230 cml refactor contributor edit metadata form affiliations handling

django/core/management/commands/populate_memberprofile_affiliations.py

@@ -1,5 +1,5 @@
 from django.core.management.base import BaseCommand
-from fuzzywuzzy import fuzz
+from rapidfuzz import fuzz
 import re
 import requests
 import time

django/core/serializers.py

@@ -287,6 +287,7 @@ class Meta:
             "email",
             "profile_url",
             "primary_affiliation_name",
+            "affiliations",
             "tags",
             "username",
         )

django/core/settings/test.py

@@ -1,11 +1,13 @@
-from .dev import *
+from .defaults import *
 
 from os import path
 
 DEPLOY_ENVIRONMENT = Environment.TEST
 
 ALLOWED_HOSTS = ["localhost", "127.0.0.1", "server"]
 
+EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
+
 LOGGING["loggers"]["core.views"] = {
     "level": "ERROR",
     "handlers": ["console"],

django/curator/management/commands/sync_user_contributors.py

@@ -0,0 +1,28 @@
+import logging
+
+from django.core.management.base import BaseCommand
+
+from library.models import Contributor
+
+
+logger = logging.getLogger(__name__)
+
+
+class Command(BaseCommand):
+    help = """Synchronize user metadata with contributor metadata for testing / development purposes."""
+
+    def handle(self, *args, **options):
+        # cannot update local model attributes to a join field attribute; this doesn't work:
+        # Contributor.objects.filter(user__isnull=False).update(given_name=F('user__first_name'), ...)
+        # see
+        # https://docs.djangoproject.com/en/dev/topics/db/queries/#updating-multiple-objects-at-once
+        # for more details
+        for contributor in Contributor.objects.select_related("user").filter(
+            user__isnull=False
+        ):
+            user = contributor.user
+            contributor.given_name = user.first_name
+            contributor.family_name = user.last_name
+            contributor.email = user.email
+            contributor.json_affiliations = user.member_profile.affiliations
+            contributor.save()

django/home/management/commands/add_comses_2019.py

@@ -55,7 +55,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Create CoMSES 2019 virtual conference conference landing page
     """

django/home/management/commands/add_open_code_page.py

@@ -29,7 +29,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Create CoMSES trusted digital repository landing page and add it as a child to the /resources/ CategoryIndexPage
     """

django/home/management/commands/add_repositories_page.py

@@ -31,7 +31,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Create CoMSES trusted digital repository landing page and add it as a child to the /resources/ CategoryIndexPage
     """

django/home/management/commands/create_or_update_education_pages.py

@@ -48,7 +48,6 @@
 
 
 class Command(BaseCommand):
-
     """
     create or update education index page and tutorial detail pages from markdown formatted files
     """

django/home/management/commands/move_community_into_about.py

@@ -33,7 +33,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Adjust the Community page for  https://github.com/comses/comses.net/issues/584
     this can't be in a data migration for arcane wagtail reasons related to CategoryIndexPage subclassing

django/home/management/commands/move_education_page.py

@@ -133,7 +133,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Move existing Education page from under Resources to a top level Page
     """

django/home/management/commands/setup_conference.py

@@ -38,7 +38,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Create CoMSES virtual conference landing pages, including wagtail replacement for archived CoMSES 2017 page.
     See https://github.com/wagtail/wagtail/issues/742 for more details - this can't be in a data migration because the

django/library/management/commands/populate_contributor_affiliations.py

@@ -0,0 +1,126 @@
+from collections import defaultdict
+from django.core.management.base import BaseCommand
+from rapidfuzz import fuzz
+from requests.adapters import HTTPAdapter
+from urllib3 import Retry
+
+import logging
+import requests
+
+from library.models import ContributorAffiliation, Contributor
+
+logger = logging.getLogger(__name__)
+
+
+class Command(BaseCommand):
+    help = """Migrate data from ContributorAffiliation Tags to Contributor.json_affiliations; attempts to augment data with a basic ROR API lookup"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "-r",
+            "--ratio",
+            type=int,
+            choices=range(1, 100),
+            metavar="[1-100]",
+            default=80,
+            help="""threshold used in fuzzy matching and ROR API score (divided by 100 for a floating point number between 0.0 and 1.0). Defaults to 80""",
+        )
+
+    def handle(self, *args, **options):
+        session = requests.Session()
+        fuzzy_match_threshold = options["ratio"]
+        ror_score_threshold = fuzzy_match_threshold / 100.0
+        adapter = HTTPAdapter(
+            max_retries=Retry(
+                total=6,
+                backoff_factor=1.5,
+                allowed_methods=None,
+                status_forcelist=[429, 500, 502, 503, 504],
+            ),
+        )
+        session.mount("http://", adapter)
+        session.mount("https://", adapter)
+
+        ordered_contributor_affiliations = (
+            ContributorAffiliation.objects.all().order_by("content_object_id")
+        )
+
+        logger.info("Looking up affiliations against ROR API")
+
+        # build affiliations_by_contributor_id dictionary
+        contributor_affiliations = defaultdict(list)
+        for ca in ordered_contributor_affiliations:
+            if not (ca.tag and ca.tag.name and ca.content_object_id):
+                continue
+
+            contributor_id = ca.content_object_id
+            affiliation_name = ca.tag.name
+            best_match = self.lookup(session, affiliation_name)
+            new_affiliation = self.to_affiliation(
+                affiliation_name,
+                best_match,
+                match_threshold=fuzzy_match_threshold,
+                ror_score_threshold=ror_score_threshold,
+            )
+            # register the new affiliation with this contributor
+            contributor_affiliations[contributor_id].append(new_affiliation)
+
+        # Loop through enriched affiliations and save the json_affiliations
+        # on each contributor
+        for contributor_id, affiliations in contributor_affiliations.items():
+            logger.info(
+                "updating [contributor_id: %s] affiliations=%s",
+                contributor_id,
+                affiliations,
+            )
+            Contributor.objects.filter(pk=contributor_id).update(
+                json_affiliations=affiliations
+            )
+
+    def lookup(self, session, name):
+        ror_api_url = f"https://api.ror.org/organizations?affiliation={name}"
+        try:
+            response = session.get(ror_api_url, timeout=10)
+            items = response.json()["items"]
+            logger.debug("[lookup %s] found %s", name, items)
+            return items[0] if items else None
+        except Exception as e:
+            logger.warning(e)
+        return None
+
+    def to_affiliation(
+        self, name, best_match, match_threshold=85, ror_score_threshold=1.0
+    ):
+        """
+        Returns a new affiliation dictionary with ROR data if a good match
+        or a dict of the original data { "name": name } otherwise
+        """
+        if best_match:
+            score = best_match["score"]
+            ror_name = best_match["organization"]["name"]
+            if (
+                score >= ror_score_threshold
+                or fuzz.partial_ratio(ror_name, name) >= match_threshold
+            ):
+                new_affiliation = {
+                    "name": ror_name,
+                    # ror id is guaranteed if lookup was successful
+                    "ror_id": best_match["organization"]["id"],
+                }
+                # acronyms and links are not guaranteed to exist
+                if best_match["organization"]["acronyms"]:
+                    new_affiliation["acronym"] = best_match["organization"]["acronyms"][
+                        0
+                    ]
+                if best_match["organization"]["links"]:
+                    new_affiliation["url"] = best_match["organization"]["links"][0]
+                # FIXME: additional geodata to include from the returned ROR API data?
+                # e.g., GRID id, 'country', 'aliases', 'types', etc.
+                return new_affiliation
+            else:
+                logger.warning("No reasonable match found for %s: %s", name, best_match)
+
+        # either no best_match or failed the match_threshold fuzz test
+        return {
+            "name": name,
+        }

django/library/management/commands/update_codemeta.py

@@ -13,7 +13,6 @@
 
 
 class Command(BaseCommand):
-
     """
     Updates all codemeta files for all Codebases and updates archive
     """

django/library/migrations/0028_contributor_json_affiliations.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.11 on 2024-05-22 23:38
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("library", "0027_codebase_spam_moderation"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="contributor",
+            name="json_affiliations",
+            field=models.JSONField(
+                default=list, help_text="JSON-LD list of affiliated institutions"
+            ),
+        ),
+    ]

django/library/models.py

@@ -41,7 +41,7 @@
 from core import fs
 from core.backends import add_to_comses_permission_whitelist
 from core.fields import MarkdownField
-from core.models import Platform, MemberProfile, ModeratedContent, SpamModeration
+from core.models import Platform, MemberProfile, ModeratedContent
 from core.queryset import get_viewable_objects_for_user
 from core.utils import send_markdown_email
 from core.view_helpers import get_search_queryset
@@ -136,6 +136,11 @@ class Contributor(index.Indexed, ClusterableModel):
     middle_name = models.CharField(max_length=100, blank=True)
     family_name = models.CharField(max_length=100, blank=True)
     affiliations = ClusterTaggableManager(through=ContributorAffiliation)
+
+    json_affiliations = models.JSONField(
+        default=list, help_text=_("JSON-LD list of affiliated institutions")
+    )
+
     type = models.CharField(
         max_length=16,
         choices=(("person", "person"), ("organization", "organization")),
@@ -151,6 +156,7 @@ class Contributor(index.Indexed, ClusterableModel):
         index.SearchField("given_name"),
         index.SearchField("family_name"),
         index.RelatedFields("affiliations", [index.SearchField("name")]),
+        index.SearchField("json_affiliations_string"),
         index.SearchField("email"),
         index.RelatedFields(
             "user",
@@ -163,11 +169,25 @@ class Contributor(index.Indexed, ClusterableModel):
         ),
     ]
 
+    @cached_property
+    def json_affiliations_string(self):
+        return ", ".join(
+            [
+                self.to_affiliation_string(affiliation)
+                for affiliation in self.json_affiliations
+            ]
+        )
+
+    @classmethod
+    def to_affiliation_string(cls, afl):
+        # e.g., "Arizona State University https://www.asu.edu ASU"
+        return f"{afl.get('name')} {afl.get('url')} {afl.get('acronym')}"
+
     @staticmethod
     def from_user(user):
         """
         Returns a tuple of (object, created) based on the
-        https://docs.djangoproject.com/en/3.1/ref/models/querysets/#get-or-create
+        https://docs.djangoproject.com/en/4.2/ref/models/querysets/#get-or-create
         contract
         """
         try:
@@ -177,6 +197,8 @@ def from_user(user):
                     "given_name": user.first_name,
                     "family_name": user.last_name,
                     "email": user.email,
+                    # FIXME: rename to affiliations eventually
+                    "json_affiliations": user.member_profile.affiliations,
                 },
             )
         except Contributor.MultipleObjectsReturned:
@@ -211,10 +233,11 @@ def to_codemeta(self):
             "givenName": self.given_name,
             "familyName": self.family_name,
         }
+        # FIXME: should we proxy to User / MemberProfile fields if User is available
         if self.orcid_url:
             codemeta["@id"] = self.orcid_url
-        if self.affiliations.exists():
-            codemeta["affiliation"] = self.formatted_affiliations
+        if self.json_affiliations:
+            codemeta["affiliation"] = self.codemeta_affiliation
         if self.email:
             codemeta["email"] = self.email
         return codemeta
@@ -259,10 +282,35 @@ def _get_person_full_name(self, family_name_first=False):
     def formatted_affiliations(self):
         return ", ".join(self.affiliations.values_list("name", flat=True))
 
+    @property
+    def codemeta_affiliation(self):
+        """
+        For now codemeta affiliations appear to be a single https://schema.org/Organization
+        """
+        if self.json_affiliations:
+            return self.to_codemeta_affiliation(self.json_affiliations[0])
+
     @property
     def primary_affiliation_name(self):
         return self.affiliations.first().name if self.affiliations.exists() else ""
 
+    @property
+    def primary_json_affiliation_name(self):
+        return self.json_affiliations[0]["name"] if self.json_affiliations else ""
+
+    def to_codemeta_affiliation(self, affiliation):
+        if affiliation:
+            return {
+                # FIXME: may switch to https://schema.org/ResearchOrganization at some point
+                "@type": "Organization",
+                "@id": affiliation.get("ror_id"),
+                "name": affiliation.get("name"),
+                "url": affiliation.get("url"),
+                "identifier": affiliation.get("ror_id"),
+                "sameAs": affiliation.get("ror_id"),
+            }
+        return {}
+
     def get_profile_url(self):
         user = self.user
         if user: