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Update dependencies and plugins.
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@meier-rene
meier-rene committed Nov 26, 2024
1 parent ff39250 commit 97fe61b
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Showing 4 changed files with 160 additions and 107 deletions.
20 changes: 13 additions & 7 deletions MassBank-Project/MassBank-lib/pom.xml
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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>
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8 changes: 4 additions & 4 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParserDefinition.java
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Original file line number Diff line number Diff line change
Expand Up @@ -542,10 +542,10 @@ public RecordParserDefinition(Set<String> config) {
)
.seq(Token.NEWLINE_PARSER)
.pick(2)
//// .map((Object value) -> {
//// System.out.println(value);
//// return value;
//// })
// .map((Object value) -> {
// System.out.println(value);
// return value;
// })

);

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161 changes: 99 additions & 62 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/cli/AddMetaData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,12 +35,15 @@
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.inchi.InChIGenerator;
import org.openscience.cdk.inchi.InChIGeneratorFactory;
import org.openscience.cdk.inchi.InChIToStructure;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmiFlavor;
import org.openscience.cdk.smiles.SmilesGenerator;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
Expand All @@ -51,6 +54,7 @@
import de.undercouch.citeproc.bibtex.BibTeXConverter;
import de.undercouch.citeproc.bibtex.BibTeXItemDataProvider;
import io.github.dan2097.jnainchi.InchiStatus;
import io.github.dan2097.jnainchi.JnaInchi;
import massbank.PubchemResolver;
import massbank.Record;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -133,7 +137,7 @@ public static String doPub(Record record, String recordstring) {
citeproc.setOutputFormat("text");
citeproc.registerCitationItems(p.getIds());
formated_citation=citeproc.makeBibliography().makeString().replace("\n", "");
citeproc.close();
//citeproc.close();
// call twice because of bug https://github.com/michel-kraemer/citeproc-java/issues/53
// formated_citation=citeproc.makeBibliography().makeString().replace("\n", "");
// remove some formating characters
Expand Down Expand Up @@ -376,77 +380,105 @@ else if (ret == InchiStatus.ERROR) {
return record.toString();
}


/**
* Automatically fix CH$LINK: PUBCHEM if possible
* if no CH$LINK: INCHIKEY is available - do nothing
* if CH$LINK: INCHIKEY is available and no CH$LINK: PUBCHEM - get and add PubChem CID
*/
public static String doAddPubchemCID(Record record) {
// get InChIKey first
if (!record.CH_LINK().containsKey("INCHIKEY")) {
// no InChIKey -> return
return record.toString();
}
String inchiKey = record.CH_LINK().get("INCHIKEY");
String ch_iupac = record.CH_IUPAC();

// fetch PubChem CIDs
PubchemResolver pr = new PubchemResolver(inchiKey);
Integer preferedCid = pr.getPreferred();
if (preferedCid == null) {
// no prefered CID -> return
logger.error("Could not fetch PubChem CID for " + inchiKey + ".");
return record.toString();
}
if ("N/A".equals(ch_iupac)) return record.toString();

//if PUBCHEM is undefined -> add
if (!record.CH_LINK().containsKey("PUBCHEM")) {
System.out.println("Add PubChem CID "+ preferedCid + ".");
LinkedHashMap<String, String> ch_link = record.CH_LINK();
ch_link.put("PUBCHEM", "CID:"+preferedCid);
//sort
ch_link = ch_link.entrySet().stream()
.sorted(Map.Entry.comparingByKey())
.collect(Collectors.toMap(Entry::getKey, Entry::getValue, (u, v) -> u, LinkedHashMap::new));
record.CH_LINK(ch_link);
return record.toString();
}
//else PUBCHEM is defined
else {
// parse existing CID
Integer cidFromCH_LINK = null;
String[] cidFromCH_LINKToken = record.CH_LINK().get("PUBCHEM").split(":");
if (cidFromCH_LINKToken.length == 2 || cidFromCH_LINKToken[0].equals("CID")) {
cidFromCH_LINK =Integer.parseInt(cidFromCH_LINKToken[1]);
}

if (cidFromCH_LINK == null) {
// no well defined CID -> return
System.out.println("PubChem CID is not correct formated: " + record.CH_LINK().get("PUBCHEM"));
try {
// Get InChIToStructure
InChIToStructure intostruct = InChIGeneratorFactory.getInstance().getInChIToStructure(ch_iupac, SilentChemObjectBuilder.getInstance());
InchiStatus ret = intostruct.getStatus();
if (ret == InchiStatus.WARNING) {
// Structure generated, but with warning message
logger.warn("InChI warning: " + intostruct.getMessage());
logger.warn(record.ACCESSION());
}
else if (ret == InchiStatus.ERROR) {
// Structure generation failed
logger.error("Can not parse InChI string in \"CH$IUPAC\" field. Structure generation failed: " + intostruct.getMessage() + " for " + ch_iupac + ".");
return record.toString();
}

if (cidFromCH_LINK.equals(preferedCid)) {
// all good -> return
System.out.println("PubChem CID is correct.");
// Structure generation succeeded
IAtomContainer m = intostruct.getAtomContainer();
// prepare an InChIGenerator
InChIGenerator inchiGen = InChIGeneratorFactory.getInstance().getInChIGenerator(m);
ret = inchiGen.getStatus();
if (ret == InchiStatus.WARNING) {
// InChI generated, but with warning message
logger.warn("InChI warning: " + inchiGen.getMessage());
logger.warn(record.ACCESSION());
} else if (ret == InchiStatus.ERROR) {
// InChI generation failed
logger.error("Can not create InChiKey from InChI string in \"CH$IUPAC\" field. Error: " + inchiGen.getMessage() + " for " + ch_iupac + ".");
return record.toString();
}
else {
if (pr.isCid(cidFromCH_LINK)) {
System.out.println("PubChem CID is correct but not preferred. Replacing...");
LinkedHashMap<String, String> ch_link = record.CH_LINK();
ch_link.put("PUBCHEM", "CID:"+preferedCid);
//sort
ch_link = ch_link.entrySet().stream()

String INCHIKEY = inchiGen.getInchiKey();
if (!record.CH_LINK().containsKey("INCHIKEY")) {
LinkedHashMap<String, String> ch_link = record.CH_LINK();
ch_link.put("INCHIKEY", INCHIKEY);
//sort
ch_link=ch_link.entrySet().stream()
.sorted(Map.Entry.comparingByKey())
.collect(Collectors.toMap(Entry::getKey, Entry::getValue, (u, v) -> u, LinkedHashMap::new));
record.CH_LINK(ch_link);
return record.toString();
}
else {
System.out.println("PubChem CID is not correct.");
record.CH_LINK(ch_link);
}
else {
if (!INCHIKEY.equals(record.CH_LINK().get("INCHIKEY"))) {
logger.error("Wrong INCHIKEY identifier in record file.");
}
}
} catch (CDKException e) {
logger.error("Can not parse InChI string in \"CH$IUPAC\" field. Error: \""+ e.getMessage() + "\" for \"" + ch_iupac + "\".");
}
return record.toString();
}

public static String doSetSMILESfromInChi(Record record) {
IAtomContainer fromCH_IUPAC = new AtomContainer();
try {
InChIToStructure intoStruct = InChIGeneratorFactory.getInstance().getInChIToStructure(record.CH_IUPAC(), SilentChemObjectBuilder.getInstance());
InchiStatus ret = intoStruct.getStatus();
if (ret == InchiStatus.WARNING) {
// Structure generated, but with warning message
logger.warn("InChI warning: " + intoStruct.getMessage());
}
else if (ret == InchiStatus.ERROR) {
logger.error("Can not parse InChI string in \"CH$IUPAC\" field. Structure generation failed.\nError:\n" + intoStruct.getMessage() + ".");
}
fromCH_IUPAC = intoStruct.getAtomContainer();
} catch (CDKException e) {
logger.error("Can not parse InChI string in \"CH$IUPAC\" field.\nError from CDK:\n"+ e.getMessage());
}

try {
InChIGenerator inchiGen = InChIGeneratorFactory.getInstance().getInChIGenerator(fromCH_IUPAC);
InchiStatus ret = inchiGen.getStatus();
if (ret == InchiStatus.WARNING) {
// Structure generated, but with warning message
logger.warn("InChI warning: " + inchiGen.getMessage());
}
else if (ret == InchiStatus.ERROR) {
// InChI generation failed
logger.error("Can not create InChIKey from SMILES string in \"CH$SMILES\" field. InChI generation failed: " + ret.toString() + " [" + inchiGen.getMessage() + "].");
}
String InChiKeyFromCH_SMILES = inchiGen.getInchiKey();
System.out.println(InChiKeyFromCH_SMILES);
} catch (CDKException e) {
logger.error("Can not create InChIKey from SMILES string in \"CH$SMILES\" field.\nError from CDK:\n"+ e.getMessage());
}

IAtomContainer inchi = record.CH_IUPAC_obj();
SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Absolute);
String smi;
try {
smi = smigen.create(inchi);
System.out.println(smi);
record.CH_SMILES(smi);
} catch (CDKException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return record.toString();
}
Expand All @@ -473,6 +505,7 @@ public static void main(String[] arguments) throws Exception {
options.addOption("ms_focused_ion", false, "Inspect MS$FOCUSED_ION");
options.addOption(null, "add-inchikey", false, "Add or fix InChIKey from the value in CH$IUPAC");
options.addOption(null, "add-pubchemcid", false, "Add or fix PubChem CID from InChIKey and flag Problems.");
options.addOption(null, "smiles-from-inchi", false, "Set SMILES from existing InChi.");
CommandLine cmd = null;
try {
cmd = new DefaultParser().parse( options, arguments);
Expand Down Expand Up @@ -512,6 +545,7 @@ public static void main(String[] arguments) throws Exception {
// validate all files
logger.trace("Validating " + recordfiles.size() + " files");
AtomicBoolean doAddPubchemCid = new AtomicBoolean(cmd.hasOption("add-pubchemcid"));
AtomicBoolean doSetSMILESfromInChi = new AtomicBoolean(cmd.hasOption("smiles-from-inchi"));
recordfiles.parallelStream().forEach(filename -> {
String recordString;
logger.info("Working on " + filename + ".");
Expand All @@ -528,7 +562,7 @@ public static void main(String[] arguments) throws Exception {
} else if (record.DEPRECATED()) {
System.exit(0);
}

String recordstring2 = recordString;
//if (cmd.hasOption("p") || cmd.hasOption("a")) recordstring2=doPub(record, recordstring2);
//if (cmd.hasOption("n") || cmd.hasOption("a")) recordstring2=doName(record, recordstring2);
Expand All @@ -542,6 +576,9 @@ public static void main(String[] arguments) throws Exception {
if (doAddPubchemCid.get()) {
recordstring2=doAddPubchemCID(record);
}
if (doSetSMILESfromInChi.get()) {
recordstring2=doSetSMILESfromInChi(record);
}

config = new HashSet<String>();
if (!recordString.equals(recordstring2)) {
Expand Down
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