Name: american-gut-rest
Owner: biocore
Description: RESTful interface into the American Gut data
Created: 2015-07-23 20:37:00.0
Updated: 2015-11-06 06:43:04.0
Pushed: 2015-08-19 01:14:14.0
Homepage: null
Size: 408
Language: Python
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A RESTful(ish) interface into the unidentified American Gut data. Any invalid response, or a query requesting an unknown sample will return a 410 HTTP status.
| endpoint | description | example | result |
| :——- | ———– | ——- | —–: |
| GET / | Endpoint detail | curl https://api.microbio.me/american-gut/1/ | {"foo_url": ...}
| GET /otu/:sample-id | A sample specific OTU table | curl https://api.microbio.me/american-gut/1/otu/000005636.1053788 | A BIOM-format 1.0.0 table |
| GET /otu/:sample-id/txt | A sample specific Excel OTU table | curl https://api.microbio.me/american-gut/1/otu/000005636.1053788/txt | A tab delimited string |
| GET /otu/:sample-id/json | A sample specific OTU table | curl https://api.microbio.me/american-gut/1/otu/000005636.1053788/json | A BIOM-format 1.0.0 table |
| GET /sample | A list of the known samples | curl https://api.microbio.me/american-gut/1/sample/ | ["foo", "bar", ...]
| GET /sequence/:sample-id | Per-sample sequences for download | curl https://api.microbio.me/american-gut/1/sequence/000005636.1053788 | {"fastq_url": "ftp://..."} |
The following is a list of the configuration options and their default value. If the environment variable $AGREST_CONFIG is defined, the configuration will be sourced from there and in which case, all configuration values must be set (i.e., defaults are all or none)
| option | description | default |
| :—– | ———– | ——: |
| serverport | The port the HTTP server will listen on | 8080 |
| base_conf_dir | The directory nginx will search for includes in | . |
| db_user | The unprivileged database user | postgres |
| db_password | The unprivileged database user password | "" |
| db_host | The database host | localhost |
| db_name | The database name | ag_rest |
| admin_db_user | The privileged database user | postgres |
| admin_db_password | The privileged database user password | "" |
| test_environment | A boolean flag to indicate if this is a test environment | True |
| ag_biom_src | The URL for the source BIOM file | https://github.com/biocore/American-Gut/blob/master/data/AG/AG_100nt_even10k.biom?raw=true |
| ag_accession_src | The URL for the per sample accession details | https://github.com/biocore/American-Gut/blob/master/data/AG/accession_to_sample.json?raw=true |
| ag_biom_src_api | The URL for the source BIOM file Github API to check its SHA | ag_biom_src_api': 'https://api.github.com/repos/biocore/American-Gut/commits?path=data/AG/AG.biom |