Merge pull request #82 from VEuPathDB/eda-analysis-migration

New classes to support EDA analysis migrations

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

@@ -0,0 +1,30 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis;
+
+import java.util.List;
+
+import org.gusdb.wdk.model.WdkModel;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces.TableRowUpdaterPlugin;
+import org.gusdb.wdk.model.fix.table.TableRowUpdater;
+
+/**
+ * Abstract class serves as a base for any plugins that need to
+ * update/migrate the rows in the EDA analysis table
+ */
+public abstract class AbstractAnalysisUpdater implements TableRowUpdaterPlugin<AnalysisRow> {
+
+  protected WdkModel _wdkModel;
+  protected boolean _writeToDb = false;
+
+  @Override
+  public void configure(WdkModel wdkModel, List<String> additionalArgs) throws Exception {
+    _wdkModel = wdkModel;
+    _writeToDb = additionalArgs.size() > 0 && additionalArgs.get(0).equals("-write");
+  }
+
+  @Override
+  public TableRowUpdater<AnalysisRow> getTableRowUpdater(WdkModel wdkModel) {
+    AnalysisRecordFactory factory = new AnalysisRecordFactory();
+    return new TableRowUpdater<AnalysisRow>(factory, factory, this, wdkModel);
+  }
+
+}

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

@@ -0,0 +1,74 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
+import java.util.Collection;
+
+import org.gusdb.fgputil.ListBuilder;
+import org.gusdb.fgputil.db.platform.DBPlatform;
+import org.gusdb.wdk.model.WdkModel;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces.TableRowFactory;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces.TableRowWriter;
+
+/**
+ * Provides the read/write mechanisms for updating EDA analysis table rows needed by the
+ * TableRowUpdater API.
+ */
+public class AnalysisRecordFactory implements TableRowFactory<AnalysisRow>, TableRowWriter<AnalysisRow> {
+
+  private String _schema;
+
+  @Override
+  public String getRecordsSql(String schema, String projectId) {
+    // reset schema based on project (userdb schema is not where eda data lives
+    switch(projectId) {
+      case "ClinEpiDB": _schema = "edauserce"; break;
+      case "MicrobiomeDB": _schema = "edausermb"; break;
+      default: _schema = "edauservb"; break;
+    }
+    return
+        "select analysis_id, study_id, analysis_descriptor, num_filters, num_computations, num_visualizations" +
+        " from " + _schema + ".analysis";
+  }
+
+  @Override
+  public AnalysisRow newTableRow(ResultSet rs, DBPlatform platform) throws SQLException {
+    return new AnalysisRow(rs, platform);
+  }
+
+  @Override
+  public String getWriteSql(String schema) {
+    return
+        "update " + _schema + ".analysis (study_id, analysis_descriptor, num_filters, num_computations, num_visualizations)" +
+        " values (?, ?, ?, ?, ?) where analysis_id = ?";
+  }
+
+  @Override
+  public Integer[] getParameterTypes() {
+    return new Integer[] {
+        Types.VARCHAR,
+        Types.CLOB,
+        Types.INTEGER,
+        Types.INTEGER,
+        Types.INTEGER,
+        Types.VARCHAR
+    };
+  }
+
+  @Override
+  public Collection<Object[]> toValues(AnalysisRow obj) {
+    return ListBuilder.asList(obj.toOrderedValues());
+  }
+
+  @Override
+  public void setUp(WdkModel wdkModel) throws Exception {
+    // nothing to do here
+  }
+
+  @Override
+  public void tearDown(WdkModel wdkModel) throws Exception {
+    // nothing to do here
+  }
+
+}

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

@@ -0,0 +1,84 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Optional;
+
+import org.gusdb.fgputil.db.platform.DBPlatform;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces.TableRow;
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+/**
+ * Stores values of a database row in the EDA analysis table
+ */
+public class AnalysisRow implements TableRow {
+
+  // basic analysis information
+  private String _analysisId;
+  private String _datasetId;
+  private JSONObject _descriptor;
+
+  // bookkeeping; update these if values change in descriptor
+  private int _numFilters;
+  private int _numComputations;
+  private int _numVisualizations;
+
+  public AnalysisRow(ResultSet rs, DBPlatform platform) throws SQLException {
+    _analysisId = rs.getString("analysis_id");
+    _datasetId = rs.getString("study_id");
+    _descriptor = new JSONObject(platform.getClobData(rs, "analysis_descriptor"));
+    _numFilters = rs.getInt("num_filters");
+    _numComputations = rs.getInt("num_computations");
+    _numVisualizations = rs.getInt("num_visualizations");
+  }
+
+  public Object[] toOrderedValues() {
+    return new Object[] {
+        _datasetId, _descriptor.toString(), _numFilters, _numComputations, _numVisualizations, _analysisId
+    };
+  }
+
+  @Override
+  public String getDisplayId() {
+    return _analysisId;
+  }
+
+  public String getDatasetId() {
+    return _datasetId;
+  }
+
+  /**
+   * Returns the current descriptor for this analysis.  Note this object can be
+   * edited in-place before returning the row result; however if the number of
+   * filters, computations, or visualizations is modified, you must also call
+   * <code>refreshStats()</code> to refresh those counts or they will be inaccurate
+   * in the database.
+   *
+   * @return descriptor for this analysis
+   */
+  public JSONObject getDescriptor() {
+    return _descriptor;
+  }
+
+  /**
+   * Sets a new descriptor and refreshes the stats (number of filters, computations,
+   * and visualizations) on this analysis.
+   *
+   * @param descriptor new descriptor
+   */
+  public void setDescriptor(JSONObject descriptor) {
+    _descriptor = descriptor;
+    refreshStats();
+  }
+
+  public void refreshStats() {
+    _numFilters = _descriptor.getJSONObject("subset").getJSONArray("descriptor").length();
+    JSONArray computations = Optional.ofNullable(_descriptor.optJSONArray("computations")).orElse(new JSONArray());
+    _numComputations = computations.length();
+    _numVisualizations = 0;
+    for (int i = 0; i < _numComputations; i++) {
+      _numVisualizations += computations.getJSONObject(i).getJSONArray("visualizations").length();
+    }
+  }
+}