From b303a9092d66313970d3e4bd030e1d6178c874fd Mon Sep 17 00:00:00 2001 From: mutantsan Date: Tue, 23 Apr 2024 15:39:02 +0300 Subject: [PATCH] feature: ap_doi plugin --- ckanext/ap_doi/__init__.py | 0 ckanext/ap_doi/collection.py | 141 +++++++++++ ckanext/ap_doi/config.py | 9 + ckanext/ap_doi/config_declaration.yaml | 44 ++++ ckanext/ap_doi/config_schema.yaml | 60 +++++ ckanext/ap_doi/const.py | 1 + ckanext/ap_doi/logic/action.py | 229 ++++++++++++++++++ ckanext/ap_doi/logic/auth.py | 9 + ckanext/ap_doi/logic/schema.py | 15 ++ ckanext/ap_doi/plugin.py | 123 ++++++++++ ckanext/ap_doi/presets.yaml | 11 + ckanext/ap_doi/templates/ap_doi/list.html | 18 ++ ckanext/ap_doi/templates/ap_doi/pager.html | 0 ckanext/ap_doi/templates/ap_doi/record.html | 17 ++ .../scheming/form_snippets/hidden.html | 4 + .../ap_doi/templates/user/dashboard_doi.html | 59 +++++ ckanext/ap_doi/utils.py | 147 +++++++++++ ckanext/ap_doi/views.py | 124 ++++++++++ ckanext/ap_example/plugin.py | 2 +- ckanext/ap_example/views.py | 3 +- ckanext/ap_main/assets/js/vendor/htmx.min.js | 3 +- .../templates/admin_panel/panel_links.html | 4 +- ckanext/ap_main/views/generics.py | 2 +- setup.cfg | 5 +- 24 files changed, 1022 insertions(+), 8 deletions(-) create mode 100644 ckanext/ap_doi/__init__.py create mode 100644 ckanext/ap_doi/collection.py create mode 100644 ckanext/ap_doi/config.py create mode 100644 ckanext/ap_doi/config_declaration.yaml create mode 100644 ckanext/ap_doi/config_schema.yaml create mode 100644 ckanext/ap_doi/const.py create mode 100644 ckanext/ap_doi/logic/action.py create mode 100644 ckanext/ap_doi/logic/auth.py create mode 100644 ckanext/ap_doi/logic/schema.py create mode 100644 ckanext/ap_doi/plugin.py create mode 100644 ckanext/ap_doi/presets.yaml create mode 100644 ckanext/ap_doi/templates/ap_doi/list.html create mode 100644 ckanext/ap_doi/templates/ap_doi/pager.html create mode 100644 ckanext/ap_doi/templates/ap_doi/record.html create mode 100644 ckanext/ap_doi/templates/scheming/form_snippets/hidden.html create mode 100644 ckanext/ap_doi/templates/user/dashboard_doi.html create mode 100644 ckanext/ap_doi/utils.py create mode 100644 ckanext/ap_doi/views.py diff --git a/ckanext/ap_doi/__init__.py b/ckanext/ap_doi/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/ckanext/ap_doi/collection.py b/ckanext/ap_doi/collection.py new file mode 100644 index 0000000..afcc6f3 --- /dev/null +++ b/ckanext/ap_doi/collection.py @@ -0,0 +1,141 @@ +from __future__ import annotations + +from dominate import tags + +import ckan.plugins.toolkit as tk + +import ckanext.ap_main.collection.base as collection_base + +from ckanext.collection.utils import ApiData +from ckanext.collection.types import InputFilter, ButtonFilter, SelectFilter +from ckanext.collection.utils import Filters + +from ckanext.ap_doi.utils import DOIProblemPackageData + + +def row_dictizer( + serializer: collection_base.ApHtmxTableSerializer, row: DOIProblemPackageData +): + row["bulk-action"] = row["id"] # type: ignore + + return row + + +class ApDOICollection(collection_base.ApCollection): + SerializerFactory = collection_base.ApHtmxTableSerializer.with_attributes( + row_dictizer=row_dictizer, + # record_template="ap_doi/record.html", + # pager_template="ap_doi/pager.html", + ) + + ColumnsFactory = collection_base.ApColumns.with_attributes( + names=[ + "bulk-action", + "title", + "doi_status", + "identifier", + "timestamp", + "published", + "row_actions", + ], + sortable={}, + labels={ + "bulk-action": tk.literal( + tags.input_( + type="checkbox", + name="bulk_check", + id="bulk_check", + data_module="ap-bulk-check", + data_module_selector='input[name="entity_id"]', + ) + ), + "title": "Title", + "doi_status": "Status", + "identifier": "DOI", + "timestamp": "Timestamp", + "published": "Publish Date", + "row_actions": "Actions", + }, + width={"title": "15%", "doi_status": "10%", "row_actions": "20%"}, + serializers={ + "timestamp": [("date", {})], + "published": [("date", {})], + }, + ) + + DataFactory = ApiData.with_attributes( + action="ap_doi_get_packages_doi", + ) + + FiltersFactory = Filters.with_attributes( + static_actions=[ + collection_base.BulkAction( + name="bulk-action", + type="bulk_action", + options={ + "label": "Action", + "options": [ + {"value": "1", "text": "Update DOI"}, + ], + }, + ), + collection_base.RowAction( + name="view", + type="row_action", + options={ + "endpoint": "doi_dashboard.create_or_update_doi", + "label": "Update DOI", + "params": { + "package_id": "$id", + }, + }, + ), + collection_base.RowAction( + name="view", + type="row_action", + options={ + "endpoint": "ap_content.entity_proxy", + "label": "View", + "params": { + "entity_id": "$name", + "entity_type": "$type", + "view": "read", + }, + }, + ), + ], + static_filters=[ + InputFilter( + name="q", + type="input", + options={ + "label": "Search", + "placeholder": "Search", + }, + ), + SelectFilter( + name="doi_status", + type="select", + options={ + "label": "Status", + "options": [ + {"value": "", "text": "Any"}, + {"value": "Published", "text": "Published"}, + {"value": "Missing", "text": "Missing"}, + {"value": "Outdated", "text": "Outdated"}, + ], + }, + ), + ButtonFilter( + name="type", + type="button", + options={ + "label": "Clear", + "type": "button", + "attrs": { + "onclick": "$(this).closest('form').find('input,select').val('').prevObject[0].requestSubmit()" + }, + }, + ), + ], + ) diff --git a/ckanext/ap_doi/config.py b/ckanext/ap_doi/config.py new file mode 100644 index 0000000..464a22d --- /dev/null +++ b/ckanext/ap_doi/config.py @@ -0,0 +1,9 @@ +import ckan.plugins.toolkit as tk + + +def is_mock_api_calls() -> bool: + return tk.asbool(tk.config.get("ckanext.ap_doi.mock_api_calls")) + + +def get_doi_prefix() -> str: + return tk.config.get("ckanext.doi.prefix") diff --git a/ckanext/ap_doi/config_declaration.yaml b/ckanext/ap_doi/config_declaration.yaml new file mode 100644 index 0000000..9d67a82 --- /dev/null +++ b/ckanext/ap_doi/config_declaration.yaml @@ -0,0 +1,44 @@ +version: 1 +groups: + - annotation: Admin panel example + options: + # The following keys are declared here, because ckanext-doi doesn't provide config declaration + + - key: ckanext.doi.account_name + required: true + description: Your DataCite Repository account + editable: true + + - key: ckanext.doi.account_password + required: true + description: Your DataCite Repository account password + editable: true + + - key: ckanext.doi.prefix + required: true + description: The prefix taken from your DataCite Repository account (from your test account if running in test mode) + editable: true + + - key: ckanext.doi.publisher + required: true + description: The name of the institution publishing the DOI + editable: true + + - key: ckanext.doi.test_mode + description: Enable dev/test mode + required: true + description: If test mode is set to true, the DOIs will use the DataCite test site. The test site uses a separate account, so you must also change your credentials and prefix. + editable: true + + - key: ckanext.doi.site_url + description: Used to build the link back to the dataset + editable: true + + - key: ckanext.doi.site_title + description: Site title to use in the citation + editable: true + + # AP_DOI config options + - key: ckanext.ap_doi.mock_api_calls + description: If enabled, the extension will not make any API calls to DataCite + editable: true diff --git a/ckanext/ap_doi/config_schema.yaml b/ckanext/ap_doi/config_schema.yaml new file mode 100644 index 0000000..cfa78d9 --- /dev/null +++ b/ckanext/ap_doi/config_schema.yaml @@ -0,0 +1,60 @@ +scheming_version: 2 +schema_id: ap_doi_config +about: Configuration options for the DOI extension + +fields: + - field_name: ckanext.ap_doi.mock_api_calls + label: Mock API calls + description: If enabled, the extension will not make any API calls to DataCite + validators: default(true), one_of([true, false]) + preset: select + required: true + choices: + - value: true + label: Enabled + - value: false + label: Disabled + + - field_name: ckanext.doi.account_name + label: Account name + required: true + description: Your DataCite Repository account + form_snippet: text.html + display_snippet: text.html + + - field_name: ckanext.doi.account_password + label: Account password + required: true + description: Your DataCite Repository account password + input_type: password + + - field_name: ckanext.doi.prefix + label: DOI prefix + required: true + description: The prefix taken from your DataCite Repository account (from your test account if running in test mode) + + - field_name: ckanext.doi.publisher + label: Publisher + required: true + description: The name of the institution publishing the DOI + + - field_name: ckanext.doi.test_mode + label: Test mode + required: true + description: If test mode is set to true, the DOIs will use the DataCite test site. The test site uses a separate account, so you must also change your credentials and prefix. + validators: default(true), one_of([true, false]) + preset: select + required: true + choices: + - value: true + label: Enabled + - value: false + label: Disabled + + - field_name: ckanext.doi.site_url + label: Site URL + description: Used to build the link back to the dataset + + - field_name: ckanext.doi.site_title + label: Site title + description: Site title to use in the citation diff --git a/ckanext/ap_doi/const.py b/ckanext/ap_doi/const.py new file mode 100644 index 0000000..b565ee6 --- /dev/null +++ b/ckanext/ap_doi/const.py @@ -0,0 +1 @@ +DOI_FLAKE_NAME = "ckanext:ap_doi:doi:" diff --git a/ckanext/ap_doi/logic/action.py b/ckanext/ap_doi/logic/action.py new file mode 100644 index 0000000..4501be6 --- /dev/null +++ b/ckanext/ap_doi/logic/action.py @@ -0,0 +1,229 @@ +from __future__ import annotations + +import random +import string +from datetime import datetime as dt +from datetime import timezone +from typing import Any + +from datacite.errors import DataCiteError + +import ckan.plugins.toolkit as tk +from ckan.logic import validate + +import ckanext.doi.model.crud as doi_crud +from ckanext.doi.lib.api import DataciteClient +from ckanext.doi.lib.metadata import build_metadata_dict, build_xml_dict +from ckanext.doi.model.doi import DOI + +import ckanext.ap_doi.logic.schema as schema +from ckanext.ap_doi import const, config +from ckanext.ap_doi.utils import DOIProblemPackageData +from ckanext.ap_doi.utils import ( + get_doi_to_update, + get_packages_to_update, + package_already_in_flake, + remove_package_from_flake, +) + + +@tk.side_effect_free +@validate(schema.ap_doi_get_packages_doi) +def ap_doi_get_packages_doi( + context: Any, data_dict: dict[str, Any] +) -> list[DOIProblemPackageData]: + """Retrieve packages data along with DOI identifiers.""" + tk.check_access("ap_doi_get_packages_doi", context, data_dict) + + model = context["model"] + packages_to_update = get_packages_to_update(const.DOI_FLAKE_NAME) + + results = ( + model.Session.query( + model.Package.id.label("package_id"), + model.Package.name.label("package_name"), + model.Package.title.label("package_title"), + model.Package.type.label("package_type"), + model.Package.metadata_modified.label("metadata_modified"), + DOI.published.label("published"), + DOI.identifier.label("identifier"), + ) + .join(DOI, model.Package.id == DOI.package_id, isouter=True) + .filter(model.Package.type != "harvest") + .filter( + model.Package.id.notin_( + ( + model.Session.query(model.PackageExtra.package_id.label("id")) + .filter(model.PackageExtra.key == "data_source") + .filter(model.PackageExtra.value != "") + .subquery() + ) + ) + ) + .all() + ) + + results = _prepare_problem_package_data(results, packages_to_update) + return filter_dois(results, data_dict) + + +def _prepare_problem_package_data( + results: Any, + packages_to_update: list[DOIProblemPackageData], +) -> list[DOIProblemPackageData]: + packages_data: list[DOIProblemPackageData] = [] + outdated_ids = [package["id"] for package in packages_to_update] + + for row in results: + if row.package_id in outdated_ids: + continue + + doi_status = "Missing" + + if row.published and row.published < row.metadata_modified: + doi_status = "Outdated" + elif row.published: + doi_status = "Published" + + packages_data.append( + { + "id": row.package_id, + "name": row.package_name, + "title": row.package_title, + "doi_status": doi_status, + "published": row.published, + "identifier": row.identifier, + "timestamp": row.metadata_modified, + "type": row.package_type, + } + ) + + for package in packages_to_update: + if package not in packages_data: + packages_data.append(package) + + # Sort packages_data, prioritizing 'Outdated' status + return sorted( + packages_data, + key=lambda x: (x["doi_status"] == "Outdated", x["timestamp"]), + # Reverse to get 'Outdated' first + reverse=True, + ) + + +def filter_dois( + results: list[DOIProblemPackageData], data_dict: dict[str, Any] +) -> list[DOIProblemPackageData]: + """Filter out packages that do not have a DOI.""" + + if q := tk.request.args.get("ap-doi:q"): + results = [result for result in results if q.lower() in result["title"].lower()] + + if doi_status := tk.request.args.get("ap-doi:doi_status"): + results = [result for result in results if doi_status == result["doi_status"]] + + return results + + +def ap_doi_update_doi(context: Any, data_dict: dict[str, Any]) -> dict[str, Any]: + """Action to update a DOI.""" + tk.check_access("ap_doi_update_doi", context, data_dict) + + package_id = data_dict.get("package_id") + + if not package_id: + raise tk.ValidationError({"package_id": "Missing package_id for DOI update"}) + + if config.is_mock_api_calls(): + errors = _mock_update_doi_metadata(context, package_id) + else: + doi_to_update = get_doi_to_update(context["model"], package_id) + pkg_dict = tk.get_action("package_show")({}, {"id": doi_to_update.package_id}) + errors = _update_doi_metadata(pkg_dict, doi_to_update) + + if not errors and package_already_in_flake(const.DOI_FLAKE_NAME, package_id): + remove_package_from_flake(const.DOI_FLAKE_NAME, package_id) + + return { + "status": "success" if not errors else "error", + # "status": "success", + "message": "DOI update completed", + "errors": errors, + } + + +def _mock_update_doi_metadata(context: Any, package_id: dict[str, Any]): + if doi_crud.DOIQuery.read_package(package_id): + context["model"].Session.query(DOI).filter(DOI.package_id == package_id).update( + {"published": dt.now(timezone.utc).isoformat()} + ) + else: + alphabet = string.ascii_lowercase + string.digits + doi = f"{config.get_doi_prefix()}/{''.join(random.choices(alphabet, k=8))}" + doi_crud.DOIQuery.create(doi, package_id) + + context["model"].Session.commit() + + return [] + + +def _update_doi_metadata(pkg_dict: dict[str, Any], doi_to_update: DOI): + """Update the DOI metadata and handle DOI creation or update as necessary.""" + title = pkg_dict.get("title", doi_to_update.package_id) + + if not pkg_dict.get("author"): + _add_author_to_pkg_dict(pkg_dict) + + metadata_dict = build_metadata_dict(pkg_dict) + xml_dict = build_xml_dict(metadata_dict) + return _handle_doi_creation_or_update(doi_to_update, xml_dict, title) + + +def _add_author_to_pkg_dict(pkg_dict: dict[str, Any]): + """Set the author full name in the package dictionary.""" + creator = tk.get_action("user_show")({}, {"id": pkg_dict["creator_user_id"]}) + full_name = creator.get("fullname") + name = creator.get("name") + pkg_dict["author"] = full_name or name + + +def _handle_doi_creation_or_update( + doi_to_update: DOI, xml_dict: dict[str, Any], title: str +): + """Handle DOI creation or update based on the DOI's publication status.""" + errors = [] + client = DataciteClient() + + if doi_to_update.published is None: + _create_doi(client, doi_to_update, xml_dict) + else: + _update_existing_doi(client, doi_to_update, xml_dict, title, errors) + return errors + + +def _create_doi(client: DataciteClient, doi_to_update: DOI, xml_dict: dict[str, Any]): + """Create a new DOI with the given metadata.""" + client.set_metadata(doi_to_update.identifier, xml_dict) + client.mint_doi(doi_to_update.identifier, doi_to_update.package_id) + + +def _update_existing_doi( + client: DataciteClient, + doi_to_update: DOI, + xml_dict: dict[str, Any], + title: str, + errors: list[str], +): + """Update an existing DOI if the metadata has changed.""" + same = client.check_for_update(doi_to_update.identifier, xml_dict) + if not same: + try: + client.set_metadata(doi_to_update.identifier, xml_dict) + except DataCiteError as e: + errors.append( + f'Error while updating "{title}"' + f" (DOI {doi_to_update.identifier}): {str(e)}" + ) + else: + errors.append(f'"{title}" is already up to date') + remove_package_from_flake(const.DOI_FLAKE_NAME, doi_to_update.package_id) diff --git a/ckanext/ap_doi/logic/auth.py b/ckanext/ap_doi/logic/auth.py new file mode 100644 index 0000000..409903f --- /dev/null +++ b/ckanext/ap_doi/logic/auth.py @@ -0,0 +1,9 @@ +from __future__ import annotations + + +def ap_doi_get_packages_doi(context, data_dict): + return {"success": False} + + +def ap_doi_update_doi(context, data_dict): + return {"success": False} diff --git a/ckanext/ap_doi/logic/schema.py b/ckanext/ap_doi/logic/schema.py new file mode 100644 index 0000000..7ee339a --- /dev/null +++ b/ckanext/ap_doi/logic/schema.py @@ -0,0 +1,15 @@ +from __future__ import annotations + +from typing import Any, Dict + +from ckan.logic.schema import validator_args + +Schema = Dict[str, Any] + + +@validator_args +def ap_doi_get_packages_doi(unicode_safe, default) -> Schema: + return { + "doi_status": [default(""), unicode_safe], + "q": [default(""), unicode_safe], + } diff --git a/ckanext/ap_doi/plugin.py b/ckanext/ap_doi/plugin.py new file mode 100644 index 0000000..8debe39 --- /dev/null +++ b/ckanext/ap_doi/plugin.py @@ -0,0 +1,123 @@ +from __future__ import annotations + +from typing import Any +from os import path + +from yaml import safe_load + +import ckan.plugins as p +import ckan.logic as logic +import ckan.plugins.toolkit as tk +from ckan.types import SignalMapping +from ckan.config.declaration import Declaration, Key + +from ckanext.doi.plugin import DOIPlugin + +import ckanext.ap_main.types as ap_types + +from ckanext.collection.interfaces import CollectionFactory, ICollection +from ckanext.ap_doi.collection import ApDOICollection + +import ckanext.ap_doi.const as const +import ckanext.ap_doi.utils as utils +import ckanext.ap_doi.config as config + + +@tk.blanket.blueprints +@tk.blanket.actions +@tk.blanket.auth_functions +class AdminPanelDoiPlugin(p.SingletonPlugin): + p.implements(p.IConfigurer) + p.implements(p.IPackageController, inherit=True) + p.implements(p.ISignal) + p.implements(p.IConfigDeclaration) + p.implements(ICollection, inherit=True) + + # IConfigurer + + def update_config(self, config_: tk.CKANConfig): + tk.add_template_directory(config_, "templates") + tk.add_public_directory(config_, "public") + tk.add_resource("assets", "ap_doi") + + # IPackageController + + def after_dataset_show(self, context: Any, pkg_dict: dict[str, Any]): + if not pkg_dict.get("author"): + pkg_dict = utils.set_package_author(pkg_dict) + + return pkg_dict + + def after_dataset_update(self, context: Any, pkg_dict: dict[str, Any]): + if not pkg_dict.get("author"): + pkg_dict = utils.set_package_author(pkg_dict) + + doi_to_update = utils.get_doi_to_update(context["model"], pkg_dict["id"]) + flake_exists = utils.package_already_in_flake( + const.DOI_FLAKE_NAME, pkg_dict["id"] + ) + is_old_doi = doi_to_update.published is not None + + # We need to create flake only for old DOIs, + # because if it is a newly generated, + # it will be shown as a package without DOI, + # and we don't have to check its metadata updates + if not flake_exists and is_old_doi: + utils.add_package_to_flake(const.DOI_FLAKE_NAME, pkg_dict["id"]) + + return pkg_dict + + # ISignal + + def get_signal_subscriptions(self) -> SignalMapping: + return { + tk.signals.ckanext.signal("ap_main:collect_config_sections"): [ + collect_config_sections_subscriber, + ], + } + + # IConfigDeclaration + + def declare_config_options(self, declaration: Declaration, key: Key): + logic.clear_validators_cache() + + with open(path.dirname(__file__) + "/config_declaration.yaml") as file: + data_dict = safe_load(file) + + return declaration.load_dict(data_dict) + + # ICollection + + def get_collection_factories(self) -> dict[str, CollectionFactory]: + return {"ap-doi": ApDOICollection} + + +def collect_config_sections_subscriber(sender: None): + return ap_types.SectionConfig( + name="DOI", + configs=[ + ap_types.ConfigurationItem( + name="Dashboard", + blueprint="doi_dashboard.list", + ), + ap_types.ConfigurationItem( + name="DOI settings", + blueprint="doi_dashboard.config", + ), + ], + ) + + +class ApDOIPlugin(DOIPlugin): + def after_dataset_create(self, context, pkg_dict): + if config.is_mock_api_calls(): + return + + super(ApDOIPlugin, self).after_dataset_create(context, pkg_dict) + + ## IPackageController + def after_dataset_update(self, context, pkg_dict): + if config.is_mock_api_calls(): + return + + super(ApDOIPlugin, self).after_dataset_update(context, pkg_dict) diff --git a/ckanext/ap_doi/presets.yaml b/ckanext/ap_doi/presets.yaml new file mode 100644 index 0000000..fbd034f --- /dev/null +++ b/ckanext/ap_doi/presets.yaml @@ -0,0 +1,11 @@ +scheming_presets_version: 2 +about: AP DOI presets +about_url: http://github.com/ckan/ckanext-scheming#preset + +presets: + - preset_name: ap_doi + values: + field_name: doi + label: Dataset DOI + form_snippet: hidden.html + display_snippet: text.html diff --git a/ckanext/ap_doi/templates/ap_doi/list.html b/ckanext/ap_doi/templates/ap_doi/list.html new file mode 100644 index 0000000..09dd631 --- /dev/null +++ b/ckanext/ap_doi/templates/ap_doi/list.html @@ -0,0 +1,18 @@ +{% extends 'admin_panel/base.html' %} + +{% block ap_main_class %} ap-doi {% endblock %} + +{% block breadcrumb_content %} +
  • {% link_for _("DOI"), request.endpoint %}
    • +{% endblock breadcrumb_content %} + +{% block ap_content %} + {% if collection.data.total %} + {{ collection.serializer.render() | safe }} + {% else %} +

    + {{ _("No packages with outdated DOI found") }} + {{ _("Clear the search") }} +

    + {% endif %} +{% endblock ap_content %} diff --git a/ckanext/ap_doi/templates/ap_doi/pager.html b/ckanext/ap_doi/templates/ap_doi/pager.html new file mode 100644 index 0000000..e69de29 diff --git a/ckanext/ap_doi/templates/ap_doi/record.html b/ckanext/ap_doi/templates/ap_doi/record.html new file mode 100644 index 0000000..955a4d0 --- /dev/null +++ b/ckanext/ap_doi/templates/ap_doi/record.html @@ -0,0 +1,17 @@ +{% set data = collection.serializer.dictize_row(record) if collection.serializer.ensure_dictized else record %} + +
    {{ data |tojson(4) }}
    + + + {% block rows %} + {% for column in collection.columns.names if column in collection.columns.visible -%} + + {% block value scoped %} +
    + {{ data[column] }} +
    + {% endblock %} + + {%- endfor %} + {% endblock rows%} + diff --git a/ckanext/ap_doi/templates/scheming/form_snippets/hidden.html b/ckanext/ap_doi/templates/scheming/form_snippets/hidden.html new file mode 100644 index 0000000..7320c7b --- /dev/null +++ b/ckanext/ap_doi/templates/scheming/form_snippets/hidden.html @@ -0,0 +1,4 @@ +{# Form snippet for fields that should be hidden from the user, but we still want + their contents to be saved and submitted with the form #} + + diff --git a/ckanext/ap_doi/templates/user/dashboard_doi.html b/ckanext/ap_doi/templates/user/dashboard_doi.html new file mode 100644 index 0000000..7e41e8b --- /dev/null +++ b/ckanext/ap_doi/templates/user/dashboard_doi.html @@ -0,0 +1,59 @@ +{% extends "user/dashboard.html" %} + +{% block primary_content_inner %} +
    +

    + {% block page_heading %} + {{ _('DATASETS WITH DOI ISSUE') }} + {% endblock %} +

    + {% with messages = get_flashed_messages(with_categories=true) %} + {% if messages %} +
    + {% for category, message in messages %} +
    + × +

    {{ message }}

    +
    + {% endfor %} +
    + {% endif %} + {% endwith %} + +
    +{% endblock %} diff --git a/ckanext/ap_doi/utils.py b/ckanext/ap_doi/utils.py new file mode 100644 index 0000000..6eaa553 --- /dev/null +++ b/ckanext/ap_doi/utils.py @@ -0,0 +1,147 @@ +from __future__ import annotations + +from datetime import datetime +from typing import Any, Optional, TypedDict, cast + +from ckanext.doi.lib.api import DataciteClient +from ckanext.doi.model.doi import DOI + +import ckan.types as types +import ckan.plugins.toolkit as tk + + +class DOIFlakesData(TypedDict): + require_doi_update: list[DOIProblemPackageData] + + +class DOIProblemPackageData(TypedDict): + id: str + name: str + title: str + doi_status: Optional[str] + timestamp: datetime + type: str + published: str + identifier: str + + +def prepare_context() -> types.Context: + return cast(types.Context, {"ignore_auth": True}) + + +def store_data_in_flake(flake_name: str, data: Any) -> dict[str, Any]: + """Save the serializable data into the flakes table.""" + return tk.get_action("flakes_flake_override")( + prepare_context(), + {"author_id": None, "name": flake_name, "data": data}, + ) + + +def get_data_from_flake(flake_name: str) -> dict[str, Any]: + """Retrieve a previously stored data from the flake.""" + try: + return tk.get_action("flakes_flake_lookup")( + prepare_context(), + {"author_id": None, "name": flake_name}, + ) + except tk.ObjectNotFound: + return tk.get_action("flakes_flake_create")( + prepare_context(), + {"author_id": None, "name": flake_name, "data": {}}, + ) + + +def package_already_in_flake(flake_name: str, package_id: str) -> bool: + packages_to_update = get_packages_to_update(flake_name) + + if not packages_to_update: + return False + + for package in packages_to_update: + if package["id"] == package_id: + return True + + return False + + +def add_package_to_flake(flake_name: str, package_id: str) -> None: + packages_to_update: list[DOIProblemPackageData] = get_packages_to_update(flake_name) + package_dict = tk.get_action("package_show")({}, {"id": package_id}) + + problem_package_dict: DOIProblemPackageData = { + "id": package_dict["id"], + "name": package_dict["name"], + "title": package_dict["title"], + "doi_status": "Outdated", + "timestamp": package_dict["metadata_modified"], + "identifier": "", + "published": "", + "type": package_dict["type"], + } + + data: DOIFlakesData = {"require_doi_update": [problem_package_dict]} + + if not packages_to_update: + store_data_in_flake(flake_name, data) + return + + packages_to_update.append(problem_package_dict) + + store_data_in_flake(flake_name, {"require_doi_update": packages_to_update}) + + +def remove_package_from_flake(flake_name: str, package_id: str) -> None: + packages_to_update = get_packages_to_update(flake_name) + + if not packages_to_update: + return + + store_data_in_flake( + flake_name, + { + "require_doi_update": [ + package for package in packages_to_update if package["id"] != package_id + ] + }, + ) + + +def get_packages_to_update(flake_name: str) -> list[DOIProblemPackageData]: + flake = get_data_from_flake(flake_name) + + doi_data = flake["data"].get("require_doi_update") + + if not doi_data: + return [] + + return doi_data + + +def get_doi_to_update(model: Any, package_id: str) -> DOI: + """Retrieve the DOI object to be updated, + or create a new one if it doesn't exist.""" + doi_to_update = model.Session.query(DOI).filter_by(package_id=package_id).first() + + if not doi_to_update: + identifier = DataciteClient().generate_doi() + doi_to_update = DOI(package_id=package_id, identifier=identifier) + + return doi_to_update + + +def set_package_author(pkg_dict: dict[str, Any]): + creator_id = pkg_dict.get("creator_user_id") + + if not creator_id: + package = tk.get_action("package_show")({}, {"id": pkg_dict["id"]}) + creator_id = package.get("creator_user_id") + + if package.get("author"): + pkg_dict["author"] = package.get("author") + return pkg_dict + + creator = tk.get_action("user_show")({}, {"id": creator_id}) + + pkg_dict["author"] = creator.get("fullname") or creator.get("name") + + return pkg_dict diff --git a/ckanext/ap_doi/views.py b/ckanext/ap_doi/views.py new file mode 100644 index 0000000..2f8eced --- /dev/null +++ b/ckanext/ap_doi/views.py @@ -0,0 +1,124 @@ +from __future__ import annotations + +import logging +from typing import Any, cast, Callable, Union + +from flask import Blueprint, Response +from flask.views import MethodView + +import ckan.lib.base as base +import ckan.plugins.toolkit as tk + +from ckan import authz, logic, model +from ckan.logic import parse_params + +from ckanext.editable_config.shared import value_as_string + +from ckanext.collection.shared import get_collection + +from ckanext.ap_main.utils import ap_before_request +from ckanext.ap_main.views.generics import ApConfigurationPageView + +log = logging.getLogger(__name__) +doi_dashboard = Blueprint("doi_dashboard", __name__, url_prefix="/admin-panel/doi") +doi_dashboard.before_request(ap_before_request) + + +class ApConfigurationDisplayPageView(MethodView): + def get(self): + self.schema = tk.h.ap_get_arbitrary_schema("ap_doi_config") + data = self.get_config_form_data() + + return tk.render( + "ap_example/display_config.html", + extra_vars={"schema": self.schema, "data": data}, + ) + + def get_config_form_data(self) -> dict[str, Any]: + """Fetch/humanize configuration values from a CKANConfig""" + + data = {} + + for field in self.schema["fields"]: + if field["field_name"] not in tk.config: + continue + + data[field["field_name"]] = value_as_string( + field["field_name"], tk.config[field["field_name"]] + ) + + return data + + +class ApDoiView(MethodView): + def get(self) -> Union[str, Response]: + + return tk.render( + "ap_doi/list.html", + extra_vars={ + "collection": get_collection("ap-doi", parse_params(tk.request.args)), + }, + ) + + def post(self) -> Response: + bulk_action = tk.request.form.get("bulk-action") + package_ids = tk.request.form.getlist("entity_id") + + action_func = self._get_bulk_action(bulk_action) if bulk_action else None + + if not action_func: + tk.h.flash_error(tk._("The bulk action is not implemented")) + return tk.redirect_to("doi_dashboard.list") + + for package_id in package_ids: + try: + action_func(package_id) + except tk.ValidationError as e: + tk.h.flash_error(str(e)) + + return tk.redirect_to("doi_dashboard.list") + + def _get_bulk_action(self, value: str) -> Callable[[str], None] | None: + return { + "1": self._remove_file, + }.get(value) + + def _remove_file(self, package_id: str) -> None: + create_or_update_doi(package_id) + + +@doi_dashboard.before_request +def before_request(): + try: + tk.check_access( + "sysadmin", + { + "model": model, + "user": tk.g.user, + "auth_user_obj": tk.g.userobj, + }, + ) + except tk.NotAuthorized: + base.abort(403, tk._("Need to be system administrator to administer")) + + +def create_or_update_doi(package_id: str): + try: + result = tk.get_action("ap_doi_update_doi")({}, {"package_id": package_id}) + if result["status"] == "error": + for err in result["errors"]: + tk.h.flash_error(err) + else: + tk.h.flash_success(result["message"]) + except Exception: + pass + + return tk.h.redirect_to("doi_dashboard.list") + + +doi_dashboard.add_url_rule("/update_doi/", view_func=create_or_update_doi) +doi_dashboard.add_url_rule("/list", view_func=ApDoiView.as_view("list")) +doi_dashboard.add_url_rule( + "/config", + view_func=ApConfigurationPageView.as_view("config", "ap_doi_config"), +) diff --git a/ckanext/ap_example/plugin.py b/ckanext/ap_example/plugin.py index abd1a6a..da3ce7e 100644 --- a/ckanext/ap_example/plugin.py +++ b/ckanext/ap_example/plugin.py @@ -1,5 +1,4 @@ from __future__ import annotations -from typing import Literal from os import path @@ -19,6 +18,7 @@ class AdminPanelExamplePlugin(p.SingletonPlugin): p.implements(p.IConfigurer) p.implements(p.IConfigDeclaration, inherit=True) p.implements(p.ISignal) + p.implements(p.IConfigDeclaration) # IConfigurer diff --git a/ckanext/ap_example/views.py b/ckanext/ap_example/views.py index 7fb5e04..82e7f0e 100644 --- a/ckanext/ap_example/views.py +++ b/ckanext/ap_example/views.py @@ -8,6 +8,8 @@ import ckan.plugins.toolkit as tk +from ckanext.editable_config.shared import value_as_string + from ckanext.ap_main.utils import ap_before_request from ckanext.ap_main.views.generics import ApConfigurationPageView @@ -29,7 +31,6 @@ def get(self): def get_config_form_data(self) -> dict[str, Any]: """Fetch/humanize configuration values from a CKANConfig""" - from ckanext.editable_config.shared import value_as_string data = {} diff --git a/ckanext/ap_main/assets/js/vendor/htmx.min.js b/ckanext/ap_main/assets/js/vendor/htmx.min.js index cc0d236..010f584 100644 --- a/ckanext/ap_main/assets/js/vendor/htmx.min.js +++ b/ckanext/ap_main/assets/js/vendor/htmx.min.js @@ -1 +1,2 @@ -(function(e,t){if(typeof define==="function"&&define.amd){define([],t)}else if(typeof 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Xr[e]}function Fr(e,r,n){if(e==undefined){return r}if(r==undefined){r=[]}if(n==undefined){n=[]}var t=te(e,"hx-ext");if(t){oe(t.split(","),function(e){e=e.replace(/ /g,"");if(e.slice(0,7)=="ignore:"){n.push(e.slice(7));return}if(n.indexOf(e)<0){var t=Xr[e];if(t&&r.indexOf(t)<0){r.push(t)}}})}return Fr(u(e),r,n)}var Vr=false;re().addEventListener("DOMContentLoaded",function(){Vr=true});function jr(e){if(Vr||re().readyState==="complete"){e()}else{re().addEventListener("DOMContentLoaded",e)}}function _r(){if(Q.config.includeIndicatorStyles!==false){re().head.insertAdjacentHTML("beforeend","")}}function zr(){var e=re().querySelector('meta[name="htmx-config"]');if(e){return E(e.content)}else{return null}}function $r(){var e=zr();if(e){Q.config=le(Q.config,e)}}jr(function(){$r();_r();var e=re().body;zt(e);var t=re().querySelectorAll("[hx-trigger='restored'],[data-hx-trigger='restored']");e.addEventListener("htmx:abort",function(e){var t=e.target;var r=ae(t);if(r&&r.xhr){r.xhr.abort()}});const r=window.onpopstate?window.onpopstate.bind(window):null;window.onpopstate=function(e){if(e.state&&e.state.htmx){ar();oe(t,function(e){ce(e,"htmx:restored",{document:re(),triggerEvent:ce})})}else{if(r){r(e)}}};setTimeout(function(){ce(e,"htmx:load",{});e=null},0)});return Q}()}); diff --git a/ckanext/ap_main/templates/admin_panel/panel_links.html b/ckanext/ap_main/templates/admin_panel/panel_links.html index aea3375..35acfb8 100644 --- a/ckanext/ap_main/templates/admin_panel/panel_links.html +++ b/ckanext/ap_main/templates/admin_panel/panel_links.html @@ -37,7 +37,5 @@ {% endmacro %} {% for button in h.ap_get_toolbar_structure() %} - {% if button.url or button.sibitems %} - {{ toolbar_button(button) }} - {% endif %} + {{ toolbar_button(button) }} {% endfor %} diff --git a/ckanext/ap_main/views/generics.py b/ckanext/ap_main/views/generics.py index 5dc200c..ea2dfa6 100644 --- a/ckanext/ap_main/views/generics.py +++ b/ckanext/ap_main/views/generics.py @@ -16,7 +16,7 @@ def __init__( breadcrum_label: str = "Configuration", page_title: str = "Configuration page", success_update_message: str = "Config options have been updated", - fields: list[dict[str, Any]] = None, + fields: list[dict[str, Any]] | None = None, ): """A generic view to render configurations for an extension based on an arbitrary schema and config_declaration.yaml diff --git a/setup.cfg b/setup.cfg index 719cea3..6abc91b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -23,11 +23,12 @@ namespace_packages = ckanext install_requires = typing-extensions ckanext-toolbelt - ckanext-collection>=0.1.0,<0.3.0 + ckanext-collection>=0.1.2,<0.3.0 ckanext-files>=0.1.0,<1.0.0 croniter>=2.0.1,<3.0.0 cron-descriptor>=1.4.0,<2.0.0 ckanext-wysiwyg>=0.1.0,<1.0.0 + ckanext-doi>=3.1.12,<4.0.0 include_package_data = True @@ -39,6 +40,8 @@ ckan.plugins = admin_panel_cron = ckanext.ap_cron.plugin:AdminPanelCronPlugin admin_panel_support = ckanext.ap_support.plugin:AdminPanelSupportPlugin admin_panel_example = ckanext.ap_example.plugin:AdminPanelExamplePlugin + admin_panel_doi = ckanext.ap_doi.plugin:AdminPanelDoiPlugin + ap_doi = ckanext.ap_doi.plugin:ApDOIPlugin ap_cron_test = ckanext.ap_cron.tests.factories:ApCronTestPlugin babel.extractors =