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Update Populate database
authored
Feb 18, 2022
by
Kenzo-Hugo Hillion
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Populate-database.md
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@@ -10,14 +10,19 @@ You can create a test database using the API directly and some test files availa
> 💬 *You can use directly the [documentation page](http://localhost/docs) 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
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
### 💀 Deprecated way
From
`backend/app`
directory:
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@@ -27,11 +32,18 @@ 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
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