Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Release version 2.2.8 #408

Merged
merged 18 commits into from
Dec 6, 2024
Merged

Release version 2.2.8 #408

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
f8ae55d
Add refactored parser
meier-rene Nov 20, 2024
ff39250
Continue on refactored RecordParserDefinition
meier-rene Nov 26, 2024
97fe61b
Update dependencies and plugins.
meier-rene Nov 26, 2024
2ce5544
Continue RecordParserDefinition refactoring, switch to java 21
meier-rene Nov 29, 2024
e5c50b9
Finish RecordParserDefinition
meier-rene Dec 2, 2024
9a9d66c
Adopt Validator to new RecordParser
meier-rene Dec 2, 2024
d28883f
Revert to java 17 because tomee supports only 17
meier-rene Dec 3, 2024
25ab0e5
Adjust to new RecordParser
meier-rene Dec 3, 2024
c397bb9
Add example for MS2 in PSI ontology
sneumann Dec 4, 2024
92ac3fc
Adjust to the RecordParser refactoring.
meier-rene Dec 4, 2024
2acbf05
Small updates to some infrastructure files.
meier-rene Dec 4, 2024
e90225f
Upgrade jquery and format some expressions with c:out.
meier-rene Dec 4, 2024
e9570f9
Small changes.
meier-rene Dec 5, 2024
54394fc
Add new jquery library
meier-rene Dec 6, 2024
3e7d59f
Fix name.
meier-rene Dec 6, 2024
3662e34
Add open bug bounty file
meier-rene Dec 6, 2024
446a940
Bumped version number to 2.2.8
meier-rene Dec 6, 2024
b724234
Merge branch 'main' into release-2.2.8
meier-rene Dec 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Documentation/MassBankRecordFormat.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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

Expand Down
34 changes: 20 additions & 14 deletions MassBank-Project/MassBank-lib/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
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>
Expand Down
30 changes: 15 additions & 15 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java
View file
Open in desktop
Original file line number Diff line number Diff line change
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;


/**
Expand Down
147 changes: 63 additions & 84 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
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));
}
}
Loading
Loading