Merge V7.12.0.5 into main

specifyweb/backend/delete_blockers/views.py

@@ -1,6 +1,7 @@
 from django import http
 from django.db import router, transaction
 from django.db.models.deletion import Collector
+from django.db.models import ForeignKey
 
 from specifyweb.middleware.general import require_http_methods
 from specifyweb.specify.api.crud import (
@@ -43,13 +44,66 @@ def _collect_delete_blockers(obj, using) -> list[dict]:
     collector.collect([obj])
     return flatten([
         [
-            {
-                'table': sub_objs[0].__class__.__name__,
-                'field': field.name,
-                'ids': [sub_obj.id for sub_obj in sub_objs]
-            }
+            _serialize_delete_blocker(field, sub_objs)
         ] for field, sub_objs in collector.delete_blockers
     ])
 
+def _serialize_delete_blocker(field, sub_objs) -> dict:
+    normalized = _normalize_many_to_many_blocker(field, sub_objs)
+    if normalized is not None:
+        return normalized
+
+    return {
+        'table': sub_objs[0].__class__.__name__,
+        'field': field.name,
+        'ids': [sub_obj.id for sub_obj in sub_objs]
+    }
+
+def _normalize_many_to_many_blocker(field, sub_objs) -> dict | None:
+    through_model = sub_objs[0].__class__
+    if hasattr(through_model, 'specify_model'):
+        return None
+
+    foreign_keys = [
+        model_field
+        for model_field in through_model._meta.fields
+        if isinstance(model_field, ForeignKey)
+    ]
+    if len(foreign_keys) != 2:
+        return None
+
+    other_field = next(
+        (
+            model_field
+            for model_field in foreign_keys
+            if model_field.name != field.name
+        ),
+        None,
+    )
+    if other_field is None:
+        return None
+
+    other_model = other_field.related_model
+    if not hasattr(other_model, 'specify_model'):
+        return None
+
+    relationship = next(
+        (
+            relationship
+            for relationship in other_model.specify_model.relationships
+            if getattr(relationship, 'through_model', None) == through_model.__name__
+            and getattr(relationship, 'through_field', None) == other_field.name
+        ),
+        None,
+    )
+    if relationship is None:
+        return None
+
+    return {
+        'table': other_model.specify_model.name,
+        'field': relationship.name,
+        'ids': [getattr(sub_obj, other_field.attname) for sub_obj in sub_objs],
+    }
+
 def flatten(l):
     return [item for sublist in l for item in sublist]

specifyweb/frontend/js_src/lib/components/FormParse/__tests__/index.test.ts

@@ -471,6 +471,30 @@ describe('parseFormDefinition', () => {
 describe('getColumnDefinitions', () => {
   requireContext();
 
+  test('prefers linux definition over generic definition', () =>
+    expect(
+      getColumnDefinitions(
+        xml(
+          `<viewdef>
+            <columnDef>Generic</columnDef>
+            <columnDef os="lnx">Linux</columnDef>
+          </viewdef>`
+        )
+      )
+    ).toBe('Linux'));
+
+  test('uses generic definition if linux definition is not available', () =>
+    expect(
+      getColumnDefinitions(
+        xml(
+          `<viewdef>
+            <columnDef os="mac">Mac</columnDef>
+            <columnDef>Generic</columnDef>
+          </viewdef>`
+        )
+      )
+    ).toBe('Generic'));
+
   test('fall back to first definition available', () =>
     expect(
       getColumnDefinitions(
@@ -510,7 +534,7 @@ theories(getColumnDefinition, [
       ),
       undefined,
     ],
-    out: 'B',
+    out: 'A',
   },
 ]);
 

specifyweb/frontend/js_src/lib/components/FormParse/index.ts

@@ -90,6 +90,8 @@ export const formTypes = ['form', 'formTable'] as const;
 export type FormType = (typeof formTypes)[number];
 export type FormMode = 'edit' | 'search' | 'view';
 
+const defaultColumnDefinitionOs = 'lnx';
+
 let views: R<ViewDefinition | undefined> = {};
 
 export const getViewSetApiUrl = (viewName: string): string =>
@@ -540,10 +542,25 @@ function getColumnDefinitions(viewDefinition: SimpleXmlNode): string {
 const getColumnDefinition = (
   viewDefinition: SimpleXmlNode,
   os: string | undefined
-): string | undefined =>
-  viewDefinition.children.columnDef?.find((child) =>
-    typeof os === 'string' ? getParsedAttribute(child, 'os') === os : true
-  )?.text;
+): string | undefined => {
+  const columnDefinitions = viewDefinition.children.columnDef;
+  if (columnDefinitions === undefined) return undefined;
+
+  if (typeof os === 'string')
+    return columnDefinitions.find(
+      (child) => getParsedAttribute(child, 'os') === os
+    )?.text;
+
+  return (
+    columnDefinitions.find(
+      (child) => getParsedAttribute(child, 'os') === defaultColumnDefinitionOs
+    )?.text ??
+    columnDefinitions.find(
+      (child) => getParsedAttribute(child, 'os') === undefined
+    )?.text ??
+    columnDefinitions[0]?.text
+  );
+};
 
 const parseRows = async (
   rawRows: RA<SimpleXmlNode>,

specifyweb/frontend/js_src/lib/components/Permissions/index.ts

@@ -64,7 +64,12 @@ export const getDerivedPermissions = () => derivedPermissions;
 const sortPolicies = (policy: typeof operationPolicies) =>
   JSON.stringify(
     Object.fromEntries(
-      Object.entries(policy).sort(sortFunction(([key]) => key))
+      Object.entries(policy)
+        .sort(sortFunction(([key]) => key))
+        .map(([key, actions]) => [
+          key,
+          Array.from(actions).sort(sortFunction((action) => action)),
+        ])
     )
   );
 

specifyweb/specify/management/commands/run_key_migration_functions.py

@@ -59,38 +59,50 @@ def apply_schema_overrides_for_all_disciplines(_apps):
                 )
             apply_schema_defaults_task.apply(args=[discipline.id])
 
+    # PERF: The vast majority of these can be collapsed to a single call to
+    # update_table_schema_config_with_defaults
     funcs = [
         # usc.update_all_table_schema_config_with_defaults,
         usc.create_geo_table_schema_config_with_defaults, # specify 0002
         usc.create_cotype_splocalecontaineritem, # specify 0003
         usc.create_strat_table_schema_config_with_defaults, # specify 0004 - getting skip warnings
         usc.create_agetype_picklist, # specify 0004
-        usc.update_cog_type_fields, # specify 0007
+        # BUG: This should really only be run in the context of the migration,
+        # and not on startup. See the below BUG comment above usc.update_hidden_prop
+        # usc.update_cog_type_fields, # specify 0007
         usc.create_cogtype_picklist, # specify 0007
-        usc.update_cogtype_splocalecontaineritem, # specify 0007
-        usc.update_systemcogtypes_picklist, # specify 0007
-        usc.update_cogtype_type_splocalecontaineritem, # specify 0007
+        # BUG: These also shouldn't be run with this suite. These are one way
+        # data migrations in the contect of migrations meant to resolve
+        # eariler migrations.
+        # The functions can be destructive as we can't really discern whether
+        # or not these functions should be applied
+        # usc.update_cogtype_splocalecontaineritem, # specify 0007
+        # usc.update_systemcogtypes_picklist, # specify 0007
+        # usc.update_cogtype_type_splocalecontaineritem, # specify 0007
         usc.update_relative_age_fields, # specify 0008
         usc.add_cojo_to_schema_config, # specify 0012
         usc.update_cog_schema_config, # specify 0013
         usc.update_age_schema_config, # specify 0015
-        usc.schemaconfig_fixes, # specify 0017
-        usc.add_cot_catnum_to_schema, # specify 0018
+        # usc.schemaconfig_fixes, # specify 0017
+        # usc.add_cot_catnum_to_schema, # specify 0018
         usc.add_tectonicunit_to_pc_in_schema_config, # specify 0020
-        usc.fix_hidden_geo_prop, # specify 0021
-        usc.update_schema_config_field_desc, # specify 0023
-        usc.update_hidden_prop, # specify 0023
+        # usc.fix_hidden_geo_prop, # specify 0021
+        # usc.update_schema_config_field_desc, # specify 0023
+        # BUG: We can't reliably run this function at startup, as there is no
+        # easy way to differentiate Schema Config tables/fields that should or
+        # should not be updated for already existing Disciplines.
+        # usc.update_hidden_prop, # specify 0023
         usc.update_storage_unique_id_fields, # specify 0024
-        usc.update_co_children_fields, # specify 0027
-        usc.remove_collectionobject_parentco, # specify 0029
-        usc.add_quantities_gift, # specify 0032
-        usc.update_paleo_desc, # specify 0033
-        usc.update_accession_date_fields, # specify 0034
+        # usc.update_co_children_fields, # specify 0027
+        # usc.remove_collectionobject_parentco, # specify 0029
+        # usc.add_quantities_gift, # specify 0032
+        # usc.update_paleo_desc, # specify 0033
+        # usc.update_accession_date_fields, # specify 0034
         usc.update_loan_and_gift_agent_fields, # specify 0039
-        usc.update_loan_and_gift_agents, # specify 0039
-        usc.componets_schema_config_migrations, # specify 0040
+        usc.remove_componentparent_item, # specify 0040
+        usc.create_table_schema_config_with_defaults, # specify 0040
         usc.create_discipline_type_picklist, # specify 0042
-        usc.update_discipline_type_splocalecontaineritem, # specify 0042
+        # usc.update_discipline_type_splocalecontaineritem, # specify 0042
         apply_schema_overrides_for_all_disciplines,
         usc.deduplicate_schema_config_orm,
     ]

specifyweb/specify/migration_utils/default_cots.py

@@ -68,7 +68,7 @@ def create_cogtype_type_picklist(apps, using='default'):
     Picklistitem = apps.get_model('specify', 'Picklistitem')
 
     for collection in Collection.objects.using(using).all():
-        cog_type_picklist, _ = Picklist.objects.using(using).get_or_create(
+        cog_type_picklist, picklist_created = Picklist.objects.using(using).get_or_create(
             name='SystemCOGTypes', # Default Collection Object Group Types
             type=0,
             collection=collection,
@@ -77,12 +77,13 @@ def create_cogtype_type_picklist(apps, using='default'):
                 "readonly": False,
             }
         )
-        for cog_type in DEFAULT_COG_TYPES:
-            Picklistitem.objects.using(using).get_or_create(
-                title=cog_type,
-                value=cog_type,
-                picklist=cog_type_picklist
-            )
+        if picklist_created:
+            for cog_type in DEFAULT_COG_TYPES:
+                Picklistitem.objects.using(using).get_or_create(
+                    title=cog_type,
+                    value=cog_type,
+                    picklist=cog_type_picklist
+                )
 
 COTYPE_PICKLIST_NAME = 'CollectionObjectType'
 FIELD_NAME = 'collectionObjectType'

specifyweb/specify/migration_utils/sp7_schemaconfig.py

@@ -411,23 +411,6 @@
     'Gift': ['agent1', 'agent2', 'agent3', 'agent4', 'agent5'],
 }
 
-MIGRATION_0038_UPDATE_FIELDS = {
-    'Loan': [
-        ('agent1','Agent 1','Agent 1'),
-        ('agent2','Agent 2','Agent 2'),
-        ('agent3','Agent 3','Agent 3'),
-        ('agent4','Agent 4','Agent 4'),
-        ('agent5','Agent 5','Agent 5'),
-    ],
-    'Gift': [
-        ('agent1','Agent 1','Agent 1'),
-        ('agent2','Agent 2','Agent 2'),
-        ('agent3','Agent 3','Agent 3'),
-        ('agent4','Agent 4','Agent 4'),
-        ('agent5','Agent 5','Agent 5'),
-    ]
-}
-
 MIGRATION_0040_TABLES = [
     ('Component', None),
 ]

specifyweb/specify/migration_utils/tectonic_ranks.py

@@ -15,14 +15,28 @@ def create_default_tectonic_ranks(apps):
         if not tectonic_tree_def:
             tectonic_tree_def, _ = TectonicTreeDef.objects.get_or_create(name="Tectonic Unit", discipline=discipline)
 
-        root, _ = TectonicUnitTreeDefItem.objects.get_or_create(
-            name="Root",
-            title="Root",
+        root, root_created = TectonicUnitTreeDefItem.objects.get_or_create(
             rankid=0,
             parent=None,
             treedef=tectonic_tree_def,
-            isenforced=True
+            defaults={
+                "name": "Root",
+                "title": "Root",
+                "isenforced": True
+            }
         )
+        # The root rank already exists in some capacity in the Discipline
+        # We can assume the user has made modifications to the tree at this
+        # point, so shouldn't go further with checking/creating lower ranks
+        if not root_created:
+            # BUG?: handle setting the tectonicunittreedef on the Discipline
+            # here? We can probably practically assume it's already set if the
+            # root node exists.
+            continue
+
+        # At this point, these get_or_create calls should always be the
+        # equivalent of create (as we know the root node didn't exist).
+        # But keeping the get_or_create here just because
         superstructure, _ = TectonicUnitTreeDefItem.objects.get_or_create(
             name="Superstructure",
             title="Superstructure",
@@ -91,23 +105,25 @@ def create_root_tectonic_node(apps):
 
     for discipline in Discipline.objects.all(): 
 
-        tectonic_tree_def = TectonicUnitTreeDef.objects.filter(name="Tectonic Unit", discipline=discipline).first()
+        tectonic_tree_def = TectonicUnitTreeDef.objects.filter(discipline=discipline).first()
         if not tectonic_tree_def:
             tectonic_tree_def, is_created = TectonicUnitTreeDef.objects.get_or_create(
                 name="Tectonic Unit",
                 discipline=discipline
             )
 
-        tectonic_tree_def_item = TectonicUnitTreeDefItem.objects.filter(treedef=tectonic_tree_def, name="Root").first()
+        tectonic_tree_def_item = TectonicUnitTreeDefItem.objects.filter(treedef=tectonic_tree_def, rankid=0, parent=None).first()
         if not tectonic_tree_def_item:
             tectonic_tree_def_item, is_created = TectonicUnitTreeDefItem.objects.get_or_create(
                 name="Root",
                 title="Root",
                 treedef=tectonic_tree_def,
+                rankid=0,
+                parent=None,
                 isenforced=True
             )
 
-        root = TectonicUnit.objects.filter(name="Root", definition=tectonic_tree_def).first()
+        root = TectonicUnit.objects.filter(definition=tectonic_tree_def, definitionitem=tectonic_tree_def_item, rankid=0, parent=None).first()
         if not root:
             root, is_created = TectonicUnit.objects.get_or_create(
                 name="Root",
@@ -123,7 +139,7 @@ def create_root_tectonic_node(apps):
             if is_created:
                 logger.info(f"Created root tectonic unit for discipline {discipline.name}")
 
-    TectonicUnitTreeDefItem.objects.filter(rankid=0, isenforced__isnull=True).update(isenforced=True)
+    TectonicUnitTreeDefItem.objects.filter(parent=None,rankid=0, isenforced__isnull=True).update(isenforced=True)
 
 def revert_create_root_tectonic_node(apps, schema_editor=None):
     TectonicUnit = apps.get_model('specify', 'TectonicUnit')