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Merge pull request mzmine#583 from robinschmid/waters_raw
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Fix Waters raw import
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@robinschmid
robinschmid authored Mar 9, 2022
2 parents 57a1ce9 + 09b9a16 commit cbbf204
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Showing 19 changed files with 92 additions and 1,433 deletions.
18 changes: 15 additions & 3 deletions ...ain/java/io/github/mzmine/modules/io/import_rawdata_waters_raw/WatersRawImportModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,13 @@
import io.github.mzmine.util.ExitCode;
import io.github.mzmine.util.MemoryMapStorage;
import io.github.mzmine.util.RawDataFileUtils;
import io.github.mzmine.util.files.FileAndPathUtil;
import java.io.File;
import java.io.IOException;
import java.time.Instant;
import java.util.Arrays;
import java.util.Collection;
import java.util.Objects;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
Expand All @@ -44,8 +46,8 @@
*/
public class WatersRawImportModule implements MZmineProcessingModule {

private Logger logger = Logger.getLogger(this.getClass().getName());

private static final Logger logger = Logger.getLogger(WatersRawImportModule.class.getName());
private static final String MODULE_NAME = "Waters RAW file import";
private static final String MODULE_DESCRIPTION = "This module imports raw data into the project.";

Expand Down Expand Up @@ -74,7 +76,16 @@ public class WatersRawImportModule implements MZmineProcessingModule {
public ExitCode runModule(final @NotNull MZmineProject project, @NotNull ParameterSet parameters,
@NotNull Collection<Task> tasks, @NotNull Instant moduleCallDate) {

File fileNames[] = parameters.getParameter(WatersRawImportParameters.fileNames).getValue();
File dir = parameters.getParameter(WatersRawImportParameters.fileNames).getValue()[0];
File fileNames[] = Arrays.stream(FileAndPathUtil.getSubDirectories(dir))
.filter(Objects::nonNull)
.filter(f -> f.isDirectory() && f.getName().toLowerCase().endsWith(".raw"))
.toArray(File[]::new);

if (fileNames.length <= 0) {
logger.warning("Select .raw folder or parent folder for waters import");
return ExitCode.ERROR;
}

if (Arrays.asList(fileNames).contains(null)) {
logger.warning("List of filenames contains null");
Expand Down Expand Up @@ -105,7 +116,8 @@ public ExitCode runModule(final @NotNull MZmineProject project, @NotNull Paramet
}

try {
RawDataFile newMZmineFile = MZmineCore.createNewFile(newName, fileNames[i].getAbsolutePath(), storage);
RawDataFile newMZmineFile = MZmineCore.createNewFile(newName,
fileNames[i].getAbsolutePath(), storage);
Task newTask = new WatersRawImportTask(project, fileNames[i], newMZmineFile,
WatersRawImportModule.class, parameters, moduleCallDate);
tasks.add(newTask);
Expand Down
103 changes: 77 additions & 26 deletions src/main/java/io/github/mzmine/modules/io/import_rawdata_waters_raw/WatersRawImportTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,18 +34,22 @@
import io.github.mzmine.taskcontrol.TaskStatus;
import io.github.mzmine.util.ExceptionUtils;
import io.github.mzmine.util.TextUtils;
import io.github.mzmine.util.ZipUtils;
import io.github.mzmine.util.scans.ScanUtils;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.file.Files;
import java.time.Instant;
import java.util.Date;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipInputStream;
import org.apache.commons.io.FileUtils;
import org.jetbrains.annotations.NotNull;

/**
Expand All @@ -54,18 +58,14 @@
*/
public class WatersRawImportTask extends AbstractTask {

private Logger logger = Logger.getLogger(this.getClass().getName());

public static final Logger logger = Logger.getLogger(WatersRawImportTask.class.getName());
private final ParameterSet parameters;
private final Class<? extends MZmineModule> module;
private File file;
private MZmineProject project;
private RawDataFile newMZmineFile;
private final ParameterSet parameters;
private final Class<? extends MZmineModule> module;

private Process dumper = null;

private int totalScans = 0, parsedScans = 0;

/*
* These variables are used during parsing of the RAW dump.
*/
Expand All @@ -78,7 +78,8 @@ public class WatersRawImportTask extends AbstractTask {
private double precursorMZ = 0;

public WatersRawImportTask(MZmineProject project, File fileToOpen, RawDataFile newMZmineFile,
@NotNull final Class<? extends MZmineModule> module, @NotNull final ParameterSet parameters, @NotNull Instant moduleCallDate) {
@NotNull final Class<? extends MZmineModule> module, @NotNull final ParameterSet parameters,
@NotNull Instant moduleCallDate) {
super(null, moduleCallDate); // storage in raw data file
this.project = project;
this.file = fileToOpen;
Expand All @@ -87,6 +88,50 @@ public WatersRawImportTask(MZmineProject project, File fileToOpen, RawDataFile n
this.module = module;
}

public static File unzipWatersParser() throws IOException {
final String tmpPath = System.getProperty("java.io.tmpdir");
File watersRawFileParserFolder = new File(tmpPath, "mzmine_waters_raw_parser");
final File watersRawFileParserExe = new File(watersRawFileParserFolder, "WatersRawDump.exe");

// Check if it has already been unzipped
if (watersRawFileParserFolder.exists() && watersRawFileParserFolder.isDirectory()
&& watersRawFileParserFolder.canRead() && watersRawFileParserExe.exists()
&& watersRawFileParserExe.isFile() && watersRawFileParserExe.canExecute()) {
logger.finest("Waters RawFileParser found in folder " + watersRawFileParserFolder);
return watersRawFileParserFolder;
}
synchronized (WatersRawImportTask.class) {
// double checked
if (watersRawFileParserFolder.exists() && watersRawFileParserFolder.isDirectory()
&& watersRawFileParserFolder.canRead() && watersRawFileParserExe.exists()
&& watersRawFileParserExe.isFile() && watersRawFileParserExe.canExecute()) {
logger.finest("Waters RawFileParser found in folder " + watersRawFileParserFolder);
return watersRawFileParserFolder;
}

// In case the folder already exists, unzip to a different folder
if (watersRawFileParserFolder.exists()) {
logger.finest("Folder " + watersRawFileParserFolder + " exists, creating a new one");
watersRawFileParserFolder = Files.createTempDirectory("mzmine_waters_raw_parser").toFile();
}

logger.finest("Unpacking Waters RawFileParser to folder " + watersRawFileParserFolder);
InputStream zipStream = WatersRawImportTask.class.getResourceAsStream(
"/vendorlib/waters/waters.zip");
if (zipStream == null) {
throw new IOException("Failed to open the resource /vendorlib/waters/waters.zip");
}
ZipInputStream zipInputStream = new ZipInputStream(zipStream);
ZipUtils.unzipStream(zipInputStream, watersRawFileParserFolder);
zipInputStream.close();

// Delete the temporary folder on application exit
FileUtils.forceDeleteOnExit(watersRawFileParserFolder);

return watersRawFileParserFolder;
}
}

/**
* @see io.github.mzmine.taskcontrol.Task#getFinishedPercentage()
*/
Expand All @@ -95,9 +140,6 @@ public double getFinishedPercentage() {
return totalScans == 0 ? 0 : (double) parsedScans / totalScans;
}

/**
* @see java.lang.Runnable#run()
*/
@Override
public void run() {

Expand All @@ -106,15 +148,25 @@ public void run() {

// Check the OS we are running
String osName = System.getProperty("os.name").toUpperCase();
String rawDumpPath =
System.getProperty("user.dir") + File.separator + "lib" + File.separator + "vendor_lib"
+ File.separator + "waters" + File.separator + "WatersRawDump.exe";
String rawDumpPath = "";

try {
final File folder = unzipWatersParser();
rawDumpPath = new File(folder, "WatersRawDump.exe").getPath();
} catch (IOException e) {
final String msg = "Error while reading waters raw library. " + e.getMessage();
logger.log(Level.WARNING, msg, e);
setErrorMessage(msg);
setStatus(TaskStatus.ERROR);
return;
}

String cmdLine[];

if (osName.toUpperCase().contains("WINDOWS")) {
cmdLine = new String[]{rawDumpPath, file.getPath()};
cmdLine = new String[]{rawDumpPath, this.file.getPath()};
} else {
cmdLine = new String[]{"wine", rawDumpPath, file.getPath()};
cmdLine = new String[]{"wine", rawDumpPath, this.file.getPath()};
}

try {
Expand Down Expand Up @@ -147,7 +199,8 @@ public void run() {
+ totalScans + ")"));
}

newMZmineFile.getAppliedMethods().add(new SimpleFeatureListAppliedMethod(module, parameters, getModuleCallDate()));
newMZmineFile.getAppliedMethods()
.add(new SimpleFeatureListAppliedMethod(module, parameters, getModuleCallDate()));
project.addFile(newMZmineFile);

} catch (Throwable e) {
Expand All @@ -166,7 +219,7 @@ public void run() {
return;
}

logger.info("Finished parsing " + file + ", parsed " + parsedScans + " scans");
logger.info("Finished parsing " + this.file + ", parsed " + parsedScans + " scans");
setStatus(TaskStatus.FINISHED);

}
Expand Down Expand Up @@ -194,7 +247,7 @@ private void readRAWDump(InputStream dumpStream) throws IOException {
}

if (line.startsWith("ERROR: ")) {
throw (new IOException(line.substring("ERROR: ".length())));
throw (new IOException(file.getAbsolutePath() + line.substring("ERROR: ".length())));
}

if (line.startsWith("NUMBER OF SCANS: ")) {
Expand Down Expand Up @@ -280,8 +333,8 @@ private void readRAWDump(InputStream dumpStream) throws IOException {
// VALUES
if (numOfDataPoints != Integer.parseInt(m.group(1))) {
throw new IOException(
"Scan " + scanNumber + " contained " + numOfDataPoints + " mass values, but " + m
.group(1) + " intensity values");
"Scan " + scanNumber + " contained " + numOfDataPoints + " mass values, but "
+ m.group(1) + " intensity values");
}
final int byteSize = Integer.parseInt(m.group(2));

Expand Down Expand Up @@ -321,9 +374,8 @@ private void readRAWDump(InputStream dumpStream) throws IOException {
msLevel != 1 && precursorMZ != 0d ? new DDAMsMsInfoImpl(precursorMZ, precursorCharge,
null, null, null, msLevel, ActivationMethod.UNKNOWN, null) : null;

SimpleScan newScan = new SimpleScan(newMZmineFile, scanNumber, msLevel, retentionTime,
info, mzValues, intensityValues, spectrumType, polarity, scanId,
mzRange);
SimpleScan newScan = new SimpleScan(newMZmineFile, scanNumber, msLevel, retentionTime, info,
mzValues, intensityValues, spectrumType, polarity, scanId, mzRange);
newMZmineFile.addScan(newScan);

parsedScans++;
Expand Down Expand Up @@ -354,5 +406,4 @@ public void cancel() {
dumper.destroy();
}
}

}
Binary file removed src/main/resources/vendorlib/waters/MassLynxRaw.dll
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Binary file removed src/main/resources/vendorlib/waters/MassLynxRaw.lib
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8 changes: 0 additions & 8 deletions src/main/resources/vendorlib/waters/README.txt
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