galaxy/scripts/api/common.py

"""
Common methods used by the API sample scripts.
"""

import json
import logging
import sys
from urllib.error import HTTPError
from urllib.request import (
    Request,
    urlopen,
)

log = logging.getLogger(__name__)


def make_url(api_key, url, args=None):
    """
    Adds the API Key to the URL if it's not already there.
    """
    if args is None:
        args = []
    argsep = '&'
    if '?' not in url:
        argsep = '?'
    if '?key=' not in url and '&key=' not in url:
        args.insert(0, ('key', api_key))
    return url + argsep + '&'.join('='.join(t) for t in args)


def get(api_key, url):
    """
    Do the actual GET.
    """
    url = make_url(api_key, url)
    try:
        return json.loads(urlopen(url).read())
    except ValueError as e:
        print("URL did not return JSON data: %s" % e)
        sys.exit(1)


def post(api_key, url, data):
    """
    Do the actual POST.
    """
    url = make_url(api_key, url)
    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
    return json.loads(urlopen(req).read())


def put(api_key, url, data):
    """
    Do the actual PUT
    """
    url = make_url(api_key, url)
    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
    req.get_method = lambda: 'PUT'
    return json.loads(urlopen(req).read())


def __del(api_key, url, data):
    """
    Do the actual DELETE
    """
    url = make_url(api_key, url)
    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
    req.get_method = lambda: 'DELETE'
    return json.loads(urlopen(req).read())


def display(api_key, url, return_formatted=True):
    """
    Sends an API GET request and acts as a generic formatter for the JSON response.
    """
    try:
        r = get(api_key, url)
    except HTTPError as e:
        print(e)
        print(e.read(1024))  # Only return the first 1K of errors.
        sys.exit(1)
    if not return_formatted:
        return r
    elif type(r) == list:
        # Response is a collection as defined in the REST style.
        print('Collection Members')
        print('------------------')
        for n, i in enumerate(r):
            # All collection members should have a name in the response.
            # url is optional
            if 'url' in i:
                print('#%d: %s' % (n + 1, i.pop('url')))
            if 'name' in i:
                print('  name: %s' % i.pop('name'))
            for k, v in i.items():
                print(f'  {k}: {v}')
        print('')
        print('%d element(s) in collection' % len(r))
    elif type(r) == dict:
        # Response is an element as defined in the REST style.
        print('Member Information')
        print('------------------')
        for k, v in r.items():
            print(f'{k}: {v}')
    elif type(r) == str:
        print(r)
    else:
        print('response is unknown type: %s' % type(r))


def submit(api_key, url, data, return_formatted=True):
    """
    Sends an API POST request and acts as a generic formatter for the JSON response.
    'data' will become the JSON payload read by Galaxy.
    """
    try:
        r = post(api_key, url, data)
    except HTTPError as e:
        if return_formatted:
            print(e)
            print(e.read(1024))
            sys.exit(1)
        else:
            return 'Error. ' + str(e.read(1024))
    if not return_formatted:
        return r
    print('Response')
    print('--------')
    if type(r) == list:
        # Currently the only implemented responses are lists of dicts, because
        # submission creates some number of collection elements.
        for i in r:
            if type(i) == dict:
                if 'url' in i:
                    print(i.pop('url'))
                else:
                    print('----')
                if 'name' in i:
                    print('  name: %s' % i.pop('name'))
                for k, v in i.items():
                    print(f'  {k}: {v}')
            else:
                print(i)
    else:
        print(r)


def update(api_key, url, data, return_formatted=True):
    """
    Sends an API PUT request and acts as a generic formatter for the JSON response.
    'data' will become the JSON payload read by Galaxy.
    """
    try:
        r = put(api_key, url, data)
    except HTTPError as e:
        if return_formatted:
            print(e)
            print(e.read(1024))
            sys.exit(1)
        else:
            return 'Error. ' + str(e.read(1024))
    if not return_formatted:
        return r
    print('Response')
    print('--------')
    print(r)


def delete(api_key, url, data, return_formatted=True):
    """
    Sends an API DELETE request and acts as a generic formatter for the JSON response.
    'data' will become the JSON payload read by Galaxy.
    """
    try:
        r = __del(api_key, url, data)
    except HTTPError as e:
        if return_formatted:
            print(e)
            print(e.read(1024))
            sys.exit(1)
        else:
            return 'Error. ' + str(e.read(1024))
    if not return_formatted:
        return r
    print('Response')
    print('--------')
    print(r)