remove all genome_browser code

api/prisma/migrations/20231213204322_remove_genome_browser/migration.sql

@@ -0,0 +1,8 @@
+/*
+  Warnings:
+
+  - You are about to drop the column `browser_enabled` on the `project` table. All the data in the column will be lost.
+
+*/
+-- AlterTable
+ALTER TABLE "project" DROP COLUMN "browser_enabled";

api/prisma/schema.prisma

@@ -214,7 +214,6 @@ model project {
   slug            String            @unique
   name            String
   description     String?
-  browser_enabled Boolean           @default(false)
   funding         String?
   metadata        Json?
   created_at      DateTime          @default(now()) @db.Timestamp(6)

api/prisma/seed_data/data.js

@@ -79,7 +79,6 @@ const _datasets = [
     archive_path: 'archive/2023/PCM230203.tar',
     workflows: ['6ca07614-bc84-4e5d-8808-71d0ebaef98b'],
     metadata: {
-      num_genome_files: 60,
       report_id: 'a577cb75-bb5c-4b1b-94ed-c4bd96de1188',
       stage_alias: 'ea497ac769f2236b6cd9ae70f288a008',
     },
@@ -97,7 +96,6 @@ const _datasets = [
     archive_path: 'archive/2023/PCM230327PL.tar',
     workflows: ['874a4b40-0534-44e3-b4ff-ae029cca5109'],
     metadata: {
-      num_genome_files: 12,
       report_id: '9b0b3fba-ccfd-4918-a5ff-ac93fa1a19ae',
     },
   },
@@ -114,7 +112,6 @@ const _datasets = [
     archive_path: 'archive/2023/PCM230215_657496842_Aborted_WF.tar',
     workflows: ['8afb902b-2ed3-47cd-9390-a262672d2d64'],
     metadata: {
-      num_genome_files: 0,
       report_id: null,
     },
     is_deleted: true,
@@ -133,7 +130,6 @@ const _datasets = [
     archive_path: 'archive/2023/PCM230306PL.tar',
     workflows: ['970e13dd-1905-493e-aa3a-13645bd439d9'],
     metadata: {
-      num_genome_files: 68,
       report_id: 'fa7d41f5-3813-43f6-9a72-5440ed6eac2b',
     },
   },
@@ -150,7 +146,6 @@ const _datasets = [
     origin_path: '/N/project/DG_Multiple_Myeloma/share/bcl_fastq',
     archive_path: 'archive/2023/bcl_fastq.tar',
     metadata: {
-      num_genome_files: 636,
     },
     workflows: ['63339ae0-9643-4d8b-aa3a-303434f6bdcd'],
   },
@@ -166,7 +161,6 @@ const _datasets = [
     origin_path: '/N/project/DG_Multiple_Myeloma/share/PCM221205',
     archive_path: 'archive/2023/PCM221205.tar',
     metadata: {
-      num_genome_files: 93,
     },
     workflows: ['02fc5cba-d4b8-4e74-8e0c-4e187c8e7f68'],
   },

api/src/routes/datasets.js

@@ -37,14 +37,7 @@ router.get(
     if (req.query.type) {
       result = await prisma.$queryRaw`
         select count(*)     as "count",
-        sum(du_size) as total_size,
-        SUM(
-                CASE
-                    WHEN metadata -> 'num_genome_files' IS NOT NULL
-                        THEN (metadata ->> 'num_genome_files')::int
-                    ELSE 0
-                    END
-            )        AS total_num_genome_files
+        sum(du_size) as total_size
         from dataset
         where is_deleted = false and type = ${req.query.type};
       `;
@@ -63,14 +56,7 @@ router.get(
       result = await prisma.$queryRaw`
         select 
           count(*) as "count", 
-          sum(du_size) as total_size, 
-          SUM(
-                CASE
-                    WHEN metadata -> 'num_genome_files' IS NOT NULL
-                        THEN (metadata ->> 'num_genome_files')::int
-                    ELSE 0
-                    END
-            )        AS total_num_genome_files
+          sum(du_size) as total_size
         from dataset 
         where is_deleted = false;
       `;

api/src/routes/projects.js

@@ -208,7 +208,6 @@ router.post(
   isPermittedTo('create'),
   validate([
     body('name').isLength({ min: 5 }),
-    body('browser_enabled').optional().toBoolean(),
   ]),
   asyncHandler(async (req, res, next) => {
     // #swagger.tags = ['Projects']
@@ -217,7 +216,7 @@ router.post(
     */
     const { user_ids, dataset_ids, ...projectData } = req.body;
     const data = _.flow([
-      _.pick(['name', 'description', 'browser_enabled', 'funding', 'metadata']),
+      _.pick(['name', 'description', 'funding', 'metadata']),
       _.omitBy(_.isNil),
     ])(projectData);
     data.slug = await projectService.generate_slug({ name: data.name });
@@ -462,7 +461,6 @@ router.patch(
   isPermittedTo('update'),
   validate([
     body('name').optional().isLength({ min: 5 }),
-    body('browser_enabled').optional().toBoolean(),
   ]),
   asyncHandler(async (req, res, next) => {
     // #swagger.tags = ['Projects']
@@ -471,7 +469,7 @@ router.patch(
     */
 
     const data = _.flow([
-      _.pick(['name', 'description', 'browser_enabled', 'funding', 'metadata']),
+      _.pick(['name', 'description', 'funding', 'metadata']),
       _.omitBy(_.isNil),
     ])(req.body);
 

ui/docs/util_components.md

@@ -78,7 +78,7 @@ Show data if it is neither null or undefined, else show default (provided it is
 
 ```html
 <template>
-  <Maybe :data="rowData?.metadata?.num_genome_files" />
+  <Maybe :data="rowData?.metadata?.num_files" />
 </template
 ```
 

ui/src/components/dashboard/Stats.vue

@@ -5,9 +5,7 @@
         <span class="text-xl"> {{ props.title }} </span>
       </va-card-title>
       <va-card-content>
-        <div
-          class="grid grid-cols-2 md:grid-cols-4 lg:grid-cols-2 gap-3 gap-y-5"
-        >
+        <div class="grid grid-cols-3 gap-3 gap-y-5">
           <div class="flex flex-col items-center justify-end">
             <h2
               v-if="props.data?.count != undefined"
@@ -44,24 +42,6 @@
             <p class="va-text-center no-wrap">Total Size</p>
           </div>
 
-          <div class="flex flex-col items-center justify-end">
-            <h2
-              v-if="props.data?.total_num_genome_files != undefined"
-              class="va-h3 ma-0 va-text-center"
-              :style="{ color: colors.success }"
-            >
-              {{ number_formatter.format(props.data.total_num_genome_files) }}
-            </h2>
-            <VaSkeleton
-              v-else
-              variant="rounded"
-              inline
-              width="64px"
-              height="32px"
-            />
-            <p class="va-text-center">Data Files</p>
-          </div>
-
           <div class="flex flex-col items-center justify-end">
             <h2
               v-if="props.data?.workflows != undefined"

ui/src/components/dataset/AssocDatasetList.vue

@@ -6,10 +6,6 @@
       </router-link>
     </template>
 
-    <template #cell(num_genome_files)="{ rowData }">
-      <Maybe :data="rowData?.metadata?.num_genome_files" />
-    </template>
-
     <template #cell(du_size)="{ source }">
       <span>{{ source != null ? formatBytes(source) : "" }}</span>
     </template>
@@ -21,9 +17,9 @@
 </template>
 
 <script setup>
-import { formatBytes } from "@/services/utils";
 import DatasetService from "@/services/dataset";
 import * as datetime from "@/services/datetime";
+import { formatBytes } from "@/services/utils";
 import { useToastStore } from "@/stores/toast";
 const toast = useToastStore();
 
@@ -46,12 +42,6 @@ const columns = ref([
     sortable: true,
     sortingOptions: ["desc", "asc", null],
   },
-  {
-    key: "num_genome_files",
-    label: "data files",
-    sortable: true,
-    sortingOptions: ["desc", "asc", null],
-  },
   {
     key: "du_size",
     label: "size",

ui/src/components/dataset/Dataset.vue

@@ -183,10 +183,6 @@
                     <i-mdi-harddisk class="text-xl" />
                     <span> {{ formatBytes(dataset.du_size) }} </span>
                   </div>
-                  <div class="flex items-center gap-1">
-                    <i-mdi-file-multiple class="text-xl" />
-                    <span> {{ dataset.metadata?.num_genome_files }} </span>
-                  </div>
                 </div>
               </div>
 
@@ -300,10 +296,10 @@
 </template>
 
 <script setup>
-import DatasetService from "@/services/dataset";
-import workflowService from "@/services/workflow";
 import config from "@/config";
+import DatasetService from "@/services/dataset";
 import { formatBytes } from "@/services/utils";
+import workflowService from "@/services/workflow";
 import { useToastStore } from "@/stores/toast";
 const toast = useToastStore();
 const router = useRouter();

ui/src/components/dataset/DatasetInfo.vue

@@ -43,10 +43,7 @@
           <td>Files</td>
           <td>{{ props.dataset.num_files }}</td>
         </tr>
-        <tr>
-          <td>Genome Files</td>
-          <td>{{ props.dataset.metadata?.num_genome_files }}</td>
-        </tr>
+
         <tr>
           <td>Directories</td>
           <td>{{ props.dataset.num_directories }}</td>
@@ -65,8 +62,8 @@
 </template>
 
 <script setup>
-import { formatBytes } from "@/services/utils";
 import * as datetime from "@/services/datetime";
+import { formatBytes } from "@/services/utils";
 
 const props = defineProps({ dataset: Object });
 

ui/src/components/dataset/DatasetList.vue

@@ -60,10 +60,6 @@
         </span>
       </template>
 
-      <template #cell(num_genome_files)="{ rowData }">
-        <Maybe :data="rowData?.metadata?.num_genome_files" />
-      </template>
-
       <template #cell(updated_at)="{ value }">
         <span>{{ datetime.fromNow(value) }}</span>
       </template>
@@ -202,10 +198,10 @@
 </template>
 
 <script setup>
+import useSearchKeyShortcut from "@/composables/useSearchKeyShortcut";
 import DatasetService from "@/services/dataset";
-import { formatBytes } from "@/services/utils";
 import * as datetime from "@/services/datetime";
-import useSearchKeyShortcut from "@/composables/useSearchKeyShortcut";
+import { formatBytes } from "@/services/utils";
 import { useToastStore } from "@/stores/toast";
 import _ from "lodash";
 
@@ -289,11 +285,6 @@ const columns = [
     width: "150px",
   },
   // { key: "status", sortable: false },
-  {
-    key: "num_genome_files",
-    label: "data files",
-    width: "80px",
-  },
   {
     key: "du_size",
     label: "size",

ui/src/components/project/CreateProjectStepper.vue

@@ -68,15 +68,6 @@
                     <td>Funding</td>
                     <td>{{ projectFormStore.project_info.funding }}</td>
                   </tr>
-
-                  <tr>
-                    <td>Genome Browser</td>
-                    <td>
-                      <BinaryStatusChip
-                        :status="projectFormStore.project_info.browser_enabled"
-                      />
-                    </td>
-                  </tr>
                 </tbody>
               </table>
             </div>
@@ -120,8 +111,8 @@
 </template>
 
 <script setup>
-import { useProjectFormStore } from "@/stores/projects/projectForm";
 import projectService from "@/services/projects";
+import { useProjectFormStore } from "@/stores/projects/projectForm";
 
 const emit = defineEmits(["update"]);
 

ui/src/components/project/datasets/ProjectDatasetsTable.vue

@@ -78,10 +78,6 @@
       </div>
     </template> -->
 
-    <template #cell(metadata)="{ rowData }">
-      <maybe :data="rowData?.metadata?.num_genome_files" />
-    </template>
-
     <template #cell(du_size)="{ source }">
       <span>{{ source != null ? formatBytes(source) : "" }}</span>
     </template>
@@ -107,14 +103,14 @@
 </template>
 
 <script setup>
+import config from "@/config";
+import DatasetService from "@/services/dataset";
 import * as datetime from "@/services/datetime";
-import { formatBytes, cmp } from "@/services/utils";
+import { formatBytes } from "@/services/utils";
 import wfService from "@/services/workflow";
-import DatasetService from "@/services/dataset";
-import config from "@/config";
+import { useAuthStore } from "@/stores/auth";
 import { HalfCircleSpinner } from "epic-spinners";
 import { useColors } from "vuestic-ui";
-import { useAuthStore } from "@/stores/auth";
 
 const { colors } = useColors();
 const auth = useAuthStore();
@@ -208,13 +204,6 @@ const columns = [
     label: "last updated",
     sortable: true,
   },
-  {
-    key: "metadata",
-    label: "data files",
-    sortable: true,
-
-    sortingFn: (a, b) => cmp(a?.num_genome_files, b?.num_genome_files),
-  },
   {
     key: "du_size",
     label: "size",

ui/src/components/project/info/ProjectInfo.vue

@@ -42,12 +42,6 @@
             </span>
           </td>
         </tr>
-        <tr>
-          <td>Genome Browser</td>
-          <td>
-            <BinaryStatusChip :status="props.project.browser_enabled" />
-          </td>
-        </tr>
         <tr>
           <td>Description</td>
           <td>