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:
parent
1f510c74a6
commit
a3c03e56dd
|
|
@ -16,154 +16,188 @@ import org.gcube.dataanalysis.ecoengine.utils.ZipTools;
|
|||
import org.gcube.dataanalysis.executor.util.LocalRScriptsManager;
|
||||
import org.gcube.dataanalysis.executor.util.StorageUtils;
|
||||
|
||||
|
||||
public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
|
||||
|
||||
//FIXED part
|
||||
protected HashMap<String,String> outputValues=new HashMap<String,String>();
|
||||
protected LinkedHashMap<String, StatisticalType> output = new LinkedHashMap<String, StatisticalType> ();
|
||||
// FIXED part
|
||||
protected HashMap<String, String> outputValues = new HashMap<String, String>();
|
||||
protected LinkedHashMap<String, StatisticalType> output = new LinkedHashMap<String, StatisticalType>();
|
||||
LocalRScriptsManager scriptmanager;
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
//in the case of forced shutdown, stop the R process
|
||||
if (scriptmanager!=null)
|
||||
// in the case of forced shutdown, stop the R process
|
||||
if (scriptmanager != null)
|
||||
scriptmanager.stop();
|
||||
System.gc();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Initializing "+this.getClass().getCanonicalName());
|
||||
AnalysisLogger.getLogger().debug("Initializing " + this.getClass().getCanonicalName());
|
||||
initVariables();
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
//init status
|
||||
boolean deletefiles = false; // for test only
|
||||
// init status
|
||||
status = 0;
|
||||
//instantiate the R Script executor
|
||||
// instantiate the R Script executor
|
||||
scriptmanager = new LocalRScriptsManager();
|
||||
//download and unzip the script in a controlled folder
|
||||
// download and unzip the script in a controlled folder
|
||||
AnalysisLogger.getLogger().debug("Starting script");
|
||||
|
||||
File localPackage = new File(config.getConfigPath(),"package"+UUID.randomUUID()+".zip");
|
||||
AnalysisLogger.getLogger().debug("Downloading package "+packageURL+"as: "+localPackage.getAbsolutePath());
|
||||
StorageUtils.downloadInputFile(packageURL, localPackage.getAbsolutePath(),true);
|
||||
File localPackage = new File(config.getConfigPath(), "package" + UUID.randomUUID() + ".zip");
|
||||
AnalysisLogger.getLogger().debug("Downloading package " + packageURL + "as: " + localPackage.getAbsolutePath());
|
||||
StorageUtils.downloadInputFile(packageURL, localPackage.getAbsolutePath(), true);
|
||||
AnalysisLogger.getLogger().debug("Generating sandbox folder");
|
||||
File folder = new File(config.getConfigPath(),"rscr_"+UUID.randomUUID());
|
||||
File folder = new File(config.getConfigPath(), "rscr_" + UUID.randomUUID());
|
||||
boolean mkdir = folder.mkdir();
|
||||
AnalysisLogger.getLogger().debug("Sandbox "+folder.getAbsolutePath()+" generated: "+mkdir);
|
||||
AnalysisLogger.getLogger().debug("Unzipping package into "+folder.getAbsolutePath());
|
||||
AnalysisLogger.getLogger().debug("Sandbox " + folder.getAbsolutePath() + " generated: " + mkdir);
|
||||
AnalysisLogger.getLogger().debug("Unzipping package into " + folder.getAbsolutePath());
|
||||
ZipTools.unZip(localPackage.getAbsolutePath(), folder.getAbsolutePath());
|
||||
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");
|
||||
//distinguish the environmental variables and the input variables
|
||||
HashMap<String,String> inputParameters = new LinkedHashMap<String, String>();
|
||||
int i=0;
|
||||
List<StatisticalType>inputs = getInputParameters();
|
||||
for (String input:inputvariables){
|
||||
// distinguish the environmental variables and the input variables
|
||||
HashMap<String, String> inputParameters = new LinkedHashMap<String, String>();
|
||||
int i = 0;
|
||||
List<StatisticalType> inputs = getInputParameters();
|
||||
for (String input : inputvariables) {
|
||||
String value = config.getParam(input);
|
||||
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++;
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Inputs: "+inputParameters.toString());
|
||||
AnalysisLogger.getLogger().debug("Inputs: " + inputParameters.toString());
|
||||
AnalysisLogger.getLogger().debug("Analysing environmental variables");
|
||||
HashMap<String,String> environmentalParameters = new LinkedHashMap<String, String>();
|
||||
for (String environment:environmentalvariables){
|
||||
HashMap<String, String> environmentalParameters = new LinkedHashMap<String, String>();
|
||||
for (String environment : environmentalvariables) {
|
||||
String value = config.getParam(environment);
|
||||
environmentalParameters.put(environment, value);
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Environmental: "+environmentalParameters.toString());
|
||||
AnalysisLogger.getLogger().debug("Environmental: " + environmentalParameters.toString());
|
||||
AnalysisLogger.getLogger().debug("Analysing output variables");
|
||||
HashMap<String,String> outputParameters = new LinkedHashMap<String, String>();
|
||||
for (String output:outputvariables){
|
||||
HashMap<String, String> outputParameters = new LinkedHashMap<String, String>();
|
||||
for (String output : outputvariables) {
|
||||
outputParameters.put(output, "");
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Output: "+outputParameters.toString());
|
||||
AnalysisLogger.getLogger().debug("Output: " + outputParameters.toString());
|
||||
|
||||
AnalysisLogger.getLogger().debug("Main script: "+mainScriptName);
|
||||
AnalysisLogger.getLogger().debug("Main script: " + mainScriptName);
|
||||
AnalysisLogger.getLogger().debug("Processing main script name");
|
||||
//build the script name
|
||||
// build the script name
|
||||
String scriptName = mainScriptName;
|
||||
String scriptSubfolder = "";
|
||||
int lioSlash = scriptName.lastIndexOf("/");
|
||||
if (lioSlash>-1){
|
||||
scriptSubfolder = scriptName.substring(0,lioSlash);
|
||||
scriptName = scriptName.substring(lioSlash+1);
|
||||
if (lioSlash > -1) {
|
||||
scriptSubfolder = scriptName.substring(0, lioSlash);
|
||||
scriptName = scriptName.substring(lioSlash + 1);
|
||||
}
|
||||
scriptSubfolder = new File (folder.getAbsoluteFile(),scriptSubfolder).getAbsolutePath();
|
||||
AnalysisLogger.getLogger().debug("Main script name: "+scriptName);
|
||||
AnalysisLogger.getLogger().debug("Main script folder: "+scriptSubfolder);
|
||||
scriptSubfolder = new File(folder.getAbsoluteFile(), scriptSubfolder).getAbsolutePath();
|
||||
AnalysisLogger.getLogger().debug("Main script name: " + scriptName);
|
||||
AnalysisLogger.getLogger().debug("Main script folder: " + scriptSubfolder);
|
||||
|
||||
boolean scriptMustReturnAFile = false;
|
||||
boolean uploadScriptOnTheInfrastructureWorkspace = false;
|
||||
status = 10;
|
||||
AnalysisLogger.getLogger().debug("Executing the script...");
|
||||
//execute the script in multi-user mode
|
||||
scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null,inputParameters, scriptMustReturnAFile,uploadScriptOnTheInfrastructureWorkspace, true, scriptSubfolder);
|
||||
// execute the script in multi-user mode
|
||||
|
||||
scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null, inputParameters, scriptMustReturnAFile, uploadScriptOnTheInfrastructureWorkspace, deletefiles, scriptSubfolder);
|
||||
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");
|
||||
for (String output:outputvariables){
|
||||
File outPath = new File(scriptSubfolder,output);
|
||||
AnalysisLogger.getLogger().debug("Output "+output +" - loading respective file from "+outPath.getAbsolutePath());
|
||||
AnalysisLogger.getLogger().debug("File exists? "+outPath.exists());
|
||||
for (String output : outputvariables) {
|
||||
File outPath = new File(scriptSubfolder, output);
|
||||
AnalysisLogger.getLogger().debug("Output " + output + " - loading respective file from " + outPath.getAbsolutePath());
|
||||
AnalysisLogger.getLogger().debug("File exists? " + outPath.exists());
|
||||
String fileContent = FileTools.loadString(outPath.getAbsolutePath(), "UTF-8");
|
||||
fileContent=analyseContent(fileContent);
|
||||
AnalysisLogger.getLogger().debug("Retrieved output content: "+output+": "+fileContent);
|
||||
fileContent = analyseContent(fileContent, scriptSubfolder);
|
||||
AnalysisLogger.getLogger().debug("Retrieved output content: " + output + ": " + fileContent);
|
||||
outputValues.put(output, fileContent);
|
||||
}
|
||||
|
||||
//delete the script folder
|
||||
// delete the script folder
|
||||
|
||||
try {
|
||||
if (deletefiles) {
|
||||
AnalysisLogger.getLogger().debug("Deleting sandbox folder");
|
||||
try{
|
||||
FileUtils.cleanDirectory(folder);
|
||||
FileUtils.deleteDirectory(folder);
|
||||
AnalysisLogger.getLogger().debug("Folder "+folder.getAbsolutePath()+ " deleted");
|
||||
}catch(Exception e){
|
||||
AnalysisLogger.getLogger().debug("Folder " + folder.getAbsolutePath() + " deleted");
|
||||
}
|
||||
|
||||
} catch (Exception 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());
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Computation finished.");
|
||||
status = 100;
|
||||
}
|
||||
|
||||
protected String analyseContent(String filecontent) throws Exception{
|
||||
String [] rows = filecontent.split("\n");
|
||||
protected String analyseContent(String filecontent, String scriptfolder) throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Analysing file content");
|
||||
String[] rows = filecontent.split(System.lineSeparator());
|
||||
List<String> files = new ArrayList<String>();
|
||||
for (String row:rows){
|
||||
if (row!=null)
|
||||
for (String row : rows) {
|
||||
AnalysisLogger.getLogger().debug("Analysing -> " + row);
|
||||
if (row != null) {
|
||||
row = row.replace("\"", "");
|
||||
if ((new File(row)).exists()){
|
||||
String preparedFile = new File(config.getConfigPath(),new File(row).getName()).getAbsolutePath();
|
||||
AnalysisLogger.getLogger().debug("Copying "+row+" to "+preparedFile);
|
||||
FileUtils.moveFileToDirectory(new File(row), new File(config.getConfigPath()), false);
|
||||
File rowFile = new File(row.trim());
|
||||
AnalysisLogger.getLogger().debug("Checking row file-> "+rowFile.getAbsolutePath());
|
||||
if (!rowFile.exists()){
|
||||
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);
|
||||
|
||||
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);
|
||||
else
|
||||
} else {
|
||||
AnalysisLogger.getLogger().debug("A String was recognized as output");
|
||||
return filecontent;
|
||||
}
|
||||
//DYNAMIC part
|
||||
protected String mainScriptName="";
|
||||
protected String packageURL="";
|
||||
}
|
||||
|
||||
// DYNAMIC part
|
||||
protected String mainScriptName = "";
|
||||
protected String packageURL = "";
|
||||
|
||||
protected List<String> environmentalvariables = new ArrayList<String>();
|
||||
protected List<String> inputvariables= new ArrayList<String>();
|
||||
protected List<String> outputvariables= new ArrayList<String>();
|
||||
protected List<String> inputvariables = new ArrayList<String>();
|
||||
protected List<String> outputvariables = new ArrayList<String>();
|
||||
|
||||
|
||||
protected void initVariables(){
|
||||
protected void initVariables() {
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue