Merge conflicts

Documentation/MassBankRecordFormat.md

@@ -904,12 +904,12 @@ Example:
 AC$MASS_SPECTROMETRY: MASS_ACCURACY 50 ppm over a range of about m/z 100-1000
 ```
 
-##### 2.4.5 Subtag: MASS\_RANGE\_MZ`
+##### 2.4.5 Subtag: MASS\_RANGE\_M/Z`
 Mass Range of the Scan (aka Scanning Range or Scan Range) in m/z.
 
 Example:
 ```
-AC$MASS_SPECTROMETRY: MASS_RANGE_MZ 100-1000
+AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 100-1000
 ```
 
 ##### 2.4.5 Subtag: REAGENT\_GAS
@@ -1321,12 +1321,12 @@ Example:
 MS$FOCUSED_ION: PRECURSOR_INT 10000
 ```
 
-##### 2.5.1 Subtag: PRECURSOR\_MZ
+##### 2.5.1 Subtag: PRECURSOR\_M/Z
 m/z of Precursor Ion in MSn spectrum.
 
 Example:
 ```
-MS$FOCUSED_ION: PRECURSOR_MZ 289.07123
+MS$FOCUSED_ION: PRECURSOR_M/Z 289.07123
 ```
 
 Calculated exact mass is preferred to the measured accurate mass of the precursor ion.
@@ -1485,8 +1485,8 @@ PK$PEAK: m/z int. rel.int.
 Line 1:  fixed string which denotes the format of Line 2 or later.
 `PK$PEAK: m/z int. rel.int.`
 
-Line 2 or later: `space` `space` `MZ` `space` `INT` `space` `REL`
-- MZ: m/z of the peak.
+Line 2 or later: `space` `space` `M/Z` `space` `INT` `space` `REL`
+- M/Z: m/z of the peak.
 - INT: intensity of the peak.
 - REL: an integer from 1 to 999 which denotes relative intensity of the peak.
 

MassBank-Project/MassBank-OpenAPI/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<artifactId>MassBank-Project</artifactId>
 		<groupId>de.ipb-halle.msbi</groupId>
-		<version>2.1.3.1</version>
+		<version>2.1.4</version>
 	</parent>
 
 	<artifactId>MassBank-OpenAPI</artifactId>
@@ -15,7 +15,7 @@
 	<name>MassBank-OpenAPI REST interface</name>
 
 	<properties>
-		<swagger-version>2.1.1</swagger-version>
+		<swagger-version>2.1.2</swagger-version>
 		<jersey2-version>2.30</jersey2-version>
 		<jackson-version>2.10.2</jackson-version>
 		<jetty-version>9.4.24.v20191120</jetty-version>

MassBank-Project/MassBank-lib/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<artifactId>MassBank-Project</artifactId>
 		<groupId>de.ipb-halle.msbi</groupId>
-		<version>2.1.3.1</version>
+		<version>2.1.4</version>
 	</parent>
 
 	<artifactId>MassBank-lib</artifactId>
@@ -16,7 +16,7 @@
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.13.1</version>
+			<version>2.13.2</version>
 		</dependency>
 		<dependency>
 			<groupId>javax.servlet</groupId>
@@ -36,12 +36,12 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.9</version>
+			<version>3.10</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-configuration2</artifactId>
-			<version>2.6</version>
+			<version>2.7</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-cli</groupId>

MassBank-Project/MassBank-lib/src/main/java/massbank/AddMetaData.java

@@ -392,6 +392,7 @@ public static void main(String[] arguments) throws Exception {
 		options.addOption("p", "publication", false, "format PUBLICATION tag from given DOI to follow the guidelines of ACS");
 		options.addOption("n", "name", false, "fix common problems in CH$NAME tag");
 		options.addOption("l", "link", false, "add links to CH$LINK tag");
+		options.addOption("r", "rewrite", false, "read and rewrite the file.");
 		options.addOption("ms_focused_ion", false, "Inspect MS$FOCUSED_ION");
 		CommandLine cmd = null;
 		try {
@@ -446,6 +447,8 @@ else if (record.DEPRECATED()) {
 		if (cmd.hasOption("l") || cmd.hasOption("a")) recordstring2=doLink(record, recordstring2);
 		if (cmd.hasOption("ms_focused_ion") || cmd.hasOption("a")) recordstring2=doFocusedIon(record, recordstring2);
 
+		if (cmd.hasOption("r")) recordstring2=record.toString();
+
 		if (!recordstring.equals(recordstring2)) {
 			Record record2 = Validator.validate(recordstring2, "");
 			if (record2 == null) {

MassBank-Project/MassBank-lib/src/main/java/massbank/DatabaseManager.java

@@ -25,6 +25,7 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.StringReader;
+import java.math.BigDecimal;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.PreparedStatement;
@@ -36,6 +37,7 @@
 import java.util.List;
 import org.apache.commons.configuration2.ex.ConfigurationException;
 import org.apache.commons.lang3.tuple.Pair;
+import org.apache.commons.lang3.tuple.Triple;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 
@@ -128,7 +130,7 @@ public class DatabaseManager {
 	private final static String insertAC_CHROMATOGRAPHY = "INSERT INTO AC_CHROMATOGRAPHY VALUES(?,?,?)";
 	private final static String insertMS_FOCUSED_ION = "INSERT INTO MS_FOCUSED_ION VALUES(?,?,?)";
 	private final static String insertMS_DATA_PROCESSING = "INSERT INTO MS_DATA_PROCESSING VALUES(?,?,?)";
-	private final static String insertPEAK = "INSERT INTO PEAK VALUES(?,?,?,?,?)";
+	private final static String insertPEAK = "INSERT INTO PEAK VALUES(?,?,?,?,?,?,?)";
 	private final static String updatePEAKs = "UPDATE PEAK SET PK_ANNOTATION = ? WHERE RECORD = ? AND PK_PEAK_MZ = ?";
 	private final static String insertANNOTATION_HEADER = "INSERT INTO ANNOTATION_HEADER VALUES(?,?)";
 
@@ -401,9 +403,10 @@ public Record getAccessionData(String accessionId) {
 				}
 
 				tmp = this.statementPEAK.executeQuery();
-//				acc.add("PK$PEAK", null, "m/z int. rel.int.");
 				while (tmp.next()) {
-					acc.PK_PEAK_ADD_LINE(Arrays.asList((Double) tmp.getDouble("PK_PEAK_MZ"), (Double) (double) tmp.getFloat("PK_PEAK_INTENSITY"), (Double) (double) tmp.getShort("PK_PEAK_RELATIVE")));
+					BigDecimal mz = (new BigDecimal(String.valueOf(tmp.getDouble("PK_PEAK_MZ")))).setScale(tmp.getInt("PK_PEAK_MZ_SIGNIFICANT"));
+					BigDecimal intensity = (new BigDecimal(String.valueOf(tmp.getDouble("PK_PEAK_INTENSITY")))).setScale(tmp.getInt("PK_PEAK_INTENSITY_SIGNIFICANT"));
+					acc.PK_PEAK_ADD_LINE(Triple.of(mz, intensity, tmp.getInt("PK_PEAK_RELATIVE")));
 					String PK_ANNOTATION	= tmp.getString("PK_ANNOTATION");
 					if(PK_ANNOTATION != null)
 						acc.PK_ANNOTATION_ADD_LINE(Arrays.asList(PK_ANNOTATION.split(" ")));
@@ -432,7 +435,7 @@ public Record getAccessionData(String accessionId) {
 			set = this.statementCOMPOUND.executeQuery();
 			while (set.next()) {
 				acc.CH_FORMULA(set.getString("CH_FORMULA"));
-				acc.CH_EXACT_MASS(set.getDouble("CH_EXACT_MASS"));
+				acc.CH_EXACT_MASS(new BigDecimal(set.getDouble("CH_EXACT_MASS")));
 				acc.CH_SMILES(set.getString("CH_SMILES"));
 				acc.CH_IUPAC(set.getString("CH_IUPAC"));
 
@@ -552,6 +555,7 @@ public Record.Structure getStructureOfAccession(String accessionId) {
 	public void persistAccessionFile(Record acc) {
 		boolean bulk=false;
 
+		// get contributor ID
 		Integer conId = -1;
 		try {
 			String sql = "SELECT ID FROM CONTRIBUTOR WHERE SHORT_NAME = ?";
@@ -602,7 +606,7 @@ public void persistAccessionFile(Record acc) {
 				//System.out.println(System.nanoTime());
 				statementInsertCompound.setNull(1, java.sql.Types.INTEGER);
 				statementInsertCompound.setString(2, acc.CH_FORMULA());
-				statementInsertCompound.setDouble(3, acc.CH_EXACT_MASS());
+				statementInsertCompound.setDouble(3, acc.CH_EXACT_MASS().doubleValue());
 				statementInsertCompound.setString(4, acc.CH_SMILES());
 				statementInsertCompound.setString(5, acc.CH_IUPAC());
 
@@ -849,16 +853,17 @@ public void persistAccessionFile(Record acc) {
 				}
 
 				//System.out.println(System.nanoTime());
-				for (List<Double> peak : acc.PK_PEAK()) {
+
+				for (Triple<BigDecimal,BigDecimal,Integer> peak : acc.PK_PEAK()) {
 					statementInsertPEAK.setString(1, accession);
-					statementInsertPEAK.setDouble(2, peak.get(0));
-					statementInsertPEAK.setFloat(3, (float)(double) peak.get(1));
-					statementInsertPEAK.setShort(4, (short)(double) peak.get(2));
-					statementInsertPEAK.setNull(5, java.sql.Types.VARCHAR);
-		//			statementInsertPEAK.setNull(5, java.sql.Types.VARCHAR);
-		//			statementInsertPEAK.setNull(6, java.sql.Types.SMALLINT);
-		//			statementInsertPEAK.setNull(7, java.sql.Types.FLOAT);
-		//			statementInsertPEAK.setNull(8, java.sql.Types.FLOAT);
+					statementInsertPEAK.setDouble(2, peak.getLeft().doubleValue());
+					statementInsertPEAK.setInt(3, peak.getLeft().scale());
+
+					statementInsertPEAK.setDouble(4, peak.getMiddle().doubleValue());
+					statementInsertPEAK.setInt(5, peak.getMiddle().scale());
+
+					statementInsertPEAK.setInt(6, peak.getRight().intValue());
+					statementInsertPEAK.setNull(7, java.sql.Types.VARCHAR);
 		//			statementInsertPEAK.executeUpdate();
 					statementInsertPEAK.addBatch();
 				}