Additional work

microbiomedata · Aug 14, 2023 · d07d31a · d07d31a
1 parent 6d2c9d1
commit d07d31a
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Showing 14 changed files with 262 additions and 116 deletions.
diff --git a/nmdc_server/api.py b/nmdc_server/api.py
diff --git a/nmdc_server/config.py b/nmdc_server/config.py
@@ -11,7 +11,7 @@ class Settings(BaseSettings):
     # Several different database urls are configured for different
     # environments.  In production, only database_uri and ingest_database_uri
     # are used.
-    database_uri: str = "postgresql:///nmdc"
+    database_uri: str = "postgresql:///nmdc_testing"
     ingest_database_uri: str = "postgresql:///nmdc_testing"
     testing_database_uri: str = "postgresql:///nmdc_testing"
 

diff --git a/nmdc_server/query.py b/nmdc_server/query.py
@@ -234,7 +234,7 @@ def compare(self) -> ClauseElement:
 # A special condition type on multiomics bitstrings
 class MultiomicsConditionSchema(BaseConditionSchema):
     table: Table
-    value: int
+    value: Union[int, List[str]]
     field: Literal["multiomics"]
     op: Literal["has"]
 

diff --git a/setup.py b/setup.py
@@ -12,7 +12,8 @@
         "authlib==0.15.5",
         "celery[redis]",
         "click",
-        "cryptography<3.4",  # https://github.com/pyca/cryptography/issues/5771
+        # "cryptography<3.4",  # https://github.com/pyca/cryptography/issues/5771
+        "cryptography",
         "fastapi==0.71.0",
         "factory-boy==3.2.1",
         "httpx<=0.18.2",

diff --git a/web/src/components/ClusterMap.vue b/web/src/components/ClusterMap.vue
@@ -93,11 +93,13 @@ export default defineComponent({
       const values: any[] = [];
       data.forEach((cluster, index) => {
         for (let i = 0; i < cluster.count; i += 1) {
-          values.push({
-            ...cluster,
-            key: `${index}_${i}`,
-            latLng: L.latLng(cluster.latitude, cluster.longitude),
-          });
+          if (cluster.latitude !== undefined && cluster.longitude !== undefined) {
+            values.push({
+              ...cluster,
+              key: `${index}_${i}`,
+              latLng: L.latLng(cluster.latitude, cluster.longitude),
+            });
+          }
         }
       });
       mapData.value = values;
@@ -108,7 +110,7 @@ export default defineComponent({
       if (bounds) {
         emit('selected', [
           {
-            field: 'latitude',
+            field: 'lat_lon.latitude',
             op: 'between',
             value: [
               //  @ts-ignore
@@ -117,7 +119,7 @@ export default defineComponent({
             table: 'biosample',
           },
           {
-            field: 'longitude',
+            field: 'lat_lon.longitude',
             op: 'between',
             value: [
               //  @ts-ignore

diff --git a/web/src/components/DataObjectTable.vue b/web/src/components/DataObjectTable.vue
@@ -87,19 +87,19 @@ export default defineComponent({
 
     const items = computed(() => flattenDeep(
       flattenDeep(props.biosample.omics_processing.filter((o) => o.omics_type.has_raw_value === props.omicsType).map(
-        (omicsProcessing) => props.biosample.analysis.filter(
-          (analysis) => analysis.was_informed_by === omicsProcessing.id,
+        (omicsProcessing) => props.biosample.activity.filter(
+          (activity) => activity.was_informed_by === omicsProcessing.id,
         ),
       )).map(
-        (analysis) => analysis.has_output.map(
+        (activity) => activity.has_output.map(
           (dataObjectId) => props.biosample.data_object.find(
             (dataObject) => dataObject.id === dataObjectId,
           ),
         ).map((dataObject, index) => ({
           ...dataObject,
-          analysis,
+          activity,
           /* TODO Hack to replace metagenome with omics type name */
-          group_name: analysis.name ? analysis.name.replace('Metagenome', props.omicsType) : '',
+          group_name: activity.name ? activity.name.replace('Metagenome', props.omicsType) : '',
           newgroup: index === 0,
         })),
       ),

diff --git a/web/src/components/Presentation/ConditionChips.vue b/web/src/components/Presentation/ConditionChips.vue
@@ -4,7 +4,6 @@ import Vue from 'vue';
 import { groupBy } from 'lodash';
 import { opMap } from '@/data/api';
 import { fieldDisplayName } from '@/util';
-import { makeSetsFromBitmask } from '@/encoding';
 
 export default Vue.extend({
   props: {
@@ -45,7 +44,7 @@ export default Vue.extend({
     valueTransform(val, field, type) {
       // Special handling for multiomics
       if (field === 'multiomics' && type === 'biosample') {
-        return Array.from(makeSetsFromBitmask(val)).join(', ');
+        return val.join(', ');
       }
       // If it's not primitive
       if (val && typeof val === 'object') {

diff --git a/web/src/components/Presentation/UpSet.vue b/web/src/components/Presentation/UpSet.vue
@@ -2,7 +2,7 @@
 import { defineComponent, watchEffect, ref } from '@vue/composition-api';
 import { select } from 'd3-selection';
 import { scaleBand, scaleLinear } from 'd3-scale';
-import { MultiomicsValue } from '@/encoding';
+import { multiomicsAbbreviations } from '@/encoding';
 
 export default defineComponent({
   props: {
@@ -39,7 +39,7 @@ export default defineComponent({
     };
     const fontSize = 12;
 
-    const setOrder = ['MG', 'MT', 'MP', 'MB', 'NOM'];
+    const setOrder = ['Metagenome', 'Metatranscriptome', 'Proteomics', 'Metabolomics', 'Organic Matter Characterization'];
     const Samples = 'Samples';
     const Studies = 'Studies';
     const seriesTitles = [Samples, Studies];
@@ -103,7 +103,7 @@ export default defineComponent({
         .attr('y', -4)
         .attr('text-anchor', 'middle')
         .attr('font-size', fontSize)
-        .text((d) => d)
+        .text((d) => multiomicsAbbreviations[d])
         .attr('fill', 'black')
         .append('svg:title')
         .text((s) => props.tooltips[s]);
@@ -153,16 +153,12 @@ export default defineComponent({
               .attr('height', y.bandwidth())
               .attr('fill', root.$vuetify.theme.currentTheme.blue)
               .classed('upset-bar-clickable', true)
-              .on('click', (event, values) => {
-                const value = values.sets.reduce((prev, cur) => {
-                  const next = prev | MultiomicsValue[cur]; //eslint-disable-line no-bitwise
-                  return next;
-                }, 0);
+              .on('click', (_event, values) => {
                 const conditions = [{
                   field: 'multiomics',
                   table: 'biosample',
                   op: 'has',
-                  value,
+                  value: values.sets,
                 }];
                 emit('select', { conditions });
               });

diff --git a/web/src/data/api.ts b/web/src/data/api.ts
@@ -109,7 +109,7 @@ export interface BiosampleSearchResult extends BaseSearchResult {
   }
   emsl_biosample_identifiers: string[];
   omics_processing: OmicsProcessingResult[];
-  analysis: AnalysisResult[];
+  activity: AnalysisResult[];
   data_object: DataObjectSearchResult[];
 }
 
@@ -472,7 +472,7 @@ async function getDatabaseStats() {
 async function getEnvironmentGeospatialAggregation(
   conditions: Condition[],
 ): Promise<EnvironmentGeospatialEntity[]> {
-  const { data } = await client.post<EnvironmentGeospatialEntity[]>('environment/geospatial', {
+  const { data } = await client.post<EnvironmentGeospatialEntity[]>('environment/mongo_geospatial', {
     conditions,
   });
   return data;
@@ -521,7 +521,7 @@ async function getEnvoTrees() {
  * Bulk Download API
  */
 async function getBulkDownloadSummary(conditions: Condition[]) {
-  const { data } = await client.post<BulkDownloadSummary>('data_object/workflow_summary', {
+  const { data } = await client.post<BulkDownloadSummary>('data_object/mongo_workflow_summary', {
     conditions,
   });
   return data;

diff --git a/web/src/encoding.ts b/web/src/encoding.ts
@@ -66,29 +66,6 @@ function stringIsKegg(v: string) {
   return Object.values(KeggPrefix).find((item) => v.match(item.pattern));
 }
 
-function makeSetsFromBitmask(mask_str: string) {
-  const mask = parseInt(mask_str, 10); // the bitmask comes in as a string
-  const sets = [];
-
-  /* eslint-disable no-bitwise */
-  if (1 & mask) {
-    sets.push('NOM');
-  }
-  if ((1 << 4) & mask) {
-    sets.push('MB');
-  }
-  if ((1 << 2) & mask) {
-    sets.push('MP');
-  }
-  if ((1 << 1) & mask) {
-    sets.push('MT');
-  }
-  if ((1 << 3) & mask) {
-    sets.push('MG');
-  }
-  return sets;
-}
-
 const types: Record<entityType, EntityData> = {
   study: {
     icon: 'mdi-book',
@@ -411,20 +388,19 @@ function getField(name: string, table?: entityType): FieldsData {
   return {};
 }
 
-const MultiomicsValue = {
-  MB: 0b10000,
-  MG: 0b01000,
-  MP: 0b00100,
-  MT: 0b00010,
-  NOM: 0b00001,
+const multiomicsAbbreviations = {
+  Metagenome: 'MG',
+  Metatranscriptome: 'MT',
+  Proteomics: 'MP',
+  Metabolomics: 'MB',
+  'Organic Matter Characterization': 'NOM',
 };
 
 export {
   types,
   ecosystems,
-  MultiomicsValue,
+  multiomicsAbbreviations,
   getField,
   keggEncode,
   stringIsKegg,
-  makeSetsFromBitmask,
 };
diff --git a/web/src/plugins/utils.ts b/web/src/plugins/utils.ts
@@ -36,6 +36,7 @@ function parseQuery(q: string) {
   const u8a = new Uint8Array(atob(b64).split('').map((c) => c.charCodeAt(0)));
   const msg = QueryParams.decode(u8a);
   const obj = QueryParams.toObject(msg, { enums: String });
+  obj.conditions = obj.conditions ?? [];
   obj.conditions.forEach((c: Condition) => {
     // @ts-ignore
     // eslint-disable-next-line no-param-reassign

diff --git a/web/src/views/Search/BiosampleVisGroup.vue b/web/src/views/Search/BiosampleVisGroup.vue
@@ -18,7 +18,6 @@ import {
   toggleConditions, removeConditions, setUniqueCondition,
 } from '@/store';
 import { api, Condition, FacetSummaryResponse } from '@/data/api';
-import { makeSetsFromBitmask } from '@/encoding';
 
 const helpBarchart = 'Displays the number of omics processing runs for each data type available. Click on a bar to filter by data type.';
 const helpMap = 'Displays geographical location (latitude, longitude) of sample collection sites. Click on a cluster to zoom in.  Click "Search this regon" to limit search to the current map bounds.';
@@ -62,27 +61,27 @@ export default defineComponent({
     const upsetData = computed(() => {
       const multiomicsObj: Record<string, { counts: any, sets: any }> = {};
       sampleFacetSummary.value.forEach(({ facet, count }) => {
-        if (parseInt(facet, 10) === 0) {
+        if (facet.length === 0) {
           return;
         }
         multiomicsObj[facet] = {
           counts: {
             Samples: count,
             Studies: 0,
           },
-          sets: makeSetsFromBitmask(facet),
+          sets: facet.split(';'),
         };
       });
       studyFacetSummary.value.forEach(({ facet, count }) => {
-        if (parseInt(facet, 10) === 0) {
+        if (facet.length === 0) {
           return;
         }
         if (!multiomicsObj[facet]) {
           multiomicsObj[facet] = {
             counts: {
               Samples: 0,
             },
-            sets: makeSetsFromBitmask(facet),
+            sets: facet.split(';'),
           };
         }
         multiomicsObj[facet].counts.Studies = count;

diff --git a/web/src/views/Search/SearchLayout.vue b/web/src/views/Search/SearchLayout.vue
@@ -285,9 +285,9 @@ export default defineComponent({
                 <template #subtitle="props">
                   <span class="pr-2">Study ID:</span>
                   <router-link
-                    :to="{name: 'Study', params: { id: props.result.study_id }}"
+                    :to="{name: 'Study', params: { id: props.result.part_of[0] }}"
                     class="pr-2 grey--text text--darken-2"
-                    v-text="props.result.study_id"
+                    v-text="props.result.part_of[0]"
                   />
                   <template
                     v-if="(props.result.alternative_identifiers && props.result.alternative_identifiers.length) ||

diff --git a/web/src/views/Search/SearchSidebar.vue b/web/src/views/Search/SearchSidebar.vue
@@ -24,16 +24,19 @@ const FunctionSearchFacets: SearchFacet[] = [
   },
   /** ENVO */
   {
-    field: 'env_broad_scale',
+    field: 'env_broad_scale.has_raw_value',
     table: 'biosample',
+    group: 'ENVO',
   },
   {
-    field: 'env_local_scale',
+    field: 'env_local_scale.has_raw_value',
     table: 'biosample',
+    group: 'ENVO',
   },
   {
-    field: 'env_medium',
+    field: 'env_medium.has_raw_value',
     table: 'biosample',
+    group: 'ENVO',
   },
   /** GOLD */
   {
@@ -52,12 +55,12 @@ const FunctionSearchFacets: SearchFacet[] = [
     group: 'Sample',
   },
   {
-    field: 'latitude',
+    field: 'lat_lon.latitude',
     table: 'biosample',
     group: 'Sample',
   },
   {
-    field: 'longitude',
+    field: 'lat_lon.longitude',
     table: 'biosample',
     group: 'Sample',
   },