[Guided Setup] Add configuration for default trees in guided setup

config/common/geography_tree.json

@@ -1,5 +1,5 @@
 {
-  "geography_tree": {
+  "tree": {
     "treedef": {
       "levels": [
         {

config/common/geologictimeperiod_tree.json

@@ -0,0 +1,44 @@
+{
+  "tree": {
+    "treedef": {
+      "levels": [
+        {
+          "name": "Time Root",
+          "rank": 0,
+          "enforced": true,
+          "infullname": false,
+          "fullnameseparator": ", "
+        },
+        {
+          "name": "Erathem/Era",
+          "rank": 100,
+          "enforced": false,
+          "infullname": false,
+          "fullnameseparator": ", "
+        },
+        {
+          "name": "System/Period",
+          "rank": 200,
+          "enforced": false,
+          "infullname": false,
+          "fullnameseparator": ", "
+        },
+        {
+          "name": "Series/Epoch",
+          "rank": 300,
+          "enforced": false,
+          "infullname": true,
+          "fullnameseparator": ", "
+        },
+        {
+          "name": "Stage/Age",
+          "rank": 400,
+          "enforced": false,
+          "infullname": true,
+          "fullnameseparator": ", "
+        }
+      ]
+    },
+    "nodes": []
+  }
+}

config/common/lithostrat_tree.json

@@ -0,0 +1,45 @@
+{
+  "tree": {
+    "treedef": {
+      "levels": [
+        {
+          "name": "Surface",
+          "enforced": true,
+          "infullname": false,
+          "rank": 0
+        },
+        {
+          "name": "Super Group",
+          "enforced": false,
+          "infullname": false,
+          "rank": 100
+        },
+        {
+          "name": "Litho Group",
+          "enforced": false,
+          "infullname": false,
+          "rank": 200
+        },
+        {
+          "name": "Formation",
+          "enforced": false,
+          "infullname": false,
+          "rank": 300
+        },
+        {
+          "name": "Member",
+          "enforced": false,
+          "infullname": false,
+          "rank": 400
+        },
+        {
+          "name": "Bed",
+          "enforced": false,
+          "infullname": false,
+          "rank": 500
+        }
+      ]
+    },
+    "nodes": []
+  }
+}

config/common/storage_tree.json

@@ -1,5 +1,5 @@
 {
-  "storage_tree": {
+  "tree": {
     "treedef": {
       "levels": [
         {
@@ -53,7 +53,7 @@
         {
           "name": "Rack",
           "enforced": false,
-          "infullname": "Rack",
+          "infullname": false,
           "rank": 450
         },
         {

config/common/tectonicunit_tree.json

@@ -0,0 +1,45 @@
+{
+  "tree": {
+    "treedef": {
+      "levels": [
+        {
+          "name": "Root",
+          "enforced": true,
+          "infullname": false,
+          "rank": 0
+        },
+        {
+          "name": "Superstructure",
+          "enforced": false,
+          "infullname": false,
+          "rank": 100
+        },
+        {
+          "name": "Tectonic Domain",
+          "enforced": false,
+          "infullname": false,
+          "rank": 200
+        },
+        {
+          "name": "Tectonic Subdomain",
+          "enforced": false,
+          "infullname": false,
+          "rank": 300
+        },
+        {
+          "name": "Tectonic Unit",
+          "enforced": false,
+          "infullname": true,
+          "rank": 400
+        },
+        {
+          "name": "Tectonic Subunit",
+          "enforced": false,
+          "infullname": true,
+          "rank": 500
+        }
+      ]
+    },
+    "nodes": []
+  }
+}

specifyweb/backend/setup_tool/api.py

@@ -17,7 +17,7 @@
 from specifyweb.backend.setup_tool.prep_type_defaults import create_default_prep_types
 from specifyweb.backend.setup_tool.setup_tasks import setup_database_background, get_active_setup_task, get_last_setup_error, set_last_setup_error
 from specifyweb.celery_tasks import MissingWorkerError
-from specifyweb.backend.setup_tool.tree_defaults import create_default_tree, update_tree_scoping
+from specifyweb.backend.setup_tool.tree_defaults import start_default_tree_from_configuration, update_tree_scoping
 from specifyweb.specify.models import Institution, Discipline
 from specifyweb.backend.businessrules.uniqueness_rules import apply_default_uniqueness_rules
 from specifyweb.specify.management.commands.run_key_migration_functions import fix_cots
@@ -193,6 +193,8 @@ def create_discipline(data):
         existing_discipline = Discipline.objects.filter(id=existing_id).first()
         if existing_discipline:
             return {"discipline_id": existing_discipline.id}
+
+    is_first_discipline = Discipline.objects.count() == 0
 
     # Resolve division
     division_url = data.get('division')
@@ -215,14 +217,13 @@ def create_discipline(data):
     # Assign a taxon tree. Not required, but its eventually needed for collection object type.
     taxontreedef_url = data.get('taxontreedef', None)
     taxontreedef = resolve_uri_or_fallback(taxontreedef_url, None, Taxontreedef)
-    if taxontreedef is not None:
+    if taxontreedef_url and taxontreedef is not None:
         data['taxontreedef_id'] = taxontreedef.id
 
     data.update({
         'datatype_id': datatype.id,
         'geographytreedef_id': geographytreedef.id,
-        'geologictimeperiodtreedef_id': geologictimeperiodtreedef.id,
-        'taxontreedef_id': taxontreedef.id if taxontreedef else None
+        'geologictimeperiodtreedef_id': geologictimeperiodtreedef.id
     })
 
     # Assign new Discipline ID
@@ -247,6 +248,12 @@ def create_discipline(data):
         update_tree_scoping(geographytreedef, new_discipline.id)
         update_tree_scoping(geologictimeperiodtreedef, new_discipline.id)
 
+        # Create a default taxon tree if the database is already set up.
+        if not is_first_discipline:
+            create_taxon_tree({
+                'discipline_id': new_discipline.id
+            })
+
         return {"discipline_id": new_discipline.id}
 
     except Exception as e:
@@ -365,9 +372,6 @@ def create_tectonicunit_tree(data):
     return create_tree('Tectonicunit', data)
 
 def create_tree(name: str, data: dict) -> dict:
-    # TODO: Use trees/create_default_trees
-    # https://github.com/specify/specify7/pull/6429
-
     # Figure out which scoping field should be used.
     use_institution = False
     use_discipline = True
@@ -393,8 +397,7 @@ def create_tree(name: str, data: dict) -> dict:
     ranks = data.pop('ranks', dict())
 
     # Pre-load Default Tree
-    # TODO: trees/create_default_trees
-    preload_tree = data.pop('default', None)
+    preload_tree = data.pop('preload', None)
 
     try:
         kwargs = {}
@@ -404,7 +407,7 @@ def create_tree(name: str, data: dict) -> dict:
         if use_discipline and discipline is not None:
             kwargs['discipline'] = discipline
 
-        treedef = create_default_tree(name, kwargs, ranks, preload_tree)
+        treedef = start_default_tree_from_configuration(name, kwargs, ranks, preload_tree)
 
         # Set as the primary tree in the discipline if its the first one
         if use_discipline and discipline:

specifyweb/backend/setup_tool/setup_tasks.py

@@ -8,6 +8,7 @@
 from celery.result import AsyncResult
 from specifyweb.backend.setup_tool import api
 from specifyweb.backend.setup_tool.app_resource_defaults import create_app_resource_defaults
+from specifyweb.backend.setup_tool.tree_defaults import start_preload_default_tree
 from specifyweb.specify.management.commands.run_key_migration_functions import fix_schema_config
 from specifyweb.specify.models_utils.model_extras import PALEO_DISCIPLINES, GEOLOGY_DISCIPLINES
 from specifyweb.celery_tasks import is_worker_alive, MissingWorkerError
@@ -80,67 +81,79 @@ def update_progress():
             logger.debug('## SETTING UP DATABASE WITH SETTINGS:##')
             logger.debug(data)
 
-            logger.debug('Creating institution')
+            logger.info('Creating institution')
             api.create_institution(data['institution'])
             update_progress()
 
-            logger.debug('Creating storage tree')
+            logger.info('Creating storage tree')
             api.create_storage_tree(data['storagetreedef'])
             update_progress()
 
-            logger.debug('Creating division')
+            logger.info('Creating division')
             api.create_division(data['division'])
             update_progress()
 
             discipline_type = data['discipline'].get('type', '')
             is_paleo_geo = discipline_type in PALEO_DISCIPLINES or discipline_type in GEOLOGY_DISCIPLINES
             default_tree = {
-                'fullnamedirection': 1,
-                'ranks': {
-                    '0': True
-                }
+                'ranks': {}
             }
 
             # if is_paleo_geo:
             # Create an empty chronostrat tree no matter what because discipline needs it.
-            logger.debug('Creating Chronostratigraphy tree')
+            logger.info('Creating Chronostratigraphy tree')
             default_chronostrat_tree = default_tree.copy()
             default_chronostrat_tree['fullnamedirection'] = -1
-            api.create_geologictimeperiod_tree(default_chronostrat_tree)
+            chronostrat_result = api.create_geologictimeperiod_tree(default_chronostrat_tree)
+            chronostrat_treedef_id = chronostrat_result.get('treedef_id')
 
-            logger.debug('Creating geography tree')
+            logger.info('Creating geography tree')
             uses_global_geography_tree = data['institution'].get('issinglegeographytree', False)
-            api.create_geography_tree(data['geographytreedef'], global_tree=uses_global_geography_tree)
+            geography_result = api.create_geography_tree(data['geographytreedef'].copy(), global_tree=uses_global_geography_tree)
+            geography_treedef_id = geography_result.get('treedef_id')
 
-            logger.debug('Creating discipline')
+            logger.info('Creating discipline')
             discipline_result = api.create_discipline(data['discipline'])
             discipline_id = discipline_result.get('discipline_id')
             default_tree['discipline_id'] = discipline_id
             update_progress()
 
             if is_paleo_geo:
-                logger.debug('Creating Lithostratigraphy tree')
+                logger.info('Creating Lithostratigraphy tree')
                 api.create_lithostrat_tree(default_tree.copy())
 
-                logger.debug('Creating Tectonic Unit tree')
+                logger.info('Creating Tectonic Unit tree')
                 api.create_tectonicunit_tree(default_tree.copy())
 
-            logger.debug('Creating taxon tree')
+            logger.info('Creating taxon tree')
             if data['taxontreedef'].get('discipline_id') is None:
                 data['taxontreedef']['discipline_id'] = discipline_id
-            api.create_taxon_tree(data['taxontreedef'])
+            taxon_result = api.create_taxon_tree(data['taxontreedef'].copy())
+            taxon_treedef_id = taxon_result.get('treedef_id')
             update_progress()
 
-            logger.debug('Creating collection')
-            api.create_collection(data['collection'])
+            logger.info('Creating collection')
+            collection_result = api.create_collection(data['collection'])
+            collection_id = collection_result.get('collection_id')
             update_progress()
 
-            logger.debug('Creating specify user')
-            api.create_specifyuser(data['specifyuser'])
+            logger.info('Creating specify user')
+            specifyuser_result = api.create_specifyuser(data['specifyuser'])
+            specifyuser_id = specifyuser_result.get('user_id')
 
-            logger.debug('Finalizing database')
+            logger.info('Finalizing database')
             fix_schema_config()
             create_app_resource_defaults()
+
+            # Pre-load trees
+            logger.info('Starting default tree downloads')
+            if is_paleo_geo:
+                start_preload_default_tree('Geologictimeperiod', discipline_id, collection_id, chronostrat_treedef_id, specifyuser_id)
+            if data['geographytreedef'].get('preload'):
+                start_preload_default_tree('Geography', discipline_id, collection_id, geography_treedef_id, specifyuser_id)
+            if data['taxontreedef'].get('preload'):
+                start_preload_default_tree('Taxon', discipline_id, collection_id, taxon_treedef_id, specifyuser_id)
+
             update_progress()
     except Exception as e:
         logger.exception(f'Error setting up database: {e}')