DON"T MERGE 1367 multiple env select

nmdc_server/fakes.py

@@ -396,7 +396,7 @@ class Meta:
             "facilities": [],
             "otherAward": "",
         },
-        "packageName": "",
+        "packageName": [],
     }
     locked_by = None
     lock_updated = None

nmdc_server/migrations/versions/afa1ff687968_convert_packagename_to_an_array.py

@@ -0,0 +1,57 @@
+"""Convert packageName to an array
+
+Revision ID: afa1ff687968
+Revises: 317274ad8137
+Create Date: 2024-08-28 22:27:28.622234
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "afa1ff687968"
+down_revision: Optional[str] = "317274ad8137"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    submission_metadata = table(
+        "submission_metadata",
+        column("id", sa.String),
+        column("metadata_submission", JSONB),
+        column("study_name", sa.String),
+        column("templates", JSONB),
+    )
+
+    connection = op.get_bind()
+    submissions = connection.execute(
+        sa.select([submission_metadata.c.id, submission_metadata.c.metadata_submission])
+    )
+
+    for submission in submissions:
+        metadata_submission = submission.metadata_submission
+        package_name = metadata_submission.get("packageName")
+
+        if isinstance(package_name, str):
+            metadata_submission["packageName"] = [package_name]
+
+        update_stmt = (
+            submission_metadata.update()
+            .where(submission_metadata.c.id == submission.id)
+            .values(metadata_submission=metadata_submission)
+        )
+        connection.execute(update_stmt)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###

nmdc_server/schemas_submission.py

@@ -73,7 +73,7 @@ class ContextForm(BaseModel):
 
 
 class MetadataSubmissionRecord(BaseModel):
-    packageName: str
+    packageName: List[str]
     contextForm: ContextForm
     addressForm: AddressForm
     templates: List[str]
@@ -83,7 +83,7 @@ class MetadataSubmissionRecord(BaseModel):
 
 
 class PartialMetadataSubmissionRecord(BaseModel):
-    packageName: Optional[str]
+    packageName: Optional[List[str]]
     contextForm: Optional[ContextForm]
     addressForm: Optional[AddressForm]
     templates: Optional[List[str]]

web/src/views/SubmissionPortal/Components/TemplateChooser.vue

@@ -32,38 +32,39 @@ export default defineComponent({
 <template>
   <div>
     <div class="text-h2">
-      Environment Package
+      Environmental Extensions
       <submission-docs-link anchor="environmental-package" />
     </div>
     <div class="text-h5">
-      Choose environment package for your data.
+      Choose environmental extensions for your data.
     </div>
     <submission-permission-banner
       v-if="!canEditSubmissionMetadata()"
     />
-    <v-radio-group
+
+    <v-checkbox
+      v-for="option in templates.filter((v) => v[1].status === 'published')"
+      :key="option[0]"
       v-model="packageName"
+      dense
+      hide-details
       class="my-6"
-      :disabled="!canEditSubmissionMetadata()"
-    >
-      <v-radio
-        v-for="option in templates.filter((v) => v[1].status === 'published')"
-        :key="option[0]"
-        :value="option[0]"
-        :disabled="templateChoiceDisabled"
-        :label="HARMONIZER_TEMPLATES[option[0]].displayName"
-      />
-      <p class="grey--text text--darken-1 my-5">
-        Under development
-      </p>
-      <v-radio
-        v-for="option in templates.filter((v) => v[1].status === 'disabled')"
-        :key="option[0]"
-        :value="option[0]"
-        :disabled="true"
-        :label="HARMONIZER_TEMPLATES[option[0]].displayName"
-      />
-    </v-radio-group>
+      :disabled="templateChoiceDisabled || !canEditSubmissionMetadata()"
+      :label="HARMONIZER_TEMPLATES[option[0]].displayName"
+      :value="option[0]"
+    />
+    <p class="grey--text text--darken-1 my-5">
+      Under development
+    </p>
+    <v-checkbox
+      v-for="option in templates.filter((v) => v[1].status === 'disabled')"
+      :key="option[0]"
+      v-model="packageName"
+      hide-details
+      :disabled="true"
+      :label="HARMONIZER_TEMPLATES[option[0]].displayName"
+      :value="option[0]"
+    />
     <v-alert
       v-if="!templateChoiceDisabled"
       color="grey lighten-2"
@@ -99,7 +100,7 @@ export default defineComponent({
       <v-btn
         color="primary"
         depressed
-        :disabled="!packageName"
+        :disabled="packageName.length === 0"
         :to="{
           name: 'Submission Sample Editor',
         }"

web/src/views/SubmissionPortal/HarmonizerView.vue

@@ -132,8 +132,10 @@ export default defineComponent({
       // WARNING: It's important to do the column settings update /before/ data. Otherwise,
       // columns will not be rendered with the correct width.
       harmonizerApi.setColumnsReadOnly(ALWAYS_READ_ONLY_COLUMNS);
-      // if we're not on the first tab, the common columns should be read-only
-      if (activeTemplateKey.value !== templateList.value[0]) {
+
+      // If the environment tab selected is a misin it should be readonly
+      const environmentList = templateList.value.filter((t) => HARMONIZER_TEMPLATES[t].status === 'mixin');
+      if (environmentList.includes(activeTemplateKey.value)) {
         harmonizerApi.setColumnsReadOnly(COMMON_COLUMNS);
         harmonizerApi.setMaxRows(activeTemplateData.value.length);
       }
@@ -294,7 +296,8 @@ export default defineComponent({
     });
 
     function rowIsVisibleForTemplate(row: Record<string, any>, templateKey: string) {
-      if (templateKey === templateList.value[0]) {
+      const environmentKeys = templateList.value.filter((t) => HARMONIZER_TEMPLATES[t].status === 'published');
+      if (environmentKeys.includes(templateKey)) {
         return true;
       }
       const row_types = row[TYPE_FIELD];
@@ -319,53 +322,65 @@ export default defineComponent({
     }
 
     function synchronizeTabData(templateKey: string) {
-      if (templateKey === templateList.value[0]) {
+      const environmentKeys = templateList.value.filter((t) => HARMONIZER_TEMPLATES[t].status === 'published');
+      if (environmentKeys.includes(templateKey)) {
         return;
       }
       const nextData = { ...sampleData.value };
       const templateSlot = HARMONIZER_TEMPLATES[templateKey].sampleDataSlot;
-      const environmentSlot = HARMONIZER_TEMPLATES[templateList.value[0]].sampleDataSlot;
 
-      if (!templateSlot || !environmentSlot) {
+      const environmentSlots = templateList.value
+        .filter((t) => HARMONIZER_TEMPLATES[t].status === 'published')
+        .map((t) => HARMONIZER_TEMPLATES[t].sampleDataSlot);
+
+      if (!templateSlot || !environmentSlots) {
         return;
       }
 
       // ensure the necessary keys exist in the data object
-      if (!nextData[environmentSlot]) {
-        nextData[environmentSlot] = [];
-      }
+      environmentSlots.forEach((slot) => {
+        if (!nextData[slot as string]) {
+          nextData[slot as string] = [];
+        }
+      });
+
       if (!nextData[templateSlot]) {
         nextData[templateSlot] = [];
       }
 
-      // add/update any rows from the first tab to the active tab if they apply and if
+      // add/update any rows from the environment tabs to the active tab if they apply and if
       // they aren't there already.
-      nextData[environmentSlot].forEach((row) => {
-        const rowId = row[SCHEMA_ID];
-        const existing = nextData[templateSlot] && nextData[templateSlot].find((r) => r[SCHEMA_ID] === rowId);
-        if (!existing && rowIsVisibleForTemplate(row, templateKey)) {
-          const newRow = {} as Record<string, any>;
-          COMMON_COLUMNS.forEach((col) => {
-            newRow[col] = row[col];
-          });
-          nextData[templateSlot].push(newRow);
-        }
-        if (existing) {
-          COMMON_COLUMNS.forEach((col) => {
-            existing[col] = row[col];
-          });
-        }
+      environmentSlots.forEach((environmentSlot) => {
+        nextData[environmentSlot as string].forEach((row) => {
+          const rowId = row[SCHEMA_ID];
+
+          const existing = nextData[templateSlot] && nextData[templateSlot].find((r) => r[SCHEMA_ID] === rowId);
+          if (!existing && rowIsVisibleForTemplate(row, templateKey)) {
+            const newRow = {} as Record<string, any>;
+            COMMON_COLUMNS.forEach((col) => {
+              newRow[col] = row[col];
+            });
+            nextData[templateSlot].push(newRow);
+          }
+          if (existing) {
+            COMMON_COLUMNS.forEach((col) => {
+              existing[col] = row[col];
+            });
+          }
+        });
       });
-      // remove any rows from the active tab if they were removed from the first tab
+      // remove any rows from the active tab if they were removed from the environment tabs
       // or no longer apply to the active tab
       if (nextData[templateSlot].length > 0) {
         nextData[templateSlot] = nextData[templateSlot].filter((row) => {
           if (!rowIsVisibleForTemplate(row, templateKey)) {
             return false;
           }
           const rowId = row[SCHEMA_ID];
-          const environmentRow = nextData[environmentSlot].findIndex((r) => r[SCHEMA_ID] === rowId);
-          return environmentRow >= 0;
+          return environmentSlots.some((environmentSlot) => {
+            const environmentRow = nextData[environmentSlot as string].findIndex((r) => r[SCHEMA_ID] === rowId);
+            return environmentRow >= 0;
+          });
         });
       }
       sampleData.value = nextData;
@@ -464,9 +479,8 @@ export default defineComponent({
       }
 
       await validate();
-
       // When changing templates we may need to populate the common columns
-      // from the first tab
+      // from the environment tabs
       const nextTemplate = templateList.value[index];
       synchronizeTabData(nextTemplate);
 

web/src/views/SubmissionPortal/harmonizerApi.ts

@@ -32,24 +32,24 @@ export const EMSL = 'emsl';
 export const JGI_MG = 'jgi_mg';
 export const JGI_MG_LR = 'jgi_mg_lr';
 export const JGT_MT = 'jgi_mt';
-export function getVariants(checkBoxes: string[], dataGenerated: boolean | undefined, base: string): string[] {
-  const templates = [base];
+export function getVariants(checkBoxes: string[], dataGenerated: boolean | undefined, base: string[]): string[] {
+  const templates = new Set(base);
   if (dataGenerated) {
-    return templates;
+    return Array.from(templates);
   }
   if (checkBoxes.includes('mp-emsl') || checkBoxes.includes('mb-emsl') || checkBoxes.includes('nom-emsl')) {
-    templates.push(EMSL);
+    templates.add(EMSL);
   }
   if (checkBoxes.includes('mg-jgi')) {
-    templates.push(JGI_MG);
+    templates.add(JGI_MG);
   }
   if (checkBoxes.includes('mg-lr-jgi')) {
-    templates.push(JGI_MG_LR);
+    templates.add(JGI_MG_LR);
   }
   if (checkBoxes.includes('mt-jgi')) {
-    templates.push(JGT_MT);
+    templates.add(JGT_MT);
   }
-  return templates;
+  return Array.from(templates);
 }
 
 /**

web/src/views/SubmissionPortal/store/api.ts

@@ -28,7 +28,7 @@ function addressToString(address: NmdcAddress): string {
 }
 
 interface MetadataSubmission {
-  packageName: keyof typeof HARMONIZER_TEMPLATES;
+  packageName: (keyof typeof HARMONIZER_TEMPLATES)[];
   contextForm: any;
   addressForm: any;
   templates: string[];

web/src/views/SubmissionPortal/store/index.ts

@@ -166,13 +166,12 @@ const multiOmicsAssociations = reactive(clone(multiOmicsAssociationsDefault));
 /**
  * Environment Package Step
  */
-const packageName = ref('soil' as keyof typeof HARMONIZER_TEMPLATES);
+const packageName = ref(['soil'] as (keyof typeof HARMONIZER_TEMPLATES)[]);
 const templateList = computed(() => {
   const checkBoxes = multiOmicsForm.omicsProcessingTypes;
   const list = getVariants(checkBoxes, contextForm.dataGenerated, packageName.value);
   return list;
 });
-
 /**
  * DataHarmonizer Step
  */
@@ -253,7 +252,7 @@ function reset() {
   multiOmicsFormValid.value = false;
   Object.assign(multiOmicsForm, multiOmicsFormDefault);
   Object.assign(multiOmicsAssociations, multiOmicsAssociationsDefault);
-  packageName.value = 'soil';
+  packageName.value = ['soil'];
   sampleData.value = {};
   status.value = submissionStatus.InProgress;
 }