Mc trainer fix cui UI

medcat-trainer/docker-compose-dev.yml

@@ -84,5 +84,5 @@ volumes:
 
 networks:
   gateway-auth_gateway-net:
+    name: ${MCT_GATEWAY_NETWORK_NAME:-gateway-auth_gateway-net}
     external: true
-

medcat-trainer/docs/installation.md

@@ -19,6 +19,7 @@ services:
 
 - Docker Engine
 - Docker Compose v2 (`docker compose` command)
+- `uv` (only needed for the local Django debug script)
 
 ## Quick start (prebuilt images)
 
@@ -47,6 +48,56 @@ docker compose -f docker-compose-dev.yml up --build
 This uses the local `webapp/` source tree and is the recommended setup for
 development work.
 
+### Local Django debug script
+
+For backend development where you want to run Django directly on your host
+machine, use the local debug helper:
+
+```bash
+./webapp/scripts/run_local_debug.sh
+```
+
+The script sources `envs/env`, syncs Python dependencies with `uv` when needed,
+runs migrations, creates a local admin user, ensures the default user group
+exists, and starts Django at `http://127.0.0.1:8001/`.
+
+By default it also starts only the `solr` service with Docker Compose:
+
+```bash
+docker compose -f docker-compose-dev.yml up -d solr
+```
+
+Before starting Solr, the script ensures the Compose gateway network exists. It
+uses `gateway-auth_gateway-net` by default, creating it if it is missing. If you
+are running MedCATtrainer alongside a different gateway stack, set the network
+name explicitly:
+
+```bash
+MCT_GATEWAY_NETWORK_NAME=my-gateway-net ./webapp/scripts/run_local_debug.sh
+```
+
+Available modes:
+
+```bash
+./webapp/scripts/run_local_debug.sh server
+./webapp/scripts/run_local_debug.sh worker
+./webapp/scripts/run_local_debug.sh shell
+./webapp/scripts/run_local_debug.sh bootstrap
+```
+
+Common overrides:
+
+| Variable | Description |
+|---|---|
+| `MCT_DEBUG_HOST` | Django bind host (default `0.0.0.0`). |
+| `MCT_DEBUG_PORT` | Django port (default `8001`). |
+| `MCT_ENV_FILE` | Env file to source instead of `envs/env`. |
+| `MCT_ADMIN_USERNAME` | Local admin username (default `admin`). |
+| `MCT_ADMIN_PASSWORD` | Local admin password (default `admin`). |
+| `MCT_START_SOLR` | Start Solr through Docker Compose (`1`/`0`, default `1`). |
+| `MCT_GATEWAY_NETWORK_NAME` | External Compose network to use/create for Solr. |
+| `MCT_SYNC_DEPS` | Run `uv sync --frozen` (`1`/`0`/`auto`, default `auto`). |
+
 ## Legacy MedCAT v0.x support
 
 If you still need the legacy MedCAT v0.x-compatible stack:
@@ -141,4 +192,4 @@ An example compose file is available at
   for the selected CDB.
 
 ## Next Steps
-Now that medcat trainer is installed and running, proceed to [Administrator Setup](admin_setup.md) to create the Admin user.
+Now that medcat trainer is installed and running, proceed to [Administrator Setup](admin_setup.md) to create the Admin user.

medcat-trainer/envs/env

@@ -2,7 +2,10 @@
 OPENBLAS_NUM_THREADS=1
 
 ### MedCAT cfg ###
+
+# when in debug mode please use ../../configs/base.txt
 MEDCAT_CONFIG_FILE=/home/configs/base.txt
+
 # number of MedCAT models that can be cached, run in bg processes at any one time
 MAX_MEDCAT_MODELS=2
 
@@ -12,9 +15,12 @@ ENV=non-prod
 # Complete once this is deployed
 CSRF_TRUSTED_ORIGINS=
 
+USE_OIDC=0
+
 ### Django debug setting - to live-reload etc. ###
 DEBUG=1
 
+
 ### Load example CDB, Vocab ###
 LOAD_EXAMPLES=1
 # URL that examples will be sent to
@@ -25,7 +31,7 @@ UNIQUE_DOC_NAMES_IN_DATASETS=True
 MAX_DATASET_SIZE=10000
 
 ### Solr Concept Search Conf ###
-CONCEPT_SEARCH_SERVICE_HOST=solr
+CONCEPT_SEARCH_SERVICE_HOST=localhost
 CONCEPT_SEARCH_SERVICE_PORT=8983
 
 ### DB backup dir ###
@@ -60,4 +66,4 @@ OTEL_METRICS_EXPORTER=none
 OTEL_LOGS_EXPORTER=none
 OTEL_PYTHON_DJANGO_EXCLUDED_URLS=/api/health/*,/metrics
 OTEL_EXPERIMENTAL_RESOURCE_DETECTORS=containerid,os
-OTEL_PYTHON_DISABLED_INSTRUMENTATIONS=sqlite3,psycopg
+OTEL_PYTHON_DISABLED_INSTRUMENTATIONS=sqlite3,psycopg

medcat-trainer/webapp/frontend/src/mixins/ConceptDetailService.js

@@ -19,12 +19,21 @@ export default {
       }
     },
     fetchConcept (selectedEnt, cdbSearchIndex, callback) {
-      this.$http.get(`/api/concepts/${cdbSearchIndex}/select?q=cui:${selectedEnt.cui}`).then(resp => {
-        if (selectedEnt && resp.data.response.docs.length > 0) {
-          const docEnt = resp.data.response.docs[0]
+      const cdbs = this.conceptSearchCdbs(cdbSearchIndex)
+      if (!cdbs) {
+        if (callback) {
+          callback()
+        }
+        return
+      }
+      const query = `search=${encodeURIComponent(selectedEnt.cui)}&cdbs=${encodeURIComponent(cdbs)}`
+      this.$http.get(`/api/search-concepts/?${query}`).then(resp => {
+        const results = resp.data?.results || []
+        if (selectedEnt && results.length > 0) {
+          const docEnt = results[0]
           selectedEnt.desc = docEnt.desc
           selectedEnt.type_ids = docEnt.type_ids
-          selectedEnt.pretty_name = docEnt.pretty_name[0]
+          selectedEnt.pretty_name = Array.isArray(docEnt.pretty_name) ? docEnt.pretty_name[0] : docEnt.pretty_name
           selectedEnt.synonyms = docEnt.synonyms
           if ((docEnt.icd10 || []).length > 0) {
             selectedEnt.icd10 = []
@@ -67,6 +76,17 @@ export default {
           callback()
         }
       })
+    },
+    conceptSearchCdbs (cdbSearchIndex) {
+      if (Array.isArray(cdbSearchIndex)) {
+        return cdbSearchIndex.filter(id => id).join(',')
+      }
+      if (!cdbSearchIndex) {
+        return null
+      }
+      const searchIndex = String(cdbSearchIndex)
+      const collectionMatch = searchIndex.match(/_id_(.+)$/)
+      return collectionMatch ? collectionMatch[1] : searchIndex
     }
   }
 }

medcat-trainer/webapp/frontend/src/tests/components/ConceptSummary.spec.ts

@@ -0,0 +1,161 @@
+import { describe, expect, it, vi } from 'vitest'
+import { flushPromises, mount } from '@vue/test-utils'
+import ConceptSummary from '@/components/common/ConceptSummary.vue'
+
+describe('ConceptSummary.vue', () => {
+  it('shows the CUI after fetching the entity label when no concept search index is configured', async () => {
+    const mockGet = vi.fn((url: string) => {
+      if (url === '/api/entities/10/') {
+        return Promise.resolve({ data: { label: 'C0022660' } })
+      }
+      return Promise.reject(new Error(`Unexpected request: ${url}`))
+    })
+
+    const wrapper = mount(ConceptSummary, {
+      props: {
+        project: {},
+        selectedEnt: null,
+        altSearch: false,
+        searchFilterDBIndex: null
+      },
+      global: {
+        mocks: {
+          $http: { get: mockGet }
+        },
+        stubs: {
+          'concept-picker': true,
+          'font-awesome-icon': true
+        }
+      }
+    })
+
+    await wrapper.setProps({
+      selectedEnt: {
+        id: 1,
+        entity: 10,
+        value: 'acute kidney failure',
+        start_ind: 10,
+        end_ind: 30,
+        acc: 0.99,
+        assignedValues: {
+          'Concept Annotation': null
+        },
+        deleted: false
+      }
+    })
+    await flushPromises()
+
+    expect(mockGet).toHaveBeenCalledTimes(1)
+    expect(mockGet).toHaveBeenCalledWith('/api/entities/10/')
+    expect(wrapper.text()).toContain('C0022660')
+  })
+
+  it('shows the CUI when the concept lookup response has no results', async () => {
+    const mockGet = vi.fn((url: string) => {
+      if (url === '/api/entities/10/') {
+        return Promise.resolve({ data: { label: 'C0022660' } })
+      }
+      if (url === '/api/search-concepts/?search=C0022660&cdbs=1') {
+        return Promise.resolve({ data: { results: [] } })
+      }
+      return Promise.reject(new Error(`Unexpected request: ${url}`))
+    })
+
+    const wrapper = mount(ConceptSummary, {
+      props: {
+        project: {},
+        selectedEnt: null,
+        altSearch: false,
+        searchFilterDBIndex: '1'
+      },
+      global: {
+        mocks: {
+          $http: { get: mockGet }
+        },
+        stubs: {
+          'concept-picker': true,
+          'font-awesome-icon': true
+        }
+      }
+    })
+
+    await wrapper.setProps({
+      selectedEnt: {
+        id: 1,
+        entity: 10,
+        value: 'acute kidney failure',
+        start_ind: 10,
+        end_ind: 30,
+        acc: 0.99,
+        assignedValues: {
+          'Concept Annotation': null
+        },
+        deleted: false
+      }
+    })
+    await flushPromises()
+
+    expect(mockGet).toHaveBeenCalledTimes(2)
+    expect(wrapper.text()).toContain('C0022660')
+  })
+
+  it('shows concept details returned by the backend concept search endpoint', async () => {
+    const mockGet = vi.fn((url: string) => {
+      if (url === '/api/entities/10/') {
+        return Promise.resolve({ data: { label: 'C0022660' } })
+      }
+      if (url === '/api/search-concepts/?search=C0022660&cdbs=1') {
+        return Promise.resolve({
+          data: {
+            results: [{
+              cui: 'C0022660',
+              pretty_name: 'Acute kidney failure',
+              type_ids: ['T047'],
+              synonyms: ['AKF']
+            }]
+          }
+        })
+      }
+      return Promise.reject(new Error(`Unexpected request: ${url}`))
+    })
+
+    const wrapper = mount(ConceptSummary, {
+      props: {
+        project: {},
+        selectedEnt: null,
+        altSearch: false,
+        searchFilterDBIndex: '1'
+      },
+      global: {
+        mocks: {
+          $http: { get: mockGet }
+        },
+        stubs: {
+          'concept-picker': true,
+          'font-awesome-icon': true
+        }
+      }
+    })
+
+    await wrapper.setProps({
+      selectedEnt: {
+        id: 1,
+        entity: 10,
+        value: 'acute kidney failure',
+        start_ind: 10,
+        end_ind: 30,
+        acc: 0.99,
+        assignedValues: {
+          'Concept Annotation': null
+        },
+        deleted: false
+      }
+    })
+    await flushPromises()
+
+    expect(mockGet).toHaveBeenCalledTimes(2)
+    expect(wrapper.text()).toContain('Acute kidney failure')
+    expect(wrapper.text()).toContain('T047')
+    expect(wrapper.text()).toContain('C0022660')
+  })
+})

medcat-trainer/webapp/frontend/src/views/Demo.vue

@@ -222,11 +222,7 @@ export default {
     },
     fetchCDBSearchIndex () {
       if (this.selectedProject?.cdb_search_filter?.length > 0) {
-        this.$http.get(`/api/concept-dbs/${this.selectedProject.cdb_search_filter[0]}/`).then(resp => {
-          if (resp.data) {
-            this.searchFilterDBIndex = `${resp.data.name}_id_${this.selectedProject.cdb_search_filter}`
-          }
-        })
+        this.searchFilterDBIndex = this.selectedProject.cdb_search_filter.join(',')
       } else {
         this.searchFilterDBIndex = null
       }

medcat-trainer/webapp/frontend/src/views/TrainAnnotations.vue

@@ -466,11 +466,9 @@ export default {
     },
     fetchCDBSearchIndex() {
       if (this.project.cdb_search_filter.length > 0) {
-        this.$http.get(`/api/concept-dbs/${this.project.cdb_search_filter[0]}/`).then(resp => {
-          if (resp.data) {
-            this.searchFilterDBIndex = `${resp.data.name}_id_${this.project.cdb_search_filter}`
-          }
-        })
+        this.searchFilterDBIndex = this.project.cdb_search_filter.join(',')
+      } else {
+        this.searchFilterDBIndex = null
       }
     },
     loadDoc(doc) {

medcat-trainer/webapp/frontend/vite.config.ts

@@ -2,13 +2,11 @@ import { fileURLToPath, URL } from 'node:url'
 
 import { defineConfig } from 'vite'
 import vue from '@vitejs/plugin-vue'
-import vueDevTools from 'vite-plugin-vue-devtools'
 
 // https://vite.dev/config/
 export default defineConfig({
   plugins: [
     vue(),
-    vueDevTools(),
   ],
   resolve: {
     alias: {
@@ -37,7 +35,7 @@ export default defineConfig({
         target: 'http://127.0.0.1:8983/solr',
         changeOrigin: true,
         secure: false,
-        rewrite: (path) => path.replace(/\/api\/concepts/, '/')
+        rewrite: (path: string) => path.replace(/\/api\/concepts/, '/')
       },
       '^/api/*': {
         target: 'http://127.0.0.1:8001'

medcat-trainer/webapp/pyproject.toml

@@ -13,7 +13,7 @@ dependencies = [
     "djangorestframework>=3.16,<4",
     "django-background-tasks-updated>=1.2",
     "openpyxl>=3.1",
-    "medcat[meta-cat,spacy,rel-cat,deid]>=2.3",
+    "medcat[meta-cat,spacy,rel-cat,deid,dict-ner]>=2.7.0",
     "psycopg[binary,pool]>=3.2",
     "cryptography>=45",
     "drf-oidc-auth>=3.0",