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fix mass calibration for compiled mzmine #2374

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Merged
merged 2 commits into from
Jan 28, 2025
Merged

fix mass calibration for compiled mzmine #2374

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5d8b400
fix mass calibration for compiled mzmine
SteffenHeu Jan 28, 2025
3d9011d
update logging message
SteffenHeu Jan 28, 2025
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25 changes: 9 additions & 16 deletions .../io/github/mzmine/modules/dataprocessing/featdet_masscalibration/MassCalibrationTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,6 @@
import io.github.mzmine.taskcontrol.TaskStatus;
import io.github.mzmine.util.MemoryMapStorage;
import java.io.InputStream;
import java.net.URL;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Collections;
Expand Down Expand Up @@ -350,22 +349,21 @@ protected boolean extractStandardsList() {
.getParameter(MassCalibrationParameters.ionizationMode).getValue();
String universalCalibrantsFilename =
MassCalibrationParameters.ionizationModeChoices.get(universalCalibrantsIonizationMode);
URL universalCalibrantsPath =
getClass().getClassLoader().getResource(universalCalibrantsFilename);
standardsListFilename = universalCalibrantsPath.getPath();
InputStream inputStream =
getClass().getClassLoader().getResourceAsStream(universalCalibrantsFilename);
UniversalCalibrantsListCsvExtractor extractor =
new UniversalCalibrantsListCsvExtractor(standardsListFilename, inputStream);
standardsListExtractor = extractor;
try (InputStream is = getClass().getClassLoader()
.getResourceAsStream(universalCalibrantsFilename)) {
UniversalCalibrantsListCsvExtractor extractor = new UniversalCalibrantsListCsvExtractor(
universalCalibrantsFilename, is);
standardsListExtractor = extractor;
standardsList = standardsListExtractor.extractStandardsList();
}
} else {
standardsListFilename = massPeakMatchingMethod.getChoices()
.get(MassPeakMatchingChoice.STANDARDS_LIST.toString())
.getParameter(MassCalibrationParameters.standardsList).getValue().getAbsolutePath();
standardsListExtractor =
StandardsListExtractorFactory.createFromFilename(standardsListFilename, false);
standardsList = standardsListExtractor.extractStandardsList();
}
standardsList = standardsListExtractor.extractStandardsList();

if (standardsList.getStandardMolecules().size() == 0) {
throw new RuntimeException(
Expand All @@ -374,12 +372,7 @@ protected boolean extractStandardsList() {
}

} catch (Exception e) {
e.printStackTrace();
logger.warning("Exception when extracting standards list from " + standardsListFilename);
logger.warning(e.toString());
setStatus(TaskStatus.ERROR);
setErrorMessage("Exception when extracting standards list from " + standardsListFilename
+ "\n" + e.toString());
error("Exception when extracting standards list from " + standardsListFilename, e);
return false;
}
return true;
Expand Down
65 changes: 32 additions & 33 deletions ...processing/featdet_masscalibration/standardslist/UniversalCalibrantsListCsvExtractor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,12 +27,14 @@

import com.opencsv.exceptions.CsvException;
import io.github.mzmine.util.CSVParsingUtils;
import java.io.File;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
import org.jetbrains.annotations.NotNull;


/**
Expand All @@ -48,29 +50,22 @@ public class UniversalCalibrantsListCsvExtractor implements StandardsListExtract
protected Logger logger = Logger.getLogger(this.getClass().getName());

protected String filename;
private final InputStream inputStream;

protected ArrayList<StandardsListItem> extractedData;

/**
* Creates the extractor
*
* @param filename csv filename
* @throws IOException exception thrown when issues opening given file occur
*/
public UniversalCalibrantsListCsvExtractor(String filename) throws IOException {
this.filename = filename;
}

/**
* Creates the extractor
*
* @param filename csv filename
* @param inputStream input stream to use.
* @throws IOException exception thrown when issues opening given file occur
*/
public UniversalCalibrantsListCsvExtractor(String filename, InputStream inputStream)
public UniversalCalibrantsListCsvExtractor(String filename, @NotNull InputStream inputStream)
throws IOException {
this.filename = filename;

this.inputStream = inputStream;
}

/**
Expand All @@ -88,30 +83,34 @@ public StandardsList extractStandardsList() throws IOException, CsvException {
}
this.extractedData = new ArrayList<>();

List<String[]> lines = CSVParsingUtils.readData(new File(filename), ",");
for (String[] lineValues : lines) {
try {
String mzRatioString = lineValues[mzRatioColumn];
String name = nameColumn < lineValues.length ? lineValues[nameColumn] : null;
double mzRatio = Double.valueOf(mzRatioString);
StandardsListItem calibrant = new StandardsListItem(mzRatio);
if (name != null && name.trim().isEmpty() == false) {
calibrant.setName(name);
try (final BufferedReader bufferedReader = new BufferedReader(
new InputStreamReader(inputStream))) {
List<String[]> lines = CSVParsingUtils.readData(bufferedReader, ",");
for (String[] lineValues : lines) {
try {
String mzRatioString = lineValues[mzRatioColumn];
String name = nameColumn < lineValues.length ? lineValues[nameColumn] : null;
double mzRatio = Double.valueOf(mzRatioString);
StandardsListItem calibrant = new StandardsListItem(mzRatio);
if (name != null && name.trim().isEmpty() == false) {
calibrant.setName(name);
}
extractedData.add(calibrant);
} catch (Exception e) {
logger.fine(
"Exception occurred when reading row index %d. Will skip this row and continue parsing.".formatted(
lines.indexOf(lineValues)));
logger.fine(e.toString());
}
extractedData.add(calibrant);
} catch (Exception e) {
logger.fine(STR."Exception occurred when reading row index \{lines.indexOf(lineValues)}");
logger.fine(e.toString());
}
}

logger.info(
STR."Extracted \{extractedData.size()} standard molecules from \{lines.size()} rows");
if (extractedData.size() < lines.size()) {
logger.warning(STR."Skipped \{lines.size()
- extractedData.size()} rows when reading standards list in csv file \{filename}");
logger.info(
STR."Extracted \{extractedData.size()} standard molecules from \{lines.size()} rows");
if (extractedData.size() < lines.size()) {
logger.warning(STR."Skipped \{lines.size()
- extractedData.size()} rows when reading standards list in csv file \{filename}");
}
return new StandardsList(extractedData);
}

return new StandardsList(extractedData);
}
}
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