one_ENCODE.py

usage: one_ENCODE.py [-h] [--infile INFILE] [--server SERVER] [--key KEY]
                     [--keyfile KEYFILE] [--authid AUTHID] [--authpw AUTHPW]
                     [--force-put] [--get-only] [--id ID] [--debug]

POST, PATCH or PUT one ENCODE JSON object

optional arguments:
  -h, --help            show this help message and exit
  --infile INFILE, -i INFILE
                        File containing the JSON object as a JSON string.
  --server SERVER       Full URL of the server.
  --key KEY             The keypair identifier from the keyfile. Default is
                        --key=default
  --keyfile KEYFILE     The keypair file. Default is --keyfile=./keypairs.json
  --authid AUTHID       The HTTP auth ID.
  --authpw AUTHPW       The HTTP auth PW.
  --force-put           Force the object to be PUT rather than PATCHed.
                        Default is False.
  --get-only            Do nothing but get the object and print it. Default is
                        False.
  --id ID               URI for an object
  --debug               Print debug messages. Default is False.

 Script to add one ENCODE object from a file or stdin

Prerequisites

• keyfile exemplified in keypairs.json
• import requests, json

Examples

$ one_ENCODE.py --id ENCBS000AAA

GET the specified object from the default server using the default keypair from the keyfile; pretty-print as a JSON string; flatten embedded objects into references.

$ one_ENCODE.py --id ENCBS000AAA --key submit

Do same but from a different server from the keyfile.

$ one_ENCODE.py --id ENCBS999JSS > ENCBS999JSS.json

Save the output to a file. To make this file postable edit it and remove the server-restricted properties like schema_version. TODO: Implement --get-postable to remove the properties that make the object unpostable.

$ echo '{"@id": "/biosamples/ENCBS999JSS/", "note": "New note text"}' | one_ENCODE.py

PATCH the object identified by the @id property. In this example, replace the note with a new one. Typically, you would save the JSON in a file and cat it to stdin.

$ one_ENCODE.py --infile newjson.json

Introspect the new JSON and if value for @id exists on the server, PATCH, otherwise POST.

$ one_ENCODE.py --infile newjson.json --force-put

Use PUT instead of PATCH.

$ one_ENCODE.py --infile newjson.json --get-only

Introspect the supplied JSON, extract the ID and get the representation of that object on the server. TODO: Implement --diff