Merge branch 'release-2.1.8' into main

Author: meier-rene

MassBank-Project/MassBank-OpenAPI/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<artifactId>MassBank-Project</artifactId>
 		<groupId>de.ipb-halle.msbi</groupId>
-		<version>2.1.7</version>
+		<version>2.1.8</version>
 	</parent>
 
 	<artifactId>MassBank-OpenAPI</artifactId>
@@ -15,8 +15,8 @@
 	<name>MassBank-OpenAPI REST interface</name>
 
 	<properties>
-		<swagger-codegen-version>3.0.21</swagger-codegen-version>
-		<swagger-core-version>2.1.4</swagger-core-version>
+		<swagger-codegen-version>3.0.23</swagger-codegen-version>
+		<swagger-core-version>2.1.5</swagger-core-version>
 		<jersey2-version>2.31</jersey2-version>
 		<jackson-version>2.11.2</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>2.1.7</version>
+		<version>2.1.8</version>
 	</parent>
 
 	<artifactId>MassBank-lib</artifactId>
@@ -16,7 +16,7 @@
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.13.3</version>
+			<version>2.14.0</version>
 		</dependency>
 		<dependency>
 			<groupId>javax.servlet</groupId>
@@ -101,7 +101,7 @@
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20200518</version>
+			<version>20201115</version>
 		</dependency>
 	</dependencies>
 	<build>

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

@@ -28,22 +28,19 @@
 import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
-
 import org.apache.commons.lang3.tuple.Pair;
 import org.apache.commons.lang3.tuple.Triple;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.json.JSONArray;
 import org.json.JSONObject;
-import org.openscience.cdk.AtomContainer;
-import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.inchi.InChIGeneratorFactory;
 import org.openscience.cdk.inchi.InChIToStructure;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IMolecularFormula;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
 
@@ -244,7 +241,7 @@ public String CH_FORMULA() {
 	* Returns the molecular formula as an String with HTML sup tags.
 	*/
 	public String CH_FORMULA1() {
-		IMolecularFormula m = MolecularFormulaManipulator.getMolecularFormula(ch_formula, DefaultChemObjectBuilder.getInstance());
+		IMolecularFormula m = MolecularFormulaManipulator.getMolecularFormula(ch_formula, SilentChemObjectBuilder.getInstance());
 		return MolecularFormulaManipulator.getHTML(m);
 	}
 	public void CH_FORMULA(String value) {
@@ -264,12 +261,12 @@ public String CH_SMILES() {
 		return ch_smiles;
 	}
 	public IAtomContainer CH_SMILES_obj() {
-		if ("N/A".equals(ch_smiles)) return new AtomContainer();
+		if ("N/A".equals(ch_smiles)) return SilentChemObjectBuilder.getInstance().newAtomContainer();
 		try {
-			return new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(ch_smiles);
+			return new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(ch_smiles);
 		} catch (InvalidSmilesException e) {
 			logger.error("Structure generation from SMILES failed. Error: \""+ e.getMessage() + "\" for \"" + ch_smiles + "\".");
-			return new AtomContainer();
+			return SilentChemObjectBuilder.getInstance().newAtomContainer();
 		}
 	}
 	public void CH_SMILES(String value) {
@@ -281,10 +278,10 @@ public String CH_IUPAC() {
 		return ch_iupac;
 	}
 	public IAtomContainer CH_IUPAC_obj() {
-		if ("N/A".equals(ch_iupac)) return new AtomContainer();
+		if ("N/A".equals(ch_iupac)) return SilentChemObjectBuilder.getInstance().newAtomContainer();
 		try {
 			// Get InChIToStructure
-			InChIToStructure intostruct = InChIGeneratorFactory.getInstance().getInChIToStructure(ch_iupac, DefaultChemObjectBuilder.getInstance());
+			InChIToStructure intostruct = InChIGeneratorFactory.getInstance().getInChIToStructure(ch_iupac, SilentChemObjectBuilder.getInstance());
 			INCHI_RET ret = intostruct.getReturnStatus();
 			if (ret == INCHI_RET.WARNING) {
 				// Structure generated, but with warning message
@@ -293,11 +290,12 @@ public IAtomContainer CH_IUPAC_obj() {
 			else if (ret != INCHI_RET.OKAY) {
 				// Structure generation failed
 				logger.error("Structure generation failed: " + ret.toString() + " [" + intostruct.getMessage() + "] for \"" + ch_iupac + "\".");
+				return  SilentChemObjectBuilder.getInstance().newAtomContainer();
 			}
 			return intostruct.getAtomContainer();
 		} catch (CDKException e) {
 			logger.error("Structure generation from InChI failed. Error: \""+ e.getMessage() + "\" for \"" + ch_iupac + "\".");
-			return new AtomContainer();
+			return  SilentChemObjectBuilder.getInstance().newAtomContainer();
 		}		 			
 	}
 	public void CH_IUPAC(String value) {
@@ -692,11 +690,22 @@ public String createStructuredData() {
 		sb.append("\"headline\": \""+RECORD_TITLE1()+"\",\n");
 		sb.append("\"name\": \""+RECORD_TITLE().get(0)+"\",\n");
 		sb.append("\"description\": \"" + description + "\",\n");
+		sb.append("\"measurementTechnique\": \"mass spectrometry\",\n");
 		String[] tokens	= DATE1();
 		sb.append("\"datePublished\": \""+tokens[0].replace(".","-")+"\",\n");
 		if(tokens.length >= 2) { sb.append("\"dateCreated\": \""+tokens[1].replace(".","-")+"\",\n"); }
 		if(tokens.length == 3) { sb.append("\"dateModified\": \""+tokens[2].replace(".","-")+"\",\n"); }
-		sb.append("\"license\": \"https://creativecommons.org/licenses\",\n");
+		// sb.append("\"license\": \"https://creativecommons.org/licenses\",\n");
+		// sb.append("\"license\": \""+LICENSE() +"\",\n");
+		// Convert licenses to URLs
+		if (LICENSE().equals("CC0")) { sb.append("\"license\": \"https://creativecommons.org/share-your-work/public-domain/cc0\",\n");
+		} else if (LICENSE().equals("CC BY-SA") || LICENSE().equals("CC BY SA") || LICENSE().equals("CC-BY SA") || LICENSE().equals("CC-BY-SA")) { sb.append("\"license\": \"https://creativecommons.org/licenses/by-sa/4.0\",\n");
+		} else if (LICENSE().equals("CC BY") || LICENSE().equals("CC-BY") || LICENSE().equals("BY CC") || LICENSE().equals("BY-CC")) { sb.append("\"license\": \"https://creativecommons.org/licenses/by/4.0\",\n");
+		} else if (LICENSE().equals("CC BY-NC") || LICENSE().equals("CC-BY-NC") || LICENSE().equals("CC BY NC") || LICENSE().equals("CC-BY NC")) { sb.append("\"license\": \"https://creativecommons.org/licenses/by-nc/4.0\",\n");
+		} else if (LICENSE().equals("CC BY-SA NC") || LICENSE().equals("CC BY-NC-SA 4.0 International") || LICENSE().equals("CC BY-NC-SA")) { sb.append("\"license\": \"https://creativecommons.org/licenses/by-nc-sa/4.0\",\n");
+		} else if (LICENSE().equals("CC BY-NC-ND")) { sb.append("\"license\": \"https://creativecommons.org/licenses/by-nc-nd/4.0\",\n");
+		} else sb.append("\"license\": \"null\",\n");
+
 		sb.append("\"citation\": \""+PUBLICATION()+"\",\n");
 		if (COMMENT().size() == 1)  sb.append("\"comment\": \""+ COMMENT().get(0) +"\",\n");
 		else if (COMMENT().size() >= 1) sb.append("\"comment\": [\""+ String.join("\", \"", COMMENT()) +"\"],\n");