Patch: Updates API request to send API key via HTTP only. Deprecates API key via parameters.

CHANGELOG.md

@@ -1,5 +1,11 @@
 ## lifebit-ai/cloudos-cli: changelog
 
+## v2.11.2 (2024-11-6)
+
+### Fix
+
+- Updates API requests to only use API key via HTTP header. Done in preparation for the upcoming deprecation of API key via parameters in CloudOS API.
+
 ## v2.11.1 (2024-10-22)
 
 ### Fix

cloudos/_version.py

@@ -1 +1 @@
-__version__ = '2.11.1'
+__version__ = '2.11.2'

cloudos/clos.py

@@ -235,10 +235,13 @@ def get_job_list(self, workspace_id, last_n_jobs=30, page=1, verify=True):
         r : list
             A list of dicts, each corresponding to a jobs from the user and the workspace.
         """
-        data = {"apikey": self.apikey}
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
         r = retry_requests_get("{}/api/v1/jobs?teamId={}&page={}".format(self.cloudos_url,
                                                                    workspace_id, page),
-                               params=data, verify=verify)
+                               headers=headers, verify=verify)
         if r.status_code >= 400:
             raise BadRequestException(r)
         content = json.loads(r.content)
@@ -329,8 +332,7 @@ def get_curated_workflow_list(self, workspace_id, get_all=True, page=1, verify=T
         r : list
             A list of dicts, each corresponding to a workflow.
         """
-        data = {"apikey": self.apikey,
-                "search": "",
+        data = {"search": "",
                 "page": page,
                 "filters": [
                     [
@@ -355,9 +357,13 @@ def get_curated_workflow_list(self, workspace_id, get_all=True, page=1, verify=T
                     ]
                  ]
                 }
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
         r = retry_requests_post("{}/api/v1/workflows/getByType?teamId={}".format(self.cloudos_url,
                                                                            workspace_id),
-                                json=data, verify=verify)
+                                json=data, headers=headers, verify=verify)
         if r.status_code >= 400:
             raise BadRequestException(r)
         content = json.loads(r.content)
@@ -391,10 +397,13 @@ def get_workflow_list(self, workspace_id, verify=True):
         r : list
             A list of dicts, each corresponding to a workflow.
         """
-        data = {"apikey": self.apikey}
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
         r = retry_requests_get("{}/api/v1/workflows?teamId={}".format(self.cloudos_url,
                                                                 workspace_id),
-                               params=data, verify=verify)
+                               headers=headers, verify=verify)
         if r.status_code >= 400:
             raise BadRequestException(r)
         return json.loads(r.content)
@@ -520,9 +529,12 @@ def get_project_list(self, workspace_id, verify=True):
         r : requests.models.Response
             The server response
         """
-        data = {"apikey": self.apikey}
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
         r = retry_requests_get("{}/api/v1/projects?teamId={}".format(self.cloudos_url, workspace_id),
-                               params=data, verify=verify)
+                               headers=headers, verify=verify)
         if r.status_code >= 400:
             raise BadRequestException(r)
         return r
@@ -615,7 +627,6 @@ def workflow_import(self, workspace_id, workflow_url, workflow_name,
         repository_name = workflow_url.split('/')[-1]
 
         data = {
-            "apikey": self.apikey,
             "workflowType": "nextflow",
             "repository": {
                 "platform": platform,
@@ -638,9 +649,13 @@ def workflow_import(self, workspace_id, workflow_url, workflow_name,
             "docsLink": workflow_docs_link,
             "team": workspace_id
         }
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
         r = retry_requests_post("{}/api/v1/workflows?teamId={}".format(self.cloudos_url,
                                                                        workspace_id),
-                                json=data, verify=verify)
+                                json=data, headers=headers, verify=verify)
         if r.status_code == 401:
             raise ValueError('It seems your API key is not authorised. Please check if ' +
                              'your workspace has support for importing workflows using cloudos-cli')

cloudos/jobs/job.py

@@ -143,11 +143,14 @@ def fetch_cloudos_id(self,
         if resource not in allowed_resources:
             raise ValueError('Your specified resource is not supported. ' +
                              f'Use one of the following: {allowed_resources}')
-        data = {"apikey": apikey}
+        headers = {
+            "Content-type": "application/json",
+            "apikey": apikey
+        }
         r = retry_requests_get("{}/api/v1/{}?teamId={}".format(cloudos_url,
                                                          resource,
                                                          workspace_id),
-                               params=data, verify=verify)
+                               headers=headers, verify=verify)
         if r.status_code >= 400:
             raise BadRequestException(r)
         content = json.loads(r.content)

tests/test_clos/test_detect_workflow.py

@@ -19,12 +19,13 @@ def test_detect_workflow():
     API request is mocked and replicated with json files
     """
     json_data = load_json_file(INPUT)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_clos/test_get_job_list.py

@@ -21,12 +21,13 @@ def test_get_job_list_correct_response():
     API request is mocked and replicated with json files
     """
     create_json = load_json_file(INPUT)
-    params = {"teamId": WORKSPACE_ID, "page": 1, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID, "page": 1}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&page=1&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}&page=1"
     # mock GET method with the .json
     responses.add(
             responses.GET,
@@ -53,12 +54,13 @@ def test_get_job_list_incorrect_response():
     error_message = {"statusCode": 400, "code": "BadRequest",
                      "message": "Bad Request.", "time": "2022-11-23_17:31:07"}
     error_json = json.dumps(error_message)
-    params = {"teamId": WORKSPACE_ID, "page": 1, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID, "page": 1}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&page=1&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}&page=1"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_clos/test_get_project_list.py

@@ -18,12 +18,13 @@ def test_get_project_list_correct_response():
     """
     Test 'get_project_list' to work as intended
     """
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,
@@ -50,12 +51,13 @@ def test_get_project_list_incorrect_response():
     error_message = {"statusCode": 400, "code": "BadRequest",
                      "message": "Bad Request.", "time": "2022-11-23_17:31:07"}
     error_json = json.dumps(error_message)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_clos/test_get_workflow_list.py

@@ -21,12 +21,13 @@ def test_get_workflow_list_correct_response():
     API request is mocked and replicated with json files
     """
     create_json = load_json_file(INPUT)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,
@@ -54,12 +55,13 @@ def test_get_workflow_list_incorrect_response():
     error_message = {"statusCode": 400, "code": "BadRequest",
                      "message": "Bad Request.", "time": "2022-11-23_17:31:07"}
     error_json = json.dumps(error_message)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_clos/test_is_module.py

@@ -19,12 +19,13 @@ def test_is_module():
     API request is mocked and replicated with json files
     """
     json_data = load_json_file(INPUT)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_errors/test_bad_request_exception.py

@@ -22,12 +22,13 @@ def test_bad_request_exception():
     API request is mocked and replicated with json files
     """
     create_json = load_json_file(INPUT)
-    params = {"teamId": WORKSPACE_ID, "page": 1, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID, "page": 1}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&page=1&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}&page=1"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_jobs/test_project_id.py

@@ -23,12 +23,13 @@ def test_project_id():
     """
     create_json_project = load_json_file(INPUT_PROJECT)
     create_json_workflow = load_json_file(INPUT_WORKFLOW)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,

tests/test_jobs/test_send_job.py

@@ -32,13 +32,11 @@ def test_send_job():
     create_json_workflow = load_json_file(INPUT_WORKFLOW)
     create_json = load_json_file(INPUT)
     params_job = {"teamId": WORKSPACE_ID}
-    params_pro_wf = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
     header = {
             "Content-type": "application/json",
             "apikey": APIKEY
         }
     search_str = f"teamId={WORKSPACE_ID}"
-    search_str_pro_wf = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
     # mock GET method with the .json
     responses.add(
             responses.POST,
@@ -49,17 +47,17 @@ def test_send_job():
             status=200)
     responses.add(
             responses.GET,
-            url=f"{CLOUDOS_URL}/api/v1/projects?{search_str_pro_wf}",
+            url=f"{CLOUDOS_URL}/api/v1/projects?{search_str}",
             body=create_json_project,
             headers=header,
-            match=[matchers.query_param_matcher(params_pro_wf)],
+            match=[matchers.query_param_matcher(params_job)],
             status=200)
     responses.add(
             responses.GET,
-            url=f"{CLOUDOS_URL}/api/v1/workflows?{search_str_pro_wf}",
+            url=f"{CLOUDOS_URL}/api/v1/workflows?{search_str}",
             body=create_json_workflow,
             headers=header,
-            match=[matchers.query_param_matcher(params_pro_wf)],
+            match=[matchers.query_param_matcher(params_job)],
             status=200)
     # start cloudOS service
     job = Job(apikey=APIKEY,

tests/test_jobs/test_workflow_id.py

@@ -23,12 +23,13 @@ def test_workflow_id():
     """
     create_json_project = load_json_file(INPUT_PROJECT)
     create_json_workflow = load_json_file(INPUT_WORKFLOW)
-    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    params = {"teamId": WORKSPACE_ID}
     header = {
         "Accept": "application/json, text/plain, */*",
-        "Content-Type": "application/json;charset=UTF-8"
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
     }
-    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    search_str = f"teamId={WORKSPACE_ID}"
     # mock GET method with the .json
     responses.add(
             responses.GET,