ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-10-14T16:19:52+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/122changes to NG6's database structure should appear in a .sql file2019-10-14T16:19:52+02:00Romain Thervillechanges to NG6's database structure should appear in a .sql fileWe should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).We should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).V3.2.6https://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/126Add a new group superadmin2019-10-29T09:36:55+01:00Celine NoirotAdd a new group superadminDuring purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interest...During purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interesting to have a new group "superadmin" which give access to all the projects.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/127Purge email should be send to all the users of the project.2019-09-20T11:37:40+02:00Celine NoirotPurge email should be send to all the users of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/128Discard some email adress from purge email.2019-09-20T10:27:40+02:00Celine NoirotDiscard some email adress from purge email.Add a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailAdd a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/129Script/workflow to migrate a list of project to from a space to another2020-11-30T11:30:50+01:00Celine NoirotScript/workflow to migrate a list of project to from a space to anotherDevelop a script to transfert a project from a storage space to another :
- change project space id
- change path of run, analyzes (of the project and of the runs)
- move filesDevelop a script to transfert a project from a storage space to another :
- change project space id
- change path of run, analyzes (of the project and of the runs)
- move filesV3.2.7.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/130In run view, the blue retention limit message should be hidden for now2019-09-12T13:12:08+02:00Romain ThervilleIn run view, the blue retention limit message should be hidden for nowThis message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")This message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")V3.2.5.3Romain ThervilleRomain Therville2019-09-12https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/131[ont-qc] Add .pdf file into ng6 analysis for nanopore runs2019-10-25T13:19:41+02:00Roxane Boyer[ont-qc] Add .pdf file into ng6 analysis for nanopore runsThe pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow.
It would be named report.pdfThe pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow.
It would be named report.pdfV3.2.6Audrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/132AligmentStats : Duplicate output is incorrect2019-10-28T10:44:11+01:00Audrey GibertAligmentStats : Duplicate output is incorrectIn Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)In Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/133[10X] Add index files to the files return by ng6workflow.py2019-10-09T14:36:00+02:00Claire Kuchly[10X] Add index files to the files return by ng6workflow.pyIl faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqi...Il faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, filtered_index_files, saved_files, concatenatefastq`Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/134Debug about add index files in sample definition2019-10-28T10:29:19+01:00Claire KuchlyDebug about add index files in sample definitionwith the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, ...with the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, sample in enumerate(self.samples) :
if sample.name :
self.samples_names.append(sample.name)
else :
sample.name = 'SAMPLE_' + str(nidx)
nidx += 1
if sample.sample_id :
if sample.sample_id in samples_ids :
display_error_message( "Sample identifier %s must be uniq ( sample %s ).\n" % sample.sample_id, sample.name )
# add an automatic id for samples
else :
sample.sample_id = 'sample_' + str(pidx)
pidx += 1
samples_ids.append(sample.sample_id)
for rfile in sample.reads1 :
self.reads1_indexes.append(sample.sample_id)
self.reads1.append(rfile)
for rfile in sample.reads2 :
self.reads2_indexes.append(sample.sample_id)
self.reads2.append(rfile)
**for rfile in sample.index :
self.index.append(rfile)**
```Claire KuchlyClaire Kuchly2019-10-24https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/135Actions on ng6 users2019-10-21T10:12:58+02:00Romain ThervilleActions on ng6 users- Create super CTD (plage user, superadmin group)
- Delete the user nG6_ADMIN (and revoke its rights on every project)
- Telling Didier about it- Create super CTD (plage user, superadmin group)
- Delete the user nG6_ADMIN (and revoke its rights on every project)
- Telling Didier about itV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137The static retention period given in the purge mail has to be computed2020-01-27T17:01:35+01:00Romain ThervilleThe static retention period given in the purge mail has to be computed"Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention..."Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention period.V3.2.6Romain ThervilleRomain Therville2019-11-21https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/138Display error in a project view : Table can not be sorted by date if the user...2020-04-03T15:58:05+02:00Audrey GibertDisplay error in a project view : Table can not be sorted by date if the user is not administratorMargot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could ...Margot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could not reproduce her bug because we were logged as CTD and it works perfectly for us...
One lead has been reported with the inspector column of web explorer :
what is sent in member view
![image](/uploads/2d8f69ffb2bbd8d28acc37314637bdeb/image.png)
what is sent in admin view
![image](/uploads/7114492349815c674d45ff5ba62c93f4/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://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/140"Random password generation" + "send mail" doesn't work with superadmin superCTD2020-06-11T17:05:46+02:00Romain Therville"Random password generation" + "send mail" doesn't work with superadmin superCTDWhen trying to regenerate a random password via the nG6 web interface, when logged as superCTD, no mail is sent to the final user.
We should check if the password is updated, and find out why no mail is sent.When trying to regenerate a random password via the nG6 web interface, when logged as superCTD, no mail is sent to the final user.
We should check if the password is updated, and find out why no mail is sent.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/141pipeline issues due to new storage space2020-06-15T09:07:03+02:00Claire Kuchlypipeline issues due to new storage spacedue to the set up of new storage space for new projet, several issues appeared :
* [x] new storage folders can not be created
* [x] data can not be found and so not be downloaded
* [x] FASTQC pictures in ReadStat analysis arent disp...due to the set up of new storage space for new projet, several issues appeared :
* [x] new storage folders can not be created
* [x] data can not be found and so not be downloaded
* [x] FASTQC pictures in ReadStat analysis arent displayedV3.2.8Claire KuchlyClaire Kuchlyhttps://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/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/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 Therville