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ecological-engine-smart-executor
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@122494 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2016-01-25 16:07:09 +00:00
parent 1f510c74a6
commit a3c03e56dd
1 changed files with 124 additions and 90 deletions
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66
src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java
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@ -16,7 +16,6 @@ import org.gcube.dataanalysis.ecoengine.utils.ZipTools;
import org.gcube.dataanalysis.executor.util.LocalRScriptsManager; import org.gcube.dataanalysis.executor.util.LocalRScriptsManager;
import org.gcube.dataanalysis.executor.util.StorageUtils; import org.gcube.dataanalysis.executor.util.StorageUtils;
public abstract class GenericRScript extends StandardLocalExternalAlgorithm { public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
// FIXED part // FIXED part
@ -31,6 +30,7 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
scriptmanager.stop(); scriptmanager.stop();
System.gc(); System.gc();
} }
@Override @Override
public void init() throws Exception { public void init() throws Exception {
AnalysisLogger.getLogger().debug("Initializing " + this.getClass().getCanonicalName()); AnalysisLogger.getLogger().debug("Initializing " + this.getClass().getCanonicalName());
@ -39,6 +39,7 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
@Override @Override
protected void process() throws Exception { protected void process() throws Exception {
boolean deletefiles = false; // for test only
// init status // init status
status = 0; status = 0;
// instantiate the R Script executor // instantiate the R Script executor
@ -57,7 +58,6 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
ZipTools.unZip(localPackage.getAbsolutePath(), folder.getAbsolutePath()); ZipTools.unZip(localPackage.getAbsolutePath(), folder.getAbsolutePath());
localPackage.delete(); localPackage.delete();
// File folder = new File("C:/Users/coro/Desktop/WorkFolder/Workspace/EcologicalEngineSmartExecutor/./cfg/rscr_7d329495-b048-4ce0-8bcc-bd74966db56d/"); // File folder = new File("C:/Users/coro/Desktop/WorkFolder/Workspace/EcologicalEngineSmartExecutor/./cfg/rscr_7d329495-b048-4ce0-8bcc-bd74966db56d/");
AnalysisLogger.getLogger().debug("Analysing inputs"); AnalysisLogger.getLogger().debug("Analysing inputs");
@ -68,7 +68,21 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
for (String input : inputvariables) { for (String input : inputvariables) {
String value = config.getParam(input); String value = config.getParam(input);
String defaultValue = inputs.get(i).getDefaultValue(); String defaultValue = inputs.get(i).getDefaultValue();
inputParameters.put(defaultValue, value); //inputParameters.put(defaultValue, value);
String punct = "[ \";]*";
String regexp = punct+input+punct+"(<-|=)"+punct+defaultValue+punct+".*";
boolean string = true;
try{
Double.parseDouble(value);
string = false;
}catch(Exception ee){
}
String line = input+"="+value;
if (string)
line = input+"=\""+value+"\"";
inputParameters.put(regexp, line);
i++; i++;
} }
AnalysisLogger.getLogger().debug("Inputs: " + inputParameters.toString()); AnalysisLogger.getLogger().debug("Inputs: " + inputParameters.toString());
@ -105,7 +119,8 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
status = 10; status = 10;
AnalysisLogger.getLogger().debug("Executing the script..."); AnalysisLogger.getLogger().debug("Executing the script...");
// execute the script in multi-user mode // execute the script in multi-user mode
scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null,inputParameters, scriptMustReturnAFile,uploadScriptOnTheInfrastructureWorkspace, true, scriptSubfolder);
scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null, inputParameters, scriptMustReturnAFile, uploadScriptOnTheInfrastructureWorkspace, deletefiles, scriptSubfolder);
AnalysisLogger.getLogger().debug("..execution finished!"); AnalysisLogger.getLogger().debug("..execution finished!");
// get the output: one file should have been produced for each output // get the output: one file should have been produced for each output
AnalysisLogger.getLogger().debug("Getting output"); AnalysisLogger.getLogger().debug("Getting output");
@ -114,17 +129,21 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
AnalysisLogger.getLogger().debug("Output " + output + " - loading respective file from " + outPath.getAbsolutePath()); AnalysisLogger.getLogger().debug("Output " + output + " - loading respective file from " + outPath.getAbsolutePath());
AnalysisLogger.getLogger().debug("File exists? " + outPath.exists()); AnalysisLogger.getLogger().debug("File exists? " + outPath.exists());
String fileContent = FileTools.loadString(outPath.getAbsolutePath(), "UTF-8"); String fileContent = FileTools.loadString(outPath.getAbsolutePath(), "UTF-8");
fileContent=analyseContent(fileContent); fileContent = analyseContent(fileContent, scriptSubfolder);
AnalysisLogger.getLogger().debug("Retrieved output content: " + output + ": " + fileContent); AnalysisLogger.getLogger().debug("Retrieved output content: " + output + ": " + fileContent);
outputValues.put(output, fileContent); outputValues.put(output, fileContent);
} }
// delete the script folder // delete the script folder
AnalysisLogger.getLogger().debug("Deleting sandbox folder");
try { try {
if (deletefiles) {
AnalysisLogger.getLogger().debug("Deleting sandbox folder");
FileUtils.cleanDirectory(folder); FileUtils.cleanDirectory(folder);
FileUtils.deleteDirectory(folder); FileUtils.deleteDirectory(folder);
AnalysisLogger.getLogger().debug("Folder " + folder.getAbsolutePath() + " deleted"); AnalysisLogger.getLogger().debug("Folder " + folder.getAbsolutePath() + " deleted");
}
} catch (Exception e) { } catch (Exception e) {
AnalysisLogger.getLogger().debug(e); AnalysisLogger.getLogger().debug(e);
AnalysisLogger.getLogger().debug("Could not delete sandbox folder " + folder.getAbsolutePath()); AnalysisLogger.getLogger().debug("Could not delete sandbox folder " + folder.getAbsolutePath());
@ -133,27 +152,43 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
status = 100; status = 100;
} }
protected String analyseContent(String filecontent) throws Exception{ protected String analyseContent(String filecontent, String scriptfolder) throws Exception {
String [] rows = filecontent.split("\n"); AnalysisLogger.getLogger().debug("Analysing file content");
String[] rows = filecontent.split(System.lineSeparator());
List<String> files = new ArrayList<String>(); List<String> files = new ArrayList<String>();
for (String row : rows) { for (String row : rows) {
if (row!=null) AnalysisLogger.getLogger().debug("Analysing -> " + row);
if (row != null) {
row = row.replace("\"", ""); row = row.replace("\"", "");
if ((new File(row)).exists()){ File rowFile = new File(row.trim());
String preparedFile = new File(config.getConfigPath(),new File(row).getName()).getAbsolutePath(); AnalysisLogger.getLogger().debug("Checking row file-> "+rowFile.getAbsolutePath());
AnalysisLogger.getLogger().debug("Copying "+row+" to "+preparedFile); if (!rowFile.exists()){
FileUtils.moveFileToDirectory(new File(row), new File(config.getConfigPath()), false); rowFile = new File(scriptfolder, row.trim());
AnalysisLogger.getLogger().debug("File does not exist - checking complete row file-> "+rowFile.getAbsolutePath());
}
if (rowFile.exists()) {
String preparedFile = new File(config.getConfigPath(), rowFile.getName()).getAbsolutePath();
AnalysisLogger.getLogger().debug("Copying " + rowFile.getAbsolutePath() + " to " + preparedFile);
FileUtils.moveFileToDirectory(rowFile, new File(config.getConfigPath()), false);
files.add(preparedFile); files.add(preparedFile);
break; break;
} }
else
AnalysisLogger.getLogger().debug("Checking row file does not exist - treating as a String");
}
} }
if (files.size()>0) if (files.size() > 0) {
AnalysisLogger.getLogger().debug("A File was recognized as output");
return files.get(0); return files.get(0);
else } else {
AnalysisLogger.getLogger().debug("A String was recognized as output");
return filecontent; return filecontent;
} }
}
// DYNAMIC part // DYNAMIC part
protected String mainScriptName = ""; protected String mainScriptName = "";
protected String packageURL = ""; protected String packageURL = "";
@ -162,7 +197,6 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
protected List<String> inputvariables = new ArrayList<String>(); protected List<String> inputvariables = new ArrayList<String>();
protected List<String> outputvariables = new ArrayList<String>(); protected List<String> outputvariables = new ArrayList<String>();
protected void initVariables() { protected void initVariables() {
} }