Amplicon fix

nmdc_server/ingest/omics_processing.py

@@ -148,7 +148,13 @@ def get_poolable_replicate_manifest(
     return omics_processing_id
 
 
-def load_omics_processing(db: Session, obj: Dict[str, Any], mongodb: Database, logger, config_map):
+def load_omics_processing(  # noqa: C901
+    db: Session,
+    obj: Dict[str, Any],
+    mongodb: Database,
+    logger,
+    config_map,
+):
     logger = get_logger(__name__)
     input_ids: list[str] = obj.pop("has_input", [""])
     biosample_input_ids: set[str] = set()
@@ -172,8 +178,18 @@ def load_omics_processing(db: Session, obj: Dict[str, Any], mongodb: Database, l
 
     data_objects = obj.pop("has_output", [])
     obj["study_id"] = obj.pop("associated_studies", [None])[0]
-    obj["analyte_category"] = omics_types[obj["analyte_category"].lower()]
-    obj["omics_type"] = omics_types[obj["analyte_category"].lower()]
+    original_analyte_category = obj["analyte_category"].lower()
+    obj["analyte_category"] = omics_types[original_analyte_category]
+    obj["omics_type"] = omics_types[original_analyte_category]
+
+    # Get amplicon specific fields
+    if obj["omics_type"] == "Amplicon":
+        obj["target_gene"] = obj.pop("target_gene", None)
+        target_subfragment = obj.pop("target_subfragment", None)
+        if isinstance(target_subfragment, dict) and "has_raw_value" in target_subfragment:
+            obj["target_subfragment"] = target_subfragment["has_raw_value"]
+        else:
+            obj["target_subfragment"] = target_subfragment
 
     # Get instrument name
     instrument_id = obj.pop("instrument_used", [])

web/src/components/AmpliconObjectDataTable.vue

@@ -0,0 +1,52 @@
+<script lang="ts">
+import { defineComponent, PropType } from '@vue/composition-api';
+import { DataTableHeader } from 'vuetify';
+import { OmicsProcessingResult } from '@/data/api';
+
+const BioprojectLinkBase = 'https://bioregistry.io/';
+
+export default defineComponent({
+  name: 'AmpliconObjectDataTable',
+  props: {
+    omicsProcessing: {
+      type: Array as PropType<OmicsProcessingResult[]>,
+      required: true,
+    },
+    omicsType: {
+      type: String,
+      required: true,
+    },
+  },
+  setup() {
+    const headers: DataTableHeader[] = [
+      { text: 'Type', value: 'type' },
+      { text: 'INSDC Expirement Identifiers', value: 'insdc_experiment_identifiers' },
+      { text: 'Target Gene', value: 'target_gene' },
+      { text: 'Target Subfragment', value: 'target_subfragment' },
+    ];
+
+    return {
+      headers,
+      BioprojectLinkBase,
+    };
+  },
+});
+
+</script>
+<template>
+  <v-data-table
+    :headers="headers"
+    :items="[omicsProcessing[0].annotations]"
+  >
+    <!-- eslint-disable-next-line -->
+    <template #item.insdc_experiment_identifiers="{ item }">
+      <a
+        :href="BioprojectLinkBase + item.insdc_experiment_identifiers"
+        target="_blank"
+        rel="noopener noreferrer"
+      >
+        {{ BioprojectLinkBase + item.insdc_experiment_identifiers }}
+      </a>
+    </template>
+  </v-data-table>
+</template>

web/src/components/SampleListExpansion.vue

@@ -4,18 +4,21 @@ import { computed, defineComponent, PropType } from '@vue/composition-api';
 import { fieldDisplayName } from '@/util';
 import { BiosampleSearchResult } from '@/data/api';
 import DataObjectTable from './DataObjectTable.vue';
+import AmpliconObjectDataTable from './AmpliconObjectDataTable.vue';
 
 const buttonOrder = [
   'metagenome',
   'metatranscriptome',
   'proteomics',
   'metabolomics',
   'organic matter characterization',
+  'amplicon',
 ];
 
 export default defineComponent({
   components: {
     DataObjectTable,
+    AmpliconObjectDataTable,
   },
 
   props: {
@@ -38,6 +41,11 @@ export default defineComponent({
       return props.expanded.resultId === props.result.id
         && props.expanded.omicsProcessingId === omicsProcessingId;
     }
+    function isDisabled(omicsType: string, projects: any[]) {
+      // TODO this is a temporary fix for the amplicon button
+      // until we have a proper way to handle amplicon data.
+      return projects[0].omics_data.length === 0 && omicsType !== 'Amplicon';
+    }
 
     const filteredOmicsProcessing = computed(() => Object.entries(groupBy(
       props.result.omics_processing,
@@ -47,9 +55,9 @@ export default defineComponent({
       const bi = buttonOrder.indexOf(bgroup.toLowerCase());
       return ai - bi;
     }));
-
     return {
       isOpen,
+      isDisabled,
       filteredOmicsProcessing,
       fieldDisplayName,
     };
@@ -69,7 +77,7 @@ export default defineComponent({
         x-small
         :outlined="!isOpen(projects[0].id)"
         :color="isOpen(projects[0].id) ? 'primary' : 'default'"
-        :disabled="projects[0].omics_data.length == 0 ? true : false"
+        :disabled="isDisabled(omicsType, projects)"
         class="mr-2 mt-2"
 
         @click="() => $emit('open-details', projects[0].id)"
@@ -80,7 +88,16 @@ export default defineComponent({
     </div>
     <template v-for="[omicsType, projects] in filteredOmicsProcessing">
       <DataObjectTable
-        v-if="isOpen(projects[0].id)"
+        v-if="isOpen(projects[0].id) && omicsType !== 'Amplicon'"
+        :key="projects[0].id"
+        class="flex-row mt-2"
+        :omics-processing="projects"
+        :omics-type="omicsType"
+        :logged-in-user="loggedInUser"
+        :biosample="result"
+      />
+      <AmpliconObjectDataTable
+        v-if="isOpen(projects[0].id) && omicsType === 'Amplicon'"
         :key="projects[0].id"
         class="flex-row mt-2"
         :omics-processing="projects"