Fix issues #9 and #11

clients/directory_client.py

@@ -128,14 +128,17 @@ def get_all_directory_services(biobanks: list[OrganizationDirectoryDTO]):
     }       
     '''
     results = requests.post(DIRECTORY_API_URL, json={'query': emx2_services_query}).json()
-    for service in results['data']['Services']:
-        service_biobank = get_biobank_by_service(biobanks, service['id'])
-        service_resource_directory = ResourceDirectoryDTO(id=service['id'], name=service['name'],
-                                                          description=service['description'], biobank=service_biobank,
-                                                          contactEmail=service['contactInformation'][
-                                                              'email'] if 'contactInformation' in service else '')
-        parsed_services.append(service_resource_directory)
-    return parsed_services
+    if('Services' in results['data'].keys()):
+        print(results['data'])
+        for service in results['data']['Services']:
+            service_biobank = get_biobank_by_service(biobanks, service['id'])
+            service_resource_directory = ResourceDirectoryDTO(id=service['id'], name=service['name'],
+                                                              description=service['description'], biobank=service_biobank,
+                                                              contactEmail=service['contactInformation'][
+                                                                  'email'] if 'contactInformation' in service else '')
+            parsed_services.append(service_resource_directory)
+        return parsed_services
+    return []
 
 
 def get_biobank_by_service(biobanks: list[OrganizationDirectoryDTO], service_id):

clients/negotiator_client.py

@@ -70,10 +70,10 @@ def get_all_negotiator_networks(self):
     def add_organizations(self, organizations: list[OrganizationDirectoryDTO]):
         self.post('organizations', data=json.dumps(organizations))
 
-    def update_organization_info(self, id, name, external_id, description, contact_email, uri):
+    def update_organization_info(self, id, name, external_id, description, contact_email, uri, withdrawn):
         self.put(f'organizations/{id}', data=json.dumps({'name': name, 'externalId': external_id,
                                                          'description': description, 'contactEmail': contact_email,
-                                                         'uri': uri}))
+                                                         'uri': uri, 'withdrawn': withdrawn}))
 
     def add_resources(self, resources: list):
         added_resources = self.post('resources', data=json.dumps(resources))

models/dto/organization.py

@@ -44,6 +44,7 @@ class NegotiatorOrganizationDTO(BaseModel):
     description: Optional[str] = Field(default='')
     contactEmail: Optional[str] = Field(default='')
     uri: Optional[str] = Field(default='')
+    withdrawn: Optional[bool] = Field(default=False)
 
     @staticmethod
     def parse(negotiator_data):

synchronization/sync_service.py

@@ -72,15 +72,17 @@ def sync_organizations(negotiator_client: NegotiatorAPIClient, directory_organzi
                     check_fields(negotiation_organization.description, directory_organization.description) or
                     (directory_organization.contact is not None and check_fields(negotiation_organization.contactEmail,
                                                                                  directory_organization.contact.email)) or
-                    check_fields(negotiation_organization.uri, directory_organization.url)):
+                    check_fields(negotiation_organization.uri, directory_organization.url) or
+                    check_fields(negotiation_organization.withdrawn, directory_organization.withdrawn)):
                 LOG.info(
-                    f'Updating name and/or description and/or contact email and/or uri for organization: {external_id}')
+                    f'Updating name and/or description and/or contact email and/or uri and/or withdrawn for organization: {external_id}')
                 LOG.info(f'Current organization name is: {negotiation_organization.name}')
                 LOG.info(f'New organization name is: {directory_organization.name}')
                 negotiator_client.update_organization_info(negotiation_organization.id, directory_organization.name,
                                                            external_id, directory_organization.description,
                                                            directory_organization.contact.email,
-                                                           directory_organization.url)
+                                                           directory_organization.url,
+                                                           directory_organization.withdrawn)
         else:
             LOG.info(
                 f'Organization with external id {external_id} not found, including it to the list of organizations to add')

tests/integration/integration_tests.py

@@ -37,7 +37,7 @@ def test_networks_initial_sync_ok():
 def test_organization_sync_when_new_added_and_then_updated():
     add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync",
                           "test negotiator sync", 'bbmri-eric:contactID:EU_network',
-                          "http://test_negotiator_sync.org", 'insert')
+                          "http://test_negotiator_sync.org", 'false', 'insert')
 
     biobanks_after_add = get_all_biobanks()
     assert len(biobanks_after_add) == len(pytest.directory_organizations) + 1
@@ -50,7 +50,7 @@ def test_organization_sync_when_new_added_and_then_updated():
 
     add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync newname",
                           "test negotiator sync", 'bbmri-eric:contactID:EU_network',
-                          "http://test_negotiator_sync.org", 'update')
+                          "http://test_negotiator_sync.org", 'false', 'update')
     biobanks_after_update_name = get_all_biobanks()
     sync_organizations(pytest.negotiator_client, biobanks_after_update_name,
                        negotiator_organizations_after_bb_add_and_sync)
@@ -61,7 +61,7 @@ def test_organization_sync_when_new_added_and_then_updated():
     assert organization_with_name_upd.name == "test negotiator sync newname"
     add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync newname",
                           "test negotiator sync newdesc", 'bbmri-eric:contactID:EU_network',
-                          "http://test_negotiator_sync.org", 'update')
+                          "http://test_negotiator_sync.org", 'false', 'update')
     biobanks_after_update_desc = get_all_biobanks()
     sync_organizations(pytest.negotiator_client, biobanks_after_update_desc,
                        negotiator_organizations_after_update_name)
@@ -73,7 +73,7 @@ def test_organization_sync_when_new_added_and_then_updated():
     assert organization_with_desc_upd.description == "test negotiator sync newdesc"
     add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync newname",
                           "test negotiator sync newdesc", 'bbmri-eric:contactID:EU_network',
-                          "http://test_negotiator_sync.org", 'update')
+                          "http://test_negotiator_sync.org", 'false', 'update')
     update_person_email_contact('[email protected]')
     biobanks_after_update_email = get_all_biobanks()
 
@@ -87,7 +87,7 @@ def test_organization_sync_when_new_added_and_then_updated():
     assert organization_with_email_upd.contactEmail == '[email protected]'
     add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync newname",
                           "test negotiator sync newdesc", 'bbmri-eric:contactID:EU_network',
-                          "http://test_negotiator_sync_newurl.org", 'update')
+                          "http://test_negotiator_sync_newurl.org", 'false', 'update')
     biobanks_after_update_url = get_all_biobanks()
     sync_organizations(pytest.negotiator_client, biobanks_after_update_url,
                        negotiator_organizations_after_update_email)
@@ -96,6 +96,17 @@ def test_organization_sync_when_new_added_and_then_updated():
     organization_with_url_upd = \
         [org for org in negotiator_organizations_after_update_url if org.externalId == "test_negotiator_sync"][0]
     assert organization_with_url_upd.uri == "http://test_negotiator_sync_newurl.org"
+    add_or_update_biobank("test_negotiator_sync", "test_negotiator_sync", "test negotiator sync newname",
+                          "test negotiator sync newdesc", 'bbmri-eric:contactID:EU_network',
+                          "http://test_negotiator_sync_newurl.org", 'true', 'update')
+    biobanks_after_update_withdrawn = get_all_biobanks()
+    sync_organizations(pytest.negotiator_client, biobanks_after_update_withdrawn,
+                       negotiator_organizations_after_update_url)
+    negotiator_organizations_after_update_withdrawn = pytest.negotiator_client.get_all_organizations()
+    assert len(negotiator_organizations_after_update_withdrawn) == len(negotiator_organizations_after_update_withdrawn)
+    organization_with_withdrawn_upd = \
+        [org for org in negotiator_organizations_after_update_withdrawn if org.externalId == "test_negotiator_sync"][0]
+    assert organization_with_withdrawn_upd.withdrawn == True
     delete_object_from_directory("test_negotiator_sync", "Biobanks")
 
 

tests/integration/utils.py

@@ -8,13 +8,13 @@
 
 
 def add_or_update_biobank(biobank_id, biobank_pid, biobank_name, biobank_description, biobank_contact, biobank_url,
-                          operation=Literal['insert', 'update']):
+                          biobank_withdrawn, operation=Literal['insert', 'update']):
     session = pytest.directory_session
     query = f'mutation {operation}($value:[BiobanksInput]){{{operation}(Biobanks:$value){{message}}}}'
     variables = {
         "value": [
             {
-                "withdrawn": "false",
+                "withdrawn": biobank_withdrawn,
                 "id": biobank_id,
 
                 "pid": biobank_pid,

utils.py

@@ -27,4 +27,7 @@ def check_fields(negotiator_field, directory_field):
     else:
         if negotiator_field is None:
             return True
-    return negotiator_field.strip() != directory_field.strip()
+    if isinstance(negotiator_field, str) and isinstance(directory_field, str):
+        return negotiator_field.strip() != directory_field.strip()
+    else:
+        return negotiator_field != directory_field