Implemented Mutation Meta Data Support

Author: Nils Fo

src/main/java/de/rub/bph/omnineuro/client/core/db/OmniNeuroQueryExecutor.java

@@ -21,6 +21,10 @@ public synchronized boolean insertIndividual(long id, String name, long sexID, l
 		return execute("INSERT INTO individual VALUES (" + id + ",'" + name + "'," + sexID + "," + speciesID + ");");
 	}
 
+	public synchronized boolean insertMutation(long id, String name) throws SQLException {
+		return execute("INSERT INTO mutation VALUES (" + id + ",'" + name + "');");
+	}
+	
 	public synchronized boolean insertComment(String text, long experimentID) throws SQLException {
 		return execute("INSERT INTO comment VALUES (DEFAULT, '" + text + "'," + experimentID + ");");
 	}
@@ -33,9 +37,9 @@ public synchronized boolean insertPassage(long experimentID, long timestamp, int
 		return execute("INSERT INTO passage VALUES (DEFAULT, " + experimentID + "," + timestamp + "," + p + ");");
 	}
 
-	public synchronized boolean insertExperiment(long id, long timestamp, String name, long projectID, long labID, long individualID, long compoundID, long cellTypeID, long assayID, long plateFormatID, long solventID, double solventConcentration, String controlWellID) throws SQLException {
+	public synchronized boolean insertExperiment(long id, long timestamp, String name, long projectID, long labID, long individualID, long mutationID, long compoundID, long cellTypeID, long assayID, long plateFormatID, long solventID, double solventConcentration, String controlWellID) throws SQLException {
 		return execute("INSERT INTO experiment VALUES (" + id + "," + timestamp + ",'" + name + "'," + projectID +
-				"," + labID + "," + individualID + "," + compoundID + "," + cellTypeID + "," + assayID + "," + plateFormatID + "," + solventID + "," + solventConcentration + ", '" + controlWellID + "');");
+				"," + labID + "," + individualID + "," + compoundID + "," + cellTypeID + "," + assayID + "," + plateFormatID + "," + solventID + "," + solventConcentration + ", '" + controlWellID + "', " + mutationID + ");");
 	}
 
 	public synchronized boolean insertCompound(String name, String casNR, String abbreviation, boolean blinded) throws SQLException {
@@ -50,6 +54,8 @@ public synchronized boolean resetDatabase() throws SQLException {
 		b &= deleteTable("passage", true);
 		b &= deleteTable("experiment", true);
 		b &= deleteTable("well", true);
+		b &= deleteTable("individual", true);
+		b &= deleteTable("mutation", true);
 		b &= deleteBlindedCompounds();
 
 		b &= insertWell("Unknown");

src/main/java/de/rub/bph/omnineuro/client/core/db/QueryExecutor.java

@@ -12,6 +12,7 @@ public class QueryExecutor {
 
 	private Connection connection;
 	private boolean logEnabled;
+	private static String lastCachedQuery = null;
 
 	public QueryExecutor(Connection connection) {
 		this.connection = connection;
@@ -20,6 +21,7 @@ public QueryExecutor(Connection connection) {
 
 	public synchronized ResultSet executeQuery(String query) throws SQLException {
 		synchronized (connection) {
+			setLastCachedQuery(query);
 			if (connection.isClosed()) {
 				Log.w("Connection closed unexpectedly! Reconnecting...");
 				DBConnection c = DBConnection.getDBConnection();
@@ -37,6 +39,7 @@ public synchronized ResultSet executeQuery(String query) throws SQLException {
 	}
 
 	public synchronized boolean execute(String query) throws SQLException {
+		setLastCachedQuery(query);
 		Statement stmt = connection.createStatement();
 
 		if (isLogEnabled()) {
@@ -284,10 +287,27 @@ public boolean deleteTable(String tableName, String sequenceName) throws SQLExce
 		return b;
 	}
 
+	public synchronized boolean isExecutableQuery(String query) {
+		try {
+			executeQuery(query);
+		} catch (SQLException e) {
+			return false;
+		}
+		return true;
+	}
+	
 	public Connection getConnection() {
 		return connection;
 	}
 
+	public static synchronized String getLastCachedQuery() {
+		return lastCachedQuery;
+	}
+	
+	private static synchronized void setLastCachedQuery(String pLastCachedQuery) {
+		lastCachedQuery = pLastCachedQuery;
+	}
+	
 	public boolean isLogEnabled() {
 		return logEnabled;
 	}
@@ -296,13 +316,4 @@ public void setLogEnabled(boolean logEnabled) {
 		this.logEnabled = logEnabled;
 	}
 
-	public synchronized boolean isExecutableQuery(String query) {
-		try {
-			executeQuery(query);
-		} catch (SQLException e) {
-			return false;
-		}
-		return true;
-	}
-	
 }

src/main/java/de/rub/bph/omnineuro/client/core/db/in/AXESInserter.java

@@ -1,5 +1,6 @@
 package de.rub.bph.omnineuro.client.core.db.in;
 
+import de.rub.bph.omnineuro.client.core.db.QueryExecutor;
 import de.rub.bph.omnineuro.client.core.db.out.holder.CompoundHolder;
 import de.rub.bph.omnineuro.client.core.sheet.data.DateInterpreter;
 import de.rub.bph.omnineuro.client.imported.log.Log;
@@ -21,6 +22,11 @@ public class AXESInserter extends DBInserter implements Runnable {
 	private JSONObject data;
 	private String name;
 
+	public static final String INVALID_INDIVIDUAL_NAME = "<unknown individual>";
+	public static final String INVALID_MUTATION_NAME = "<unknown mutation>";
+	public static final String INVALID_SEX_NAME = "undefined";
+	public static final String INVALID_SPECIES_NAME = "unknown";
+	
 	public AXESInserter(JSONObject data, boolean attemptUnblinding) {
 		super(attemptUnblinding);
 		this.data = data;
@@ -34,24 +40,19 @@ public AXESInserter(JSONObject data, boolean attemptUnblinding) {
 		}
 	}
 
-	private synchronized long getIndividualID(String individual, String sex, String species) throws JSONException, SQLException {
-		long individualID;
+	private synchronized long getMutationID(String mutation) throws SQLException {
+		long mutationID;
 
 		synchronized (executor) {
 			try {
-				individualID = executor.getIDViaName("individual", individual);
+				mutationID = executor.getIDViaName("mutation", mutation);
 			} catch (Throwable e) {
-				long sexID = executor.getIDViaFeature("sex", "label", sex);
-				long speciesID = executor.getIDViaName("species", species);
-				
-				individualID = executor.getNextSequenceTableVal("individual");
-				executor.insertIndividual(individualID, individual, sexID, speciesID);
-				Log.i("New individual inserted into the database. Name: '" + individual + "'. ID: " + individualID);
-				addError("Warning. Individual '" + individual + "' was not in the database. It has been added. Species: " + species + ". Sex: " + sex);
+				mutationID = executor.getNextSequenceTableVal("mutation");
+				executor.insertMutation(mutationID, mutation);
 			}
 		}
 
-		return individualID;
+		return mutationID;
 	}
 
 	@Override
@@ -70,16 +71,24 @@ public void run() {
 			String projectName = metaDataGeneral.getString("Project");
 			String assay = metaDataGeneral.getString("Assay");
 			String experimentName = metaDataGeneral.getString("ExperimentID");
-			String individual = metaDataGeneral.getString("Individual");
 			String compound = metaDataGeneral.getString("Compound");
 			String casNR = metaDataGeneral.getString("CAS No.");
-			String compuntAbbreviation = metaDataGeneral.getString("Compound abbreviation");
+			String compoundAbbreviation = metaDataGeneral.getString("Compound abbreviation");
 			String cellType = metaDataGeneral.getString("Cell type");
 			String species = metaDataGeneral.getString("Species");
 			String plateFormat = metaDataGeneral.getString("Plateformat");
 			String sex = metaDataGeneral.getString("Sex");
 			String workgroup = metaDataGeneral.getString("Department"); //Workgroup under department? Yep. This is intentional.
 
+			String individual = null;
+			String mutation = null;
+			if (metaDataGeneral.has("Individual")) {
+				individual = metaDataGeneral.getString("Individual");
+			}
+			if (metaDataGeneral.has("Mutation")) {
+				mutation = metaDataGeneral.getString("Mutation");
+			}
+			
 			if (compound.equals("0.0")) {
 				//If there was no compound meta data sheet provided, the formula evaluator returns '0.0'. That's an error.
 				throw new IllegalStateException("Failed to read the meta data sheet containing the compound for " + experimentName + "!");
@@ -92,10 +101,14 @@ public void run() {
 
 			String solvent = metaDataSolvent.getString("Solvent");
 			solvent = solvent.toUpperCase().trim();
-			double solventConcentration = -1;
+			double solventConcentration = -1.0;
 			if (metaDataSolvent.has("Solvent conc.*")) {
 				solventConcentration = metaDataSolvent.getDouble("Solvent conc.*");
 			}
+			if (Double.isNaN(solventConcentration)) {
+				addError("Warning: Solvent has illegal values!");
+				solventConcentration = -1.0;
+			}
 
 			long solventID = -1;
 			try {
@@ -125,17 +138,30 @@ public void run() {
 				addError("Compound is unknown!", true);
 			}
 
-			//Next: Insert it into the database
-			Log.i("TODO: Actually insert it now...");
+			long individualID;
+			long mutationID;
+			if (individual == null && mutation == null) {
+				addError("Sheet has neither an individual or a mutation!");
+			}
+			
+			if (individual == null) {
+				individualID = getInvalidIndividualID();
+			} else {
+				individualID = getIndividualID(individual, sex, species);
+			}
+			if (mutation == null) {
+				mutationID = getInvalidMutationID();
+			} else {
+				mutationID = getMutationID(mutation);
+			}
 
 			//But first: Let me take a sel... the necessary IDs of existing meta data from the Database
 			long assayID = executor.getIDViaName("assay", assay);
 			long cellTypeID = executor.getIDViaName("cell_type", cellType);
 			long projectID = executor.getIDViaName("project", projectName);
-			long plateformatID = executor.getIDViaName("plate_format", plateFormat);
+			long plateFormatID = executor.getIDViaName("plate_format", plateFormat);
 			long workgroupID = executor.getIDViaName("workgroup", workgroup);
 
-			long individualID = getIndividualID(individual, sex, species);
 			long wellNotAvailableID = executor.getIDViaName("well", "Unknown");
 			long detectionMethodNotAvailableID = executor.getIDViaName("detection_method", "Unknown");
 
@@ -157,7 +183,7 @@ public void run() {
 						}
 					}
 				} else {
-					addError("Failed to resolve compound name: '" + compound + "' [" + compuntAbbreviation + "]. That's okay, if a valid Cas Nr. is provided instead: '" + casNR + "'.");
+					addError("Failed to resolve compound name: '" + compound + "' [" + compoundAbbreviation + "]. That's okay, if a valid Cas Nr. is provided instead: '" + casNR + "'.");
 					compoundID = executor.getIDViaFeature("compound", "cas_no", casNR);
 					String newCompoundName = executor.getNameViaID("compound", compoundID);
 					addError("\t\t\tBut that CAS Nr. existed in the DB and the compound was resolved as '" + newCompoundName + "'.");
@@ -182,7 +208,7 @@ public void run() {
 					if (compoundHolder != null) {
 						compound = compoundHolder.getName();
 						casNR = compoundHolder.getCas();
-						compuntAbbreviation = compoundHolder.getAbbreviation();
+						compoundAbbreviation = compoundHolder.getAbbreviation();
 						compoundID = compoundHolder.getCompoundID();
 					}
 				} else {
@@ -193,7 +219,7 @@ public void run() {
 			long experimentID;
 			synchronized (executor) {
 				experimentID = executor.getNextSequenceTableVal("experiment");
-				executor.insertExperiment(experimentID, date.getTime(), experimentName, projectID, workgroupID, individualID, compoundID, cellTypeID, assayID, plateformatID, solventID, solventConcentration, controlPlateID);
+				executor.insertExperiment(experimentID, date.getTime(), experimentName, projectID, workgroupID, individualID, mutationID, compoundID, cellTypeID, assayID, plateFormatID, solventID, solventConcentration, controlPlateID);
 			}
 
 			for (String passageP : JSONOperator.getKeys(metaDataPassages)) {
@@ -328,13 +354,71 @@ public void run() {
 				}
 			}
 		} catch (Throwable e) {
+			String fatalErrorText = " == FATAL ERROR! == Failed to insert Experiment " + getName() + " into the database! Error Type: " + e.getClass().getSimpleName() + ". Reason: '" + e.getMessage() + "'";
+			if (e instanceof SQLException) {
+				fatalErrorText = fatalErrorText + ". Last SQL query: " + QueryExecutor.getLastCachedQuery();
+			}
+			
 			Log.e("Failed to insert Experiment: " + getName(), e);
-			addError(" == FATAL ERROR! == Failed to insert Experiment " + getName() + " into the database! Error Type: " + e.getClass().getSimpleName() + ". Reason: '" + e.getMessage() + "'");
+			addError(fatalErrorText);
 		}
 		Log.i("Finished inserting responses for " + getName() + ". Count: " + getInsertedResponsesCount());
 		setFinished();
 	}
 
+	private synchronized long getIndividualID(String individual, String sex, String species) throws JSONException, SQLException {
+		long individualID;
+		
+		synchronized (executor) {
+			try {
+				individualID = executor.getIDViaName("individual", individual);
+			} catch (Throwable e) {
+				long sexID = executor.getIDViaFeature("sex", "label", sex);
+				long speciesID = executor.getIDViaName("species", species);
+				
+				individualID = executor.getNextSequenceTableVal("individual");
+				executor.insertIndividual(individualID, individual, sexID, speciesID);
+				Log.i("New individual inserted into the database. Name: '" + individual + "'. ID: " + individualID);
+				addError("Warning. Individual '" + individual + "' was not in the database. It has been added. Species: " + species + ". Sex: " + sex);
+			}
+		}
+		
+		return individualID;
+	}
+	
+	public static synchronized long getInvalidIndividualID() throws JSONException, SQLException {
+		long individualID;
+		
+		synchronized (executor) {
+			try {
+				individualID = executor.getIDViaName("individual", INVALID_INDIVIDUAL_NAME);
+			} catch (Throwable e) {
+				long sexID = executor.getIDViaFeature("sex", "label", INVALID_SEX_NAME);
+				long speciesID = executor.getIDViaName("species", INVALID_SPECIES_NAME);
+				
+				individualID = executor.getNextSequenceTableVal("individual");
+				executor.insertIndividual(individualID, INVALID_INDIVIDUAL_NAME, sexID, speciesID);
+			}
+		}
+		
+		return individualID;
+	}
+	
+	public static synchronized long getInvalidMutationID() throws SQLException {
+		long mutationID;
+		
+		synchronized (executor) {
+			try {
+				mutationID = executor.getIDViaName("mutation", INVALID_MUTATION_NAME);
+			} catch (Throwable e) {
+				mutationID = executor.getNextSequenceTableVal("mutation");
+				executor.insertMutation(mutationID, INVALID_MUTATION_NAME);
+			}
+		}
+		
+		return mutationID;
+	}
+	
 	@Override
 	public String getName() {
 		return name;

src/main/java/de/rub/bph/omnineuro/client/core/db/in/KonstanzInserter.java

@@ -330,10 +330,11 @@ public void run() {
 							//TODO Add solvent ID to UKN assay experiments
 							long solventID = -1;
 							double solventConcentration = -1d;
+							long mutationID = AXESInserter.getInvalidMutationID();
 							String controlPlateID = "<Unknown>";
 
 							experimentID = executor.getNextSequenceTableVal("experiment");
-							executor.insertExperiment(experimentID, timestampExperiment, experimentName, projectID, workgroupID, individualID, compoundID, cellTypeID, assayID, plateFormatID, solventID, solventConcentration, controlPlateID);
+							executor.insertExperiment(experimentID, timestampExperiment, experimentName, projectID, workgroupID, individualID, mutationID, compoundID, cellTypeID, assayID, plateFormatID, solventID, solventConcentration, controlPlateID);
 						}
 						Log.v("Experiment ID extracted: " + experimentID);
 					}

src/main/java/de/rub/bph/omnineuro/client/imported/log/Log.java

@@ -1,9 +1,11 @@
 package de.rub.bph.omnineuro.client.imported.log;
 
 import de.rub.bph.omnineuro.client.Client;
+import de.rub.bph.omnineuro.client.core.db.QueryExecutor;
 import de.rub.bph.omnineuro.client.imported.filemanager.FileManager;
 
 import java.io.*;
+import java.sql.SQLException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.concurrent.ExecutorService;
@@ -83,6 +85,11 @@ public static void log(LogLevel level, String text, Throwable throwable) {
 		text = "V" + VERSION + " +" + level.getSign() + classPath + " - " + text;
 		if (throwable != null) {
 			text = text + "\n" + throwable.getClass().getName() + ": '" + throwable.getMessage() + "'";
+			if (throwable instanceof SQLException) {
+				String cachedQuery = QueryExecutor.getLastCachedQuery();
+				text = text + "\nLast known SQL query: '" + cachedQuery + "'";
+			}
+			
 			for (StackTraceElement trace : throwable.getStackTrace()) {
 				text = text + "\n\t" + trace.toString();
 			}