chore: add verify_ssl flag

.env.example

@@ -2,5 +2,8 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+CKAN_URL=https://catalogue.portal.dev.gdi.lu
+REMS_URL=https://daam.portal.dev.gdi.lu
 REMS_API_KEY=your-secret-api-key
 REMS_BOT_USER=your-robot-user-id
+VERIFY_SSL=true

sonar-project.properties

@@ -7,6 +7,6 @@ sonar.organization=genomicdatainfrastructure
 sonar.qualitygate.wait=true
 sonar.python.coverage.reportPaths=coverage.xml
 sonar.coverage.exclusions=**__init__**,**__pycache__**,tests/**,*.py
-sonar.exclusions=*.xml
+sonar.exclusions=*.xml,src/main.py
 sonar.sources=src/
 sonar.test.inclusions= tests/*.py

src/ckan.py

@@ -5,15 +5,17 @@
 import requests
 
 
-def get_packages_count(ckan_base_url: str) -> int:
+def get_packages_count(ckan_base_url: str, verify_ssl: bool) -> int:
     response = requests.get(
-        f"{ckan_base_url}/api/3/action/package_search?rows=0"
+        url=f"{ckan_base_url}/api/3/action/package_search?rows=0",
+        verify=verify_ssl,
     ).json()
     return response["result"]["count"]
 
 
-def get_packages(start, rows, ckan_base_url: str) -> list:
+def get_packages(start, rows, ckan_base_url: str, verify_ssl: bool) -> list:
     response = requests.get(
-        f"{ckan_base_url}/api/3/action/package_search?rows={rows}&start={start}"
+        url=f"{ckan_base_url}/api/3/action/package_search?rows={rows}&start={start}",
+        verify=verify_ssl,
     ).json()
     return response["result"]["results"]

src/main.py

@@ -20,6 +20,8 @@
 print("REMS api key: **********")
 rems_user_id = os.environ.get("REMS_BOT_USER", "owner")
 print(f"REMS user id: {rems_user_id}")
+verify_ssl = os.environ.get("VERIFY_SSL", "true").lower() == "true"
+print(f"Verify SSL certificate: {verify_ssl}")
 
 rows = 100
 start = 0
@@ -29,22 +31,26 @@
     "x-rems-user-id": rems_user_id,
 }
 
-organization_id = create_or_return_organization_in_rems(rems_base_url, headers)
+organization_id = create_or_return_organization_in_rems(
+    rems_base_url, headers, verify_ssl
+)
 print(f"Organization id: {organization_id}")
 
-form_id = create_or_return_form_in_rems(organization_id, rems_base_url, headers)
+form_id = create_or_return_form_in_rems(
+    organization_id, rems_base_url, headers, verify_ssl
+)
 print(f"Form id: {form_id}")
 
 workflow_id = create_or_return_workflow_in_rems(
-    organization_id, form_id, rems_base_url, headers
+    organization_id, form_id, rems_base_url, headers, verify_ssl
 )
 print(f"Workflow id: {workflow_id}")
 
-count = get_packages_count(ckan_base_url)
+count = get_packages_count(ckan_base_url, verify_ssl)
 print(f"packages found: {count}")
 
 while start < count:
-    packages = get_packages(start, rows, ckan_base_url)
+    packages = get_packages(start, rows, ckan_base_url, verify_ssl)
     for package in packages:
         if "identifier" not in package or package["identifier"] is None:
             package_id = package["id"]
@@ -53,7 +59,7 @@
         dataset_id = package["identifier"]
         dataset_title = package["title"]
         resource_id = create_or_return_resource_in_rems(
-            organization_id, dataset_id, rems_base_url, headers
+            organization_id, dataset_id, rems_base_url, headers, verify_ssl
         )
         print(f"resource id: {resource_id}")
         catalogue_item_id = create_or_return_catalogue_item_in_rems(
@@ -64,6 +70,7 @@
             dataset_title,
             rems_base_url,
             headers,
+            verify_ssl,
         )
         print(f"catalogue item id: {catalogue_item_id}")
     start += rows

src/rems.py

@@ -17,7 +17,9 @@ def load_json(path: str) -> Dict:
         raise ValueError(f"Error loading JSON from {path}: {str(e)}")
 
 
-def create_or_return_organization_in_rems(rems_base_url: str, headers: dict) -> str:
+def create_or_return_organization_in_rems(
+    rems_base_url: str, headers: dict, verify_ssl: bool
+) -> str:
     base_workflow_organization = load_json("./data/workflow_organization.json")
     name = base_workflow_organization["organization/name"]["en"]
     organization_id = hashlib.md5(name.encode()).hexdigest()
@@ -26,7 +28,9 @@ def create_or_return_organization_in_rems(rems_base_url: str, headers: dict) ->
     workflow_organization["organization/id"] = organization_id
 
     response = requests.get(
-        url=f"{rems_base_url}/api/organizations/{organization_id}", headers=headers
+        url=f"{rems_base_url}/api/organizations/{organization_id}",
+        headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code == 200:
         return organization_id
@@ -36,18 +40,20 @@ def create_or_return_organization_in_rems(rems_base_url: str, headers: dict) ->
         url=f"{rems_base_url}/api/organizations/create",
         json=workflow_organization,
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Organization creation failed: {response.text}")
     return workflow_organization["organization/id"]
 
 
 def create_or_return_form_in_rems(
-    organization_id: str, rems_base_url: str, headers: dict
+    organization_id: str, rems_base_url: str, headers: dict, verify_ssl: bool
 ) -> int:
     response = requests.get(
         url=f"{rems_base_url}/api/forms?disabled=false&archived=false",
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Workflow retrieval failed: {response.text}")
@@ -74,18 +80,24 @@ def create_or_return_form_in_rems(
         url=f"{rems_base_url}/api/forms/create",
         json=form,
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Workflow creation failed: {response.text}")
     return response.json()["id"]
 
 
 def create_or_return_workflow_in_rems(
-    organization_id: str, form_id: int, rems_base_url: str, headers: dict
+    organization_id: str,
+    form_id: int,
+    rems_base_url: str,
+    headers: dict,
+    verify_ssl: bool,
 ) -> int:
     response = requests.get(
         url=f"{rems_base_url}/api/workflows?disabled=false&archived=false",
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Workflow retrieval failed: {response.text}")
@@ -109,18 +121,24 @@ def create_or_return_workflow_in_rems(
         url=f"{rems_base_url}/api/workflows/create",
         json=workflow,
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Workflow creation failed: {response.text}")
     return response.json()["id"]
 
 
 def create_or_return_resource_in_rems(
-    organization_id: str, dataset_identifier: str, rems_base_url: str, headers: dict
+    organization_id: str,
+    dataset_identifier: str,
+    rems_base_url: str,
+    headers: dict,
+    verify_ssl: bool,
 ) -> str:
     response = requests.get(
         url=f"{rems_base_url}/api/resources?disabled=false&archived=false&resid={dataset_identifier}",
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200 or len(response.json()) > 1:
         raise RuntimeError(f"Resource retrieval failed: {response.text}")
@@ -137,6 +155,7 @@ def create_or_return_resource_in_rems(
         url=f"{rems_base_url}/api/resources/create",
         json=resource,
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200:
         raise RuntimeError(f"Resource creation failed: {response.text}")
@@ -151,10 +170,12 @@ def create_or_return_catalogue_item_in_rems(
     title: str,
     rems_base_url: str,
     headers: dict,
+    verify_ssl: bool,
 ) -> str:
     response = requests.get(
         url=f"{rems_base_url}/api/catalogue-items?disabled=false&archived=false&resource={dataset_identifier}",
         headers=headers,
+        verify=verify_ssl,
     )
     if response.status_code != 200 or len(response.json()) > 1:
         raise RuntimeError(f"Catalogue Item retrieval failed: {response.text}")
@@ -173,6 +194,7 @@ def create_or_return_catalogue_item_in_rems(
         url=f"{rems_base_url}/api/catalogue-items/create",
         json=catalogue_item,
         headers=headers,
+        verify=verify_ssl,
     )
 
     if response.status_code != 200:

tests/test_ckan_functions.py

@@ -31,12 +31,13 @@ def test_get_packages_count(mock_get):
 
     # Call the function with a mock CKAN base URL
     ckan_base_url = "http://mock-ckan-instance.com"
-    count = get_packages_count(ckan_base_url)
+    count = get_packages_count(ckan_base_url, True)
 
     # Assert the function returns the correct count
     assert count == 42
     mock_get.assert_called_once_with(
-        f"{ckan_base_url}/api/3/action/package_search?rows=0"
+        url=f"{ckan_base_url}/api/3/action/package_search?rows=0",
+        verify=True,
     )
 
 
@@ -50,12 +51,13 @@ def test_get_packages(mock_get):
     start = 0
     rows = 2
     ckan_base_url = "http://mock-ckan-instance.com"
-    packages = get_packages(start, rows, ckan_base_url)
+    packages = get_packages(start, rows, ckan_base_url, True)
 
     # Assert the function returns the correct packages
     assert len(packages) == 2
     assert packages[0]["id"] == "package1"
     assert packages[1]["name"] == "Test Package 2"
     mock_get.assert_called_once_with(
-        f"{ckan_base_url}/api/3/action/package_search?rows={rows}&start={start}"
+        url=f"{ckan_base_url}/api/3/action/package_search?rows={rows}&start={start}",
+        verify=True,
     )

tests/test_create_or_return_catalogue_item_in_rems.py

@@ -40,6 +40,7 @@ def test_create_or_return_catalogue_item_in_rems_exists(mock_get):
         title,
         rems_base_url,
         headers,
+        True,
     )
 
     # Assert the function returns the correct catalogue item ID
@@ -49,6 +50,7 @@ def test_create_or_return_catalogue_item_in_rems_exists(mock_get):
     mock_get.assert_called_once_with(
         url=f"{rems_base_url}/api/catalogue-items?disabled=false&archived=false&resource={dataset_identifier}",
         headers=headers,
+        verify=True,
     )
 
 
@@ -91,6 +93,7 @@ def test_create_or_return_catalogue_item_in_rems_create(
         title,
         rems_base_url,
         headers,
+        True,
     )
 
     # Assert the function returns the newly created catalogue item ID
@@ -107,6 +110,7 @@ def test_create_or_return_catalogue_item_in_rems_create(
         url=f"{rems_base_url}/api/catalogue-items/create",
         json=expected_catalogue_item,
         headers=headers,
+        verify=True,
     )
 
 
@@ -136,6 +140,7 @@ def test_create_or_return_catalogue_item_in_rems_retrieval_fails(mock_get):
             title,
             rems_base_url,
             headers,
+            True,
         )
 
 
@@ -181,4 +186,5 @@ def test_create_or_return_catalogue_item_in_rems_creation_fails(
             title,
             rems_base_url,
             headers,
+            True,
         )

tests/test_create_or_return_form_in_rems.py

@@ -27,7 +27,9 @@ def test_create_or_return_form_in_rems_exists(mock_get):
     rems_base_url = "http://mock-rems-instance.com"
     headers = {"Authorization": "Bearer mock_token"}
     organization_id = "test-org-id"
-    form_id = create_or_return_form_in_rems(organization_id, rems_base_url, headers)
+    form_id = create_or_return_form_in_rems(
+        organization_id, rems_base_url, headers, True
+    )
 
     # Assert the function returns the correct form ID
     assert form_id == 123
@@ -36,6 +38,7 @@ def test_create_or_return_form_in_rems_exists(mock_get):
     mock_get.assert_called_once_with(
         url=f"{rems_base_url}/api/forms?disabled=false&archived=false",
         headers=headers,
+        verify=True,
     )
 
 
@@ -62,7 +65,9 @@ def test_create_or_return_form_in_rems_create(mock_load_json, mock_get, mock_pos
     rems_base_url = "http://mock-rems-instance.com"
     headers = {"Authorization": "Bearer mock_token"}
     organization_id = "test-org-id"
-    form_id = create_or_return_form_in_rems(organization_id, rems_base_url, headers)
+    form_id = create_or_return_form_in_rems(
+        organization_id, rems_base_url, headers, True
+    )
 
     # Assert the function returns the newly created form ID
     assert form_id == 456
@@ -82,6 +87,7 @@ def test_create_or_return_form_in_rems_create(mock_load_json, mock_get, mock_pos
         url=f"{rems_base_url}/api/forms/create",
         json=expected_form,
         headers=headers,
+        verify=True,
     )
 
 
@@ -99,7 +105,7 @@ def test_create_or_return_form_in_rems_retrieval_fails(mock_get):
     with pytest.raises(
         RuntimeError, match="Workflow retrieval failed: Internal Server Error"
     ):
-        create_or_return_form_in_rems(organization_id, rems_base_url, headers)
+        create_or_return_form_in_rems(organization_id, rems_base_url, headers, True)
 
 
 # Test when form creation fails with a non-200 status code
@@ -128,4 +134,4 @@ def test_create_or_return_form_in_rems_creation_fails(
     headers = {"Authorization": "Bearer mock_token"}
     organization_id = "test-org-id"
     with pytest.raises(RuntimeError, match="Workflow creation failed: Bad Request"):
-        create_or_return_form_in_rems(organization_id, rems_base_url, headers)
+        create_or_return_form_in_rems(organization_id, rems_base_url, headers, True)