#!/usr/bin/env groovy

/**
** 	This assumes that you have installed Groovy and 
** 	that you have the command groovy available in your path. 
** 	On Debian/Ubuntu systems, installing Groovy should be as easy as apt-get install groovy.
** 	You can download groovy from http://groovy.codehaus.org/
** 	The first run may be slow since it needs to download all of the dependencies.
**  Usage: $groovy cTAKES-without-resources.groovy [inputDir]
** 	or enable more verbose status $groovy -Dgroovy.grape.report.downloads=true cTAKES-without-resources.groovy [inputDir]
**/

// @GrabResolver from Richard Eckart de Castilho, needed while using OpenNLP pre-1.5.3 version.
// To fix issue with jwnl unresolved dependency
@GrabResolver(name='opennlp.sf.net', 
      root='http://opennlp.sourceforge.net/maven2')

// Tried getting core-res first in hopes it will get added to classpath and that can avoid:
//Caused by: java.io.FileNotFoundException: org\apache\ctakes\core\sentdetect\sd-med-model.zip (The system cannot find the path specified)
// but it didn't make a difference....
@Grapes([	  

 @Grab(group='org.scala-lang', module='scala-library', version='2.9.0'),
 @Grab(group='org.scala-tools.sbinary', module='sbinary_2.9.0', version='0.4.0'),
                        
			
// @Grab(group='org.apache.ctakes',
//      module='ctakes-core-res',
//            version='3.1.1'),
			
 @Grab(group='org.apache.ctakes',
      module='ctakes-clinical-pipeline',
            version='3.1.1'),
			
 //@Grab(group='net.sf.mastif', module='mastif-i2b2', version='1.4'),
 //@Grab(group='net.sf.mastif', module='mastif-zoner', version='1.4'),
 //@Grab(group='net.sf.carafe.jcarafe', module='jcarafe-ext_2.9.1', version='0.9.8.3.RC4'),
 //@Grab(group='net.sf.carafe.jcarafe', module='jcarafe-core_2.9.1', version='0.9.8.3.RC4'),
            
                                               			
								
// @Grab(group='org.apache.ctakes',
//      module='ctakes-dependency-parser-res',
//            version='3.1.1'),
			
			
 //<groupId>net.sourceforge.ctakesresources</groupId>
 //<artifactId>ctakes-resources-umls2011ab</artifactId>
 //<version>3.1.1</version>
 @Grab(group='net.sourceforge.ctakesresources',
      module='ctakes-resources-umls2011ab',
            version='3.1.1')
])

import java.io.File;
import org.apache.uima.jcas.JCas;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.cleartk.util.cr.FilesCollectionReader;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.AggregateBuilder;
import org.uimafit.pipeline.SimplePipeline;	
import org.uimafit.component.JCasAnnotator_ImplBase;
import org.uimafit.component.xwriter.XWriter;
import org.uimafit.factory.TypeSystemDescriptionFactory;
import org.uimafit.factory.TypePrioritiesFactory;
import static org.uimafit.util.JCasUtil.*;

import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.ae.SentenceDetector;
import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
import org.apache.ctakes.core.util.CtakesFileNamer;

String path = null;
File cwd = new File(".");
path = cwd.getCanonicalPath();
System.out.println(path);


//this.class.classLoader.rootLoader.addURL( new URL("file:///C:/lib/my.jar") )
String libLocation = "file:///" + path + "/lib/";
String modelName;
modelName = "med-facts-i2b2-1.2-SNAPSHOT.jar";
this.class.classLoader.rootLoader.addURL( new URL(libLocation + modelName) );
modelName = "med-facts-zoner-1.1.jar";
this.class.classLoader.rootLoader.addURL( new URL(libLocation + modelName) );
modelName = "jcarafe-ext_2.9.1-0.9.8.3.RC4.jar";
this.class.classLoader.rootLoader.addURL( new URL(libLocation + modelName) );
modelName = "jcarafe-core_2.9.1-0.9.8.3.RC4.jar";
this.class.classLoader.rootLoader.addURL( new URL(libLocation + modelName) );


if(args.length < 1) {
	System.out.println("Please specify input directory");
	System.exit(1);
}
		
//scala.ScalaObject o = new scala.ScalaObject();
//System.out.println("HERE! I was able to get an error about abstract interface 'scala.ScalaObject' so it is findable here");
		
System.out.println("Reading from directory: " + args[0]);

CollectionReader collectionReader = FilesCollectionReader.getCollectionReader(args[0]);

		//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
		// Start of section to be replaced/deleted once get resolving to models (jars and zips) to work properly from groovy//
		//Download Models
		//TODO: Separate downloads from URL here is a hack.  
		//Models should really be automatically downloaded from 
		//maven central as part of ctakes-*-res projects/artifacts via @grab.
		File downloadDir;
		String ctakesRepoUrl = "http://svn.apache.org/repos/asf/ctakes/trunk/";
		String modelUrl;
		String modelRelative;
		String modelRelativeName;
		
		downloadDir = new File("org/apache/ctakes/core/sentdetect");
		downloadDir.mkdirs();
		modelUrl = ctakesRepoUrl + "ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/sd-med-model.zip";
		downloadFile(modelUrl, "org/apache/ctakes/core/sentdetect/sd-med-model.zip");
		
		downloadDir = new File("org/apache/ctakes/constituency/parser/models");
		downloadDir.mkdirs();
		modelUrl = ctakesRepoUrl + "ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/models/sharpacq-3.1.bin"
		downloadFile(modelUrl, "org/apache/ctakes/constituency/parser/models/sharpacq-3.1.bin");
		
		downloadDir = new File("org/apache/ctakes/postagger/models/");
		downloadDir.mkdirs();
		modelUrl = ctakesRepoUrl + "ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/mayo-pos.zip";
		downloadFile(modelUrl, "org/apache/ctakes/postagger/models/mayo-pos.zip");
		
		modelRelative = "org/apache/ctakes/dependency/parser/models/pred/";
		modelName = "mayo-en-pred-1.3.0.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-dependency-parser-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/dependency/parser/models/role/";
		modelName = "mayo-en-role-1.3.0.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-dependency-parser-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/dependency/parser/models/srl/";
		modelName = "mayo-en-srl-1.3.0.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-dependency-parser-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/chunker/models/";
		modelName = "chunker-model.zip";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-chunker-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "i2b2.model";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "cue.model";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "scope.model";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "pos.model";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "featureFile11b";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "generic.txt";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "history.txt";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "polarity.txt";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "org/apache/ctakes/assertion/models/";
		modelName = "uncertainty.txt";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		
		// sharpPolarityFrags.txt
		// sharpUncertaintyFrags.txt
		
		modelRelative = "org/apache/ctakes/dictionary/lookup/";
		modelName = "LookupDesc_Db.xml";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-dictionary-lookup-res/src/main/resources/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);

		// get some jars that can't get using grapes/@grab
		modelRelative = "lib/";
		modelName = "jcarafe-core_2.9.1-0.9.8.3.RC4.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "lib/";
		modelName = "jcarafe-ext_2.9.1-0.9.8.3.RC4.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "lib/";
		modelName = "med-facts-zoner-1.1.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		modelRelative = "lib/";
		modelName = "med-facts-i2b2-1.2-SNAPSHOT.jar";
		modelRelativeName = modelRelative + modelName;
		modelUrl = ctakesRepoUrl + "ctakes-assertion/" + modelRelativeName;
		downloadDir = new File(modelRelative);
		downloadDir.mkdirs();
		downloadFile(modelUrl, modelRelativeName);
		
		// tried using net.sf.mastif grapes but dep errors....
		
		System.err.println("TODO YET - DEAL WITH GETTING rxnorm_index");
		System.err.println("TODO YET - DEAL WITH GETTING OrangeBook");
		
		File curDir = new File(".");
		String depDepDir = "org/apache/ctakes/dependency/parser/models/dependency";
		String depLemDir = "org/apache/ctakes/dependency/parser/models/lemmatizer";
		//File depParserDir = new File(curDir, "org/apache/ctakes/dependency/parser/models/dependency";)
		//File depParserLemDir = new File(curDir, "org/apache/ctakes/dependency/parser/models/lemmatizer";)
		
		String dictionaryJar = "dictionary-1.3.1.jar";
		String dictionaryJarWithRelPath = depLemDir + "/" + dictionaryJar;

		String mayoEnDepJar = "mayo-en-dep-1.3.0.jar";
		String mayoEnDepJarWithRelPath = depDepDir + "/" + mayoEnDepJar;
		
		File f1 = new File(depDepDir);
		File f2 = new File(depLemDir);
		String absPath;

		absPath = f1.getAbsolutePath();
		System.out.println("Creating dirs for " + absPath);
		f1.mkdirs();

		absPath = f2.getAbsolutePath();
		System.out.println("Creating dirs for " + absPath);
		f2.mkdirs();

		
		String modelsURL = "https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-dependency-parser-res/src/main/resources/org/apache/ctakes/dependency/parser/models/"
		String dictionaryJarURL = modelsURL + "lemmatizer/" + dictionaryJar;
		String mayoEnDepJarURL = modelsURL + "dependency/" + mayoEnDepJar;
		System.out.println("Downloading resources not available separately from maven central: " + dictionaryJar);
		downloadFile(dictionaryJarURL, dictionaryJarWithRelPath);
		downloadFile(mayoEnDepJarURL, mayoEnDepJarWithRelPath);
		//downloadFile("https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-dependency-parser-res/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/dictionary-1.3.1.jar", "dictionary-1.3.1.jar");
		
		//   End of section to be replaced/deleted once get resolving to models (jars and zips) to work properly from groovy//
		//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
		
		
		

		//Build the pipeline to run
		AggregateBuilder aggregateBuilder = new AggregateBuilder();
		
		AnalysisEngineDescription clinicalPipelineWithUmls = AnalysisEngineFactory.createAnalysisEngineDescription("desc/analysis_engine/AggregatePlaintextUMLSProcessor" // Note, do not include .xml in the name here
		);
		aggregateBuilder.add(clinicalPipelineWithUmls);

		
		//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
		//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
            //SentenceDetector.class,
            //SentenceDetector.SD_MODEL_FILE_PARAM,
            //"sd-med-model.zip"));
		//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class));			
		//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
			//ConstituencyParser.class,
			//ConstituencyParser.PARAM_MODELFILE,
            //"sharpacq-3.1.bin"));
		//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(Writer.class));
		TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription("org.apache.ctakes.typesystem.types.TypeSystem");
		AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
			  XWriter.class,
			  typeSystemDescription,
			  XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
			  "output-dir",
			  XWriter.PARAM_FILE_NAMER_CLASS_NAME,
			  CtakesFileNamer.class.getName()
			  );

		aggregateBuilder.add(xWriter);

		
		SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());

// Custom writer class used at the end of the pipeline to write results to screen
class Writer extends org.uimafit.component.JCasAnnotator_ImplBase {
  void process(JCas jcas) {
	System.out.println("Commented out most of process() for Writer");
  }
}

def downloadFile(String url, String filename) {
	System.out.println("Downloading: " + url);
	def file = new File(filename);
	String savingAs = file.getAbsolutePath();
	System.out.println("Saving as " + savingAs);
	if(file.exists()) {
	  System.out.println("File already exists:" + filename);
	  return;
	}
    def f = new FileOutputStream(file)
    def out = new BufferedOutputStream(f)
    out << new URL(url).openStream()
    out.close()
}