Hard code to support JGI data

Author: matthewma7

client/src/components/MetagenomePropertiesTable.vue

@@ -83,7 +83,7 @@ export default {
   },
   methods: {
     getPorjectName(sample) {
-      return sample["Genome Name / Sample Name"].split(" - ")[1];
+      return sample.name;
     },
     table7Sum(property) {
       return _.sum(

client/src/components/SampleList.vue

@@ -14,7 +14,7 @@ export default {
   },
   methods: {
     getPorjectName(sample) {
-      return sample["Genome Name / Sample Name"].split(" - ")[1];
+      return sample.name;
     },
     toggle(sample) {
       if (this.selectedSamples.indexOf(sample) !== -1) {
@@ -41,7 +41,10 @@ export default {
     },
     checkAll(checked) {
       if (checked) {
-        this.$emit("update:selectedSamples", this.meta.slice());
+        this.$emit(
+          "update:selectedSamples",
+          this.meta.filter(meta => meta.source === "LLNL").slice()
+        );
       } else {
         this.$emit("update:selectedSamples", []);
       }
@@ -84,9 +87,11 @@ export default {
         v-for="sample in this.meta"
         :key="sample['taxon_oid']"
         :class="{ selected: selectedSamples.indexOf(sample) !== -1 }"
-        @click="123"
+        v-on="sample.source === 'LLNL' ? { click: () => 123 } : {}"
       >
-        <v-list-tile-content @click="toggle(sample)">
+        <v-list-tile-content
+          v-on="sample.source === 'LLNL' ? { click: () => toggle(sample) } : {}"
+        >
           <v-list-tile-title>
             <v-tooltip right open-delay="500">
               <template #activator="data">
@@ -107,6 +112,7 @@ export default {
           }"
         >
           <v-checkbox
+            v-if="sample.source === 'LLNL'"
             :value="selectedSamples.indexOf(sample) !== -1"
             @change="check($event, sample)"
           ></v-checkbox>

client/src/components/SamplesLocation.vue

@@ -13,7 +13,7 @@ export default {
   computed: {
     ...mapState(["meta"]),
     sitesFeature() {
-      var grouped = _.groupBy(this.meta, sample => {
+      var grouped = _.groupBy(this.meta.filter(sample=>sample.Lat&&sample.Long), sample => {
         return sample.Lat + sample.Long;
       });
       return {

client/src/store/index.js

@@ -18,8 +18,25 @@ const store = new Vuex.Store({
   actions: {
     async load({ state }) {
       var { data: records } = await girder.rest.get("record");
-      state.meta = records.meta;
-      Object.assign(state, records);
+
+      Object.assign(state, {
+        meta: records.map(record => ({
+          ...record.meta.meta_,
+          ...record.meta.meta
+        })),
+        summary: records
+          .filter(record => record.meta.summary)
+          .map(record => record.meta.summary),
+        table7: records
+          .filter(record => record.meta.table7)
+          .map(record => record.meta.table7),
+        table8: records
+          .filter(record => record.meta.table8)
+          .map(record => record.meta.table8),
+        table9: records
+          .filter(record => record.meta.table9)
+          .map(record => record.meta.table9)
+      });
       console.log(state);
     }
   }

client/src/views/Home.vue

@@ -31,31 +31,15 @@ export default {
   computed: {
     ...mapState(["meta", "summary", "table7", "table8", "table9"]),
     metaNames() {
-      return this.meta.map(meta => meta["Genome Name / Sample Name"]);
+      return this.meta.map(meta => meta.name);
     },
     sampleTypes() {
-      var types = this.metaNames
-        .map(name => {
-          if (/soil/i.exec(name)) {
-            return "Soil";
-          } else if (/water/.exec(name)) {
-            return "Water";
-          } else if (/vegetation/.exec(name)) {
-            return "Vegetation";
-          }
-        })
-        .filter(value => value);
+      var types = this.meta.map(meta => meta.material).filter(value => value);
       return _.uniq(types);
     },
     ecosystems() {
-      var types = this.metaNames
-        .map(name => {
-          if (/arctic/i.exec(name)) {
-            return "Arctic";
-          }
-        })
-        .filter(value => value);
-      return _.uniq(types);
+      var ecosystems = this.meta.map(meta => meta.ecosystem).filter(value => value);
+      return _.uniq(ecosystems);
     },
     numberOfMetagenomes() {
       return this.meta.filter(meta => meta.Sequencing === "Metagenome").length;
@@ -179,7 +163,7 @@ export default {
           Across all projects and samples
         </template>
         <template v-else-if="selectedSamples.length === 1">
-          {{ selectedSamples[0]["Genome Name / Sample Name"] }}
+          {{ selectedSamples[0].name }}
         </template>
         <template v-else>
           Multiple items

server/data/ingest.py

@@ -67,7 +67,7 @@ def parseTable(directory, filename):
 
 
 def extractMeta(data):
-    def getSampleType(name):
+    def getMaterial(name):
         if re.search('soil', name, re.IGNORECASE):
             return 'Soil'
         elif re.search('water', name, re.IGNORECASE):
@@ -81,17 +81,17 @@ def getEcosystem(name):
     name = data['meta_']['Genome Name / Sample Name'].split(' - ')[1]
     latitude = data['meta_']['Lat']
     longitude = data['meta_']['Long']
-    sampleType = getSampleType(data['meta_']['Genome Name / Sample Name'])
+    material = getMaterial(data['meta_']['Genome Name / Sample Name'])
     ecosystem = getEcosystem(data['meta_']['Genome Name / Sample Name'])
     return {
         'name': name,
         'latitude': latitude,
         'longitude': longitude,
         'timestemp': None,
-        'sampleType': sampleType,
-        'omicsType': None,
+        'material': material,
+        'feature': None,
+        'biome': None,
         'ecosystem': ecosystem,
-        'ontology': None,
         'source': 'LLNL'
     }
 

server/resonanteco_server/rest/record.py

@@ -7,12 +7,6 @@
 from girder.models.folder import Folder
 from girder.models.item import Item
 
-from ..model.meta import Meta
-from ..model.summary import Summary
-from ..model.table7 import Table7
-from ..model.table8 import Table8
-from ..model.table9 import Table9
-
 
 class Record(Resource):
     def __init__(self):
@@ -26,10 +20,4 @@ def __init__(self):
         Description('')
         .errorResponse())
     def getAll(self, params):
-        return {
-            'meta': list(Meta().find()),
-            'summary': list(Summary().find()),
-            'table7': list(Table7().find()),
-            'table8': list(Table8().find()),
-            'table9': list(Table9().find())
-        }
+        return Item().find({'meta.meta':{'$exists':1}})