dcor-shared 0.12.0__tar.gz → 0.12.2__tar.gz

dcor_shared-0.12.2/.github/workflows/check.yml

@@ -0,0 +1,105 @@
+name: Checks
+on: [push, pull_request]
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        ckan-version: ["2.11"]
+        dcor_control: ["develop", "pypi"]
+      fail-fast: false
+
+    name: DCOR-CKAN ${{ matrix.ckan-version }} ${{ matrix.dcor_control }}
+    runs-on: ubuntu-latest
+    container:
+      image: ckan/ckan-dev:${{ matrix.ckan-version }}
+      options: --user root --hostname dcor-dev-docker
+
+    services:
+      solr:
+        image: ckan/ckan-solr:${{ matrix.ckan-version }}-solr9
+      postgres:
+        image: ckan/ckan-postgres-dev:${{ matrix.ckan-version }}
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        options: >-
+          --health-cmd "pg_isready" 
+          --health-interval 10s 
+          --health-timeout 5s 
+          --health-retries 10
+      redis:
+        image: redis:3
+      minio:
+        image: raghavaalajangi95/dcor-minio:latest
+        # Note:
+        # The official MinIO setup uses standalone mode, which has limitations:
+        # - Certain 'mc admin' commands, such as user and policy management, are not supported.
+        # - Using these commands will result in errors like:
+        #   "This 'admin' API is not supported by server in 'mode-server-fs'"
+        # - `minio/minio:edge-cicd` container from MinIO is a good alternative,
+        # but it is still not supporting 'mc admin policy' command and the container is not managed properly.
+        # References:
+        # - https://github.com/minio/minio/discussions/16099
+        # - https://github.com/orgs/community/discussions/26688#discussioncomment-4183701
+        # - https://stackoverflow.com/questions/64031598/creating-a-minios3-container-inside-a-github-actions-yml-file/64188150#64188150
+        env:
+          MINIO_ROOT_USER: minioadmin
+          MINIO_ROOT_PASSWORD: minioadmin
+          MINIO_NEW_USER: dcor
+          MINIO_NEW_SECRET_KEY: secretkey12345678
+        options: >-
+          --health-cmd "curl -f http://localhost:9000/minio/health/ready || exit 1"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+        ports:
+          - 9000:9000
+          - 9001:9001
+
+    env:
+      CKAN_SQLALCHEMY_URL: postgresql://ckan_default:pass@postgres/ckan_test
+      CKAN_DATASTORE_WRITE_URL: postgresql://datastore_write:pass@postgres/datastore_test
+      CKAN_DATASTORE_READ_URL: postgresql://datastore_read:pass@postgres/datastore_test
+      CKAN_SOLR_URL: http://solr:8983/solr/ckan
+      CKAN_REDIS_URL: redis://redis:6379/1
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install and setup DCOR
+        run: |
+          pip3 install dcor_control
+
+          # use test-core.ini as default
+          cp /srv/app/src/ckan/test-core.ini /srv/app/ckan.ini
+          # initialize CKAN database
+          ckan -c /srv/app/ckan.ini db init
+          # fix location of allowed datastore commands
+          # https://github.com/ckan/ckan/issues/8926
+          mkdir -p /srv/app/ckanext/datastore/tests/
+          printf 'upper\n"count"\n' > /srv/app/ckanext/datastore/tests/allowed_functions.txt
+          # complement configuration
+          dcor inspect --assume-yes
+
+      - name: Install latest DCOR extensions from GitHub
+        if: matrix.dcor_control == 'develop'
+        run: |
+          dcor develop --yes
+          dcor inspect --assume-yes
+
+      - name: Install extension and requirements
+        run: |
+          pip install -e .
+          pip install -r ./tests/requirements.txt
+
+      - name: Run tests
+        run: |
+          pytest -v --ckan-ini=/srv/app/ckan.ini \
+             --cov=dcor_shared \
+             --cov-report=xml \
+             --cov-append \
+             tests

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/CHANGELOG

@@ -1,3 +1,8 @@
+0.12.2
+ - fix: testing did not append S3 resources
+0.12.1
+ - ci: migrate to docker
+ - ref: deprecate `get_resource_path`, `make_dataset`, `make_resource`
 0.12.0
  - feat: introduce rqjob submodule for managing CKAN background jobs
 0.11.5

{dcor_shared-0.12.0/dcor_shared.egg-info → dcor_shared-0.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: dcor_shared
-Version: 0.12.0
+Version: 0.12.2
 Summary: Functionalities shared by the DCOR CKAN extensions
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -18,6 +18,7 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: boto3
 Requires-Dist: dclab[s3]>=0.60.9
+Dynamic: license-file
 
 dcor_shared
 ===========
@@ -37,22 +38,14 @@ To install the latest release, simply run:
 
 Testing
 -------
-Testing is done via vagrant in a virtualmachine using the
-`dcor-test <https://app.vagrantup.com/paulmueller/boxes/dcor-test/>` image.
-Make sure that `vagrant` and `virtualbox` are installed and run the
-following commands in the root of this repository:
-
-::
-
-    # Setup virtual machine using `Vagrantfile`
-    vagrant up
-    # Run the tests
-    vagrant ssh -- sudo bash /testing/vagrant-run-tests.sh
+Testing is implemented via GitHub Actions. You may also set up a local
+docker container with CKAN and MinIO. Take a look at the GitHub Actions
+workflow for more information.
 
 
 .. |PyPI Version| image:: https://img.shields.io/pypi/v/dcor_shared.svg
    :target: https://pypi.python.org/pypi/dcor_shared
 .. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/DCOR-dev/dcor_shared/check.yml
-   :target: https://travis-ci.com/DCOR-dev/dcor_shared
+   :target: https://github.com/DCOR-dev/dcor_shared/actions/workflows/check.yml
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/DCOR-dev/dcor_shared
    :target: https://codecov.io/gh/DCOR-dev/dcor_shared

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/README.rst

@@ -16,22 +16,14 @@ To install the latest release, simply run:
 
 Testing
 -------
-Testing is done via vagrant in a virtualmachine using the
-`dcor-test <https://app.vagrantup.com/paulmueller/boxes/dcor-test/>` image.
-Make sure that `vagrant` and `virtualbox` are installed and run the
-following commands in the root of this repository:
-
-::
-
-    # Setup virtual machine using `Vagrantfile`
-    vagrant up
-    # Run the tests
-    vagrant ssh -- sudo bash /testing/vagrant-run-tests.sh
+Testing is implemented via GitHub Actions. You may also set up a local
+docker container with CKAN and MinIO. Take a look at the GitHub Actions
+workflow for more information.
 
 
 .. |PyPI Version| image:: https://img.shields.io/pypi/v/dcor_shared.svg
    :target: https://pypi.python.org/pypi/dcor_shared
 .. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/DCOR-dev/dcor_shared/check.yml
-   :target: https://travis-ci.com/DCOR-dev/dcor_shared
+   :target: https://github.com/DCOR-dev/dcor_shared/actions/workflows/check.yml
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/DCOR-dev/dcor_shared
    :target: https://codecov.io/gh/DCOR-dev/dcor_shared

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/dcor_shared/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.12.0'
-__version_tuple__ = version_tuple = (0, 12, 0)
+__version__ = version = '0.12.2'
+__version_tuple__ = version_tuple = (0, 12, 2)

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/dcor_shared/ckan.py

@@ -1,5 +1,6 @@
 import os
 import pathlib
+import warnings
 
 from .parse import get_ini_config_option
 
@@ -77,6 +78,9 @@ def get_resource_path(resource_id, create_dirs=False):
 
     If `create_dirs` is True, create the parent directory tree.
     """
+    warnings.warn("`get_resource_path` should not be used since DCOR moved "
+                  "to storing data solely on S3",
+                  DeprecationWarning)
     rid = resource_id
     resources_path = get_ckan_storage_path() / "resources"
     pdir = resources_path / rid[:3] / rid[3:6]

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/dcor_shared/testing.py

@@ -5,6 +5,7 @@ import numbers
 import pathlib
 from typing import Dict, List
 import uuid
+import warnings
 
 import ckan.authz
 import ckan.tests.factories as factories
@@ -47,6 +48,10 @@ def create_with_upload_no_temp(clean_db, ckan_config, monkeypatch):
 def make_dataset(create_context=None, owner_org=None, create_with_upload=None,
                  resource_path=None, activate=False, **kwargs):
     """Create a dataset with a resource for testing"""
+    warnings.warn(
+        "`make_dataset` is deprecated, use `make_dataset_via_s3` instead",
+        DeprecationWarning)
+
     if create_context is None:
         user = factories.User()
         create_context = {'ignore_auth': False,
@@ -163,7 +168,6 @@ def make_dataset_via_s3(
         rid = make_resource_via_s3(resource_path=resource_path,
                                    organization_id=owner_org["id"],
                                    dataset_id=ds_dict["id"],
-                                   create_context=create_context,
                                    private=ds_dict.get("private", False)
                                    )
     else:
@@ -188,6 +192,9 @@ def make_dataset_via_s3(
 
 def make_resource(resource_path, create_with_upload, create_context,
                   dataset_id):
+    warnings.warn(
+        "`make_resource` is deprecated, use `make_resource_via_s3` instead",
+        DeprecationWarning)
     content = resource_path.read_bytes()
     rs = create_with_upload(
         data=content,
@@ -200,9 +207,25 @@ def make_resource(resource_path, create_with_upload, create_context,
     return resource
 
 
-def make_resource_via_s3(resource_path, organization_id, dataset_id,
-                         create_context, private=False):
+def make_resource_via_s3(
+        resource_path: pathlib.Path | str,
+        organization_id: str,
+        dataset_id: str,
+        create_context: Dict = None,
+        private: bool = False,
+        ret_dict: bool = False,
+        ):
     """Upload a resource to S3 and register it with CKAN"""
+    if create_context is not None:
+        warnings.warn("Create context has no effect for creating resources "
+                      f"via S3 for testing (got {create_context})",
+                      DeprecationWarning)
+
+    user = factories.Sysadmin()
+    create_context = {'ignore_auth': False,
+                      'user': user['name'],
+                      'api_version': 3}
+
     bucket_name = get_ckan_config_option(
         "dcor_object_store.bucket_name").format(
         organization_id=organization_id)
@@ -216,15 +239,18 @@ def make_resource_via_s3(resource_path, organization_id, dataset_id,
 
     revise_dict = {
         "match": {"id": dataset_id},
-        "update": {"resources": [{"id": rid,
-                                  "name": resource_path.name,
-                                  "s3_available": True,
-                                  }
-                                 ]
-                   }
+        "update__resources__extend": [{
+            "id": rid,
+            "name": resource_path.name,
+            "s3_available": True,
+            }]
         }
     helpers.call_action("package_revise", create_context, **revise_dict)
-    return rid
+    if ret_dict:
+        res_dict = helpers.call_action("resource_show", id=rid)
+        return res_dict
+    else:
+        return rid
 
 
 def synchronous_enqueue_job(job_func, args=None, kwargs=None, title=None,

{dcor_shared-0.12.0 → dcor_shared-0.12.2/dcor_shared.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: dcor_shared
-Version: 0.12.0
+Version: 0.12.2
 Summary: Functionalities shared by the DCOR CKAN extensions
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -18,6 +18,7 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: boto3
 Requires-Dist: dclab[s3]>=0.60.9
+Dynamic: license-file
 
 dcor_shared
 ===========
@@ -37,22 +38,14 @@ To install the latest release, simply run:
 
 Testing
 -------
-Testing is done via vagrant in a virtualmachine using the
-`dcor-test <https://app.vagrantup.com/paulmueller/boxes/dcor-test/>` image.
-Make sure that `vagrant` and `virtualbox` are installed and run the
-following commands in the root of this repository:
-
-::
-
-    # Setup virtual machine using `Vagrantfile`
-    vagrant up
-    # Run the tests
-    vagrant ssh -- sudo bash /testing/vagrant-run-tests.sh
+Testing is implemented via GitHub Actions. You may also set up a local
+docker container with CKAN and MinIO. Take a look at the GitHub Actions
+workflow for more information.
 
 
 .. |PyPI Version| image:: https://img.shields.io/pypi/v/dcor_shared.svg
    :target: https://pypi.python.org/pypi/dcor_shared
 .. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/DCOR-dev/dcor_shared/check.yml
-   :target: https://travis-ci.com/DCOR-dev/dcor_shared
+   :target: https://github.com/DCOR-dev/dcor_shared/actions/workflows/check.yml
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/DCOR-dev/dcor_shared
    :target: https://codecov.io/gh/DCOR-dev/dcor_shared

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/dcor_shared.egg-info/SOURCES.txt

@@ -3,9 +3,7 @@ CHANGELOG
 LICENSE
 MANIFEST.in
 README.rst
-Vagrantfile
 pyproject.toml
-vagrant-run-tests.sh
 .github/workflows/check.yml
 .github/workflows/deploy_pypi.yml
 dcor_shared/__init__.py

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/tests/test_ckan.py

@@ -1,12 +1,10 @@
 import pathlib
 from unittest import mock
 
-import ckanext.dcor_schemas.plugin
-
 from dcor_shared import get_resource_dc_config, get_resource_info
 
 import pytest
-from dcor_shared.testing import make_dataset, synchronous_enqueue_job
+from dcor_shared.testing import make_dataset_via_s3, synchronous_enqueue_job
 
 data_path = pathlib.Path(__file__).parent / "data"
 
@@ -15,15 +13,8 @@ data_path = pathlib.Path(__file__).parent / "data"
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
-def test_get_resource_dc_config(enqueue_job_mock, create_with_upload,
-                                monkeypatch):
-    monkeypatch.setattr(
-        ckanext.dcor_schemas.plugin,
-        'DISABLE_AFTER_DATASET_CREATE_FOR_CONCURRENT_JOB_TESTS',
-        True)
-
-    _, res_dict = make_dataset(
-        create_with_upload=create_with_upload,
+def test_get_resource_dc_config(enqueue_job_mock):
+    _, res_dict = make_dataset_via_s3(
         resource_path=data_path / "calibration_beads_47.rtdc",
         activate=True)
 
@@ -37,14 +28,8 @@ def test_get_resource_dc_config(enqueue_job_mock, create_with_upload,
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
-def test_get_resource_info(enqueue_job_mock, create_with_upload, monkeypatch):
-    monkeypatch.setattr(
-        ckanext.dcor_schemas.plugin,
-        'DISABLE_AFTER_DATASET_CREATE_FOR_CONCURRENT_JOB_TESTS',
-        True)
-
-    ds_dict, res_dict = make_dataset(
-        create_with_upload=create_with_upload,
+def test_get_resource_info(enqueue_job_mock):
+    ds_dict, res_dict = make_dataset_via_s3(
         resource_path=data_path / "calibration_beads_47.rtdc",
         activate=True)
 

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/tests/test_data.py

@@ -5,15 +5,14 @@ from unittest import mock
 import uuid
 
 from ckan import logic
-import ckanext.dcor_schemas.plugin
 
 from dcor_shared import (
-    get_dc_instance, get_resource_path, s3, sha256sum, wait_for_resource
+    get_dc_instance, s3, sha256sum, wait_for_resource
 )
 
 import pytest
 import ckan.tests.factories as factories
-from dcor_shared.testing import make_dataset, synchronous_enqueue_job
+from dcor_shared.testing import make_dataset_via_s3, synchronous_enqueue_job
 
 data_path = pathlib.Path(__file__).parent / "data"
 
@@ -22,23 +21,14 @@ data_path = pathlib.Path(__file__).parent / "data"
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
-def test_get_dc_instance_file(enqueue_job_mock, create_with_upload,
-                              monkeypatch):
-    monkeypatch.setattr(
-        ckanext.dcor_schemas.plugin,
-        'DISABLE_AFTER_DATASET_CREATE_FOR_CONCURRENT_JOB_TESTS',
-        True)
-
-    ds_dict, _ = make_dataset(
-        create_with_upload=create_with_upload,
+def test_get_dc_instance_file(enqueue_job_mock):
+    ds_dict, _ = make_dataset_via_s3(
         resource_path=data_path / "calibration_beads_47.rtdc",
         activate=True)
 
     rid = ds_dict["resources"][0]["id"]
-    resource_path = pathlib.Path(get_resource_path(rid))
-    assert resource_path.exists(), "sanity check"
     with get_dc_instance(rid) as ds:
-        assert str(ds.path) == str(resource_path)
+        assert len(ds)
 
 
 @pytest.mark.ckan_config('ckan.storage_path',
@@ -60,24 +50,13 @@ def test_get_dc_instance_file_fails_without_actual_resource():
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
-def test_get_dc_instance_s3(enqueue_job_mock, create_with_upload,
-                            monkeypatch):
-    monkeypatch.setattr(
-        ckanext.dcor_schemas.plugin,
-        'DISABLE_AFTER_DATASET_CREATE_FOR_CONCURRENT_JOB_TESTS',
-        True)
-
-    ds_dict, _ = make_dataset(
-        create_with_upload=create_with_upload,
+def test_get_dc_instance_s3(enqueue_job_mock):
+    ds_dict, _ = make_dataset_via_s3(
         resource_path=data_path / "calibration_beads_47.rtdc",
         activate=True)
 
     res_dict = ds_dict["resources"][0]
     rid = res_dict["id"]
-    resource_path = pathlib.Path(get_resource_path(rid))
-    # remove the file, so DCOR falls back to the S3 resource
-    resource_path.unlink()
-    assert not resource_path.exists(), "sanity check"
     with get_dc_instance(rid) as ds:
         assert ds.path.startswith("http")
         assert res_dict["s3_available"]
@@ -85,6 +64,8 @@ def test_get_dc_instance_s3(enqueue_job_mock, create_with_upload,
 
 
 @pytest.mark.ckan_config('ckan.plugins', 'dcor_depot dcor_schemas')
+@pytest.mark.ckan_config('dcor_object_store.bucket_name',
+                         'circle-{organization_id}')
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
@@ -125,38 +106,6 @@ def test_wait_for_resource_s3(monkeypatch):
     wait_for_resource(res_id)
 
 
-@pytest.mark.ckan_config('ckan.plugins', '')  # disable plugins
-def test_wait_for_resource_no_s3_url_no_plugins(monkeypatch):
-    res_id = str(uuid.uuid4())
-    monkeypatch.setattr(logic, "get_action",
-                        lambda x: lambda context, data_dict: {
-                            "id": res_id})
-    # Create the actual path
-    rp = pathlib.Path(get_resource_path(res_id))
-    rp.parent.mkdir(parents=True, exist_ok=True)
-    rp.write_bytes(b"This is not a dummy file, but a fake DC file!")
-    # Should not raise an exception
-    wait_for_resource(res_id)
-
-
-@pytest.mark.ckan_config('ckan.plugins', 'dcor_depot')
-def test_wait_for_resource_no_s3_url_with_dcor_depot_plugin(monkeypatch):
-    res_id = str(uuid.uuid4())
-    monkeypatch.setattr(logic, "get_action",
-                        lambda x: lambda context, data_dict: {
-                            "id": res_id})
-    # Create the actual path
-    rp = pathlib.Path(get_resource_path(res_id))
-    rp.parent.mkdir(parents=True, exist_ok=True)
-    rp.write_bytes(b"This is not a dummy file, but a fake DC file!")
-    rp2 = rp.with_name("test.rtdc")
-    rp.rename(rp2)
-    rp.symlink_to(rp2)
-
-    # Should not raise an exception
-    wait_for_resource(res_id)
-
-
 def test_wait_resource_not_available(monkeypatch):
     res_id = str(uuid.uuid4())
     monkeypatch.setattr(logic, "get_action",

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/tests/test_s3.py

@@ -1,14 +1,13 @@
 import hashlib
 from unittest import mock
 import pathlib
-import random
 import uuid
 
 import botocore.exceptions
 import pytest
 import requests
 
-from dcor_shared import get_ckan_config_option, s3, sha256sum
+from dcor_shared import s3, sha256sum
 from dcor_shared.testing import upload_presigned_to_s3
 
 

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/tests/test_s3cc.py

@@ -7,10 +7,9 @@ import pytest
 from ckan import model
 import ckan.tests.helpers as helpers
 import ckan.tests.factories as factories
-import ckanext.dcor_schemas.plugin
 
 from dcor_shared.testing import (
-    make_dataset, synchronous_enqueue_job, upload_presigned_to_s3
+    make_dataset_via_s3, synchronous_enqueue_job, upload_presigned_to_s3
 )
 from dcor_shared import s3, s3cc, sha256sum
 
@@ -140,6 +139,8 @@ def test_get_s3_attributes_for_artifact(enqueue_job_mock):
 
 
 @pytest.mark.ckan_config('ckan.plugins', 'dcor_schemas')
+@pytest.mark.ckan_config('dcor_object_store.bucket_name',
+                         'circle-{organization_id}')
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
@@ -170,20 +171,13 @@ def test_get_s3_handle(enqueue_job_mock):
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 @mock.patch('ckan.plugins.toolkit.enqueue_job',
             side_effect=synchronous_enqueue_job)
-def test_get_s3_dc_handle_basin_based(enqueue_job_mock, create_with_upload,
-                                      monkeypatch, tmp_path):
-    monkeypatch.setattr(
-        ckanext.dcor_schemas.plugin,
-        'DISABLE_AFTER_DATASET_CREATE_FOR_CONCURRENT_JOB_TESTS',
-        True)
-
+def test_get_s3_dc_handle_basin_based(enqueue_job_mock, tmp_path):
     resource_path = tmp_path / "data.rtdc"
     shutil.copy2(data_path / "calibration_beads_47.rtdc", resource_path)
     with h5py.File(resource_path, "a") as h5:
         del h5["events/volume"]
 
-    _, res_dict = make_dataset(
-        create_with_upload=create_with_upload,
+    _, res_dict = make_dataset_via_s3(
         resource_path=resource_path,
         activate=True)
     rid = res_dict["id"]

{dcor_shared-0.12.0 → dcor_shared-0.12.2}/tests/test_testing.py

@@ -4,48 +4,12 @@ import pytest
 import ckan.tests.factories as factories
 import requests
 
-from dcor_shared.testing import make_dataset, make_dataset_via_s3
+from dcor_shared.testing import make_dataset_via_s3
 from dcor_shared import s3cc, sha256sum
 
 data_path = pathlib.Path(__file__).parent / "data"
 
 
-@pytest.mark.ckan_config('ckan.plugins', 'dcor_schemas')
-@pytest.mark.usefixtures('clean_db', 'with_request_context')
-def test_make_dataset():
-    user = factories.User()
-    owner_org = factories.Organization(users=[{
-        'name': user['id'],
-        'capacity': 'admin'
-    }])
-    # Note: `call_action` bypasses authorization!
-    create_context = {'ignore_auth': False,
-                      'user': user['name'], 'api_version': 3}
-    ds_dict = make_dataset(create_context, owner_org,
-                           activate=False)
-    assert ds_dict["state"] == "draft"
-
-
-@pytest.mark.ckan_config('ckan.plugins', 'dcor_schemas')
-@pytest.mark.usefixtures('clean_db', 'with_request_context')
-def test_make_dataset_no_user_specified():
-    ds_dict = make_dataset(activate=False)
-    assert ds_dict["state"] == "draft"
-
-
-@pytest.mark.ckan_config('ckan.plugins', 'dcor_schemas')
-@pytest.mark.usefixtures('clean_db', 'with_request_context')
-def test_make_dataset_with_resource(create_with_upload):
-    # upload a *valid* [sic] .rtdc File (this is the control)
-    ds_dict, res_dict = make_dataset(
-        create_with_upload=create_with_upload,
-        resource_path=data_path / "calibration_beads_47.rtdc",
-        activate=True)
-    assert len(ds_dict["resources"]) == 1
-    assert "id" in res_dict
-    assert res_dict["package_id"] == ds_dict["id"]
-
-
 @pytest.mark.ckan_config('ckan.plugins', 'dcor_schemas')
 @pytest.mark.usefixtures('clean_db', 'with_request_context')
 def test_make_dataset_via_s3():

dcor_shared-0.12.0/.github/workflows/check.yml

@@ -1,49 +0,0 @@
-name: Checks
-
-on:
-  push:
-  pull_request:
-
-# only allow one job to run
-concurrency: general_workflow
-
-jobs:
-  checks:
-    runs-on: macos-12
-    steps:
-    - uses: actions/checkout@main
-    - name: Set up Python 3.8
-      uses: actions/setup-python@main
-      with:
-        python-version: "3.8"
-    - name: Install flake8 dependencies
-      run: |
-        # prerequisites
-        python -m pip install --upgrade pip wheel
-        python -m pip install flake8
-    - name: Lint with flake8
-      run: |
-        flake8 --exclude _version.py .
-    - name: Cache vagrant images
-      uses: actions/cache@v3
-      env:
-        cache-name: vagrant-image
-      with:
-        path: ~/.vagrant.d
-        key: macos-build-${{ env.cache-name }}-${{ hashFiles('Vagrantfile') }}
-        restore-keys: |
-          macos-build-${{ env.cache-name }}-
-    - name: save environment variables for codecov in VM
-      run: |
-        env | grep GITHUB > environment.txt
-        cat environment.txt
-    - name: Get the latest box and remove old boxes from the GH Actions cache
-      run: |
-        vagrant box update
-        vagrant box prune
-    - name: Setup vagrant VM
-      run: |
-        vagrant up
-    - name: Run tests in vagrant VM
-      run: |
-        vagrant ssh -- sudo bash /testing/vagrant-run-tests.sh

dcor_shared-0.12.0/Vagrantfile

@@ -1,72 +0,0 @@
-# -*- mode: ruby -*-
-# vi: set ft=ruby :
-
-# All Vagrant configuration is done below. The "2" in Vagrant.configure
-# configures the configuration version (we support older styles for
-# backwards compatibility). Please don't change it unless you know what
-# you're doing.
-Vagrant.configure("2") do |config|
-  # The most common configuration options are documented and commented below.
-  # For a complete reference, please see the online documentation at
-  # https://docs.vagrantup.com.
-
-  # Every Vagrant development environment requires a box. You can search for
-  # boxes at https://vagrantcloud.com/search.
-  config.vm.box = "paulmueller/dcor-test"
-
-  # Disable automatic box update checking. If you disable this, then
-  # boxes will only be checked for updates when the user runs
-  # `vagrant box outdated`. This is not recommended.
-  # config.vm.box_check_update = false
-
-  # Create a forwarded port mapping which allows access to a specific port
-  # within the machine from a port on the host machine. In the example below,
-  # accessing "localhost:8080" will access port 80 on the guest machine.
-  # NOTE: This will enable public access to the opened port
-  # config.vm.network "forwarded_port", guest: 80, host: 8080
-
-  # Create a forwarded port mapping which allows access to a specific port
-  # within the machine from a port on the host machine and only allow access
-  # via 127.0.0.1 to disable public access
-  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
-
-  # Create a private network, which allows host-only access to the machine
-  # using a specific IP.
-  # config.vm.network "private_network", ip: "192.168.33.10"
-
-  # Create a public network, which generally matched to bridged network.
-  # Bridged networks make the machine appear as another physical device on
-  # your network.
-  # config.vm.network "public_network"
-
-  # Share an additional folder to the guest VM. The first argument is
-  # the path on the host to the actual folder. The second argument is
-  # the path on the guest to mount the folder. And the optional third
-  # argument is a set of non-required options.
-  # config.vm.synced_folder "../data", "/vagrant_data"
-  # config.vm.synced_folder ".", "/vagrant", disabled: true
-  config.vm.synced_folder ".", "/testing", type: "rsync",
-    rsync__args: ["-vzra", "--delete"],
-    rsync__exclude: ["*.pyc", "__pycache__"],
-    owner: "www-data"
-  # Provider-specific configuration so you can fine-tune various
-  # backing providers for Vagrant. These expose provider-specific options.
-  # Reduce requirements so everythin runs on GitHub Actions
-  config.vm.provider "virtualbox" do |v|
-    v.memory = 2048
-    v.cpus = 1
-  end
-
-
-  # Enable provisioning with a shell script. Additional provisioners such as
-  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
-  # documentation for more information about their specific syntax and use.
-  # config.vm.provision "shell", inline: <<-SHELL
-  #   apt-get update
-  #   apt-get install -y apache2
-  # SHELL
-
-  # Prevent reinstallation of guest additinos on every vagrant up
-  # (Uncomment the next line in your CI tests)
-  # config.vbguest.auto_update = false
-end

dcor_shared-0.12.0/vagrant-run-tests.sh

@@ -1,22 +0,0 @@
-set -e
-set -x
-# Set CKAN_INI to testing
-export CKAN_INI=/etc/ckan/default/ckan.ini
-# Go to the directory of this script
-cd "$(dirname "${BASH_SOURCE[0]}")"
-# Source the CKAN environment
-source /usr/lib/ckan/default/bin/activate
-# Update pip
-pip install --upgrade pip wheel
-# Update all DCOR extensions
-dcor update --yes
-# Install the current package in editable mode for testing
-pip install -e .
-pip install -r tests/requirements.txt
-# run tests with coverage
-coverage run --source=dcor_shared -m pytest -p no:warnings tests
-# Get GitHub environment variables so codecov detects GH Actions (allow command to fail)
-export $(grep -v '^#' environment.txt | xargs) || exit 0
-curl -Os https://uploader.codecov.io/latest/linux/codecov
-chmod +x codecov
-./codecov