diff utilities.py @ 0:35d52820e7c7 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utilities.py	Tue Jun 26 09:01:39 2018 -0400
@@ -0,0 +1,226 @@
+# Helper functions to perform REST calls on the GMQL server.
+# ----------------------------------------------------------------------------
+# Luana Brancato, [e-mail]
+# ----------------------------------------------------------------------------
+
+import sys
+import os
+import yaml
+import requests
+
+
+def load_parts(module, call) :
+    """Given the module and the single operation, returns the fragments for the url to call"""
+
+    y_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),'gmql_rest.yaml')
+
+    with open(y_path,'r') as yamlf :
+        cfg = yaml.load(yamlf)
+
+    parts = list ()
+
+    gmql = cfg['GMQL_URL']
+    prefix = cfg[module]['prefix']
+    op = cfg[module]['operations'][call]
+
+    parts.append(gmql)
+    if prefix :
+        parts.append(prefix)
+
+    for p in op :
+        parts.append(p)
+
+    return parts
+
+def compose_url(module, call) :
+    """Given the fragments of a url, return the composite one"""
+
+    parts = load_parts(module,call)
+    url = '/'.join(parts)
+
+    return url
+
+def add_url_param(params, module, op, value,) :
+    """Given the params dict, add a new pair of key:value with the given value and the key set for given module and operation"""
+
+    y_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'gmql_rest.yaml')
+
+    with open(y_path, 'r') as yamlf:
+        cfg = yaml.load(yamlf)
+    yamlf.close()
+
+    key = cfg[module]['params'][op]
+
+    params.update({key : value})
+
+    return params
+
+
+def read_token(input):
+    """It takes the tabular file with the information over the user
+     name   authToken   valid_flag
+     It checks if the user is still valid and extract the authToken for the REST calls"""
+
+    with open(input,'r') as f_in :
+        user = f_in.readline().rstrip('\n').split('\t')
+
+    if user[2] :
+        token = user[1]
+    else :
+        stop_err("This session is no longer valid")
+
+
+    return token
+
+def expire_user(input):
+    """Set the validity flag of a user token to false"""
+
+    with open(input,'r') as f:
+        user = f.readline().rstrip('\n').split('\t')
+
+    user[2] = False
+
+    with open(input,'w') as f :
+         f.write('{fullName}\t{token}\t{valid}\n'.format(fullName=user[0], token=user[1],
+                                                            valid=user[2]))
+
+
+def get(url, user=None, response_type='json') :
+    """GET Request
+    :param url: url where to fetch the requested resource
+    :param user: for authenticated requests; if not provided make an unauthenticated request (es. for login)
+    :param response_type: type of the fetched response.
+        JSON ( Default )
+        TEXT
+        ZIP
+        FILE
+    """
+
+    #Set request headers
+    headers = dict ()
+
+    if user :
+        headers.update({'X-AUTH-TOKEN' : read_token(user)})
+
+    if response_type == 'text' :
+        headers.update({'Accept' : 'text/plain'})
+    elif response_type == 'zip' :
+        pass
+    elif response_type == 'file' :
+        headers.update({'Accept' : 'file'})
+    else :
+        headers.update({'Accept' : 'application/json'})
+
+
+    #Make the request
+    response = requests.get(url, headers=headers)
+
+    #Check returned server status
+    status_code = response.status_code
+
+    #Read result. If Server OK, read according to response_type. Raise an error otherwise.
+    if status_code == requests.codes.ok :
+        if response_type == 'json' :
+            return response.json()
+        elif response_type == 'text' :
+            return response.text
+        else :
+            return response
+    elif status_code == requests.codes.unauthorized :
+        expire_user(user)
+        stop_err("You are not authorized to do this. \nPlease login first.")
+    elif status_code == requests.codes.not_found :
+        stop_err("Resource not found for this user.")
+    else :
+        stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
+                                                            reason=response.reason,
+                                                            message=response.content))
+
+
+def post(url, payload, user=None, params=None, content_type='json', response_type='json') :
+    """ POST Request
+    :param url: url where to post data
+    :param payload: payload for the post request. Type is specified by content_type.
+    :param user:  for authenticated requests; if not provided make an unauthenticated request (es. for registration)
+    :param params: optional query parameters
+    :param content_type
+    :param response_type: Default is json
+    """
+
+
+    # Set request headers
+    headers = dict()
+
+    if user:
+        headers.update({'X-AUTH-TOKEN': read_token(user)})
+
+    headers.update({'Accept': 'application/json'})
+
+    if content_type == 'text' :
+        headers.update({'Content-Type' : 'text/plain'})
+        response = requests.post(url, params=params, headers=headers, data=payload)
+    elif content_type == 'multiform' :
+        response = requests.post(url, params=params, headers=headers, files=payload)
+    else :
+        headers.update({'Content-Type': 'application/json'})
+        response = requests.post(url, params=params, headers=headers, json=payload)
+
+    # Check returned server status
+    status_code = response.status_code
+
+
+    if status_code == requests.codes.ok :
+       return response.json()
+    elif status_code == requests.codes.unauthorized :
+       content = response.content
+       if content.__contains__("The username or password you entered don't match") :
+           stop_err("The username or password you entered don't match")
+       else:
+           expire_user(user)
+           stop_err("You are not authorized to do this. \nPlease login first.")
+    else :
+        stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
+                                                 reason=response.reason,
+                                                 message=response.content))
+
+
+
+def delete(url, user=None, response_type='json') :
+    """DELETE request
+    :param url: url where to post data
+    :param user:  for authenticated requests; if not provided make an unauthenticated request (es. for registration)
+    :param response_type: Default is json
+    """
+
+    # Set request headers
+    headers = dict()
+
+    if user:
+        headers.update({'X-AUTH-TOKEN': read_token(user)})
+
+    headers.update({'Accept': 'application/json'})
+
+    #Make the request
+    response = requests.delete(url, headers=headers)
+
+    #Check returned server status
+    status_code = response.status_code
+
+
+    #If Server OK, read result. Raise an error otherwise.
+    if status_code == requests.codes.ok :
+            return response.json()
+    elif status_code == requests.codes.unauthorized :
+        expire_user(user)
+        stop_err("You are not authorized to do this. \nPlease login first.")
+    elif status_code == requests.codes.not_found :
+        stop_err("Resource not found for this user.")
+    else :
+        stop_err("Error {code}: {reason}".format(code=status_code,
+                                                 reason=response.reason))
+
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()