D-GENIES issueshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues2018-01-23T10:26:58+01:00https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/103Remove BDD2018-01-23T10:26:58+01:00Floreal CabanettesRemove BDDTest with 240 concurrent jobs splitted in 4 groups (4 users). 8 jobs failed because of two much opened connections.
For jobs, we can replace BDD by a file in each job folder.
For sessions, may be we can replace BDD by a storage in memo...Test with 240 concurrent jobs splitted in 4 groups (4 users). 8 jobs failed because of two much opened connections.
For jobs, we can replace BDD by a file in each job folder.
For sessions, may be we can replace BDD by a storage in memory...1.0Floreal CabanettesFloreal Cabanettes2018-01-19https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/107Clean session status links and job status links on clear sessions/jobs and pe...2018-01-23T10:24:20+01:00Floreal CabanettesClean session status links and job status links on clear sessions/jobs and periodicallySome fails may keep bad links...Some fails may keep bad links...1.0Floreal CabanettesFloreal Cabanettes2018-01-22https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/109Run a job: if we choose a file, and then we switch to URL, the size of the fi...2018-01-29T10:50:50+01:00Floreal CabanettesRun a job: if we choose a file, and then we switch to URL, the size of the file don't disappearMake it hiddenMake it hidden1.0Floreal CabanettesFloreal Cabanettes2018-01-25https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/108Error: MySQL server has gone away2018-01-29T11:58:46+01:00Floreal CabanettesError: MySQL server has gone awayHappens after 1 day. We must restart mysql and apache to restore the website.Happens after 1 day. We must restart mysql and apache to restore the website.1.0Floreal CabanettesFloreal Cabanettes2018-01-26https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/111Summary: fail for big data: timeout2018-01-31T15:12:42+01:00Floreal CabanettesSummary: fail for big data: timeout1.0Floreal CabanettesFloreal Cabanettes2018-02-02https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/110Download of query: remove contigs not present in the index2018-01-29T16:06:39+01:00Floreal CabanettesDownload of query: remove contigs not present in the indexBecause they has been filtered outBecause they has been filtered out1.0Floreal CabanettesFloreal Cabanettes2018-02-02https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/106Fix big data in all-vs-all mode2018-02-05T17:09:07+01:00Floreal CabanettesFix big data in all-vs-all modeIn all-vs-all mode (only target is given), no split is done. Probably for that reason, we need too much memory and time...
Solutions:
- Limit all-vs-all mode to small or medium analysis (done in 1/2 h)
- Split target (so target and quer...In all-vs-all mode (only target is given), no split is done. Probably for that reason, we need too much memory and time...
Solutions:
- Limit all-vs-all mode to small or medium analysis (done in 1/2 h)
- Split target (so target and query [the same as the target] will be splitted... We must change the code to take that in account: needs more work (1/2 day)1.0Floreal CabanettesFloreal Cabanettes2018-02-02https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/113Summary stats failed on big data2018-02-02T16:23:06+01:00Floreal CabanettesSummary stats failed on big dataHuman VS Chimp for example.
Too much memory is used, it make the server unresponding...
Fixes propals:
- Change the algorithm to use less memory
- Make summary on job run, save it and just show it on button clickHuman VS Chimp for example.
Too much memory is used, it make the server unresponding...
Fixes propals:
- Change the algorithm to use less memory
- Make summary on job run, save it and just show it on button click1.0Floreal CabanettesFloreal Cabanettes2018-02-09https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/121Check XSS and other security breaches2018-02-19T14:48:41+01:00Floreal CabanettesCheck XSS and other security breaches1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/118Sometimes (on windows at least) flask is really long to start. Check flask is...2018-02-15T14:12:14+01:00Floreal CabanettesSometimes (on windows at least) flask is really long to start. Check flask is already started before launch the browser1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/117Standalone version: problem with treatments which requires mail2018-02-16T14:08:51+01:00Floreal CabanettesStandalone version: problem with treatments which requires mailTwo possibilities:
- disable them on standalone version
- change code to be compatible withTwo possibilities:
- disable them on standalone version
- change code to be compatible with1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/116Remove "you will receive a mail...." on standalone version2018-02-15T14:12:14+01:00Floreal CabanettesRemove "you will receive a mail...." on standalone version1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/130Check index files are correct, like other files2018-04-11T18:23:57+02:00Floreal CabanettesCheck index files are correct, like other files1.1Floreal CabanettesFloreal Cabanettes2018-04-12https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/133Job fail if input files contains spaces2018-07-05T17:53:35+02:00Floreal CabanettesJob fail if input files contains spacesFix: after upload, replace spaces by underscoreFix: after upload, replace spaces by underscore1.1.*Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/97Concurrent jobs failed2018-01-12T14:21:32+01:00Floreal CabanettesConcurrent jobs failedIf we have a lot of jobs (more than 10), we have errors due to no correct update of the BDD. It happens with Sqlite. We must check with Mysql and check it solves the problem.If we have a lot of jobs (more than 10), we have errors due to no correct update of the BDD. It happens with Sqlite. We must check with Mysql and check it solves the problem.1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/95Catch malformed errors server side and client side2018-01-04T13:31:38+01:00Floreal CabanettesCatch malformed errors server side and client sideFor example, must start with http(s)?:// or ftp://
Server side, catch the exceptionFor example, must start with http(s)?:// or ftp://
Server side, catch the exception1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/94Add check on file upload size server side2018-01-04T13:05:59+01:00Floreal CabanettesAdd check on file upload size server side1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/88Si on met le même id plus de 2 fois dans la soumission d'un job, ça plante (o...2017-12-05T17:25:12+01:00Floreal CabanettesSi on met le même id plus de 2 fois dans la soumission d'un job, ça plante (on passe pas à _3)1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/86Reverse contigs: do a reverse complement, not just reverse the sequence2017-11-21T10:15:25+01:00Floreal CabanettesReverse contigs: do a reverse complement, not just reverse the sequence1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/73Timeout if sort is too long2017-11-14T17:23:18+01:00Floreal CabanettesTimeout if sort is too longAs sort is done server-side, if it's too long we have a timeout (because we are not asynchronous).
Solutions:
- Limit number of lines taken in account for the sort (not sure it solves the problem, may be a problem for export fasta etc.....As sort is done server-side, if it's too long we have a timeout (because we are not asynchronous).
Solutions:
- Limit number of lines taken in account for the sort (not sure it solves the problem, may be a problem for export fasta etc...)
- Make it asynchronous:
- By a websocket connection. If chosen, could also be used for the status page
- By a regular server call by the client (it's not the best choice... :-( )
- Make the sort on job launch and save it. Just load it on click on the sort button. Solves the problem, but job takes more time (juste few seconds in general...) and the server could do it while the user will never want the sorted version.1.0Floreal CabanettesFloreal Cabanettes