vidjil issueshttps://gitlab.inria.fr/vidjil/vidjil/-/issues2024-02-13T12:48:37+01:00https://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/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/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/5176Similarity between clones; Add shortcut to select similar clonotype.2023-10-19T14:51:18+02:00THONIER FlorianSimilarity between clones; Add shortcut to select similar clonotype.Thinking about shourtcut on similarity:
* Shift+click on a clonotype: Select clone + similar clonotype. Doable after #5175
* Shift+ctrl+click on a clonotype: Select all clone with same V/J ?Thinking about shourtcut on similarity:
* Shift+click on a clonotype: Select clone + similar clonotype. Doable after #5175
* Shift+ctrl+click on a clonotype: Select all clone with same V/J ?https://gitlab.inria.fr/vidjil/vidjil/-/issues/5175Warning similarity; Position not correct after a fuse2023-10-19T14:51:00+02:00THONIER FlorianWarning similarity; Position not correct after a fuseFor the moment, we throw some warning on similarities between clones. (Similar to clone "\#1 - TRGV9*01 0/AC/1 TRGJ1*02").
After a fuse, clone \#1 is not correct. We need to update this position at the fuse.
In fact, even without fuse w...For the moment, we throw some warning on similarities between clones. (Similar to clone "\#1 - TRGV9*01 0/AC/1 TRGJ1*02").
After a fuse, clone \#1 is not correct. We need to update this position at the fuse.
In fact, even without fuse with other sample, position is false (see https://app.vidjil.org/3296-25?clone=42,64).https://gitlab.inria.fr/vidjil/vidjil/-/issues/5174Show N in sequence with a color2023-10-18T14:51:01+02:00THONIER FlorianShow N in sequence with a colorSome sequences have a N. We could probably give them a specific color to easily identify them in the interface.Some sequences have a N. We could probably give them a specific color to easily identify them in the interface.THONIER FlorianTHONIER Florianhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5172consensus sequence length: mix of sequence with a nucleotide mix at a positio...2023-10-18T17:56:11+02:00THONIER Florianconsensus sequence length: mix of sequence with a nucleotide mix at a position in the V geneSee sample 59910-50, with either configurations [IGH](https://app.vidjil.org/59910-2?clone=26) or [no-clusterign](https://app.vidjil.org/59910-50?).
We can see that in multi, top clonotype have a short consensus length for read that are...See sample 59910-50, with either configurations [IGH](https://app.vidjil.org/59910-2?clone=26) or [no-clusterign](https://app.vidjil.org/59910-50?).
We can see that in multi, top clonotype have a short consensus length for read that are able to get entire V gene. We can see in no clustering that top 2 clonotypes have a mix of C/T at this specific position that cut the consensus sequence.
In these case, maybe we can extend consensus but show (but how?) the mix of nucleotides.
* bypass mix with a color scale to represent variation. Can also be used to show variation in case of merge of clonotype.
* hover can show precise values variationhttps://gitlab.inria.fr/vidjil/vidjil/-/issues/5167Can create generic set with some rules to select samples to import2023-10-11T18:14:43+02:00THONIER FlorianCan create generic set with some rules to select samples to importI want for a meta-analysis create a set with some samples that have in my case a similar tags.
That make me think about a dynamic playlist for music, with a list of rules to compose it.
It could be usefull to be able de to create a set...I want for a meta-analysis create a set with some samples that have in my case a similar tags.
That make me think about a dynamic playlist for music, with a list of rules to compose it.
It could be usefull to be able de to create a set by giving some rules, for example tags, number of reads, age of patient, disease, ...).
In this case, sample of a set should probably be constant with a refresh button if needed to update list.
This would improve usage of server for research purpose I presume.
This usage could also be benifit for appstats.
A button to generate a fuse without needing of relaunch an analysis should also be present I think.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5153Envoyer les données vers vdj.online2023-07-13T09:22:10+02:00Mikaël SalsonEnvoyer les données vers vdj.onlinehttps://vdj.online/
Service de MiXCR.
À discuter, peut-être pas très pratique à intégrer, car il faut renseigner pas mal d'info sur le protocole expérimental.https://vdj.online/
Service de MiXCR.
À discuter, peut-être pas très pratique à intégrer, car il faut renseigner pas mal d'info sur le protocole expérimental.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5150Follow-up from "Feature sc/remove watir testing complete"2023-11-06T14:31:53+01:00THONIER FlorianFollow-up from "Feature sc/remove watir testing complete"The following discussion from !1324 should be addressed:
- [ ] @fthonier started a [discussion](https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1324#note_847594):
> Make a new MR to import these testsThe following discussion from !1324 should be addressed:
- [ ] @fthonier started a [discussion](https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1324#note_847594):
> Make a new MR to import these testshttps://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/5148Open an analysis by drag and drop2023-05-24T15:25:31+02:00THONIER FlorianOpen an analysis by drag and dropSometimes, I want to open a local vidjil file in the client. It is always frustratting to navigate to the correct file that is 10 click away from the current location but to see it in my navigator and not be able to draging it in the cli...Sometimes, I want to open a local vidjil file in the client. It is always frustratting to navigate to the correct file that is 10 click away from the current location but to see it in my navigator and not be able to draging it in the client directly.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5142Huge lengths in the read length distribution2023-06-21T15:20:21+02:00Mikaël SalsonHuge lengths in the read length distributionIn those samples, the read length distribution plot ranges from 0 to 6,500, which seems quite a lot: https://app.vidjil.org/57055-2?plot=Reads%20length,J/3%27%20gene,bar
The data doesn't look like 3rd generation sequencing.In those samples, the read length distribution plot ranges from 0 to 6,500, which seems quite a lot: https://app.vidjil.org/57055-2?plot=Reads%20length,J/3%27%20gene,bar
The data doesn't look like 3rd generation sequencing.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5141Read length distribution shows wrong sizes2024-01-22T15:22:21+01:00Mikaël SalsonRead length distribution shows wrong sizesOn these samples, I find that the read length distribution plot starts at -10% (!): https://app.vidjil.org/57056-25?plot=Reads%20length,Size,bar
It seems that the labels are not at their correct place. Even the main clone which is at 36...On these samples, I find that the read length distribution plot starts at -10% (!): https://app.vidjil.org/57056-25?plot=Reads%20length,Size,bar
It seems that the labels are not at their correct place. Even the main clone which is at 36%, only reaches 20% on the plot.Web 2024.04https://gitlab.inria.fr/vidjil/vidjil/-/issues/5138Upload: Avertir dans le client quand les noms de fichiers ne respectent pas R...2023-05-04T15:44:06+02:00Mathieu GiraudUpload: Avertir dans le client quand les noms de fichiers ne respectent pas R1/R2
Normalement, on s'attend à exactement le même nom, avec juste R1 qui est changé en R2.
Si ce n'est pas le cas, avertir.
Soucis humains possibles qui seront diagnostiqués ainsi:
- deux fois le même fichier R1 (et ensuite flash fait des ...
Normalement, on s'attend à exactement le même nom, avec juste R1 qui est changé en R2.
Si ce n'est pas le cas, avertir.
Soucis humains possibles qui seront diagnostiqués ainsi:
- deux fois le même fichier R1 (et ensuite flash fait des choses, mais on ne détecte pas d'où vient le problème)
- ou on se plante de fichier R1/R2
- ou on inverse R1/R2https://gitlab.inria.fr/vidjil/vidjil/-/issues/5124Fuse; How to merge clonotype with various windows/ids length ?2023-03-01T10:54:49+01:00THONIER FlorianFuse; How to merge clonotype with various windows/ids length ?I was looking on analysis made with multiple configurations on the same sample file.
Window length parameter is not constant and the fuse don't work.
How can we resolve this ? I was naively thinking about `if the smaller window fit ins...I was looking on analysis made with multiple configurations on the same sample file.
Window length parameter is not constant and the fuse don't work.
How can we resolve this ? I was naively thinking about `if the smaller window fit inside the bigger we can merge`. But in this case, with the longer windows configuration, a clonotype on configuration `multi` (windows of 60nt length) is splitted into multiple smaller clonotype for configuration `clonality` (full sequence windows).
It is a one-to-many relationship. If it is easy to create a link at the fuse step, how to use it in client ?https://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/5117artifact sequence; be able to substract them from number of reads2023-01-25T17:30:48+01:00THONIER Florianartifact sequence; be able to substract them from number of readsWhen a clone is tagged as noise/artifact, we should offer the possiblity to subsrat is value from what is proportion of reads shown.
ex: IGH D7-27//J1. If it is seen at 50% and hidden or tagged as noise, other clone still at the same s...When a clone is tagged as noise/artifact, we should offer the possiblity to subsrat is value from what is proportion of reads shown.
ex: IGH D7-27//J1. If it is seen at 50% and hidden or tagged as noise, other clone still at the same size.https://gitlab.inria.fr/vidjil/vidjil/-/issues/5101Sample; show a little bar graph to show segmentation repartition and locus2022-12-20T13:48:58+01:00Thonier FlorianSample; show a little bar graph to show segmentation repartition and locusSomething like [on old ipod](https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcR6AmcfB2oBlMiTXDv5LzvJK8ArsuMCTacF3A&usqp=CAU)
Need to convert our log into structured data. (And to be able to retro-convert old data from string values).Something like [on old ipod](https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcR6AmcfB2oBlMiTXDv5LzvJK8ArsuMCTacF3A&usqp=CAU)
Need to convert our log into structured data. (And to be able to retro-convert old data from string values).https://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 2023.10