diff --git a/Pipfile b/Pipfile index f60483ce..49dca939 100644 --- a/Pipfile +++ b/Pipfile @@ -10,14 +10,14 @@ sphinx = ">=4.5" isort = "<6.0" # Unpin when isort==6.0.0 is released [packages] -invenio-app-rdm = {version = "~=13.0.0b1.dev17", extras = ["opensearch2"]} +invenio-app-rdm = {version = "~=13.0.0b1.dev18", extras = ["opensearch2"]} invenio-logging = {extras = ["sentry_sdk"], version = "~=2.0"} sentry-sdk = ">=1.45,<2.0.0" zenodo_rdm = {editable="True", path="./site"} zenodo_legacy = {editable="True", path="./legacy"} # TODO: Remove once we fix PyPI package issues -invenio-swh = {git = "https://github.com/inveniosoftware/invenio-swh", ref = "v0.10.2"} +invenio-swh = {git = "https://github.com/inveniosoftware/invenio-swh", ref = "v0.10.3"} jsonschema = ">=4.17.0,<4.18.0" # due to compatibility issues with alpha ipython = "!=8.1.0" uwsgi = ">=2.0" diff --git a/Pipfile.lock b/Pipfile.lock index 88b6e9f6..8285f3a9 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "624b582a21b5d836ec50cf631a0f572c49c26f256e8ee1af6ea5d40eddbda9f2" + "sha256": "c8773ce002ca56066b6c228f14d3d591c206f55a51b61f51cf6f327b5f228240" }, "pipfile-spec": 6, "requires": { @@ -34,11 +34,11 @@ }, "amqp": { "hashes": [ - "sha256:827cb12fb0baa892aad844fd95258143bce4027fdac4fccddbc43330fd281637", - "sha256:a1ecff425ad063ad42a486c902807d1482311481c8ad95a72694b2975e75f7fd" + "sha256:43b3319e1b4e7d1251833a93d672b4af1e40f3d632d479b98661a95f117880a2", + "sha256:cddc00c725449522023bad949f70fff7b48f0b1ade74d170a6f10ab044739432" ], "markers": "python_version >= '3.6'", - "version": "==5.2.0" + "version": "==5.3.1" }, "aniso8601": { "hashes": [ @@ -526,11 +526,11 @@ }, "deprecated": { "hashes": [ - "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c", - "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3" + "sha256:353bc4a8ac4bfc96800ddab349d89c25dec1079f65fd53acdcc1e0b975b21320", + "sha256:683e561a90de76239796e6b6feac66b99030d2dd3fcf61ef996330f14bbb9b0d" ], "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", - 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"version": "==7.6.4" + "version": "==7.6.7" }, "docker-services-cli": { "hashes": [ @@ -4168,11 +4168,11 @@ }, "setuptools": { "hashes": [ - "sha256:f2504966861356aa38616760c0f66568e535562374995367b4e69c7143cf6bcd", - "sha256:fba5dd4d766e97be1b1681d98712680ae8f2f26d7881245f2ce9e40714f1a686" + "sha256:5c4ccb41111392671f02bb5f8436dfc5a9a7185e80500531b133f5775c4163ef", + "sha256:87cb777c3b96d638ca02031192d40390e0ad97737e27b6b4fa831bea86f2f829" ], - "markers": "python_version >= '3.8'", - "version": "==75.3.0" + "markers": "python_version >= '3.9'", + "version": "==75.5.0" }, "snowballstemmer": { "hashes": [ @@ -4247,11 +4247,11 @@ }, "tomli": { "hashes": [ - "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38", - "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed" + "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8", + "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391" ], "markers": "python_version < '3.11'", - "version": "==2.0.2" + "version": "==2.1.0" }, "typing-extensions": { "hashes": [ diff --git a/assets/js/components/react_invenio_forms/CustomAffiliationsSuggestions.js b/assets/js/components/react_invenio_forms/CustomAffiliationsSuggestions.js new file mode 100644 index 00000000..eb92cfe9 --- /dev/null +++ b/assets/js/components/react_invenio_forms/CustomAffiliationsSuggestions.js @@ -0,0 +1,59 @@ +import React from "react"; +import { Header, Grid } from "semantic-ui-react"; +import { makeIdEntry, makeSubheader } from "react-invenio-forms"; + + +export const CustomAffiliationsSuggestions = (creatibutors) => { + // Ensure creatibutors is always an array + const creatibutorsArray = Array.isArray(creatibutors) ? creatibutors : [creatibutors]; + + return creatibutorsArray.map((creatibutor) => { + const { creatibutor: creatibutorData } = creatibutor; + const { name, acronym, identifiers = [], id } = creatibutorData; + + const subheader = makeSubheader(creatibutorData, creatibutor.isOrganization); + const displayName = acronym ? `${name} (${acronym})` : name; + + const sources = []; + const idStrings = []; + + identifiers.forEach((identifier) => { + const { scheme, identifier: value } = identifier; + + if (scheme === "ror") { + sources.push( + + Source: {scheme.toUpperCase()} (Preferred) + + ); + } else if (scheme === "edmo") { + sources.push( + Source: {scheme.toUpperCase()} + ); + } else { + const idEntry = makeIdEntry(identifier); + if (idEntry) idStrings.push(idEntry); + } + }); + + return ( + + + +
+ {displayName} {idStrings.length > 0 && <>({idStrings})} + {subheader && {subheader}} +
+ + + {sources.length > 0 && ( +
+ {sources} +
+ )} + + + + ); + }); +}; diff --git a/assets/js/invenio_app_rdm/overridableRegistry/mapping.js b/assets/js/invenio_app_rdm/overridableRegistry/mapping.js index 594c4f22..dc541dda 100644 --- a/assets/js/invenio_app_rdm/overridableRegistry/mapping.js +++ b/assets/js/invenio_app_rdm/overridableRegistry/mapping.js @@ -7,10 +7,12 @@ import { UpgradeLegacyRecordButton } from "../../components/landing_page/overrides/UpgradeLegacyRecordButton"; import { FileUploaderNewVersion } from "../../components/landing_page/overrides/FileUploaderNewVersion"; import SubcommunityCreateForm from "../../components/community/overrides/SubcommunityCreateForm"; +import { CustomAffiliationsSuggestions } from "../../components/react_invenio_forms/CustomAffiliationsSuggestions"; export const overriddenComponents = { "InvenioAppRdm.RecordLandingPage.RecordManagement.container": UpgradeLegacyRecordButton, "ReactInvenioDeposit.FileUploader.NewVersionButton.container": FileUploaderNewVersion, + "ReactInvenioForms.AffiliationsSuggestions.content": CustomAffiliationsSuggestions, "InvenioCommunities.CommunityCreateForm.layout": SubcommunityCreateForm }; diff --git a/docker-compose.full.yml b/docker-compose.full.yml index 1f07c2d0..fe30b975 100644 --- a/docker-compose.full.yml +++ b/docker-compose.full.yml @@ -1,4 +1,3 @@ -version: '2.2' services: cache: extends: diff --git a/docker-compose.yml b/docker-compose.yml index e660e2a6..7ab226fa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,4 +1,3 @@ -version: '2.2' services: cache: extends: diff --git a/docker-services.yml b/docker-services.yml index b4ad9566..d9185eb7 100644 --- a/docker-services.yml +++ b/docker-services.yml @@ -1,4 +1,3 @@ -version: "2.2" services: app: build: diff --git a/invenio.cfg b/invenio.cfg index ddfeed9b..b1b685e9 100644 --- a/invenio.cfg +++ b/invenio.cfg @@ -20,68 +20,48 @@ from datetime import timedelta from celery.schedules import crontab from flask_resources import create_error_handler from invenio_administration.permissions import administration_permission -from invenio_app_rdm.config import ( - APP_RDM_DEPOSIT_FORM_DEFAULTS as DEPOSIT_FORM_DEFAULTS, -) -from invenio_app_rdm.config import ( - APP_RDM_ROUTES, - CELERY_BEAT_SCHEDULE, -) -from invenio_app_rdm.config import ( - COMMUNITIES_ERROR_HANDLERS as BASE_COMMUNITIES_ERROR_HANDLERS, -) +from invenio_app_rdm.config import \ + APP_RDM_DEPOSIT_FORM_DEFAULTS as DEPOSIT_FORM_DEFAULTS +from invenio_app_rdm.config import APP_RDM_ROUTES, CELERY_BEAT_SCHEDULE, APP_RDM_IDENTIFIER_SCHEMES_UI +from invenio_app_rdm.config import \ + COMMUNITIES_ERROR_HANDLERS as BASE_COMMUNITIES_ERROR_HANDLERS from invenio_communities.communities.services import facets as community_facets from invenio_github.oauth.remote_app import github_app as github_remote_app from invenio_i18n import lazy_gettext as _ from invenio_oauthclient.contrib.keycloak import KeycloakSettingsHelper -from invenio_oauthclient.contrib.orcid import ( - REMOTE_MEMBER_APP, - REMOTE_SANDBOX_MEMBER_APP, -) +from invenio_oauthclient.contrib.orcid import (REMOTE_MEMBER_APP, + REMOTE_SANDBOX_MEMBER_APP) from invenio_oauthclient.views.client import auto_redirect_login -from invenio_rdm_records.config import ( - RDM_FACETS, -) -from invenio_rdm_records.config import ( - RDM_SORT_OPTIONS as BASE_SORT_OPTIONS, -) +from invenio_rdm_records.config import (RDM_FACETS, + RDM_RECORDS_PERSONORG_SCHEMES) +from invenio_rdm_records.config import RDM_SORT_OPTIONS as BASE_SORT_OPTIONS from invenio_rdm_records.contrib.journal import JOURNAL_SORT_OPTIONS from invenio_rdm_records.contrib.meeting import MEETING_SORT_OPTIONS -from invenio_rdm_records.resources.config import ( - error_handlers as base_records_error_handlers, -) +from invenio_rdm_records.resources.config import \ + error_handlers as base_records_error_handlers from invenio_rdm_records.resources.errors import HTTPJSONException from invenio_rdm_records.services.components import DefaultRecordsComponents from invenio_rdm_records.services.components.signal import SignalComponent from invenio_records_resources.services.records.queryparser import ( - FieldValueMapper, - QueryParser, - SearchFieldTransformer, -) -from invenio_vocabularies.services.custom_fields import ( - SUBJECT_FIELDS, - SUBJECT_FIELDS_UI, -) + FieldValueMapper, QueryParser, SearchFieldTransformer) +from invenio_vocabularies.services.custom_fields import (SUBJECT_FIELDS, + SUBJECT_FIELDS_UI) from zenodo_rdm import facets as zenodo_community_facets from zenodo_rdm import providers as zenodo_providers from zenodo_rdm.api import ZenodoRDMDraft, ZenodoRDMRecord -from zenodo_rdm.custom_fields import ( - CUSTOM_FIELDS, - CUSTOM_FIELDS_FACETS, - CUSTOM_FIELDS_UI, - NAMESPACES, -) +from zenodo_rdm.custom_fields import (CUSTOM_FIELDS, CUSTOM_FIELDS_FACETS, + CUSTOM_FIELDS_UI, NAMESPACES) +from zenodo_rdm.custom_schemes import is_edmo from zenodo_rdm.files import storage_factory from zenodo_rdm.github.schemas import CitationMetadataSchema from zenodo_rdm.legacy.resources import record_serializers from zenodo_rdm.metrics.config import METRICS_CACHE_UPDATE_INTERVAL from zenodo_rdm.moderation.errors import UserBlockedException -from zenodo_rdm.moderation.handlers import CommunityScoreHandler, RecordScoreHandler +from zenodo_rdm.moderation.handlers import (CommunityScoreHandler, + RecordScoreHandler) from zenodo_rdm.openaire.records.components import OpenAIREComponent -from zenodo_rdm.permissions import ( - ZenodoCommunityPermissionPolicy, - ZenodoRDMRecordPermissionPolicy, -) +from zenodo_rdm.permissions import (ZenodoCommunityPermissionPolicy, + ZenodoRDMRecordPermissionPolicy) from zenodo_rdm.queryparser import word_communities, word_doi from zenodo_rdm.subcommunities import ( ZenodoSubCommunityRequest, @@ -740,16 +720,10 @@ USERPROFILES_READ_ONLY = ( THEME_SHOW_FRONTPAGE_INTRO_SECTION = False APP_RDM_RECORD_LANDING_PAGE_TEMPLATE = "zenodo_rdm/records/detail.html" -from zenodo_rdm.utils import ( - annostor_link_render, - blr_link_render, - briefideas_link_render, - f1000_link_render, - github_link_render, - openaire_link_render, - reana_link_render, - swh_link_render, -) +from zenodo_rdm.utils import (annostor_link_render, blr_link_render, + briefideas_link_render, f1000_link_render, + github_link_render, openaire_link_render, + reana_link_render, swh_link_render) APP_RDM_RECORD_LANDING_PAGE_EXTERNAL_LINKS = [ {"id": "f1000", "render": f1000_link_render}, @@ -926,6 +900,22 @@ OAISERVER_XSL_URL = "/static/oai2.xsl" RDM_DATACITE_FUNDER_IDENTIFIERS_PRIORITY = ("doi", "ror", "grid", "isni", "gnd") """Priority of funder identifiers types for Datacite serialization, prioritize DOI.""" +RDM_RECORDS_PERSONORG_SCHEMES = { +**RDM_RECORDS_PERSONORG_SCHEMES, + "edmo": {"label": _("EDMO"), "validator": is_edmo, "datacite": "URL"}, +} +"""Person and Organization Schemes.""" + +APP_RDM_IDENTIFIER_SCHEMES_UI = { + **APP_RDM_IDENTIFIER_SCHEMES_UI, + "edmo": { + "url_prefix": "https://edmo.seadatanet.org/report/", + "icon": "images/edmo-icon.svg", + "label": "EDMO", + } +} +"""Identifier Schemes UI config.""" + RECORDS_RESOURCES_ALLOW_EMPTY_FILES = False """Disable empty files for Zenodo.""" diff --git a/scripts/run_script.py b/scripts/run_script.py old mode 100644 new mode 100755 index 9d0eb868..78a2db0e --- a/scripts/run_script.py +++ b/scripts/run_script.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python # -*- coding: utf-8 -*- # # Copyright (C) 2024 CERN. @@ -5,7 +6,7 @@ # Invenio-RDM is free software; you can redistribute it and/or modify # it under the terms of the MIT License; see LICENSE file for more details. """Script to run a Python script in a job on OpenShift.""" -#!/usr/bin/env python + import json import subprocess import sys @@ -22,9 +23,9 @@ def _abort(message): if len(sys.argv) < 1: print(f"Usage: {PROGRAM} \n") - print(f" file: the path to the script to run") + print(" file: the path to the script to run") print( - f" image: the image version to be used by the job. If not provided, the script will try to infer it from the deployed image." + " image: the image version to be used by the job. If not provided, the script will try to infer it from the deployed image." ) print(f" Example: {PROGRAM} /home/script.py 7.3.0") sys.exit(1) @@ -60,7 +61,9 @@ def infer_deployed_version(): script_path = sys.argv[1] -image_version = sys.argv[2].removeprefix("v") if len(sys.argv) > 2 else infer_deployed_version() +image_version = ( + sys.argv[2].removeprefix("v") if len(sys.argv) > 2 else infer_deployed_version() +) # verify the file exists in local filesystem if not Path(script_path).is_file(): @@ -103,7 +106,7 @@ def infer_deployed_version(): - copy the script {script_path} to {terminal_pod_name} - run a pod with Zenodo {image_version} - execute the script inside the created pod -Proceed? (y/n): +Proceed? (y/n): """ if input(str_) != "y": _abort("Aborted.") diff --git a/site/setup.cfg b/site/setup.cfg index 7bd0290c..58bfa192 100644 --- a/site/setup.cfg +++ b/site/setup.cfg @@ -88,6 +88,8 @@ invenio_previewer.previewers = image_previewer = zenodo_rdm.previewer.image_previewer invenio_search.index_templates = zenodo_rdm = zenodo_rdm.index_templates +idutils.custom_schemes = + edmo = zenodo_rdm.custom_schemes:get_scheme_config_func [bdist_wheel] universal = 1 diff --git a/site/zenodo_rdm/custom_schemes.py b/site/zenodo_rdm/custom_schemes.py new file mode 100644 index 00000000..ce643f35 --- /dev/null +++ b/site/zenodo_rdm/custom_schemes.py @@ -0,0 +1,57 @@ +# -*- coding: utf-8 -*- +# +# Copyright (C) 2024 CERN. +# +# ZenodoRDM is free software; you can redistribute it and/or modify it +# under the terms of the MIT License; see LICENSE file for more details. + +"""Custom scheme config.""" + +import re + +# Regular expression to validate EDMO identifiers in the format "edmo:" +edmo_regexp = re.compile(r"^edmo:(\d+)$") + +# Regular expression to match the EDMO URL format +edmo_url_regexp = re.compile( + r"(?:https?://)?(?:edmo\.seadatanet\.org/report/)?(\d+)$", re.IGNORECASE +) + + +def is_edmo(val): + """ + Validate and normalize an EDMO identifier or URL. + + Returns the normalized 'edmo:' format if valid, otherwise None. + """ + # Match against the URL or the edmo: format + match = edmo_url_regexp.match(val) or edmo_regexp.match(val) + if match: + # Extract the numeric ID from the matched group + return f"edmo:{match.group(1)}" + return None + + +def normalize_edmo(val): + """Normalize an EDMO identifier or URL to the 'edmo:' format.""" + return is_edmo(val) + + +def generate_edmo_url(_, normalized_pid): + """ + Generate a URL for a given normalized EDMO identifier. + + Assumes the input is in the form 'edmo:'. + """ + edmo_id = normalized_pid.split(":")[1] + return f"https://edmo.seadatanet.org/report/{edmo_id}" + + +def get_scheme_config_func(): + """Return the configuration for the EDMO custom scheme.""" + return { + "validator": is_edmo, + "normalizer": normalize_edmo, + "filter": [], + "url_generator": generate_edmo_url, + } diff --git a/site/zenodo_rdm/legacy/services.py b/site/zenodo_rdm/legacy/services.py index 7eb2c57e..8656356d 100644 --- a/site/zenodo_rdm/legacy/services.py +++ b/site/zenodo_rdm/legacy/services.py @@ -152,7 +152,7 @@ class LegacyRecordServiceConfig(RDMRecordServiceConfig): ), "doi": RecordPIDLink("https://doi.org/{+pid_doi}", when=has_doi), "parent_doi": RecordParentPIDLink( - "{+ui}/doi/{+pid_doi}", + "https://doi.org/{+pid_doi}", when=is_record_and_has_parent_doi, ), "badge": RecordPIDLink("{+ui}/badge/doi/{pid_doi}.svg"), diff --git a/static/images/edmo-icon.svg b/static/images/edmo-icon.svg new file mode 100644 index 00000000..a602f24a --- /dev/null +++ b/static/images/edmo-icon.svg @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/templates/semantic-ui/zenodo_rdm/macros/creators.html b/templates/semantic-ui/zenodo_rdm/macros/creators.html index 24f94a26..caf3d1b1 100644 --- a/templates/semantic-ui/zenodo_rdm/macros/creators.html +++ b/templates/semantic-ui/zenodo_rdm/macros/creators.html @@ -53,6 +53,11 @@ {% set link = "https://ror.org/{identifier}".format(identifier=id.identifier) %} {% set link_title = _("ROR profile") %} {% set icon = "/static/images/ror-icon.svg" %} + + {% elif id.scheme == "edmo" %} + {% set link = "https://edmo.seadatanet.org/report/{identifier}".format(identifier=id.identifier) %} + {% set link_title = _("EDMO profile") %} + {% set icon = "/static/images/edmo-icon.svg" %} {% elif id.scheme == "gnd" %} {% set link = "https://d-nb.info/gnd/{identifier}".format(identifier=id.identifier) %}