undo changes to auth configuration

Author: jaeddy

test/test_client_util.py

@@ -19,9 +19,9 @@ def setUp(self):
         dirname, filename = os.path.split(os.path.abspath(__file__))
         self.testdata_dir = dirname + 'data'
         self.local = {'cwl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.cwl'),
-                      'wdl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.wdl'),
-                      'py': 'file://' + os.path.join(os.getcwd() + '/test/test_integration.py'),
-                      'unsupported': 'fake.txt'}
+                 'wdl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.wdl'),
+                 'py': 'file://' + os.path.join(os.getcwd() + '/test/test_integration.py'),
+                 'unsupported': 'fake.txt'}
 
         self.remote = {
             'cwl': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.cwl',
@@ -31,9 +31,9 @@ def setUp(self):
             'unreachable': 'https://fake.py'}
 
         self.expected = {'cwl': ('v1.0', 'CWL'),
-                         'wdl': ('draft-2', 'WDL'),
-                         'py': ('2.7', 'PY'),
-                         'pyWithPrefix': ('2.7', 'PY')}
+                    'wdl': ('draft-2', 'WDL'),
+                    'py': ('2.7', 'PY'),
+                    'pyWithPrefix': ('2.7', 'PY')}
 
     def tearDown(self):
         unittest.TestCase.tearDown(self)

test/test_integration.py

@@ -33,7 +33,7 @@ def setUpClass(cls):
         cls.wdl_attachments = ['file://' + os.path.abspath('testdata/md5sum.input')]
 
         # client for the swagger API methods
-        cls.client = WESClient({'auth': '', 'auth_type': None, 'proto': 'http', 'host': 'localhost:8080'})
+        cls.client = WESClient({'auth': '', 'proto': 'http', 'host': 'localhost:8080'})
 
         # manual test (wdl only working locally atm)
         cls.manual = False

wes_client/util.py

@@ -110,11 +110,8 @@ def build_wes_request(workflow_file, json_path, attachments=None):
             wf_params = json.dumps(json.load(f))
     elif json_path.startswith("http"):
         wf_params = modify_jsonyaml_paths(json_path)
-    else:
+    else: 
         wf_params = json_path
-        with open(json_path) as f:
-            wf_params = json.dumps(json.load(f))
-
     wf_version, wf_type = wf_info(workflow_file)
 
     parts = [("workflow_params", wf_params),
@@ -130,7 +127,7 @@ def build_wes_request(workflow_file, json_path, attachments=None):
     if attachments:
         for attachment in attachments:
             if attachment.startswith("file://"):
-                attachment = attachment[7:]
+                attachment = attachment[7:] 
                 attach_f = open(attachment, "rb")
             elif attachment.startswith("http"):
                 attach_f = urlopen(attachment)
@@ -166,10 +163,6 @@ def __init__(self, service):
         self.auth = service['auth']
         self.proto = service['proto']
         self.host = service['host']
-        auth_param = {'token': 'Authorization',
-                      'api_key': 'X-API-KEY',
-                      None: 'Authorization'}
-        self.param_in = auth_param[service['auth_type']]
 
     def get_service_info(self):
         """
@@ -185,7 +178,7 @@ def get_service_info(self):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get("%s://%s/ga4gh/wes/v1/service-info" % (self.proto, self.host),
-                                  headers={self.param_in: self.auth})
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def list_runs(self):
@@ -201,7 +194,7 @@ def list_runs(self):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
-                                  headers={self.param_in: self.auth})
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def run(self, wf, jsonyaml, attachments):
@@ -221,7 +214,7 @@ def run(self, wf, jsonyaml, attachments):
         parts = build_wes_request(wf, jsonyaml, attachments)
         postresult = requests.post("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
                                    files=parts,
-                                   headers={self.param_in: self.auth})
+                                   headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def cancel(self, run_id):
@@ -235,7 +228,7 @@ def cancel(self, run_id):
         :return: The body of the delete result as a dictionary.
         """
         postresult = requests.delete("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
-                                     headers={self.param_in: self.auth})
+                                     headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def get_run_log(self, run_id):
@@ -249,7 +242,7 @@ def get_run_log(self, run_id):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
-                                  headers={self.param_in: self.auth})
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def get_run_status(self, run_id):
@@ -263,5 +256,5 @@ def get_run_status(self, run_id):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get("%s://%s/ga4gh/wes/v1/runs/%s/status" % (self.proto, self.host, run_id),
-                                  headers={self.param_in: self.auth})
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)

wes_client/wes_client_main.py

@@ -16,7 +16,6 @@ def main(argv=sys.argv[1:]):
     parser.add_argument("--host", type=str, default=os.environ.get("WES_API_HOST"),
                         help="Example: '--host=localhost:8080'.  Defaults to WES_API_HOST.")
     parser.add_argument("--auth", type=str, default=os.environ.get("WES_API_AUTH"), help="Defaults to WES_API_AUTH.")
-    parser.add_argument("--auth_type", type=str, default=None, help="Defaults to None.")
     parser.add_argument("--proto", type=str, default=os.environ.get("WES_API_PROTO", "https"),
                         help="Options: [http, https].  Defaults to WES_API_PROTO (https).")
     parser.add_argument("--quiet", action="store_true", default=False)
@@ -50,7 +49,7 @@ def main(argv=sys.argv[1:]):
         print(u"%s %s" % (sys.argv[0], pkg[0].version))
         exit(0)
 
-    client = WESClient({'auth': args.auth, 'auth_type': args.auth_type, 'proto': args.proto, 'host': args.host})
+    client = WESClient({'auth': args.auth, 'proto': args.proto, 'host': args.host})
 
     if args.list:
         response = client.list_runs()  # how to include: page_token=args.page, page_size=args.page_size ?