Support for importing pepXML files from PEAKS searches

ms2/src/org/labkey/ms2/MS2Run.java

@@ -24,19 +24,20 @@
 import org.labkey.api.protein.MassType;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.util.MemTracker;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ViewContext;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.Serializable;
-import java.util.ArrayList;
+import java.lang.reflect.InvocationTargetException;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 public abstract class MS2Run implements Serializable
 {
-    private static Logger _log = LogManager.getLogger(MS2Run.class);
+    private static final Logger _log = LogHelper.getLogger(MS2Run.class, "MS2 runs");
 
     protected final static String[] EMPTY_STRING_ARRAY = new String[0];
 
@@ -187,11 +188,11 @@ public static MS2Run getRunFromTypeString(String type, String version)
 
         try
         {
-            MS2Run run = runType.getRunClass().newInstance();
+            MS2Run run = runType.getRunClass().getDeclaredConstructor().newInstance();
             run.setType(runType.name());
             return run;
         }
-        catch (IllegalAccessException | InstantiationException e)
+        catch (IllegalAccessException | InstantiationException | NoSuchMethodException | InvocationTargetException e)
         {
             throw new RuntimeException(e);
         }
@@ -238,62 +239,6 @@ public int[] getFastaIds()
         return _fastaIds;
     }
 
-    // CONSIDER: extend Apache ListOrderedSet (ideally) or our ArrayListMap.
-    public static class ColumnNameList extends ArrayList<String>
-    {
-        public ColumnNameList(Collection<String> columnNames)
-        {
-            for (String s : columnNames)
-            {
-                add(s);
-            }
-        }
-
-        public ColumnNameList(String csvColumnNames)
-        {
-            super(20);
-
-            String[] arrayColumnNames = csvColumnNames.split(",");
-            for (String arrayColumnName : arrayColumnNames)
-                add(arrayColumnName.trim());
-        }
-
-        @Override
-        public boolean add(String o)
-        {
-            return super.add(o.toLowerCase());
-        }
-
-        public ColumnNameList()
-        {
-            super(20);
-        }
-
-        @Override
-        public boolean contains(Object elem)
-        {
-            if (elem instanceof String)
-            {
-                return super.contains(((String)elem).toLowerCase());
-            }
-            return super.contains(elem);
-        }
-
-        public String toCSVString()
-        {
-            StringBuffer sb = new StringBuffer();
-            for (Object o : this)
-            {
-                if (sb.length() > 0)
-                    sb.append(',');
-
-                sb.append(o);
-            }
-            return sb.toString();
-        }
-    }
-
-
     public int getRun()
     {
         return run;

ms2/src/org/labkey/ms2/MS2RunType.java

@@ -26,6 +26,7 @@
 import org.labkey.ms2.pipeline.comet.CometRun;
 import org.labkey.ms2.pipeline.comet.LegacyCometRun;
 import org.labkey.ms2.pipeline.mascot.MascotRun;
+import org.labkey.ms2.pipeline.peaks.PeaksRun;
 import org.labkey.ms2.pipeline.phenyx.PhenyxRun;
 import org.labkey.ms2.pipeline.sequest.SequestRun;
 import org.labkey.ms2.pipeline.tandem.XCometRun;
@@ -114,6 +115,8 @@ public boolean isPeptideTableHidden()
             return true;
         }
     },
+    PeaksDb(PeaksRun.class,
+            new ScoreInfo("-10lgP", "-10lgP")),
     Unknown(UnknownMS2Run.class)
     {
         @Override

ms2/src/org/labkey/ms2/PeptideImporter.java

@@ -26,7 +26,10 @@
 import org.labkey.api.protein.fasta.FastaDbLoader;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.NetworkDrive;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.ms2.pipeline.MS2PipelineManager;
 import org.labkey.ms2.reader.AbstractQuantAnalysisResult;
 import org.labkey.ms2.reader.MS2Loader;
 import org.labkey.ms2.reader.PeptideProphetHandler;
@@ -127,6 +130,42 @@ public void writeRunInfo(MS2Loader.PeptideFraction fraction, MS2Progress progres
             dbPaths.add(dbPath);
         }
 
+        // Handle PEAKS FASTA references
+        for (String dbName : fraction.getDatabaseParameterValues())
+        {
+            File database = null;
+
+            // First look in the FASTA directory, with and without a .fasta extension
+            File databaseRoot = MS2PipelineManager.getSequenceDatabaseRoot(_container, true);
+            if (NetworkDrive.exists(databaseRoot))
+            {
+                database = FileUtil.appendName(databaseRoot, dbName);
+                if (!NetworkDrive.exists(database))
+                {
+                    database = FileUtil.appendName(databaseRoot, dbName + ".fasta");
+                }
+            }
+
+            // Also try relative to the file being imported, with and without a .fasta extension
+            if (!NetworkDrive.exists(database))
+            {
+                database = FileUtil.appendName(new File(_path), dbName);
+            }
+            if (!NetworkDrive.exists(database))
+            {
+                database = FileUtil.appendName(new File(_path), dbName + ".fasta");
+            }
+
+            if (NetworkDrive.exists(database))
+            {
+                dbPaths.add(database.getAbsolutePath());
+            }
+            else
+            {
+                _log.warn("Could not find FASTA " + dbName);
+            }
+        }
+
         try
         {
             // Clear any stale values so we can re-insert
@@ -192,7 +231,7 @@ protected String getTableColumnNames()
         columnNames.append(", HitRank");
         columnNames.append(", Decoy");
 
-        return super.getTableColumnNames() + columnNames.toString();
+        return super.getTableColumnNames() + columnNames;
     }
 
 
@@ -299,7 +338,7 @@ public void write(MS2Loader.Peptide peptide, PeptideProphetSummary peptideProphe
         // If we have quantitation, use the statement that reselects the rowId; otherwise, use the simple insert statement
         PeptideProphetHandler.PeptideProphetResult pp = peptide.getPeptideProphetResult();
         boolean hasProphet = (_scoringAnalysis && pp != null && pp.isSummaryLoaded());
-        boolean hasQuant = (null != _quantSummaries && _quantSummaries.size() > 0);
+        boolean hasQuant = (null != _quantSummaries && !_quantSummaries.isEmpty());
 
         if (hasProphet || hasQuant)
         {

ms2/src/org/labkey/ms2/filterHeader.jsp

@@ -50,12 +50,12 @@
 <labkey:form method="post" action="<%=bean.applyViewURL%>">
     <table id="ms2RunViewConfig" class="lk-fields-table">
         <tr>
-            <td valign=bottom><%=bean.applyView%></td>
-            <td valign=bottom><%= button("Go").submit(true) %></td>
+            <td style="vertical-align: bottom"><%=bean.applyView%></td>
+            <td  style="vertical-align: bottom"><%= button("Go").submit(true) %></td>
             <td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
-            <td valign=bottom><% if (!user.isGuest()) { %>
+            <td  style="vertical-align: bottom"><% if (!user.isGuest()) { %>
                 <%= button("Save View").href(bean.saveViewURL) %><% } %></td>
-            <td valign=bottom><% if (!user.isGuest()) { %>
+            <td  style="vertical-align: bottom"><% if (!user.isGuest()) { %>
                 <%= button("Manage Views").href(bean.manageViewsURL) %><% } %></td>
         </tr>
     </table>

ms2/src/org/labkey/ms2/pipeline/peaks/PeaksRun.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright (c) 2008-2019 LabKey Corporation
+ *
+ * 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 org.labkey.ms2.pipeline.peaks;
+
+import org.labkey.ms2.MS2Run;
+import org.labkey.ms2.MS2RunType;
+
+/**
+ * Support for PEAKS data, exported as pepXML
+ */
+public class PeaksRun extends MS2Run
+{
+    @Override
+    public MS2RunType getRunType()
+    {
+        return MS2RunType.PeaksDb;
+    }
+
+    @Override
+    public String getParamsFileName()
+    {
+        return "peaks.xml";
+    }
+
+    @Override
+    public String getChargeFilterColumnName()
+    {
+        return "-10lgP";
+    }
+
+    @Override
+    public String getChargeFilterParamName()
+    {
+        return "-10lgP";
+    }
+
+    @Override
+    public String getDiscriminateExpressions()
+    {
+        return null;
+    }
+
+    @Override
+    public String[] getGZFileExtensions()
+    {
+        return new String[0];
+    }
+}