Added everything Andy asked for. Added version info in MsftbxInfo.java

MSFileToolbox/src/umich/ms/datatypes/lcmsrun/Hash.java

@@ -20,11 +20,11 @@
  * @author Dmitry Avtonomov
  */
 public class Hash {
-    public final String hash;
+    public final String value;
     public final TYPE type;
 
-    public Hash(String hash, TYPE type) {
-        this.hash = hash;
+    public Hash(String value, TYPE type) {
+        this.value = value;
         this.type = type;
     }
 

MSFileToolbox/src/umich/ms/datatypes/lcmsrun/LCMSRunInfo.java

@@ -171,12 +171,10 @@ public List<OriginalFile> getOriginalFiles() {
     public String toString() {
         return "LCMSRunInfo{" +
                 "instruments=" + instruments +
+                ", date=" + date +
                 ", defaultInstrumentID='" + defaultInstrumentID + '\'' +
                 ", isCentroided=" + isCentroided +
                 ", isDefaultExplicitlySet=" + isDefaultExplicitlySet +
-                ", date=" + date +
-                ", software=" + software +
-                ", originalFiles=" + originalFiles +
                 '}';
     }
 }

MSFileToolbox/src/umich/ms/fileio/filetypes/mzxml/MZXMLRunHeaderParser.java

@@ -1,33 +1,42 @@
-/* 
- * Copyright 2016 Dmitry Avtonomov.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+/* 
+ * Copyright 2016 Dmitry Avtonomov.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package umich.ms.fileio.filetypes.mzxml;
 
 import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.RandomAccessFile;
+import java.net.URI;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.List;
+
+import umich.ms.datatypes.lcmsrun.Hash;
 import umich.ms.datatypes.lcmsrun.LCMSRunInfo;
+import umich.ms.datatypes.lcmsrun.MsSoftware;
+import umich.ms.datatypes.lcmsrun.OriginalFile;
 import umich.ms.datatypes.scan.props.Instrument;
 import umich.ms.fileio.exceptions.RunHeaderBoundsNotFound;
 import umich.ms.fileio.exceptions.RunHeaderParsingException;
 import umich.ms.fileio.filetypes.mzxml.jaxb.MsRun;
 import umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType;
+import umich.ms.fileio.filetypes.mzxml.jaxb.Software;
 import umich.ms.fileio.filetypes.util.AbstractFile;
 import umich.ms.fileio.filetypes.xmlbased.OffsetLength;
 import umich.ms.logging.LogHelper;
@@ -64,6 +73,41 @@ public LCMSRunInfo parse() throws RunHeaderParsingException {
         MsRun parsedInfo = parseHeaderWithJAXB(MsRun.class, msRunLocation);
         LCMSRunInfo runInfo = new LCMSRunInfo();
 
+
+        // original files
+        List<MsRun.ParentFile> parentFiles = parsedInfo.getParentFile();
+        for (MsRun.ParentFile parentFile : parentFiles) {
+            String file = parentFile.getFileName();
+            file = file.replaceAll("\\\\", "/");
+            String location = "";
+            String fileName = file;
+            try {
+                Path path = Paths.get(file);
+                location = path.getParent().toString();
+                fileName = path.getFileName().toString();
+            } catch (InvalidPathException e) {
+                // could not parse path, try URI
+                try {
+                    URI uri = URI.create(file).normalize();
+                    String uriPath = uri.getPath();
+                    while (uriPath.startsWith("/")) uriPath = uriPath.substring(1);
+
+                    Path path = Paths.get(uriPath);
+                    location = path.getParent().toString();
+                    fileName = path.getFileName().toString();
+                } catch (IllegalArgumentException e2) {
+                    // URI also didn't work, forget it
+                }
+            }
+
+            Hash hash = null;
+            if (parentFile.getFileSha1() != null && !parentFile.getFileSha1().isEmpty()) {
+                hash = new Hash(parentFile.getFileSha1(), Hash.TYPE.SHA1);
+            }
+            runInfo.getOriginalFiles().add(new OriginalFile(location, fileName, hash));
+        }
+
+
         List<MsRun.MsInstrument> msInstruments = parsedInfo.getMsInstrument();
         if (msInstruments.size() > 0) {
             for (MsRun.MsInstrument i : msInstruments) {
@@ -113,7 +157,12 @@ public LCMSRunInfo parse() throws RunHeaderParsingException {
         for (MsRun.DataProcessing dataProcessing : dataProcessings) {
             if (dataProcessing.isCentroided() != null) {
                 runInfo.setCentroided(dataProcessing.isCentroided());
-                break;
+            }
+
+            Software software = dataProcessing.getSoftware();
+            if (software != null) {
+                MsSoftware msSoftware = new MsSoftware(software.getName(), software.getVersion());
+                runInfo.getSoftware().add(msSoftware);
             }
         }
 

MSFileToolbox/src/umich/ms/msfiletoolbox/MsftbxInfo.java

@@ -0,0 +1,24 @@
+/*
+ * Copyright (c) 2016 Dmitry Avtonomov
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package umich.ms.msfiletoolbox;
+
+/**
+ * @author Dmitry Avtonomov
+ */
+public class MsftbxInfo {
+    public static final String version = "1.1.0";
+}