add dev configs and db dump to seed db, disclaimer, update readme. Re…

…ady for first release

.env

@@ -1,9 +1,23 @@
 DB_NAME=biogenome-db
 DB_USER=biogenome-user
 DB_PASS=biogenome-password
-DB_HOST=mydatabase
+
+# declare production db host here
+# DB_PROD_HOST=
+
+# default dev db host
+DB_DEV_HOST=mydev-db
+
 DB_PORT=27017
+DB_DUMP=dump_2022-05-18.gz
 
+MONGO_INITDB_ROOT_USERNAME=root
+MONGO_INITDB_ROOT_PASSWORD=root
+MONGO_INITDB_DATABASE=admin
+MONGODB_DATA_DIR=/var/lib/mongodb-data
+MONDODB_LOG_DIR=/dev/null
+
+# change to 'production' or null in prod!!
 FLASK_ENV=development
 APP_NAME=RNAmaps
 API_PORT=80
@@ -14,6 +28,8 @@ THREADS=2
 USR=admin
 JWT_SECRET_KEY=secret_restKey 
 RESTKEY=secretPassword
+
+
 PROJECT_ACCESSION=PRJNA533106
 PROJECTS=DTOL, VGP
 EXEC_TIME=600

README.md

@@ -85,27 +85,31 @@ This project is built with the following stack:
 <!-- GETTING STARTED -->
 ## Getting Started
 
-Before building the application it is necessary to configure the .env file in the project's root directory:
-The .env file contains many parts that have to be configured depending on the needs:
+By default the portal is configured to retrieve public data under the EBP umbrella (https://www.earthbiogenome.org/) it will load (at building stage) and seed the database with the last dump (/dump-db directory)
 
-	The API KEY part:
-  	Configure this part if you want to enter samples locally
+If you want to customize the portal follow the steps below:
 
-	USER=admin --> Define the user name that will be inserted to access the admin area
-	JWT_SECRET_KEY=secret_restKey #change this in production!! --> key to encrypt the RESTKEY (below)
-	RESTKEY=secretPassword #change this in production!! --> password that will be inserted to access the admin area
+  General configurations:
+  - Set the ROOT_NODE env variable with the Taxon name you want to use as a root (default: Eukaryota)
+
+  Public data management:
+  - in the .env file insert the PROJECT_ACCESSION (The INSDC BioProject accession) of the project you want to use as a root:
+      if the bioproject you want to use as a root is not under the EBP umbrella, you have to comment the volumes of the biogenome_mongo service in the docker-compose-dev file:
+                  - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh
+                  - ./mongo-restore.sh:/docker-entrypoint-initdb.d/mongo-restore.sh
+                  - ./db-dump:/db-dump
+  - if the same project or sub projects are defined as attributes of the sample metadata (ex: project name: 'YOUR_PROJECT_NAME') submitted in INSDC, set the list of comma separated project names in the PROJECTS env variable (default values: VGP(https://vertebrategenomesproject.org/), DTOL(https://www.darwintreeoflife.org/)) 
+
+  -EXEC_TIME: how often, in seconds, the job should be performed it does nothing if PROJECTS OR PROJECT_ACCESSION are empty
 
-	The CRONJOB part:
-  Configure this part if you want to retrieve public data from ENA/BioSamples and/or NCBI (the sample metadata format must be compliant with the ENA checklist).
-	The cronjob will automatically check for read data in ENA if PROJECTS and/or PROJECT_ACCESSION are present
-	PROJECTS=  --> list of projects (comma separated) wich name figures in the sample metadata submitted to the ENA/BioSamples
-	PROJECT_ACCESSION --> bioproject accession to retrieve data from NCBI 
-	EXEC_TIME=600 --> how often, in seconds, the job should be performed
+  NOTE: if you are just interested in local data management remove the default values of PROJECTS and PROJECT_ACCESSION
 
-	The DATA PORTAL part:
-  	This part have some default values that can be modified
+  Local data management:
 
-    ROOT_NODE=the INSDC bioproject acccession which will be used as the root project of the application
+  Configure this part if you want to enter samples locally
+	USR=admin --> Define the user name that will be inserted to access the admin area
+	JWT_SECRET_KEY=secret_restKey #change this in production!! --> key to encrypt the RESTKEY (below)
+	RESTKEY=secretPassword #change this in production!! --> password that will be inserted to access the admin area
 
 
 To add a custom logo and an icon follow this steps:
@@ -129,12 +133,14 @@ To get a local copy up and running follow these simple example steps.
 
 ### Installation
 
-You need to have docker compose installed (https://docs.docker.com/compose/)
+You need to have docker compose installed (https://docs.docker.com/compose/). 
 
-1. Configure the .env file as above
-2. Run this command in the root directory:
-	sudo docker-compose -f docker-compose.yml up --build
-3. To start creating data go to: /admin from the home page and login
+1. Run this command in the root directory:
+	sudo docker-compose -f docker-compose.dev.yml up --build
+
+  This will load the last generated db dump containing all the public data under the EBP scope (https://www.earthbiogenome.org/)
+
+2. To start creating data go to: /admin from the home page and login
 
 
 <p align="right">(<a href="#top">back to top</a>)</p>
@@ -175,11 +181,10 @@ The import function uses the BioSamples API to retrieve samples metadata via the
 ## Roadmap
 
 - [ ] Add Changelog
-- [ ] Add JSON schema (OAS docs)
-- [X] Add local names management
-- [X] Add organism photo management
-- [X] Add sample accession import feature
-- [ ] Add custom fields management
+- [ ] Add API Documentation
+- [ ] Add tests (I know..)
+
+
 
 
 

client/src/App.vue

@@ -4,6 +4,21 @@
     <b-overlay :show="loading">
     <b-container fluid class="router-container">
       <b-row>
+        <b-col lg="6">
+          <b-alert dismissible show variant="success">
+            <p>
+              This data portal is an instance of the <a href="https://github.com/guigolab/biogenome-portal" class="alert-link">BioGenome portal</a> software.
+            </p>
+            <p>
+              It tracks the <a href="https://www.insdc.org/" class="alert-link">INSDC</a> public data under the <a href="https://www.earthbiogenome.org/" class="alert-link">Earth BioGenome Project</a> umbrella.
+            </p>
+            <hr>
+            <p class="mb-0">
+              <strong>IMPORTANT</strong>: This is <strong>NOT</strong> the official data portal of the Earth BioGenome Project.
+              Refer to <a href="https://goat.genomehubs.org/" class="alert-link">GoaT</a> to view the Earth BioGenome Project sequencing progress.
+            </p>
+          </b-alert>
+        </b-col>
         <alert-component/>
       </b-row>
       <b-row>
@@ -25,7 +40,7 @@
 </template>
 
 <script>
-import {BOverlay} from 'bootstrap-vue'
+import {BOverlay,BAlert} from 'bootstrap-vue'
 import BreadCrumbComponent from './components/base/BreadCrumbComponent.vue';
 import NavBarComponent from './components/base/NavBarComponent.vue'
 import AlertComponent from './components/base/AlertComponent.vue';
@@ -42,6 +57,7 @@ components: {
   NavBarComponent,
   BreadCrumbComponent,
   BOverlay,
+  BAlert,
   AlertComponent,
   LoginModal,
   }

client/src/components/data/AnnotationsComponent.vue

@@ -1,21 +1,26 @@
 <template>
 <div ref="annotationsTable">
-  <table-component stacked :sticky-header="stickyHeader" :items="annotations">
+  <table-component stacked :sticky-header="stickyHeader" :items="annotations" :fields="fields">
     <template #cell(pageURL)="data">
-        <b-link class="no-underline" target="_blank" :href="data.value">Genome browser</b-link>
+        <b-link class="no-underline" target="_blank" :href="data.value">Open</b-link>
     </template>
     <template #cell(gffGzLocation)="data">
-        <b-link class="no-underline" target="_blank" :href="data.value">GFF3</b-link>
+        <b-link class="no-underline" target="_blank" :href="data.value">Download</b-link>
     </template>
         <template #cell(tabIndexLocation)="data">
-        <b-link class="no-underline" target="_blank" :href="data.value">GFF3 (Tabix)</b-link>
+        <b-link class="no-underline" target="_blank" :href="data.value">Download</b-link>
     </template>
-    <template #cell(targetGenome)="data">
+    <template #cell(assemblyAccession)="data">
         <b-link class="no-underline" target="_blank" :href="'https://www.ebi.ac.uk/ena/browser/view/' + data.value">{{data.value}}</b-link>
     </template>
     <template #cell(annotationSource)="data">
         <b-link class="no-underline" target="_blank" :href="data.value">{{data.value}}</b-link>
     </template>
+    <template #cell(evidenceSource)="data">
+        <div v-for="value in data.value.split('.')" :key="value">
+            {{value}}
+        </div>
+    </template>
 </table-component>
 </div>
 </template>
@@ -27,6 +32,20 @@ import TableComponent from '../base/TableComponent.vue'
 export default{
   components: { TableComponent,BLink },
   props: ['annotations'],
+  data(){
+      return {
+          fields:[
+              {key:'name', label: 'Name'},
+              {key:'gffGzLocation', label: 'GFF3 (.gz)'},
+              {key:'tabIndexLocation', label: 'GFF3 (gz.tbi)'},
+              {key:'pageURL', label: 'Genome Browser'},
+              {key:'annotationSource', label: 'Annotation Pipeline'},
+              {key:'evidenceSource', label: 'Evidence Source'},
+              {key:'targetGenome', label: 'Assembly Name'},
+              {key:'assemblyAccession', label: 'Assembly Accession'}
+          ]
+      }
+  }
 }
 </script>
 <style>

client/src/components/organism/OrganismFilterComponent.vue

@@ -20,7 +20,7 @@
             <b-tooltip target="switch-description">
                Retrieve only selected data ex: retrieve <stong>only</stong> organisms with 'Submitted Samples' or <stong>only</stong> 'Submitted Samples' and 'Submitted Assemblies'
             </b-tooltip>
-            <b-form-checkbox-group :options="checkboxOptions" v-model="selectedCheckboxes"/>
+            <b-form-checkbox-group :options="checkboxOptions" v-model="selectedData"/>
             <b-icon-arrow-clockwise variant="primary" @mouseenter="animation='spin-pulse'" @mouseleave="animation=''" :animation="animation" font-scale="2" id="refresh-action" @click="resetFilters()"/>
             <b-tooltip target="refresh-action">
                 Refresh filters
@@ -37,52 +37,36 @@ import FilterComponent from '../base/FilterComponent.vue'
 import portalService from '../../services/DataPortalService'
 import {PROJECT_ACCESSION} from '../../utils/static-config'
 import MultiSelectComponent from '../base/MultiSelectComponent.vue'
-
+import {dataOptions} from '../../utils/static-config'
 export default {
     data(){
         return {
             options: [{name:'Species name',item:'species_name'},{name:'TaxID',item:'taxid'}, {name:'Common name',item:'common_name'},{name:'ToLID', item:'tolid'}],
-            checkboxOptions:[
-                {text: 'Acquired samples', value: 'local_samples'},
-                {text: 'Submitted samples', value: 'insdc_samples'},
-                {text: 'Submitted reads', value: 'experiments'},
-                {text: 'Submitted assemblies', value: 'assemblies'},
-                {text: 'Annotations', value: 'annotations'}
-            ],
-            selectedCheckboxes:[],
+            checkboxOptions:dataOptions,
             animation:'',
             projectAccession: PROJECT_ACCESSION
         }
     },
     computed: {
         ...mapFields({
-            fields: ['onlySelectedData','selectedBioproject'],
+            fields: ['selectedData','onlySelectedData','selectedBioproject'],
             module: 'portal',
             mutation: 'portal/setField'      
-        })
+        }),
     },
     watch:{
-        selectedCheckboxes(values){
-            this.checkboxOptions
-            .map(it => {return it.value})
-            .forEach(it => {
-                if (values.filter(v => v === it).length){
-                    this.$store.commit('portal/setField', {label: it, value:true})
-                }else{
-                    this.$store.commit('portal/setField', {label: it, value:false})
-                }
-            })
-            this.$root.$emit('bv::refresh::table', 'organisms-table')
-        },
         selectedBioproject(){
             this.$root.$emit('bv::refresh::table', 'organisms-table')
         },
         onlySelectedData(){
             this.$root.$emit('bv::refresh::table', 'organisms-table')
+        },
+        selectedData(){
+            this.$root.$emit('bv::refresh::table', 'organisms-table')
         }
     },
     components:{
-    BFormCheckbox,BFormCheckboxGroup,BTooltip,
+        BFormCheckbox,BFormCheckboxGroup,BTooltip,
         BIconArrowClockwise,FilterComponent,MultiSelectComponent
     },
     created(){
@@ -101,7 +85,6 @@ export default {
     },
     methods:{
         resetFilters(){
-            this.selectedCheckboxes=[]
             this.$store.dispatch('portal/resetFilters')
         }
     }

client/src/components/organism/OrganismsComponent.vue

@@ -89,6 +89,7 @@ import SubmissionService from '../../services/SubmissionService';
 import DataModal from '../modal/DataModal.vue';
 import EditOrganismModal from '../modal/EditOrganismModal.vue';
 import PaginationComponent from '../base/PaginationComponent.vue';
+import {dataOptions} from '../../utils/static-config'
 
 export default {
   components: 
@@ -103,9 +104,7 @@ export default {
       fields: ['filter','perPage',
        'onlySelectedData','selectedBioproject',
        'option','taxName',
-       'totalRows','currentPage',
-       'insdc_samples','local_samples',
-       'experiments','assemblies','annotations'],
+       'totalRows','currentPage','selectedData'],
       module: 'portal',
       mutation: 'portal/setField'      
     }),
@@ -144,43 +143,18 @@ export default {
       organism:null,
       commonNames: '',
       model:'',
+      dataOptions: dataOptions
     }
   },
   watch: {
-      insdc_samples(value){
-      if (value){
-        this.fields.filter(f => f.key === 'insdc_samples').forEach(f => f.variant = "success")
-      }else{
-        this.fields.filter(f => f.key === 'insdc_samples').forEach(f => f.variant = "")
-      }
-    },
-    local_samples(value){
-      if (value){
-        this.fields.filter(f => f.key === 'local_samples').forEach(f => f.variant = "info")
-      }else{
-        this.fields.filter(f => f.key === 'local_samples').forEach(f => f.variant = "")
-      }
-    },
-    assemblies(value){
-      if (value){
-        this.fields.filter(f => f.key === 'assemblies').forEach(f => f.variant = "primary")
-      }else{
-        this.fields.filter(f => f.key === 'assemblies').forEach(f => f.variant = "")
-      }
-    },
-    experiments(value){
-      if (value){
-        this.fields.filter(f => f.key === 'experiments').forEach(f => f.variant = "warning")
-      }else{
-        this.fields.filter(f => f.key === 'experiments').forEach(f => f.variant = "")
-      }
-    },
-    annotations(value){
-      if (value){
-        this.fields.filter(f => f.key === 'annotations').forEach(f => f.variant = "secondary")
-      }else{
-        this.fields.filter(f => f.key === 'annotations').forEach(f => f.variant = "")
-      }
+     selectedData(values){
+        this.dataOptions.forEach(opt => {
+          if (values.includes(opt.value)){
+            this.fields.filter(f => f.key === opt.value).forEach(f => f.variant = opt.variant)
+          }else{
+              this.fields.filter(f => f.key === opt.value).forEach(f => f.variant = "")
+          }
+        })
     },
     option(){
       this.filter=''
@@ -241,21 +215,26 @@ export default {
     },
     organismsProvider(ctx,callback){
       const fromParam = (ctx.currentPage - 1) * ctx.perPage
+      const selectedData = this.dataOptions.map(opt => {
+        var data = {}
+        if (this.selectedData.includes(opt.value)){
+          data[opt.value] = true
+        }else{
+          data[opt.value] = false
+        }
+        return data
+      })
       const params = {
         filter: ctx.filter,
         offset: fromParam,
         limit: ctx.perPage,
         sortColumn: ctx.sortBy,
         sortOrder: ctx.sortDesc,
         taxName: this.taxName,
-        insdc_samples: this.insdc_samples,
-        local_samples: this.local_samples,
-        assemblies: this.assemblies,
-        experiments: this.experiments,
-        annotations: this.annotations,
         option: this.option,
         onlySelectedData: this.onlySelectedData,
-        bioproject:this.selectedBioproject
+        bioproject:this.selectedBioproject,
+        ...Object.assign({}, ...selectedData)
         }
       this.defaultSearch(params,callback)
     }