Merge pull request #761 from robinschmid/tomasmaster_gnps_new_fbmn_site

[GNPS] New FBMN submission URL and GNPS GC-MS workflow in MZmine

src/main/java/net/sf/mzmine/main/MZmineModulesList.java

@@ -64,6 +64,7 @@
 import net.sf.mzmine.modules.peaklistmethods.io.adap.mspexport.AdapMspExportModule;
 import net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule;
 import net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.fbmn.GnpsFbmnExportAndSubmitModule;
+import net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.gc.GnpsGcExportAndSubmitModule;
 import net.sf.mzmine.modules.peaklistmethods.io.metaboanalystexport.MetaboAnalystExportModule;
 import net.sf.mzmine.modules.peaklistmethods.io.mztabexport.MzTabExportModule;
 import net.sf.mzmine.modules.peaklistmethods.io.mztabimport.MzTabImportModule;
@@ -108,6 +109,7 @@
 import net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule;
 import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule;
 import net.sf.mzmine.modules.tools.isotopepatternpreview.IsotopePatternPreviewModule;
+import net.sf.mzmine.modules.tools.kovats.KovatsIndexExtractionModule;
 import net.sf.mzmine.modules.tools.msmsspectramerge.MsMsSpectraMergeModule;
 import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule;
 import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeMassCalculatorModule;
@@ -197,7 +199,7 @@ public class MZmineModulesList {
       AdapMspExportModule.class, //
       AdapMgfExportModule.class, //
       GnpsFbmnExportAndSubmitModule.class, //
-      // Not finished: GnpsGcExportAndSubmitModule.class, //
+      GnpsGcExportAndSubmitModule.class, //
       SiriusExportModule.class, //
 
       // Gap filling
@@ -286,7 +288,7 @@ public class MZmineModulesList {
       MzRangeMassCalculatorModule.class, //
       MzRangeFormulaCalculatorModule.class, //
       IsotopePatternPreviewModule.class, //
-      // Not finished: KovatsIndexExtractionModule.class,
+      KovatsIndexExtractionModule.class, //
 
       // all other regular MZmineModule (not MZmineRunnableModule) NOT LISTED IN MENU
       SpectraIdentificationSpectralDatabaseModule.class, //

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/GNPSUtils.java

@@ -37,7 +37,6 @@
 import org.apache.http.util.EntityUtils;
 import org.json.JSONException;
 import org.json.JSONObject;
-import io.github.msdk.MSDKRuntimeException;
 import net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.fbmn.GnpsFbmnSubmitParameters;
 import net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.gc.GnpsGcSubmitParameters;
 import net.sf.mzmine.util.files.FileAndPathUtil;
@@ -53,9 +52,9 @@ public class GNPSUtils {
   private static final Logger LOG = Logger.getLogger(GNPSUtils.class.getName());
 
   public static final String FBMN_SUBMIT_SITE =
-      "http://dorresteinappshub.ucsd.edu:5050/uploadanalyzefeaturenetworking";
+      "https://gnps-quickstart.ucsd.edu/uploadanalyzefeaturenetworking";
   public static final String GC_SUBMIT_SITE =
-      "http://gnps-quickstart.ucsd.edu/uploadanalyzegcnetworking";
+      "https://gnps-quickstart.ucsd.edu/uploadanalyzegcnetworking";
 
   /**
    * Submit feature-based molecular networking (FBMN) job to GNPS
@@ -64,8 +63,7 @@ public class GNPSUtils {
    * @param param
    * @return
    */
-  public static String submitFbmnJob(File file, GnpsFbmnSubmitParameters param)
-      throws MSDKRuntimeException {
+  public static String submitFbmnJob(File file, GnpsFbmnSubmitParameters param) throws IOException {
     // optional
     boolean useMeta = param.getParameter(GnpsFbmnSubmitParameters.META_FILE).getValue();
     boolean openWebsite = param.getParameter(GnpsFbmnSubmitParameters.OPEN_WEBSITE).getValue();
@@ -103,68 +101,59 @@ public static String submitFbmnJob(File file, GnpsFbmnSubmitParameters param)
    */
   public static String submitFbmnJob(File mgf, File quan, File meta, File[] additionalEdges,
       String title, String email, String username, String password, String presets,
-      boolean openWebsite) throws MSDKRuntimeException {
-    try {
-      // NEEDED files
-      if (mgf.exists() && quan.exists() && !presets.isEmpty()) {
-        CloseableHttpClient httpclient = HttpClients.createDefault();
+      boolean openWebsite) throws IOException {
+    // NEEDED files
+    if (mgf.exists() && quan.exists() && !presets.isEmpty()) {
+      CloseableHttpClient httpclient = HttpClients.createDefault();
+      try {
+        MultipartEntity entity = new MultipartEntity();
+
+        // ######################################################
+        // NEEDED
+        // tool, presets, quant table, mgf
+        entity.addPart("featuretool", new StringBody("MZMINE2"));
+        entity.addPart("description", new StringBody(title == null ? "" : title));
+        entity.addPart("networkingpreset", new StringBody(presets));
+        entity.addPart("featurequantification", new FileBody(quan));
+        entity.addPart("featurems2", new FileBody(mgf));
+
+        // ######################################################
+        // OPTIONAL
+        // email, meta data, additional edges
+        entity.addPart("email", new StringBody(email));
+        entity.addPart("username", new StringBody(username));
+        entity.addPart("password", new StringBody(password));
+        if (meta != null && meta.exists())
+          entity.addPart("samplemetadata", new FileBody(meta));
+
+        // add additional edges
+        if (additionalEdges != null)
+          for (File edge : additionalEdges)
+            if (edge != null && edge.exists())
+              entity.addPart("additionalpairs", new FileBody(edge));
+
+        HttpPost httppost = new HttpPost(FBMN_SUBMIT_SITE);
+        httppost.setEntity(entity);
+
+        LOG.info("Submitting GNPS job " + httppost.getRequestLine());
+        CloseableHttpResponse response = httpclient.execute(httppost);
         try {
-          MultipartEntity entity = new MultipartEntity();
-
-          // ######################################################
-          // NEEDED
-          // tool, presets, quant table, mgf
-          entity.addPart("featuretool", new StringBody("MZMINE2"));
-          entity.addPart("description", new StringBody(title == null ? "" : title));
-          entity.addPart("networkingpreset", new StringBody(presets));
-          entity.addPart("featurequantification", new FileBody(quan));
-          entity.addPart("featurems2", new FileBody(mgf));
-
-          // ######################################################
-          // OPTIONAL
-          // email, meta data, additional edges
-          entity.addPart("email", new StringBody(email));
-          entity.addPart("username", new StringBody(username));
-          entity.addPart("password", new StringBody(password));
-          if (meta != null && meta.exists())
-            entity.addPart("samplemetadata", new FileBody(meta));
-
-          // add additional edges
-          if (additionalEdges != null)
-            for (File edge : additionalEdges)
-              if (edge != null && edge.exists())
-                entity.addPart("additionalpairs", new FileBody(edge));
-
-          // old address
-          // HttpPost httppost =
-          // new HttpPost("http://mingwangbeta.ucsd.edu:5050/uploadanalyzefeaturenetworking");
-          HttpPost httppost =
-              new HttpPost("http://dorresteinappshub.ucsd.edu:5050/uploadanalyzefeaturenetworking");
-          httppost.setEntity(entity);
-
-          LOG.info("Submitting GNPS job " + httppost.getRequestLine());
-          CloseableHttpResponse response = httpclient.execute(httppost);
-          try {
-            LOG.info("GNPS submit response status: " + response.getStatusLine());
-            HttpEntity resEntity = response.getEntity();
-            if (resEntity != null) {
-              LOG.info("GNPS submit response content length: " + resEntity.getContentLength());
-
-              // open job website
-              if (openWebsite)
-                openWebsite(resEntity);
-              EntityUtils.consume(resEntity);
-            }
-          } finally {
-            response.close();
+          LOG.info("GNPS submit response status: " + response.getStatusLine());
+          HttpEntity resEntity = response.getEntity();
+          if (resEntity != null) {
+            LOG.info("GNPS submit response content length: " + resEntity.getContentLength());
+
+            // open job website
+            if (openWebsite)
+              openWebsite(resEntity);
+            EntityUtils.consume(resEntity);
           }
         } finally {
-          httpclient.close();
+          response.close();
         }
+      } finally {
+        httpclient.close();
       }
-    } catch (IOException e) {
-      LOG.log(Level.SEVERE, "Error while submitting GNPS job", e);
-      throw new MSDKRuntimeException(e);
     }
     return "";
   }

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/fbmn/GnpsFbmnExportAndSubmitTask.java

@@ -170,7 +170,7 @@ private void submit(File fileName, GnpsFbmnSubmitParameters param) {
     try {
       String url = GNPSUtils.submitFbmnJob(fileName, param);
       if (url == null || url.isEmpty())
-        LOG.log(Level.WARNING, "GNPS submit failed (url empty)");
+        LOG.log(Level.WARNING, "GNPS submit failed (response url empty)");
     } catch (Exception e) {
       LOG.log(Level.WARNING, "GNPS submit failed", e);
     }

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/fbmn/help/help.html

@@ -1,12 +1,12 @@
 <html>
 <head>
-    <title>Export - GNPS Export/Submit</title>
+    <title>Export - Export/Submit to GNPS-FBMN</title>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
     <link rel="stylesheet" type="text/css" href="/net/sf/mzmine/desktop/impl/helpsystem/HelpStyles.css">
 </head>
 <body>
 
-<h1>GNPS Export/Submit</h1>
+<h1>Export/Submit to GNPS-FBMN</h1>
 
 <h2>Description</h2>
 <p>

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/gc/GnpsGcExportAndSubmitModule.java

@@ -42,18 +42,18 @@
 import net.sf.mzmine.util.ExitCode;
 
 /**
- * Exports all files needed for GNPS feature based molecular networking (quant table (csv export)),
- * MS2 mgf, additional edges (ion identity networks)
+ * Exports all files needed for GNPS GC-MS (quant table (csv export)), mgf (ADAP mgf export)
+ * 
  * 
  * @author Robin Schmid ([email protected])
  *
  */
 public class GnpsGcExportAndSubmitModule implements MZmineProcessingModule {
   private final Logger LOG = Logger.getLogger(getClass().getName());
 
-  private static final String MODULE_NAME = "Export/Submit to GNPS-GC-MS (with ADAP)";
+  private static final String MODULE_NAME = "Export to GNPS-GC-MS (with ADAP)";
   private static final String MODULE_DESCRIPTION =
-      "GNPS GC-EI-MS workflow. Export the mgf, quant table and Kovats reference file (optionally). Allows to directly submit to GNPS analysis.";
+      "GNPS GC-EI-MS workflow. Export the mgf, quant table and Kovats reference file (optionally).";
 
   @Override
   public String getDescription() {

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/gc/GnpsGcExportAndSubmitParameters.java

@@ -69,7 +69,8 @@ public class GnpsGcExportAndSubmitParameters extends SimpleParameterSet {
 
 
   public GnpsGcExportAndSubmitParameters() {
-    super(new Parameter[] {PEAK_LISTS, FILENAME, REPRESENTATIVE_MZ, PEAK_INTENSITY, SUBMIT,
+    super(new Parameter[] {PEAK_LISTS, FILENAME, REPRESENTATIVE_MZ, PEAK_INTENSITY,
+        // SUBMIT,
         OPEN_FOLDER});
   }
 

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/gc/GnpsGcExportAndSubmitTask.java

@@ -90,10 +90,11 @@ public class GnpsGcExportAndSubmitTask extends AbstractTask {
     this.peakMeasure =
         parameters.getParameter(GnpsGcExportAndSubmitParameters.PEAK_INTENSITY).getValue();
     openFolder = parameters.getParameter(GnpsGcExportAndSubmitParameters.OPEN_FOLDER).getValue();
-    submit = parameters.getParameter(GnpsGcExportAndSubmitParameters.SUBMIT).getValue();
     file = parameters.getParameter(GnpsGcExportAndSubmitParameters.FILENAME).getValue();
     file = FileAndPathUtil.eraseFormat(file);
     parameters.getParameter(GnpsGcExportAndSubmitParameters.FILENAME).setValue(file);
+    // submit = parameters.getParameter(GnpsGcExportAndSubmitParameters.SUBMIT).getValue();
+    submit = false;
   }
 
   @Override

src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/gc/help/help.html

@@ -0,0 +1,53 @@
+<html>
+<head>
+    <title>Export - Export GNPS GC-MS (with ADAP)</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <link rel="stylesheet" type="text/css" href="/net/sf/mzmine/desktop/impl/helpsystem/HelpStyles.css">
+</head>
+<body>
+
+<h1>Export to GNPS GC-MS (with ADAP)</h1>
+
+<h2>Description</h2>
+<p>
+    The GNPS GC-MS module exports all files needed for the <strong>GC-MS</strong> workflow on the <a href="http://gnps.ucsd.edu/">GNPS web-platform</a>. 
+    This includes the <strong>feature quantification table</strong> (CSV file) and the <strong>spectral summary</strong> (.MGF file) with representative clustered GC-EI-MS spectra for the row in an (aligned) feature list.
+</p>
+
+<h2>Instructions</h2>
+<p>
+    Run this method on any (aligned) feature List. One of the spectral deconvolution methods need to be run (refer to the ADAP manual).
+</p>
+
+
+<h2>Parameters</h2>
+<dl>
+    <dt>Filename</dt>
+    <dd>Base name for the output files</dd>
+
+    <dt>Representative m/z</dt>
+    <dd>The m/z value that is exported to the mgf and used in GNPS GC-MS (Options: As in feature table, highest m/z, heighest intensity)</dd>
+
+    <dt>Open folder</dt>
+    <dd>Opens the folder containing the output files</dd>
+</dl>
+
+<h2>Documentation</h2>
+<p>
+    Please refer to the following documentation for a detailed tutorial:
+    <ul>    
+        <li>If you use the <em>GNPS GC-MS</em> export please cite:
+            <ul>
+                <li>our upcoming paper on GC-MS within the GNPS environment: Aksenov et al.</li>
+                <li>the ADAP paper: Smirnov et al.: <a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00633">J. Proteome Res 2017, DOI: 10.1021/acs.jproteome.7b00633</a></li>
+                <li>the <a href="http://gnps.ucsd.edu/">GNPS</a> paper: Wang et al.: <a href="https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html">Nature Biotechnology 34.8 (2016): 828-837</a><a href="http://gnps.ucsd.edu/">.</a></li>
+                <li>and the MZmine paper: Pluskal et al.: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395">BMC Bioinformatics, 11, 395 (2010)</a></li>
+            </ul>
+        </li>
+        <li><a href="https://ccms-ucsd.github.io/GNPSDocumentation/gc-ms-library-molecular-network/">See the documentation</a> about GC-MS within GNPS or <a href="https://ccms-ucsd.github.io/GNPSDocumentation">GNPS</a> on how to perform molecular networking, MS/MS spectral library search, and benefit from other tools available in GNPS environment.</li>
+        <li>Or check out the <a href="https://www.youtube.com/playlist?list=PL4L2Xw5k8ITwb4TzDKTAQ1UzrkVoBYkng">youtube playlist</a> on GNPS GC-MS (and MZmine) related videos</li>
+    </ul>
+</p>
+
+</body>
+</html>

src/main/java/net/sf/mzmine/modules/tools/kovats/KovatsIndexExtractionDialog.java

@@ -73,7 +73,6 @@
 import net.sf.mzmine.datamodel.RawDataFile;
 import net.sf.mzmine.framework.listener.DelayedDocumentListener;
 import net.sf.mzmine.main.MZmineCore;
-import net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.view.ScanSelectPanel;
 import net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex;
 import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule;
 import net.sf.mzmine.modules.visualization.tic.TICPlot;
@@ -508,13 +507,16 @@ private String getCsvTable(TreeMap<KovatsIndex, Double> values) {
     StringBuilder s = new StringBuilder();
     String nl = "\n";
     // header for GNPS
-    s.append("Compound_Name,RT_Query" + nl);
+    // alkane name, num carbon(int), rt (seconds)
+    s.append("Compound_Name,Carbon_Number,RT" + nl);
     DecimalFormat f = new DecimalFormat("0.##");
 
     for (Entry<KovatsIndex, Double> e : values.entrySet()) {
-      s.append(e.getKey().getCombinedName());
+      s.append(e.getKey().getAlkaneName());
       s.append(",");
-      // expor tin seconds for GNPS GC
+      s.append(String.valueOf(e.getKey().getNumCarbon()));
+      s.append(",");
+      // export rt in seconds for GNPS GC
       s.append(f.format(e.getValue() * 60.0));
       s.append(nl);
     }
@@ -877,7 +879,7 @@ private void combineFiles() {
 
 
   private static Icon createIcon(String path) {
-    return new ImageIcon(new ImageIcon(ScanSelectPanel.class.getClassLoader().getResource(path))
-        .getImage().getScaledInstance(SIZE, SIZE, Image.SCALE_SMOOTH));
+    return new ImageIcon(
+        new ImageIcon(path).getImage().getScaledInstance(SIZE, SIZE, Image.SCALE_SMOOTH));
   }
 }