init

.github/workflows/build.yaml

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+name: Build and test
+
+on:
+  workflow_call:
+    inputs:
+      oarepo:
+        description: OARepo version (11, 12, ...)
+        required: true
+        default: 11
+        type: string
+
+env:
+  OAREPO_VERSION: ${{ inputs.oarepo }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          # This path is specific to Ubuntu
+          path: ~/.cache/pip
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+
+      - name: Configure sysctl limits
+        run: |
+          sudo swapoff -a
+          sudo sysctl -w vm.swappiness=1
+          sudo sysctl -w fs.file-max=262144
+          sudo sysctl -w vm.max_map_count=262144
+
+      - name: Runs Opensearch
+        uses: ankane/setup-opensearch@v1
+        with:
+          plugins: analysis-icu
+
+      - name: Start Redis
+        uses: supercharge/[email protected]
+        with:
+          redis-version: ${{ matrix.redis-version }}
+
+      - name: Run tests
+        run: |
+          ./run-tests.sh
+
+      - name: Build package to publish
+        run: |
+          .venv-builder/bin/python setup.py sdist bdist_wheel
+
+      - name: Freeze packages
+        run: |
+          .venv-builder/bin/pip freeze > requirements.txt
+          .venv-tests/bin/pip freeze >>requirements.txt
+
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist
+
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: requirements.txt
+          path: requirements.txt

.github/workflows/manual.yaml

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+name: Dispatch
+
+on:
+  workflow_dispatch:
+    inputs:
+      oarepo:
+        description: OARepo version (11, 12, ...)
+        required: true
+        default: 11
+
+jobs:
+  build:
+    uses: ./.github/workflows/build.yaml
+    with:
+      oarepo: ${{ github.event.inputs.oarepo }}

.github/workflows/push.yaml

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+name: Build, test and publish
+
+on: push
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+  build11:
+    uses: ./.github/workflows/build.yaml
+    with:
+      oarepo: 11
+
+  build12:
+    uses: ./.github/workflows/build.yaml
+    with:
+      oarepo: 12
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: build11
+    steps:
+      - name: Use built artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist
+
+      - name: List files
+        run: |
+          ls -la
+          ls -la dist
+
+      - name: Publish package
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip_existing: true
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# Idea software family
+.idea/
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+venv/
+.venv/
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+
+# Translations
+*.mo
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Vim swapfiles
+.*.sw?
+
+tests/test.db
+
+.venv*
+.direnv
+
+docs/migration/data
+
+.env
+.envrc
+/.python-version
+/poetry.lock
+example/data
+.DS_Store
+
+test-model
+
+# Testing
+sample/
+
+tests/test-sample-app
+tests/test-sample-site
+
+example_document/
+dist/
+
+.model_venv/
+.vscode
+
+thesis

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (C) 2021 CESNET.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include oarepo_doi *
+prune tests
+prune thesis

README.md

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+# OARepo DOI

format.sh

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+black oarepo_requests tests --target-version py310
+autoflake --in-place --remove-all-unused-imports --recursive oarepo_requests tests
+isort oarepo_requests tests  --profile black

oarepo_doi/actions/doi.py

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+from invenio_requests.customizations import SubmitAction
+from invenio_requests.resolvers.registry import ResolverRegistry
+from invenio_records_resources.proxies import current_service_registry
+
+from oarepo_doi.api import create_doi
+
+
+class DoiDraftAction(SubmitAction):
+    def execute(self, identity, uow):
+        topic = self.request.topic.resolve()
+        # create_doi(topic, event=None)
+        super().execute(identity, uow)

oarepo_doi/api.py

@@ -0,0 +1,59 @@
+import requests
+import json
+from invenio_base.utils import obj_or_import_string
+from flask import current_app
+
+
+def create_doi(service, record, data, event = None ):
+    """ if event = None, doi will be created as a draft."""
+
+    mapping = obj_or_import_string(service.mapping[record.schema])()
+    errors = mapping.metadata_check(data)
+    if len(errors) > 0 and event:
+        return #todo: dois can not be published with missing mandatory values
+
+    request_metadata = mapping.create_datacite_payload(data)
+
+    if event:
+        request_metadata["data"]["attributes"]["event"] = event
+
+    request_metadata["data"]["attributes"]["prefix"] = service.prefix
+
+    request = requests.post(url=service.url, json=request_metadata, headers={'Content-type': 'application/vnd.api+json'},
+                            auth=(service.username, service.password)
+                            )
+
+    if request.status_code != 201:
+        raise requests.ConnectionError("Expected status code 201, but got {}".format(request.status_code))
+
+    content = request.content.decode('utf-8')
+    json_content = json.loads(content)
+    doi_value = json_content['data']['id']
+    mapping.add_doi(record, data, doi_value)
+
+
+def edit_doi(service, record, event = None):
+    """ edit existing draft """
+
+    mapping = obj_or_import_string(service.mapping[record.schema])()
+    errors = mapping.metadata_check(record)
+    if len(errors) > 0 and event:
+        return #todo: dois can not be published with missing mandatory values
+    doi_value = mapping.get_doi(record)
+    if doi_value:
+        if not service.url.endswith('/'):
+            url = service.url + '/'
+        else:
+            url = service.url
+        url = url + doi_value.replace("/", "%2F")
+
+        request_metadata = mapping.create_datacite_payload(record)
+        if event:
+            request_metadata["data"]["attributes"]["event"] = event
+
+        request = requests.put(url=url, json=request_metadata, headers={'Content-type': 'application/vnd.api+json'},
+                    auth=(service.username, service.password))
+
+        if request.status_code != 200:
+            raise requests.ConnectionError("Expected status code 200, but got {}".format(request.status_code))
+

oarepo_doi/ext.py

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+
+class OARepoDOI(object):
+    """OARepo DOI extension."""
+
+    def __init__(self, app=None):
+        """Extension initialization."""
+        if app:
+            self.init_app(app)
+
+    def init_app(self, app):
+        """Flask application initialization."""
+        self.init_config(app)
+        app.extensions["oarepo-doi"] = self
+
+    def init_config(self, app):
+        """Initialize configuration."""
+        if "DATACITE_URL" not in app.config:
+            app.config["DATACITE_URL"] = 'https://api.datacite.org/dois'
+        if "DATACITE_MODE" not in app.config:
+            app.config["DATACITE_MODE"] = "ON_EVENT"

oarepo_doi/services/components/__init__.py

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+import json
+import requests
+from invenio_records_resources.services.records.components import ServiceComponent
+from flask import current_app
+from invenio_base.utils import obj_or_import_string
+
+from oarepo_doi.api import create_doi, edit_doi
+
+
+class DoiComponent(ServiceComponent):
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.mode = current_app.config.get("DATACITE_MODE")
+        self.username = current_app.config.get("DATACITE_USERNAME")
+        self.password = current_app.config.get("DATACITE_PASSWORD")
+        self.url = current_app.config.get("DATACITE_URL")
+        self.prefix = current_app.config.get("DATACITE_PREFIX")
+        self.mapping = current_app.config.get("DATACITE_MAPPING")
+
+    def create(self, identity, data=None, record=None, **kwargs):
+        if self.mode == "AUTOMATIC_DRAFT":
+            create_doi(self, record,data, None)
+
+    def update_draft(self, identity, data=None, record=None, **kwargs):
+        if self.mode == "AUTOMATIC_DRAFT":
+            edit_doi(self, record)
+
+    def update(self, identity, data=None, record=None, **kwargs):
+        if self.mode == "AUTOMATIC_DRAFT" or self.mode == "AUTOMATIC":
+            edit_doi(self, record)
+
+    def publish(self, identity, data=None, record=None, **kwargs):
+        if self.mode == "AUTOMATIC":
+            create_doi(self, record, data, "publish")
+        if self.mode == "AUTOMATIC_DRAFT":
+            edit_doi(self, record, "publish")