some fixes, ready to release

README.md

@@ -5,16 +5,13 @@ This project aims to provide a user-friendly interface to show and manage biodiv
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10363191.svg)](https://doi.org/10.5281/zenodo.10363191)
 
 
-## Online instances
-* [CBP](https://dades.biogenoma.cat)
-* [EBP](https://ebp.biogenoma.cat/)
+## API specs and Instances
 
-## API specs
-[API](https://guigolab.github.io/biogenome-portal/)
+See the API specs [here](https://guigolab.github.io/biogenome-portal/)
 
-## Full Documentation
+## Docs
 
-Full documentation is now [HERE](https://github.com/guigolab/biogenome-portal/wiki)
+Full documentation is now [here](https://github.com/guigolab/biogenome-portal/wiki)
 
 <!-- CONTRIBUTING -->
 ## Contributing
@@ -30,14 +27,10 @@ Don't forget to give the project a star! Thanks again!
 4. Push to the Branch (`git push origin feature/AmazingFeature`)
 5. Open a Pull Request
 
-<!-- LICENSE -->
 ## License
 
 Distributed under the MIT License. See `LICENSE.txt` for more information.
 
-<p align="right">(<a href="#top">back to top</a>)</p>
-
-<!-- CONTACT -->
 ## Contact
 
 Emilio Righi - emilio.righi@crg.eu

biogenome-client/src/components/charts/BarChart.vue

@@ -33,7 +33,7 @@ await fetchData()
 
 
 const chartOptions = computed(() => {
-    const total = itemStore.stores[model].total || Object.values(data.value).reduce((acc, val) => acc + val, 0)
+    const total = Object.values(data.value).reduce((acc, val) => acc + val, 0)
     return getChartOptions(type, total)
 })
 const chartData = computed(() => {

biogenome-client/src/components/charts/PieChart.vue

@@ -34,7 +34,7 @@ await fetchData()
 
 
 const chartOptions = computed(() => {
-  const total = itemStore.stores[model].total || Object.values(data.value).reduce((acc, val) => acc + val, 0)
+  const total = Object.values(data.value).reduce((acc, val) => acc + val, 0)
   return getChartOptions(type, total)
 })
 const chartData = computed(() => {

biogenome-client/src/layouts/Layout.vue

@@ -27,13 +27,21 @@ import { useBreakpoint } from 'vuestic-ui'
 import { useGlobalStore } from "../stores/global-store"
 import NavBar from '../components/navbar/Navbar.vue'
 import Sidebar from '../components/sidebar/Sidebar.vue'
-import { onMounted } from 'vue';
+import { onMounted, watch } from 'vue';
+import { useItemStore } from '../stores/items-store';
+import { useRoute } from 'vue-router';
 
+const itemStore = useItemStore()
 const globalStore = useGlobalStore()
 const breakpoints = useBreakpoint()
+const route = useRoute()
 
 onMounted(async () => {
     if (!globalStore.isAuthenticated) await globalStore.checkUserIsLoggedIn()
 })
 
+watch(() => route.name, () => {
+    itemStore.isDashBoard = route.name === 'dashboard'
+})
+
 </script>

biogenome-client/src/pages/cms/annotation/components/FileForm.vue

@@ -62,6 +62,7 @@ import { useAnnotationStore } from '../../../../stores/annotation-store'
 import AuthService from '../../../../services/clients/AuthService'
 import AnnotationService from '../../../../services/clients/AnnotationService'
 import { AxiosError } from 'axios'
+import { useRouter } from 'vue-router'
 
 const { init } = useToast()
 const annotationStore = useAnnotationStore()
@@ -74,6 +75,7 @@ const props = defineProps<{
     name?: string
 }>()
 
+const router = useRouter()
 const emits = defineEmits(['onLoading'])
 
 watch(() => props.name, (v) => {
@@ -135,7 +137,8 @@ async function handleSubmit() {
     try {
         emits('onLoading', true)
         const { data } = props.name ? await AuthService.updateAnnotation(props.name, requestData) : await AuthService.createAnnotation(requestData)
-        init({ message: data, color: 'success' })
+        init({ message: data  + ' saved!', color: 'success' })
+        router.push({name:'cms-assemblies'})
     } catch (error) {
         const axiosError = error as AxiosError
         if (axiosError.response && axiosError.response.data) {

biogenome-client/src/pages/cms/assembly/Assemblies.vue

@@ -3,33 +3,21 @@
     <p class="mb-4">Add genome annotations, chromosome aliases or delete assemblies </p>
     <va-form @submit.prevent="handleSubmit">
         <div class="row align-end">
-            <va-input v-model="filter" label="search assembly" class="flex lg4 md4 sm12 xs12"></va-input>
             <div class="flex">
-                <va-checkbox indeterminate v-model="hasAliases" label="Has chromosome aliases?"></va-checkbox>
+                <va-input v-model="filter" label="search assembly"/>
             </div>
             <div class="flex">
-                <va-button icon="search" @click="handleSubmit"> </va-button>
-                <va-button icon="cancel" color="danger" @click="reset"> </va-button>
+                <va-button icon="search" @click="handleSubmit">Search </va-button>
+            </div>
+            <div class="flex">
+                <va-button style="margin-left: 3px;" icon="cancel" color="danger" @click="reset"> Reset </va-button>
             </div>
         </div>
     </va-form>
-    <va-data-table :items="assemblies"
-        :columns="['accession', 'scientific_name', 'assembly_name', 'metadata.assembly_info.assembly_level', 'chromosome_aliases', 'delete']">
+    <va-data-table :items="assemblies" :columns="['accession', 'scientific_name', 'assembly_name', 'delete']">
         <template #cell(delete)="{ rowData }">
             <va-icon color="danger" name="delete" @click="deleteConfirmation(rowData)" />
         </template>
-        <template #cell(chromosome_aliases)="{ rowData }">
-            <div class="row">
-                <div v-if="rowData.has_chromosomes_aliases" class="flex">
-                    <va-button size="small" :href="`${baseURL}/assemblies/${rowData.accession}/chr_aliases`"
-                        icon="download"></va-button>
-                </div>
-                <div v-if="rowData.metadata && rowData.metadata.assembly_info.assembly_level === 'Chromosome'" class="flex">
-                    <va-button :to="{ name: 'chr-aliases', params: { accession: rowData.accession } }" size="small"
-                        icon="add" />
-                </div>
-            </div>
-        </template>
     </va-data-table>
     <div class="row justify-center">
         <div class="flex">
@@ -56,9 +44,6 @@ import AssemblyService from '../../../services/clients/AssemblyService'
 import AuthService from '../../../services/clients/AuthService'
 import { useToast } from 'vuestic-ui/web-components'
 
-const baseURL = import.meta.env.VITE_BASE_PATH ? import.meta.env.VITE_BASE_PATH + '/api' : '/api'
-
-
 const { init } = useToast()
 const initPagination = {
     offset: 0,

biogenome-client/src/router/cms-routes.ts

@@ -81,13 +81,6 @@ export const cmsRoutes = [
                 beforeEnter: [isAdmin],
                 component: () => import('../pages/cms/annotation/AnnotationForm.vue'),
             },
-            {
-                name: 'chr-aliases',
-                path: 'chr-aliases/:accession',
-                props: true,
-                beforeEnter: [isAdmin],
-                component: () => import('../pages/cms/uploads/ChrAliasesForm.vue')
-            },
             {
                 name: 'insdc-form',
                 path: 'insdc-form',

biogenome-client/src/services/clients/AuthService.js

@@ -78,9 +78,6 @@ class AuthService {
   importAssembly(accession) {
     return auth.post(`/assemblies/${accession}`)
   }
-  uploadRefNameAliases(accession, formData) {
-    return auth.post(`/assemblies/${accession}/chr_aliases`, formData)
-  }
   deleteAssembly(accession) {
     return auth.delete(`/assemblies/${accession}`)
   }

biogenome-client/src/stores/items-store.ts

@@ -76,6 +76,7 @@ export const useItemStore = defineStore('item', {
             showChartModal: false,
             currentModel: "",
             isTableLoading: false,
+            isDashBoard: false,
             isTSVLoading: false,
             toast: useToast().init
         }
@@ -118,11 +119,16 @@ export const useItemStore = defineStore('item', {
         //incoming model may not correspond to currentModel
         async getStats(model: string, field: string) {
             try {
-                //filter out filter, and sort fields
-                const filteredEntries = Object.entries(this.stores[model].searchForm).filter(([k, v]) => !Object.keys(staticFilters).includes(k))
-                const query = Object.fromEntries(filteredEntries)
-                if (this.country) query['countries'] = this.country
-                if (this.parentTaxon) query['taxon_lineage'] = this.parentTaxon
+                let query = {}
+                if (!this.isDashBoard) {
+
+                    const filteredEntries = Object.entries(this.stores[model].searchForm).filter(([k, v]) => !Object.keys(staticFilters).includes(k))
+                    if (this.country) filteredEntries.push(['countries', this.country])
+                    if (this.parentTaxon) filteredEntries.push(['taxon_lineage', this.parentTaxon])
+
+                    query = Object.fromEntries(filteredEntries)
+                }
+
 
                 const { data } = await StatisticsService.getModelFieldStats(model, field, query)
                 return data

server/db/enums.py

@@ -26,6 +26,7 @@ class INSDCStatus(Enum):
     SAMPLE = 'Biosample Submitted'
     READS = 'Reads Submitted'
     ASSEMBLIES = 'Assemblies Submitted'
+    ANNOTATIONS = 'Annotation Completed'
 
 class Roles(Enum):
     ##CRUD LOCAL_SAMPLES

server/helpers/assembly.py

@@ -18,8 +18,6 @@ def save_chromosomes(assembly_obj):
             new_chromosomes = [chr for chr in chromosomes_to_save if chr.accession_version and chr.accession_version not in existing_chromosomes]
             if new_chromosomes:
                 print(f"Saving a total of {len(new_chromosomes)} chromosomes")
-
                 Chromosome.objects.insert(new_chromosomes)
-            assembly_obj.chromosomes = [chr.accession_version for chr in chromosomes_to_save if chr.accession_version]
     else:
         print(f"Chromosomes not found for {accession}")

server/jobs/assemblies.py

@@ -83,7 +83,7 @@ def import_assemblies_by_bioproject(project_accession=None):
         except Exception as e:
             print(e)
             print(f"Impossible to save assembly {new_accession}, 'skipping it..")
-            Chromosome.objects(accession_version__in=parsed_assembly.chromosomes).delete()
+            Chromosome.objects(metadata__assembly_accession=new_accession).delete()
             continue
 
     print(f"Job executed. Saved {saved_assemblies} out of {new_ids_length}")

server/rest/assembly/assemblies_controller.py

@@ -36,12 +36,6 @@ class AssemblyChrAliasesApi(Resource):
     def get(self,accession):
         return assemblies_service.get_chr_aliases_file(accession)
 
-    @data_manager_required()
-    @jwt_required()
-    def post(self,accession):
-        msg = assemblies_service.store_chromosome_aliases(accession, request)
-        return Response(json.dumps(msg), mimetype="application/json", status=200)
-
 class AssembliesRelatedChromosomesApi(Resource):
     def get(self,accession):
         chromosomes = assemblies_service.get_related_chromosomes(accession)

server/rest/assembly/assemblies_service.py

@@ -7,8 +7,11 @@
 import io
 
 def get_related_chromosomes(accession):
-    assembly = get_assembly(accession)
-    return Chromosome.objects(accession_version__in=assembly.chromosomes).exclude('id')
+    ass = get_assembly(accession)
+    chromosomes = Chromosome.objects(metadata__assembly_accession=accession)
+    if not chromosomes.count():
+        chromosomes = Chromosome.objects(accession_version__in=ass.chromosomes)
+    return chromosomes.exclude('id')
 
 def get_assemblies(args):
     return data.get_items('assemblies', args)
@@ -77,28 +80,35 @@ def delete_assembly(accession):
 
     return accession
 
-def store_chromosome_aliases(accession, request):
-    assembly = get_assembly(accession)
-    aliases_file = request.files.get('chr_aliases')
-    if not aliases_file:
-        raise BadRequest(description=f"chr_aliases file is required!")
-
-    assembly.chromosomes_aliases = aliases_file.read()
-    assembly.has_chromosomes_aliases = True
-    assembly.save()
-    return "Chromosome aliases successfully updated"
 
 def get_related_annotations(accession):
     get_assembly(accession)
     return GenomeAnnotation.objects(assembly_accession=accession).exclude('id','created').to_json()
 
 def get_chr_aliases_file(accession):
     assembly_obj = get_assembly(accession)
-    if not assembly_obj.has_chromosomes_aliases:
-        raise BadRequest(description=f"Assembly {accession} lacks of chromosome aliases file")
+
+    # Query chromosomes based on accession_version
+    chromosomes = Chromosome.objects(accession_version__in=assembly_obj.chromosomes).as_pymongo()
+
+    if not chromosomes:
+        raise BadRequest(description=f"Assembly {accession} lacks chromosomes")
+
+    # Prepare the TSV data
+    tsv_data = io.StringIO()
+
+    # Assuming chromosomes is a list of dictionaries with fields 'name' and 'accession_version'
+    for chromosome in chromosomes:
+        chr_name = chromosome.get('metadata', {}).get('name')
+        accession_version = chromosome.get('accession_version')
+        tsv_data.write(f"{chr_name}\t{accession_version}\n")
+
+    tsv_data.seek(0)  # Go back to the start of the StringIO object
+
+    # Send the TSV as a downloadable file
     return send_file(
-    io.BytesIO(assembly_obj.chromosomes_aliases),
-    mimetype='text/plain',
-    as_attachment=True,
-    download_name=f'{assembly_obj.accession}_chr_aliases.txt')
-
+        io.BytesIO(tsv_data.getvalue().encode('utf-8')),  # Convert StringIO to bytes
+        mimetype='text/tab-separated-values',
+        as_attachment=True,
+        download_name=f'{assembly_obj.accession}_chr_aliases.tsv'
+    )

server/rest/stats/stats_controller.py

@@ -6,6 +6,6 @@
 
 class FieldStatsApi(Resource):
     def get(self, model, field):
-        resp,status = stats_service.get_stats(model, field, request.args)
-        return Response(json.dumps(resp, default=str),mimetype="application/json", status=status)
+        json_resp,status = stats_service.get_stats(model, field, request.args)
+        return Response(json_resp,mimetype="application/json", status=status)
 

server/rest/stats/stats_service.py

@@ -49,8 +49,7 @@ def get_stats(model, field, query):
         }
         # Sort the response dictionary
         sorted_response = {key : response[key] for key in sorted(response)}
-
-        return sorted_response, 200
+        return data_helper.dump_json(sorted_response), 200
 
     except Exception as e:
         print(e)