Add correlation refactor migration plugin

Model/src/main/java/org/gusdb/wdk/model/fix/table/edaanalysis/plugins/CorrelationRefactorPlugin.java

@@ -0,0 +1,99 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis.plugins;
+
+import org.apache.log4j.Logger;
+import org.gusdb.wdk.model.WdkModel;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces;
+import org.gusdb.wdk.model.fix.table.edaanalysis.AbstractAnalysisUpdater;
+import org.gusdb.wdk.model.fix.table.edaanalysis.AnalysisRow;
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+public class CorrelationRefactorPlugin extends AbstractAnalysisUpdater {
+  private static final Logger LOG = Logger.getLogger(CorrelationRefactorPlugin.class);
+
+  @Override
+  public void configure(WdkModel wdkModel, List<String> additionalArgs) throws Exception {
+    super.configure(wdkModel, additionalArgs);
+  }
+
+  @Override
+  public TableRowInterfaces.RowResult<AnalysisRow> processRecord(AnalysisRow nextRow) throws Exception {
+    JSONObject descriptor = nextRow.getDescriptor();
+    JSONArray computations = descriptor.getJSONArray("computations");
+
+    LOG.info("Descriptor before migration: " + descriptor);
+
+    boolean updateNeeded = computations.toList().stream()
+        .anyMatch(CorrelationRefactorPlugin::needsUpdate);
+
+    if (!updateNeeded) {
+      // Short-circuit to avoid doing migration work.
+      return new TableRowInterfaces.RowResult<>(nextRow)
+          .setShouldWrite(false);
+    }
+
+    List<JSONObject> updatedComputations = computations.toList().stream()
+        .map(computation -> migrateComputation(new JSONObject((Map<?, ?>) computation)))
+        .collect(Collectors.toList());
+
+    descriptor.put("computations", updatedComputations);
+
+    LOG.info("Descriptor after migration: " + descriptor);
+
+    return new TableRowInterfaces.RowResult<>(nextRow)
+        .setShouldWrite(_writeToDb);
+  }
+
+  private static boolean needsUpdate(Object computation) {
+    List<String> migratableComputeTypes = List.of("correlationassaymetadata", "correlationassayassay");
+    return migratableComputeTypes.contains(new JSONObject((Map<?, ?>) computation).getJSONObject("descriptor").getString("type"));
+  }
+
+  /**
+   * Migrates a computation, mutating it in-place and returning the migrated object.
+   *
+   * Only migrates computations of type:
+   *   - correlationassaymetadata
+   *   - correlationassayassay
+   * @param computation Specification of the computation to migrate.
+   * @return Migrated computation.
+   */
+  private JSONObject migrateComputation(JSONObject computation) {
+    String computationType = computation.getJSONObject("descriptor").getString("type");
+    JSONObject descriptor = computation.getJSONObject("descriptor");
+    if (computationType.equals("correlationassaymetadata")) {
+      JSONObject configuration = descriptor.getJSONObject("configuration");
+      descriptor.put("type", "correlation");
+
+      configuration.put("data1", configuration.getJSONObject("collectionVariable"));
+      configuration.getJSONObject("data1").put("dataType", "collection");
+      configuration.remove("collectionVariable");
+
+      configuration.put("data2", new JSONObject());
+      configuration.getJSONObject("data2").put("dataType", "metadata");
+      return computation;
+    } else if (computationType.equals("correlationassayassay")) {
+      JSONObject configuration = descriptor.getJSONObject("configuration");
+      descriptor.put("type", "correlation");
+
+      configuration.put("data1", configuration.getJSONObject("collectionVariable1"));
+      configuration.getJSONObject("data1").put("dataType", "collection");
+      configuration.remove("collectionVariable1");
+
+      configuration.put("data2", configuration.getJSONObject("collectionVariable2"));
+      configuration.getJSONObject("data2").put("dataType", "collection");
+      configuration.remove("collectionVariable2");
+      return computation;
+    }
+    return computation;
+  }
+
+  @Override
+  public void dumpStatistics() {
+
+  }
+}

Model/src/test/java/org/gusdb/wdk/model/fix/table/edaanalysis/plugins/CorrelationRefactorPluginTest.java

@@ -0,0 +1,143 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis.plugins;
+
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces;
+import org.gusdb.wdk.model.fix.table.edaanalysis.AnalysisRow;
+import org.json.JSONObject;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CorrelationRefactorPluginTest {
+
+  @Test
+  public void test() throws Exception {
+    CorrelationRefactorPlugin plugin = new CorrelationRefactorPlugin();
+    TableRowInterfaces.RowResult<AnalysisRow> result = plugin.processRecord(new AnalysisRow("id", "id", new JSONObject(testConfig()), 3, 3, 3));
+    String descriptorAsString = result.getRow().getDescriptor().toString();
+    Assert.assertTrue(descriptorAsString.contains("data1"));
+    Assert.assertTrue(descriptorAsString.contains("data2"));
+  }
+
+  private static String testConfig() {
+    return "{\n" +
+        "  \"subset\": {\n" +
+        "    \"descriptor\": [],\n" +
+        "    \"uiSettings\": {}\n" +
+        "  },\n" +
+        "  \"computations\": [\n" +
+        "    {\n" +
+        "      \"computationId\": \"iopsx\",\n" +
+        "      \"descriptor\": {\n" +
+        "        \"type\": \"correlationassaymetadata\",\n" +
+        "        \"configuration\": {\n" +
+        "          \"prefilterThresholds\": {\n" +
+        "            \"proportionNonZero\": 0.05,\n" +
+        "            \"variance\": 0,\n" +
+        "            \"standardDeviation\": 0\n" +
+        "          },\n" +
+        "          \"collectionVariable\": {\n" +
+        "            \"entityId\": \"EUPATH_0000808\",\n" +
+        "            \"collectionId\": \"EUPATH_0009256\"\n" +
+        "          },\n" +
+        "          \"correlationMethod\": \"spearman\"\n" +
+        "        }\n" +
+        "      },\n" +
+        "      \"visualizations\": [\n" +
+        "        {\n" +
+        "          \"visualizationId\": \"e7411924-0ecb-48c9-9a8f-f8ea3ed73468\",\n" +
+        "          \"displayName\": \"Taxa correlated with age\",\n" +
+        "          \"descriptor\": {\n" +
+        "            \"type\": \"bipartitenetwork\",\n" +
+        "            \"configuration\": {\n" +
+        "              \"correlationCoefThreshold\": 0.5,\n" +
+        "              \"significanceThreshold\": 0.05\n" +
+        "            },\n" +
+        "            \"currentPlotFilters\": []\n" +
+        "          }\n" +
+        "        }\n" +
+        "      ]\n" +
+        "    },\n" +
+        "    {\n" +
+        "      \"computationId\": \"jwdb9\",\n" +
+        "      \"descriptor\": {\n" +
+        "        \"type\": \"abundance\",\n" +
+        "        \"configuration\": {\n" +
+        "          \"collectionVariable\": {\n" +
+        "            \"collectionId\": \"EUPATH_0009256\",\n" +
+        "            \"entityId\": \"EUPATH_0000808\"\n" +
+        "          },\n" +
+        "          \"rankingMethod\": \"variance\"\n" +
+        "        }\n" +
+        "      },\n" +
+        "      \"visualizations\": [\n" +
+        "        {\n" +
+        "          \"visualizationId\": \"6e6afcbf-fbf0-4d3c-bfa3-ab7bbc92dda9\",\n" +
+        "          \"displayName\": \"Top taxa by age (genus); faceted by case/control status\",\n" +
+        "          \"descriptor\": {\n" +
+        "            \"type\": \"boxplot\",\n" +
+        "            \"configuration\": {\n" +
+        "              \"dependentAxisValueSpec\": \"Full\",\n" +
+        "              \"overlayVariable\": {\n" +
+        "                \"entityId\": \"EUPATH_0000096\",\n" +
+        "                \"variableId\": \"EUPATH_0051008\"\n" +
+        "              },\n" +
+        "              \"facetVariable\": {\n" +
+        "                \"entityId\": \"EUPATH_0000096\",\n" +
+        "                \"variableId\": \"EUPATH_0010375\"\n" +
+        "              }\n" +
+        "            },\n" +
+        "            \"currentPlotFilters\": []\n" +
+        "          }\n" +
+        "        }\n" +
+        "      ]\n" +
+        "    },\n" +
+        "    {\n" +
+        "      \"computationId\": \"pia0q\",\n" +
+        "      \"descriptor\": {\n" +
+        "        \"type\": \"alphadiv\",\n" +
+        "        \"configuration\": {\n" +
+        "          \"collectionVariable\": {\n" +
+        "            \"collectionId\": \"EUPATH_0009256\",\n" +
+        "            \"entityId\": \"EUPATH_0000808\"\n" +
+        "          },\n" +
+        "          \"alphaDivMethod\": \"shannon\"\n" +
+        "        }\n" +
+        "      },\n" +
+        "      \"visualizations\": [\n" +
+        "        {\n" +
+        "          \"visualizationId\": \"e7d48cfb-aeb4-4f2a-9c68-699a27ebefa6\",\n" +
+        "          \"displayName\": \"Alpha div (genus) by age w/ case/control status as overlay\",\n" +
+        "          \"descriptor\": {\n" +
+        "            \"type\": \"boxplot\",\n" +
+        "            \"configuration\": {\n" +
+        "              \"dependentAxisValueSpec\": \"Full\",\n" +
+        "              \"xAxisVariable\": {\n" +
+        "                \"entityId\": \"EUPATH_0000096\",\n" +
+        "                \"variableId\": \"EUPATH_0051008\"\n" +
+        "              },\n" +
+        "              \"overlayVariable\": {\n" +
+        "                \"entityId\": \"EUPATH_0000096\",\n" +
+        "                \"variableId\": \"EUPATH_0010375\"\n" +
+        "              }\n" +
+        "            },\n" +
+        "            \"currentPlotFilters\": []\n" +
+        "          }\n" +
+        "        }\n" +
+        "      ]\n" +
+        "    }\n" +
+        "  ],\n" +
+        "  \"starredVariables\": [\n" +
+        "    {\n" +
+        "      \"entityId\": \"EUPATH_0000096\",\n" +
+        "      \"variableId\": \"EUPATH_0010375\"\n" +
+        "    },\n" +
+        "    {\n" +
+        "      \"entityId\": \"EUPATH_0000096\",\n" +
+        "      \"variableId\": \"EUPATH_0010367\"\n" +
+        "    }\n" +
+        "  ],\n" +
+        "  \"dataTableConfig\": {},\n" +
+        "  \"derivedVariables\": []\n" +
+        "}";
+  }
+}