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keep improving robustness in windows
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@carlosuc3m
carlosuc3m committed Mar 18, 2024
1 parent 66aa515 commit 6dd606a
Showing 1 changed file with 32 additions and 24 deletions.
56 changes: 32 additions & 24 deletions src/main/java/io/bioimage/modelrunner/apposed/appose/Mamba.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@

import org.apache.commons.compress.archivers.ArchiveException;

import com.sun.jna.Platform;

import io.bioimage.modelrunner.apposed.appose.CondaException.EnvironmentExistsException;
import io.bioimage.modelrunner.bioimageio.download.DownloadModel;
import io.bioimage.modelrunner.engine.installation.FileDownloader;
Expand Down Expand Up @@ -488,7 +490,7 @@ public void updateIn( final String envName, final String... args ) throws IOExce
{
checkMambaInstalled();
if (!installed) throw new MambaInstallException("Micromamba is not installed");
final List< String > cmd = new ArrayList<>( Arrays.asList( "update", "-p", checkExecutablePath(this.envsdir + File.separator + envName )) );
final List< String > cmd = new ArrayList<>( Arrays.asList( "update", "-p", this.envsdir + File.separator + envName ) );
cmd.addAll( Arrays.asList( args ) );
if (!cmd.contains("--yes") && !cmd.contains("-y")) cmd.add("--yes");
runMamba( cmd.stream().toArray( String[]::new ) );
Expand Down Expand Up @@ -545,7 +547,7 @@ public void createWithYaml( final String envName, final String envYaml, final bo
if ( !isForceCreation && getEnvironmentNames().contains( envName ) )
throw new EnvironmentExistsException();
runMamba("env", "create", "--prefix",
checkExecutablePath(envsdir + File.separator + envName), "-f", envYaml, "-y", "-vv" );
envsdir + File.separator + envName, "-f", envYaml, "-y", "-vv" );
}

/**
Expand Down Expand Up @@ -593,7 +595,7 @@ public void create( final String envName, final boolean isForceCreation ) throws
if (!installed) throw new MambaInstallException("Micromamba is not installed");
if ( !isForceCreation && getEnvironmentNames().contains( envName ) )
throw new EnvironmentExistsException();
runMamba( "create", "-y", "-p", checkExecutablePath(envsdir + File.separator + envName) );
runMamba( "create", "-y", "-p", envsdir + File.separator + envName );
}

/**
Expand Down Expand Up @@ -647,7 +649,7 @@ public void create( final String envName, final boolean isForceCreation, final S
if (!installed) throw new MambaInstallException("Micromamba is not installed");
if ( !isForceCreation && getEnvironmentNames().contains( envName ) )
throw new EnvironmentExistsException();
final List< String > cmd = new ArrayList<>( Arrays.asList( "create", "-p", checkExecutablePath(envsdir + File.separator + envName) ) );
final List< String > cmd = new ArrayList<>( Arrays.asList( "create", "-p", envsdir + File.separator + envName ) );
cmd.addAll( Arrays.asList( args ) );
if (!cmd.contains("--yes") && !cmd.contains("-y")) cmd.add("--yes");
runMamba( cmd.stream().toArray( String[]::new ) );
Expand Down Expand Up @@ -821,7 +823,7 @@ public void installIn( final String envName, List<String> channels, List<String>
checkMambaInstalled();
if (!installed) throw new MambaInstallException("Micromamba is not installed");
Objects.requireNonNull(envName, "The name of the environment of interest needs to be provided.");
final List< String > cmd = new ArrayList<>( Arrays.asList( "install", "-y", "-p", checkExecutablePath(this.envsdir + File.separator + envName )) );
final List< String > cmd = new ArrayList<>( Arrays.asList( "install", "-y", "-p", this.envsdir + File.separator + envName ) );
if (channels == null) channels = new ArrayList<String>();
for (String chan : channels) { cmd.add("-c"); cmd.add(chan);}
if (packages == null) packages = new ArrayList<String>();
Expand Down Expand Up @@ -850,7 +852,7 @@ public void installIn( final String envName, final String... args ) throws IOExc
{
checkMambaInstalled();
if (!installed) throw new MambaInstallException("Micromamba is not installed");
final List< String > cmd = new ArrayList<>( Arrays.asList( "install", "-p", checkExecutablePath(this.envsdir + File.separator + envName )) );
final List< String > cmd = new ArrayList<>( Arrays.asList( "install", "-p", this.envsdir + File.separator + envName ) );
cmd.addAll( Arrays.asList( args ) );
if (!cmd.contains("--yes") && !cmd.contains("-y")) cmd.add("--yes");
runMamba( cmd.stream().toArray( String[]::new ) );
Expand Down Expand Up @@ -960,9 +962,9 @@ public void runPythonIn( final String envName, final String... args ) throws IOE
if ( envName.equals( DEFAULT_ENVIRONMENT_NAME ) )
argsList.add( PYTHON_COMMAND );
else
argsList.add( checkExecutablePath(Paths.get( ENVS_NAME, envName, PYTHON_COMMAND ).toString()) );
argsList.add( coverArgWithDoubleQuotes(Paths.get( ENVS_NAME, envName, PYTHON_COMMAND ).toString()) );
argsList.addAll( Arrays.asList( args ).stream().map(aa -> {
if (aa.contains(" ") && PlatformDetection.isWindows()) return checkExecutablePath(aa);
if (aa.contains(" ") && PlatformDetection.isWindows()) return coverArgWithDoubleQuotes(aa);
else return aa;
}).collect(Collectors.toList()) );
boolean containsSpaces = argsList.stream().filter(aa -> aa.contains(" ")).collect(Collectors.toList()).size() > 0;
Expand Down Expand Up @@ -1009,8 +1011,11 @@ public static void runPythonIn( final File envFile, final String... args ) throw
+ "file does not exist: " + Paths.get( envFile.getAbsolutePath(), PYTHON_COMMAND ).toAbsolutePath());
final List< String > cmd = getBaseCommand();
List<String> argsList = new ArrayList<String>();
argsList.add( checkExecutablePath(Paths.get( envFile.getAbsolutePath(), PYTHON_COMMAND ).toAbsolutePath().toString()) );
argsList.addAll( Arrays.asList( args ) );
argsList.add( coverArgWithDoubleQuotes(Paths.get( envFile.getAbsolutePath(), PYTHON_COMMAND ).toAbsolutePath().toString()) );
argsList.addAll( Arrays.asList( args ).stream().map(aa -> {
if (Platform.isWindows() && aa.contains(" ")) return coverArgWithDoubleQuotes(aa);
else return aa;
}).collect(Collectors.toList()) );
boolean containsSpaces = argsList.stream().filter(aa -> aa.contains(" ")).collect(Collectors.toList()).size() > 0;

if (!containsSpaces || !PlatformDetection.isWindows()) cmd.addAll(argsList);
Expand Down Expand Up @@ -1049,9 +1054,9 @@ public String getVersion() throws IOException, InterruptedException, MambaInstal
{
final List< String > cmd = getBaseCommand();
if (mambaCommand.contains(" ") && PlatformDetection.isWindows())
cmd.add( surroundWithQuotes(Arrays.asList( checkExecutablePath(mambaCommand), "--version" )) );
cmd.add( surroundWithQuotes(Arrays.asList( coverArgWithDoubleQuotes(mambaCommand), "--version" )) );
else
cmd.addAll( Arrays.asList( checkExecutablePath(mambaCommand), "--version" ) );
cmd.addAll( Arrays.asList( coverArgWithDoubleQuotes(mambaCommand), "--version" ) );
final Process process = getBuilder( false ).command( cmd ).start();
if ( process.waitFor() != 0 )
throw new RuntimeException("Error getting Micromamba version");
Expand Down Expand Up @@ -1085,8 +1090,11 @@ public void runMamba(boolean isInheritIO, final String... args ) throws RuntimeE

final List< String > cmd = getBaseCommand();
List<String> argsList = new ArrayList<String>();
argsList.add( checkExecutablePath(mambaCommand) );
argsList.addAll( Arrays.asList( args ) );
argsList.add( coverArgWithDoubleQuotes(mambaCommand) );
argsList.addAll( Arrays.asList( args ).stream().map(aa -> {
if (aa.contains(" ") && PlatformDetection.isWindows()) return coverArgWithDoubleQuotes(aa);
else return aa;
}).collect(Collectors.toList()) );
boolean containsSpaces = argsList.stream().filter(aa -> aa.contains(" ")).collect(Collectors.toList()).size() > 0;

if (!containsSpaces || !PlatformDetection.isWindows()) cmd.addAll(argsList);
Expand Down Expand Up @@ -1588,22 +1596,22 @@ public boolean checkEnvFromYamlExists(String envYaml) throws MambaInstallExcepti
}

/**
* In Windows, if the path to the wanted executable contains spaces, it is surrounded by
* double quotes
* @param path
* path to the wanted executable
* @return a robust executable path
* In Windows, if a command prompt argument contains and space " " it needs to
* start and end with double quotes
* @param arg
* the cmd argument
* @return a robust argument
*/
private static String checkExecutablePath(String path) {
private static String coverArgWithDoubleQuotes(String arg) {
String[] specialChars = new String[] {" "};
for (String schar : specialChars) {
if (path.startsWith("\"") && path.endsWith("\""))
if (arg.startsWith("\"") && arg.endsWith("\""))
continue;
if (path.contains(schar) && PlatformDetection.isWindows()) {
return "\"" + path + "\"";
if (arg.contains(schar) && PlatformDetection.isWindows()) {
return "\"" + arg + "\"";
}
}
return path;
return arg;
}

/**
Expand Down

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