From d6d450a70804a0f9234f9613ca7039e08a3099ab Mon Sep 17 00:00:00 2001 From: Gianpaolo Coro Date: Fri, 17 Apr 2015 14:37:42 +0000 Subject: [PATCH] bug fixes on FAOMSY git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@114220 82a268e6-3cf1-43bd-a215-b396298e98cf --- .../executor/nodes/algorithms/FAOMSY.java | 43 ++++++++++++++----- .../executor/util/StorageUtils.java | 4 +- 2 files changed, 34 insertions(+), 13 deletions(-) diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java index 2c91d71..a3fc61d 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java +++ b/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java @@ -3,6 +3,7 @@ package org.gcube.dataanalysis.executor.nodes.algorithms; import java.io.File; import java.util.ArrayList; import java.util.HashMap; +import java.util.LinkedHashMap; import java.util.List; import java.util.UUID; @@ -39,14 +40,20 @@ public class FAOMSY extends ActorNode { @Override public String getDescription() { - return "An algorithm to estimate the Maximum Sustainable Yield from a catch statistic by FAO."; + return "An algorithm to be used by Fisheries managers for stock assessment. " + + "Estimates the Maximum Sustainable Yield (MSY) of a stock, based on a catch trend. " + + "The algorithm has been developed by the Resource Use and Conservation Division of the FAO Fisheries and Aquaculture Department (contact: Yimin Ye, yimin.ye@fao.org). " + + "It is applicable to a CSV file containing metadata and catch statistics for a set of marine species and produces MSY estimates for each species. " + + "The CSV must follow a FAO-defined format (e.g. http://goo.gl/g6YtVx). " + + "The output is made up of two (optional) files: one for sucessfully processed species and another one for species that could not be processed because data were not sufficient to estimate MSY."; } static String stocksFile = "StocksFile"; static String processOutput= "ProcessOutput"; static String nonProcessedOutput= "NonProcessedOutput"; static String scriptName = "CatchMSY_Dec2014.R"; - + String processedSpOutputFile=""; + String nonProcessedSpOutputFile=""; @Override public List getInputParameters() { @@ -57,20 +64,26 @@ public class FAOMSY extends ActorNode { @Override public StatisticalType getOutput() { - File outfile = new File(config.getPersistencePath(),config.getParam(processOutput)); - File outfile2 = new File(config.getPersistencePath(),config.getParam(nonProcessedOutput)); - PrimitiveTypesList list = new PrimitiveTypesList(File.class.getName(), PrimitiveTypes.FILE, "OutputFiles", "Textual output files - processed and non-processed species",false); + File outfile = new File(processedSpOutputFile); + File outfile2 = new File(nonProcessedSpOutputFile); + AnalysisLogger.getLogger().debug("FAOMSY Output 1: "+outfile.getAbsolutePath()+" : "+outfile.exists()); + AnalysisLogger.getLogger().debug("FAOMSY Output 2: "+outfile2.getAbsolutePath()+" : "+outfile2.exists()); + + LinkedHashMap outputmap = new LinkedHashMap(); + if (outfile.exists()){ - PrimitiveType o = new PrimitiveType(File.class.getName(), outfile, PrimitiveTypes.FILE, "ProcessedSpecies", "Output file"); - list.add(o); + PrimitiveType o = new PrimitiveType(File.class.getName(), outfile, PrimitiveTypes.FILE, "ProcessedSpecies", "Output file with processed species"); + outputmap.put("File containing Processed Species", o); } if (outfile2.exists()){ - PrimitiveType o2 = new PrimitiveType(File.class.getName(), outfile2, PrimitiveTypes.FILE, "NonProcessedSpecies", "Output file"); - list.add(o2); + PrimitiveType o2 = new PrimitiveType(File.class.getName(), outfile2, PrimitiveTypes.FILE, "NonProcessedSpecies", "Output file with non processed species"); + outputmap.put("File containing Non Processed Species", o2); } + PrimitiveType output = new PrimitiveType(HashMap.class.getName(), outputmap, PrimitiveTypes.MAP, "ResultsMap", "Results Map"); + AnalysisLogger.getLogger().debug("FAOMSY Output Managed"); - return list; + return output; } @Override @@ -152,7 +165,13 @@ public class FAOMSY extends ActorNode { config.setParam(processOutput, "FAOMSY_"+"output_"+uuid); config.setParam(nonProcessedOutput, "FAOMSY_nonprocessed_"+"output_"+uuid); File tempfile = new File(config.getPersistencePath(),"FAOMSY_input_"+(UUID.randomUUID()+".csv").replace("-", "")); - StorageUtils.downloadInputFile(config.getParam(stocksFile), tempfile.getAbsolutePath()); + try{ + if (config.getParam(stocksFile).toLowerCase().startsWith("https:")) + throw new Exception("Error in FAOMSY: https link not supported!"); + StorageUtils.downloadInputFile(config.getParam(stocksFile), tempfile.getAbsolutePath()); + }catch(Exception e){ + throw new Exception("Error in FAOMSY: error in accessing file (alert: https not supported)"); + } nstocks = StorageUtils.calcFileRows(tempfile, true); AnalysisLogger.getLogger().info("FAOMSY Found "+nstocks+" stocks!"); if (nstocks==0) @@ -212,6 +231,8 @@ public class FAOMSY extends ActorNode { try { String mainOutputfilename = config.getParam(processOutput); String optionalOutputfilename = config.getParam(nonProcessedOutput); + processedSpOutputFile = new File(config.getPersistencePath(),mainOutputfilename).getAbsolutePath(); + nonProcessedSpOutputFile = new File(config.getPersistencePath(),optionalOutputfilename).getAbsolutePath(); assembleFiles(mainOutputfilename); assembleFiles(optionalOutputfilename); AnalysisLogger.getLogger().debug("FAOMSY - Postprocess complete"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/StorageUtils.java b/src/main/java/org/gcube/dataanalysis/executor/util/StorageUtils.java index 6882260..e661d9b 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/util/StorageUtils.java +++ b/src/main/java/org/gcube/dataanalysis/executor/util/StorageUtils.java @@ -131,9 +131,9 @@ public class StorageUtils { try { int nfiles = filenames.size(); - BufferedWriter bw = new BufferedWriter(new FileWriter(outputfile)); + BufferedWriter bw = new BufferedWriter(new FileWriter(new File(localFolder,outputfile))); for (int i=0;i