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Merge pull request #408 from MassBank/release-2.2.8
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Release version 2.2.8
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@meier-rene
meier-rene authored Dec 6, 2024
2 parents 88f58e0 + b724234 commit 6eb858a
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Showing 36 changed files with 3,126 additions and 2,998 deletions.
2 changes: 1 addition & 1 deletion Documentation/MassBankRecordFormat.md
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Expand Up @@ -755,7 +755,7 @@ MSn

Brief definition of terms used in `MS_TYPE`:
* `MS` - [MS1 spectrum(MS:1000579)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000579)
* `MS2` - [MSn spectrum(MS:1000580)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000580)
* `MS2` - [MSn spectrum(MS:1000580)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000580) with [ms level(MS:1000511)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000580) = 2
* `MS3` - [MSn spectrum(MS:1000580)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000580) with [ms level(MS:1000511)](https://terminology.tib.eu/ts/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000580) = 3
* `MSn` - use for any other multi stage acquisition method, which does not fit in the above scheme, like merged MS spectra from different stages

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34 changes: 20 additions & 14 deletions MassBank-Project/MassBank-lib/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>MassBank-Project</artifactId>
<groupId>de.ipb-halle.msbi</groupId>
<version>2.2.7-hotfix1</version>
<version>2.2.8</version>
</parent>

<artifactId>MassBank-lib</artifactId>
Expand All @@ -18,7 +18,7 @@
</dependency>
<dependency>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-api</artifactId>
<artifactId>jakarta.jakartaee-web-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -47,13 +47,19 @@
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-bundle</artifactId>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
</exclusions>
<artifactId>cdk-data</artifactId>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-depict</artifactId>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-inchi</artifactId>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-formula</artifactId>
</dependency>
<dependency>
<groupId>org.mariadb.jdbc</groupId>
Expand Down Expand Up @@ -83,11 +89,11 @@
<groupId>io.github.dan2097</groupId>
<artifactId>jna-inchi-all</artifactId>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>5.5.0</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>net.sourceforge.owlapi</groupId>-->
<!-- <artifactId>owlapi-distribution</artifactId>-->
<!-- <version>5.5.0</version>-->
<!-- </dependency>-->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
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30 changes: 15 additions & 15 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java
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Expand Up @@ -10,21 +10,21 @@
import java.util.ArrayList;
import java.util.Set;

import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.BufferingMode;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.model.OWLClass;
//import org.semanticweb.owlapi.apibinding.OWLManager;
//import org.semanticweb.owlapi.model.IRI;
//import org.semanticweb.owlapi.model.OWLAxiom;
//import org.semanticweb.owlapi.model.OWLDataFactory;
//import org.semanticweb.owlapi.model.OWLOntology;
//import org.semanticweb.owlapi.model.OWLOntologyCreationException;
//import org.semanticweb.owlapi.model.OWLOntologyManager;
//import org.semanticweb.owlapi.reasoner.BufferingMode;
//import org.semanticweb.owlapi.reasoner.InferenceType;
//import org.semanticweb.owlapi.reasoner.OWLReasoner;
//import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
//import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
//import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
//import org.semanticweb.owlapi.reasoner.NodeSet;
//import org.semanticweb.owlapi.model.OWLClass;


/**
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147 changes: 63 additions & 84 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java
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Expand Up @@ -20,16 +20,11 @@
******************************************************************************/
package massbank;

import java.math.BigDecimal;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import io.github.dan2097.jnainchi.InchiStatus;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.commons.lang3.tuple.Triple;
import org.apache.logging.log4j.LogManager;
Expand All @@ -44,12 +39,11 @@
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;

import io.github.dan2097.jnainchi.InchiStatus;
import java.math.BigDecimal;
import java.time.Instant;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
* This class keeps all data of a record.
Expand Down Expand Up @@ -93,42 +87,42 @@ public class Record {
private List<Pair<String, String>> MS$DATA_PROCESSING; // optional
private String PK$SPLASH;
private List<String> PK$ANNOTATION_HEADER; // optional
private List<Pair<BigDecimal, List<String>>> PK$ANNOTATION; // optional
private List<Triple<BigDecimal,BigDecimal,Integer>> PK$PEAK;
private final List<Pair<BigDecimal, List<String>>> PK$ANNOTATION; // optional
private final List<Triple<BigDecimal,BigDecimal,Integer>> PK$PEAK;

public Record() {
contributor = new String();
ACCESSION = new String();
contributor = "";
ACCESSION = "";
deprecated = false;
deprecated_content = new String();
deprecated_content = "";
RECORD_TITLE = new ArrayList<String>();
DATE = new String();
AUTHORS = new String();
LICENSE = new String();
COPYRIGHT = new String(); // optional
PUBLICATION = new String(); // optional
PROJECT = new String(); // optional
DATE = "";
AUTHORS = "";
LICENSE = "";
COPYRIGHT = ""; // optional
PUBLICATION = ""; // optional
PROJECT = ""; // optional
COMMENT = new ArrayList<String>(); // optional
CH$NAME = new ArrayList<String>();
CH$COMPOUND_CLASS = new ArrayList<String>();
CH$FORMULA = new String();
CH$FORMULA = "";
CH$EXACT_MASS = new BigDecimal(0);
CH$SMILES = new String();
CH$IUPAC = new String();
CH$SMILES = "";
CH$IUPAC = "";
CH$LINK = new LinkedHashMap<String, String>(); // optional
SP$SCIENTIFIC_NAME = new String(); // optional
SP$LINEAGE = new String(); // optional
SP$SCIENTIFIC_NAME = ""; // optional
SP$LINEAGE = ""; // optional
SP$LINK = new LinkedHashMap<String, String>(); // optional
SP$SAMPLE = new ArrayList<String>(); // optional
AC$INSTRUMENT = new String();
AC$INSTRUMENT_TYPE = new String();
AC$MASS_SPECTROMETRY_MS_TYPE = new String();
AC$MASS_SPECTROMETRY_ION_MODE = new String();
AC$INSTRUMENT = "";
AC$INSTRUMENT_TYPE = "";
AC$MASS_SPECTROMETRY_MS_TYPE = "";
AC$MASS_SPECTROMETRY_ION_MODE = "";
AC$MASS_SPECTROMETRY = new ArrayList<Pair<String, String>>(); // optional
AC$CHROMATOGRAPHY = new ArrayList<Pair<String, String>>(); // optional
MS$FOCUSED_ION = new ArrayList<Pair<String, String>>(); // optional
MS$DATA_PROCESSING = new ArrayList<Pair<String, String>>(); // optional
PK$SPLASH = new String();
PK$SPLASH = "";
PK$ANNOTATION_HEADER = new ArrayList<String>(); // optional
PK$ANNOTATION = new ArrayList<Pair<BigDecimal, List<String>>>(); // optional
PK$PEAK = new ArrayList<Triple<BigDecimal,BigDecimal,Integer>>();
Expand Down Expand Up @@ -474,54 +468,53 @@ public void PK_PEAK_ADD_LINE(Triple<BigDecimal,BigDecimal,Integer> peak) {
public String toString() {
StringBuilder sb = new StringBuilder();

sb.append("ACCESSION: " + ACCESSION() + "\n");
sb.append("ACCESSION: ").append(ACCESSION()).append("\n");
if (DEPRECATED()) {
sb.append("DEPRECATED: ");
sb.append(DEPRECATED_CONTENT());
sb.append("DEPRECATED: ").append(DEPRECATED_CONTENT());
return sb.toString();
}
sb.append("RECORD_TITLE: " + RECORD_TITLE1() + "\n");
sb.append("DATE: " + DATE() + "\n");
sb.append("AUTHORS: " + AUTHORS() + "\n");
sb.append("LICENSE: " + LICENSE() + "\n");
sb.append("RECORD_TITLE: ").append(RECORD_TITLE1()).append("\n");
sb.append("DATE: ").append(DATE()).append("\n");
sb.append("AUTHORS: ").append(AUTHORS()).append("\n");
sb.append("LICENSE: ").append(LICENSE()).append("\n");
if (!"".equals(COPYRIGHT()))
sb.append("COPYRIGHT: " + COPYRIGHT() + "\n");
sb.append("COPYRIGHT: ").append(COPYRIGHT()).append("\n");
if (!"".equals(PUBLICATION()))
sb.append("PUBLICATION: " + PUBLICATION() + "\n");
sb.append("PUBLICATION: ").append(PUBLICATION()).append("\n");
if (!"".equals(PROJECT()))
sb.append("PROJECT: " + PROJECT() + "\n");
sb.append("PROJECT: ").append(PROJECT()).append("\n");
for (String comment : COMMENT())
sb.append("COMMENT: " + comment + "\n");
sb.append("COMMENT: ").append(comment).append("\n");

for (String ch_name : CH_NAME())
sb.append("CH$NAME: " + ch_name + "\n");
sb.append("CH$NAME: ").append(ch_name).append("\n");
if (!CH_COMPOUND_CLASS().isEmpty()) {
sb.append("CH$COMPOUND_CLASS: " + String.join("; ", CH_COMPOUND_CLASS()) + "\n");
sb.append("CH$COMPOUND_CLASS: ").append(String.join("; ", CH_COMPOUND_CLASS())).append("\n");
}
sb.append("CH$FORMULA: " + CH_FORMULA() + "\n");
sb.append("CH$EXACT_MASS: " + CH_EXACT_MASS() + "\n");
sb.append("CH$SMILES: " + CH_SMILES() + "\n");
sb.append("CH$IUPAC: " + CH_IUPAC() + "\n");
sb.append("CH$FORMULA: ").append(CH_FORMULA()).append("\n");
sb.append("CH$EXACT_MASS: ").append(CH_EXACT_MASS()).append("\n");
sb.append("CH$SMILES: ").append(CH_SMILES()).append("\n");
sb.append("CH$IUPAC: ").append(CH_IUPAC()).append("\n");
CH_LINK().forEach((key,value) -> {
sb.append("CH$LINK: " + key + " " + value + "\n");
sb.append("CH$LINK: ").append(key).append(" ").append(value).append("\n");
});

if (!"".equals(SP_SCIENTIFIC_NAME()))
sb.append("SP$SCIENTIFIC_NAME: " + SP_SCIENTIFIC_NAME() + "\n");
sb.append("SP$SCIENTIFIC_NAME: ").append(SP_SCIENTIFIC_NAME()).append("\n");
if (!"".equals(SP_LINEAGE()))
sb.append("SP$LINEAGE: " + SP_LINEAGE() + "\n");
sb.append("SP$LINEAGE: ").append(SP_LINEAGE()).append("\n");
SP_LINK().forEach((key,value) -> {
sb.append("SP$LINK: " + key + " " + value + "\n");
sb.append("SP$LINK: ").append(key).append(" ").append(value).append("\n");
});
for (String sample : SP_SAMPLE())
sb.append("SP$SAMPLE: " + sample + "\n");
sb.append("SP$SAMPLE: ").append(sample).append("\n");

sb.append("AC$INSTRUMENT: " + AC_INSTRUMENT() + "\n");
sb.append("AC$INSTRUMENT_TYPE: " + AC_INSTRUMENT_TYPE() + "\n");
sb.append("AC$MASS_SPECTROMETRY: MS_TYPE " + AC_MASS_SPECTROMETRY_MS_TYPE() + "\n");
sb.append("AC$MASS_SPECTROMETRY: ION_MODE " + AC_MASS_SPECTROMETRY_ION_MODE() + "\n");
sb.append("AC$INSTRUMENT: ").append(AC_INSTRUMENT()).append("\n");
sb.append("AC$INSTRUMENT_TYPE: ").append(AC_INSTRUMENT_TYPE()).append("\n");
sb.append("AC$MASS_SPECTROMETRY: MS_TYPE ").append(AC_MASS_SPECTROMETRY_MS_TYPE()).append("\n");
sb.append("AC$MASS_SPECTROMETRY: ION_MODE ").append(AC_MASS_SPECTROMETRY_ION_MODE()).append("\n");
for (Pair<String,String> ac_mass_spectrometry : AC_MASS_SPECTROMETRY())
sb.append("AC$MASS_SPECTROMETRY: " + ac_mass_spectrometry.getKey() + " " + ac_mass_spectrometry.getValue() + "\n");
sb.append("AC$MASS_SPECTROMETRY: ").append(ac_mass_spectrometry.getKey()).append(" ").append(ac_mass_spectrometry.getValue()).append("\n");
for (Pair<String,String> ac_chromatography : AC_CHROMATOGRAPHY())
sb.append("AC$CHROMATOGRAPHY: " + ac_chromatography.getKey() + " " + ac_chromatography.getValue() + "\n");
for (Pair<String,String> ms_focued_ion : MS_FOCUSED_ION())
Expand Down Expand Up @@ -580,7 +573,7 @@ public String createRecordString() {
if (!"".equals(PUBLICATION())) {
String pub=PUBLICATION();
String regex_doi = "10\\.\\d{3,9}\\/[\\-\\._;\\(\\)\\/:a-zA-Z0-9]+[a-zA-Z0-9]";
String regex_pmid = "PMID:[ ]?\\d{8,8}";
String regex_pmid = "PMID:[ ]?\\d{8}";
Pattern pattern_doi = Pattern.compile(".*" + "(" + regex_doi+ ")" + ".*");
Pattern pattern_pmid = Pattern.compile(".*" + "(" + regex_pmid + ")" + ".*");
Matcher matcher_doi = pattern_doi.matcher(pub);
Expand Down Expand Up @@ -841,7 +834,7 @@ public JsonArray createStructuredDataJsonArray() {
chemicalSubstance.addProperty("url", "https://massbank.eu/MassBank/RecordDisplay?id="+ACCESSION());
chemicalSubstance.addProperty("chemicalComposition", CH_FORMULA());
if (CH_NAME().size() == 1) chemicalSubstance.addProperty("alternateName", CH_NAME().get(0));
else if (CH_NAME().size() >= 1) chemicalSubstance.add("alternateName", gson.toJsonTree(CH_NAME()));
else if (!CH_NAME().isEmpty()) chemicalSubstance.add("alternateName", gson.toJsonTree(CH_NAME()));

JsonArray molecularEntitys = new JsonArray();

Expand Down Expand Up @@ -901,25 +894,11 @@ public JsonObject createPeakListData() {
result.add("peaks", peaklist);
return result;
}

public static class Structure{
public final String CH_SMILES;
public final String CH_IUPAC;
public Structure(String CH_SMILES, String CH_IUPAC) {
this.CH_SMILES = CH_SMILES;
this.CH_IUPAC = CH_IUPAC;
}

public record Structure(String CH_SMILES, String CH_IUPAC) {
}

public static class Contributor{
public final String ACRONYM;
public final String SHORT_NAME;
public final String FULL_NAME;
public Contributor(String ACRONYM, String SHORT_NAME, String FULL_NAME) {
this.ACRONYM = ACRONYM;
this.SHORT_NAME = SHORT_NAME;
this.FULL_NAME = FULL_NAME;
}

public record Contributor(String ACRONYM, String SHORT_NAME, String FULL_NAME) {
}

private static Map<String, String> listToMap(List<Pair<String, String>> list) {
Expand Down
22 changes: 7 additions & 15 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParser.java
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Original file line number Diff line number Diff line change
@@ -1,20 +1,12 @@
package massbank;

import java.util.Set;

import org.petitparser.tools.GrammarParser;

/**
* Record parser. To parse an Record consider the following code:
*
* <pre>
* Parser record = new RecordParser();
* Object result = record.parse(your_record_content);
* System.out.println(result.value);
* </pre>
*/
import java.util.Set;

public class RecordParser extends GrammarParser {
public RecordParser(Record callback, Set<String> config) {
super(new RecordParserDefinition(callback, config));
}
}

public RecordParser(Set<String> config) {
super(new RecordParserDefinition(config));
}
}
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