feat(trees): add tree repair utility

specifyweb/backend/trees/extras.py

@@ -560,7 +560,13 @@ def definition_joins(table, depth):
         for j in range(depth)
     ])
 
-def set_fullnames(treedef, null_only=False, node_number_range=None):
+def set_fullnames(
+    treedef,
+    null_only: bool = False,
+    node_number_range=None,
+    include_synonyms: bool = False,
+    synonyms_only: bool = False,
+):
     table = treedef.treeentries.model._meta.db_table
     depth = treedef.treedefitems.count()
     reverse = treedef.fullnamedirection == -1
@@ -569,29 +575,55 @@ def set_fullnames(treedef, null_only=False, node_number_range=None):
     if depth < 1:
         return
     cursor = connection.cursor()
+
+    if synonyms_only:
+        accepted_filter = "and t0.acceptedid is not null"
+    elif include_synonyms:
+        accepted_filter = ""
+    else:
+        accepted_filter = "and t0.acceptedid is null"
+
+    fullname_sql_expr = fullname_expr(depth, reverse)
+
+    diff_condition = (
+        "and (t0.fullname is null OR t0.fullname <> {expr})".format(
+            expr=fullname_sql_expr
+        )
+        if not null_only
+        else ""
+    )
+
     sql = (
         "update {table} t0\n"
         "{parent_joins}\n"
         "{definition_joins}\n"
         "set {set_expr}\n"
         "where t{root}.parentid is null\n"
         "and t0.{table}treedefid = {treedefid}\n"
-        "and t0.acceptedid is null\n"
+        "{accepted_filter}\n"
         "{null_only}\n"
         "{node_number_range}\n"
+        "{diff_condition}\n"
     ).format(
         root=depth-1,
         table=table,
         treedefid=treedefid,
-        set_expr=f"t0.fullname = {fullname_expr(depth, reverse)}",
+        set_expr=f"t0.fullname = {fullname_sql_expr}",
         parent_joins=parent_joins(table, depth),
         definition_joins=definition_joins(table, depth),
+        accepted_filter=accepted_filter,
         null_only="and t0.fullname is null" if null_only else "",
-        node_number_range=f"and t0.nodenumber between {node_number_range[0]} and {node_number_range[1]}" if not (node_number_range is None) else ''
+        node_number_range=(
+            f"and t0.nodenumber between {node_number_range[0]} and {node_number_range[1]}"
+            if node_number_range is not None
+            else ''
+        ),
+        diff_condition=diff_condition,
     )
 
     logger.debug('fullname update sql:\n%s', sql)
-    return cursor.execute(sql)
+    cursor.execute(sql)
+    return cursor.rowcount
 
 def predict_fullname(table, depth, parentid, defitemid, name, reverse=False):
     cursor = connection.cursor()

specifyweb/backend/trees/urls.py

@@ -13,6 +13,7 @@
         path('<int:id>/bulk_move/', views.bulk_move),
         path('<int:id>/synonymize/', views.synonymize),
         path('<int:id>/desynonymize/', views.desynonymize),
+        path('<int:id>/rebuild_fullname/', views.rebuild_fullname),
         path('<int:rankid>/tree_rank_item_count/', views.tree_rank_item_count),
         path('<int:parentid>/predict_fullname/', views.predict_fullname),
         re_path(r'^(?P<treedef>\d+)/(?P<parentid>\w+)/stats/$', views.tree_stats),

specifyweb/backend/trees/views.py

@@ -411,6 +411,54 @@ def repair_tree(request, tree: TREE_TABLE):
     extras.renumber_tree(table)
     extras.validate_tree_numbering(table)
 
+@login_maybe_required
+@require_POST
+@transaction.atomic
+def rebuild_fullname(request, tree: TREE_TABLE, id: int):
+    """Rebuild fullname values for the specified tree definition.
+
+    By default only accepted (preferred) nodes are processed. Pass
+    ?rebuild_synonyms=true to also rebuild fullname values for synonym nodes.
+    """
+    check_permission_targets(
+        request.specify_collection.id,
+        request.specify_user.id,
+        [perm_target(tree).rebuild_fullname],
+    )
+
+    rebuild_synonyms = request.GET.get('rebuild_synonyms', 'false').lower() == 'true'
+
+    tree_name = tree.title()
+    treedef = get_object_or_404(f"{tree_name}treedef", id=id)
+
+    accepted_changed = extras.set_fullnames(
+        treedef,
+        null_only=False,
+        include_synonyms=False,
+        synonyms_only=False,
+    )
+
+    synonyms_changed = 0
+    if rebuild_synonyms:
+        synonyms_changed = extras.set_fullnames(
+            treedef,
+            null_only=False,
+            include_synonyms=True,
+            synonyms_only=True,
+        )
+
+    payload = {
+        "success": True,
+        "rebuild_synonyms": rebuild_synonyms,
+        "changed": {
+            "accepted": accepted_changed,
+            "synonyms": synonyms_changed,
+            "total": accepted_changed + synonyms_changed,
+        },
+    }
+
+    return HttpResponse(toJson(payload), content_type="application/json")
+
 @tree_mutation
 def add_root(request, tree, treeid): 
     "Creates a root node in a specific tree."
@@ -550,6 +598,7 @@ class TaxonMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 
 class GeographyMutationPT(PermissionTarget):
@@ -559,6 +608,7 @@ class GeographyMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 
 class StorageMutationPT(PermissionTarget):
@@ -569,6 +619,7 @@ class StorageMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 
 class GeologictimeperiodMutationPT(PermissionTarget):
@@ -578,6 +629,7 @@ class GeologictimeperiodMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 
 class LithostratMutationPT(PermissionTarget):
@@ -587,6 +639,7 @@ class LithostratMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 class TectonicunitMutationPT(PermissionTarget):
     resource = "/tree/edit/tectonicunit"
@@ -595,6 +648,7 @@ class TectonicunitMutationPT(PermissionTarget):
     synonymize = PermissionTargetAction()
     desynonymize = PermissionTargetAction()
     repair = PermissionTargetAction()
+    rebuild_fullname = PermissionTargetAction()
 
 def perm_target(tree):
     return {

specifyweb/frontend/js_src/lib/components/Atoms/Icons.tsx

@@ -137,6 +137,7 @@ export const icons = {
   userCircle: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M18 10a8 8 0 11-16 0 8 8 0 0116 0zm-6-3a2 2 0 11-4 0 2 2 0 014 0zm-2 4a5 5 0 00-4.546 2.916A5.986 5.986 0 0010 16a5.986 5.986 0 004.546-2.084A5 5 0 0010 11z" fillRule="evenodd" /></svg>,
   variable: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M4.649 3.084A1 1 0 015.163 4.4 13.95 13.95 0 004 10c0 1.993.416 3.886 1.164 5.6a1 1 0 01-1.832.8A15.95 15.95 0 012 10c0-2.274.475-4.44 1.332-6.4a1 1 0 011.317-.516zM12.96 7a3 3 0 00-2.342 1.126l-.328.41-.111-.279A2 2 0 008.323 7H8a1 1 0 000 2h.323l.532 1.33-1.035 1.295a1 1 0 01-.781.375H7a1 1 0 100 2h.039a3 3 0 002.342-1.126l.328-.41.111.279A2 2 0 0011.677 14H12a1 1 0 100-2h-.323l-.532-1.33 1.035-1.295A1 1 0 0112.961 9H13a1 1 0 100-2h-.039zm1.874-2.6a1 1 0 011.833-.8A15.95 15.95 0 0118 10c0 2.274-.475 4.44-1.332 6.4a1 1 0 11-1.832-.8A13.949 13.949 0 0016 10c0-1.993-.416-3.886-1.165-5.6z" fillRule="evenodd" /></svg>,
   viewList: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M3 4a1 1 0 011-1h12a1 1 0 110 2H4a1 1 0 01-1-1zm0 4a1 1 0 011-1h12a1 1 0 110 2H4a1 1 0 01-1-1zm0 4a1 1 0 011-1h12a1 1 0 110 2H4a1 1 0 01-1-1zm0 4a1 1 0 011-1h12a1 1 0 110 2H4a1 1 0 01-1-1z" fillRule="evenodd" /></svg>,
+  wrench: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M19 5.5a4.5 4.5 0 0 1-4.791 4.49c-.873-.055-1.808.128-2.368.8l-6.024 7.23a2.724 2.724 0 1 1-3.837-3.837L9.21 8.16c.672-.56.855-1.495.8-2.368a4.5 4.5 0 0 1 5.873-4.575c.324.105.39.51.15.752L13.34 4.66a.455.455 0 0 0-.11.494 3.01 3.01 0 0 0 1.617 1.617c.17.07.363.02.493-.111l2.692-2.692c.241-.241.647-.174.752.15.14.435.216.9.216 1.382ZM4 17a1 1 0 1 0 0-2 1 1 0 0 0 0 2Z" fillRule="evenodd" /></svg>,
   x: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M4.293 4.293a1 1 0 011.414 0L10 8.586l4.293-4.293a1 1 0 111.414 1.414L11.414 10l4.293 4.293a1 1 0 01-1.414 1.414L10 11.414l-4.293 4.293a1 1 0 01-1.414-1.414L8.586 10 4.293 5.707a1 1 0 010-1.414z" fillRule="evenodd" /></svg>,
   zoomIn: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path d="M5 8a1 1 0 011-1h1V6a1 1 0 012 0v1h1a1 1 0 110 2H9v1a1 1 0 11-2 0V9H6a1 1 0 01-1-1z" /><path clipRule="evenodd" d="M2 8a6 6 0 1110.89 3.476l4.817 4.817a1 1 0 01-1.414 1.414l-4.816-4.816A6 6 0 012 8zm6-4a4 4 0 100 8 4 4 0 000-8z" fillRule="evenodd" /></svg>,
   zoomOut: <svg aria-hidden className={iconClassName} fill="currentColor" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg"><path clipRule="evenodd" d="M8 4a4 4 0 100 8 4 4 0 000-8zM2 8a6 6 0 1110.89 3.476l4.817 4.817a1 1 0 01-1.414 1.414l-4.816-4.816A6 6 0 012 8z" fillRule="evenodd" /><path clipRule="evenodd" d="M5 8a1 1 0 011-1h4a1 1 0 110 2H6a1 1 0 01-1-1z" fillRule="evenodd" /></svg>,  

specifyweb/frontend/js_src/lib/components/Header/userToolDefinitions.ts

@@ -89,7 +89,7 @@ const rawUserTools = ensure<IR<IR<Omit<MenuItem, 'name'>>>>()({
     repairTree: {
       title: headerText.repairTree(),
       url: '/specify/overlay/tree-repair/',
-      icon: icons.checkCircle,
+      icon: icons.wrench,
       enabled: () =>
         getDisciplineTrees().some((treeName) =>
           hasPermission(`/tree/edit/${toLowerCase(treeName)}`, 'repair')

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

@@ -24,13 +24,21 @@ export const operationPolicies = {
     'copy_from_library',
   ],
   '/permissions/library/roles': ['read', 'create', 'update', 'delete'],
-  '/tree/edit/taxon': ['merge', 'move', 'synonymize', 'desynonymize', 'repair'],
+  '/tree/edit/taxon': [
+    'merge',
+    'move',
+    'synonymize',
+    'desynonymize',
+    'repair',
+    'rebuild_fullname',
+  ],
   '/tree/edit/geography': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
+    'rebuild_fullname',
   ],
   '/tree/edit/storage': [
     'merge',
@@ -39,27 +47,31 @@ export const operationPolicies = {
     'desynonymize',
     'repair',
     'bulk_move',
+    'rebuild_fullname',
   ],
   '/tree/edit/geologictimeperiod': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
+    'rebuild_fullname',
   ],
   '/tree/edit/lithostrat': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
+    'rebuild_fullname',
   ],
   '/tree/edit/tectonicunit': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
+    'rebuild_fullname',
   ],
   '/querybuilder/query': [
     'execute',