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Vet paths in Windows registry before using them
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Registry paths can contain illegal path characters, which caused
Paths.get() calls to throw, which in turn cancelled Python binary
search.
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@chhh
chhh committed Nov 16, 2018
1 parent f8f17f2 commit 068c082
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Showing 3 changed files with 31 additions and 10 deletions.
4 changes: 2 additions & 2 deletions MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.form
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
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4 changes: 2 additions & 2 deletions MSFragger-GUI/src/umich/msfragger/gui/MsfraggerGuiFrame.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down Expand Up @@ -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);

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33 changes: 27 additions & 6 deletions MSFragger-GUI/src/umich/msfragger/util/PythonInfo.java
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Expand Up @@ -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"};

Expand All @@ -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()));
}
}

Expand All @@ -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;
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