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 |