refactor: move logic to CodeMetaSchema

django/core/view_helpers.py

@@ -107,10 +107,6 @@ def get_search_queryset(
         criteria.update(tags__name__in=[t.lower() for t in tags])
         operator = 'and'
     """
-
-    """ 
-    Build text search query
-    """
     if query:
         Query.get(query).add_hit()
 
@@ -120,6 +116,7 @@ def get_search_queryset(
         # filters, query = parse_query_string(query, operator="and")
         # criteria.update(filters)
 
+        # generate search query from text
         query = build_search_query(query)
     else:
         query = MATCH_ALL
@@ -176,7 +173,6 @@ def retrieve_with_perms(self, request, *args, **kwargs):
 
 
 def add_user_retrieve_perms(instance, data, user):
-    print(user.get_all_permissions())
     data["has_change_perm"] = user.has_perm(
         f"{instance._meta.app_label}.change_{instance._meta.model_name}",
         instance,

django/curator/fs.py

@@ -18,15 +18,15 @@ def fsck(queryset):
 def pretty_print_fsck_results(results):
     for id, result in results.items():
         release, errors = result
-        print("ID: {}".format(id))
-        print("Release: {}".format(release))
-        print("Errors")
+        print(f"ID: {id}")
+        print(f"Release: {release}")
+        print("Errors:")
         for error in errors:
             if isinstance(error, FileNotFoundError):
-                error_msg = "FileNotFoundError({})".format(repr(error.filename))
+                error_msg = f"FileNotFoundError({error.filename})"
             else:
                 error_msg = error
-            print("  {}".format(error_msg))
+            print(f"    {error_msg}")
         print("\n")
 
 

django/library/models.py

@@ -190,11 +190,14 @@ def to_affiliation_string(cls, afl):
     @property
     def codemeta_affiliation(self):
         """
-        FIXME: move to CodeMeta class
         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])
+            return CodeMetaSchema.convert_affiliation(self.json_affiliations[0])
+
+    @property
+    def primary_affiliation(self):
+        return self.json_affiliations[0] if self.json_affiliations else {}
 
     @property
     def primary_affiliation_name(self):
@@ -204,20 +207,6 @@ def primary_affiliation_name(self):
     def primary_json_affiliation_name(self):
         return self.json_affiliations[0]["name"] if self.json_affiliations else ""
 
-    def to_codemeta_affiliation(self, affiliation):
-        # FIXME: move to CodeMeta class
-        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 {}
-
     @staticmethod
     def from_user(user):
         """
@@ -274,21 +263,8 @@ def member_profile_url(self):
     def get_markdown_link(self):
         return f"[{self.get_full_name()}]({self.member_profile_url})"
 
-    # FIXME: move to CodeMeta transformer class
     def to_codemeta(self):
-        codemeta = {
-            "@type": "Person",
-            # FIXME: Contributor should proxy to User / MemberProfile fields if User is available and given_name and family_name are not set
-            "givenName": self.given_name,
-            "familyName": self.family_name,
-        }
-        if self.orcid_url:
-            codemeta["@id"] = self.orcid_url
-        if self.json_affiliations:
-            codemeta["affiliation"] = self.codemeta_affiliation
-        if self.email:
-            codemeta["email"] = self.email
-        return codemeta
+        return CodeMetaSchema.convert_contributor(self)
 
     def get_aggregated_search_fields(self):
         return " ".join(
@@ -1688,6 +1664,7 @@ def get_fs_api(
 
     def add_contributor(self, contributor: Contributor, role=Role.AUTHOR, index=None):
         # Check if a ReleaseContributor with the same contributor already exists
+        logger.debug("Adding contributor with role: %s, %s", contributor, role)
         existing_release_contributor = self.codebase_contributors.filter(
             contributor=contributor
         ).first()
@@ -2596,7 +2573,7 @@ def convert_platforms(self):
     def license_url(self):
         if self.license:
             return self.license.url
-        return "DEFAULT LICENSE - https://opensource.org/licenses/MIT"
+        return "DEFAULT LICENSE: https://opensource.org/licenses/MIT"
 
     @property
     def descriptions(self):
@@ -2670,13 +2647,14 @@ def build(cls, codebase_release: CodebaseRelease):
 
     @classmethod
     def convert(cls, codebase_release: CodebaseRelease):
+        """
+        Converts the given CodebaseRelease into a Python dictionary.
+        """
         common_metadata = codebase_release.common_metadata
         metadata = {
             **cls.INITIAL_METADATA,
-            # FIXME: inherit fields from common_metadata, look into how to do this
-            # better, snake_case to camelCase of variable names is also an issue
-            **common_metadata.to_dict(),
             "@id": common_metadata.permanent_url,
+            "name": common_metadata.name,
             "copyrightYear": common_metadata.copyright_year,
             "dateCreated": common_metadata.date_created.isoformat(),
             "dateModified": common_metadata.date_modified.isoformat(),
@@ -2693,8 +2671,7 @@ def convert(cls, codebase_release: CodebaseRelease):
             metadata.update(codeRepository=common_metadata.code_repository)
         if hasattr(common_metadata, "release_notes"):
             metadata.update(releaseNotes=common_metadata.release_notes)
-
-        return CodeMetaSchema(metadata)
+        return metadata
 
     @classmethod
     def convert_programming_languages(cls, common_metadata: CommonMetadata):
@@ -2717,10 +2694,42 @@ def to_creative_work(cls, text):
     @classmethod
     def convert_authors(cls, common_metadata: CommonMetadata):
         return [
-            author.contributor.to_codemeta()
+            cls.convert_contributor(author.contributor)
             for author in common_metadata.release_contributor_authors
         ]
 
+    @classmethod
+    def convert_ror_affiliation(cls, affiliation: dict):
+        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 {}
+
+    @classmethod
+    def convert_contributor(cls, contributor: Contributor):
+        codemeta = {
+            "@type": "Person",
+            # FIXME: Contributor should proxy to User / MemberProfile fields if User is available and given_name and family_name are not set
+            "givenName": contributor.given_name,
+            "familyName": contributor.family_name,
+        }
+        if contributor.orcid_url:
+            codemeta["@id"] = contributor.orcid_url
+        if contributor.json_affiliations:
+            codemeta["affiliation"] = cls.convert_ror_affiliation(
+                contributor.primary_affiliation
+            )
+        if contributor.email:
+            codemeta["email"] = contributor.email
+        return codemeta
+
     @classmethod
     def convert_target_product(cls, common_metadata: CommonMetadata):
         target_product = {

django/library/tests/base.py

@@ -1,4 +1,5 @@
 import io
+import logging
 import random
 from uuid import UUID
 
@@ -16,6 +17,9 @@
 from library.serializers import CodebaseSerializer
 
 
+logger = logging.getLogger(__name__)
+
+
 class CodebaseFactory(ContentModelFactory):
     model = Codebase
     serializer = CodebaseSerializer
@@ -32,6 +36,9 @@ def get_default_data(self):
             "uuid": uuid,
             "identifier": str(uuid),
             "submitter": self.submitter,
+            "references_text": "Wilensky, U. (1997). NetLogo Wolf Sheep Predation model.",
+            "replication_text": "This model is a replication of the NetLogo model.",
+            "associated_publication_text": "This model is associated with a publication.",
         }
 
     def data_for_create_request(self, **overrides):
@@ -41,6 +48,13 @@ def data_for_create_request(self, **overrides):
         del serialized["id"]
         return serialized
 
+    def create_published_release(self, codebase=None, **overrides):
+        if codebase is None:
+            codebase = self.create(**overrides)
+        release = ReleaseSetup.setUpPublishableDraftRelease(codebase)
+        release.publish()
+        return release
+
 
 class ContributorFactory:
     def __init__(self, user):
@@ -58,9 +72,17 @@ def get_default_data(self, user):
         }
 
     def create(self, **overrides) -> Contributor:
-        kwargs = self.get_default_data(overrides.get("user"))
-        kwargs.update(overrides)
-        return Contributor.objects.create(**kwargs)
+        default_data = self.get_default_data(overrides.get("user"))
+        default_data.update(overrides)
+        user = default_data.pop("user")
+        contributor, created = Contributor.objects.get_or_create(
+            user=user, defaults=default_data
+        )
+        if created:
+            return contributor
+        else:
+            logger.warning("Contributor with user already exists: %s", user)
+            return contributor
 
 
 class ReleaseContributorFactory:
@@ -79,38 +101,6 @@ def create(self, contributor: Contributor, **overrides):
         return ReleaseContributor.objects.create(contributor=contributor, **kwargs)
 
 
-class CodebaseReleaseFactory:
-    def __init__(self, codebase, submitter=None):
-        if submitter is None:
-            submitter = codebase.submitter
-        self.submitter = submitter
-        self.codebase = codebase
-
-    def get_default_data(self):
-        return {
-            "description": "Added rational utility decision making to wolves",
-            "submitter": self.submitter,
-            "codebase": self.codebase,
-            "live": True,
-        }
-
-    def create(self, **defaults) -> CodebaseRelease:
-        kwargs = self.get_default_data()
-        kwargs.update(defaults)
-
-        codebase = kwargs.pop("codebase")
-        submitter = kwargs.pop("submitter")
-
-        codebase_release = codebase.create_release(submitter=submitter)
-        for k, v in kwargs.items():
-            if hasattr(codebase_release, k):
-                setattr(codebase_release, k, v)
-            else:
-                raise KeyError('Key "{}" is not a property of codebase'.format(k))
-        codebase_release.save()
-        return codebase_release
-
-
 class PeerReviewFactory:
     def __init__(self, submitter, codebase_release):
         self.submitter = submitter

django/library/tests/test_codemeta.py

@@ -270,13 +270,8 @@ def setup(self, data):
         Create Codebase and CodebaseRelease
         """
         codebase_factory = CodebaseFactory(submitter=self.submitter)
-        self.codebase = codebase_factory.create()
-        self.codebase_release = self.codebase.create_release(initialize=False)
-
-        #  set initial texts used for citation
-        self.codebase_release.codebase.references_text = ""
-        self.codebase_release.codebase.replication_text = ""
-        self.codebase_release.codebase.associated_publication_text = ""
+        self.codebase_release = codebase_factory.create_published_release()
+        self.codebase = self.codebase_release.codebase
 
         logger.debug("setup() done.")
 
@@ -295,7 +290,7 @@ def add_unique_contributor(self, role):
         logger.debug(f"adding unique contributor: {contributor.name}")
 
         # Function under test: CodebaseRelease.add_contributor()
-        release_contributor = self.codebase_release.add_contributor(contributor, role)
+        self.codebase_release.add_contributor(contributor, role)
         self.codebase_release.save()
 
         # since we are always adding a unique user, the contributors count will always increase by one
@@ -325,7 +320,7 @@ def add_existing_contributor(self, role):
         logger.debug(f"adding existing contributor: {contributor.id}")
 
         # Function under test: CodebaseRelease.add_contributor()
-        release_contributor = self.codebase_release.add_contributor(contributor, role)
+        self.codebase_release.add_contributor(contributor, role)
         self.codebase_release.save()
 
         # if an existing contributor is added again, but with AUTHOR role -> it will be considered "author" and not "nonauthor"
@@ -454,7 +449,7 @@ def length_agrees(self):
                 if citation
             ]
 
-            fresh_codemeta = CodeMetaSchema.build(CommonMetadata(self.codebase_release))
+            fresh_codemeta = CodeMetaSchema.build(self.codebase_release)
             # Extract text from CodeMeta.metadata
             real_codemeta_citation_flat_text = [
                 creative_work["text"]
@@ -472,7 +467,7 @@ def validate_against_schema(self):
         """
         logger.debug("validate_against_schema()")
 
-        fresh_codemeta = CodeMetaSchema.build(CommonMetadata(self.codebase_release))
+        fresh_codemeta = CodeMetaSchema.build(self.codebase_release)
         try:
             jsonschema.validate(
                 json.loads(fresh_codemeta.to_json()),

django/library/tests/test_views.py

@@ -414,20 +414,12 @@ def test_list_files(self):
             self.assertEqual(
                 response.status_code,
                 expected_status_code,
-                msg="{} {}".format(repr(user), response.data),
+                msg=f"{user} {response.data}",
             )
 
     def test_delete_file(self):
         path_to_foo = pathlib.Path("foo.txt")
         api = self.codebase_release.get_fs_api()
-        print(self.codebase_release)
-        print(
-            "CodebaseRelease perm %s"
-            % self.submitter.has_perm(
-                "library.delete_codebaserelease", self.codebase_release
-            )
-        )
-
         # Unpublished codebase release permissions
         response = self.client.delete(
             api.get_absolute_url(