refactoring custom props

src/mol-model-props/pdbe/structure-quality-report.ts

@@ -33,7 +33,7 @@ export namespace StructureQualityReport {
             id: Column.Schema.int,
             ...mmCIF_residueId_schema,
             pdbx_PDB_model_num: Column.Schema.int,
-            issue_group_id: Column.Schema.int
+            issue_type_group_id: Column.Schema.int
         },
         pdbe_structure_quality_report_issue_types: {
             group_id: Column.Schema.int,
@@ -129,7 +129,7 @@ export namespace StructureQualityReport {
 const _structure_quality_report_issues_fields = CifWriter.fields<number, ReportExportContext['models'][0]>()
     .index('id')
     .many(residueIdFields((i, d) => d.elements[i], { includeModelNum: true }))
-    .int('group_id', (i, d) => d.groupId[i])
+    .int('issue_type_group_id', (i, d) => d.groupId[i])
     .getFields();
 
 interface ReportExportContext {
@@ -208,18 +208,16 @@ function createIssueMapFromCif(modelData: Model,
     groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): StructureQualityReport.IssueMap | undefined {
 
     const ret = new Map<ResidueIndex, string[]>();
-    const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issue_group_id, pdbx_PDB_model_num, _rowCount } = residueData;
+    const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issue_type_group_id, pdbx_PDB_model_num, _rowCount } = residueData;
 
     const groups = parseIssueTypes(groupData);
 
     for (let i = 0; i < _rowCount; i++) {
         if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue;
         const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
-        ret.set(idx, groups.get(issue_group_id.value(i))!);
+        ret.set(idx, groups.get(issue_type_group_id.value(i))!);
     }
 
-    console.log(ret);
-
     return IndexedCustomProperty.fromResidueMap(ret);
 }
 

src/servers/model/test.ts

@@ -34,22 +34,28 @@ function wrapFile(fn: string) {
     return w;
 }
 
-const basePath = path.join(__dirname, '..', '..', '..', '..')
-const examplesPath = path.join(basePath, 'examples')
-const outPath = path.join(basePath, 'build', 'test')
+export const basePath = path.join(__dirname, '..', '..', '..', '..')
+export const examplesPath = path.join(basePath, 'examples')
+export const outPath = path.join(basePath, 'build', 'test')
 if (!fs.existsSync(outPath)) fs.mkdirSync(outPath);
 
 async function run() {
     try {
         // const testFile = '1crn.cif'
+        // const testFile = '1grm_updated.cif'
+        // const testFile = 'C:/Projects/mol-star/molstar-proto/build/test/in/1grm_updated.cif'
+        // const request = createJob({
+        //     entryId: testFile,
+        //     queryName: 'full',
+        //     queryParams: { },
+        // });
         const testFile = '1grm_updated.cif'
-        //const testFile = 'C:/Projects/mol-star/molstar-proto/build/test/1grm_updated.cif'
         const request = createJob({
             entryId: path.join(examplesPath, testFile),
             queryName: 'full',
-            queryParams: { },
-            // options: { modelNums: [ 2, 3 ] }
+            queryParams: { }
         });
+
         // const request = createJob({
         //     entryId: path.join(examplesPath, testFile),
         //     queryName: 'atoms',
@@ -67,6 +73,7 @@ async function run() {
         // });
         const encoder = await resolveJob(request);
         const writer = wrapFile(path.join(outPath, testFile));
+        // const writer = wrapFile(path.join(outPath, '1grm_test.cif'));
         encoder.writeTo(writer);
         writer.end();
     } catch (e) {