From 79602f5bab81c4ae39e8eefc08667d895a56da2a Mon Sep 17 00:00:00 2001
From: Ryan Doherty <tech@conical.org>
Date: Tue, 4 Nov 2025 16:13:11 -0500
Subject: [PATCH] Special processing for gene orthologs table when downloading
 result

---
 .../model/report/TranscriptTableReporter.java | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/TranscriptTableReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/TranscriptTableReporter.java
index 88b0a09f8..efa7fb6c5 100644
--- a/Model/src/main/java/org/apidb/apicommon/model/report/TranscriptTableReporter.java
+++ b/Model/src/main/java/org/apidb/apicommon/model/report/TranscriptTableReporter.java
@@ -1,18 +1,29 @@
 package org.apidb.apicommon.model.report;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 import org.apidb.apicommon.model.TranscriptUtil;
+import org.gusdb.fgputil.json.JsonUtil;
 import org.gusdb.wdk.model.WdkModelException;
 import org.gusdb.wdk.model.WdkRuntimeException;
 import org.gusdb.wdk.model.WdkUserException;
+import org.gusdb.wdk.model.answer.stream.RecordStream;
+import org.gusdb.wdk.model.answer.stream.SingleTableRecordStream;
+import org.gusdb.wdk.model.query.param.FlatVocabParam;
 import org.gusdb.wdk.model.report.ReporterConfigException;
 import org.gusdb.wdk.model.report.reporter.TableTabularReporter;
+import org.json.JSONArray;
 import org.json.JSONObject;
 
 public class TranscriptTableReporter extends TableTabularReporter {
 
   private String _originalQuestionName;
+  private String _customTableSql;
 
   @Override
   public TranscriptTableReporter configure(Map<String, String> config) {
@@ -24,8 +35,24 @@ public TranscriptTableReporter configure(JSONObject config) throws ReporterConfi
     try {
       _originalQuestionName = _baseAnswer.getQuestion().getName();
       _baseAnswer = TranscriptUtil.transformToGeneAnswer(_baseAnswer);
+
       // now that base answer is a Gene answer, check and assign selected table field name
       super.configure(config);
+
+      // need special processing for orthologs table
+      if (_tableField.getName().equals("OrthologsLite")) {
+
+        // look up ortholog organism option on config and convert to abbrevs
+        List<String> orgAbbrevs = findOrgAbbrevs(config);
+
+        // use ortholog table with organism filtering based on reporter config
+        _tableField = _baseAnswer.getQuestion().getRecordClass().getTableFieldMap().get("OrthologsLiteForDownload");
+
+        // build custom table SQL
+        String rawSql = _baseAnswer.getTableFieldResultSql(_tableField);
+        _customTableSql = rawSql.replace("$$orthologPartitionKeys$$", orgAbbrevs.stream().collect(Collectors.joining("','","'","'")));
+
+      }
       return this;
     }
     catch (WdkUserException e) {
@@ -36,6 +63,37 @@ public TranscriptTableReporter configure(JSONObject config) throws ReporterConfi
     }
   }
 
+  private List<String> findOrgAbbrevs(JSONObject config) throws ReporterConfigException, WdkModelException {
+
+    // look for org filtering parameter on reporter config
+    JSONArray orgsJson = config.optJSONArray("orthologOrganisms");
+    if (orgsJson == null)
+      throw new ReporterConfigException("OrthologsLite table requires an additional config value 'orthologOrganisms', an array of organism terms");
+    List<String> orgTerms = Arrays.asList(JsonUtil.toStringArray(orgsJson));
+
+    // look up term to internal map for organism param; internal value is org_abbrev
+    FlatVocabParam orgParam = (FlatVocabParam)_baseAnswer.getWdkModel().getQuestionByName("GenesByTaxon").get().getParamMap().get("organism");
+    Map<String,String> termsToInternalMap = orgParam.getVocabInstance(_baseAnswer.getRequestingUser(), Collections.emptyMap()).getVocabMap();
+
+    // convert terms to internal values
+    List<String> orgAbbrevs = new ArrayList<>();
+    for (String term : orgTerms) {
+      String internal = termsToInternalMap.get(term);
+      if (internal == null) {
+        throw new ReporterConfigException("At least one passed ortholog organsim is invalid ('" + term + "').");
+      }
+      orgAbbrevs.add(internal);
+    }
+    return orgAbbrevs;
+  }
+
+  @Override
+  protected RecordStream getSingleTableRecordStream() throws WdkModelException {
+    return _customTableSql == null
+      ? super.getSingleTableRecordStream()
+      : new SingleTableRecordStream(_baseAnswer, _tableField, _customTableSql);
+  }
+
   @Override
   public String getDownloadFileName() {
     return getDownloadFileName(_originalQuestionName);