Merge branch 'master' into subcom-invitation

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"

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(
+          <span key={value}>
+            Source: {scheme.toUpperCase()} <span>(Preferred)</span>
+          </span>
+        );
+      } else if (scheme === "edmo") {
+        sources.push(
+          <span key={value}>Source: {scheme.toUpperCase()}</span>
+        );
+      } else {
+        const idEntry = makeIdEntry(identifier);
+        if (idEntry) idStrings.push(idEntry);
+      }
+    });
+
+    return (
+      <Grid key={id}>
+        <Grid.Row columns={2} verticalAlign="middle">
+          <Grid.Column width={12}>
+            <Header>
+              {displayName} {idStrings.length > 0 && <>({idStrings})</>}
+              {subheader && <Header.Subheader>{subheader}</Header.Subheader>}
+            </Header>
+          </Grid.Column>
+          <Grid.Column width={4} textAlign="right">
+            {sources.length > 0 && (
+              <Header as="h6" color="grey" style={{ margin: 0 }}>
+                {sources}
+              </Header>
+            )}
+          </Grid.Column>
+        </Grid.Row>
+      </Grid>
+    );
+  });
+};

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
 };

docker-compose.full.yml

@@ -1,4 +1,3 @@
-version: '2.2'
 services:
   cache:
     extends:

docker-compose.yml

@@ -1,4 +1,3 @@
-version: '2.2'
 services:
   cache:
     extends:

docker-services.yml

@@ -1,4 +1,3 @@
-version: "2.2"
 services:
   app:
     build:

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."""
 

scripts/run_script.py

@@ -1,11 +1,12 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright (C) 2024 CERN.
 #
 # 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} <file> <image>\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.")

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

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:<ID>"
+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:<ID>' format if valid, otherwise None.
+    """
+    # Match against the URL or the edmo:<ID> 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:<ID>' 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:<ID>'.
+    """
+    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,
+    }

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"),

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) %}