feat: Add page about version of services we use (#603) (#604)

backend/app/api/internal/api.py

@@ -1,7 +1,9 @@
+import datetime
 import subprocess
 
 from fastapi import APIRouter, Response
 from fastapi.responses import JSONResponse
+from pydantic import BaseModel
 
 from app.api.internal.endpoints import proxy, remote
 from app.core.config import settings
@@ -12,6 +14,184 @@
 api_router.include_router(remote.router, prefix="/remote", tags=["remote"])
 
 
+class DataVersions(BaseModel):
+    """Container with data versions."""
+
+    #: Annonars version.
+    annonars: str
+    #: Viguno version.
+    viguno: str
+    #: Mehari version.
+    mehari: str
+    #: Cada-prio version.
+    cada_prio: str
+    #: Dotty version.
+    dotty: str
+    #: Variant validator version.
+    variant_validator: str
+    #: InterVar version.
+    intervar: str
+    #: AutoCNV version.
+    autocnv: str
+    #: PubTator3 version.
+    pubtator3: str
+    #: Beacon Network version.
+    beacon_network: str
+    #: String to use for AlphaMissense version.
+    alphamissense: str
+    #: String to use for ClinGen gene curation version.
+    clingen_gene: str
+    #: String to use for ClinGen variant curation version.
+    clingen_variant: str
+    #: String to use for GRCh37 ENSEMBL version.
+    ensembl_37: str
+    #: String to use for GRCh38 ENSEMBL version.
+    ensembl_38: str
+    #: String to use for ENSEMBL version.
+    ensembl: str
+    #: Version of dbNSFP.
+    dbnsfp: str
+    #: Version of dbscSNV.
+    dbscsnv: str
+    #: Version of CADD.
+    cadd: str
+    #: Version of gnomAD for constraints.
+    gnomad_constraints: str
+    #: Version of gnomAD mtDNA.
+    gnomad_mtdna: str
+    #: Version of gnomAD v2.
+    gnomad_v2: str
+    #: Version of gnomAD v3.
+    gnomad_v3: str
+    #: Version of gnomAD v4.
+    gnomad_v4: str
+    #: Version of gnomAD SV.
+    gnomad_sv: str
+    #: Version of gnomAD CNV v4.
+    gnomad_cnv4: str
+    #: Version of gnomAD SV v4.
+    gnomad_sv4: str
+    #: Version of dbVar.
+    dbvar: str
+    #: Version of DGV.
+    dgv: str
+    #: Version of DGV Gold Standard.
+    dgv_gs: str
+    #: ExAC CNVs.
+    exac_cnv: str
+    #: Thousand Genomes SVs.
+    g1k_svs: str
+    #: HelixMtDb
+    helixmtdb: str
+    #: UCSC conservation (GRCh37).
+    ucsc_cons_37: str
+    #: UCSC conservation (GRCh38).
+    ucsc_cons_38: str
+    #: UCSC repeat masker (GRCh37).
+    ucsc_rmsk_37: str
+    #: UCSC repeat masker (GRCh38).
+    ucsc_rmsk_38: str
+    #: UCSC genomicSuperDups (GRCh37).
+    ucsc_genomic_super_dups_37: str
+    #: UCSC genomicSuperDups (GRCh38).
+    ucsc_genomic_super_dups_38: str
+    #: UCSC genome browser altSeqLiftOverPsl (GRCh37).
+    ucsc_alt_seq_liftover_37: str
+    #: UCSC genome browser altSeqLiftOverPsl (GRCh38).
+    ucsc_alt_seq_liftover_38: str
+    #: UCSC genome browser fixSeqLiftOverPsl (GRCh37).
+    ucsc_fix_seq_liftover_37: str
+    #: UCSC genome browser fixSeqLiftOverPsl (GRCh38).
+    ucsc_fix_seq_liftover_38: str
+    #: RefSeq version (GRCh37).
+    refseq_37: str
+    #: RefSeq version (GRCh38).
+    refseq_38: str
+    #: dbSNP version.
+    dbsnp: str
+    #: ACMG secondary findings version.
+    acmg_sf: str
+    #: HPO
+    hpo: str
+    #: Orphadata
+    orphadata: str
+    #: Pathogenic MMS
+    patho_mms: str
+    #: Mehari transcript data.
+    mehari_tx: str
+    #: ClinVar release.
+    clinvar_release: str
+    #: ClinVar version.
+    clinvar_version: str
+    #: RefSeq functional elements for GRCh37.
+    refseq_fe_37: str
+    #: RefSeq functional elements for GRCh38.
+    refseq_fe_38: str
+
+
+#: The current date.
+TODAY = datetime.date.strftime(datetime.date.today(), "%Y%m%d")
+
+#: The data versions to use.
+DATA_VERSIONS = DataVersions(
+    annonars="0.2.1",
+    viguno="0.36.1",
+    mehari="0.25.4",
+    cada_prio="0.6.1",
+    dotty="0.4.1",
+    variant_validator="2.2.1",
+    intervar="2021-08",
+    autocnv="latest",
+    pubtator3="latest",
+    beacon_network="latest",
+    alphamissense="1",
+    clingen_gene=TODAY,
+    clingen_variant=TODAY,
+    ensembl_37="87",
+    ensembl_38="109",
+    ensembl="111",
+    dbnsfp="4.5",
+    dbscsnv="1.1",
+    cadd="1.6",
+    gnomad_constraints="4.0",
+    gnomad_mtdna="3.1",
+    gnomad_v2="2.1.1",
+    gnomad_v3="3.1.2",
+    gnomad_v4="4.0",
+    gnomad_sv="2.1.1",
+    gnomad_cnv4="4.0",
+    gnomad_sv4="4.0",
+    dbvar="20231030",
+    dgv="20200225",
+    dgv_gs="20160515",
+    exac_cnv="0.3.1",
+    g1k_svs="phase3v2",
+    helixmtdb="20200327",
+    ucsc_cons_37="20161007",
+    ucsc_cons_38="20190906",
+    ucsc_rmsk_37="20200322",
+    ucsc_rmsk_38="20221018",
+    ucsc_genomic_super_dups_37="20111025",
+    ucsc_genomic_super_dups_38="20141019",
+    ucsc_alt_seq_liftover_37="20200322",
+    ucsc_alt_seq_liftover_38="20221103",
+    ucsc_fix_seq_liftover_37="20200524",
+    ucsc_fix_seq_liftover_38="20221103",
+    refseq_37="105",
+    refseq_38="GCF_000001405.40+RS_2023_03",
+    dbsnp="b151",
+    acmg_sf="3.1",
+    hpo="20240116",
+    orphadata=TODAY,
+    patho_mms="20220730",
+    mehari_tx="0.4.4",
+    clinvar_release="2023_09",
+    clinvar_version="v2.0",
+    refseq_fe_37="105.20201022",
+    refseq_fe_38="110",
+)
+
+
 @api_router.get("/version")
 @api_router.post("/version")
 async def version():
@@ -42,3 +222,15 @@ async def frontend_settings():
         "matomo_site_id": settings.MATOMO_SITE_ID,
     }
     return JSONResponse(content=frontend_settings)
+
+
+@api_router.get("/data-versions")
+@api_router.post("/data-versions")
+async def data_versions():
+    """
+    Return versions of data and services used in the application.
+
+    :return: A JSON response containing the versions of various data and services.
+    :rtype: dict
+    """
+    return JSONResponse(content=DATA_VERSIONS.dict())

frontend/src/api/misc/api.ts

@@ -17,4 +17,11 @@ export class MiscClient {
     })
     return await response.text()
   }
+
+  async fetchDataVersions(): Promise<any> {
+    const response = await fetch(`${this.apiBaseUrl}data-versions`, {
+      method: 'GET'
+    })
+    return await response.json()
+  }
 }

frontend/src/components/PageHeader/PageHeader.vue

@@ -112,6 +112,9 @@ function toggleTheme() {
           <v-list-item id="terms" to="/info#terms-of-use">
             <v-list-item-title> Terms of Use </v-list-item-title>
           </v-list-item>
+          <v-list-item id="data-versions" to="/info#data-versions">
+            <v-list-item-title> Data Versions </v-list-item-title>
+          </v-list-item>
         </v-list>
       </v-menu>
     </v-container>

frontend/src/components/StaticViews/DataVersionsView.spec.ts

@@ -0,0 +1,34 @@
+import { setupMountedComponents } from '@bihealth/reev-frontend-lib/lib/testUtils'
+import { describe, it, vi } from 'vitest'
+
+import { StoreState } from '@/stores'
+
+import DataVersionsView from './DataVersionsView.vue'
+
+describe.concurrent('DataVersionsView', async () => {
+  it.skip('renders the main content', async () => {
+    // arrange:
+    const mockInitialize = vi.fn().mockImplementation(async () => {})
+    const { wrapper } = await setupMountedComponents(
+      { component: DataVersionsView },
+      {
+        initialStoreState: {
+          misc: {
+            storeState: StoreState.Active,
+            appVersion: 'v0.0.0',
+            dataVersions: {
+              alphamissense: '2021-01-01',
+              clingen_gene: '2021-01-01'
+            },
+            initialize: mockInitialize
+          }
+        }
+      }
+    )
+
+    // act: nothing, only test rendering
+
+    // assert:
+    console.log(wrapper.html())
+  })
+})

frontend/src/components/StaticViews/DataVersionsView.vue

@@ -0,0 +1,62 @@
+<script setup lang="ts">
+import { onMounted, ref } from 'vue'
+
+import { useMiscStore } from '@/stores/misc'
+
+const miscStore = useMiscStore()
+
+/** Data version to display. */
+const transformedDataVersions = ref<{ name: string; version: string }[]>([])
+
+/** Define table headers */
+const headers = ref([
+  { text: 'Resource', value: 'name' },
+  { text: 'Version', value: 'version' }
+])
+
+const initializeDataVersions = async () => {
+  await miscStore.initialize()
+  const transformDataVersions = () => {
+    if (miscStore.dataVersions) {
+      return Object.entries(miscStore.dataVersions).map(([name, version]) => ({
+        name,
+        version: version ? String(version) : ''
+      }))
+    } else {
+      return []
+    }
+  }
+  transformedDataVersions.value = transformDataVersions()
+}
+
+onMounted(initializeDataVersions)
+</script>
+
+<template>
+  <v-card>
+    <v-card-title>Data Sources</v-card-title>
+    <v-card-subtitle>
+      The following data sources and service versions are used in REEV application.
+    </v-card-subtitle>
+    <v-card-text>
+      <div v-if="transformedDataVersions && transformedDataVersions.length > 0"></div>
+      <v-table>
+        <thead>
+          <tr>
+            <!-- Table Headers -->
+            <th v-for="header in headers" :key="header.value">
+              {{ header.text }}
+            </th>
+          </tr>
+        </thead>
+        <tbody>
+          <!-- Table Rows -->
+          <tr v-for="(item, index) in transformedDataVersions" :key="index">
+            <td>{{ item.name }}</td>
+            <td>{{ item.version }}</td>
+          </tr>
+        </tbody>
+      </v-table>
+    </v-card-text>
+  </v-card>
+</template>

frontend/src/stores/misc/store.spec.ts

@@ -28,15 +28,23 @@ describe('miscInfo Store', () => {
 
   it('should load data', async () => {
     // arrange:
-    fetchMocker.mockResponseOnce('v0.0.0')
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('version') && !req.url.includes('data')) {
+        return Promise.resolve(JSON.stringify('v0.0.0'))
+      } else if (req.url.includes('data')) {
+        return Promise.resolve(JSON.stringify({ dataVersions: { data: 'versions' } }))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
     const store = useMiscStore()
 
     // act:
     await store.initialize()
 
     // assert:
     expect(store.storeState).toBe(StoreState.Active)
-    expect(store.appVersion).toBe('v0.0.0')
+    expect(store.appVersion).toBe('"v0.0.0"')
+    expect(store.dataVersions).toStrictEqual({ dataVersions: { data: 'versions' } })
   })
 
   it('should handle error', async () => {