed
nothing left to do.
sending incremental file list
./
test.txt
sent 166 bytes received 34 bytes 400.00 bytes/sec
total size is 61 speedup is 0.30
###########
# Results #
###########
> V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/154Visual inconsistency in the project list page2020-06-11T17:03:16+02:00Romain ThervilleVisual inconsistency in the project list pageIf a user has the "member" rights on a hidden project, the number of results displayed is wrong.
![Capture_du_2020-01-07_16-00-19](/uploads/d60798b007b269bbb1a1b38f4e94c0cc/Capture_du_2020-01-07_16-00-19.png)
(Every view has already bee...If a user has the "member" rights on a hidden project, the number of results displayed is wrong.
![Capture_du_2020-01-07_16-00-19](/uploads/d60798b007b269bbb1a1b38f4e94c0cc/Capture_du_2020-01-07_16-00-19.png)
(Every view has already been updated with a new hidden column)V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/153The DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex2020-01-10T10:24:16+01:00Romain ThervilleThe DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run ...**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run and analyzes are deployed and selected:
![2019-12-16_172422](/uploads/b95a120a14968d72406ad2d2d27e7f77/2019-12-16_172422.png)
**Why?**
In utils.py:
*12-16 13:19 Utils DEBUG get_directories_structure_and_content. src_directories = /save/ng6///data/run/fb3cdcb00, /save/ng6///data/analyze/e3df5acbb, /save/ng6///data/analyze/2753b0457, /save/ng6///data/run/b2e7de531, /save/ng6///data/analyze/ae6d2ec97, /save/ng6///data/analyze/cfec28f91
12-16 13:19 Utils DEBUG get_directories_structure_and_content. dest_directories = /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_RUNStats.64567*
(The destination tab contains 2 versions of the same runs and analyzes, one with '-' separatores, one with '_'.)
This may be fixed with an update to the download page's javascript call:
http://ng6-test.toulouse.inra.fr:8080//run_workflow?username=ng6-test&password=aCYLKVdYzI8AaTcB%25C2%25A4%25C3%2596%25C3%25B3i%2540%25C3%2598%2515%25C3%25B6%2522&user_directory=/work/ng6-test/jflow_rtherville/&admin_login=CTD&data_id=15032&run_id=15032&analysis_id=57729::-::57730&workflow_class=DownloadSymlink&callback=jQuery111105034437105204775_1576513683378&_=1576513683383
(By removing the analyzes that have no directory.)
The workflow tries the following treatment:
ln -s /save/ng6/data/run/fb3cdcb00 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData
ln -s /save/ng6/data/analyze/e3df5acbb /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606
ln -s /save/ng6/data/analyze/2753b0457 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608
ln -s /save/ng6/data/run/b2e7de531 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData
ln -s /save/ng6/data/analyze/ae6d2ec97 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568
ln -s /save/ng6/data/analyze/cfec28f91 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567
But fails, BECAUSE /save/ng6/data/analyze/2753b0457 AND /save/ng6/data/analyze/ae6d2ec97 DO NOT EXIST!V3.2.6Romain ThervilleRomain Thervillehttps://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/146There are hard-coded links in Admin>Extend Project>Project name column2020-06-11T17:01:31+02:00Romain ThervilleThere are hard-coded links in Admin>Extend Project>Project name columnEx: href="index.php?id=3&tx_nG6_pi1[project_id]=1"
The "id=3" has to be recovered from the typo3 "plugin.tx_nG6_pi6.redirection_page" template value.
This is defined in tx_nG6_pi6.js, line 706.
The expected result would be href="index.p...Ex: href="index.php?id=3&tx_nG6_pi1[project_id]=1"
The "id=3" has to be recovered from the typo3 "plugin.tx_nG6_pi6.redirection_page" template value.
This is defined in tx_nG6_pi6.js, line 706.
The expected result would be href="index.php?**id=55**&tx_nG6_pi1[project_id]=1" .V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/145"The run data has been purged." wrong in single run view2020-06-11T17:07:36+02:00Romain Therville"The run data has been purged." wrong in single run viewExemple :
Project CfDAILY(1353), Run CfDAILY(15511).
https://ng6.toulouse.inra.fr/index.php?id=55&tx_nG6_pi1%5Brun_id%5D=15511&tx_nG6_pi1%5Bproject_id%5D=1353
"The run data has been purged." is wrong, the run's data state is "extended"...Exemple :
Project CfDAILY(1353), Run CfDAILY(15511).
https://ng6.toulouse.inra.fr/index.php?id=55&tx_nG6_pi1%5Brun_id%5D=15511&tx_nG6_pi1%5Bproject_id%5D=1353
"The run data has been purged." is wrong, the run's data state is "extended".
The code should be checked to verify if this case is handled correctly.V3.2.7Romain ThervilleRomain Thervillehttps://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 Therville