Vet paths in Windows registry before using them

chhh · chhh · commit 068c0820eed5 · 2018-11-16T11:04:22.000-08:00
Registry paths can contain illegal path characters, which caused
Paths.get() calls to throw, which in turn cancelled Python binary
search.
diff --git a/MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.form b/MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.form
@@ -510,7 +510,7 @@
                     <TitledBorder title="DB Slicing"/>
                   </Border>
                 </Property>
-                <Property name="toolTipText" type="java.lang.String" value="&lt;html&gt;Requires &lt;b&gt;Python 3&lt;/b&gt; with packages &lt;b&gt;Numpy, Pandas&lt;/b&gt;&#xa;Ways to get everything set up:&lt;br&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;Install Python 3 if you don&apos;t yet have it.&lt;/li&gt;&#xa;&lt;li&gt;Install required python modules using &lt;i&gt;pip&lt;/i&gt;, the python package manager, with commands:&lt;/li&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;pip install numpy&lt;/li&gt;&#xa;&lt;li&gt;pip install pandas&lt;/li&gt;&#xa;&lt;li&gt;pip install cython&lt;/li&gt;&#xa;&lt;li&gt;pip install msproteomicstools&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;/ul&gt;&#xa;"/>
+                <Property name="toolTipText" type="java.lang.String" value="&lt;html&gt;Requires &lt;b&gt;Python 3&lt;/b&gt; with packages &lt;b&gt;Numpy, Pandas&lt;/b&gt;&#xa;Ways to get everything set up:&lt;br&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;Install Python 3 if you don&apos;t yet have it.&lt;/li&gt;&#xa;&lt;li&gt;Install required python modules using &lt;i&gt;pip&lt;/i&gt;, the python package manager, with command:&lt;/li&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;pip install numpy pandas&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;/ul&gt;&#xa;"/>
               </Properties>
 
               <Layout>
@@ -571,7 +571,7 @@
                     <TitledBorder title="Spectral Lib generation"/>
                   </Border>
                 </Property>
-                <Property name="toolTipText" type="java.lang.String" value="&lt;html&gt;Requires &lt;b&gt;Python 3&lt;/b&gt; with packages &lt;b&gt;Cython, Msproteomicstools&lt;/b&gt;.&lt;br/&gt;&#xa;Ways to get everything set up:&lt;br&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;Install Python 3 if you don&apos;t yet have it.&lt;/li&gt;&#xa;&lt;li&gt;Install required python modules using &lt;i&gt;pip&lt;/i&gt;, the python package manager, with commands:&lt;/li&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;pip install numpy&lt;/li&gt;&#xa;&lt;li&gt;pip install pandas&lt;/li&gt;&#xa;&lt;li&gt;pip install cython&lt;/li&gt;&#xa;&lt;li&gt;pip install msproteomicstools&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;/ul&gt;&#xa;"/>
+                <Property name="toolTipText" type="java.lang.String" value="&lt;html&gt;Requires &lt;b&gt;Python 3&lt;/b&gt; with packages &lt;b&gt;Cython, Msproteomicstools&lt;/b&gt;.&lt;br/&gt;&#xa;Ways to get everything set up:&lt;br&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;Install Python 3 if you don&apos;t yet have it.&lt;/li&gt;&#xa;&lt;li&gt;Install required python modules using &lt;i&gt;pip&lt;/i&gt;, the python package manager, with commands:&lt;/li&gt;&#xa;&lt;ul&gt;&#xa;&lt;li&gt;pip install numpy pandas cython&lt;/li&gt;&#xa;&lt;li&gt;pip install msproteomicstools&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;/ul&gt;&#xa;"/>
               </Properties>
 
               <Layout>
diff --git a/MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.java b/MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.java
@@ -1069,7 +1069,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
     });
 
     jPanel2.setBorder(javax.swing.BorderFactory.createTitledBorder("DB Slicing"));
-    jPanel2.setToolTipText("<html>Requires <b>Python 3</b> with packages <b>Numpy, Pandas</b>\nWays to get everything set up:<br>\n<ul>\n<li>Install Python 3 if you don't yet have it.</li>\n<li>Install required python modules using <i>pip</i>, the python package manager, with commands:</li>\n<ul>\n<li>pip install numpy</li>\n<li>pip install pandas</li>\n<li>pip install cython</li>\n<li>pip install msproteomicstools</li>\n</ul>\n</ul>\n");
+    jPanel2.setToolTipText("<html>Requires <b>Python 3</b> with packages <b>Numpy, Pandas</b>\nWays to get everything set up:<br>\n<ul>\n<li>Install Python 3 if you don't yet have it.</li>\n<li>Install required python modules using <i>pip</i>, the python package manager, with command:</li>\n<ul>\n<li>pip install numpy pandas</li>\n</ul>\n</ul>\n");
 
     lblDbsliceInfo1.setText(DbSlice.DEFAULT_MESSAGE);
 
@@ -1105,7 +1105,7 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
     });
 
     jPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder("Spectral Lib generation"));
-    jPanel1.setToolTipText("<html>Requires <b>Python 3</b> with packages <b>Cython, Msproteomicstools</b>.<br/>\nWays to get everything set up:<br>\n<ul>\n<li>Install Python 3 if you don't yet have it.</li>\n<li>Install required python modules using <i>pip</i>, the python package manager, with commands:</li>\n<ul>\n<li>pip install numpy</li>\n<li>pip install pandas</li>\n<li>pip install cython</li>\n<li>pip install msproteomicstools</li>\n</ul>\n</ul>\n");
+    jPanel1.setToolTipText("<html>Requires <b>Python 3</b> with packages <b>Cython, Msproteomicstools</b>.<br/>\nWays to get everything set up:<br>\n<ul>\n<li>Install Python 3 if you don't yet have it.</li>\n<li>Install required python modules using <i>pip</i>, the python package manager, with commands:</li>\n<ul>\n<li>pip install numpy pandas cython</li>\n<li>pip install msproteomicstools</li>\n</ul>\n</ul>\n");
 
     lblSpeclibInfo1.setText(SpecLibGen.DEFAULT_MESSAGE);
 
diff --git a/MSFragger-GUI/src/umich/msfragger/util/PythonInfo.java b/MSFragger-GUI/src/umich/msfragger/util/PythonInfo.java
@@ -156,7 +156,20 @@ private String tryPythonCommandVersion(String cmd) throws Exception {
   public boolean setPythonCommand(String command) throws Exception {
       return trySetPythonCommand(command);
   }
-  
+
+  /**
+   * Checks that a registry location can be converted to {@link java.nio.file.Path}
+   * via {@link Paths#get(String, String...)} method.
+   */
+  private boolean vetRegistryLocation(String loc) {
+    try {
+      Paths.get(loc);
+    } catch (Exception ignored) {
+      return false;
+    }
+    return true;
+  }
+
   public void findPythonCommand() throws Exception {
     String[] commands = {"python", "python3"};
 
@@ -169,7 +182,10 @@ public void findPythonCommand() throws Exception {
       List<String> potentialLocs = new ArrayList<>();
       for (String root : roots) {
         for (String loc : locations) {
-          potentialLocs.addAll(RegQuery.query(root + loc));
+          List<String> query = RegQuery.query(root + loc);
+          potentialLocs.addAll(query.stream()
+              .filter(this::vetRegistryLocation)
+              .collect(Collectors.toList()));
         }
       }
 
@@ -178,11 +194,16 @@ public void findPythonCommand() throws Exception {
           .sorted(Comparator.reverseOrder())
           .collect(Collectors.toList());
       for (String possiblePython3InstallPath : possiblePython3InstallPaths) {
-        List<String> res = RegQuery.query(possiblePython3InstallPath + "\\InstallPath", "");
-        for (String r : res) {
-          for(String cmd : commands) {
+        final List<String> qureyInstallPath;
+        try {
+          qureyInstallPath = RegQuery.query(possiblePython3InstallPath + "\\InstallPath", "");
+        } catch (Exception ignored) {
+          continue;
+        }
+        for (String installPath : qureyInstallPath) {
+          for (String cmd : commands) {
             try {
-              final String rVal = RegQuery.getTokenValue(RegQuery.TOKEN_REGSZ, r);
+              final String rVal = RegQuery.getTokenValue(RegQuery.TOKEN_REGSZ, installPath);
               final String pythonBinPath = Paths.get(rVal, cmd).toString();
               if (trySetPythonCommand(pythonBinPath))
                 return;
