metagenedb merge requestshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests2020-03-20T10:13:12+01:00https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/44Use the same image as the deployed one2020-03-20T10:13:12+01:00Bryan BRANCOTTEUse the same image as the deployed oneUse the same image, and wait after the service to be started to run the testsUse the same image, and wait after the service to be started to run the testshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/43Celery and Redis2021-12-16T18:04:40+01:00Kenzo-Hugo HillionCelery and RedisDoes not close the issue since some new pods needs to be added to Kubernetes too.Does not close the issue since some new pods needs to be added to Kubernetes too.https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/45Add independant service to query external APIs2020-04-08T17:57:13+02:00Kenzo-Hugo HillionAdd independant service to query external APIsCloses #113
* [x] Set up the structure on docker-compose with hello world example
* [x] Add endpoints to obtain information from external APIs
* [x] Think about a common structure for response from this service
* [x] Handle er...Closes #113
* [x] Set up the structure on docker-compose with hello world example
* [x] Add endpoints to obtain information from external APIs
* [x] Think about a common structure for response from this service
* [x] Handle error and return a common way of handling them for API consumers
* [ ] Set Kubernetes podhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/46Integrate VIRGO genes2020-05-11T17:06:50+02:00Kenzo-Hugo HillionIntegrate VIRGO genesCloses #111
## TO DO
* [x] Create VIRGO source in the model and have the corresponding migration
* [x] Create all Genes
* [x] IDs
* [x] Sequences
* [x] KEGG annotations
* [x] EggNOG annotations
* [x] Taxonom...Closes #111
## TO DO
* [x] Create VIRGO source in the model and have the corresponding migration
* [x] Create all Genes
* [x] IDs
* [x] Sequences
* [x] KEGG annotations
* [x] EggNOG annotations
* [x] Taxonomy
* [x] Display source on frontend and possibility to filterhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/47Compute statistics for Virgo2020-05-14T14:11:16+02:00Kenzo-Hugo HillionCompute statistics for VirgoNeed to go step by step:
* [x] Add method to clean up everything on the table
* [x] Make each steps source specific
* [x] Gene counts
* [x] Computation on backend
* [x] Use from frontend
* [x] Gene length repart...Need to go step by step:
* [x] Add method to clean up everything on the table
* [x] Make each steps source specific
* [x] Gene counts
* [x] Computation on backend
* [x] Use from frontend
* [x] Gene length repartition
* [x] Computation on backend
* [x] Use from frontend
* [x] Taxonomy repartition
* [x] Computation on backend
* [x] Use from frontend
* [x] Compute for both source
* [x] Add way to display one or another on dashboard
Closes #116https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/48add simple way of comparing taxonomy between catalogs2020-05-15T12:11:55+02:00Kenzo-Hugo Hillionadd simple way of comparing taxonomy between catalogsCloses #121
This MR allows to display side by side two taxonomical distribution.Closes #121
This MR allows to display side by side two taxonomical distribution.https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/49Filter on a specific taxonomical annotation2020-06-02T12:16:49+02:00Kenzo-Hugo HillionFilter on a specific taxonomical annotation* Also remove bioapi service from this app since it is now available as its own service
### TO DO
* [x] Compute representated taxonomy
* [x] Use this list to display available filter for a given taxonomy level
* [x] Update filte...* Also remove bioapi service from this app since it is now available as its own service
### TO DO
* [x] Compute representated taxonomy
* [x] Use this list to display available filter for a given taxonomy level
* [x] Update filter interface on frontend
* [x] Create filtering on backend
* [x] Use new filtering on frontend
The filter takes into account not only direct annotation but also all those at a higher level. It means that if a gene is annotated at the species level, it is also retrieved if we filter for its genus, order...
Closes #92https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/50Take into account gene source filter to display available taxonomic annotation2020-06-02T16:16:00+02:00Kenzo-Hugo HillionTake into account gene source filter to display available taxonomic annotationCloses #124Closes #124https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/51Browse trough pages on gene list2020-06-03T17:06:37+02:00Kenzo-Hugo HillionBrowse trough pages on gene listCloses #91Closes #91https://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 #128https://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/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/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/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/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/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/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/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/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/62COG to have links to NCBI pages2020-06-24T17:23:11+02:00Kenzo-Hugo HillionCOG to have links to NCBI pagesCloses #138Closes #138