ng6 issues
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues
2019-10-24T09:38:56+02:00
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/121
purge email configuration
2019-10-24T09:38:56+02:00
Gerald Salin
gerald.salin@inra.fr
purge email configuration
check the recipient field, I think there were multiple copies of support.ng6 in the last purge session.
check the recipient field, I think there were multiple copies of support.ng6 in the last purge session.
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/131
[ont-qc] Add .pdf file into ng6 analysis for nanopore runs
2019-10-25T13:19:41+02:00
Roxane Boyer
[ont-qc] Add .pdf file into ng6 analysis for nanopore runs
The 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.pdf
The 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.pdf
V3.2.6
Audrey Gibert
Audrey Gibert
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/134
Debug about add index files in sample definition
2019-10-28T10:29:19+01:00
Claire Kuchly
Debug about add index files in sample definition
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, ...
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 Kuchly
Claire Kuchly
2019-10-24
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/132
AligmentStats : Duplicate output is incorrect
2019-10-28T10:44:11+01:00
Audrey Gibert
AligmentStats : Duplicate output is incorrect
In 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/126
Add a new group superadmin
2019-10-29T09:36:55+01:00
Celine Noirot
Add a new group superadmin
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 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.
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/85
Error addanalysis from graphic interface (firefox)
2019-11-12T13:44:01+01:00
Maxime Manno
Error addanalysis from graphic interface (firefox)
I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)
I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/153
The DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex
2020-01-10T10:24:16+01:00
Romain Therville
The 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!
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/155
Warning on hidden column while create a run, analyse or projet
2020-01-10T10:24:43+01:00
Celine Noirot
Warning 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 #
###########
>
V3.2.6
Celine Noirot
Celine Noirot
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/119
add the run/analysis status in the summary table
2020-01-10T10:28:33+01:00
Gerald Salin
gerald.salin@inra.fr
add the run/analysis status in the summary table
![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge state
![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge state
V3.2.6
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/151
Add a space id column in Administration > Mail obsolete project
2020-01-16T17:33:08+01:00
Romain Therville
Add a space id column in Administration > Mail obsolete project
- New space_id column
- Replace the "size greater than" filter with a "space_id" selection
- New space_id column
- Replace the "size greater than" filter with a "space_id" selection
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/120
add the retention policy to project view
2020-01-22T11:28:03+01:00
Gerald Salin
gerald.salin@inra.fr
add the retention policy to project view
V3.2.6
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/9
Regenerate a password for users added by the project manager
2020-01-22T16:22:03+01:00
Audrey Gibert
Regenerate a password for users added by the project manager
For now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be added
For now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be added
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137
The static retention period given in the purge mail has to be computed
2020-01-27T17:01:35+01:00
Romain Therville
The 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.
V3.2.6
Romain Therville
Romain Therville
2019-11-21
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/169
FAQ style is ugly
2020-02-11T14:32:56+01:00
Celine Noirot
FAQ style is ugly
Do it less ugly
Do it less ugly
V3.2.6
Celine Noirot
Celine Noirot
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/161
A rework of the purge processes is needed
2020-03-04T09:25:59+01:00
Romain Therville
A rework of the purge processes is needed
With the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going ...
With the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going to be deleted.
No extention is allowed in this case.
* A new CRON that sends the purge mail one month before the data deletion and opens a purge request (Admin > Mail obsolete projects).
* A new CRON (every week) to send to the ng6 administrators the list of the last purge mails sent.
V3.2.7
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/156
Style error
2020-04-03T14:00:13+02:00
Celine Noirot
Style error
- Cadre pour les projets chevauchant et n'utilise pas tout l'espace
- foooter non centré
- Cadre pour les projets chevauchant et n'utilise pas tout l'espace
- foooter non centré
V3.2.6
Celine Noirot
Celine Noirot
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/138
Display error in a project view : Table can not be sorted by date if the user...
2020-04-03T15:58:05+02:00
Audrey Gibert
Display error in a project view : Table can not be sorted by date if the user is not administrator
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 ...
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 - Maintenance
Audrey Gibert
Audrey Gibert
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/177
No error message if login failed
2020-06-11T16:56:51+02:00
Celine Noirot
No error message if login failed
Since last upgrade no error message :/
Since last upgrade no error message :/
V3.2.7
Romain Therville
Romain Therville
2020-04-03
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/171
Unable to add an analysis on web interface
2020-06-11T16:58:26+02:00
Celine Noirot
Unable to add an analysis on web interface
with 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 !
V3.2.7
Romain Therville
Romain Therville
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/172
When creating a project, the 'space' is not a select field
2020-06-11T16:58:50+02:00
Romain Therville
When creating a project, the 'space' is not a select field
There 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.
V3.2.7
Romain Therville
Romain Therville