vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2024-01-15T09:39:47+01:00https://gitlab.inria.fr/vidjil/vidjil/-/issues/5191py4web; return that a server error occured when it is2024-01-15T09:39:47+01:00THONIER Florianpy4web; return that a server error occured when it isFor the moment, when an `internal server error` occur, a modal with text about ssl is open.
This is false and we should show a flash message to say that an error occured.
Maybe use code error 500 to detect it with ajax.
As with py4web ...For the moment, when an `internal server error` occur, a modal with text about ssl is open.
This is false and we should show a flash message to say that an error occured.
Maybe use code error 500 to detect it with ajax.
As with py4web migration these types of error can occure more than usual, it can be important to return a correct message to user and that they don't waste time to search about ssl error.Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5190py4web; restore unittest pipeline2023-12-21T17:05:05+01:00THONIER Florianpy4web; restore unittest pipelineSince we change for py4web, pipeline haven't been converted. We are curently unable to check them.
We need to do it before use py4web in production.
Another issue is open for the content of these tests (#5179)Since we change for py4web, pipeline haven't been converted. We are curently unable to check them.
We need to do it before use py4web in production.
Another issue is open for the content of these tests (#5179)Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5189py4web: check that all download function work2024-01-08T09:27:35+01:00THONIER Florianpy4web: check that all download function workWith this migration, we should convert download process. Some download controller have already been change, but some other don't.
For the moment, we can't check if it work as we have an old version of cypress (see MR !1308 and more prec...With this migration, we should convert download process. Some download controller have already been change, but some other don't.
For the moment, we can't check if it work as we have an old version of cypress (see MR !1308 and more precisely !1319).Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5187py4web; Lauch without uwsgi2024-01-22T15:38:13+01:00THONIER Florianpy4web; Lauch without uwsgiIs uwsgi mandatory to launch application ? Is it possible to use only py4web application and command line to set up out server ?
@clement.chesnin said that maybe py4web is not fully multithreaded and that it can be a pain to use in thi...Is uwsgi mandatory to launch application ? Is it possible to use only py4web application and command line to set up out server ?
@clement.chesnin said that maybe py4web is not fully multithreaded and that it can be a pain to use in this case.
We already need to (partially) launch py4web by CLI for coverage and unit testing.
Maybe an optional issue as it work well as it.Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5185py4web: some error on DB2023-12-08T14:33:50+01:00THONIER Florianpy4web: some error on DBDuring convertion of web2py to py4web; I fall on some error in controller that return a `none` value for an existing entry in database.
In some case, same call of type `db.sequence_file[id]` return fisrt a correct value, and a second ...During convertion of web2py to py4web; I fall on some error in controller that return a `none` value for an existing entry in database.
In some case, same call of type `db.sequence_file[id]` return fisrt a correct value, and a second call one line under return none value.
Hard to reproduce, not constant, ...
@clement.chesnin sugfgest to use `row.update(**values)` and `row.validate_and_update(**values)`.
Don't know if it will be enough.Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5182Py4web, Clean up demo file (bulma, ...)2023-12-21T17:06:27+01:00THONIER FlorianPy4web, Clean up demo file (bulma, ...)During dev, some demo file have been used (as bulma css pipeline, vue ,...) that don't occur in our vidjil app.
Need to make some cleaning now that py4web work enough.
Link to !1355During dev, some demo file have been used (as bulma css pipeline, vue ,...) that don't occur in our vidjil app.
Need to make some cleaning now that py4web work enough.
Link to !1355Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5180py4web; database migration from web2py2024-01-22T14:18:05+01:00THONIER Florianpy4web; database migration from web2pyIs there any point to fiollow to change backend server from web2py to py4web ?
@clement.chesnin think about make a diff on tables on web2py database and py4web.
After that, we should make some tests on a backup of prod database to be ...Is there any point to fiollow to change backend server from web2py to py4web ?
@clement.chesnin think about make a diff on tables on web2py database and py4web.
After that, we should make some tests on a backup of prod database to be sure that everything work well.Server - py4webTHONIER FlorianTHONIER Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5179Py4web; unit tests2023-12-21T17:05:47+01:00THONIER FlorianPy4web; unit testsServer - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5178py4web; Bad HTML rendering after request return error2023-12-08T14:32:14+01:00THONIER Florianpy4web; Bad HTML rendering after request return errorSometimes, when request return error (or flash ?), a modal open and all html rendering become ugly and inconstant.
A simple close of this modal allow to restore aspect.
Need to investigate to find exact cause of this (unclosed div ?)Sometimes, when request return error (or flash ?), a modal open and all html rendering become ugly and inconstant.
A simple close of this modal allow to restore aspect.
Need to investigate to find exact cause of this (unclosed div ?)Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5169py4web: after user creation, redirection fails2023-12-05T14:51:37+01:00Mikaël Salsonpy4web: after user creation, redirection failsAfter user creation (which succeeds), redirection to the index page fails.After user creation (which succeeds), redirection to the index page fails.Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5157API and Py4web: make it work2023-11-28T13:07:50+01:00THONIER FlorianAPI and Py4web: make it workFor the moment, API don't work out of the box:
* some forms have variation on dom ids
* Auth user is not directly accessible
* Use of generic.json as in web2py seem to be impossible (or at least modified and not documented).For the moment, API don't work out of the box:
* some forms have variation on dom ids
* Auth user is not directly accessible
* Use of generic.json as in web2py seem to be impossible (or at least modified and not documented).Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5078py4web : impersonnate2023-12-08T15:08:19+01:00Mathieu Giraudpy4web : impersonnate
@duez: "il faut convertir les fonctions impersonate() et is_impersonating() de web2py et les ajouter a VidjilAuth.py"
@duez: "il faut convertir les fonctions impersonate() et is_impersonating() de web2py et les ajouter a VidjilAuth.py"Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5155Follow-up from "Draft: Py4web; apply mulitple changes to backend server code."2023-11-06T15:04:09+01:00THONIER FlorianFollow-up from "Draft: Py4web; apply mulitple changes to backend server code."The following discussion from !1338 should be addressed:
- [ ] @fthonier started a [discussion](https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1338#note_862390):
> Supprimer aussi les règles associées.The following discussion from !1338 should be addressed:
- [ ] @fthonier started a [discussion](https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1338#note_862390):
> Supprimer aussi les règles associées.Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5143Add D primers in the set of primers2023-05-11T17:49:33+02:00Mikaël SalsonAdd D primers in the set of primersAs requested by ~"NAN - Nantes" during 2023 Vidjil day.
Beware to the prioritization of primers (V/J primers should have the priority over D).As requested by ~"NAN - Nantes" during 2023 Vidjil day.
Beware to the prioritization of primers (V/J primers should have the priority over D).Web 2023.10THONIER FlorianTHONIER Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5140Show percentage by locus in addition that by sample2023-06-29T14:57:42+02:00THONIER FlorianShow percentage by locus in addition that by sampleA feature asked by some users: Be able to show percentage of clonotype inside his own locus in the client.
An alternative inside scatterplot exist with preset 17; locus by size, but not in list of clonotype.
Warning, a locus with only ...A feature asked by some users: Be able to show percentage of clonotype inside his own locus in the client.
An alternative inside scatterplot exist with preset 17; locus by size, but not in list of clonotype.
Warning, a locus with only few reads (wet lab/sequencing failure) can easily have a clonotype at a high level.Web 2023.10THONIER FlorianTHONIER Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5123Warning view; Ugly display on chrome2023-03-28T16:14:38+02:00THONIER FlorianWarning view; Ugly display on chromeWhile I was testing to take screenshot for documentation, I found that warning view is not similar that the view on firefox.
![Screenshot_20230228_102853](/uploads/7e5eff9708e63deadfb4961ff384b425/Screenshot_20230228_102853.png)While I was testing to take screenshot for documentation, I found that warning view is not similar that the view on firefox.
![Screenshot_20230228_102853](/uploads/7e5eff9708e63deadfb4961ff384b425/Screenshot_20230228_102853.png)Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5097Report; include image in comment section or in other place2023-03-28T16:14:57+02:00Thonier FlorianReport; include image in comment section or in other placeA feature asked by ~"LIL-Lille" : A way to add an external image inside the report.
If saved, we should include these pictures.
In the present case, we can also try to import raw data from the page that generate picture and rerender ...A feature asked by ~"LIL-Lille" : A way to add an external image inside the report.
If saved, we should include these pictures.
In the present case, we can also try to import raw data from the page that generate picture and rerender that inside report... But it is another point.Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5096Report; shortcut to hide all other sample2023-03-28T16:15:28+02:00Thonier FlorianReport; shortcut to hide all other sampleAs for locus, a shortcut shift+click to hide all other samples present in the report.
Also, if we choose to directly hide sample from graph-list, update export menu too.As for locus, a shortcut shift+click to hide all other samples present in the report.
Also, if we choose to directly hide sample from graph-list, update export menu too.Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5094Report; allow to set generic clone information (% locus; %locus+inc, ...)2023-03-28T16:28:32+02:00Thonier FlorianReport; allow to set generic clone information (% locus; %locus+inc, ...)Asked by ~"LIL-Lille" : Use the same mechanism than clonotype settings ? Particular format as splitted by sample.Asked by ~"LIL-Lille" : Use the same mechanism than clonotype settings ? Particular format as splitted by sample.Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5091menu export; bypass shortcut2023-03-28T16:07:18+02:00Thonier Florianmenu export; bypass shortcutAt the opening of this menu, no more shortcut is possible.
The last button `save as` seem to get a focus call and all keyboard action will be listen by it. (click on enter will call his action for example).At the opening of this menu, no more shortcut is possible.
The last button `save as` seem to get a focus call and all keyboard action will be listen by it. (click on enter will call his action for example).Web 2023.10