vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2024-01-10T17:54:22+01:00https://gitlab.inria.fr/vidjil/vidjil/-/issues/5211CGI, custom_fuse, workers: unify ?2024-01-10T17:54:22+01:00THONIER FlorianCGI, custom_fuse, workers: unify ?Discuss with @clement.chesnin : We have 3 ways to make call to softwares on our server:
* CGI by nginx
* custom fuse with an ad-hoc server, transfert by py4web
* task with workers
At least CGI and custom_fuse could be unify in a same a...Discuss with @clement.chesnin : We have 3 ways to make call to softwares on our server:
* CGI by nginx
* custom fuse with an ad-hoc server, transfert by py4web
* task with workers
At least CGI and custom_fuse could be unify in a same ad-hoc server ? Other option ?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/5209py4web : when the server is not responding, we get an error regarding ssl ins...2024-01-11T16:53:55+01:00CHESNIN Clementpy4web : when the server is not responding, we get an error regarding ssl instead of a more significant error![Screenshot from 2024-01-09 16-32-12.png](/uploads/ef1c0e71c72d0f5685ba18b1883d5dee/Screenshot_from_2024-01-09_16-32-12.png){width=775 height=397}![Screenshot from 2024-01-09 16-32-12.png](/uploads/ef1c0e71c72d0f5685ba18b1883d5dee/Screenshot_from_2024-01-09_16-32-12.png){width=775 height=397}Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5208py4web: design and link is messed up with 500 error2024-01-11T16:53:17+01:00CHESNIN Clementpy4web: design and link is messed up with 500 errorWhen getting a 500 error, the design is quite messed up, and we get a link to the ticket (not displayable unless you get the dashboard password but...
Note that with the dark palette, display seems to be a bit better (see capture under)...When getting a 500 error, the design is quite messed up, and we get a link to the ticket (not displayable unless you get the dashboard password but...
Note that with the dark palette, display seems to be a bit better (see capture under)
![Screenshot from 2024-01-09 16-24-34.png](/uploads/dafea2fe31b88dd53eda7eb5437cf49b/Screenshot_from_2024-01-09_16-24-34.png){width=579 height=297}
![Screenshot from 2024-01-09 16-24-40.png](/uploads/38be39d2653c8fcbfa77fdfe0eea25ed/Screenshot_from_2024-01-09_16-24-40.png){width=581 height=298}
![Screenshot from 2024-01-09 16-29-45.png](/uploads/3b40e6072b2e2a3418f131db1b0c2571/Screenshot_from_2024-01-09_16-29-45.png){width=638 height=327}Server - py4webhttps://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/5206assignsubset link don't work2024-01-11T10:22:33+01:00THONIER Florianassignsubset link don't workTest and fix before release of next version of serverTest and fix before release of next version of serverServer - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5205custom fuse should return name of sample if only one sample present2024-01-08T15:58:49+01:00THONIER Floriancustom fuse should return name of sample if only one sample presentWhen we open a custom fuse and when multiple samples is present, we have name of samples present in timeline, but not if we call only one sample. In this case, the `generic_info` value is set to `Sample X` where X is the number of sample...When we open a custom fuse and when multiple samples is present, we have name of samples present in timeline, but not if we call only one sample. In this case, the `generic_info` value is set to `Sample X` where X is the number of sample.
I suggest to modify function `get_custom_data` from default controller to adapt this value.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5204py4web: Open results from process line fails (compare samples)2024-01-10T17:25:23+01:00CHESNIN Clementpy4web: Open results from process line fails (compare samples)When running an analysis and try to open it from the processing line using the arrow, the result first waits for quite long, then display an error (see capture below)
To reproduce
1. Import a sample (for example Demo-X5.fa)
2. Run a p...When running an analysis and try to open it from the processing line using the arrow, the result first waits for quite long, then display an error (see capture below)
To reproduce
1. Import a sample (for example Demo-X5.fa)
2. Run a process (from example multi+inc+xxx)
3. When process is complete, reload page
4. Click on the right arrow at the end of the line
5. A "waiting" is first displayed
6. After some time, "Gateway Time-out" is displayed
Note that this works when doing the same on app
Note also that the result is correctly opened when click on the "multi+inc+xxx" link at the bottom of the page
![Screenshot from 2024-01-03 12-08-26.png](/uploads/65b5456a0446ad8019c0176553ed08b8/Screenshot_from_2024-01-03_12-08-26.png)Server - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5203Heuristics: Improve estimation of combined V/J probabilities ?2023-12-22T14:06:58+01:00Mathieu GiraudHeuristics: Improve estimation of combined V/J probabilities ?
Seen by @mikael-s.
We roughly estimate the $p$-value of a recombination as $p_V + p_J$. But... this is not a probability.
Something such as $1 - (1 - p_V)(1 - p_J)$ is a bit better (and it's still an estimation), but... it's almost eq...
Seen by @mikael-s.
We roughly estimate the $p$-value of a recombination as $p_V + p_J$. But... this is not a probability.
Something such as $1 - (1 - p_V)(1 - p_J)$ is a bit better (and it's still an estimation), but... it's almost equivalent when these probabilites are small.
So ~"wont-fix" ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/5202Check pre-process with py4web2024-01-09T16:34:15+01:00CHESNIN ClementCheck pre-process with py4webCheck that pre-process correctly works in py4webCheck that pre-process correctly works in py4webServer - py4webCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5201Include fontello in our docker image ?2023-12-20T14:38:12+01:00THONIER FlorianInclude fontello in our docker image ?Since some days, we have error dues to fontello curl request. Maybe are we launch to much test and are "partially" black listed.
Can we include directly these font in our docker image to only get it on by commit, even from another adre...Since some days, we have error dues to fontello curl request. Maybe are we launch to much test and are "partially" black listed.
Can we include directly these font in our docker image to only get it on by commit, even from another adress that don't fail ?
We also have sometimes somes problems with server that don't have a full access to internet.
Questions
* license allow it ?
* Where to easily store this file ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/5200Make top by system the default.2023-12-13T18:02:45+01:00Mikaël SalsonMake top by system the default.See !1381See !1381https://gitlab.inria.fr/vidjil/vidjil/-/issues/5199Add missing controllers unit tests2023-12-21T17:05:47+01:00CHESNIN ClementAdd missing controllers unit testsIn #5179, some unit tests were added. However, some functions/controllers were not added due to a lack of time. We also had issues with some tests implementation. Here is a list of the missing tests :
- [ ] admin.py controller
- [ ] ad...In #5179, some unit tests were added. However, some functions/controllers were not added due to a lack of time. We also had issues with some tests implementation. Here is a list of the missing tests :
- [ ] admin.py controller
- [ ] add tests for make_backup
- [ ] add tests for load_backup
- [ ] add tests for repair
- [ ] add tests for reset_workers
- [ ] add some more tests for repair missing files
- [ ] default.py controller
- [ ] add tests for init_db
- [ ] add tests for init_db_form
- [ ] add tests for get_custom_data
- [ ] add tests for get_analysis
- [ ] add tests for get_analysis
- [ ] add tests for stop_impersonate
- [ ] file.py controller
- [ ] add tests for restart_pre_process
- [ ] my_account.py controller
- [ ] add tests for index
- [ ] add tests for jobs
- [ ] proxy.py controller
- [ ] add tests for all methods
- [ ] results_file.py controller
- [ ] add tests for run_all_patients
- [ ] add tests for info
- [ ] add tests for download
- [ ] sample_set.py controller
- [ ] add tests for custom
- [ ] add tests for confirm
- [ ] add tests for delete
- [ ] add tests for permission
- [ ] add tests for change_permission
- [ ] add tests for get_sample_set_list
- [ ] add tests for auto_complete
- [ ] should we test stats methods ?
- [ ] segmenter.py controller
- [ ] add tests for all methods
- [ ] tag.py controller
- [ ] add tests for all methods
After this, most of the endpoints will be tested.
A next step could be to check the coverage in order to identify missing tests. Another step would be to add unit tests for modules too?https://gitlab.inria.fr/vidjil/vidjil/-/issues/5198Speed up cypress ci jobs2024-01-18T10:12:44+01:00THONIER FlorianSpeed up cypress ci jobs* [ ] improve docker build of testing images
* [ ] reduce time of starting of server
* [ ] Pull cypress image at the same time that other images* [ ] improve docker build of testing images
* [ ] reduce time of starting of server
* [ ] Pull cypress image at the same time that other imagesDev-cihttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5197CI; gain some time by using some pre-updated image server/client2024-02-07T14:19:38+01:00THONIER FlorianCI; gain some time by using some pre-updated image server/clientI was thinking to a way to increase our time of CI.
Major part of the build time is taken by apt-get update & installation of third-party softwares as a base image before pull vidjil content.
We could probably split our Dockerfile as...I was thinking to a way to increase our time of CI.
Major part of the build time is taken by apt-get update & installation of third-party softwares as a base image before pull vidjil content.
We could probably split our Dockerfile as base/top image that we will be able to speed up build time.
Problem is that if we change content of dockerfile, we will have error. We could probably use branch name to take that into account.
* build a first image for that, push it as vidjil/vidjil-{client/server}:latest-base
* have a new branche type `docker` that will launch a job to build a new base image and propagate it to his derived CI jobs to ensure that everything work well
* Other branch will use default latest-base image
* When merge in dev, we could [detect a change in file](https://forum.gitlab.com/t/how-to-trigger-a-job-when-specific-files-have-changed-at-any-commit-in-the-branch/89945) to launch jobs to build latest-base images.
... Something like that I think...Dev-cihttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5196Taille de la fenêtre ID d'un clone - analyses IGL/IGK2024-03-06T15:31:03+01:00Anne de SeptenvilleTaille de la fenêtre ID d'un clone - analyses IGL/IGKBonjour,
J'ai depuis peu ajouté des séquences générées par amplicon sur des réarrangements KAPPA et les analyses sont visuellement pas très jolies, c'est à dire que les clones sont très fragmentés. La/les amorces côté JK sont suffisamm...Bonjour,
J'ai depuis peu ajouté des séquences générées par amplicon sur des réarrangements KAPPA et les analyses sont visuellement pas très jolies, c'est à dire que les clones sont très fragmentés. La/les amorces côté JK sont suffisamment proches pour être incluses dans la séquences ID du clone. Sur les chaînes légères, les CDR3 sont beaucoup plus courts à cause de l'absence de gène D. Est-ce nécessaire d'avoir une ID de 50 nucléotides tout de même ? Ne pourrait-on pas réduire un peu la fenêtre ?
Exemple de résultat KAPPA :
https://app.vidjil.org/60432-46?https://gitlab.inria.fr/vidjil/vidjil/-/issues/5195API + py4web : tests d'intégration2023-11-17T09:49:05+01:00Mathieu GiraudAPI + py4web : tests d'intégrationévoqué avec @fthonierévoqué avec @fthonierhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5194Problème de récupération de gosu2023-11-10T15:06:47+01:00Mikaël SalsonProblème de récupération de gosuErreur 502 avec un wget sur github : https://gitlab.inria.fr/vidjil/vidjil/-/jobs/3571211#L1510
Est-ce un ban de github ?
Discuté avec @clement.chesnin. Peut-être tester en faisant un gitlab-ci.yml sur un autre repo, juste avec un wget...Erreur 502 avec un wget sur github : https://gitlab.inria.fr/vidjil/vidjil/-/jobs/3571211#L1510
Est-ce un ban de github ?
Discuté avec @clement.chesnin. Peut-être tester en faisant un gitlab-ci.yml sur un autre repo, juste avec un wget sur l'URL et un autre sur un autre dépôt Github.CHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5193log flash; add a copy to clipboard icon2023-11-09T10:49:36+01:00THONIER Florianlog flash; add a copy to clipboard iconI change a flash message, including now the url called.
I dont' know if it is usefull to include this type of information (server internal error url) in flash message as we should have a ticket on our side with this value.
But is ther...I change a flash message, including now the url called.
I dont' know if it is usefull to include this type of information (server internal error url) in flash message as we should have a ticket on our side with this value.
But is there some case where it can be usefull to user to keep a trace of error ?
Another reason is that if you try to select text in it, it close.https://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 2024.04