Derive Excel worksheet names from schema annotations

nmdc_server/static_files.py

@@ -38,10 +38,6 @@ def generate_submission_schema_files(directory: Path) -> None:
     # The entire submission schema in JSON format
     json_dumper.dump(sv.schema, out_dir / "submission_schema.json")
 
-    # Each class of the submission schema in JSON format
-    for class_name, class_definition in sv.all_classes().items():
-        json_dumper.dump(class_definition, out_dir / f"{class_name}.json")
-
     # The GOLD ecosystem tree that the submission schema re-exports
     gold_tree_path = submission_schema_files / "project/thirdparty/GoldEcosystemTree.json"
     shutil.copyfile(str(gold_tree_path), out_dir / "GoldEcosystemTree.json")

pyproject.toml

@@ -23,8 +23,8 @@ dependencies = [
     "ipython==7.31.1",
     "itsdangerous==2.0.1",
     "mypy<0.920",
-    "nmdc-schema==10.5.5",
-    "nmdc-submission-schema==10.5.1",
+    "nmdc-schema==10.7.0",
+    "nmdc-submission-schema==10.7.0",
     "pint==0.18",
     "psycopg2==2.9.3",
     "pydantic==1.10.2",

web/package.json

@@ -34,7 +34,7 @@
     "linkify-it": "^4.0.1",
     "lodash": "^4.17.21",
     "moment": "^2.29.4",
-    "nmdc-schema": "https://github.com/microbiomedata/nmdc-schema#v10.5.5",
+    "nmdc-schema": "https://github.com/microbiomedata/nmdc-schema#v10.7.0",
     "popper.js": "1.16.1",
     "protobufjs": "^6.11.3",
     "serialize-javascript": "^6.0.0",

web/src/views/SubmissionPortal/HarmonizerView.vue

@@ -123,6 +123,8 @@ export default defineComponent({
     const submitDialog = ref(false);
 
     const snackbar = ref(false);
+    const importErrorSnackbar = ref(false);
+    const notImportedWorksheetNames = ref([] as string[]);
 
     watch(activeTemplate, () => {
       // WARNING: It's important to do the column settings update /before/ data. Otherwise,
@@ -384,7 +386,7 @@ export default defineComponent({
         ], {
           skipHeader: true,
         });
-        utils.book_append_sheet(workbook, worksheet, template.displayName);
+        utils.book_append_sheet(workbook, worksheet, template.excelWorksheetName || template.displayName);
       });
       writeFile(workbook, EXPORT_FILENAME, { compression: true });
     }
@@ -401,9 +403,13 @@ export default defineComponent({
         }
         const workbook = read(event.target.result);
         const imported = {} as Record<string, any>;
+        const notImported = [] as string[];
         Object.entries(workbook.Sheets).forEach(([name, worksheet]) => {
-          const template = Object.values(HARMONIZER_TEMPLATES).find((template) => template.displayName === name);
+          const template = Object.values(HARMONIZER_TEMPLATES).find((template) => (
+            template.excelWorksheetName === name || template.displayName === name
+          ));
           if (!template || !template.sampleDataSlot || !template.schemaClass) {
+            notImported.push(name);
             return;
           }
 
@@ -422,6 +428,11 @@ export default defineComponent({
             template.schemaClass,
           );
         });
+
+        // Alert the user if any worksheets were not imported
+        notImportedWorksheetNames.value = notImported;
+        importErrorSnackbar.value = notImported.length > 0;
+
         // Load imported data
         sampleData.value = imported;
 
@@ -497,6 +508,8 @@ export default defineComponent({
       submitDialog,
       snackbar,
       schemaLoading,
+      importErrorSnackbar,
+      notImportedWorksheetNames,
       /* methods */
       doSubmit,
       downloadSamples,
@@ -572,6 +585,13 @@ export default defineComponent({
         >
           Validation Passed! You can now submit or continue editing.
         </v-snackbar>
+        <v-snackbar
+          v-model="importErrorSnackbar"
+          color="error"
+          timeout="5000"
+        >
+          The following worksheet names were not recognized: {{ notImportedWorksheetNames.join(', ') }}
+        </v-snackbar>
         <v-card
           v-if="validationErrorGroups.length"
           color="error"

web/src/views/SubmissionPortal/harmonizerApi.ts

@@ -60,6 +60,8 @@ interface HarmonizerTemplateInfo {
   schemaClass?: string,
   sampleDataSlot?: string,
   status: 'published' | 'mixin' | 'disabled',
+  // This value comes from annotations in the schema. It will be populated once the schema is loaded.
+  excelWorksheetName?: string,
 }
 export const HARMONIZER_TEMPLATES: Record<string, HarmonizerTemplateInfo> = {
   air: {
@@ -208,6 +210,20 @@ export class HarmonizerApi {
     this.schema = schema;
     this.goldEcosystemTree = goldEcosystemTree;
 
+    // Attempt to find each template's underlying schema class, pull the excel_worksheet_name annotation from it
+    // and add it to the template object.
+    Object.values(HARMONIZER_TEMPLATES).forEach((template) => {
+      if (!template.schemaClass) {
+        return;
+      }
+      const classDefinition = schema.classes[template.schemaClass];
+      if (!classDefinition) {
+        return;
+      }
+      // eslint-disable-next-line no-param-reassign
+      template.excelWorksheetName = classDefinition.annotations?.excel_worksheet_name?.value;
+    });
+
     this.dh = new DataHarmonizer(r, {
       modalsRoot: document.querySelector('.harmonizer-style-container'),
       fieldSettings: this._getFieldSettings(),

web/yarn.lock

@@ -7635,9 +7635,9 @@ nice-try@^1.0.4:
   resolved "https://registry.yarnpkg.com/nice-try/-/nice-try-1.0.5.tgz#a3378a7696ce7d223e88fc9b764bd7ef1089e366"
   integrity sha512-1nh45deeb5olNY7eX82BkPO7SSxR5SSYJiPTrTdFUVYwAl8CKMA5N9PjTYkHiRjisVcxcQ1HXdLhx2qxxJzLNQ==
 
-"nmdc-schema@https://github.com/microbiomedata/nmdc-schema#v10.5.5":
+"nmdc-schema@https://github.com/microbiomedata/nmdc-schema#v10.7.0":
   version "0.0.0"
-  resolved "https://github.com/microbiomedata/nmdc-schema#0ed6dfd1823deaa8ede6ca8250188429d7d86305"
+  resolved "https://github.com/microbiomedata/nmdc-schema#ad1440736c1e088705a8b09f88727c0e195abfb3"
 
 no-case@^2.2.0:
   version "2.3.2"