D-GENIES issueshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues2018-02-19T14:48:41+01:00https://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/120Add a button to delete a job2018-02-16T18:03:13+01:00Floreal CabanettesAdd a button to delete a jobAdd protected jobs (for webserver mode) which cannot be deleted by this button. Or all gallery jobs are protected.Add protected jobs (for webserver mode) which cannot be deleted by this button. Or all gallery jobs are protected.1.0Floreal CabanettesFloreal Cabanettes2018-02-20https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/119In standalone mode, load all jobs on startup to add them in the result menu2018-02-16T18:51:10+01:00Floreal CabanettesIn standalone mode, load all jobs on startup to add them in the result menu1.0Floreal CabanettesFloreal Cabanettes2018-02-20https://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/115Windows compatibility2018-02-22T10:55:48+01:00Floreal CabanettesWindows compatibilityCheck program is compatible for windows in standalone mode, and make required changes to make it compatible.Check program is compatible for windows in standalone mode, and make required changes to make it compatible.1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/114Standalone version2018-02-08T17:44:09+01:00Floreal CabanettesStandalone versionTo launch D-Genies on a local computer, with only 1 user.To launch D-Genies on a local computer, with only 1 user.1.0Floreal CabanettesFloreal Cabanettes2018-02-23https://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/112Add a table beside the gallery items with times and memory usage for all items2018-02-05T16:21:19+01:00Floreal CabanettesAdd a table beside the gallery items with times and memory usage for all items1.0Floreal CabanettesFloreal Cabanettes2018-02-02https://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/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/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/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/105Improve databases2018-01-18T11:04:46+01:00Floreal CabanettesImprove databasesFor Job and Session:
- new is a classe method that create the new object from informations given (as now, but as class method) and returns it. It's called without instance a new object.
- So when we instance a new object, the Job/Sessi...For Job and Session:
- new is a classe method that create the new object from informations given (as now, but as class method) and returns it. It's called without instance a new object.
- So when we instance a new object, the Job/Session already exists. So we execute the load method in the __init__, and load method becomes private (_load)
- So we remove the load calling from other methods, not needed anymore1.0Floreal CabanettesFloreal Cabanettes2018-01-18https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/104Sort: still store sorted version on unsort2018-01-29T15:31:00+01:00Floreal CabanettesSort: still store sorted version on unsortJust set if current vision is sorted or not (.sorted file)Just set if current vision is sorted or not (.sorted file)1.0Floreal CabanettesFloreal Cabanettes2018-01-19https://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/99List of query-target associations table: add coordinates2018-02-06T15:21:28+01:00Floreal CabanettesList of query-target associations table: add coordinates1.0Floreal CabanettesFloreal Cabanettes