metagenedb merge requestshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests2019-06-20T15:37:09+02:00https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/1Front vue2019-06-20T15:37:09+02:00Kenzo-Hugo HillionFront vueAdd front part for the app :
* Add it to the docker compose
* use Vue js
* Add NginxAdd front part for the app :
* Add it to the docker compose
* use Vue js
* Add Nginxhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/2Usepipenv2019-06-28T10:04:40+02:00Kenzo-Hugo HillionUsepipenvUse pipenv instead of requirements handled by `requirements.txt` and `requirements_dev.txt`.
Closes #9Use pipenv instead of requirements handled by `requirements.txt` and `requirements_dev.txt`.
Closes #9https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/3Integrate taxonomy to database2019-07-19T10:13:03+02:00Kenzo-Hugo HillionIntegrate taxonomy to database### Description
This integrates NCBI taxonomy to the DB. It performs:
* Creation of all taxonomy entries
* linkage to direct parental node
* generation of full parental hierarchy from a given node
### Test to be done:
* [ ]...### Description
This integrates NCBI taxonomy to the DB. It performs:
* Creation of all taxonomy entries
* linkage to direct parental node
* generation of full parental hierarchy from a given node
### Test to be done:
* [ ] Run the import script of the full database
Closes #23https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/4add superkingdom and improve performances2019-07-19T16:40:51+02:00Kenzo-Hugo Hillionadd superkingdom and improve performancesCloses #23 add missing commits to masterCloses #23 add missing commits to masterhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/5Set up Kubernetes for the project2019-08-01T10:16:23+02:00Kenzo-Hugo HillionSet up Kubernetes for the projectFirst set up of Kubernetes for the project.
This need to be revised :
* Dev Kubernetes to only be deployed for dev branch
Closes #11First set up of Kubernetes for the project.
This need to be revised :
* Dev Kubernetes to only be deployed for dev branch
Closes #11https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/6Replace custom insertion_model by serializers2019-08-01T18:19:55+02:00Kenzo-Hugo HillionReplace custom insertion_model by serializersAlso added few tests for insertion of Genes to DB in the `import_from_igc.py` script.
Maybe we could externalize the functions used to make them reusable by other scripts.
Closes #28Also added few tests for insertion of Genes to DB in the `import_from_igc.py` script.
Maybe we could externalize the functions used to make them reusable by other scripts.
Closes #28https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/7Resolve "Reorganize backend architecture"2019-08-05T12:21:30+02:00Kenzo-Hugo HillionResolve "Reorganize backend architecture"Big reorganization of backend to separate api from the rest of the application.
Also moved `gene_length` to the `GeneViewSet`.
Closes #27
Close #33Big reorganization of backend to separate api from the rest of the application.
Also moved `gene_length` to the `GeneViewSet`.
Closes #27
Close #33https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/8Add taxonomy information to IGC genes2019-08-05T18:21:10+02:00Kenzo-Hugo HillionAdd taxonomy information to IGC genes* adds the field `taxonomy` to the `Gene` model.
* adds method to create genes from IGC with taxonomical information.
* moved parser for IGC to `common/utils/parsers` and reorganize as a module
Closes #40* adds the field `taxonomy` to the `Gene` model.
* adds method to create genes from IGC with taxonomical information.
* moved parser for IGC to `common/utils/parsers` and reorganize as a module
Closes #40https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/9Resolve "Create secrets for postgres from gitlab CI"2019-08-06T14:43:10+02:00Kenzo-Hugo HillionResolve "Create secrets for postgres from gitlab CI"Closes #39
Closes #36Closes #39
Closes #36https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/10Generate Documentation for the backend API2019-08-07T18:10:39+02:00Kenzo-Hugo HillionGenerate Documentation for the backend API* Give the basis for API documentation
* Also changed attribute `gene_length` to `length` in `Gene` model
Closes #43* Give the basis for API documentation
* Also changed attribute `gene_length` to `length` in `Gene` model
Closes #43https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/11start using factory boy for tests2019-08-09T17:01:00+02:00Kenzo-Hugo Hillionstart using factory boy for testsStarted using factory boy when items in db are required
Closes #31Started using factory boy when items in db are required
Closes #31https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/12Resolve "Use POST in scripts to create elements instead of doing it manually ...2019-09-10T15:22:07+02:00Kenzo-Hugo HillionResolve "Use POST in scripts to create elements instead of doing it manually for Taxonomy"Closes #48
Closes #49
Closes #50Closes #48
Closes #49
Closes #50https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/13Use axios2019-09-13T17:32:01+02:00Kenzo-Hugo HillionUse axioshttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/14Resolve "Update scripts to use new `PUT` and `POST` to populate database"2019-10-28T17:14:21+01:00Kenzo-Hugo HillionResolve "Update scripts to use new `PUT` and `POST` to populate database"Needs to make sure also:
* [x] Deal with many to many relationships (for `Gene` <-> `Function` for instance)
* [x] Fix script to import KEGG to make the right source (currently making : unknown)
Closes #55Needs to make sure also:
* [x] Deal with many to many relationships (for `Gene` <-> `Function` for instance)
* [x] Fix script to import KEGG to make the right source (currently making : unknown)
Closes #55https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/15Deal with functions in importing IGC genes2019-10-30T16:16:26+01:00Kenzo-Hugo HillionDeal with functions in importing IGC genesCloses #57Closes #57https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/16Add endpoint to generate hierarchy of taxonomy from the backend2019-11-04T16:48:40+01:00Kenzo-Hugo HillionAdd endpoint to generate hierarchy of taxonomy from the backendStrategy was to generate hierarchy directly once the item is requested through a `GET`. Therefore, to generate full hierarchy of the taxonomy, just need to iterate through all entries and request them through a `GET` on the API.
Closes #58Strategy was to generate hierarchy directly once the item is requested through a `GET`. Therefore, to generate full hierarchy of the taxonomy, just need to iterate through all entries and request them through a `GET` on the API.
Closes #58https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/17Add gene detail page on frontend2019-11-12T18:23:58+01:00Kenzo-Hugo HillionAdd gene detail page on frontendThis was a bit of benchmark to build a gene page that can access external API (here KEGG through togows.org).
Edit: Since I needed the API to return more information, this also deal with two issues:
Closes #61
Closes #56 This was a bit of benchmark to build a gene page that can access external API (here KEGG through togows.org).
Edit: Since I needed the API to return more information, this also deal with two issues:
Closes #61
Closes #56 Simon Malesyssimon.malesys@pasteur.frSimon Malesyssimon.malesys@pasteur.frhttps://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/18Resolve "Create backend service to perform request to external APIs"2019-11-21T16:00:55+01:00Kenzo-Hugo HillionResolve "Create backend service to perform request to external APIs"## Still need to be done
* [x] Validation of query_params for function
* [x] Test custom methods for `function.py`
* [x] Test for `togows.py` in common
Closes #63## Still need to be done
* [x] Validation of query_params for function
* [x] Test custom methods for `function.py`
* [x] Test for `togows.py` in common
Closes #63https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/19mprove the way mapping between taxonomy names and id is done during IGC gene ...2019-11-22T15:08:11+01:00Kenzo-Hugo Hillionmprove the way mapping between taxonomy names and id is done during IGC gene creationThe whole mapping between genus and phylum names are done locally to prevent the number of requests done during creation. This should improve the speed of creation. Still need to deal with #65 to be able to load IGC smoothly to the db.
...The whole mapping between genus and phylum names are done locally to prevent the number of requests done during creation. This should improve the speed of creation. Still need to deal with #65 to be able to load IGC smoothly to the db.
Closes #66https://gitlab.pasteur.fr/metagenomics/metagenedb/-/merge_requests/20Check if function exists in the db or remove it from payload2019-11-22T17:34:11+01:00Kenzo-Hugo HillionCheck if function exists in the db or remove it from payloadThis MR allows to prevent the use of function IDs that do not exist in the database. It was too complicated to set up from the server side and at the end it makes sure we know what we do as a consumer of the API.
Closes #65This MR allows to prevent the use of function IDs that do not exist in the database. It was too complicated to set up from the server side and at the end it makes sure we know what we do as a consumer of the API.
Closes #65