Quilt native Groovy #18
Comments
drernie
changed the title
drernie
changed the title
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Proposed Integration Plan End Result:
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Implementation Proposal
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Things you can steal from nf-quilt:
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Requires Download (via Makefile?) from https://github.com/nextflow-io/nf-amazon/releases |
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Almost: java.lang.NullPointerException: Cannot invoke "org.pf4j.Plugin.start()" because the return value of "org.pf4j.PluginWrapper.getPlugin()" is null |
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Different error if 'prod' versus 'dev'. Oddly: java.lang.IllegalStateException: Missing plugin 'nf-amazon' required to read file: s3://quilt-example/.quilt |
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Same problem as before: |
log.info("Start plugin '{}'", getPluginLabel(pluginDescriptor));
pluginWrapper.getPlugin().start();https://github.com/pf4j/pf4j/blob/master/pf4j/src/main/java/org/pf4j/PluginWrapper.java plugin = pluginFactory.create(this);
// Plugin create(PluginWrapper pluginWrapper); for (ClassLoadingStrategy.Source classLoadingSource : classLoadingStrategy.getSources()) {
Class<?> c = null;
try {
switch (classLoadingSource) {
case APPLICATION:
c = super.loadClass(className);
break;
case PLUGIN:
c = findClass(className);
break;
case DEPENDENCIES:
c = loadClassFromDependencies(className);
break;
}
} catch (ClassNotFoundException ignored) {}
if (c != null) {
log.trace("Found class '{}' in {} classpath", className, classLoadingSource);
return c;
} else {
log.trace("Couldn't find class '{}' in {} classpath", className, classLoadingSource);
}
}
throw new ClassNotFoundException(className);https://github.com/pf4j/pf4j/blob/master/pf4j/src/main/java/org/pf4j/ClassLoadingStrategy.java |
/**
* One instance of this class should be created by plugin manager for every available plug-in.
* By default, this class loader is a Parent Last ClassLoader - it loads the classes from the plugin's jars
* before delegating to the parent class loader.
* Use {@link #classLoadingStrategy} to change the loading strategy.
*
* @author Decebal Suiu
*/
public class PluginClassLoader extends URLClassLoader {
public PluginClassLoader(PluginManager pluginManager, PluginDescriptor pluginDescriptor, ClassLoader parent, ClassLoadingStrategy classLoadingStrategy) {
super(new URL[0], parent);
this.pluginManager = pluginManager;
this.pluginDescriptor = pluginDescriptor;
this.classLoadingStrategy = classLoadingStrategy;
}
import java.net.URLClassLoader public String loadPlugin(Path pluginPath) {
if ((pluginPath == null) || Files.notExists(pluginPath)) {
throw new IllegalArgumentException(String.format("Specified plugin %s does not exist!", pluginPath));
}
log.debug("Loading plugin from '{}'", pluginPath);
PluginWrapper pluginWrapper = loadPluginFromPath(pluginPath);
// try to resolve the loaded plugin together with other possible plugins that depend on this plugin
resolvePlugins();
return pluginWrapper.getDescriptor().getPluginId();
} |
case APPLICATION:
c = super.loadClass(className);
break;
case PLUGIN:
c = findClass(className);
break;
case DEPENDENCIES:
c = loadClassFromDependencies(className);
break; |
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Manually loading plugin finally failed on: class AmazonPlugin extends BasePlugin {
AmazonPlugin(PluginWrapper wrapper) {
super(wrapper)
}
@Override
void start() {
super.start()
FileHelper.getOrInstallProvider(S3FileSystemProvider)
}
}with: The simplest solution might be to just catch the error and re-implement FileHelper. |
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Hmm. Others seem to have had this issue:
But, their solution still seems to (obviously) require running nextflow. Hmm. |
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Completed via quiltcore-java. |
Call Quilt from Groovy: bypass quilt3 command-line tool
Right now the plugin uses the command-line tool from the quilt3 pip package, specifically the 'install' and 'push' actions.
This is both an added dependency, and a 'blunt instrument'. For example, the only way to get a list of all the files in a package is to first install the package then
lsthe install directory.Alternatives include:
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