vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2020-06-25T19:53:21+02:00https://gitlab.inria.fr/vidjil/vidjil/-/issues/4261Upgrade issue with classification2020-06-25T19:53:21+02:00Mikaël SalsonUpgrade issue with classification@meidanis points out that his upgrade failed following !627:
>Hi Guys! That's great! You created a field to allow administrators to sort the analysis configs in a custom order, instead of alphabetical order. At least that's what I under...@meidanis points out that his upgrade failed following !627:
>Hi Guys! That's great! You created a field to allow administrators to sort the analysis configs in a custom order, instead of alphabetical order. At least that's what I understood with my so-so- French reading the comment to merge request !627 (merged).
>
>This, however, posed a problem for me. My database doesn't have this field. So, I guess I'll have to do the procedure under "Migrating data" in the documentation, re-create a Vidjil installation from scratch, and, when I load back my database, the field will be there, and the vidjil_utils.py script will take care of initializing the classification field.
>
>Is that it? I'll be glad to do it. Just confirm that this is indeed the process. And I guess I will have to do that every time the database changes.https://gitlab.inria.fr/vidjil/vidjil/-/issues/4024Clones with different analyses at diagnosis and follow-up2019-10-28T12:56:03+01:00Mathieu GiraudClones with different analyses at diagnosis and follow-upUsers sometimes report sequences with different analyses at diagnosis and follow-up (link to old issue ?)
@meidanis has recently seen such sequences (could you share them?).
The main reason is probably #3970. See also #2726.
We have to ...Users sometimes report sequences with different analyses at diagnosis and follow-up (link to old issue ?)
@meidanis has recently seen such sequences (could you share them?).
The main reason is probably #3970. See also #2726.
We have to be sure and to investigate and/or document things.
cc @flothoni https://gitlab.inria.fr/vidjil/vidjil/-/issues/3964Running MiXCR through Vidjil2020-09-28T16:44:10+02:00Mathieu GiraudRunning MiXCR through VidjilReported by @meidanis :
> The first thing his analysis does is to combine R1 and R2. Shall I do
this as a pre-processing step? That was my inclination, but I'm not sure
the resulting file from "mixcr align" is a fastq file. Maybe it ...Reported by @meidanis :
> The first thing his analysis does is to combine R1 and R2. Shall I do
this as a pre-processing step? That was my inclination, but I'm not sure
the resulting file from "mixcr align" is a fastq file. Maybe it is
written in some other format. How can I continue the analysis then?
> Even if I continue the analysis calling mixcr again for the next step,
will it produce a `.vidjil` file? Does it know how to do that?
> Finally, is mixcr (the binary, executable) already installed in the
containers?
cc @flothoni @mikael-sThonier FlorianThonier Florian2019-12-20https://gitlab.inria.fr/vidjil/vidjil/-/issues/3929conf.js : addons2022-10-04T16:35:32+02:00Mathieu Giraudconf.js : addonsSee #2444
`addons = ['foo.js', 'bar.js']` in `conf.js` should load these files at the end of `app.js`See #2444
`addons = ['foo.js', 'bar.js']` in `conf.js` should load these files at the end of `app.js`https://gitlab.inria.fr/vidjil/vidjil/-/issues/3927Mounted files / network : docker, documentation2020-03-23T13:03:53+01:00Mathieu GiraudMounted files / network : docker, documentation@meidanis had a question on the "from my computer" / "from the network" choice when uploading.
- Is it normal that he sees this choice as this is not configured ?
- Did we document this feature ?@meidanis had a question on the "from my computer" / "from the network" choice when uploading.
- Is it normal that he sees this choice as this is not configured ?
- Did we document this feature ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/3925No spike normalization and disconnected lines2019-07-15T11:33:22+02:00Mathieu GiraudNo spike normalization and disconnected lines@meidanis has situations where the diagnosis point was not normalized (when there is no / a few spike-ins, this is the good way to go).
In this case, there were no lines between the clones in the ~"client-graph". He will send us the `.v...@meidanis has situations where the diagnosis point was not normalized (when there is no / a few spike-ins, this is the good way to go).
In this case, there were no lines between the clones in the ~"client-graph". He will send us the `.vidjil` files before and after normalization.
cc @flothonihttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3838Flexible strategy for MRD (and other things)2019-10-14T18:00:34+02:00Mathieu GiraudFlexible strategy for MRD (and other things)Discussed with @meidanis @mikael\-s @flothoni
- In `/spikes/spikes-A.json` :
```
'config': {
'labels': [
{ 'name': 'foobar', 'sequence': 'ACGTG...', 'copies': xxx, 'family'... }
```
- the ~"server\-config" says:
- la...Discussed with @meidanis @mikael\-s @flothoni
- In `/spikes/spikes-A.json` :
```
'config': {
'labels': [
{ 'name': 'foobar', 'sequence': 'ACGTG...', 'copies': xxx, 'family'... }
```
- the ~"server\-config" says:
- launch `vidjil-algo --label-json /spikes/spikes-A.json ....`
- launch `fuse.py --pre normalize.py`
- `vidil-algo` will understand only `name` and `sequence`, but will copy everything from `spikes-A.json`, including `copies` or other fields, to its `.vidjil` output #3837 #3839
- `normalize.py` adds `normalized_reads` where he wants (@meidanis)https://gitlab.inria.fr/vidjil/vidjil/-/issues/3684Mieux documenter --label2019-03-14T09:27:42+01:00Mathieu GiraudMieux documenter --labelLe filtrage est fait dans `WindowsStorage::getLabel(junction window) `, introduit en partie par 14602c2292.Le filtrage est fait dans `WindowsStorage::getLabel(junction window) `, introduit en partie par 14602c2292.Algo 2018.12https://gitlab.inria.fr/vidjil/vidjil/-/issues/3663Bikeshedding normalisation2022-04-25T16:58:09+02:00Mathieu GiraudBikeshedding normalisationAprès !378 :
- libellé exact des menus
- icône
Je m'en occuperai la semaine prochaineAprès !378 :
- libellé exact des menus
- icône
Je m'en occuperai la semaine prochainehttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3662Afficher dans getHtmlInfo les valeurs normalized_reads2018-12-28T11:39:43+01:00Mathieu GiraudAfficher dans getHtmlInfo les valeurs normalized_readscc @flothonicc @flothonihttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3661Enlever les choix "External" et "Expected" s'il ne sont pas pertinents2018-12-31T09:15:06+01:00Mathieu GiraudEnlever les choix "External" et "Expected" s'il ne sont pas pertinentscc @flothonicc @flothonihttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3650How does the user see the normalized_reads field?2019-01-10T15:21:23+01:00Mathieu GiraudHow does the user see the normalized_reads field?Raised by @meidanis on #3645.
(We do not directly display `normalized_reads`, but ratios computed with this number, and depending on what is selected)
We could have something like `(17 reads (0.19%), 18.5 normalized (0.23%))` that coul...Raised by @meidanis on #3645.
(We do not directly display `normalized_reads`, but ratios computed with this number, and depending on what is selected)
We could have something like `(17 reads (0.19%), 18.5 normalized (0.23%))` that could be shown on the detailed information window, but we definitely need a short version.
It could be (17 reads is the actual number of reads, 0.23% is the ratio computed with `normalized_reads`):
- `17 reads (0.23%)`
- `17 reads (0.23%N)`
- `17 reads (0.23)`
Note that most of the people that will use this feature will probabibly always have normalized reads (even with #3648). It's probably better not to disturb them with too many information and to show them something simple.
cc @mikael\-s @flothoni https://gitlab.inria.fr/vidjil/vidjil/-/issues/3648Enable to switch between normalized_reads and other modes of normalization (i...2019-03-22T14:52:17+01:00Mathieu GiraudEnable to switch between normalized_reads and other modes of normalization (including no normalization)See #3645.See #3645.Thonier FlorianThonier Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3647Pre-/post- options in fuse to implement a post-process2020-12-11T12:32:00+01:00Mathieu GiraudPre-/post- options in fuse to implement a post-processInstead of resolving #3538 (that is ~"!\-hard"), @flothoni proposed a solution with ~"server\-fuse" to implement a post-process and still to be admin-configurable by configs.
A post-process programm is something that takes a `.vidjil` f...Instead of resolving #3538 (that is ~"!\-hard"), @flothoni proposed a solution with ~"server\-fuse" to implement a post-process and still to be admin-configurable by configs.
A post-process programm is something that takes a `.vidjil` file and give back another `.vidjil` file.
We implement two `--pre` and `--post` options to ~"server\-fuse"
- `--pre progname` will lauch `progname in.vidjil in2.vidjil` on each `in.vidjil` input file.
- `--post progname` will lauch `progname out.vidjil out2.vidjil` on the collated `out.vidjil` filehttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3646Document normalize_reads in doc/vidjil-format.md2023-03-28T16:34:30+02:00Mathieu GiraudDocument normalize_reads in doc/vidjil-format.md#3645#3645Web 2021.05https://gitlab.inria.fr/vidjil/vidjil/-/issues/3645Extend normalization with custom normalized_reads2018-12-28T08:13:10+01:00Mathieu GiraudExtend normalization with custom normalized_readsAter #3644, implement `normalized_reads` handling in `normalize()`Ater #3644, implement `normalized_reads` handling in `normalize()`Thonier FlorianThonier Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3644Refactor normalisation2018-12-28T08:13:43+01:00Mathieu GiraudRefactor normalisationTalked with @mikael\-s et @flothoni
Proposed solution:
- model.js: normalize() looks directly to `m.norm`
- clone.js: a new `getNormalizedReads()` *always* calls `m.normalize()`
- clone.js: all `get*Size()` functions call `getNormalize...Talked with @mikael\-s et @flothoni
Proposed solution:
- model.js: normalize() looks directly to `m.norm`
- clone.js: a new `getNormalizedReads()` *always* calls `m.normalize()`
- clone.js: all `get*Size()` functions call `getNormalizedReads()`
Thonier FlorianThonier Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/3472L'image docker pose des soucis sur l'accès des configurations2018-12-20T17:45:44+01:00Thonier FlorianL'image docker pose des soucis sur l'accès des configurationsEn testant l'installation par docker, je me rends compte que les utilisateurs n'ont accès ni aux configurations ni au preprocess si l'accès ne leur a pas été *spécifiquement fourni* en tant qu'user.
Cela signifie que le configurations ...En testant l'installation par docker, je me rends compte que les utilisateurs n'ont accès ni aux configurations ni au preprocess si l'accès ne leur a pas été *spécifiquement fourni* en tant qu'user.
Cela signifie que le configurations `public` ne sont pas accessibles.
Je ne sais pas si il s'agit d'un bug car j'installe avec des erreurs ou bien si c'est la dernière image qui est buggé. A noter que l'installation par docker au Brésil présente la même anomalie.
cc @RyanHerb ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/2444Customisation du client pour certains utilisateurs ou groupes2021-04-17T06:24:27+02:00Mathieu GiraudCustomisation du client pour certains utilisateurs ou groupesPour #1684 ou d'autres, on pourrait être tenté de faire des axes d'analyse pour certains utilisateurs, non visibles des autres. Plus généralement, on aimerait aussi parfois donner "certaines" fonctionnalités à certains utilisateurs, qu'e...Pour #1684 ou d'autres, on pourrait être tenté de faire des axes d'analyse pour certains utilisateurs, non visibles des autres. Plus généralement, on aimerait aussi parfois donner "certaines" fonctionnalités à certains utilisateurs, qu'elles soient en développement ou pertinentes pour quelques utilisateurs (#2043). Le `devel-mode` et le `beta-mode` peuvent être une solution, mais ce n'est pas très flexible...
On pourrait donner accès à un autre client, statique, quelque part, avec du `.js` modifié. Ou souhaite-t-on pouvoir donner un bout de `.js` en fonction de l'utilisateur ? Le ~server serait agnostique par rapport à cela, on aurait juste un `lille.js` quelque part ? ou bien en champ un base de données ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/1726Évolution clonale : changement de V (V switch), similarité VDJ-aware2022-06-17T12:39:29+02:00Vidjil TeamÉvolution clonale : changement de V (V switch), similarité VDJ-awareEuh ? Demander à Bruxelles ?
***
Je ne me souviens plus des détails, mais c'était venu à Zurich lors d'une discussion avec Marleen ~"BRU-Bruxelles" et Hélène ~"PAR-Debré". Les relancer avant, ou au pire en discuter lors du VW.
***
Disc...Euh ? Demander à Bruxelles ?
***
Je ne me souviens plus des détails, mais c'était venu à Zurich lors d'une discussion avec Marleen ~"BRU-Bruxelles" et Hélène ~"PAR-Debré". Les relancer avant, ou au pire en discuter lors du VW.
***
Discuté au VW. Mail de Cristina ~"PAR-Debré" :
> voici l'URL correspondant au patient que nous avons regardé tout à l'heure (locus IgH oligoclonal), passé sur le Miseq en V3 avec le kit LymphoTrack FR1 : http://app.vidjil.org/browser/?patient=1292&config=25. Il s'agit d'un VH4DH3JH6 et d'un VH6DH3JH6, partageant donc le même D-J.
***
Faire un calcul de similarité V/D/J-aware, capable de dire : "oh, ces séquences sont très similaires avec une certaine e-valeur car N2/J similaire"... Et le lancer par exemple via le browser comme "plot by similarity"
(Problème: sera dépendant du seuil de détection de D.)
En lien aussi avec modèle de proba d'une recombinaison (Bristol fait cela).
***
- soit un calcul de similarité directement sur la représentation sortie du FineSegmenter
- soit, plus précis, on fait cela directement en programmation dynamique, aligner deux séquences en connaissant leur AligBox, et avoir un score différent pour les N.
***
@magiraud @mikael-s