Fix some issues with protein prophet

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")
 }

build.xml

@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- You may freely edit this file. See commented blocks below for -->
+<!-- some examples of how to customize the build. -->
+<!-- (If you delete it and reopen the project it will be recreated.) -->
+<!-- By default, only the Clean and Build commands use this build script. -->
+<!-- Commands such as Run, Debug, and Test only use this build script if -->
+<!-- the Compile on Save feature is turned off for the project. -->
+<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
+<!-- in the project's Project Properties dialog box.-->
+<project basedir="." default="default" name="DeltaMass">
+  <description>Builds, tests, and runs the project DeltaMass.</description>
+  <import file="nbproject/build-impl.xml"/>
+  <!--
+
+  There exist several targets which are by default empty and which can be
+  used for execution of your tasks. These targets are usually executed
+  before and after some main targets. They are:
+
+    -pre-init:                 called before initialization of project properties
+    -post-init:                called after initialization of project properties
+    -pre-compile:              called before javac compilation
+    -post-compile:             called after javac compilation
+    -pre-compile-single:       called before javac compilation of single file
+    -post-compile-single:      called after javac compilation of single file
+    -pre-compile-test:         called before javac compilation of JUnit tests
+    -post-compile-test:        called after javac compilation of JUnit tests
+    -pre-compile-test-single:  called before javac compilation of single JUnit test
+    -post-compile-test-single: called after javac compilation of single JUunit test
+    -pre-jar:                  called before JAR building
+    -post-jar:                 called after JAR building
+    -post-clean:               called after cleaning build products
+
+  (Targets beginning with '-' are not intended to be called on their own.)
+
+  Example of inserting an obfuscator after compilation could look like this:
+
+      <target name="-post-compile">
+          <obfuscate>
+              <fileset dir="${build.classes.dir}"/>
+          </obfuscate>
+      </target>
+
+  For list of available properties check the imported
+  nbproject/build-impl.xml file.
+
+
+  Another way to customize the build is by overriding existing main targets.
+  The targets of interest are:
+
+    -init-macrodef-javac:     defines macro for javac compilation
+    -init-macrodef-junit:     defines macro for junit execution
+    -init-macrodef-debug:     defines macro for class debugging
+    -init-macrodef-java:      defines macro for class execution
+    -do-jar:                  JAR building
+    run:                      execution of project
+    -javadoc-build:           Javadoc generation
+    test-report:              JUnit report generation
+
+  An example of overriding the target for project execution could look like this:
+
+      <target name="run" depends="DeltaMass-impl.jar">
+          <executorDefSize dir="bin" executable="launcher.exe">
+              <arg file="${dist.jar}"/>
+          </executorDefSize>
+      </target>
+
+  Notice that the overridden target depends on the jar target and not only on
+  the compile target as the regular run target does. Again, for a list of available
+  properties which you can use, check the target you are overriding in the
+  nbproject/build-impl.xml file.
+
+  -->
+
+  <target depends="jar" name="package-for-store">
+    <property name="store.jar.name" value="DeltaMass"/>
+    <property name="store.dir" value="dist"/>
+    <property name="store.jar" value="${store.dir}/${store.jar.name}.jar"/>
+    <echo message="Packaging ${application.title} into a single JAR at ${store.jar}"/>
+    <delete dir="${store.dir}"/>
+    <mkdir dir="${store.dir}"/>
+    <jar destfile="${store.dir}/temp_final.jar" filesetmanifest="skip">
+      <zipgroupfileset dir="dist" includes="*.jar"/>
+      <zipgroupfileset dir="dist/lib" includes="*.jar"/>
+      <manifest>
+        <attribute name="Main-Class" value="${main.class}"/>
+      </manifest>
+    </jar>
+    <zip destfile="${store.jar}">
+      <zipfileset excludes="META-INF/*.SF, META-INF/*.DSA, META-INF/*.RSA"
+        src="${store.dir}/temp_final.jar"/>
+    </zip>
+    <delete file="${store.dir}/temp_final.jar"/>
+  </target>
+
+  <!-- Creating manifest for NetBeans Ant builds -->
+  <target name="-pre-init">
+    <!-- Not needed, turns out you can just put stuff in manifest.mf file in
+         the project root directory -->
+  </target>
+
+</project>

master/src/main/java/com/dmtavt/deltamass/Bundle.properties

@@ -1 +1 @@
-deltamass.version.current=0.1-SNAPSHOT
+deltamass.version.current=1.1

src/main/java/com/dmtavt/deltamass/Bundle.properties

@@ -1 +1 @@
-deltamass.version.current=1.0
+deltamass.version.current=1.1

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() {

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<Path> 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<Path> modifyInputPathsForCacheDeletion(List<Path> paths) {
+    List<Path> 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<Path> getScheduledForDeletion() {
     List<Path> delete = new ArrayList<>();
+    final List<Path> 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;
   }
@@ -89,73 +97,34 @@ 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);
         }
       }
     }
     return new ArrayList<>(delete);
   }
 
-  private class DeletionStats {
-    int scheduled = 0;
-    int deleted = 0;
-    ConcurrentLinkedQueue<Path> skipped = new ConcurrentLinkedQueue<>();
+  private static class DeletionStats {
+    ConcurrentLinkedQueue<Path> scheduled = new ConcurrentLinkedQueue<>();
+    ConcurrentLinkedQueue<Path> deleted = new ConcurrentLinkedQueue<>();
     ConcurrentLinkedQueue<Path> error = new ConcurrentLinkedQueue<>();
   }
 
-  private DeletionStats deleteMatchingFilesInSubtrees(Iterable<? extends Path> paths, Predicate<? super Path> condition, boolean dryRun) {
-    final ConcurrentLinkedQueue<Path> delete = new ConcurrentLinkedQueue<>();
-    final DeletionStats stats = new DeletionStats();
-
-    for (Path path : paths) {
-      if (Files.isDirectory(path)) {
-        try {
-          Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
-            @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<Path> 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;
   }
+
 }

src/main/java/com/dmtavt/deltamass/logic/LogicInputFiles.java

@@ -259,6 +259,11 @@ private List<Path> inputFiles(List<Path> inputPaths, final Pattern regex, boolea
     return matched;
   }
 
+  private boolean isPepFileSupported(Path pepFilePath) {
+    IParserFactory<IPepidParser> parser = PepidParserRegistry.find(pepFilePath);
+    return parser != null;
+  }
+
   private List<Path> collectSupportedFiles(Iterable<? extends Path> paths, boolean recursive) {
     final ConcurrentLinkedQueue<Path> supported = new ConcurrentLinkedQueue<>();
 
@@ -280,8 +285,7 @@ public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) {
 
             @Override
             public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
-              IParserFactory<IPepidParser> 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);