vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2024-03-19T12:34:55+01:00https://gitlab.inria.fr/vidjil/vidjil/-/issues/5266Delete old fashion distributions computed in reads2024-03-19T12:34:55+01:00THONIER FlorianDelete old fashion distributions computed in readsWe still compute a reads->distributions values.
This values seem to ne never used.
It is made on server side.
Check if really never use and delete in that case.We still compute a reads->distributions values.
This values seem to ne never used.
It is made on server side.
Check if really never use and delete in that case.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5261Preprocess with vdj filter for large capture files ?2024-03-27T14:00:29+01:00THONIER FlorianPreprocess with vdj filter for large capture files ?We have number of user that load large file with small part of vdj in it. Should we make a preprocess that launch a vidjil-algo filter on it and delete temp data to save disk space and gain fluidity on real analysis ?
We still have iss...We have number of user that load large file with small part of vdj in it. Should we make a preprocess that launch a vidjil-algo filter on it and delete temp data to save disk space and gain fluidity on real analysis ?
We still have issue on upload data to server but it is already the case.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5259search field; include creator user ?2024-02-21T14:18:06+01:00THONIER Floriansearch field; include creator user ?A specific case for ~"LIL-Lille" : a patient have the same last name that a user of the team.
The search return all patients created by this users and inside the list the expected patient. Should we ?
A search with both last and firs...A specific case for ~"LIL-Lille" : a patient have the same last name that a user of the team.
The search return all patients created by this users and inside the list the expected patient. Should we ?
A search with both last and first name don't work.
One day, we will probably improve search we capacity to include field for search.
Until this time, what should we do ?Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5256Better configuration files for docker2024-02-14T14:28:30+01:00THONIER FlorianBetter configuration files for dockerWe nned to have default configuration that we can override by other files if available.
This will be better to rebase repository for some server instances.We nned to have default configuration that we can override by other files if available.
This will be better to rebase repository for some server instances.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5255Add a direct download icon to config result on set page2024-02-13T12:48:37+01:00THONIER FlorianAdd a direct download icon to config result on set pageTo download result of fuse for a given configuration, add a down arrow to result button to easily download all conf results
![Screenshot_20240213_124613](/uploads/e3955fac8c275ad8c476f65a040a2fbe/Screenshot_20240213_124613.png)To download result of fuse for a given configuration, add a down arrow to result button to easily download all conf results
![Screenshot_20240213_124613](/uploads/e3955fac8c275ad8c476f65a040a2fbe/Screenshot_20240213_124613.png)Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5243Speed up users page2024-02-06T12:01:30+01:00CHESNIN ClementSpeed up users pagePour le moment, l'ouverture de la page users sur app met 30s...
Quelques idées :
- voir si on peut optimiser les requêtes sb
- paginer la réponse (cf ce qu'on a fait pour les sample_sets)
- avoir un chargement dynamique des infos sur les...Pour le moment, l'ouverture de la page users sur app met 30s...
Quelques idées :
- voir si on peut optimiser les requêtes sb
- paginer la réponse (cf ce qu'on a fait pour les sample_sets)
- avoir un chargement dynamique des infos sur les users
- ...Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5239Slow request to IMGT2024-02-14T15:20:43+01:00THONIER FlorianSlow request to IMGTSince some times, we got slow answer from imgt in our CI pipeline (probably the same in current usage).
It take from 4sec to 30sec.
We need to increase timeout in our cypress jobs that are usually of 4sec by default.Since some times, we got slow answer from imgt in our CI pipeline (probably the same in current usage).
It take from 4sec to 30sec.
We need to increase timeout in our cypress jobs that are usually of 4sec by default.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5231Refacto .env and .env-default handling to prevent issue if .env is not define...2024-01-31T13:45:03+01:00CHESNIN ClementRefacto .env and .env-default handling to prevent issue if .env is not defined on local configC'est embêtant, parce qu'on a une erreur lorsqu'il n'y a rien dans le .env (ce qui est le cas par défaut)C'est embêtant, parce qu'on a une erreur lorsqu'il n'y a rien dans le .env (ce qui est le cas par défaut)Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5221Tag; add them to doc2024-01-24T18:04:04+01:00THONIER FlorianTag; add them to docWe can extract default list of tags to insert them in doc.
Maybe class them by type (disease, locus, sequencing protocol, ...).We can extract default list of tags to insert them in doc.
Maybe class them by type (disease, locus, sequencing protocol, ...).Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5218docker env; add rules for worker concurrency2024-01-31T19:03:16+01:00THONIER Floriandocker env; add rules for worker concurrencyWe need to be able to set number of concurrency of workers from an env.
For the moment, workers use the number of cpu threads as limit. We can set it by modifying entrypoint (--concurrency value).
The value should be taken from env.We need to be able to set number of concurrency of workers from an env.
For the moment, workers use the number of cpu threads as limit. We can set it by modifying entrypoint (--concurrency value).
The value should be taken from env.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5216Roadmap hiver/printemps 2024 suite au CST 2023-122024-03-27T14:21:24+01:00Mathieu GiraudRoadmap hiver/printemps 2024 suite au CST 2023-12
Discuté à l'AG puis affiné entre @mikael-s @fthonier @clement.chesnin @magiraud en janvier
Fenêtre de dev: 3 mois, fév/mars/avril
- mi-mai: déploy sur app
- juste avant le workshop
- mi-juin: déploy health
## Priorités
### Points ...
Discuté à l'AG puis affiné entre @mikael-s @fthonier @clement.chesnin @magiraud en janvier
Fenêtre de dev: 3 mois, fév/mars/avril
- mi-mai: déploy sur app
- juste avant le workshop
- mi-juin: déploy health
## Priorités
### Points majeurs décidés par le CST
- [Bioinformatics] Better tools for quality assessment and massification of analyses ==> statsQC, API
- [Bioinformatics] Better tools for full repertoire analysis (including app-stats)
- [Technical] Technical foundations (Py4web, more flexible workflows, CI, librairies)
### Points que l'on fait tout de même
- [Technical] Tools to improve support, admin, and monitoring
- Better communication with the community (documentation, feature tours, Vidjil Workshop)
- Better communication with developers/bioinformaticians
### Autres points
- [Bioinformatics] Better sequence and recombination analysis [Research in algorithms] ==> on reparle dans 6 mois, sauf éventuellement merge Aho XXXX et tranlocation
- [Bioinformatics] Profiles/scenarios ==> pas d'intérêt fort, on en reparle dans 6 mois
## Concrètement
### Tâches majeures février-mars-(avril)
- [ ] [ensemble] Finir py4web, suivi deploy prod #5073
- [x] [C] NSX
- [ ] [C] QCstats ~"server-qc-stats"
- [ ] [F] app-stats (démo en février) ~"app-stats"
- [ ] [F] bioinfo (lecture, support, recherche) :)
- [ ] [Ensemble] MySQL 8 ? #3582
### Tâches continues
[Ensemble] vie du consortium
- Feature Tour
- Vidjil Workshop vdj#1392
- EuroClonality-NGS
- Com
- Panel beta: début avril (statsQC + autres choses) (séparé du Tour ? à voir)
### Autres tâches
ensemble
- [ ] [ensemble] Nettoyer web2py
- [ ] [ensemble] Documenter py4web
- [ ] [ensemble] Article 2024 sur la plateforme vdj#1180
F
- [ ] [F] Merger première MR à QCstats, transférer à Clément !1224
- [ ] [F] Promotheus/Grafana: passer à Clément !1343
- [ ] [F] Premier vendredi du mois, présentation biblio
- [ ] [F] Créer vijdil-community-bioinfo
- [ ] [F] API: Lille, Nantes, Strasbourg?
C
- [ ] [C] Promotheus/Grafana !1343 vdj#1073
- [ ] [C] task.py, workflows #2358
- [ ] [C] Création de compte, avec vérification de mail
- [ ] [C] Config SMTP (reçoit-on les mails ?)
- [ ] [C] Autres updates de frameworks/librairies Python3, Ubuntu 24.04 LTS, Cypress 14, ..., fixer version…Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5210Test external, add a server side for CGI/proxy that are not fully tested2024-01-22T14:12:36+01:00THONIER FlorianTest external, add a server side for CGI/proxy that are not fully testedFor the moment, our external tests are launch on client, and use CGI from db.vidjil.org.
This cause an error as we don't really test server cgi service. And indeed, py4web cgi don't work.
We need to add some tests on CGI on the serve...For the moment, our external tests are launch on client, and use CGI from db.vidjil.org.
This cause an error as we don't really test server cgi service. And indeed, py4web cgi don't work.
We need to add some tests on CGI on the server side (and on feature-s branches).Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5207py4web : 404 error page2024-01-31T16:52:32+01:00CHESNIN Clementpy4web : 404 error pageWhen we get to a 404 page with py4web, we get a single link on the middle on the page, which points towards _vidjil_url_/vidjil, which leads to a new 404 error
![Screenshot from 2024-01-09 16-20-37.png](/uploads/109cc7fad983a620e9c125a7...When we get to a 404 page with py4web, we get a single link on the middle on the page, which points towards _vidjil_url_/vidjil, which leads to a new 404 error
![Screenshot from 2024-01-09 16-20-37.png](/uploads/109cc7fad983a620e9c125a781a3e10c/Screenshot_from_2024-01-09_16-20-37.png){width=726 height=372}Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5192py4web; check that an email is send at error ticket occured2024-01-22T14:14:08+01:00THONIER Florianpy4web; check that an email is send at error ticket occuredWe should check if it still work from web2py to py4web.We should check if it still work from web2py to py4web.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5186py4web; fix review server2024-01-22T14:13:34+01:00THONIER Florianpy4web; fix review serverSince conversion to py4web; job to start a review server don't work.
Job success, but opening link return to error nginx 404.
Proxy, conf.js, docker env ?Since conversion to py4web; job to start a review server don't work.
Job success, but opening link return to error nginx 404.
Proxy, conf.js, docker env ?Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5183Py4web; update documentation2024-01-22T14:14:19+01:00THONIER FlorianPy4web; update documentationSome documentation need to be added and updated, on dev, usage, migration, ...Some documentation need to be added and updated, on dev, usage, migration, ...Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5181py4web; Is script create_clone_db_py working well ?2024-01-22T15:39:10+01:00THONIER Florianpy4web; Is script create_clone_db_py working well ?Make some tests to know if everything work well with new backend server.Make some tests to know if everything work well with new backend server.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5149Replace vidjil (beta) by vidjil (version)2024-01-19T19:06:19+01:00THONIER FlorianReplace vidjil (beta) by vidjil (version)I think it time to change it.
We could also have a button in help menu with "À propos" properties; as a complete list of version of server, client, algo, external softwares ...
For the moment, we only show version of client in the con...I think it time to change it.
We could also have a button in help menu with "À propos" properties; as a complete list of version of server, client, algo, external softwares ...
For the moment, we only show version of client in the console, and server in the admin page.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5145Upload by network; merge create hard file and no symlink2024-01-19T19:03:58+01:00THONIER FlorianUpload by network; merge create hard file and no symlinkIf you use a network to load data and choose a preprocess with merge, the resulting file will be store as a real file and no as a symlink. In this case, it will take more space.If you use a network to load data and choose a preprocess with merge, the resulting file will be store as a real file and no as a symlink. In this case, it will take more space.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5133No log in database2024-01-22T15:28:47+01:00Mikaël SalsonNo log in databaseIt appears that we are not logging actions anymore in the database, since 52158ac0 (which came a few days after this attempt: 6fce80e1db).
Anyone knows why?
It should be fixed.It appears that we are not logging actions anymore in the database, since 52158ac0 (which came a few days after this attempt: 6fce80e1db).
Anyone knows why?
It should be fixed.Web 2024.04