diff --git a/build.gradle b/build.gradle
index 72f2e63..aabec3f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -9,7 +9,7 @@ plugins {
}
group = 'com.dmtavt'
-version = '1.0'
+version = '1.1'
description = """DeltaMass - detection and visualization of common mass shifts in proteomic searches."""
@@ -29,7 +29,12 @@ jar {
shadowJar {
classifier = null
- minimize()
+ minimize {
+ exclude(dependency('javax.xml.bind:jaxb-api:.*'))
+ exclude(dependency('org.glassfish.jaxb:jaxb-runtime:.*'))
+ exclude(dependency('javax.activation:javax.activation-api:.*'))
+ exclude(dependency('com.sun.istack:istack-commons-runtime:.*'))
+ }
}
launch4j {
@@ -46,19 +51,19 @@ repositories {
}
dependencies {
// our projects
- implementation("com.github.chhh:dmtavt-utils:0.4.4")
- implementation("com.github.chhh:msftbx:1.8.6")
- implementation("com.github.chhh:ptm-factory:1.0")
- implementation("edu.umich.andykong:mscalibrator:1.1")
+ compile("com.github.chhh:dmtavt-utils:0.4.4")
+ compile("com.github.chhh:msftbx:1.8.6")
+ compile("com.github.chhh:ptm-factory:1.0")
+ compile("edu.umich.andykong:mscalibrator:1.1")
// basic
- implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.2.3'
- implementation group: 'org.slf4j', name: 'slf4j-api', version: '1.7.25'
- implementation group: 'com.beust', name: 'jcommander', version: '1.72'
+ compile group: 'ch.qos.logback', name: 'logback-classic', version: '1.2.3'
+ compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.25'
+ compile group: 'com.beust', name: 'jcommander', version: '1.72'
// commons
- implementation group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'
- implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.8.1'
+ compile group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'
+ compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.8.1'
compile 'commons-io:commons-io:2.6'
// other
@@ -67,17 +72,22 @@ dependencies {
compile 'com.miglayout:miglayout-swing:5.2'
compile 'org.jfree:jfreechart:1.5.0'
- implementation group: 'com.edwardraff', name: 'JSAT', version: '0.0.9'
- implementation(group: 'com.github.haifengl', name: 'smile-core', version: '1.5.2') {
+ compile(group: 'com.edwardraff', name: 'JSAT', version: '0.0.9')
+ compile(group: 'com.github.haifengl', name: 'smile-core', version: '1.5.2') {
exclude(module: 'smile-data')
exclude(module: 'smile-graph')
}
+ // JAXB stuff for parsing mods from databases
+ compile 'javax.xml.bind:jaxb-api:2.3.1'
+ compile 'org.glassfish.jaxb:jaxb-runtime:2.3.1'
+ compile 'javax.activation:javax.activation-api:1.2.0'
+
// downloaded / precompiled jars
compile fileTree(dir: 'libs', include: '*.jar')
// test
- testImplementation(group: 'org.apache.maven', name: 'maven-model', version: '3.6.0')
- testImplementation group: 'junit', name: 'junit', version: '4.12'
+ testCompile(group: 'org.apache.maven', name: 'maven-model', version: '3.6.0')
+ testCompile group: 'junit', name: 'junit', version: '4.12'
testCompile("org.assertj:assertj-core:3.11.1")
}
diff --git a/build.xml b/build.xml
new file mode 100644
index 0000000..5bc5c76
--- /dev/null
+++ b/build.xml
@@ -0,0 +1,101 @@
+
+
+
+
+
+
+
+
+
+
+ Builds, tests, and runs the project DeltaMass.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/master/src/main/java/com/dmtavt/deltamass/Bundle.properties b/master/src/main/java/com/dmtavt/deltamass/Bundle.properties
index a112905..4f8c8d0 100644
--- a/master/src/main/java/com/dmtavt/deltamass/Bundle.properties
+++ b/master/src/main/java/com/dmtavt/deltamass/Bundle.properties
@@ -1 +1 @@
-deltamass.version.current=0.1-SNAPSHOT
+deltamass.version.current=1.1
diff --git a/src/main/java/com/dmtavt/deltamass/Bundle.properties b/src/main/java/com/dmtavt/deltamass/Bundle.properties
index 266e39b..35438c1 100644
--- a/src/main/java/com/dmtavt/deltamass/Bundle.properties
+++ b/src/main/java/com/dmtavt/deltamass/Bundle.properties
@@ -1 +1 @@
-deltamass.version.current=1.0
+deltamass.version.current=1.1
diff --git a/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java b/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java
index a99ee42..bd49eb1 100644
--- a/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java
+++ b/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java
@@ -20,15 +20,14 @@ public final class DeltaMassInfo {
private static final EventBus bus = EventBus.getDefault();
public static final String Name = "DeltaMass";
- public static final String Ver = "1.0";
+ public static final String Ver = "1.1";
private static final String PROP_VER = "deltamass.version.current";
private static final String PROP_DOWNLOAD_URL = "deltamass.download.url";
private static final String DEFAULT_DOWNLOAD_URL = "https://github.com/chhh/deltamass/releases";
- private static final String BUNDLE_PATH = "com/dmtavt/deltamass/Bundle";
+ private static final String BUNDLE_PATH = "com/dmtavt/deltamass/Bundle.properties";
private static final String BUNDLE_URL =
- "https://raw.githubusercontent.com/chhh/deltamass/master/src/main/java/" + BUNDLE_PATH
- + ".properties";
+ "https://raw.githubusercontent.com/chhh/deltamass/master/src/main/java/" + BUNDLE_PATH;
private static final URI BUNDLE_URI = URI.create(BUNDLE_URL);
private DeltaMassInfo() {
diff --git a/src/main/java/com/dmtavt/deltamass/logic/LogicClean.java b/src/main/java/com/dmtavt/deltamass/logic/LogicClean.java
index c428d78..c16b564 100644
--- a/src/main/java/com/dmtavt/deltamass/logic/LogicClean.java
+++ b/src/main/java/com/dmtavt/deltamass/logic/LogicClean.java
@@ -25,37 +25,45 @@ public LogicClean(CommandClean cmd) {
public void run() {
log.info("Running cleanup");
- if (cmd.dryRun) log.info("Dry-run, won't take any action.");
- int stepsPerformed = 0;
+ final List scheduledForDeletion = getScheduledForDeletion();
- if (!cmd.noPep) {
- stepsPerformed++;
- log.info("Cleaning up peptide identification files.");
- DeletionStats stats = deleteMatchingFilesInSubtrees(cmd.inputFiles,
- CacheLocator::isPepCacheFile, cmd.dryRun);
- log.info("Pep ID cleanup summary: scheduled: {}, deleted: {}, skipped: {}, error: {}",
- stats.scheduled, stats.deleted, stats.skipped.size(), stats.error.size());
- }
+ final String list = scheduledForDeletion.stream().map(Path::toString)
+ .collect(Collectors.joining("\n"));
+ log.info("Files to delete:\n" + list);
- if (!cmd.noLcms) {
- stepsPerformed++;
- log.info("Cleaning up LC-MS calibration files.");
- DeletionStats stats = deleteMatchingFilesInSubtrees(cmd.inputFiles,
- CacheLocator::isCalCacheFile, cmd.dryRun);
- log.info("Calibration cleanup summary: scheduled: {}, deleted: {}, skipped: {}, error: {}",
- stats.scheduled, stats.deleted, stats.skipped.size(), stats.error.size());
+ if (cmd.dryRun) {
+ log.info("Dry-run, won't take any action.");
+ return;
}
- if (stepsPerformed == 0) log.info("You made it clear that nothing should be cleaned up. Doing nothing.");
+ DeletionStats stats = delete(scheduledForDeletion);
+ log.info("Cleanup: deleted {}/{}, errors: {}", stats.deleted.size(), stats.scheduled.size(), stats.error.size());
+ }
+
+ private static List modifyInputPathsForCacheDeletion(List paths) {
+ List possibleCachePaths = new ArrayList<>();
+ for (Path inputFile : paths) {
+ if (Files.isDirectory(inputFile)) {
+ possibleCachePaths.add(inputFile);
+ } else {
+ Path parent = inputFile.getParent();
+ Path fn = inputFile.getFileName();
+ possibleCachePaths.add(parent.resolve(fn.toString() + CacheLocator.CACHE_EXT_PEP));
+ possibleCachePaths.add(parent.resolve(fn.toString() + CacheLocator.CACHE_EXT_CAL));
+ }
+ }
+ return possibleCachePaths;
}
public List getScheduledForDeletion() {
List delete = new ArrayList<>();
+ final List putativeCachePaths = modifyInputPathsForCacheDeletion(cmd.inputFiles);
+
if (!cmd.noPep) {
- delete.addAll(getScheduledForDeletion(cmd.inputFiles, CacheLocator::isPepCacheFile));
+ delete.addAll(getScheduledForDeletion(putativeCachePaths, CacheLocator::isPepCacheFile));
}
if (!cmd.noLcms) {
- delete.addAll(getScheduledForDeletion(cmd.inputFiles, CacheLocator::isCalCacheFile));
+ delete.addAll(getScheduledForDeletion(putativeCachePaths, CacheLocator::isCalCacheFile));
}
return delete;
}
@@ -89,7 +97,7 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
log.warn("Error collecting files for deletion in subtree: {}" + path, e);
}
} else {
- if (condition.test(path)) {
+ if (Files.exists(path) && condition.test(path)) {
delete.add(path);
}
}
@@ -97,65 +105,26 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
return new ArrayList<>(delete);
}
- private class DeletionStats {
- int scheduled = 0;
- int deleted = 0;
- ConcurrentLinkedQueue skipped = new ConcurrentLinkedQueue<>();
+ private static class DeletionStats {
+ ConcurrentLinkedQueue scheduled = new ConcurrentLinkedQueue<>();
+ ConcurrentLinkedQueue deleted = new ConcurrentLinkedQueue<>();
ConcurrentLinkedQueue error = new ConcurrentLinkedQueue<>();
}
- private DeletionStats deleteMatchingFilesInSubtrees(Iterable paths, Predicate condition, boolean dryRun) {
- final ConcurrentLinkedQueue delete = new ConcurrentLinkedQueue<>();
- final DeletionStats stats = new DeletionStats();
-
- for (Path path : paths) {
- if (Files.isDirectory(path)) {
- try {
- Files.walkFileTree(path, new SimpleFileVisitor() {
- @Override
- public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) {
- if (!Files.isReadable(dir)) return FileVisitResult.SKIP_SUBTREE;
- return FileVisitResult.CONTINUE;
- }
-
- @Override
- public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
- if (!Files.isWritable(file)) {
- log.warn("File not writeable, skipping: {}", file);
- stats.skipped.add(file);
- return FileVisitResult.CONTINUE;
- }
- if (condition.test(file)) delete.add(file);
- return FileVisitResult.CONTINUE;
- }
- });
- } catch (IOException e) {
- log.error("Error collecting files for deletion in subtree: {}" + path, e);
- }
- } else {
- if (CacheLocator.isPepCacheFile(path))
- delete.add(path);
- }
- }
-
- if (!delete.isEmpty()) {
- log.info("Files scheduled for deletion:\n {}",
- delete.stream().map(Path::toString).collect(Collectors.joining("\n ")));
- } else {
- log.info("Found no files to delete.");
- }
- stats.scheduled = delete.size();
-
- if (!dryRun) delete.forEach(path -> {
+ public static DeletionStats delete(List pathsToDelete) {
+ DeletionStats ds = new DeletionStats();
+ ds.scheduled.addAll(pathsToDelete);
+ for (Path path : pathsToDelete) {
try {
- Files.deleteIfExists(path);
- stats.deleted++;
+ if (Files.deleteIfExists(path)) {
+ ds.deleted.add(path);
+ }
} catch (IOException e) {
- log.error("Could not delete file: " + path, e);
- stats.error.add(path);
+ log.error("Error deleting file: " + path.toString() + "\nDetails:\n" + e.getMessage());
+ ds.error.add(path);
}
- });
-
- return stats;
+ }
+ return ds;
}
+
}
diff --git a/src/main/java/com/dmtavt/deltamass/logic/LogicInputFiles.java b/src/main/java/com/dmtavt/deltamass/logic/LogicInputFiles.java
index c454f78..dac1463 100644
--- a/src/main/java/com/dmtavt/deltamass/logic/LogicInputFiles.java
+++ b/src/main/java/com/dmtavt/deltamass/logic/LogicInputFiles.java
@@ -259,6 +259,11 @@ private List inputFiles(List inputPaths, final Pattern regex, boolea
return matched;
}
+ private boolean isPepFileSupported(Path pepFilePath) {
+ IParserFactory parser = PepidParserRegistry.find(pepFilePath);
+ return parser != null;
+ }
+
private List collectSupportedFiles(Iterable paths, boolean recursive) {
final ConcurrentLinkedQueue supported = new ConcurrentLinkedQueue<>();
@@ -280,8 +285,7 @@ public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) {
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
- IParserFactory parser = PepidParserRegistry.find(file);
- if (parser != null) {
+ if (isPepFileSupported(file)) {
supported.add(file);
}
return FileVisitResult.CONTINUE;
@@ -292,8 +296,10 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
log.warn("Error collecting files for deletion in subtree: {}" + path, e);
}
} else {
- if (CacheLocator.isPepCacheFile(path))
+ // given a regular file, not a directory
+ if (isPepFileSupported(path)) {
supported.add(path);
+ }
}
}
return new ArrayList<>(supported);
diff --git a/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java b/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java
index b1b1bed..6c82308 100644
--- a/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java
+++ b/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java
@@ -156,7 +156,6 @@ public PepSearchFile parse(final Pattern decoyRegex) throws IOException {
if (charge != 0) {
// TODO: is this value really not present in pepxml and need to be computed?
spm.mzObs = (precMassZ0 + charge * PROTON_MASS) / charge;
- int a = 1;
}
spm.spectrumId = spectrumId;
spm.seq = sh.getPeptide();
@@ -206,23 +205,28 @@ public PepSearchFile parse(final Pattern decoyRegex) throws IOException {
+ "spectrum query `%s`", i, sq.getSpectrum()));
}
}
- if (pepProphIdx > -1) {
- Object analysis = sh.getAnalysisResult().stream()
- .flatMap(analysisResult -> analysisResult.getAny().stream())
- .filter(o -> o instanceof PeptideprophetResult).findAny()
- .orElseThrow(() -> new IllegalStateException(String.format(
- "PeptideProphet score could not be found in file `%s`, SpectrumQuery `%s`",
- path, sq.getSpectrum())));
- spm.scores[pepProphIdx] = ((PeptideprophetResult) analysis).getProbability();
- }
- if (iProphIdx> -1) {
- Object analysis = sh.getAnalysisResult().stream()
- .flatMap(analysisResult -> analysisResult.getAny().stream())
- .filter(o -> o instanceof InterprophetResult).findAny()
- .orElseThrow(() -> new IllegalStateException(String.format(
- "iProphet score could not be found in file `%s`, SpectrumQuery `%s`", path,
- sq.getSpectrum())));
- spm.scores[iProphIdx] = ((InterprophetResult) analysis).getProbability();
+ try {
+ if (pepProphIdx > -1) {
+ Object analysis = sh.getAnalysisResult().stream()
+ .flatMap(analysisResult -> analysisResult.getAny().stream())
+ .filter(o -> o instanceof PeptideprophetResult).findAny()
+ .orElseThrow(() -> new IllegalStateException(String.format(
+ "PeptideProphet score could not be found in file `%s`, SpectrumQuery `%s`",
+ path, sq.getSpectrum())));
+ spm.scores[pepProphIdx] = ((PeptideprophetResult) analysis).getProbability();
+ }
+ if (iProphIdx > -1) {
+ Object analysis = sh.getAnalysisResult().stream()
+ .flatMap(analysisResult -> analysisResult.getAny().stream())
+ .filter(o -> o instanceof InterprophetResult).findAny()
+ .orElseThrow(() -> new IllegalStateException(String.format(
+ "iProphet score could not be found in file `%s`, SpectrumQuery `%s`", path,
+ sq.getSpectrum())));
+ spm.scores[iProphIdx] = ((InterprophetResult) analysis).getProbability();
+ }
+ } catch (IllegalStateException e) {
+ log.warn(e.getMessage());
+ throw e;
}
spms.add(spm);
}
@@ -254,7 +258,7 @@ private HashMap mapScoreNames(List queries) thro
scoreMapping.put(scoreName, scoreIndex);
}
- // try get peptide prophet score
+ // try get peptidepprophet/iprophet score
List analysisResults = sh.getAnalysisResult();
for (AnalysisResult analysisResult : analysisResults) {
String analysis = analysisResult.getAnalysis();
diff --git a/src/main/java/com/dmtavt/deltamass/ui/DeltaMassOptionsForm.java b/src/main/java/com/dmtavt/deltamass/ui/DeltaMassOptionsForm.java
index 98fb9ba..2762be6 100644
--- a/src/main/java/com/dmtavt/deltamass/ui/DeltaMassOptionsForm.java
+++ b/src/main/java/com/dmtavt/deltamass/ui/DeltaMassOptionsForm.java
@@ -18,6 +18,7 @@
import com.dmtavt.deltamass.messages.MsgRunPlot;
import com.dmtavt.deltamass.messages.MsgStop;
import com.dmtavt.deltamass.messages.MsgVersionUpdateInfo;
+import com.dmtavt.deltamass.utils.OsUtils;
import com.github.chhh.utils.StringUtils;
import com.github.chhh.utils.SwingUtils;
import com.github.chhh.utils.ser.SwingCachePropsStore;
@@ -56,6 +57,7 @@
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTable;
+import javax.swing.SwingUtilities;
import javax.swing.border.TitledBorder;
import javax.swing.table.DefaultTableModel;
import net.java.balloontip.BalloonTip;
@@ -332,11 +334,22 @@ private void init() {
bus.post(new MsgStop(uiBtnStop));
});
+
+
bus.register(this);
// Try to fetch new version info from remote. Runs in a separate thread.
DeltaMassInfo.checkForNewVersions();
cache.load(this);
+ logSysInfo();
+ }
+
+ /** Log system info. */
+ private void logSysInfo() {
+ final StringBuilder sb = new StringBuilder("System info:\n");
+ sb.append(OsUtils.osInfo()).append("\n");
+ sb.append(OsUtils.javaInfo());
+ log.info(sb.toString());
}
@Subscribe
diff --git a/src/main/java/com/dmtavt/deltamass/utils/OsUtils.java b/src/main/java/com/dmtavt/deltamass/utils/OsUtils.java
new file mode 100644
index 0000000..0c5c06b
--- /dev/null
+++ b/src/main/java/com/dmtavt/deltamass/utils/OsUtils.java
@@ -0,0 +1,92 @@
+package com.dmtavt.deltamass.utils;
+
+import com.github.chhh.utils.StringUtils;
+import java.util.Arrays;
+import java.util.List;
+
+public class OsUtils {
+
+ private OsUtils() {
+ }
+
+ public static String osInfo() {
+ String os = OsUtils.getOsName();
+ os = StringUtils.isNullOrWhitespace(os) ? "?" : os;
+ String arch = OsUtils.getSystemArch();
+ arch = StringUtils.isNullOrWhitespace(arch) ? "?" : arch;
+ return "System OS: " + os + ", Architecture: " + arch;
+ }
+
+ public static String javaInfo() {
+ List propNames = Arrays.asList(
+ "java.version",
+ "java.vm.name",
+ "java.vm.vendor"
+ );
+ StringBuilder sb = new StringBuilder("Java Info: ");
+ for (int i = 0; i < propNames.size(); i++) {
+ String p = propNames.get(i);
+ String val = System.getProperty(p);
+ if (!StringUtils.isNullOrWhitespace(val)) {
+ sb.append(val);
+ }
+ if (i < propNames.size() - 1) {
+ sb.append(", ");
+ }
+ }
+
+ return sb.toString();
+ }
+
+ public static boolean isWindows() {
+ String osName = System.getProperty("os.name");
+ if (osName == null) {
+ return true; // just the default
+ }
+ return osName.toLowerCase().startsWith("win");
+ }
+
+ /**
+ * OS name. E.g. 'Linux' or 'Windows XP'.
+ *
+ * @return
+ */
+ public static String getOsName() {
+ String osName = System.getProperty("os.name");
+ return osName;
+ }
+
+ /**
+ * Tries to determine processor architecture from system properties.
+ *
+ * @return null if could not determine.
+ */
+ public static String getSystemArch() {
+
+ try {
+ if (isWindows()) {
+ String wow64 = System.getenv("PROCESSOR_ARCHITEW6432");
+ if (wow64 != null) {
+ return wow64;
+ }
+ String arch = System.getenv("PROCESSOR_ARCHITECTURE");
+ if (arch != null) {
+ return arch;
+ }
+
+ } else {
+ String osArch = System.getProperty("os.arch");
+ if (osArch != null) {
+ return osArch;
+ }
+ }
+ } catch (IllegalArgumentException e) {
+ // could not map os.arch or whatever to our enum values, not a biggie
+ }
+
+ // if all else fails, at least try to get the bitness of the JRE
+ // which might still be null
+ String osArch = System.getProperty("os.arch");
+ return osArch;
+ }
+}