Package qupath.ext.biop.cmd

Class VirtualEnvironmentRunner

java.lang.Object

qupath.ext.biop.cmd.VirtualEnvironmentRunner

public class VirtualEnvironmentRunner
extends Object

A wrapper to run python virtualenvs, that tries to figure out the commands to run based on the environment type

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	VirtualEnvironmentRunner.EnvType	This enum helps us figure out the type of virtualenv.

Constructor Summary

Constructors

Constructor	Description
VirtualEnvironmentRunner(String environmentNameOrPath, VirtualEnvironmentRunner.EnvType type, String name)
VirtualEnvironmentRunner(String environmentNameOrPath, VirtualEnvironmentRunner.EnvType type, String condaPath, String name)

Method Summary

Modifier and Type	Method	Description
void	closeWatchService()
List<String>	getChangedFiles()
Process	getProcess()
List<String>	getProcessLog()
void	runCommand(boolean waitUntilDone)	This builds, runs the command and outputs it to the logger as it is being run
void	setArguments(List<String> arguments)	This is the code you actually want to run after 'python'.
void	startWatchService(Path folderToListen)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

VirtualEnvironmentRunner

public VirtualEnvironmentRunner(String environmentNameOrPath,
 VirtualEnvironmentRunner.EnvType type,
 String name)

VirtualEnvironmentRunner

public VirtualEnvironmentRunner(String environmentNameOrPath,
 VirtualEnvironmentRunner.EnvType type,
 String condaPath,
 String name)

Method Details

setArguments

public void setArguments(List<String> arguments)

This is the code you actually want to run after 'python'. For example adding Arrays.asList("--version") should return the version of python that is being run.

Parameters:

arguments - any cellpose or omnipose command line argument

runCommand

public void runCommand(boolean waitUntilDone)
                throws IOException

This builds, runs the command and outputs it to the logger as it is being run

Parameters:

waitUntilDone - whether to wait for the process to end or not before exiting this method

Throws:

IOException - in case there is an issue with the process

getProcess

public Process getProcess()

getProcessLog

public List<String> getProcessLog()

startWatchService

public void startWatchService(Path folderToListen)
                       throws IOException

Throws:

IOException

getChangedFiles

public List<String> getChangedFiles()
                             throws InterruptedException

Throws:

InterruptedException

closeWatchService

public void closeWatchService()
                       throws IOException

Throws:

IOException