D-GENIES issueshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues2018-01-29T18:17:18+01:00https://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/72If more than 75% of contigs have length < 1% of the full fasta, do the sort a...2018-01-29T18:17:18+01:00Floreal CabanettesIf more than 75% of contigs have length < 1% of the full fasta, do the sort automaticallyChange borns if necessary!Change borns if necessary!1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/98Proposer plusieurs palettes de couleur2018-01-29T17:17:28+01:00Floreal CabanettesProposer plusieurs palettes de couleur- Normal (actuelle)
- Daltonien+
- Noir & Blanc- Normal (actuelle)
- Daltonien+
- Noir & Blanc1.0Floreal CabanettesFloreal Cabanetteshttps://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/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/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/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/2Analyser le fasta avant de lancer l'alignement pour éviter les traitements tr...2018-01-25T15:34:56+01:00Floreal CabanettesAnalyser le fasta avant de lancer l'alignement pour éviter les traitements trop longs ou donnant des résultats inexploitablesÉviter d'avoir trop de contigs de petite taille. Il faudra faire des tests pour définir les valeurs limitesÉviter d'avoir trop de contigs de petite taille. Il faudra faire des tests pour définir les valeurs limites1.0Floreal 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/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/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/18Add stats2018-01-15T18:08:02+01:00Floreal CabanettesAdd statsÇa serait bien d'avoir aussi une la liste des contigs de chaque fichier qui n'ont pas d'alignement et une synthèse des alignements du type 50% > 75% d'identité, 20% entre 50 et 75%..., pet-être sous la forme d'un graphique en barre comme...Ça serait bien d'avoir aussi une la liste des contigs de chaque fichier qui n'ont pas d'alignement et une synthèse des alignements du type 50% > 75% d'identité, 20% entre 50 et 75%..., pet-être sous la forme d'un graphique en barre comme dans jvenn, mais pour faire cela il ne faut prendre dans chaque carré que les alignements qui sont significatifs. Ceci permettrait de comparer des assemblages de manière globale...1.0Floreal 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/96Prepare big jobs on cluster2018-01-05T16:26:38+01:00Floreal CabanettesPrepare big jobs on clusterBecause prepare step can be huge...Because prepare step can be huge...1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/22Show size of fasta files before upload2018-01-04T13:51:24+01:00Floreal CabanettesShow size of fasta files before upload1.0Floreal 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/26Add max size for files and check it2017-12-18T11:17:33+01:00Floreal CabanettesAdd max size for files and check it1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/90Add support to local+cluster batch system type2017-12-15T16:10:53+01:00Floreal CabanettesAdd support to local+cluster batch system typeLaunch small jobs locally and big jobs on clusterLaunch small jobs locally and big jobs on cluster1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/91Change ORM2017-12-13T16:55:46+01:00Floreal CabanettesChange ORMPony ORM has some problems until the beginning. With new implementations it is really a problem. Try to found another ORM...Pony ORM has some problems until the beginning. With new implementations it is really a problem. Try to found another ORM...1.0Floreal CabanettesFloreal Cabanetteshttps://forgemia.inra.fr/genotoul-bioinfo/dgenies/-/issues/89Add cluster submission support2017-12-13T14:10:48+01:00Floreal CabanettesAdd cluster submission support1.0Floreal CabanettesFloreal Cabanettes