ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2023-10-04T11:13:50+02:00https://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/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/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/166Infinite loop when trying to expand the 1QELD project in the download page2022-12-16T16:21:28+01:00Romain ThervilleInfinite loop when trying to expand the 1QELD project in the download pageWhen logged as CTD, on the download page, there is an infinite loop trying to call the AJAX "raw_data_description".
The project doesn't expand, the page is not stuck, but this results in a lot a pointless calls.
Screenshot below:
![scr...When logged as CTD, on the download page, there is an infinite loop trying to call the AJAX "raw_data_description".
The project doesn't expand, the page is not stuck, but this results in a lot a pointless calls.
Screenshot below:
![screenshot_bug_nG6_1QELD](/uploads/8c59366a852bc9f4616a3a18720fe205/screenshot_bug_nG6_1QELD.png)Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/159On the "Download" page, selecting a whole project without expanding it bugs2022-12-16T16:21:27+01:00Romain ThervilleOn the "Download" page, selecting a whole project without expanding it bugsOn the download page:
https://ng6.toulouse.inra.fr/index.php?id=59
For the project "GutSpodo"
![Screen_Shot_2020-01-17_at_15.49.24](/uploads/3a8a01797b32ac31e6e9628e5a736202/Screen_Shot_2020-01-17_at_15.49.24.png)
"No run neither any a...On the download page:
https://ng6.toulouse.inra.fr/index.php?id=59
For the project "GutSpodo"
![Screen_Shot_2020-01-17_at_15.49.24](/uploads/3a8a01797b32ac31e6e9628e5a736202/Screen_Shot_2020-01-17_at_15.49.24.png)
"No run neither any analysis selected".
When expanding the project, there is no problem.Romain ThervilleRomain Thervillehttps://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/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 Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/139Debug about add raw files due to 10X dev2020-06-15T10:26:45+02:00Claire KuchlyDebug about add raw files due to 10X devhttps://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.https://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.V3.2.8Claire KuchlyClaire Kuchly2019-11-07https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/83copy to clipboard from download windows does not work2020-06-11T17:09:25+02:00Gerald Salingerald.salin@inra.frcopy to clipboard from download windows does not work![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe w...![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe we have to upgrade the ZeroClipBoard.min.js file (3 yers old)Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/124Analysis added to a run have no space_id2019-09-27T14:50:59+02:00Romain ThervilleAnalysis added to a run have no space_idError:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --ana...Error:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
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" --admin-login sigenae --project-id 1144
**Error: 'NoneType' object has no attribute 'space_id'**
Origin:
Issue#114
src/ng6/ng6workflow.py
```
if addto == "project": cmpt_object.project = self.project
elif addto == "run": cmpt_object.run = self.runobj
#We replace the default space_id
if cmpt_object.space_id == "default" and cmpt_object.space_id != cmpt_object.run.space_id:
cmpt_object.space_id = cmpt_object.run.space_id
```
We should set the space_id according to the project containing the run, not the run itself.V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/104loadin icon go on display while an error is raised2019-08-30T13:22:58+02:00Roxane Boyerloadin icon go on display while an error is raisedwhile downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)while downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/95Ajout d'analyse à un projet2019-10-21T11:52:25+02:00Philippe BardouAjout d'analyse à un projetImpossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)Impossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/27Project view : hidden run and analyses are counted2019-09-18T17:27:36+02:00Celine NoirotProject view : hidden run and analyses are countedIn data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)In data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/8Metacharacter "&" in password creates a bug2019-09-12T09:27:13+02:00Audrey GibertMetacharacter "&" in password creates a bugWhen "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"When "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"V3.2.6Romain ThervilleRomain Thervillehttps://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/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.fr