Merge pull request #27 from pepkit/dev

Release 0.2.1

Author: khoroshevskyi

.github/workflows/black.yml .github/workflows/black_linter.yml

@@ -4,11 +4,10 @@ on:
   pull_request:
     branches: [main]
 
-
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - uses: psf/black@stable

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  # Run the Ruff linter.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.3
+    hooks:
+      # Run the Ruff linter.
+      - id: ruff
+      # Run the Ruff formatter.
+      - id: ruff-format

Makefile

@@ -1,6 +1,5 @@
 lint:
-	# black should be last in the list, as it lint the code. Tests can fail if order will be different
-	flake8 && isort . && black .
+	ruff format .
 
 run-coverage:
 	coverage run -m pytest

docs/changelog.md

@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.2.1] - 2023-11-01
+### Added
+- is_registry_path checker function
+
 ## [0.2.0] - 2023-10-02
 ### Added
 - Project search functionality

pephubclient/__init__.py

@@ -1,7 +1,7 @@
 from pephubclient.pephubclient import PEPHubClient
 
 __app_name__ = "pephubclient"
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

pephubclient/helpers.py

@@ -4,7 +4,11 @@
 import requests
 from requests.exceptions import ConnectionError
 
+from ubiquerg import parse_registry_path
+from pydantic.error_wrappers import ValidationError
+
 from pephubclient.exceptions import PEPExistsError, ResponseError
+from pephubclient.constants import RegistryPath
 
 
 class RequestManager:
@@ -84,3 +88,18 @@ def call_client_func(func: Callable[..., Any], **kwargs) -> Any:
         MessageHandler.print_warning(f"PEP already exists. {err}")
     except OSError as err:
         MessageHandler.print_error(f"{err}")
+
+
+def is_registry_path(input_string: str) -> bool:
+    """
+    Check if input is a registry path to pephub
+    :param str input_string: path to the PEP (or registry path)
+    :return bool: True if input is a registry path
+    """
+    if input_string.endswith(".yaml"):
+        return False
+    try:
+        RegistryPath(**parse_registry_path(input_string))
+    except (ValidationError, TypeError):
+        return False
+    return True

requirements/requirements-all.txt

@@ -3,3 +3,4 @@ peppy>=0.35.7
 requests>=2.28.2
 pydantic<2.0
 pandas>=2.0.0
+ubiquerg>=0.6.3

requirements/requirements-test.txt

@@ -1,7 +1,9 @@
 black
+ruff
 pytest
 python-dotenv
 pytest-mock
 flake8
 coveralls
-pytest-cov
+pytest-cov
+pre-commit

tests/test_pephubclient.py

@@ -5,6 +5,7 @@
 
 from pephubclient.exceptions import ResponseError
 from pephubclient.pephubclient import PEPHubClient
+from pephubclient.helpers import is_registry_path
 
 SAMPLE_PEP = os.path.join(
     os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
@@ -150,11 +151,53 @@ def test_push_with_pephub_error_response(
 
     def test_search_prj(self, mocker):
         return_value = b'{"count":1,"limit":100,"offset":0,"items":[{"namespace":"namespace1","name":"basic","tag":"default","is_private":false,"number_of_samples":2,"description":"None","last_update_date":"2023-08-27 19:07:31.552861+00:00","submission_date":"2023-08-27 19:07:31.552858+00:00","digest":"08cbcdbf4974fc84bee824c562b324b5","pep_schema":"random_schema_name"}],"session_info":null,"can_edit":false}'
-        requests_mock = mocker.patch(
+        mocker.patch(
             "requests.request",
             return_value=Mock(content=return_value, status_code=200),
         )
 
         return_value = PEPHubClient().find_project(namespace="namespace1")
         assert return_value.count == 1
         assert len(return_value.items) == 1
+
+
+class TestHelpers:
+    @pytest.mark.parametrize(
+        "input_str, expected_output",
+        [
+            (
+                "databio/pep:default",
+                True,
+            ),
+            (
+                "pephub.databio.org::databio/pep:default",
+                True,
+            ),
+            (
+                "pephub.databio.org://databio/pep:default",
+                True,
+            ),
+            (
+                "databio/pep",
+                True,
+            ),
+            (
+                "databio/pep/default",
+                False,
+            ),
+            (
+                "some/random/path/to.yaml",
+                False,
+            ),
+            (
+                "path_to.csv",
+                False,
+            ),
+            (
+                "this/is/path/to.csv",
+                False,
+            ),
+        ],
+    )
+    def test_is_registry_path(self, input_str, expected_output):
+        assert is_registry_path(input_str) is expected_output