vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2023-03-28T16:18:06+02:00https://gitlab.inria.fr/vidjil/vidjil/-/issues/4539stats-qc : Pouvoir afficher d'un coup tous les échantillons d'un set2023-03-28T16:18:06+02:00Mathieu Giraudstats-qc : Pouvoir afficher d'un coup tous les échantillons d'un setCertains usagers, avec des runs avec 50+ échantillons, souhaiteraient visualiser ~"server-qc-stats" d'un coup. Ce n'est pas possible pour l'instant (~~limite à 10, et en plus~~ il faut cliquer sur les échantillons un par un).
Avoir sur ...Certains usagers, avec des runs avec 50+ échantillons, souhaiteraient visualiser ~"server-qc-stats" d'un coup. Ce n'est pas possible pour l'instant (~~limite à 10, et en plus~~ il faut cliquer sur les échantillons un par un).
Avoir sur la page d'un set un bouton "preview all samples" qui fait tout cela d'un coup ? (Derrière, le ~"server-fuse" a déjà été lancé s'ils sont dans le même set #4538)Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/3901Faire une première config spike/MRD de test2023-06-28T17:34:41+02:00Mathieu GiraudFaire une première config spike/MRD de testvidjil#3838
Prendre le script de Joao ?
Un autre "jouet" (par exemple divise par 2 IGH mais pas TRG) ?vidjil#3838
Prendre le script de Joao ?
Un autre "jouet" (par exemple divise par 2 IGH mais pas TRG) ?Web 2023.10Thonier FlorianThonier Florian2021-09-24https://gitlab.inria.fr/vidjil/vidjil/-/issues/3332Client : aligner avec EndWithSomeDeletions pour l'alignement contre les germl...2023-03-28T16:19:43+02:00Mathieu GiraudClient : aligner avec EndWithSomeDeletions pour l'alignement contre les germlinesQuand le V se termine par 7 délétions, actuellement ces 7 nucléotides sont répartis de manière non optimale.
- Avoir un alignement comme il faut
- Améliorer l'affichage (grisés, barrés ?) #2599
(@mikael\-s: une telle issue existait p...Quand le V se termine par 7 délétions, actuellement ces 7 nucléotides sont répartis de manière non optimale.
- Avoir un alignement comme il faut
- Améliorer l'affichage (grisés, barrés ?) #2599
(@mikael\-s: une telle issue existait peut-être déjà)Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/2710Méta-données de démo réalistes, utiliser ci.sql dans les tests, tests unitair...2024-01-25T14:15:00+01:00Mathieu GiraudMéta-données de démo réalistes, utiliser ci.sql dans les tests, tests unitaire qui vérifient vraiment les réponsesJe suis en train de mettre sur `dev` (user `u3`) un jeu de données crédible, notamment avec des tags #2683 un peu cohérents. Essai d'une liste de noms un peu variée, bien que fort occidentale, mais bon, ~"ec-ngs". Voir si, quand ce sera ...Je suis en train de mettre sur `dev` (user `u3`) un jeu de données crédible, notamment avec des tags #2683 un peu cohérents. Essai d'une liste de noms un peu variée, bien que fort occidentale, mais bon, ~"ec-ngs". Voir si, quand ce sera fait, on essaie de récupérer les tags pour une série de screenshots.
```
Florbela Espanca 1894-12-08
Paulina Wilkońska 1815
Camilla Collett 1813-01-23
Διονύσιος Σολωμός 1798-04-08
Vasile Alecsandri 1801-07-21
Sophia Elisabet Brenner 1659-04-29
Marin Držić 1508
老子 6 BCE
Emil Aarestrup 1800-12-04
Božena Němcová 1820-02-04
ابن خلدون (Ibn Khaldoûn), 1332-05-27
Willem Bilderdijk 1756-09-07
Johann Wolfgang Goethe, 1749-08-28
George Sand 1804-02-01
Dante Alighieri 1265
Friedrich von Schiller 1759
Miguel de Cervantes 1547-09-29
Jane Austeen 1775-12-16
```Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/2443Updated ERIC recommendations2023-03-28T16:20:07+02:00Mathieu GiraudUpdated ERIC recommendationsTransmis par Stéphanie ~"LIL-Lille" :
Rosenquist et al., [Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia: updated ERIC recommendations](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508071/), doi:10.1038/leu.2017.1...Transmis par Stéphanie ~"LIL-Lille" :
Rosenquist et al., [Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia: updated ERIC recommendations](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508071/), doi:10.1038/leu.2017.125
Quelles sont les recommandations ? A-t-on des choses à implémenter/corriger dans le ~"client-segmenter" ?
cc @flothoniWeb 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/2309UMI / traitement des identifiants moléculaires uniques2023-06-28T17:22:53+02:00Mathieu GiraudUMI / traitement des identifiants moléculaires uniquesÀ ma grande surprise, je n'ai pas retrouvé d'issue parlant de ces barcodes. Existe-t-il des scripts standard pour traiter ces données ? On en ferait un ~"server-pre-process" ? Des jeux publics sur lesquels on pourrait tester cela, ou bi...À ma grande surprise, je n'ai pas retrouvé d'issue parlant de ces barcodes. Existe-t-il des scripts standard pour traiter ces données ? On en ferait un ~"server-pre-process" ? Des jeux publics sur lesquels on pourrait tester cela, ou bien un jeu de @mfigeac ?
cc @mikael-sWeb 2023.10Thonier FlorianThonier Florian2023-07-05https://gitlab.inria.fr/vidjil/vidjil/-/issues/1614Faire une CSS de présentation / screenshot2023-03-28T16:21:06+02:00Vidjil TeamFaire une CSS de présentation / screenshotUtilisation : démo, mais aussi discussion patients autour d'une table. On se focalise sur le graphe, la grid, éventuellement sur les séquences.
- tous les textes plus gros (labels, séquences)
- masquer l'info / la liste des clones
...Utilisation : démo, mais aussi discussion patients autour d'une table. On se focalise sur le graphe, la grid, éventuellement sur les séquences.
- tous les textes plus gros (labels, séquences)
- masquer l'info / la liste des clones
(ou sinon, les compresser)
- masquer des boutons non essentiels
Comme ce sera dans le menu "palette", on pourra aisément basculer de la vue normale à cette vue.
***
@nobodyWeb 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/1589API des controlleurs : documenter2023-06-29T10:23:44+02:00Vidjil TeamAPI des controlleurs : documenterPour que Martin puisse faire ce qu'il veut, il faudrait documenter quelques controlleurs.Pour que Martin puisse faire ce qu'il veut, il faudrait documenter quelques controlleurs.Web 2023.10https://gitlab.inria.fr/vidjil/vidjil/-/issues/5215py4web; wrong link to open results in sets pages (all configs appear)2024-01-19T15:21:19+01:00THONIER Florianpy4web; wrong link to open results in sets pages (all configs appear)We got link to results with all availabel configs launched. (https://localhost/index.html?sample_set_id=1&config=2,3).
In this case, we cannot open a result.
Need to be fixed before release.We got link to results with all availabel configs launched. (https://localhost/index.html?sample_set_id=1&config=2,3).
In this case, we cannot open a result.
Need to be fixed before release.Server - py4webhttps://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/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/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/5214Release 2024.012024-02-16T14:06:16+01:00THONIER FlorianRelease 2024.01
### Before the deploy
- [x] Set the deploy day (Most servers are busy on Mondays and Tuesdays. Web deploys are usually done on Wednesday.) : 23-24 January
- [x] Before the MR freeze, discuss regularly in the team what remains to do
W...
### Before the deploy
- [x] Set the deploy day (Most servers are busy on Mondays and Tuesdays. Web deploys are usually done on Wednesday.) : 23-24 January
- [x] Before the MR freeze, discuss regularly in the team what remains to do
Wednesday (D-8)
- [x] Notification on the server
- [x] MR Freeze (everything except urgent fixes or bikeshed strings/~doc)
- [x] Move issues/MR that are still opened to a new milestone for the next release
- [x] Push on `feature-cs/release`
### Deploy week
- [x] Deploy on `dev`, either with `git pull` or with Docker
- [x] Live tests on `dev`
On `feature-cs/release`:
- [x] Bikeshed strings
- [x] List all the changes, checking that the milestone contains all relevant issues/MR
- [x] Finalize `CHANGELOG.web`
- [x] Finalize ~doc
- [x] Finalize `docker/CHANGELOG`
Monday 22 (D-1)
- [x] MR Freeze (everything)
### Deploy day
Tuesday 23 (D0)
- [x] Morning: update notification on the server
- [x] MR `feature-cs/release` to `prod-client` !1318 and `prod-server` !1401
- [x] Disconnect the client through `conf.js`
- [x] Deploy
- [x] Link vidjil-algo to latest if needed
- [x] Live test on the prod server
- [x] Reconnect the client
- [x] Notification "Maintenance finished" + news
- [x] Possibly mail to users
- [x] Merge `feature-cs/release` into `dev` and `master`, and `git push github`Server - py4webhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5213py4web; loading analysis is not working2024-01-18T08:10:49+01:00THONIER Florianpy4web; loading analysis is not workingWhen we try to load an analysis from a py4web server, we got an error.
It seem to be some minor change between python 2.7 and python3 (`AttributeError: 'dict' object has no attribute 'iterkeys'`).
I take a look to fix that.When we try to load an analysis from a py4web server, we got an error.
It seem to be some minor change between python 2.7 and python3 (`AttributeError: 'dict' object has no attribute 'iterkeys'`).
I take a look to fix that.Server - py4webTHONIER FlorianTHONIER Florianhttps://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/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/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/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 Clement