Merge remote-tracking branch 'origin/develop' into feature/CSCKAN-276

backend/composer/admin.py

@@ -1,9 +1,13 @@
+from typing import Any
+from django.db.models.query import QuerySet
+from django.http import HttpRequest
 import nested_admin
 from adminsortable2.admin import SortableAdminBase, SortableStackedInline
 from django.contrib import admin
 from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
 from django.contrib.auth.models import User
 from fsm_admin.mixins import FSMTransitionMixin
+from django import forms
 
 from composer.models import (
     Phenotype,
@@ -38,6 +42,10 @@ class ProvenanceInline(admin.StackedInline):
     model = Provenance
     extra = 1
 
+class SynonymInline(admin.StackedInline):
+    model = Synonym
+    extra = 1
+
 
 class ProvenanceNestedInline(nested_admin.NestedStackedInline):
     model = Provenance
@@ -89,26 +97,32 @@ class SentenceAdmin(
         NoteSentenceInline,
     )
 
-
-class SynonymInline(admin.TabularInline):
-    model = Synonym
-    extra = 1
-
-
 class AnatomicalEntityAdmin(admin.ModelAdmin):
     search_fields = ('simple_entity__name', 'region_layer__layer__name', 'region_layer__region__name')
+    autocomplete_fields = ('simple_entity', 'region_layer')
+    list_display = ('simple_entity', 'region_layer', "synonyms")
+    list_display_links = ('simple_entity', 'region_layer')
+    inlines = (SynonymInline,)
 
-    def get_model_perms(self, request):
-        """
-        Return empty dict to hide the model from admin index.
-        """
-        return {}
+    # we need to make efficient queries to the database to get the list of anatomical entities
+    def get_queryset(self, request: HttpRequest) -> QuerySet[Any]:
+        return super().get_queryset(request) \
+            .select_related('simple_entity', 'region_layer__layer', 'region_layer__region') \
+            .prefetch_related('synonyms')
+
+    @admin.display(description="Synonyms")
+    def synonyms(self, obj):
+        synonyms = obj.synonyms.all()
+        return ', '.join([synonym.name for synonym in synonyms])
 
 
 class AnatomicalEntityMetaAdmin(admin.ModelAdmin):
     list_display = ("name", "ontology_uri")
     list_display_links = ("name", "ontology_uri")
-    search_fields = ("name",)
+    search_fields = ("name", "ontology_uri")
+
+    def get_model_perms(self, request):
+        return {}
 
 
 class LayerAdmin(admin.ModelAdmin):
@@ -122,11 +136,15 @@ class RegionAdmin(admin.ModelAdmin):
     filter_horizontal = ('layers',)
 
 
-class AnatomicalEntityIntersectionAdmin(admin.ModelAdmin):
-    list_display = ('layer', 'region',)
+class AnatomicalEntityIntersectionAdmin(nested_admin.NestedModelAdmin, admin.ModelAdmin):
+    list_display = ('layer', 'region')
+    search_fields = ("region__name", "layer__name")
     list_filter = ('layer', 'region',)
     raw_id_fields = ('layer', 'region',)
 
+    def get_model_perms(self, request):
+        return {}
+
 
 class ViaInline(SortableStackedInline):
     model = Via

backend/composer/migrations/0051_alter_anatomicalentity_region_layer.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.1.4 on 2024-04-03 13:57
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0050_alter_anatomicalentityintersection_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="anatomicalentity",
+            name="region_layer",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                to="composer.anatomicalentityintersection",
+            ),
+        ),
+    ]

backend/composer/models.py

@@ -255,28 +255,35 @@ class Meta:
         verbose_name_plural = "Region/Layer Combinations"
 
     def __str__(self):
-        return f"{self.region.name} - {self.layer.name}"
+        return f'{self.region.name} - {self.layer.name}'
 
 
 class AnatomicalEntity(models.Model):
     simple_entity = models.OneToOneField(AnatomicalEntityMeta, on_delete=models.CASCADE, null=True, blank=True)
-    region_layer = models.ForeignKey(AnatomicalEntityIntersection, on_delete=models.CASCADE, null=True, blank=True)
+    region_layer = models.OneToOneField(AnatomicalEntityIntersection, on_delete=models.CASCADE, null=True, blank=True)
 
     @property
     def name(self):
-        return self.simple_entity.name if self.simple_entity \
-            else f'{self.region_layer.region.name},{self.region_layer.layer.name}'
+        if self.simple_entity:
+            return self.simple_entity.name
+        elif self.region_layer:
+            return f'{self.region_layer.region.name},{self.region_layer.layer.name}'
+        return 'Unknown Anatomical Entity'
 
     @property
     def ontology_uri(self):
-        return self.simple_entity.ontology_uri if self.simple_entity \
-            else f'{self.region_layer.region.ontology_uri},{self.region_layer.layer.ontology_uri}'
-
+        if self.simple_entity:
+            return self.simple_entity.ontology_uri
+        elif self.region_layer:
+            return f'{self.region_layer.region.ontology_uri},{self.region_layer.layer.ontology_uri}'
+        return 'Unknown URI'
 
     def __str__(self):
         return self.name
 
     class Meta:
+        verbose_name = "Anatomical Entity"
+        verbose_name_plural = "Anatomical Entities"
         constraints = [
             CheckConstraint(
                 check=(
@@ -519,7 +526,8 @@ def __str__(self):
         source=[
             CSState.DRAFT,
             CSState.IN_PROGRESS,
-            CSState.INVALID
+            CSState.INVALID,
+            CSState.EXPORTED,
         ],
         target=CSState.COMPOSE_NOW,
         permission=ConnectivityStatementStateService.has_permission_to_transition_to_compose_now,

backend/composer/signals.py

@@ -5,8 +5,8 @@
 from django_fsm.signals import post_transition
 
 from .enums import CSState, NoteType
-from .models import ConnectivityStatement, ExportBatch, Note, Sentence, AnatomicalEntity, AnatomicalEntityIntersection, \
-    AnatomicalEntityMeta
+from .models import ConnectivityStatement, ExportBatch, Note, Sentence, Synonym, \
+    AnatomicalEntity, Layer, Region
 from .services.export_services import compute_metrics, ConnectivityStatementStateService
 
 
@@ -48,14 +48,12 @@ def post_transition_cs(sender, instance, name, source, target, **kwargs):
             # add important tag to CS when transition to COMPOSE_NOW from NPO Approved or Exported
             instance = ConnectivityStatementStateService.add_important_tag(instance)
 
-
-@receiver(post_save, sender=AnatomicalEntityIntersection)
-def create_region_layer_anatomical_entity(sender, instance=None, created=False, **kwargs):
+@receiver(post_save, sender=Layer)
+def create_layer_anatomical_entity(sender, instance=None, created=False, **kwargs):
     if created and instance:
-        AnatomicalEntity.objects.create(region_layer=instance)
-
+        AnatomicalEntity.objects.create(simple_entity=instance) 
 
-@receiver(post_save, sender=AnatomicalEntityMeta)
-def create_simple_anatomical_entity(sender, instance=None, created=False, **kwargs):
+@receiver(post_save, sender=Region)
+def create_region_anatomical_entity(sender, instance=None, created=False, **kwargs):
     if created and instance:
         AnatomicalEntity.objects.create(simple_entity=instance)

frontend/src/apiclient/backend/api.ts

@@ -2216,7 +2216,7 @@ export const ComposerApiAxiosParamCreator = function (configuration?: Configurat
         },
         /**
          * AnatomicalEntity
-         * @param {number} id A unique integer value identifying this anatomical entity.
+         * @param {number} id A unique integer value identifying this Anatomical Entity.
          * @param {*} [options] Override http request option.
          * @throws {RequiredError}
          */
@@ -4730,7 +4730,7 @@ export const ComposerApiFp = function(configuration?: Configuration) {
         },
         /**
          * AnatomicalEntity
-         * @param {number} id A unique integer value identifying this anatomical entity.
+         * @param {number} id A unique integer value identifying this Anatomical Entity.
          * @param {*} [options] Override http request option.
          * @throws {RequiredError}
          */
@@ -5333,7 +5333,7 @@ export const ComposerApiFactory = function (configuration?: Configuration, baseP
         },
         /**
          * AnatomicalEntity
-         * @param {number} id A unique integer value identifying this anatomical entity.
+         * @param {number} id A unique integer value identifying this Anatomical Entity.
          * @param {*} [options] Override http request option.
          * @throws {RequiredError}
          */
@@ -5885,7 +5885,7 @@ export class ComposerApi extends BaseAPI {
 
     /**
      * AnatomicalEntity
-     * @param {number} id A unique integer value identifying this anatomical entity.
+     * @param {number} id A unique integer value identifying this Anatomical Entity.
      * @param {*} [options] Override http request option.
      * @throws {RequiredError}
      * @memberof ComposerApi

frontend/src/components/Forms/StatementForm.tsx

@@ -198,7 +198,7 @@ const StatementForm = (props: any) => {
           await api.composerViaDestroy(element.children.props.formData.id);
           refreshStatement();
         }}
-        onElementAdd={async (element: any) => {
+        onElementAdd={async () => {
           await api.composerViaCreate({
             id: -1,
             order: statement?.vias?.length,
@@ -354,7 +354,7 @@ const StatementForm = (props: any) => {
           },
           refreshStatement: () => refreshStatement(),
           errors: "",
-          mapValueToOption: (anatomicalEntities: any[], formId: any) => {
+          mapValueToOption: (anatomicalEntities: any[]) => {
             const entities: Option[] = [];
             const selected = findMatchingEntities(
               statement,
@@ -386,7 +386,7 @@ const StatementForm = (props: any) => {
           );
           refreshStatement();
         }}
-        onElementAdd={async (element: any) => {
+        onElementAdd={async () => {
           await api.composerDestinationCreate({
             id: -1,
             connectivity_statement: statement.id,
@@ -536,7 +536,7 @@ const StatementForm = (props: any) => {
           },
           refreshStatement: () => refreshStatement(),
           errors: "",
-          mapValueToOption: (anatomicalEntities: any[], formId: any) => {
+          mapValueToOption: (anatomicalEntities: any[]) => {
             const entities: Option[] = [];
             const selected = findMatchingEntities(
               statement,
@@ -573,6 +573,7 @@ const StatementForm = (props: any) => {
   copiedUISchema.forward_connection = {
     "ui:widget": CustomEntitiesDropdown,
     "ui:options": {
+      chipsNumber: 10,
       isDisabled,
       placeholder: "Forward connection(s)",
       searchPlaceholder: "Search for Connectivity Statements",

frontend/src/components/Widgets/CustomChipBoxComponent.tsx

@@ -2,7 +2,6 @@ import {Box, Chip, Tooltip} from "@mui/material";
 import {Option} from "../../types";
 import ClearOutlinedIcon from "@mui/icons-material/ClearOutlined";
 import React from "react";
-
 const CustomChipBoxComponent = ({
    selectedOptions,
    CustomInputChip,
@@ -21,41 +20,47 @@ const CustomChipBoxComponent = ({
       width: 'fit-content',
       maxWidth: 'fit-content',
     }
+
+  const renderChipOrCustomInput = (item: Option) => (
+    <Tooltip
+      title={item?.label}
+      placement="top"
+      arrow
+      key={item.id}
+    >
+      {CustomInputChip ? (
+        <CustomInputChip sx={styles.chip} entity={item} />
+      ) : (
+        <Chip
+          sx={{
+            ...styles.chip,
+            ...extraChipStyle
+          }}
+          variant={"outlined"}
+          onClick={(e) => {
+            e.stopPropagation();
+          }}
+          deleteIcon={<ClearOutlinedIcon />}
+          onDelete={!isDisabled ? (e) => {
+            e.stopPropagation();
+            handleChipRemove(item);
+          } : undefined}
+          label={item?.label}
+        />
+      )}
+    </Tooltip>
+  );
+
+
   return (
     <Box gap={1} display="flex" flexWrap="wrap" alignItems="center">
-      {selectedOptions?.length ? (
+      {!isDisabled && selectedOptions?.length ? (
         selectedOptions
           .slice(0, chipsNumber)
-          .map((item: Option, index: number) => (
-            <Tooltip
-              title={item?.label}
-              placement="top"
-              arrow
-              key={item.id}
-            >
-              {CustomInputChip ? (
-                <CustomInputChip sx={styles.chip} entity={item} />
-              ) : (
-                <Chip
-                  sx={{
-                    ...styles.chip,
-                    ...extraChipStyle
-                  }}
-                  variant={"outlined"}
-                  onClick={(e) => {
-                    e.stopPropagation();
-                  }}
-                  deleteIcon={<ClearOutlinedIcon />}
-                  onDelete={!isDisabled ? (e) => {
-                    e.stopPropagation();
-                    handleChipRemove(item);
-                  } : undefined}
-                  label={item?.label}
-                />
-              )}
-            </Tooltip>
-          ))
-      ) : null}
+          .map((item: Option) => renderChipOrCustomInput(item))
+      ) : (
+        selectedOptions?.map((item: Option) => renderChipOrCustomInput(item))
+      )}
       {!isDisabled && selectedOptions.length > chipsNumber && (
         <span style={{ marginRight: ".5rem" }}>
           +{selectedOptions.length - chipsNumber}

frontend/src/components/Widgets/CustomEntitiesDropdown.tsx

@@ -98,7 +98,6 @@ const styles = {
     height: "1.5rem",
     borderRadius: "0.375rem",
     fontSize: "0.875rem",
-    maxWidth: "8rem",
     fontWeight: 500,
 
     "&.MuiChip-filled": {
@@ -489,7 +488,6 @@ export default function CustomEntitiesDropdown({
                   gap={1}
                   sx={{
                     borderBottom: `0.0625rem solid ${popperBorderColor}`,
-                    height: autocompleteOptions.length > 0 ? "2.75rem" : "auto",
                     padding:
                       autocompleteOptions.length > 0 ? "0 0.875rem" : "0.875rem",
                   }}

frontend/src/helpers/anatomicalEntityHelper.ts

@@ -1,4 +1,4 @@
-import {AnatomicalEntity} from "../apiclient/backend";
+import { AnatomicalEntity } from "../apiclient/backend";
 import { OptionDetail } from "../types";
 
 export const DROPDOWN_MAPPER_ONTOLOGY_URL = "Ontology URI";