FastGenes merge requestshttps://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests2022-03-11T16:14:59+01:00https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/16gene annotations from csv file2022-03-11T16:14:59+01:00Kenzo-Hugo Hilliongene annotations from csv fileCurrent API does not work but example of usage of WIP is available in `notebooks/create annotations`
Closes #25Current API does not work but example of usage of WIP is available in `notebooks/create annotations`
Closes #25https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/14Test files and documentation2022-02-18T16:25:25+01:00Kenzo-Hugo HillionTest files and documentation# Content
* Creation of `data_test` directory that contains small dataset to tests different endpoints based on file url:
* Update README
* `ncbi_taxonomy/taxdump.tar.gz` small taxonomy with **Escherichia coli** and **Lactobacillus ...# Content
* Creation of `data_test` directory that contains small dataset to tests different endpoints based on file url:
* Update README
* `ncbi_taxonomy/taxdump.tar.gz` small taxonomy with **Escherichia coli** and **Lactobacillus casei group**.
* *No data for KEGG which is quick to create.*
* `genes/genes.fa`: few genes with random sequences.https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/15Set up frontend from metagenedb2022-01-19T16:02:19+01:00Kenzo-Hugo HillionSet up frontend from metagenedbCloses #2Closes #2https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/13DB migrations with alembic2022-01-12T10:28:43+01:00Kenzo-Hugo HillionDB migrations with alembic* Set alembic for migrations
* Add initial migration
* update sqlmodel to 0.0.6 (#20)
# Related issues
Closes #1
Closes #22* Set alembic for migrations
* Add initial migration
* update sqlmodel to 0.0.6 (#20)
# Related issues
Closes #1
Closes #22https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/12Creation of genes from fasta2022-01-11T09:48:43+01:00Kenzo-Hugo HillionCreation of genes from fasta### TO DO
- [x] Use case
- [x] Update repository
- [x] Add catalog to use case that is created if not existing
- [x] Endpoint to create gene from fasta url to be downloaded
### Related issue
Closes #14### TO DO
- [x] Use case
- [x] Update repository
- [x] Add catalog to use case that is created if not existing
- [x] Endpoint to create gene from fasta url to be downloaded
### Related issue
Closes #14https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/11Update operation on NCBI taxonomy2022-01-04T17:06:34+01:00Kenzo-Hugo HillionUpdate operation on NCBI taxonomy### Content
* Generate NCBI taxonomy hierarchy
* Create link to parent for NCBI tax
### Related Issue
Closes #16### Content
* Generate NCBI taxonomy hierarchy
* Create link to parent for NCBI tax
### Related Issue
Closes #16https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/10NCBI taxonomy creation2021-12-29T14:04:38+01:00Kenzo-Hugo HillionNCBI taxonomy creation* Also improve performances for KEGG orthology creation
Closes #13* Also improve performances for KEGG orthology creation
Closes #13https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/9Celery workers2021-12-21T16:55:16+01:00Kenzo-Hugo HillionCelery workersCloses #20Closes #20https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/8use case to create or update KEGG entries2021-12-16T18:02:38+01:00Kenzo-Hugo Hillionuse case to create or update KEGG entries## To do left
- [x] Pagination of all KEGG KO items
- [ ] ~~Route to compute all KEGG KO~~ -> #20
- [x] Tests
## Related issue
Closes #11## To do left
- [x] Pagination of all KEGG KO items
- [ ] ~~Route to compute all KEGG KO~~ -> #20
- [x] Tests
## Related issue
Closes #11https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/7CRUD for gene2021-12-15T11:28:04+01:00Kenzo-Hugo HillionCRUD for geneCloses #8Closes #8All simple CRUDshttps://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/6CRUD annotations and add id to most items2021-12-10T18:04:54+01:00Kenzo-Hugo HillionCRUD annotations and add id to most itemsCloses #9Closes #9All simple CRUDshttps://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/5add Entity CRUDs and endpoints2021-12-08T15:23:39+01:00Kenzo-Hugo Hillionadd Entity CRUDs and endpointsCloses #7Closes #7All simple CRUDshttps://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/4Catalog creation using clean architecture2021-12-03T19:35:33+01:00Kenzo-Hugo HillionCatalog creation using clean architectureFirst approach to set up Catalog creation trying to respect [Clean Architecture philosophy](https://breadcrumbscollector.tech/the-clean-architecture-in-python-how-to-write-testable-and-flexible-code/).
Closes #4First approach to set up Catalog creation trying to respect [Clean Architecture philosophy](https://breadcrumbscollector.tech/the-clean-architecture-in-python-how-to-write-testable-and-flexible-code/).
Closes #4https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/3Draft: Catalog Creation2021-12-01T18:02:16+01:00Kenzo-Hugo HillionDraft: Catalog CreationFirst approach to set up Catalog creation trying to respect [Clean Architecture philosophy](https://breadcrumbscollector.tech/the-clean-architecture-in-python-how-to-write-testable-and-flexible-code/).
Closes #4First approach to set up Catalog creation trying to respect [Clean Architecture philosophy](https://breadcrumbscollector.tech/the-clean-architecture-in-python-how-to-write-testable-and-flexible-code/).
Closes #4Kenzo-Hugo HillionKenzo-Hugo Hillionhttps://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/2Update archi and first small CI2021-11-22T14:27:03+01:00Kenzo-Hugo HillionUpdate archi and first small CIUpdate architecture to be more restrictive about annotations.Update architecture to be more restrictive about annotations.https://gitlab.pasteur.fr/metagenomics/fastgenes/-/merge_requests/1Base archi model for app2021-11-16T17:58:48+01:00Kenzo-Hugo HillionBase archi model for appCreate base modes architecture for the project.Create base modes architecture for the project.