Test: fetch_cloudos_id function

.gitignore

@@ -142,3 +142,9 @@ old_scripts/
 
 # pychache
 __pycache__
+
+# .DS_Store
+.DS_Store
+._.DS_Store
+**/.DS_Store
+**/._.DS_Store

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## lifebit-ai/cloudos-cli: changelog
 
+### 1.3.1 - 2022-12-01
+- Patch: fixes `BarRequestException` and `TimeOutException` messages when the response from
+the API server is empty.
+
 ### 1.3.0 - 2022-11-07
 - All Cromwell functionality works now with personal API key. The
 `--cromwell-token` argument is maintained for backwards compatibility, but can

README.md

@@ -1,7 +1,7 @@
 # cloudos
 
-__Date:__ 2022-11-07\
-__Version:__ 1.3.0
+__Date:__ 2022-12-01\
+__Version:__ 1.3.1
 
 
 Python package for interacting with CloudOS
@@ -25,7 +25,7 @@ and the `environment.yml` files provided.
 To run the existing docker image at `quay.io`:
 
 ```bash
-docker run --rm -it quay.io/lifebitaiorg/cloudos-cli:v1.3.0
+docker run --rm -it quay.io/lifebitaiorg/cloudos-cli:v1.3.1
 ```
 
 ### From Github
@@ -78,7 +78,7 @@ cloudos job run --help
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -220,7 +220,7 @@ If everything went well, you should see something like:
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -263,7 +263,7 @@ previous command should have an output similar to:
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -292,7 +292,7 @@ The expected output should be something similar to:
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -327,7 +327,7 @@ The expected output is something similar to:
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -350,7 +350,7 @@ cloudos job list \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 
@@ -383,7 +383,7 @@ The expected output is something similar to:
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS workflow functionality: list workflows in CloudOS.
 
@@ -405,7 +405,7 @@ cloudos workflow list \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS workflow functionality: list workflows in CloudOS.
 
@@ -432,7 +432,7 @@ cloudos cromwell status \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 Cromwell server functionality: check status, start and stop.
 
@@ -451,7 +451,7 @@ cloudos cromwell start \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 Cromwell server functionality: check status, start and stop.
 
@@ -472,7 +472,7 @@ cloudos cromwell stop \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 Cromwell server functionality: check status, start and stop.
 
@@ -538,7 +538,7 @@ cloudos job run \
 ```console
 CloudOS python package: a package for interacting with CloudOS.
 
-Version: 1.3.0
+Version: 1.3.1
 
 CloudOS job functionality: run and check jobs in CloudOS.
 

cloudos/_version.py

@@ -1 +1 @@
-__version__ = '1.3.0'
+__version__ = '1.3.1'

cloudos/utils/errors.py

@@ -2,21 +2,17 @@
 Specific classes to handle errors.
 """
 
-import json
-
 
 class BadRequestException(Exception):
     """Handle bad request exceptions and shows improved messages.
 
     Parameters
     ----------
-    rv : request variable
+    rv : requests.Response
         The request variable returned that caused the error.
     """
     def __init__(self, rv):
-        msg = "Server returned status {}. Response:\n{}".format(
-                    rv.status_code, json.dumps(rv.json())
-                )
+        msg = "Server returned status {}. Reason: {}".format(rv.status_code, rv.reason)
         super(BadRequestException, self).__init__(msg)
         self.rv = rv
 
@@ -26,11 +22,11 @@ class TimeOutException(Exception):
 
     Parameters
     ----------
-    rv : request variable
+    rv : requests.Response
         The request variable returned that caused the error.
     """
     def __init__(self, rv):
         msg = ("Server exceeded the max time to process request. " +
-               "Response:\n{}".format(json.dumps(rv)))
+               "Status: {}; Reason: {}".format(rv.status_code, rv.reason))
         super(TimeOutException, self).__init__(msg)
         self.rv = rv

tests/test_clos/test_create_cromwell_header.py

@@ -0,0 +1,35 @@
+from cloudos.clos import Cloudos
+
+TOKEN = "lifebit_test_token"
+URL = "lifebit.ai"
+
+EXPECTED_OUTPUT_APIKEY = {
+                "Accept": "application/json",
+                "apikey": TOKEN
+            }
+
+EXPECTED_OUTPUT_CROMWELL_TOKEN = {
+                "Accept": "application/json",
+                "Authorization": f'Bearer {TOKEN}'
+            }
+
+
+def test_create_cromwell_header_apikey():
+    """Testing only apikey is provided."""
+    clos = Cloudos(apikey=TOKEN, cromwell_token=None, cloudos_url=URL)
+    output = clos._create_cromwell_header()
+    assert output == EXPECTED_OUTPUT_APIKEY
+
+
+def test_create_cromwell_header_cromwell_token():
+    """Test only cromwell_token is provided."""
+    clos = Cloudos(apikey=None, cromwell_token=TOKEN, cloudos_url=URL)
+    output = clos._create_cromwell_header()
+    assert output == EXPECTED_OUTPUT_CROMWELL_TOKEN
+
+
+def test_create_cromwell_header_both():
+    """Test both cromwell_token and apikey are provided."""
+    clos = Cloudos(apikey=TOKEN, cromwell_token=TOKEN, cloudos_url=URL)
+    output = clos._create_cromwell_header()
+    assert output == EXPECTED_OUTPUT_CROMWELL_TOKEN

tests/test_clos/test_detect_workflow.py

@@ -0,0 +1,40 @@
+"""Pytest for method Cloudos.detect_workflow"""
+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_detect_workflow():
+    """
+    Test 'get_workflow_list' 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.detect_workflow(workspace_id=WORKSPACE_ID, workflow_name="picard")
+    assert response == 'docker'

tests/test_clos/test_get_job_list.py

@@ -0,0 +1,77 @@
+import mock
+import json
+import pytest
+import requests
+import responses
+from responses import matchers
+from cloudos.clos import Cloudos
+from cloudos.utils.errors import BadRequestException
+from tests.functions_for_pytest import load_json_file
+
+INPUT = "tests/test_data/process_job_list_initial_json.json"
+APIKEY = 'vnoiweur89u2ongs'
+CLOUDOS_URL = 'http://cloudos.lifebit.ai'
+WORKSPACE_ID = 'lv89ufc838sdig'
+
+
+@mock.patch('cloudos.clos', mock.MagicMock())
+@responses.activate
+def test_get_job_list_correct_response():
+    """
+    Test 'get_job_list' to work as intended
+    API request is mocked and replicated with json files
+    """
+    create_json = 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/jobs?{search_str}",
+            body=create_json,
+            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.get_job_list(WORKSPACE_ID)
+    # check the response
+    assert response.status_code == 200
+    assert isinstance(response, requests.models.Response)
+
+
+@mock.patch('cloudos.clos', mock.MagicMock())
+@responses.activate
+def test_get_job_list_incorrect_response():
+    """
+    Test 'get_job_list' to fail with '400' response
+    """
+    # prepare error message
+    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}
+    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/jobs?{search_str}",
+            body=error_json,
+            headers=header,
+            match=[matchers.query_param_matcher(params)],
+            status=400)
+    # raise 400 error
+    with pytest.raises(BadRequestException) as error:
+        # check if it failed
+        clos = Cloudos(apikey=APIKEY, cromwell_token=None, cloudos_url=CLOUDOS_URL)
+        clos.get_job_list(WORKSPACE_ID)
+    assert "Bad Request" in (str(error))