Tests integration with ON/OFF switch (#237)

* created `HAS_INTEGRATION_TESTS_ENABLED` boolean in conftest.py

* test_api.py skipping tests if `HAS_INTEGRATION_TESTS_ENABLED` is turned OFF

* turning `ON/OFF` integration API test with a simple boolean

* skipping some tests in file and uncommenting them

* updated `test_user.py` to remove unneeded fixture

updated test to use standard fixture

* added boolean variable for integration test ON/OFF switch `HAS_INTEGRATION_TESTS_ENABLED`

* formatted with trunk

* switched `HAS_INTEGRATION_TESTS_ENABLED` to `False`

tests/api/test_api.py

@@ -8,6 +8,7 @@
 
 import pytest
 import requests
+from conftest import HAS_INTEGRATION_TESTS_ENABLED
 
 import cript
 from cript.api.exceptions import InvalidVocabulary
@@ -41,7 +42,7 @@ def test_api_with_invalid_host() -> None:
         cript.API(host="no_http_host.org", api_token="123456789", storage_token="987654321")
 
 
-@pytest.mark.skip(reason="skipping for now because it needs an API container")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="skipping because API client needs API token")
 def test_api_context(cript_api: cript.API) -> None:
     assert cript.api.api._global_cached_api is not None
     assert cript.api.api._get_global_cached_api() is not None
@@ -252,7 +253,7 @@ def test_download_file_from_url(cript_api: cript.API, tmp_path) -> None:
     assert response == saved_file_contents
 
 
-@pytest.mark.skip(reason="this test requires a real storage_token from a real frontend, and this cannot be done via CI")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="requires a real storage_token from a real frontend")
 def test_upload_and_download_local_file(cript_api, tmp_path_factory) -> None:
     """
     tests file upload to cloud storage
@@ -292,7 +293,7 @@ def test_upload_and_download_local_file(cript_api, tmp_path_factory) -> None:
     assert downloaded_file_contents == file_text
 
 
-@pytest.mark.skip(reason="requires a real cript_api_token and not currently available on CI")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="requires a real cript_api_token")
 def test_api_search_node_type(cript_api: cript.API) -> None:
     """
     tests the api.search() method with just a node type material search
@@ -323,7 +324,7 @@ def test_api_search_node_type(cript_api: cript.API) -> None:
     assert materials_paginator.current_page_results[0]["name"] == "(2-Chlorophenyl) 2,4-dichlorobenzoate"
 
 
-@pytest.mark.skip(reason="requires a real cript_api_token and not currently available on CI")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="requires a real cript_api_token")
 def test_api_search_contains_name(cript_api: cript.API) -> None:
     """
     tests that it can correctly search with contains name mode
@@ -336,7 +337,7 @@ def test_api_search_contains_name(cript_api: cript.API) -> None:
     assert contains_name_paginator.current_page_results[0]["name"] == "Pilocarpine polyacrylate"
 
 
-@pytest.mark.skip(reason="requires a real cript_api_token and not currently available on CI")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="requires a real cript_api_token")
 def test_api_search_exact_name(cript_api: cript.API) -> None:
     """
     tests search method with exact name search
@@ -349,7 +350,7 @@ def test_api_search_exact_name(cript_api: cript.API) -> None:
     assert exact_name_paginator.current_page_results[0]["name"] == "Sodium polystyrene sulfonate"
 
 
-@pytest.mark.skip(reason="requires a real cript_api_token and not currently available on CI")
+@pytest.mark.skipif(not HAS_INTEGRATION_TESTS_ENABLED, reason="requires a real cript_api_token")
 def test_api_search_uuid(cript_api: cript.API) -> None:
     """
     tests search with UUID

tests/conftest.py

@@ -16,6 +16,8 @@
 
 import cript
 
+HAS_INTEGRATION_TESTS_ENABLED: bool = False
+
 
 @pytest.fixture(scope="session", autouse=True)
 def cript_api():

tests/nodes/supporting_nodes/test_file.py

@@ -3,6 +3,7 @@
 import os
 import uuid
 
+import pytest
 from test_integration import integrate_nodes_helper
 from util import strip_uid_from_dict
 
@@ -55,6 +56,7 @@ def test_source_is_local(tmp_path, tmp_path_factory) -> None:
     assert _is_local_file(file_source=relative_file_path) is True
 
 
+@pytest.mark.skip(reason="test is outdated because files now upload on api.save()")
 def test_local_file_source_upload_and_download(tmp_path_factory) -> None:
     """
     upload a file and download it and be sure the contents are the same
@@ -68,70 +70,64 @@ def test_local_file_source_upload_and_download(tmp_path_factory) -> None:
     1. download the file to a temporary path
         1. read that file text and assert that the string written and read are the same
     """
-    # import uuid
-    # import datetime
-    # file_text: str = (
-    #     f"This is an automated test from the Python SDK within "
-    #     f"`tests/nodes/supporting_nodes/test_file.py/test_local_file_source_upload_and_download()` "
-    #     f"checking that the file source is automatically and correctly uploaded to AWS S3. "
-    #     f"The test is conducted on UTC time of '{datetime.datetime.utcnow()}' "
-    #     f"with the unique UUID of '{str(uuid.uuid4())}'"
-    # )
-    #
-    # # create a temp file and write to it
-    # upload_file_dir = tmp_path_factory.mktemp("file_test_upload_file_dir")
-    # local_file_path = upload_file_dir / "my_upload_file.txt"
-    # local_file_path.write_text(file_text)
-    #
-    # # create a file node with a local file path
-    # my_file = cript.File(name="my local file source node", source=str(local_file_path), type="data")
-    #
-    # # check that the file source has been uploaded to cloud storage and source has changed to reflect that
-    # assert my_file.source.startswith("tests/")
-    #
-    # # Get the temporary directory path and clean up handled by pytest
-    # download_file_dir = tmp_path_factory.mktemp("file_test_download_file_dir")
-    # download_file_name = "my_downloaded_file.txt"
-    #
-    # # download file
-    # my_file.download(destination_directory_path=download_file_dir, file_name=download_file_name)
-    #
-    # # the path the file was downloaded to and can be read from
-    # downloaded_local_file_path = download_file_dir / download_file_name
-    #
-    # # read file contents from where the file was downloaded
-    # downloaded_file_contents = downloaded_local_file_path.read_text()
-    #
-    # # assert file contents for upload and download are the same
-    # assert downloaded_file_contents == file_text
-    pass
+    import datetime
+    import uuid
+
+    file_text: str = (
+        f"This is an automated test from the Python SDK within "
+        f"`tests/nodes/supporting_nodes/test_file.py/test_local_file_source_upload_and_download()` "
+        f"checking that the file source is automatically and correctly uploaded to AWS S3. "
+        f"The test is conducted on UTC time of '{datetime.datetime.utcnow()}' "
+        f"with the unique UUID of '{str(uuid.uuid4())}'"
+    )
+
+    # create a temp file and write to it
+    upload_file_dir = tmp_path_factory.mktemp("file_test_upload_file_dir")
+    local_file_path = upload_file_dir / "my_upload_file.txt"
+    local_file_path.write_text(file_text)
+
+    # create a file node with a local file path
+    my_file = cript.File(name="my local file source node", source=str(local_file_path), type="data")
+
+    # check that the file source has been uploaded to cloud storage and source has changed to reflect that
+    assert my_file.source.startswith("tests/")
+
+    # Get the temporary directory path and clean up handled by pytest
+    download_file_dir = tmp_path_factory.mktemp("file_test_download_file_dir")
+    download_file_name = "my_downloaded_file.txt"
+
+    # download file
+    my_file.download(destination_directory_path=download_file_dir, file_name=download_file_name)
 
+    # the path the file was downloaded to and can be read from
+    downloaded_local_file_path = download_file_dir / download_file_name
 
-def test_create_file_local_source(tmp_path) -> None:
+    # read file contents from where the file was downloaded
+    downloaded_file_contents = downloaded_local_file_path.read_text()
+
+    # assert file contents for upload and download are the same
+    assert downloaded_file_contents == file_text
+
+
+def test_create_file_with_local_source(tmp_path) -> None:
     """
     tests that a simple file with only required attributes can be created
     with source pointing to a local file on storage
 
     create a temporary directory with temporary file
     """
-
-    # TODO since no S3 client token for GitHub CI this test will always fail. Commenting it out so tests run well
     # create a temporary file in the temporary directory to test with
-    # file_path = tmp_path / "test.txt"
-    # with open(file_path, "w") as temporary_file:
-    #     temporary_file.write("hello world!")
-    #
-    # assert cript.File(name="my file node with local source", source=str(file_path), type="calibration")
-    pass
+    file_path = tmp_path / "test.txt"
+    with open(file_path, "w") as temporary_file:
+        temporary_file.write("hello world!")
+
+    assert cript.File(name="my file node with local source", source=str(file_path), type="calibration")
 
 
+@pytest.mark.skip(reason="validating file type automatically with DB schema and test not currently needed")
 def test_file_type_invalid_vocabulary() -> None:
     """
     tests that setting the file type to an invalid vocabulary word gives the expected error
-
-    Returns
-    -------
-    None
     """
     pass
 

tests/nodes/supporting_nodes/test_user.py

@@ -36,47 +36,20 @@ def test_user_serialization_and_deserialization(complex_user_dict, complex_user_
     assert strip_uid_from_dict(json.loads(user_node.json)) == user_node_dict
 
 
-@pytest.fixture(scope="session")
-def user_node() -> cript.User:
-    """
-    create a user node for other tests to use
-
-    Notes
-    -----
-    User node should only be created from JSON and not from instantiation
-
-    Returns
-    -------
-    User
-    """
-    # TODO create this user node from JSON instead of instantiation
-    # create User node
-    my_user = cript.User(
-        username="my username",
-        email="my_email@email.com",
-        orcid="123456",
-    )
-    # use user node in test
-    yield my_user
-
-    # reset user node
-    my_user = my_user
-
-
-def test_set_user_properties(user_node):
+def test_set_user_properties(complex_user_node):
     """
     tests that setting any user property throws an AttributeError
     """
     with pytest.raises(AttributeError):
-        user_node.username = "my new username"
+        complex_user_node.username = "my new username"
 
     with pytest.raises(AttributeError):
-        user_node.email = "my new email"
+        complex_user_node.email = "my new email"
 
     with pytest.raises(AttributeError):
-        user_node.orcid = "my new orcid"
+        complex_user_node.orcid = "my new orcid"
 
     with pytest.raises(AttributeError):
         # TODO try setting it via a group node
         #   either way it should give the same error
-        user_node.orcid = ["my new group"]
+        complex_user_node.orcid = ["my new group"]

tests/test_integration.py

@@ -1,6 +1,8 @@
 import json
 import warnings
 
+import pytest
+from conftest import HAS_INTEGRATION_TESTS_ENABLED
 from deepdiff import DeepDiff
 
 import cript
@@ -42,8 +44,10 @@ def integrate_nodes_helper(cript_api: cript.API, project_node: cript.Project):
     * ignoring the UID field through all the JSON because those the API changes when responding
     """
 
-    # TODO remove skip test
-    return
+    if not HAS_INTEGRATION_TESTS_ENABLED:
+        pytest.skip("Integration tests with API requires real API and Storage token")
+        return
+
     print("\n\n=================== Project Node ============================")
     print(project_node.get_json(sort_keys=False, condense_to_uuid={}, indent=2).json)
     print("==============================================================")