metagenedb merge requestshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests2021-04-01T11:33:16+02:00https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/71add logs and dependencies to build UML2021-04-01T11:33:16+02:00Kenzo-Hugo Hillionadd logs and dependencies to build UMLhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/70set indexes on gene columns2021-03-26T15:14:15+01:00Kenzo-Hugo Hillionset indexes on gene columnsTry to improve queries
* Setting indexesTry to improve queries
* Setting indexeshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/69Resolve "Allow filtering on genes with KEGG or EggNOG annotations"2021-03-24T13:14:04+01:00Kenzo-Hugo HillionResolve "Allow filtering on genes with KEGG or EggNOG annotations"Closes #157Closes #157https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/68Retrieve taxonomy details from gene list2020-09-21T15:19:32+02:00Kenzo-Hugo HillionRetrieve taxonomy details from gene listCloses #155Closes #155https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/67Use new fields for KEGG details2020-08-14T15:53:58+02:00Kenzo-Hugo HillionUse new fields for KEGG detailsThis MR also contains the following changes:
* provide choice of links for redirection to NCBI taxonomy
* provide rediction to IntEnz for EC numbers
* update version for factory boy to 3.x
* update dabeplech version
Closes #146This MR also contains the following changes:
* provide choice of links for redirection to NCBI taxonomy
* provide rediction to IntEnz for EC numbers
* update version for factory boy to 3.x
* update dabeplech version
Closes #146https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/66replace TOGOWS by KEGGAPI from dabeplech2020-08-10T17:24:25+02:00Kenzo-Hugo Hillionreplace TOGOWS by KEGGAPI from dabeplechCloses #145Closes #145https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/65Dev documentation to run metageneDB locally2020-07-02T13:19:19+02:00Kenzo-Hugo HillionDev documentation to run metageneDB locally## Description
Most of the work is done on the Wiki.
There is also a part to generate a light DB when first setting up the project locally.
## Definition of Done
* [x] ~~New code added is tested (*only apply for Python at the...## Description
Most of the work is done on the Wiki.
There is also a part to generate a light DB when first setting up the project locally.
## Definition of Done
* [x] ~~New code added is tested (*only apply for Python at the moment*)~~
* [x] ~~Merge request has been revised and validated~~
## Related issue(s)
Closes #140https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/64Update prod with new features2020-07-01T13:10:22+02:00Kenzo-Hugo HillionUpdate prod with new featureshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/63Handle no data for histograms and doughnut2020-06-25T15:39:26+02:00Kenzo-Hugo HillionHandle no data for histograms and doughnutCloses #135Closes #135https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/62COG to have links to NCBI pages2020-06-24T17:23:11+02:00Kenzo-Hugo HillionCOG to have links to NCBI pagesCloses #138Closes #138https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/61Resolve "Improve download of csv and fasta"2020-06-24T16:53:43+02:00Kenzo-Hugo HillionResolve "Improve download of csv and fasta"User is now aware that a download is occuring and errors are displayed when an error occurs on the backend.
Closes #139
Closes #134User is now aware that a download is occuring and errors are displayed when an error occurs on the backend.
Closes #139
Closes #134https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/60Extract table from gene list2020-06-23T14:53:53+02:00Kenzo-Hugo HillionExtract table from gene listAllow to download `.csv` of metadata for a filtered list of genes.
Limited to 100000 for the moment, like the fasta files
Closes #126Allow to download `.csv` of metadata for a filtered list of genes.
Limited to 100000 for the moment, like the fasta files
Closes #126https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/59Prod2020-06-18T11:55:01+02:00Kenzo-Hugo HillionProdFirst merging to master to run prod instance at https://metagenedb.pasteur.cloudFirst merging to master to run prod instance at https://metagenedb.pasteur.cloudhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/58Obtain fasta for a given query2020-06-18T10:56:30+02:00Kenzo-Hugo HillionObtain fasta for a given queryThis allow to obtain sequences at the fasta format if the `fasta=true` qparam is given to the genes endpoint.
Frontend only allows to download until the limit of 100000 genes.
Closes #99This allow to obtain sequences at the fasta format if the `fasta=true` qparam is given to the genes endpoint.
Frontend only allows to download until the limit of 100000 genes.
Closes #99https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/57fix listing when more than one kegg (or eggnog)2020-06-16T11:40:05+02:00Kenzo-Hugo Hillionfix listing when more than one kegg (or eggnog)Also updated about page
Closes #86Also updated about page
Closes #86https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/56Resolve "Create eggnog card"2020-06-11T18:21:29+02:00Kenzo-Hugo HillionResolve "Create eggnog card"Closes #71
Closes #108
Closes #106Closes #71
Closes #108
Closes #106https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/55About and Home pages2020-06-10T17:01:54+02:00Kenzo-Hugo HillionAbout and Home pagesCloses #132
Closes #131Closes #132
Closes #131https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/54Add build number based on commit hash2020-06-08T12:31:15+02:00Kenzo-Hugo HillionAdd build number based on commit hashAlso updated the navigation bar to make links alive:
* Link to Gitlab repository
* Starting Help section with meaningful links...
Closes #42Also updated the navigation bar to make links alive:
* Link to Gitlab repository
* Starting Help section with meaningful links...
Closes #42https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/53Resolve Endpoints to allow updating by admin without computing2020-06-04T16:53:23+02:00Kenzo-Hugo HillionResolve Endpoints to allow updating by admin without computingThis would allow to easily send statistics already computed locally since the DB are identical for the moment.
Closes #130This would allow to easily send statistics already computed locally since the DB are identical for the moment.
Closes #130https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/52Limits page number and display loading when changing page2020-06-04T14:48:44+02:00Kenzo-Hugo HillionLimits page number and display loading when changing pageCloses #127
Closes #128Closes #127
Closes #128