Update Schema Config to include new geo fields and COG picklists

specifyweb/businessrules/rules/cogtype_rules.py

@@ -10,7 +10,6 @@ def cogtype_pre_save(cog_type):
     # NOTE: Maybe add constraint on the cog_type name in the future.
     default_cog_types_picklist = Picklist.objects.get(
         name="Default Collection Object Group Types",
-        tablename="collectionobjectgrouptype",
         collection=cog_type.collection
     )
     if Picklistitem.objects.filter(picklist=default_cog_types_picklist, value=cog_type.type).count() == 0:

specifyweb/frontend/js_src/lib/components/PickLists/definitions.ts

@@ -60,6 +60,12 @@ export const userTypes = [
   'Guest',
 ] as const;
 
+export const collectionObjectGroupTypeTypes = [
+  'Discrete',
+  'Consolidated',
+  'Drill Core',
+] as const;
+
 export const PickListTypes = {
   // Items are defined in the PickListItems table
   ITEMS: 0,
@@ -210,6 +216,18 @@ export const getFrontEndPickLists = f.store<{
         .set('tableName', 'collectionobjecttype')
         .set('fieldName', 'name'),
     },
+    CollectionObjectGroupType: {
+      name: definePicklist('_CollectionObjectGroupType', [])
+        .set('type', PickListTypes.FIELDS)
+        .set('tableName', 'collectionobjectgrouptype')
+        .set('fieldName', 'name'),
+      type: definePicklist(
+        '_CollectionObjectGroupTypeType',
+        collectionObjectGroupTypeTypes.map((title) =>
+          createPickListItem(title, title)
+        )
+      ),
+    },
     CollectionRelType: {
       name: definePicklist('_CollectionRelType', [])
         .set('type', PickListTypes.FIELDS)

specifyweb/frontend/js_src/lib/components/SchemaConfig/README.md

@@ -5,11 +5,14 @@ fields and formatters/aggregators.
 
 Tables used:
 
-- SpLocaleContainer
-- SpLocaleContainerItem
-- SpLocaleItemStr
+- SpLocaleContainer: Refers to each table in Schema Config. Each Specify table has one `SpLocaleContainer` record for each discipline.
+- SpLocaleContainerItem: Contains the entries (fields/relations) for tables in Schema Config.
+- SpLocaleItemStr: Contains the name and description strings for each `SpLocaleContainerItem`.
 
 Also, the PickList tables:
 
-- PickList
-- PickListItem
+- PickList: Defines a picklist in the database. Picklists can be one of 3 types:
+    - `type=0`: Refers to user-defined picklists. i.e: picklists containing explicitly specified values.
+    - `type=1`: Picklists that are related to a table. The values of the picklist are based on a specified formatter. e.g: CollectionObject > CollectionObjectType.
+    - `type=2`: Picklists that generates its values from a field in a given table. Essentially works as a user-defined picklist, but with autogenerated values.
+- PickListItem: Contains the values for user-defined picklists. Only used for `type 1` picklists.

specifyweb/frontend/js_src/lib/components/Toolbar/QueryTablesEdit.tsx

@@ -45,7 +45,6 @@ export const HIDDEN_GEO_TABLES = new Set([
   'CollectionObjectType',
   'CollectionObjectGroup',
   'CollectionObjectGroupJoin',
-  'CollectionObjectGroupType',
 ]);
 export function TablesListEdit({
   isNoRestrictionMode,

specifyweb/specify/migrations/0002_geo.py

@@ -123,9 +123,8 @@ def create_default_collection_object_types():
     for collection in Collection.objects.all():
         cog_type_picklist = Picklist.objects.create(
             name='Default Collection Object Group Types',
-            tablename='Collectionobjectgrouptype',
             issystem=False,
-            type=1,
+            type=0,
             readonly=False,
             collection=collection
         )
@@ -140,7 +139,6 @@ def revert_default_collection_object_types():
     for collection in Collection.objects.all():
         cog_type_picklist_qs = Picklist.objects.filter(
             name='Default Collection Object Group Types',
-            tablename='Collectionobjectgrouptype',
             collection=collection
         )
         if cog_type_picklist_qs.exists():

specifyweb/specify/migrations/0004_schema_config_update.py

@@ -0,0 +1,177 @@
+"""
+This migration updates the Schema Config entries for pre-geo tables. 
+Geo migration added new fields to already existing tables. This migration updates the Schema Config to reflect those changes.
+
+Fields added:
+Collection -> collectionObjectType
+GeographyTreeDef -> discipline
+GeologicTimePeriodTreeDef -> discipline
+LithostratTreeDef -> discipline
+StorageTreeDef -> institution
+TaxonTreeDef -> discipline
+"""
+from django.db import migrations
+
+FIELD_DATA = [
+    {
+        "table": "Collection",
+        "field": "collectionObjectType",
+        "isrequired": False,
+    },
+    {
+        "table": "GeographyTreeDef",
+        "field": "discipline",
+        "isrequired": True,
+    },
+    {
+        "table": "GeologicTimePeriodTreeDef",
+        "field": "discipline",
+        "isrequired": True,
+    },
+    {
+        "table": "LithostratTreeDef",
+        "field": "discipline",
+        "isrequired": True,
+    },
+    {
+        "table": "StorageTreeDef",
+        "field": "institution",
+        "isrequired": True,
+    },
+    {
+        "table": "TaxonTreeDef",
+        "field": "discipline",
+        "isrequired": True,
+    },
+]
+
+PICKLIST_NAME = 'CollectionObjectGroupType'
+COGTYPE_FIELD_NAME = 'cogType'
+PICKLIST_TEXT = 'Collection Object Group Type'
+
+def add_fields(apps):
+    Splocalecontainer = apps.get_model('specify', 'Splocalecontainer')
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+    Splocaleitemstr = apps.get_model('specify', 'Splocaleitemstr')
+
+    for data in FIELD_DATA:
+        for container in Splocalecontainer.objects.filter(name=data['table'], schematype=0):
+            container_item, _ = Splocalecontaineritem.objects.get_or_create(
+                name=data["field"],
+                type='ManyToOne',
+                container=container,
+                isrequired=data["isrequired"]
+            )
+            Splocaleitemstr.objects.get_or_create(
+                language='en',
+                text=data["field"],
+                itemname=container_item
+            )
+            Splocaleitemstr.objects.get_or_create(
+                language='en',
+                text=data["field"],
+                itemdesc=container_item
+            )
+
+def remove_fields(apps):
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+    Splocaleitemstr = apps.get_model('specify', 'Splocaleitemstr')
+
+    for data in FIELD_DATA:
+        Splocaleitemstr.objects.filter(
+            text=data["field"].title(),
+            itemname__name=data["field"],
+            itemname__container__name=data["table"], 
+            itemname__container__schematype=0
+        ).delete()
+        Splocaleitemstr.objects.filter(
+            text=data["field"],
+            itemdesc__name=data["field"],
+            itemdesc__container__name=data["table"], 
+            itemdesc__container__schematype=0
+        ).delete()
+        Splocalecontaineritem.objects.filter(
+            name=data["field"],
+            container__name=data["table"],
+            container__schematype=0,
+        ).delete()
+
+def create_cogtype_picklist(apps):
+    Collection = apps.get_model('specify', 'Collection')
+    Picklist = apps.get_model('specify', 'Picklist')
+
+    # Create a cogtype picklist for each collection
+    for collection in Collection.objects.all():
+        Picklist.objects.get_or_create(
+            name=PICKLIST_NAME,
+            issystem=True,
+            readonly=True,
+            sizelimit=-1,
+            sorttype=1,
+            type=1,
+            tablename='collectionobjectgrouptype',
+            collection=collection,
+            formatter=PICKLIST_NAME
+        )
+
+def revert_cogtype_picklist(apps):
+    Picklist = apps.get_model('specify', 'Picklist')
+
+    Picklist.objects.filter(name=PICKLIST_NAME).delete()
+
+# Updates COG -> cogtype to use the type 1 picklist created above
+def update_cogtype_splocalecontaineritem(apps):
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+
+    Splocalecontaineritem.objects.filter(container__name='collectionobjectgroup', container__schematype=0, name=COGTYPE_FIELD_NAME).update(
+        picklistname=PICKLIST_NAME,
+        type='ManyToOne',
+        isrequired=True
+    )
+
+def revert_cogtype_splocalecontaineritem(apps):
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+
+    Splocalecontaineritem.objects.filter(container__name='collectionobjectgroup', container__schematype=0, name=COGTYPE_FIELD_NAME).update(
+        picklistname=None,
+        type=None,
+        isrequired=None
+    )
+
+# Updates cogtype -> type to use the Default COGType picklist (Drill Core, Discrete, Consolidated)
+def update_cogtype_type_splocalecontaineritem(apps):
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+
+    Splocalecontaineritem.objects.filter(container__name='collectionobjectgrouptype', container__schematype=0, name='type').update(
+        picklistname='Default Collection Object Group Types',
+        isrequired=True
+    )
+
+def revert_cogtype_type_splocalecontaineritem(apps):
+    Splocalecontaineritem = apps.get_model('specify', 'Splocalecontaineritem')
+
+    Splocalecontaineritem.objects.filter(container__name='collectionobjectgrouptype', container__schematype=0, name='type').update(
+        picklistname=None,
+        isrequired=None
+    )
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('specify', '0003_cotype_picklist'),
+    ]
+
+    def apply_migration(apps, schema_editor):
+        add_fields(apps)
+        create_cogtype_picklist(apps)
+        update_cogtype_splocalecontaineritem(apps)
+        update_cogtype_type_splocalecontaineritem(apps)
+
+    def revert_migration(apps, schema_editor):
+        remove_fields(apps)
+        revert_cogtype_picklist(apps)
+        revert_cogtype_splocalecontaineritem(apps)
+        revert_cogtype_type_splocalecontaineritem(apps)
+
+    operations = [
+        migrations.RunPython(apply_migration, revert_migration, atomic=True)
+    ]