Creating the database
To create new entries, everything goes through the API using the /api/admin_db route.
🐤 Create and Populate Test DB
You can create a test database using the API directly and some test files available on the repository.
💬 You can use directly the documentation page to run the different commands.
📔 Entities
| Title | route | input path |
|---|---|---|
| Create KEGG database | /api/admin_db/create_kegg_ko |
no input file necessary, process is quick for all KEGG KO. |
| NCBI taxonomy | /api/admin_db/create_ncbi_taxonomy |
https://gitlab.pasteur.fr/metagenomics/fastgenes/-/raw/25-gene-annotations/data_test/ncbi_taxonomy/taxdump.tar.gz?inline=false |
| NCBI taxonomy hierarchy | /api/admin_db/generate_ncbi_taxonomy_hierarchy |
No file necessary, based on existing db |
📕 Genes
| Title | route | input path |
|---|---|---|
| Genes | /api/admin_db/create_genes |
https://gitlab.pasteur.fr/metagenomics/fastgenes/-/raw/25-gene-annotations/data_test/genes/genes.fa?inline=false |
💀 Deprecated way
From backend/app directory:
poetry run create_test_db
🐔 Populate DB with real data
📔 Entities
| Title | route | input path |
|---|---|---|
| Create KEGG database | /api/admin_db/create_kegg_ko |
no input file necessary, process is quick for all KEGG KO. |
| NCBI taxonomy | /api/admin_db/create_ncbi_taxonomy |
https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz |
| NCBI taxonomy hierarchy | /api/admin_db/generate_ncbi_taxonomy_hierarchy |
No file necessary, based on existing db |
📕 Genes
| Title | route | input path |
|---|---|---|
| Genes | /api/admin_db/create_genes |
Link to your fasta file |
📂 Empty DB
poetry run empty_db