pytest

README.md

@@ -11,6 +11,7 @@ The package requires Python >= 3.7 and the following python packages:
 ```
 click>=8.0.1
 pandas>=1.3.4
+numpy==1.26.4
 requests>=2.26.0
 ```
 

cloudos/__init__.py

@@ -8,4 +8,4 @@
 from .clos import Cloudos
 from ._version import __version__
 
-__all__ = ['jobs', 'utils', 'clos', 'cohorts']
+__all__ = ['jobs', 'utils', 'clos', 'queue']

cloudos/__main__.py

@@ -345,7 +345,7 @@ def run(apikey,
         print('\t' + str(j))
         print('\t...Sending job to CloudOS\n')
     if is_module:
-        if job_queue != None:
+        if job_queue is not None:
             print(f'\t\t[Message] Job queue "{job_queue}" was specified but a the ' +
                   'workflow is a platform workflow that uses a fixed queue provided ' +
                   f'by CloudOS. Ignoring job queue "{job_queue}" and using the ' +

cloudos/clos.py

@@ -418,6 +418,7 @@ def process_workflow_list(r, all_fields=False):
         """
         COLUMNS = ['_id',
                    'name',
+                   'isModule',
                    'archived.status',
                    'mainFile',
                    'workflowType',
@@ -495,8 +496,8 @@ def is_module(self, workflow_name, workspace_id, verify=True):
         if len(is_module) == 0:
             raise ValueError(f'No workflow found with name: {workflow_name}')
         if len(is_module) > 1:
-            raise ValueError(f'More than one workflow type detected for {workflow_name}: {wt}')
-        return is_module.values[0].upper() == 'TRUE'
+            raise ValueError(f'More than one workflow found with name: {workflow_name}')
+        return is_module.values[0]
 
     def get_project_list(self, workspace_id, verify=True):
         """Get all the project from a CloudOS workspace.

environment.yml

@@ -8,3 +8,4 @@ dependencies:
     - requests
     - click
     - pandas
+    - numpy==1.26.4

requirements.txt

@@ -2,6 +2,7 @@ click>=8.0.1
 requests>=2.26.0
 requests-mock>=1.9.3
 pandas>=1.3.4
+numpy==1.26.4
 pytest>=6.2.5
 responses>=0.21.0
-mock>=3.0.5
+mock>=3.0.5

tests/test_clos/test_is_module.py

@@ -0,0 +1,41 @@
+"""Pytest for method Cloudos.is_module"""
+import mock
+import responses
+from responses import matchers
+from cloudos.clos import Cloudos
+from tests.functions_for_pytest import load_json_file
+
+INPUT = "tests/test_data/process_workflow_list_initial_request.json"
+APIKEY = 'vnoiweur89u2ongs'
+CLOUDOS_URL = 'http://cloudos.lifebit.ai'
+WORKSPACE_ID = 'lv89ufc838sdig'
+
+
+@mock.patch('cloudos.clos', mock.MagicMock())
+@responses.activate
+def test_is_module():
+    """
+    Test 'is_module' to work as intended
+    API request is mocked and replicated with json files
+    """
+    json_data = load_json_file(INPUT)
+    params = {"teamId": WORKSPACE_ID, "apikey": APIKEY}
+    header = {
+        "Accept": "application/json, text/plain, */*",
+        "Content-Type": "application/json;charset=UTF-8"
+    }
+    search_str = f"teamId={WORKSPACE_ID}&apikey={APIKEY}"
+    # mock GET method with the .json
+    responses.add(
+            responses.GET,
+            url=f"{CLOUDOS_URL}/api/v1/workflows?{search_str}",
+            body=json_data,
+            headers=header,
+            match=[matchers.query_param_matcher(params)],
+            status=200)
+    # start cloudOS service
+    clos = Cloudos(apikey=APIKEY, cromwell_token=None, cloudos_url=CLOUDOS_URL)
+    # get mock response
+    response = clos.is_module(workspace_id=WORKSPACE_ID,
+                              workflow_name="multiqc")
+    assert response

tests/test_data/process_workflow_list_initial_request.json

@@ -292,7 +292,7 @@
         "isPredefined": false,
         "isCurated": false,
         "isFeatured": false,
-        "isModule": false,
+        "isModule": true,
         "isPublic": false,
         "priceAmount": 0,
         "priceUnit": "PER_SAMPLE",
@@ -309,4 +309,4 @@
         "workflowType": "docker",
         "containerName": "ewels/multiqc"
     }
-]
+]

tests/test_data/process_workflow_list_results.csv

@@ -1,4 +1,4 @@
-_id,name,archived.status,mainFile,workflowType,repository.name,repository.platform,repository.url,repository.isPrivate
-XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX
-XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX
-XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX
+_id,name,isModule,archived.status,mainFile,workflowType,repository.name,repository.platform,repository.url,repository.isPrivate
+XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX
+XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX
+XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX,XXX