Branching to have a new version depending on new SmartExecutor
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@112013 82a268e6-3cf1-43bd-a215-b396298e98cf
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/classes" path="src/main/java"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>
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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>EcologicalEngineExecutor</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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||||||
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<buildCommand>
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||||||
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<name>org.eclipse.m2e.core.maven2Builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.m2e.core.maven2Nature</nature>
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<nature>org.eclipse.jdt.core.javanature</nature>
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</natures>
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</projectDescription>
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#Fri Jun 22 18:05:41 CEST 2012
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eclipse.preferences.version=1
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encoding//src/main/java=UTF-8
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encoding/<project>=UTF-8
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#Fri Jun 22 18:05:41 CEST 2012
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eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
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org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
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org.eclipse.jdt.core.compiler.compliance=1.6
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org.eclipse.jdt.core.compiler.debug.lineNumber=generate
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org.eclipse.jdt.core.compiler.debug.localVariable=generate
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org.eclipse.jdt.core.compiler.debug.sourceFile=generate
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org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
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org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.source=1.6
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#Fri Jun 22 17:51:31 CEST 2012
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activeProfiles=
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eclipse.preferences.version=1
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resolveWorkspaceProjects=true
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version=1
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<?xml version='1.0' encoding='UTF-8'?>
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<hibernate-configuration>
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<session-factory>
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<property name="connection.driver_class">org.postgresql.Driver</property>
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<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
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<property name="connection.url">jdbc:postgresql://localhost/testdb</property>
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<property name="connection.username">gcube</property>
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||||||
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<property name="connection.password">d4science2</property>
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||||||
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<property name="dialect">org.hibernate.dialect.PostgreSQLDialect</property>
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||||||
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<property name="transaction.factory_class">org.hibernate.transaction.JDBCTransactionFactory</property>
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||||||
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<property name="c3p0.timeout">0</property>
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||||||
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<property name="c3p0.max_size">1</property>
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||||||
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<property name="c3p0.max_statements">0</property>
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||||||
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<property name="c3p0.min_size">1</property>
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||||||
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<property name="current_session_context_class">thread</property>
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</session-factory>
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</hibernate-configuration>
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#!/bin/sh
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# AQUAMAPS_SUITABLE
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cd $1
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java -Xmx1024M -classpath ./:./aquamapsnode.jar:./c3p0-0.9.1.2.jar:./commons-collections-3.1.jar:./dom4j-1.6.1.jar:./ecologicalDataMining.jar:./hibernate3.jar:./jaxen-1.1.2.jar:./jta-1.1.jar:./log4j-1.2.16.jar:./postgresql-8.4-702.jdbc4.jar:./slf4j-api-1.6.0.jar:./slf4j-log4j12-1.6.0.jar:./xpp3_min-1.1.4c.jar:./xstream-1.3.1.jar org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode $2 execution.output
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##--------------------------------------------------------
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## CMSY analysis with estimation of total biomass, including Bayesian Schaefer
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## written by Rainer Froese with support from Gianpaolo Coro in 2013-2014
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## This version adjusts biomass to average biomass over the year
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## It also contains the FutureCrash option to improve prediction of final biomass
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## Version 21 adds the purple point to indicate the 25th percentile of final biomass
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## Version 22 accepts that no biomass or CPUE area available
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##--------------------------------------------------------
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library(R2jags) # Interface with JAGS
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library(coda)
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||||||
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#-----------------------------------------
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# Some general settings
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#-----------------------------------------
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# set.seed(999) # use for comparing results between runs
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rm(list=ls(all=TRUE)) # clear previous variables etc
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options(digits=3) # displays all numbers with three significant digits as default
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graphics.off() # close graphics windows from previous sessions
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|
||||||
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#-----------------------------------------
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||||||
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# General settings for the analysis
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#-----------------------------------------
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||||||
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sigR <- 0.02 # overall process error; 0.05 works reasonable for simulations, 0.02 for real data; 0 if deterministic model
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n <- 10000 # initial number of r-k pairs
|
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batch.mode <- T # set to TRUE to suppress graphs
|
||||||
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write.output <- T # set to true if table of output is wanted
|
||||||
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FutureCrash <- "No"
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|
||||||
|
#-----------------------------------------
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||||||
|
# Start output to screen
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||||||
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#-----------------------------------------
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cat("-------------------------------------------\n")
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cat("Catch-MSY Analysis,", date(),"\n")
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cat("-------------------------------------------\n")
|
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|
||||||
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#------------------------------------------
|
||||||
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# Read data and assign to vectors
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||||||
|
#------------------------------------------
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||||||
|
# filename_1 <- "AllStocks_Catch4.csv"
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# filename_2 <- "AllStocks_ID4.csv"
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# filename_1 <- "SimCatch.csv"
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||||||
|
# filename_2 <- "SimSpec.csv"
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||||||
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# filename_2 <- "SimSpecWrongS.csv"
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# filename_2 <- "SimSpecWrongI.csv"
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||||||
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# filename_2 <- "SimSpecWrongF.csv"
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||||||
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# filename_2 <- "SimSpecWrongH.csv"
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||||||
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# filename_2 <- "SimSpecWrongL.csv"
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||||||
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# filename_1 <- "FishDataLim.csv"
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||||||
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# filename_2 <- "FishDataLimSpec.csv"
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filename_1 <- "WKLIFE4Stocks.csv"
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filename_2 <- "WKLIFE4ID.csv"
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|
||||||
|
outfile<-"outfile"
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outfile.txt <- "outputfile.txt"
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||||||
|
cdat <- read.csv(filename_1, header=T, dec=".", stringsAsFactors = FALSE)
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||||||
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cinfo <- read.csv(filename_2, header=T, dec=".", stringsAsFactors = FALSE)
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||||||
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cat("Files", filename_1, ",", filename_2, "read successfully","\n")
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||||||
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||||||
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# Stocks with total biomass data and catch data from StartYear to EndYear
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# stocks <- sort(as.character(cinfo$stock)) # All stocks
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stocks<-"HLH_M07"
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||||||
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# select one stock after the other
|
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for(stock in stocks) {
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# assign data from cinfo to vectors
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res <- as.character(cinfo$Resilience[cinfo$stock==stock])
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StartYear <- as.numeric(cinfo$StartYear[cinfo$stock==stock])
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||||||
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EndYear <- as.numeric(cinfo$EndYear[cinfo$stock==stock])
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r_low <- as.numeric(cinfo$r_low[cinfo$stock==stock])
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r_hi <- as.numeric(cinfo$r_hi[cinfo$stock==stock])
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||||||
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stb_low <- as.numeric(cinfo$stb_low[cinfo$stock==stock])
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stb_hi <- as.numeric(cinfo$stb_hi[cinfo$stock==stock])
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intyr <- as.numeric(cinfo$intyr[cinfo$stock==stock])
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intbio_low <- as.numeric(cinfo$intbio_low[cinfo$stock==stock])
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||||||
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intbio_hi <- as.numeric(cinfo$intbio_hi[cinfo$stock==stock])
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||||||
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endbio_low <- as.numeric(cinfo$endbio_low[cinfo$stock==stock])
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endbio_hi <- as.numeric(cinfo$endbio_hi[cinfo$stock==stock])
|
||||||
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Btype <- as.character(cinfo$Btype[cinfo$stock==stock])
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||||||
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FutureCrash <- as.character(cinfo$FutureCrash[cinfo$stock==stock])
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||||||
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comment <- as.character(cinfo$comment[cinfo$stock==stock])
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||||||
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||||||
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||||||
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# extract data on stock
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||||||
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yr <- as.numeric(cdat$yr[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])
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ct <- as.numeric(cdat$ct[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that catch is given in tonnes, transforms to '000 tonnes
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if(Btype=="observed" | Btype=="CPUE" | Btype=="simulated") {
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bt <- as.numeric(cdat$TB[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that biomass is in tonnes, transforms to '000 tonnes
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} else {bt <- NA}
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nyr <- length(yr) # number of years in the time series
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if(Btype!="observed") {bio <- bt}
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# change biomass to moving average as assumed by Schaefer (but not for simulations or CPUE)
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# for last year use reported bio
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if(Btype=="observed") {
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ma <- function(x){filter(x,rep(1/2,2),sides=2)}
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bio <- ma(bt)
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bio[length(bio)] <- bt[length(bt)] }
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# initialize vectors for viable r, k, bt
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rv.all <- vector()
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kv.all <- vector()
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btv.all <- matrix(data=vector(),ncol=nyr+1)
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#----------------------------------------------------
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# Determine initial ranges for parameters and biomass
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#----------------------------------------------------
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# initial range of r from input file
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if(is.na(r_low)==F & is.na(r_hi)==F) {
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start_r <- c(r_low,r_hi)
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} else {
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# initial range of r and CatchMult values based on resilience
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if(res == "High") {
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start_r <- c(0.6,1.5)} else if(res == "Medium") {
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start_r <- c(0.2,0.8)} else if(res == "Low") {
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start_r <- c(0.05,0.5)} else { # i.e. res== "Very low"
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start_r <- c(0.015,0.1)}
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}
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||||||
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# initial range of k values, assuming k will always be larger than max catch
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# and max catch will never be smaller than a quarter of MSY
|
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||||||
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start_k <- c(max(ct),16*max(ct)/start_r[1])
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||||||
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# initial biomass range from input file
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if(is.na(stb_low)==F & is.na(stb_hi)==F) {
|
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startbio <- c(stb_low,stb_hi)
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} else {
|
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# us low biomass at start as default
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||||||
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startbio <- c(0.1,0.5)
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||||||
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}
|
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|
||||||
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MinYear <- yr[which.min(ct)]
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MaxYear <- yr[which.max(ct)]
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||||||
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# use year and biomass range for intermediate biomass from input file
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||||||
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if(is.na(intbio_low)==F & is.na(intbio_hi)==F) {
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||||||
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intyr <- intyr
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||||||
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intbio <- c(intbio_low,intbio_hi)
|
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# else if year of minimum catch is at least 3 years away from StartYear and EndYear of series, use min catch
|
||||||
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} else if((MinYear - StartYear) > 3 & (EndYear - MinYear) > 3 ) {
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||||||
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# assume that biomass range in year before minimum catch was 0.01 - 0.4
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intyr <- MinYear-1
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intbio <- c(0.01,0.4)
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||||||
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# else if year of max catch is at least 3 years away from StartYear and EndYear of series, use max catch
|
||||||
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} else if((MaxYear - StartYear) > 3 & (EndYear - MaxYear) > 3 ) {
|
||||||
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# assume that biomass range in year before maximum catch was 0.3 - 0.9
|
||||||
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intyr <- MaxYear-1
|
||||||
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intbio <- c(0.3,0.9)
|
||||||
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} else {
|
||||||
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# assume uninformative range 0-1 in mid-year
|
||||||
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intyr <- as.integer(mean(c(StartYear, EndYear)))
|
||||||
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intbio <- c(0,1) }
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||||||
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# end of intbio setting
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||||||
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|
||||||
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# final biomass range from input file
|
||||||
|
if(is.na(endbio_low)==F & is.na(endbio_hi)==F) {
|
||||||
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endbio <- c(endbio_low,endbio_hi)
|
||||||
|
} else {
|
||||||
|
# else use Catch/maxCatch to estimate final biomass
|
||||||
|
endbio <- if(ct[nyr]/max(ct) > 0.5) {c(0.4,0.8)} else {c(0.01,0.4)}
|
||||||
|
} # end of final biomass setting
|
||||||
|
|
||||||
|
|
||||||
|
#----------------------------------------------
|
||||||
|
# MC with Schaefer Function filtering
|
||||||
|
#----------------------------------------------
|
||||||
|
Schaefer <- function(ri, ki, startbio, intyr, intbio, endbio, sigR, pt) {
|
||||||
|
|
||||||
|
# if stock is not expected to crash within 3 years if last catch continues
|
||||||
|
if(FutureCrash == "No") {
|
||||||
|
yr.s <- c(yr,EndYear+1,EndYear+2,EndYear+3)
|
||||||
|
ct.s <- c(ct,ct[yr==EndYear],ct[yr==EndYear],ct[yr==EndYear])
|
||||||
|
nyr.s <- length(yr.s)
|
||||||
|
} else{
|
||||||
|
yr.s <- yr
|
||||||
|
ct.s <- ct
|
||||||
|
nyr.s <- nyr
|
||||||
|
}
|
||||||
|
|
||||||
|
# create vector for initial biomasses
|
||||||
|
startbt <-seq(from =startbio[1], to=startbio[2], by = (startbio[2]-startbio[1])/10)
|
||||||
|
# create vectors for viable r, k and bt
|
||||||
|
rv <- array(-1:-1,dim=c(length(ri)*length(startbt))) #initialize array with -1. The -1 remaining after the process will be removed
|
||||||
|
kv <- array(-1:-1,dim=c(length(ri)*length(startbt)))
|
||||||
|
btv <- matrix(data=NA, nrow = (length(ri)*length(startbt)), ncol = nyr+1)
|
||||||
|
intyr.i <- which(yr.s==intyr) # get index of intermediate year
|
||||||
|
|
||||||
|
#loop through r-k pairs
|
||||||
|
npoints = length(ri)
|
||||||
|
nstartb = length(startbt)
|
||||||
|
|
||||||
|
for(i in 1 : npoints) {
|
||||||
|
if (i%%1000==0)
|
||||||
|
cat(".")
|
||||||
|
|
||||||
|
# create empty vector for annual biomasses
|
||||||
|
bt <- vector()
|
||||||
|
|
||||||
|
# loop through range of relative start biomasses
|
||||||
|
for(j in startbt) {
|
||||||
|
# set initial biomass, including process error
|
||||||
|
bt[1]=j*ki[i]*exp(rnorm(1,0, sigR)) ## set biomass in first year
|
||||||
|
|
||||||
|
#loop through years in catch time series
|
||||||
|
for(t in 1:nyr.s) { # for all years in the time series
|
||||||
|
xt=rnorm(1,0, sigR) # set new random process error for every year
|
||||||
|
|
||||||
|
# calculate biomass as function of previous year's biomass plus surplus production minus catch
|
||||||
|
bt[t+1]=(bt[t]+ri[i]*bt[t]*(1-bt[t]/ki[i])-ct.s[t])*exp(xt)
|
||||||
|
|
||||||
|
# if biomass < 0.01 k or > 1.1 k, discard r-k pair
|
||||||
|
if(bt[t+1] < 0.01*ki[i] || bt[t+1] > 1.1*ki[i]) { break } # stop looping through years, go to next upper level
|
||||||
|
|
||||||
|
if ((t+1)==intyr.i && (bt[t+1]>(intbio[2]*ki[i]) || bt[t+1]<(intbio[1]*ki[i]))) { break } #intermediate year check
|
||||||
|
|
||||||
|
} # end of loop of years
|
||||||
|
|
||||||
|
# if last biomass falls without expected ranges goto next r-k pair
|
||||||
|
if(t < nyr.s || bt[yr.s==EndYear] > (endbio[2]*ki[i]) || bt[yr.s==EndYear] < (endbio[1]*ki[i])) {
|
||||||
|
next } else {
|
||||||
|
# store r, k, and bt, plot point, then go to next startbt
|
||||||
|
rv[((i-1)*nstartb)+j] <- ri[i]
|
||||||
|
kv[((i-1)*nstartb)+j] <- ki[i]
|
||||||
|
btv[((i-1)*nstartb)+j,] <- bt[1:(nyr+1)]/ki[i] #substitute a row into the matrix, exclude FutureCrash years
|
||||||
|
if(pt==T) {points(x=ri[i], y=ki[i], pch=".", cex=2, col="black")
|
||||||
|
next }
|
||||||
|
}
|
||||||
|
} # end of loop of initial biomasses
|
||||||
|
} # end of loop of r-k pairs
|
||||||
|
|
||||||
|
rv=rv[rv!=-1]
|
||||||
|
kv=kv[kv!=-1]
|
||||||
|
btv=na.omit(btv) #delete first line
|
||||||
|
|
||||||
|
cat("\n")
|
||||||
|
return(list(rv, kv,btv))
|
||||||
|
} # end of Schaefer function
|
||||||
|
|
||||||
|
#------------------------------------------------------------------
|
||||||
|
# Uniform sampling of the r-k space
|
||||||
|
#------------------------------------------------------------------
|
||||||
|
# get random set of r and k from log space distribution
|
||||||
|
ri1 = exp(runif(n, log(start_r[1]), log(start_r[2])))
|
||||||
|
ki1 = exp(runif(n, log(start_k[1]), log(start_k[2])))
|
||||||
|
|
||||||
|
#-----------------------------------------------------------------
|
||||||
|
# Plot data and progress
|
||||||
|
#-----------------------------------------------------------------
|
||||||
|
#windows(14,9)
|
||||||
|
par(mfcol=c(2,3))
|
||||||
|
# plot catch
|
||||||
|
plot(x=yr, y=ct, ylim=c(0,1.2*max(ct)), type ="l", bty="l", main=paste(stock,"catch"), xlab="Year",
|
||||||
|
ylab="Catch", lwd=2)
|
||||||
|
points(x=yr[which.max(ct)], y=max(ct), col="red", lwd=2)
|
||||||
|
points(x=yr[which.min(ct)], y=min(ct), col="red", lwd=2)
|
||||||
|
|
||||||
|
# plot r-k graph
|
||||||
|
plot(ri1, ki1, xlim = start_r, ylim = start_k, log="xy", xlab="r", ylab="k", main="Finding viable r-k", pch=".", cex=2, bty="l", col="lightgrey")
|
||||||
|
|
||||||
|
#1 - Call MC-Schaefer function to preliminary explore the space without prior information
|
||||||
|
cat(stock, ": First Monte Carlo filtering of r-k space with ",n," points\n")
|
||||||
|
MCA <- Schaefer(ri=ri1, ki=ki1, startbio=startbio, intyr=intyr, intbio=intbio, endbio=endbio, sigR=sigR, pt=T)
|
||||||
|
rv.all <- append(rv.all,MCA[[1]])
|
||||||
|
kv.all <- append(kv.all,MCA[[2]])
|
||||||
|
btv.all <- rbind(btv.all,MCA[[3]])
|
||||||
|
#take viable r and k values
|
||||||
|
nviablepoints = length(rv.all)
|
||||||
|
cat("* Found ",nviablepoints," viable points from ",n," samples\n");
|
||||||
|
|
||||||
|
|
||||||
|
#if few points were found then resample and shrink the k log space
|
||||||
|
if (nviablepoints<=1000){
|
||||||
|
log.start_k.new <- log(start_k)
|
||||||
|
max_attempts = 3
|
||||||
|
current_attempts = 1
|
||||||
|
while (nviablepoints<=1000 && current_attempts<=max_attempts){
|
||||||
|
if(nviablepoints > 0) {
|
||||||
|
log.start_k.new[1] <- mean(c(log.start_k.new[1], min(log(kv.all))))
|
||||||
|
log.start_k.new[2] <- mean(c(log.start_k.new[2], max(log(kv.all)))) }
|
||||||
|
n.new=n*current_attempts #add more points
|
||||||
|
ri1 = exp(runif(n.new, log(start_r[1]), log(start_r[2])))
|
||||||
|
ki1 = exp(runif(n.new, log.start_k.new[1], log.start_k.new[2]))
|
||||||
|
cat("Shrinking k space: repeating Monte Carlo in the interval [",exp(log.start_k.new[1]),",",exp(log.start_k.new[2]),"]\n")
|
||||||
|
cat("Attempt ",current_attempts," of ",max_attempts," with ",n.new," points","\n")
|
||||||
|
MCA <- Schaefer(ri=ri1, ki=ki1, startbio=startbio, intyr=intyr, intbio=intbio, endbio=endbio, sigR=sigR, pt=T)
|
||||||
|
rv.all <- append(rv.all,MCA[[1]])
|
||||||
|
kv.all <- append(kv.all,MCA[[2]])
|
||||||
|
btv.all <- rbind(btv.all,MCA[[3]])
|
||||||
|
nviablepoints = length(rv.all) #recalculate viable points
|
||||||
|
cat("* Found altogether",nviablepoints," viable points \n");
|
||||||
|
current_attempts=current_attempts+1 #increment the number of attempts
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# If tip of viable r-k pairs is 'thin', do extra sampling there
|
||||||
|
gm.rv = exp(mean(log(rv.all)))
|
||||||
|
if(length(rv.all[rv.all > 0.9*start_r[2]]) < 10) {
|
||||||
|
l.sample.r <- (gm.rv + max(rv.all))/2
|
||||||
|
cat("Final sampling in the tip area above r =",l.sample.r,"\n")
|
||||||
|
log.start_k.new <- c(log(0.8*min(kv.all)),log(max(kv.all[rv.all > l.sample.r])))
|
||||||
|
ri1 = exp(runif(50000, log(l.sample.r), log(start_r[2])))
|
||||||
|
ki1 = exp(runif(50000, log.start_k.new[1], log.start_k.new[2]))
|
||||||
|
MCA <- Schaefer(ri=ri1, ki=ki1, startbio=startbio, intyr=intyr, intbio=intbio, endbio=endbio, sigR=sigR, pt=T)
|
||||||
|
rv.all <- append(rv.all,MCA[[1]])
|
||||||
|
kv.all <- append(kv.all,MCA[[2]])
|
||||||
|
btv.all <- rbind(btv.all,MCA[[3]])
|
||||||
|
nviablepoints = length(rv.all) #recalculate viable points
|
||||||
|
cat("Found altogether", length(rv.all), "unique viable r-k pairs and biomass trajectories\n")
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
# ------------------------------------------------------------
|
||||||
|
# Bayesian analysis of catch & biomass with Schaefer model
|
||||||
|
# ------------------------------------------------------------
|
||||||
|
if(Btype == "observed" | Btype=="simulated") {
|
||||||
|
cat("Running Schaefer MCMC analysis....\n")
|
||||||
|
mcmc.burn <- as.integer(30000)
|
||||||
|
mcmc.chainLength <- as.integer(60000) # burn-in plus post-burn
|
||||||
|
mcmc.thin = 10 # to reduce autocorrelation
|
||||||
|
mcmc.chains = 3 # needs to be at least 2 for DIC
|
||||||
|
|
||||||
|
# Parameters to be returned by JAGS
|
||||||
|
jags.save.params=c('r','k','sigma.b', 'alpha', 'sigma.r') #
|
||||||
|
|
||||||
|
# JAGS model
|
||||||
|
Model = "model{
|
||||||
|
# to avoid crash due to 0 values
|
||||||
|
eps<-0.01
|
||||||
|
# set a quite narrow variation from the expected value
|
||||||
|
sigma.b <- 1/16
|
||||||
|
tau.b <- pow(sigma.b,-2)
|
||||||
|
|
||||||
|
Bm[1] <- log(alpha*k)
|
||||||
|
bio[1] ~ dlnorm(Bm[1],tau.b)
|
||||||
|
|
||||||
|
|
||||||
|
for (t in 2:nyr){
|
||||||
|
bio[t] ~ dlnorm(Bm[t],tau.b)
|
||||||
|
Bm[t] <- log(max(bio[t-1] + r*bio[t-1]*(1 - (bio[t-1])/k) - ct[t-1], eps))
|
||||||
|
}
|
||||||
|
|
||||||
|
# priors
|
||||||
|
alpha ~ dunif(0.01,1) # needed for fit of first biomass
|
||||||
|
#inverse cubic root relationship between the range of viable r and the size of the search space
|
||||||
|
inverseRangeFactor <- 1/((start_r[2]-start_r[1])^1/3)
|
||||||
|
|
||||||
|
# give sigma some variability in the inverse relationship
|
||||||
|
sigma.r ~ dunif(0.001*inverseRangeFactor,0.02*inverseRangeFactor)
|
||||||
|
tau.r <- pow(sigma.r,-2)
|
||||||
|
rm <- log((start_r[1]+start_r[2])/2)
|
||||||
|
r ~ dlnorm(rm,tau.r)
|
||||||
|
|
||||||
|
# search in the k space from the center of the range. Allow high variability
|
||||||
|
km <- log((start_k[1]+start_k[2])/2)
|
||||||
|
tau.k <- pow(km,-2)
|
||||||
|
k ~ dlnorm(km,tau.k)
|
||||||
|
|
||||||
|
#end model
|
||||||
|
}"
|
||||||
|
|
||||||
|
# Write JAGS model to file
|
||||||
|
cat(Model, file="r2jags.bug")
|
||||||
|
|
||||||
|
### random seed
|
||||||
|
set.seed(runif(1,1,500)) # needed in JAGS
|
||||||
|
|
||||||
|
### run model
|
||||||
|
jags_outputs <- jags(data=c('ct','bio','nyr', 'start_r', 'start_k'),
|
||||||
|
working.directory=NULL, inits=NULL,
|
||||||
|
parameters.to.save= jags.save.params,
|
||||||
|
model.file="r2jags.bug", n.chains = mcmc.chains,
|
||||||
|
n.burnin = mcmc.burn, n.thin = mcmc.thin, n.iter = mcmc.chainLength,
|
||||||
|
refresh=mcmc.burn/20, )
|
||||||
|
|
||||||
|
# ------------------------------------------------------
|
||||||
|
# Results from JAGS Schaefer
|
||||||
|
# ------------------------------------------------------
|
||||||
|
r_out <- as.numeric(mcmc(jags_outputs$BUGSoutput$sims.list$r))
|
||||||
|
k_out <- as.numeric(mcmc(jags_outputs$BUGSoutput$sims.list$k))
|
||||||
|
## sigma_out <- as.numeric(mcmc(jags_outputs$BUGSoutput$sims.list$sigma.b))
|
||||||
|
alpha_out <- as.numeric(mcmc(jags_outputs$BUGSoutput$sims.list$alpha))
|
||||||
|
## sigma.r_out <- as.numeric(mcmc(jags_outputs$BUGSoutput$sims.list$sigma.r))
|
||||||
|
|
||||||
|
mean.log.r.jags <- mean(log(r_out))
|
||||||
|
SD.log.r.jags <- sd(log(r_out))
|
||||||
|
lcl.log.r.jags <- mean.log.r.jags-1.96*SD.log.r.jags
|
||||||
|
ucl.log.r.jags <- mean.log.r.jags+1.96*SD.log.r.jags
|
||||||
|
gm.r.jags <- exp(mean.log.r.jags)
|
||||||
|
lcl.r.jags <- exp(lcl.log.r.jags)
|
||||||
|
ucl.r.jags <- exp(ucl.log.r.jags)
|
||||||
|
mean.log.k.jags <- mean(log(k_out))
|
||||||
|
SD.log.k.jags <- sd(log(k_out))
|
||||||
|
lcl.log.k.jags <- mean.log.k.jags-1.96*SD.log.k.jags
|
||||||
|
ucl.log.k.jags <- mean.log.k.jags+1.96*SD.log.k.jags
|
||||||
|
gm.k.jags <- exp(mean.log.k.jags)
|
||||||
|
lcl.k.jags <- exp(lcl.log.k.jags)
|
||||||
|
ucl.k.jags <- exp(ucl.log.k.jags)
|
||||||
|
mean.log.MSY.jags<- mean(log(r_out)+log(k_out)-log(4))
|
||||||
|
SD.log.MSY.jags <- sd(log(r_out)+log(k_out)-log(4))
|
||||||
|
gm.MSY.jags <- exp(mean.log.MSY.jags)
|
||||||
|
lcl.MSY.jags <- exp(mean.log.MSY.jags-1.96*SD.log.MSY.jags)
|
||||||
|
ucl.MSY.jags <- exp(mean.log.MSY.jags+1.96*SD.log.MSY.jags)
|
||||||
|
|
||||||
|
} # end of MCMC Schaefer loop
|
||||||
|
|
||||||
|
#------------------------------------
|
||||||
|
# get results from CMSY
|
||||||
|
#------------------------------------
|
||||||
|
# get estimate of most probable r as median of mid log.r-classes above cut-off
|
||||||
|
# get remaining viable log.r and log.k
|
||||||
|
rem.log.r <- log(rv.all[rv.all > gm.rv])
|
||||||
|
rem.log.k <- log(kv.all[rv.all>gm.rv])
|
||||||
|
# get vectors with numbers of r and mid values in about 25 classes
|
||||||
|
hist.log.r <- hist(x=rem.log.r, breaks=25, plot=F)
|
||||||
|
log.r.counts <- hist.log.r$counts
|
||||||
|
log.r.mids <- hist.log.r$mids
|
||||||
|
# get most probable log.r as mean of mids with counts > 0
|
||||||
|
log.r.est <- median(log.r.mids[which(log.r.counts > 0)])
|
||||||
|
lcl.log.r <- as.numeric(quantile(x=log.r.mids[which(log.r.counts > 0)], 0.025))
|
||||||
|
ucl.log.r <- as.numeric(quantile(x=log.r.mids[which(log.r.counts > 0)], 0.975))
|
||||||
|
r.est <- exp(log.r.est)
|
||||||
|
lcl.r.est <- exp(lcl.log.r)
|
||||||
|
ucl.r.est <- exp(ucl.log.r)
|
||||||
|
|
||||||
|
# do linear regression of log k ~ log r with slope fixed to -1 (from Schaefer)
|
||||||
|
reg <- lm(rem.log.k ~ 1 + offset(-1*rem.log.r))
|
||||||
|
int.reg <- as.numeric(reg[1])
|
||||||
|
sd.reg <- sd(resid(reg))
|
||||||
|
se.reg <- summary(reg)$coefficients[2]
|
||||||
|
# get estimate of log(k) from y where x = log.r.est
|
||||||
|
log.k.est <- int.reg + (-1) * log.r.est
|
||||||
|
# get estimates of CL of log.k.est from y +/- SD where x = lcl.log r or ucl.log.r
|
||||||
|
lcl.log.k <- int.reg + (-1) * ucl.log.r - sd.reg
|
||||||
|
ucl.log.k <- int.reg + (-1) * lcl.log.r + sd.reg
|
||||||
|
k.est <- exp(log.k.est)
|
||||||
|
lcl.k.est <- exp(lcl.log.k)
|
||||||
|
ucl.k.est <- exp(ucl.log.k)
|
||||||
|
|
||||||
|
# get MSY from remaining log r-k pairs
|
||||||
|
log.MSY.est <- mean(rem.log.r + rem.log.k - log(4))
|
||||||
|
sd.log.MSY.est <- sd(rem.log.r + rem.log.k - log(4))
|
||||||
|
lcl.log.MSY.est <- log.MSY.est - 1.96*sd.log.MSY.est
|
||||||
|
ucl.log.MSY.est <- log.MSY.est + 1.96*sd.log.MSY.est
|
||||||
|
MSY.est <- exp(log.MSY.est)
|
||||||
|
lcl.MSY.est <- exp(lcl.log.MSY.est)
|
||||||
|
ucl.MSY.est <- exp(ucl.log.MSY.est)
|
||||||
|
|
||||||
|
# get predicted biomass vectors as median and quantiles of trajectories
|
||||||
|
median.btv <- apply(btv.all,2, median)
|
||||||
|
lastyr.bio <- median.btv[length(median.btv)-1]
|
||||||
|
nextyr.bio <- median.btv[length(median.btv)]
|
||||||
|
lcl.btv <- apply(btv.all,2, quantile, probs=0.025)
|
||||||
|
q.btv <- apply(btv.all,2, quantile, probs=0.25)
|
||||||
|
ucl.btv <- apply(btv.all,2, quantile, probs=0.975)
|
||||||
|
lcl.lastyr.bio <- lcl.btv[length(lcl.btv)-1]
|
||||||
|
ucl.lastyr.bio <- ucl.btv[length(lcl.btv)-1]
|
||||||
|
lcl.nextyr.bio <- lcl.btv[length(lcl.btv)]
|
||||||
|
ucl.nextyr.bio <- ucl.btv[length(lcl.btv)]
|
||||||
|
|
||||||
|
# -----------------------------------------
|
||||||
|
# Plot results
|
||||||
|
# -----------------------------------------
|
||||||
|
# Analysis of viable r-k pairs
|
||||||
|
plot(x=rv.all, y=kv.all, xlim=start_r,
|
||||||
|
ylim=c(0.9*min(kv.all, ifelse(Btype == "observed",k_out,NA), na.rm=T), 1.1*max(kv.all)),
|
||||||
|
pch=16, col="grey",log="xy", bty="l",
|
||||||
|
xlab="r", ylab="k", main="Analysis of viable r-k")
|
||||||
|
abline(v=gm.rv, lty="dashed")
|
||||||
|
|
||||||
|
# plot points and best estimate from full Schaefer analysis
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
# plot r-k pairs from MCMC
|
||||||
|
points(x=r_out, y=k_out, pch=16,cex=0.5)
|
||||||
|
# plot best r-k pair from MCMC
|
||||||
|
points(x=gm.r.jags, y=gm.k.jags, pch=19, col="green")
|
||||||
|
lines(x=c(lcl.r.jags, ucl.r.jags),y=c(gm.k.jags,gm.k.jags), col="green")
|
||||||
|
lines(x=c(gm.r.jags,gm.r.jags),y=c(lcl.k.jags, ucl.k.jags), col="green")
|
||||||
|
}
|
||||||
|
|
||||||
|
# if data are from simulation, plot true r and k
|
||||||
|
if(Btype=="simulated") {
|
||||||
|
l.stock <- nchar(stock) # get length of sim stock name
|
||||||
|
r.char <- substr(stock,l.stock-1,l.stock) # get last character of sim stock name
|
||||||
|
r.sim <- NA # initialize vector for r used in simulation
|
||||||
|
if(r.char=="_H") {r.sim=1; lcl.r.sim=0.8; ucl.r.sim=1.25} else
|
||||||
|
if(r.char=="_M") {r.sim=0.5;lcl.r.sim=0.4;ucl.r.sim=0.62} else
|
||||||
|
if(r.char=="_L") {r.sim=0.25;lcl.r.sim=0.2;ucl.r.sim=0.31} else {r.sim=0.05;lcl.r.sim=0.04;ucl.r.sim=0.062}
|
||||||
|
# plot true r-k point with error bars
|
||||||
|
points(x=r.sim, y=1000, pch=19, col="red")
|
||||||
|
# add +/- 20% error bars
|
||||||
|
lines(x=c(lcl.r.sim,ucl.r.sim), y=c(1000,1000), col="red")
|
||||||
|
lines(x=c(r.sim,r.sim), y=c(800,1250), col="red")
|
||||||
|
}
|
||||||
|
|
||||||
|
# plot blue dot for proposed r-k, with 95% CL lines
|
||||||
|
points(x=r.est, y=k.est, pch=19, col="blue")
|
||||||
|
lines(x=c(lcl.r.est, ucl.r.est),y=c(k.est,k.est), col="blue")
|
||||||
|
lines(x=c(r.est,r.est),y=c(lcl.k.est, ucl.k.est), col="blue")
|
||||||
|
|
||||||
|
# plot biomass graph
|
||||||
|
# determine k to use for red line in b/k plot
|
||||||
|
if(Btype=="simulated") {k2use <- 1000} else
|
||||||
|
if(Btype == "observed") {k2use <- gm.k.jags} else {k2use <- k.est}
|
||||||
|
# determine hight of y-axis in plot
|
||||||
|
max.y <- max(c(bio/k2use,ucl.btv,0.6,startbio[2], intbio[2],endbio[2]),na.rm=T)
|
||||||
|
|
||||||
|
plot(x=yr,y=median.btv[1:nyr], lwd=2, xlab="Year", ylab="Relative biomass b/k", type="l",
|
||||||
|
ylim=c(0,max.y), bty="l", main=paste("Pred. biomass vs ", Btype,sep=""))
|
||||||
|
lines(x=yr, y=lcl.btv[1:nyr],type="l")
|
||||||
|
lines(x=yr, y=ucl.btv[1:nyr],type="l")
|
||||||
|
points(x=EndYear,y=q.btv[yr==EndYear], col="purple", cex=1.5, lwd=2)
|
||||||
|
abline(h=0.5, lty="dashed")
|
||||||
|
abline(h=0.25, lty="dotted")
|
||||||
|
lines(x=c(yr[1],yr[1]), y=startbio, col="blue")
|
||||||
|
lines(x=c(intyr,intyr), y=intbio, col="blue")
|
||||||
|
lines(x=c(max(yr),max(yr)), y=endbio, col="blue")
|
||||||
|
|
||||||
|
# if observed biomass is available, plot red biomass line
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
lines(x=yr, y=bio/k2use,type="l", col="red", lwd=1)
|
||||||
|
}
|
||||||
|
|
||||||
|
# if CPUE data are available, scale to predicted biomass range, plot red biomass line
|
||||||
|
if(Btype == "CPUE") {
|
||||||
|
par(new=T) # prepares for new plot on top of previous
|
||||||
|
plot(x=yr, y=bio, type="l", col="red", lwd=1,
|
||||||
|
ann=F,axes=F,ylim=c(0,1.2*max(bio, na.rm=T))) # forces this plot on top of previous one
|
||||||
|
axis(4, col="red", col.axis="red")
|
||||||
|
}
|
||||||
|
|
||||||
|
# plot yield and biomass against equilibrium surplus parabola
|
||||||
|
max.y <-max(c(ct/MSY.est,ifelse(Btype=="observed"|Btype=="simulated",ct/gm.MSY.jags,NA),1.2),na.rm=T)
|
||||||
|
# plot parabola
|
||||||
|
x=seq(from=0,to=2,by=0.001)
|
||||||
|
y=4*x-(2*x)^2
|
||||||
|
plot(x=x, y=y, xlim=c(0,1), ylim=c(0,max.y), type="l", bty="l",xlab="Relative biomass b/k",
|
||||||
|
ylab="Catch / MSY", main="Equilibrium curve")
|
||||||
|
# plot catch against CMSY biomass estimates
|
||||||
|
points(x=median.btv[1:nyr], y=ct/MSY.est, pch=16, col="grey")
|
||||||
|
points(x=q.btv[yr==EndYear],y=ct[yr==EndYear]/MSY.est, col="purple", cex=1.5, lwd=2)
|
||||||
|
# plot catch against observed biomass or CPUE
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
points(x=bio/k2use, y=ct/gm.MSY.jags, pch=16, cex=0.5)
|
||||||
|
}
|
||||||
|
|
||||||
|
# plot exploitation rate u against u.msy
|
||||||
|
# get u derived from predicted CMSY biomass
|
||||||
|
u.CMSY <- ct/(median.btv[1:nyr]*k.est)
|
||||||
|
u.msy.CMSY <- 1-exp(-r.est/2) # # Fmsy from CMSY expressed as exploitation rate
|
||||||
|
# get u from observed or simulated biomass
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
u.bio <- ct/bio
|
||||||
|
u.msy.bio <- 1-exp(-gm.r.jags/2)
|
||||||
|
}
|
||||||
|
# get u from CPUE
|
||||||
|
if(Btype == "CPUE") {
|
||||||
|
q=max(median.btv[1:nyr][is.na(bio)==F],na.rm=T)*k.est/max(bio,na.rm=T)
|
||||||
|
u.CPUE <- ct/(q*bio)
|
||||||
|
}
|
||||||
|
|
||||||
|
# determine upper bound of Y-axis
|
||||||
|
max.y <- max(c(1.5, 1.2*u.CMSY/u.msy.CMSY,ct[yr==EndYear]/(q.btv[yr==EndYear]*k.est)/u.msy.CMSY,
|
||||||
|
ifelse(Btype=="observed"|Btype=="simulated",max(u.bio[is.na(u.bio)==F]/u.msy.bio),0),
|
||||||
|
na.rm=T))
|
||||||
|
# plot u from CMSY
|
||||||
|
plot(x=yr,y=u.CMSY/u.msy.CMSY, type="l", bty="l", ylim=c(0,max.y), xlab="Year",
|
||||||
|
ylab="u / u_msy", main="Exploitation rate")
|
||||||
|
abline(h=1, lty="dashed")
|
||||||
|
points(x=EndYear,y=ct[yr==EndYear]/(q.btv[yr==EndYear]*k.est)/u.msy.CMSY, col="purple", cex=1.5, lwd=2)
|
||||||
|
# plot u from biomass
|
||||||
|
if(Btype == "observed"|Btype=="simulated") lines(x=yr, y=u.bio/u.msy.bio, col="red")
|
||||||
|
# plot u from CPUE
|
||||||
|
if(Btype == "CPUE") {
|
||||||
|
par(new=T) # prepares for new plot on top of previous
|
||||||
|
plot(x=yr, y=u.CPUE, type="l", col="red", ylim=c(0, 1.2*max(u.CPUE,na.rm=T)),ann=F,axes=F)
|
||||||
|
axis(4, col="red", col.axis="red")
|
||||||
|
}
|
||||||
|
if(batch.mode == TRUE) {dev.off()} # close plot window
|
||||||
|
|
||||||
|
# ------------------------------------------
|
||||||
|
# print input and results to screen
|
||||||
|
cat("---------------------------------------\n")
|
||||||
|
|
||||||
|
cat("Species:", cinfo$ScientificName[cinfo$stock==stock], "\n")
|
||||||
|
cat("Name and region:", cinfo$EnglishName[cinfo$stock==stock], ",", cinfo$Name[cinfo$stock==stock], "\n")
|
||||||
|
cat("Stock:",stock,"\n")
|
||||||
|
cat("Catch data used from years", min(yr),"-", max(yr), "\n")
|
||||||
|
cat("Prior initial relative biomass =", startbio[1], "-", startbio[2], "\n")
|
||||||
|
cat("Prior intermediate rel. biomass=", intbio[1], "-", intbio[2], "in year", intyr, "\n")
|
||||||
|
cat("Prior final relative biomass =", endbio[1], "-", endbio[2], "\n")
|
||||||
|
cat("If current catches continue, is the stock likely to crash within 3 years?",FutureCrash,"\n")
|
||||||
|
cat("Prior range for r =", format(start_r[1],digits=2), "-", format(start_r[2],digits=2),
|
||||||
|
", prior range for k =", start_k[1], "-", start_k[2],"\n")
|
||||||
|
|
||||||
|
# if data are simulated, print true r-k
|
||||||
|
if(filename_1=="SimCatch.csv") {
|
||||||
|
cat("True r =", r.sim, "(because input data were simulated with Schaefer model)\n")
|
||||||
|
cat("True k = 1000 \n")
|
||||||
|
cat("True MSY =", 1000*r.sim/4,"\n")
|
||||||
|
cat("True biomass in last year =",bio[length(bio)],"or",bio[length(bio)]/1000,"k \n")
|
||||||
|
cat("True mean catch / MSY ratio =", mean(ct)/(1000*r.sim/4),"\n")
|
||||||
|
}
|
||||||
|
# print results from full Schaefer if available
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
cat("Results from Bayesian Schaefer model using catch & biomass (",Btype,")\n")
|
||||||
|
cat("MSY =", gm.MSY.jags,", 95% CL =", lcl.MSY.jags, "-", ucl.MSY.jags,"\n")
|
||||||
|
cat("Mean catch / MSY =", mean(ct)/gm.MSY.jags,"\n")
|
||||||
|
if(Btype != "CPUE") {
|
||||||
|
cat("r =", gm.r.jags,", 95% CL =", lcl.r.jags, "-", ucl.r.jags,"\n")
|
||||||
|
cat("k =", gm.k.jags,", 95% CL =", lcl.k.jags, "-", ucl.k.jags,"\n")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
# results of CMSY analysis
|
||||||
|
cat("Results of CMSY analysis \n")
|
||||||
|
cat("Altogether", nviablepoints,"unique viable r-k pairs were found \n")
|
||||||
|
cat(nviablepoints-length(rem.log.r),"r-k pairs above the initial geometric mean of r =", gm.rv, "were analysed\n")
|
||||||
|
cat("r =", r.est,", 95% CL =", lcl.r.est, "-", ucl.r.est,"\n")
|
||||||
|
cat("k =", k.est,", 95% CL =", lcl.k.est, "-", ucl.k.est,"\n")
|
||||||
|
cat("MSY =", MSY.est,", 95% CL =", lcl.MSY.est, "-", ucl.MSY.est,"\n")
|
||||||
|
cat("Predicted biomass in last year =", lastyr.bio, "2.5th perc =", lcl.lastyr.bio,
|
||||||
|
"97.5th perc =", ucl.lastyr.bio,"\n")
|
||||||
|
cat("Predicted biomass in next year =", nextyr.bio, "2.5th perc =", lcl.nextyr.bio,
|
||||||
|
"97.5th perc =", ucl.nextyr.bio,"\n")
|
||||||
|
cat("----------------------------------------------------------\n")
|
||||||
|
|
||||||
|
## Write some results into outfile
|
||||||
|
if(write.output == TRUE) {
|
||||||
|
# write data into csv file
|
||||||
|
output = data.frame(cinfo$ScientificName[cinfo$stock==stock], stock, StartYear, EndYear, mean(ct)*1000,
|
||||||
|
ifelse(Btype=="observed"|Btype=="simulate",bio[length(bio)],NA), # last biomass on record
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",gm.MSY.jags,NA), # full Schaefer
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",lcl.MSY.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",ucl.MSY.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",gm.r.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",lcl.r.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",ucl.r.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",gm.k.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",lcl.k.jags,NA),
|
||||||
|
ifelse(Btype == "observed"|Btype=="simulated",ucl.k.jags,NA),
|
||||||
|
r.est, lcl.r.est, ucl.r.est, # CMSY r
|
||||||
|
k.est, lcl.k.est, ucl.k.est, # CMSY k
|
||||||
|
MSY.est, lcl.MSY.est, ucl.MSY.est, # CMSY r
|
||||||
|
lastyr.bio, lcl.lastyr.bio, ucl.lastyr.bio, # last year bio
|
||||||
|
nextyr.bio, lcl.nextyr.bio, ucl.nextyr.bio)# last year + 1 bio
|
||||||
|
|
||||||
|
write.table(output, file=outfile, append = T, sep = ",",
|
||||||
|
dec = ".", row.names = FALSE, col.names = FALSE)
|
||||||
|
|
||||||
|
# write some text into text outfile.txt
|
||||||
|
|
||||||
|
cat("Species:", cinfo$ScientificName[cinfo$stock==stock], "\n",
|
||||||
|
"Name:", cinfo$EnglishName[cinfo$stock==stock], "\n",
|
||||||
|
"Region:", cinfo$Name[cinfo$stock==stock], "\n",
|
||||||
|
"Stock:",stock,"\n",
|
||||||
|
"Catch data used from years", min(yr),"-", max(yr),", biomass =", Btype, "\n",
|
||||||
|
"Prior initial relative biomass =", startbio[1], "-", startbio[2], "\n",
|
||||||
|
"Prior intermediate rel. biomass=", intbio[1], "-", intbio[2], "in year", intyr, "\n",
|
||||||
|
"Prior final relative biomass =", endbio[1], "-", endbio[2], "\n",
|
||||||
|
"Future crash with current catches?", FutureCrash, "\n",
|
||||||
|
"Prior range for r =", format(start_r[1],digits=2), "-", format(start_r[2],digits=2),
|
||||||
|
", prior range for k =", start_k[1], "-", start_k[2],"\n",
|
||||||
|
file=outfile.txt,append=T)
|
||||||
|
|
||||||
|
if(filename_1=="SimCatch.csv") {
|
||||||
|
cat(" True r =", r.sim, "(because input data were simulated with Schaefer model)\n",
|
||||||
|
"True k = 1000, true MSY =", 1000*r.sim/4,"\n",
|
||||||
|
"True biomass in last year =",bio[length(bio)],"or",bio[length(bio)]/1000,"k \n",
|
||||||
|
"True mean catch / MSY ratio =", mean(ct)/(1000*r.sim/4),"\n",
|
||||||
|
file=outfile.txt,append=T)
|
||||||
|
}
|
||||||
|
if(Btype == "observed"|Btype=="simulated") {
|
||||||
|
cat(" Results from Bayesian Schaefer model using catch & biomass \n",
|
||||||
|
"r =", gm.r.jags,", 95% CL =", lcl.r.jags, "-", ucl.r.jags,"\n",
|
||||||
|
"k =", gm.k.jags,", 95% CL =", lcl.k.jags, "-", ucl.k.jags,"\n",
|
||||||
|
"MSY =", gm.MSY.jags,", 95% CL =", lcl.MSY.jags, "-", ucl.MSY.jags,"\n",
|
||||||
|
"Mean catch / MSY =", mean(ct)/gm.MSY.jags,"\n",
|
||||||
|
file=outfile.txt,append=T)
|
||||||
|
}
|
||||||
|
cat(" Results of CMSY analysis with altogether", nviablepoints,"unique viable r-k pairs \n",
|
||||||
|
nviablepoints-length(rem.log.r),"r-k pairs above the initial geometric mean of r =", gm.rv, "were analysed\n",
|
||||||
|
"r =", r.est,", 95% CL =", lcl.r.est, "-", ucl.r.est,"\n",
|
||||||
|
"k =", k.est,", 95% CL =", lcl.k.est, "-", ucl.k.est,"\n",
|
||||||
|
"MSY =", MSY.est,", 95% CL =", lcl.MSY.est, "-", ucl.MSY.est,"\n",
|
||||||
|
"Predicted biomass last year b/k =", lastyr.bio, "2.5th perc b/k =", lcl.lastyr.bio,
|
||||||
|
"97.5th perc b/k =", ucl.lastyr.bio,"\n",
|
||||||
|
"Precautionary 25th percentile b/k =",q.btv[yr==EndYear],"\n",
|
||||||
|
"----------------------------------------------------------\n",
|
||||||
|
file=outfile.txt,append=T)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
} # end of stocks loop
|
||||||
|
|
@ -0,0 +1,119 @@
|
||||||
|
##--------------------------------------------------------
|
||||||
|
## CMSY analysis with estimation of total biomass, including Bayesian Schaefer
|
||||||
|
## written by Rainer Froese with support from Gianpaolo Coro in 2013-2014
|
||||||
|
## This version adjusts biomass to average biomass over the year
|
||||||
|
## It also contains the FutureCrash option to improve prediction of final biomass
|
||||||
|
## Version 21 adds the purple point to indicate the 25th percentile of final biomass
|
||||||
|
## Version 22 accepts that no biomass or CPUE area available
|
||||||
|
##--------------------------------------------------------
|
||||||
|
library(R2jags) # Interface with JAGS
|
||||||
|
library(coda)
|
||||||
|
|
||||||
|
#-----------------------------------------
|
||||||
|
# Some general settings
|
||||||
|
#-----------------------------------------
|
||||||
|
# set.seed(999) # use for comparing results between runs
|
||||||
|
rm(list=ls(all=TRUE)) # clear previous variables etc
|
||||||
|
options(digits=3) # displays all numbers with three significant digits as default
|
||||||
|
graphics.off() # close graphics windows from previous sessions
|
||||||
|
|
||||||
|
#-----------------------------------------
|
||||||
|
# General settings for the analysis
|
||||||
|
#-----------------------------------------
|
||||||
|
sigR <- 0.02 # overall process error; 0.05 works reasonable for simulations, 0.02 for real data; 0 if deterministic model
|
||||||
|
n <- 10000 # initial number of r-k pairs
|
||||||
|
batch.mode <- T # set to TRUE to suppress graphs
|
||||||
|
write.output <- T # set to true if table of output is wanted
|
||||||
|
FutureCrash <- "No"
|
||||||
|
|
||||||
|
#-----------------------------------------
|
||||||
|
# Start output to screen
|
||||||
|
#-----------------------------------------
|
||||||
|
cat("-------------------------------------------\n")
|
||||||
|
cat("Catch-MSY Analysis,", date(),"\n")
|
||||||
|
cat("-------------------------------------------\n")
|
||||||
|
|
||||||
|
#------------------------------------------
|
||||||
|
# Read data and assign to vectors
|
||||||
|
#------------------------------------------
|
||||||
|
# filename_1 <- "AllStocks_Catch4.csv"
|
||||||
|
# filename_2 <- "AllStocks_ID4.csv"
|
||||||
|
# filename_1 <- "SimCatch.csv"
|
||||||
|
# filename_2 <- "SimSpec.csv"
|
||||||
|
# filename_2 <- "SimSpecWrongS.csv"
|
||||||
|
# filename_2 <- "SimSpecWrongI.csv"
|
||||||
|
# filename_2 <- "SimSpecWrongF.csv"
|
||||||
|
# filename_2 <- "SimSpecWrongH.csv"
|
||||||
|
# filename_2 <- "SimSpecWrongL.csv"
|
||||||
|
# filename_1 <- "FishDataLim.csv"
|
||||||
|
# filename_2 <- "FishDataLimSpec.csv"
|
||||||
|
filename_1 <- "WKLIFE4Stocks.csv"
|
||||||
|
filename_2 <- "WKLIFE4ID.csv"
|
||||||
|
|
||||||
|
outfile<-"outfile"
|
||||||
|
outfile.txt <- "outputfile.txt"
|
||||||
|
|
||||||
|
cdat <- read.csv(filename_1, header=T, dec=".", stringsAsFactors = FALSE)
|
||||||
|
cinfo <- read.csv(filename_2, header=T, dec=".", stringsAsFactors = FALSE)
|
||||||
|
cat("Files", filename_1, ",", filename_2, "read successfully","\n")
|
||||||
|
|
||||||
|
# Stocks with total biomass data and catch data from StartYear to EndYear
|
||||||
|
# stocks <- sort(as.character(cinfo$stock)) # All stocks
|
||||||
|
stocks<-"HLH_M07"
|
||||||
|
|
||||||
|
# select one stock after the other
|
||||||
|
for(stock in stocks) {
|
||||||
|
# assign data from cinfo to vectors
|
||||||
|
res <- as.character(cinfo$Resilience[cinfo$stock==stock])
|
||||||
|
StartYear <- as.numeric(cinfo$StartYear[cinfo$stock==stock])
|
||||||
|
EndYear <- as.numeric(cinfo$EndYear[cinfo$stock==stock])
|
||||||
|
r_low <- as.numeric(cinfo$r_low[cinfo$stock==stock])
|
||||||
|
r_hi <- as.numeric(cinfo$r_hi[cinfo$stock==stock])
|
||||||
|
stb_low <- as.numeric(cinfo$stb_low[cinfo$stock==stock])
|
||||||
|
stb_hi <- as.numeric(cinfo$stb_hi[cinfo$stock==stock])
|
||||||
|
intyr <- as.numeric(cinfo$intyr[cinfo$stock==stock])
|
||||||
|
intbio_low <- as.numeric(cinfo$intbio_low[cinfo$stock==stock])
|
||||||
|
intbio_hi <- as.numeric(cinfo$intbio_hi[cinfo$stock==stock])
|
||||||
|
endbio_low <- as.numeric(cinfo$endbio_low[cinfo$stock==stock])
|
||||||
|
endbio_hi <- as.numeric(cinfo$endbio_hi[cinfo$stock==stock])
|
||||||
|
Btype <- as.character(cinfo$Btype[cinfo$stock==stock])
|
||||||
|
FutureCrash <- as.character(cinfo$FutureCrash[cinfo$stock==stock])
|
||||||
|
comment <- as.character(cinfo$comment[cinfo$stock==stock])
|
||||||
|
|
||||||
|
|
||||||
|
# extract data on stock
|
||||||
|
yr <- as.numeric(cdat$yr[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])
|
||||||
|
ct <- as.numeric(cdat$ct[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that catch is given in tonnes, transforms to '000 tonnes
|
||||||
|
if(Btype=="observed" | Btype=="CPUE" | Btype=="simulated") {
|
||||||
|
bt <- as.numeric(cdat$TB[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that biomass is in tonnes, transforms to '000 tonnes
|
||||||
|
} else {bt <- NA}
|
||||||
|
nyr <- length(yr) # number of years in the time series
|
||||||
|
|
||||||
|
cat("->---------------------------------------
|
||||||
|
Species: NA
|
||||||
|
Name and region: NA , NA
|
||||||
|
Stock: HLH_M07
|
||||||
|
Catch data used from years 1 - 50
|
||||||
|
Prior initial relative biomass = 0.5 - 0.9
|
||||||
|
Prior intermediate rel. biomass= 0.01 - 0.4 in year 25
|
||||||
|
Prior final relative biomass = 0.4 - 0.8
|
||||||
|
If current catches continue, is the stock likely to crash within 3 years? No
|
||||||
|
Prior range for r = 0.2 - 0.8 , prior range for k = 125 - 9965
|
||||||
|
Results from Bayesian Schaefer model using catch & biomass ( simulated )
|
||||||
|
MSY = 91.7 , 95% CL = 83.9 - 100
|
||||||
|
Mean catch / MSY = 0.882
|
||||||
|
r = 0.425 , 95% CL = 0.374 - 0.483
|
||||||
|
k = 863 , 95% CL = 783 - 951
|
||||||
|
Results of CMSY analysis
|
||||||
|
Altogether 2055 unique viable r-k pairs were found
|
||||||
|
1142 r-k pairs above the initial geometric mean of r = 0.343 were analysed
|
||||||
|
r = 0.522 , 95% CL = 0.349 - 0.782
|
||||||
|
k = 683 , 95% CL = 438 - 1067
|
||||||
|
MSY = 89.2 , 95% CL = 82.2 - 96.7
|
||||||
|
Predicted biomass in last year = 0.676 2.5th perc = 0.435 97.5th perc = 0.768
|
||||||
|
Predicted biomass in next year = 0.673 2.5th perc = 0.433 97.5th perc = 0.758
|
||||||
|
----------------------------------------------------------
|
||||||
|
",file=outfile.txt,append=T)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
<?xml version='1.0' encoding='UTF-8'?>
|
||||||
|
<hibernate-configuration>
|
||||||
|
<session-factory>
|
||||||
|
<property name="connection.driver_class">org.postgresql.Driver</property>
|
||||||
|
<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
|
||||||
|
<property name="connection.url">jdbc:postgresql://localhost/testdb</property>
|
||||||
|
<property name="connection.username">gcube</property>
|
||||||
|
<property name="connection.password">d4science2</property>
|
||||||
|
<property name="dialect">org.hibernate.dialect.PostgreSQLDialect</property>
|
||||||
|
<property name="transaction.factory_class">org.hibernate.transaction.JDBCTransactionFactory</property>
|
||||||
|
<property name="c3p0.timeout">0</property>
|
||||||
|
<property name="c3p0.max_size">1</property>
|
||||||
|
<property name="c3p0.max_statements">0</property>
|
||||||
|
<property name="c3p0.min_size">1</property>
|
||||||
|
<property name="current_session_context_class">thread</property>
|
||||||
|
</session-factory>
|
||||||
|
</hibernate-configuration>
|
||||||
Binary file not shown.
|
|
@ -0,0 +1,530 @@
|
||||||
|
#### R and JAGS code for estimating LWR-parameters from previous studies
|
||||||
|
#### Meant for updating the ESTIMATE table in FishBase
|
||||||
|
#### Created by Rainer Froese in March 2013, including JAGS models by James Thorston
|
||||||
|
#### Modified in June 2013 to include subfamilies
|
||||||
|
|
||||||
|
rm(list=ls(all=TRUE)) # remove previous variables and data
|
||||||
|
options(digits=3) # 3 significant digits as default
|
||||||
|
library(R2jags) # Interface with JAGS
|
||||||
|
runif(1) # sets random seed
|
||||||
|
|
||||||
|
#### Read in data
|
||||||
|
DataFile = "RF_LWR2.csv" # RF_LWR4 was extracted from FishBase in June 2013
|
||||||
|
Data = read.csv(DataFile, header=TRUE)
|
||||||
|
cat("Start", date(), "\n")
|
||||||
|
cat("Data file =", DataFile, "\n")
|
||||||
|
# Get unique, sorted list of Families
|
||||||
|
Fam.All <- sort(unique(as.character(Data$Family)))
|
||||||
|
Families <- Fam.All[Fam.All== "Acanthuridae" | Fam.All == "Achiridae"]
|
||||||
|
|
||||||
|
OutFile = "LWR_Test1.csv"
|
||||||
|
JAGSFILE = "dmnorm_0.bug"
|
||||||
|
|
||||||
|
# Get unique, sorted list of body shapes
|
||||||
|
Bshape <- sort(unique(as.character(Data$BodyShapeI)))
|
||||||
|
|
||||||
|
#------------------------------------------
|
||||||
|
# Functions
|
||||||
|
#------------------------------------------
|
||||||
|
|
||||||
|
#---------------------------------------------------------
|
||||||
|
# Function to get the priors for the respective body shape
|
||||||
|
#---------------------------------------------------------
|
||||||
|
Get.BS.pr <- function(BS) {
|
||||||
|
### Assignment of priors based on available body shape information
|
||||||
|
# priors derived from 5150 LWR studies in FishBase 02/2013
|
||||||
|
|
||||||
|
if (BS == "eel-like") { # eel-like prior for log(a) and b
|
||||||
|
prior_mean_log10a = -2.99
|
||||||
|
prior_sd_log10a = 0.175
|
||||||
|
prior_tau_log10a = 1/prior_sd_log10a^2
|
||||||
|
prior_mean_b = 3.06
|
||||||
|
prior_sd_b = 0.0896
|
||||||
|
prior_tau_b = 1/prior_sd_b^2
|
||||||
|
} else
|
||||||
|
if (BS == "elongated") { # elongate prior for log(a) and b
|
||||||
|
prior_mean_log10a = -2.41
|
||||||
|
prior_sd_log10a = 0.171
|
||||||
|
prior_tau_log10a = 1/prior_sd_log10a^2
|
||||||
|
prior_mean_b = 3.12
|
||||||
|
prior_sd_b = 0.09
|
||||||
|
prior_tau_b = 1/prior_sd_b^2
|
||||||
|
} else
|
||||||
|
if (BS == "fusiform / normal") { # fusiform / normal prior for log(a) and b
|
||||||
|
prior_mean_log10a = -1.95
|
||||||
|
prior_sd_log10a = 0.173
|
||||||
|
prior_tau_log10a = 1/prior_sd_log10a^2
|
||||||
|
prior_mean_b = 3.04
|
||||||
|
prior_sd_b = 0.0857
|
||||||
|
prior_tau_b = 1/prior_sd_b^2
|
||||||
|
} else
|
||||||
|
if (BS == "short and / or deep") { # short and / or deep prior for log(a) and b
|
||||||
|
prior_mean_log10a = -1.7
|
||||||
|
prior_sd_log10a = 0.175
|
||||||
|
prior_tau_log10a = 1/prior_sd_log10a^2
|
||||||
|
prior_mean_b = 3.01
|
||||||
|
prior_sd_b = 0.0905
|
||||||
|
prior_tau_b = 1/prior_sd_b^2
|
||||||
|
} else
|
||||||
|
# priors across all shapes, used for missing or other BS
|
||||||
|
{
|
||||||
|
prior_mean_log10a = -2.0
|
||||||
|
prior_sd_log10a = 0.313
|
||||||
|
prior_tau_log10a = 1/prior_sd_log10a^2
|
||||||
|
prior_mean_b = 3.04
|
||||||
|
prior_sd_b = 0.119
|
||||||
|
prior_tau_b = 1/prior_sd_b^2
|
||||||
|
}
|
||||||
|
|
||||||
|
# Priors for measurement error (= sigma) based on 5150 studies
|
||||||
|
# given here as shape mu and rate r, for gamma distribution
|
||||||
|
SD_rObs_log10a = 6520
|
||||||
|
SD_muObs_log10a = 25076
|
||||||
|
SD_rObs_b = 6808
|
||||||
|
SD_muObs_b = 37001
|
||||||
|
# Priors for between species variability (= sigma) based on 5150 studies for 1821 species
|
||||||
|
SD_rGS_log10a = 1372
|
||||||
|
SD_muGS_log10a = 7933
|
||||||
|
SD_rGS_b = 572
|
||||||
|
SD_muGS_b = 6498
|
||||||
|
|
||||||
|
prior.list <- list(mean_log10a=prior_mean_log10a, sd_log10a=prior_sd_log10a,
|
||||||
|
tau_log10a=prior_tau_log10a, mean_b=prior_mean_b, sd_b=prior_sd_b,
|
||||||
|
tau_b=prior_tau_b, SD_rObs_log10a=SD_rObs_log10a, SD_muObs_log10a=SD_muObs_log10a,
|
||||||
|
SD_rObs_b=SD_rObs_b, SD_muObs_b=SD_muObs_b, SD_rGS_log10a=SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=SD_muGS_log10a, SD_rGS_b=SD_rGS_b, SD_muGS_b=SD_muGS_b)
|
||||||
|
return(prior.list)
|
||||||
|
}
|
||||||
|
|
||||||
|
#--------------------------------------------------------------------
|
||||||
|
# Function to do a Bayesian analysis including LWR from relatives
|
||||||
|
#--------------------------------------------------------------------
|
||||||
|
SpecRelLWR <- function(a, b, wts, GenusSpecies, Nspecies, prior_mean_b, prior_tau_b,
|
||||||
|
prior_mean_log10a, prior_tau_log10a, SD_rObs_log10a, SD_muObs_log10a,
|
||||||
|
SD_rObs_b, SD_muObs_b, SD_rGS_log10a, SD_muGS_log10a,
|
||||||
|
SD_rGS_b, SD_muGS_b){
|
||||||
|
### Define JAGS model
|
||||||
|
Model = "
|
||||||
|
model {
|
||||||
|
#### Process model -- effects of taxonomy
|
||||||
|
# given the likelihood distributions and the priors,
|
||||||
|
# create normal posterior distributions for log10a, b,
|
||||||
|
# and for the process error (=between species variability sigmaGS)
|
||||||
|
|
||||||
|
abTrue[1] ~ dnorm(prior_mean_log10a,prior_tau_log10a)
|
||||||
|
abTrue[2] ~ dnorm(prior_mean_b,prior_tau_b)
|
||||||
|
sigmaGSlog10a ~ dgamma( SD_rGS_log10a, SD_muGS_log10a)
|
||||||
|
sigmaGSb ~ dgamma( SD_rGS_b, SD_muGS_b)
|
||||||
|
|
||||||
|
# given the posterior distributions and the process errors,
|
||||||
|
# establish for every species the expected witin-species
|
||||||
|
# parameter distributions; no correlation roGS between species
|
||||||
|
|
||||||
|
roGS <- 0
|
||||||
|
tauGenusSpecies[1] <- pow(sigmaGSlog10a,-2)
|
||||||
|
tauGenusSpecies[2] <- pow(sigmaGSb,-2)
|
||||||
|
for(k in 1:Nspecies){
|
||||||
|
abGenusSpecies[k,1] ~ dnorm(abTrue[1],tauGenusSpecies[1])
|
||||||
|
abGenusSpecies[k,2] ~ dnorm(abTrue[2],tauGenusSpecies[2])
|
||||||
|
}
|
||||||
|
|
||||||
|
### Observation model
|
||||||
|
## Errors
|
||||||
|
# given the data and the priors, establish distributions
|
||||||
|
# for the observation errors sigmaObs
|
||||||
|
|
||||||
|
sigmaObslog10a ~ dgamma( SD_rObs_log10a, SD_muObs_log10a)
|
||||||
|
sigmaObsb ~ dgamma( SD_rObs_b, SD_muObs_b)
|
||||||
|
|
||||||
|
# create inverse covariance matrix, with negative parameter correlation roObs
|
||||||
|
roObs ~ dunif(-0.99,0)
|
||||||
|
CovObs[1,1] <- pow(sigmaObslog10a,2)
|
||||||
|
CovObs[2,2] <- pow(sigmaObsb,2)
|
||||||
|
CovObs[1,2] <- roObs * sigmaObslog10a * sigmaObsb
|
||||||
|
CovObs[2,1] <- CovObs[1,2]
|
||||||
|
TauObs[1:2,1:2] <- inverse(CovObs[1:2,1:2])
|
||||||
|
|
||||||
|
## likelihood
|
||||||
|
# given the data, the priors and the covariance,
|
||||||
|
# create multivariate likelihood distributions for log10(a) and b
|
||||||
|
|
||||||
|
for(i in 1:N){
|
||||||
|
TauObsI[i,1:2,1:2] <- TauObs[1:2,1:2] * pow(Weights[i],2) # weighted precision
|
||||||
|
ab[i,1:2] ~ dmnorm(abGenusSpecies[GenusSpecies[i],1:2],TauObsI[i,1:2,1:2])
|
||||||
|
}
|
||||||
|
}
|
||||||
|
"
|
||||||
|
|
||||||
|
# Write JAGS model
|
||||||
|
cat(Model, file=JAGSFILE)
|
||||||
|
# JAGS settings
|
||||||
|
Nchains = 3 # number of MCMC chains to be used in JAGS
|
||||||
|
Nburnin = 1e4 # number of burn-in iterations, to be discarded; 1e4 = 10000 iterations for burn-in
|
||||||
|
Niter = 3e4 # number of iterations after burn-in; 3e4 = 30000 iterations
|
||||||
|
Nthin = 1e1 # subset of iterations to be used for analysis; 1e1 = every 10th iteration
|
||||||
|
|
||||||
|
# Run JAGS: define data to be passed on in DataJags;
|
||||||
|
# determine parameters to be returned in Param2Save;
|
||||||
|
# call JAGS with function Jags()
|
||||||
|
DataJags = list(ab=cbind(log10(a),b), N=length(a), Weights=wts, Nspecies=Nspecies, GenusSpecies=GenusSpecies,
|
||||||
|
prior_mean_b=prior_mean_b, prior_tau_b=prior_tau_b,
|
||||||
|
prior_mean_log10a=prior_mean_log10a, prior_tau_log10a=prior_tau_log10a,
|
||||||
|
SD_rObs_log10a=SD_rObs_log10a, SD_muObs_log10a=SD_muObs_log10a,
|
||||||
|
SD_rObs_b=SD_rObs_b, SD_muObs_b=SD_muObs_b,
|
||||||
|
SD_rGS_log10a=SD_rGS_log10a, SD_muGS_log10a=SD_muGS_log10a,
|
||||||
|
SD_rGS_b=SD_rGS_b, SD_muGS_b=SD_muGS_b)
|
||||||
|
Params2Save = c("abTrue","abGenusSpecies","sigmaGSlog10a","sigmaGSb","sigmaObslog10a","sigmaObsb","roObs")
|
||||||
|
Jags <- jags(inits=NULL, model.file=JAGSFILE, working.directory=NULL, data=DataJags,
|
||||||
|
parameters.to.save=Params2Save, n.chains=Nchains, n.thin=Nthin, n.iter=Niter, n.burnin=Nburnin)
|
||||||
|
Jags$BUGSoutput # contains the results from the JAGS run
|
||||||
|
|
||||||
|
# Analyze output for the relatives
|
||||||
|
abTrue <- Jags$BUGSoutput$sims.list$abTrue
|
||||||
|
R_mean_log10a <- mean(abTrue[,1]) # true mean of log10(a)
|
||||||
|
R_sd_log10a <- sd(abTrue[,1]) # true SE of log10(a)
|
||||||
|
R_mean_b <- mean(abTrue[,2]) # true mean of b
|
||||||
|
R_sd_b <- sd(abTrue[,2]) # true SE of b
|
||||||
|
|
||||||
|
# Analyze output for the target species
|
||||||
|
abGenusSpecies <- Jags$BUGSoutput$sims.list$abGenusSpecies
|
||||||
|
mean_log10a <- mean(abGenusSpecies[,1,1]) # true mean of log10(a) for the first species= target species
|
||||||
|
sd_log10a <- sd(abGenusSpecies[,1,1]) # true SE of log10(a)
|
||||||
|
mean_b <- mean(abGenusSpecies[,1,2]) # true mean of b
|
||||||
|
sd_b <- sd(abGenusSpecies[,1,2]) # true SE of b
|
||||||
|
mean_sigma_log10a <- mean(Jags$BUGSoutput$sims.list$sigmaObslog10a) # measurement error of log10(a)
|
||||||
|
sd_sigma_log10a <- apply(as.matrix(Jags$BUGSoutput$sims.list$sigmaObslog10a), 2, sd)
|
||||||
|
mean_sigma_b <- mean(Jags$BUGSoutput$sims.list$sigmaObsb) # measurement error of b
|
||||||
|
sd_sigma_b <- apply(as.matrix(Jags$BUGSoutput$sims.list$sigmaObsb), 2, sd)
|
||||||
|
ro_ab <- mean(Jags$BUGSoutput$sims.list$roObs) # measurement correlation of log10(a),b
|
||||||
|
|
||||||
|
out.list <- list(N=length(a), mean_log10a=mean_log10a, sd_log10a=sd_log10a, mean_b=mean_b, sd_b=sd_b,
|
||||||
|
R_mean_log10a=R_mean_log10a, R_sd_log10a=R_sd_log10a, R_mean_b=R_mean_b, R_sd_b=R_sd_b)
|
||||||
|
return(out.list)
|
||||||
|
}
|
||||||
|
|
||||||
|
#-----------------------------------------------------------------------------
|
||||||
|
# Function to do a Bayesian LWR analysis with studies for target species only
|
||||||
|
#-----------------------------------------------------------------------------
|
||||||
|
SpecLWR <- function(a, b, wts, prior_mean_b, prior_tau_b,
|
||||||
|
prior_mean_log10a, prior_tau_log10a, SD_rObs_log10a, SD_muObs_log10a,
|
||||||
|
SD_rObs_b, SD_muObs_b, SD_rGS_log10a, SD_muGS_log10a,
|
||||||
|
SD_rGS_b, SD_muGS_b){
|
||||||
|
|
||||||
|
# Define JAGS model
|
||||||
|
Model = "
|
||||||
|
model {
|
||||||
|
sigma1 ~ dgamma( SD_rObs_log10a, SD_muObs_log10a) # posterior distribution for measurement error in log10a
|
||||||
|
sigma2 ~ dgamma( SD_rObs_b, SD_muObs_b) # posterior distribution for measurement error in log10a
|
||||||
|
|
||||||
|
ro ~ dunif(-0.99,0) # uniform prior for negative correlation between log10a and b
|
||||||
|
abTrue[1] ~ dnorm(prior_mean_log10a,prior_tau_log10a) # normal posterior distribution for log10a
|
||||||
|
abTrue[2] ~ dnorm(prior_mean_b,prior_tau_b) # normal posterior distribution for b
|
||||||
|
CovObs[1,1] <- pow(sigma1,2)
|
||||||
|
CovObs[2,2] <- pow(sigma2,2)
|
||||||
|
CovObs[1,2] <- ro * sigma1 * sigma2
|
||||||
|
CovObs[2,1] <- CovObs[1,2]
|
||||||
|
TauObs[1:2,1:2] <- inverse(CovObs[1:2,1:2]) # create inverse covariance matrix
|
||||||
|
for(i in 1:N){
|
||||||
|
TauObsI[i,1:2,1:2] <- TauObs[1:2,1:2] * pow(Weights[i],2) # converts prior SD into prior weighted precision
|
||||||
|
|
||||||
|
# given the data, the priors and the covariance, create multivariate normal posteriors for log(a) and b
|
||||||
|
ab[i,1:2] ~ dmnorm(abTrue[1:2],TauObsI[i,1:2,1:2])
|
||||||
|
}
|
||||||
|
}
|
||||||
|
"
|
||||||
|
|
||||||
|
# Write JAGS model
|
||||||
|
cat(Model, file=JAGSFILE)
|
||||||
|
# JAGS settings
|
||||||
|
Nchains = 3 # number of MCMC chains to be used in JAGS
|
||||||
|
Nburnin = 1e4 # number of burn-in runs, to be discarded; 10000 iterations for burn-in
|
||||||
|
Niter = 3e4 # number of iterations after burn-in; 3e4 = 30000 iterations
|
||||||
|
Nthin = 1e1 # subset of iterations to be used for analysis; 1e1 = every 10th iteration
|
||||||
|
# Run JAGS: define data to be passed on in DataJags; determine parameters to be returned in Param2Save; call JAGS with function Jags()
|
||||||
|
DataJags = list(ab=cbind(log10(a),b), N=length(a), Weights=wts, prior_mean_b=prior_mean_b,
|
||||||
|
prior_tau_b=prior_tau_b, prior_mean_log10a=prior_mean_log10a, prior_tau_log10a=prior_tau_log10a,
|
||||||
|
SD_rObs_log10a=SD_rObs_log10a, SD_muObs_log10a=SD_muObs_log10a,
|
||||||
|
SD_rObs_b=SD_rObs_b, SD_muObs_b=SD_muObs_b)
|
||||||
|
Params2Save = c("abTrue","sigma1","sigma2","ro")
|
||||||
|
Jags <- jags(inits=NULL, model.file=JAGSFILE, working.directory=NULL, data=DataJags, parameters.to.save=Params2Save, n.chains=Nchains, n.thin=Nthin, n.iter=Niter, n.burnin=Nburnin)
|
||||||
|
Jags$BUGSoutput # contains the results from the JAGS run
|
||||||
|
# Analyze output
|
||||||
|
abTrue <- Jags$BUGSoutput$sims.list$abTrue
|
||||||
|
mean_log10a <- mean(abTrue[,1]) # true mean of log10(a)
|
||||||
|
sd_log10a <- sd(abTrue[,1]) # true SE of log10(a)
|
||||||
|
mean_b <- mean(abTrue[,2]) # true mean of b
|
||||||
|
sd_b <- sd(abTrue[,2]) # true SE of b
|
||||||
|
mean_sigma_log10a <- mean(Jags$BUGSoutput$sims.list$sigma1) # measurement error of log10(a)
|
||||||
|
sd_sigma_log10a <- apply(as.matrix(Jags$BUGSoutput$sims.list$sigma1), 2, sd)
|
||||||
|
mean_sigma_b <- mean(Jags$BUGSoutput$sims.list$sigma2) # measurement error of b
|
||||||
|
sd_sigma_b <- apply(as.matrix(Jags$BUGSoutput$sims.list$sigma2), 2, sd)
|
||||||
|
ro_ab <- mean(Jags$BUGSoutput$sims.list$ro) # measurement correlation of log10(a),b
|
||||||
|
|
||||||
|
out.list <- list(N=length(a), mean_log10a=mean_log10a, sd_log10a=sd_log10a, mean_b=mean_b, sd_b=sd_b)
|
||||||
|
return(out.list)
|
||||||
|
|
||||||
|
} # End of Functions section
|
||||||
|
|
||||||
|
#--------------------------------
|
||||||
|
# Analysis by Family
|
||||||
|
#--------------------------------
|
||||||
|
# Do LWR analysis by Family, Subfamily and Body shape, depending on available LWR studies
|
||||||
|
# for(Fam in "Acanthuridae") {
|
||||||
|
for(Fam in Families) {
|
||||||
|
Subfamilies <- sort(unique(Data$Subfamily[Data$Family==Fam]))
|
||||||
|
for(SF in Subfamilies) {
|
||||||
|
for(BS in Bshape) {
|
||||||
|
# get species (SpecCodes) in this Subfamily and with this body shape
|
||||||
|
SpecCode.SF.BS <- unique(Data$SpecCode[Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS])
|
||||||
|
# if there are species with this body shape
|
||||||
|
if(length(SpecCode.SF.BS > 0)) {
|
||||||
|
# get priors for this body shape
|
||||||
|
prior <- Get.BS.pr(BS)
|
||||||
|
# get LWR data for this body shape
|
||||||
|
b_raw <- Data$b[Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS]
|
||||||
|
cat("\n")
|
||||||
|
cat("Family =", Fam, ", Subfamily =", SF, ", Body shape =", BS, ", Species =", length(SpecCode.SF.BS), ", LWR =",
|
||||||
|
length(b_raw[is.na(b_raw)==F]), "\n")
|
||||||
|
# if no LWR studies exist for this body shape, assign the respective priors to all species
|
||||||
|
if(length(b_raw[is.na(b_raw)==F])==0) {
|
||||||
|
# assign priors to species with no LWR in this Subfamily with this body shape
|
||||||
|
cat("Assigning overall body shape prior to", length(SpecCode.SF.BS), " species \n")
|
||||||
|
for(SpC in SpecCode.SF.BS) {
|
||||||
|
out.prior <- data.frame(Fam, SF, BS, SpC, 0, prior$mean_log10a, prior$sd_log10a, prior$mean_b, prior$sd_b,
|
||||||
|
paste("all LWR estimates for this BS"))
|
||||||
|
write.table(out.prior, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
|
||||||
|
# Update priors for this body shape using existing LWR studies
|
||||||
|
# get LWR data for this Subfamily and body shape
|
||||||
|
Keep <- which(Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS & is.na(Data$b)==F & Data$Score>0)
|
||||||
|
wts <- Data$Score[Keep] # Un-normalized weights (so that Cov is comparable among analyses)
|
||||||
|
a <- Data$a[Keep]
|
||||||
|
b <- Data$b[Keep]
|
||||||
|
GenSpec <- paste(Data$Genus[Keep],Data$Species[Keep])
|
||||||
|
# add a first dummy record with prior LWR and low score = 0.3, as pseudo target species
|
||||||
|
# Name of dummy target species is Dum1 dum1
|
||||||
|
TargetSpec = paste("Dum1", "dum1")
|
||||||
|
wts <- c(0.3, wts)
|
||||||
|
a <- c(10^(prior$mean_log10a), a)
|
||||||
|
b <- c(prior$mean_b, b)
|
||||||
|
GenSpec <- c(TargetSpec, GenSpec)
|
||||||
|
# Relabel GenSpec so that TargetSpec = level 1
|
||||||
|
OtherSpecies = unique(GenSpec[GenSpec != TargetSpec])
|
||||||
|
GenusSpecies = factor(GenSpec, levels=c(TargetSpec, OtherSpecies))
|
||||||
|
Nspecies = nlevels(GenusSpecies) # number of species
|
||||||
|
# run Bayesian analysis for pseudo target species with Subfamily members
|
||||||
|
# The resulting R_mean_log10a, R_sd_log10a, R_mean_b, R_sd_b will be used for species without LWR
|
||||||
|
cat("Updating Subfamily-Bodyshape prior using", Nspecies-1, "species with LWR studies \n")
|
||||||
|
prior.SFam.BS <- SpecRelLWR(a, b, wts, GenusSpecies, Nspecies, prior_mean_b=prior$mean_b,
|
||||||
|
prior_tau_b=prior$tau_b, prior_mean_log10a=prior$mean_log10a,
|
||||||
|
prior_tau_log10a=prior$tau_log10a, SD_rObs_log10a=prior$SD_rObs_log10a,
|
||||||
|
SD_muObs_log10a=prior$SD_muObs_log10a, SD_rObs_b=prior$SD_rObs_b,
|
||||||
|
SD_muObs_b=prior$SD_muObs_b, SD_rGS_log10a=prior$SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=prior$SD_muGS_log10a, SD_rGS_b=prior$SD_rGS_b,
|
||||||
|
SD_muGS_b=prior$SD_muGS_b)
|
||||||
|
|
||||||
|
#------------------------------------------------------------------------------------------
|
||||||
|
# if there are Genera with >= 5 species with LWR, update body shape priors for these Genera
|
||||||
|
#------------------------------------------------------------------------------------------
|
||||||
|
Genera <- unique(as.character(Data$Genus[Keep]))
|
||||||
|
# create empty list of lists for storage of generic priors
|
||||||
|
prior.Gen.BS <- rep(list(list()),length(Genera)) # create a list of empty lists
|
||||||
|
names(prior.Gen.BS) <- Genera # name the list elements according to the Genera
|
||||||
|
for(Genus in Genera){
|
||||||
|
# check if Genus contains >= 5 species with LWR data
|
||||||
|
if(length(unique(Data$SpecCode[Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS & is.na(Data$b)==F &
|
||||||
|
Data$Score>0 & Data$Genus==Genus]))>=5) {
|
||||||
|
# run Subfamily analysis with only data for this genus
|
||||||
|
Keep <- which(Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS & is.na(Data$b)==F & Data$Score>0 &
|
||||||
|
Data$Genus==Genus)
|
||||||
|
wts <- Data$Score[Keep] # Un-normalized weights (so that Cov is comparable among analyses)
|
||||||
|
a <- Data$a[Keep]
|
||||||
|
b <- Data$b[Keep]
|
||||||
|
GenSpec <- paste(Data$Genus[Keep],Data$Species[Keep])
|
||||||
|
# add a first dummy record with prior LWR and low score = 0.3, as pseudo target species
|
||||||
|
# Name of dummy target species is Dum1 dum1
|
||||||
|
TargetSpec = paste("Dum1", "dum1")
|
||||||
|
wts <- c(0.3, wts)
|
||||||
|
a <- c(10^(prior$mean_log10a), a)
|
||||||
|
b <- c(prior$mean_b, b)
|
||||||
|
GenSpec <- c(TargetSpec, GenSpec)
|
||||||
|
# Relabel GenSpec so that TargetSpec = level 1
|
||||||
|
OtherSpecies = unique(GenSpec[GenSpec != TargetSpec])
|
||||||
|
GenusSpecies = factor(GenSpec, levels=c(TargetSpec, OtherSpecies))
|
||||||
|
Nspecies = nlevels(GenusSpecies) # number of species
|
||||||
|
# run Bayesian analysis for pseudo target species with Genus members
|
||||||
|
# R_mean_log10a, R_sd_log10a, R_mean_b, R_sd_b will be used for species without LWR
|
||||||
|
cat("Updating prior for Genus =", Genus, ", with", Nspecies -1, "LWR Species \n")
|
||||||
|
prior.Gen.BS[[Genus]] <- SpecRelLWR(a, b, wts, GenusSpecies, Nspecies,
|
||||||
|
prior_mean_b=prior.SFam.BS$R_mean_b,
|
||||||
|
prior_tau_b=1/prior.SFam.BS$R_sd_b^2,
|
||||||
|
prior_mean_log10a=prior.SFam.BS$R_mean_log10a,
|
||||||
|
prior_tau_log10a=1/prior.SFam.BS$R_sd_log10a,
|
||||||
|
SD_rObs_log10a=prior$SD_rObs_log10a,
|
||||||
|
SD_muObs_log10a=prior$SD_muObs_log10a, SD_rObs_b=prior$SD_rObs_b,
|
||||||
|
SD_muObs_b=prior$SD_muObs_b, SD_rGS_log10a=prior$SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=prior$SD_muGS_log10a, SD_rGS_b=prior$SD_rGS_b,
|
||||||
|
SD_muGS_b=prior$SD_muGS_b)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
# new Subfamily-BS priors have been generated
|
||||||
|
# for some genera, new Genus-BS priors have been generated
|
||||||
|
# ---------------------------------------------------------------------
|
||||||
|
# Loop through all species in this Subfamily-BS; assign LWR as appropriate
|
||||||
|
# ---------------------------------------------------------------------
|
||||||
|
for(SpC in SpecCode.SF.BS) {
|
||||||
|
Genus <- as.character(unique(Data$Genus[Data$SpecCode==SpC]))
|
||||||
|
Species <- as.character(unique(Data$Species[Data$SpecCode==SpC]))
|
||||||
|
TargetSpec = paste(Genus, Species)
|
||||||
|
LWR <- length(Data$b[Data$SpecCode==SpC & is.na(Data$b)==F & Data$Score>0])
|
||||||
|
LWRGenspec <- length(unique(Data$SpecCode[Data$BodyShapeI==BS & is.na(Data$b)==F &
|
||||||
|
Data$Score>0 & Data$Genus==Genus]))
|
||||||
|
LWRSFamspec <- length(unique(Data$SpecCode[Data$BodyShapeI==BS & is.na(Data$b)==F &
|
||||||
|
Data$Score>0 & Data$Family==Fam & Data$Subfamily==SF]))
|
||||||
|
#---------------------------------------------------------
|
||||||
|
# >= 5 LWR in target species, run single species analysis
|
||||||
|
if(LWR >= 5) {
|
||||||
|
# Run analysis with data only for this species
|
||||||
|
Keep <- which(Data$SpecCode==SpC & is.na(Data$b)==F & Data$Score>0)
|
||||||
|
wts = Data$Score[Keep] # Un-normalized weights (so that Cov is comparable among analyses)
|
||||||
|
a = Data$a[Keep]
|
||||||
|
b = Data$b[Keep]
|
||||||
|
|
||||||
|
# determine priors to be used
|
||||||
|
if(LWRGenspec >= 5) {
|
||||||
|
prior_mean_b=prior.Gen.BS[[Genus]]$R_mean_b
|
||||||
|
prior_tau_b=1/prior.Gen.BS[[Genus]]$R_sd_b^2
|
||||||
|
prior_mean_log10a=prior.Gen.BS[[Genus]]$R_mean_log10a
|
||||||
|
prior_tau_log10a=1/prior.Gen.BS[[Genus]]$R_sd_log10a^2
|
||||||
|
} else
|
||||||
|
if (LWRSFamspec > 0) {
|
||||||
|
prior_mean_b=prior.SFam.BS$R_mean_b
|
||||||
|
prior_tau_b=1/prior.SFam.BS$R_sd_b^2
|
||||||
|
prior_mean_log10a=prior.SFam.BS$R_mean_log10a
|
||||||
|
prior_tau_log10a=1/prior.SFam.BS$R_sd_log10a^2
|
||||||
|
} else {
|
||||||
|
prior_mean_b=prior$mean_b
|
||||||
|
prior_tau_b=prior$tau_b
|
||||||
|
prior_mean_log10a=prior$mean_log10a
|
||||||
|
prior_tau_log10a=prior$tau_log10a
|
||||||
|
}
|
||||||
|
cat("Running single species analysis for", TargetSpec, "LWR =", LWR, ", LWR species in Genus=",LWRGenspec,"\n" )
|
||||||
|
# call function for single species analysis
|
||||||
|
post <- SpecLWR(a, b, wts, prior_mean_b=prior_mean_b,
|
||||||
|
prior_tau_b=prior_tau_b, prior_mean_log10a=prior_mean_log10a,
|
||||||
|
prior_tau_log10a=prior_tau_log10a, SD_rObs_log10a=prior$SD_rObs_log10a,
|
||||||
|
SD_muObs_log10a=prior$SD_muObs_log10a, SD_rObs_b=prior$SD_rObs_b,
|
||||||
|
SD_muObs_b=prior$SD_muObs_b, SD_rGS_log10a=prior$SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=prior$SD_muGS_log10a, SD_rGS_b=prior$SD_rGS_b,
|
||||||
|
SD_muGS_b=prior$SD_muGS_b)
|
||||||
|
out.SpC <- data.frame(Fam, SF, BS, SpC, LWR, format(post$mean_log10a, digits=3), format(post$sd_log10a, digits=3), format(post$mean_b, disgits=3), format(post$sd_b, digits=3),
|
||||||
|
paste("LWR estimates for this species"))
|
||||||
|
write.table(out.SpC, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
|
||||||
|
} else
|
||||||
|
#--------------------------------------------------------
|
||||||
|
# 1-4 LWR in target species and >= 5 LWR species in Genus
|
||||||
|
# run hierarchical analysis for genus members, with Subfamily-BS prior
|
||||||
|
if(LWR >= 1 & LWRGenspec >=5) {
|
||||||
|
# run Subfamily analysis with only data for this genus
|
||||||
|
Keep <- which(Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS & is.na(Data$b)==F & Data$Score>0 &
|
||||||
|
Data$Genus==Genus)
|
||||||
|
wts <- Data$Score[Keep] # Un-normalized weights (so that Cov is comparable among analyses)
|
||||||
|
a <- Data$a[Keep]
|
||||||
|
b <- Data$b[Keep]
|
||||||
|
GenSpec <- paste(Data$Genus[Keep],Data$Species[Keep])
|
||||||
|
|
||||||
|
# Relabel GenSpec so that TargetSpec = level 1
|
||||||
|
OtherSpecies = unique(GenSpec[GenSpec != TargetSpec])
|
||||||
|
GenusSpecies = factor(GenSpec, levels=c(TargetSpec, OtherSpecies))
|
||||||
|
Nspecies = nlevels(GenusSpecies) # number of species
|
||||||
|
# run Bayesian analysis for target species with Genus members
|
||||||
|
cat("Running analysis with congeners for", TargetSpec, ", LWR =", LWR,", LWR species in Genus =", LWRGenspec,"\n")
|
||||||
|
post <- SpecRelLWR(a, b, wts, GenusSpecies, Nspecies,
|
||||||
|
prior_mean_b=prior.SFam.BS$R_mean_b,
|
||||||
|
prior_tau_b=1/prior.SFam.BS$R_sd_b^2,
|
||||||
|
prior_mean_log10a=prior.SFam.BS$R_mean_log10a,
|
||||||
|
prior_tau_log10a=1/prior.SFam.BS$R_sd_log10a^2,
|
||||||
|
SD_rObs_log10a=prior$SD_rObs_log10a,
|
||||||
|
SD_muObs_log10a=prior$SD_muObs_log10a, SD_rObs_b=prior$SD_rObs_b,
|
||||||
|
SD_muObs_b=prior$SD_muObs_b, SD_rGS_log10a=prior$SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=prior$SD_muGS_log10a, SD_rGS_b=prior$SD_rGS_b,
|
||||||
|
SD_muGS_b=prior$SD_muGS_b)
|
||||||
|
out.SpC <- data.frame(Fam, SF, BS, SpC, LWR, format(post$mean_log10a, digits=3), format(post$sd_log10a, digits=3), format(post$mean_b, disgits=3), format(post$sd_b, digits=3),
|
||||||
|
paste("LWR estimates for species & Genus-BS"))
|
||||||
|
write.table(out.SpC, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
} else
|
||||||
|
|
||||||
|
#-------------------------------------------------------
|
||||||
|
# 1-4 LWR in target species and < 5 LWR species in Genus
|
||||||
|
# run hierarchical analysis for Subfamily members, with bodyshape prior
|
||||||
|
|
||||||
|
if(LWR >= 1 & LWRSFamspec > 1) {
|
||||||
|
# run Subfamily analysis
|
||||||
|
Keep <- which(Data$Family==Fam & Data$Subfamily==SF & Data$BodyShapeI==BS & is.na(Data$b)==F & Data$Score>0)
|
||||||
|
wts <- Data$Score[Keep] # Un-normalized weights (so that Cov is comparable among analyses)
|
||||||
|
a <- Data$a[Keep]
|
||||||
|
b <- Data$b[Keep]
|
||||||
|
GenSpec <- paste(Data$Genus[Keep],Data$Species[Keep])
|
||||||
|
# Relabel GenSpec so that TargetSpec = level 1
|
||||||
|
OtherSpecies = unique(GenSpec[GenSpec != TargetSpec])
|
||||||
|
GenusSpecies = factor(GenSpec, levels=c(TargetSpec, OtherSpecies))
|
||||||
|
Nspecies = nlevels(GenusSpecies) # number of species
|
||||||
|
# run Bayesian analysis for target species with Subfamily members
|
||||||
|
cat("Running analysis with Subfamily members for", TargetSpec, ", LWR =", LWR,", LWR species in Subfamily-BS =",
|
||||||
|
LWRSFamspec, "\n")
|
||||||
|
post <- SpecRelLWR(a, b, wts, GenusSpecies, Nspecies,
|
||||||
|
prior_mean_b=prior$mean_b,
|
||||||
|
prior_tau_b=prior$tau_b,
|
||||||
|
prior_mean_log10a=prior$mean_log10a,
|
||||||
|
prior_tau_log10a=prior$tau_log10a,
|
||||||
|
SD_rObs_log10a=prior$SD_rObs_log10a,
|
||||||
|
SD_muObs_log10a=prior$SD_muObs_log10a, SD_rObs_b=prior$SD_rObs_b,
|
||||||
|
SD_muObs_b=prior$SD_muObs_b, SD_rGS_log10a=prior$SD_rGS_log10a,
|
||||||
|
SD_muGS_log10a=prior$SD_muGS_log10a, SD_rGS_b=prior$SD_rGS_b,
|
||||||
|
SD_muGS_b=prior$SD_muGS_b)
|
||||||
|
out.SpC <- data.frame(Fam, SF, BS, SpC, LWR, format(post$mean_log10a, digits=3), format(post$sd_log10a, digits=3),
|
||||||
|
format(post$mean_b, disgits=3), format(post$sd_b, digits=3),
|
||||||
|
paste("LWR estimates for species & Subfamily-BS"))
|
||||||
|
write.table(out.SpC, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
} else
|
||||||
|
#--------------------------------------------------
|
||||||
|
# assign Genus-BS priors to target species
|
||||||
|
if(LWRGenspec >= 5) {
|
||||||
|
cat("Assign Genus-BS prior for", TargetSpec, "\n")
|
||||||
|
out.SpC <- data.frame(Fam, SF, BS, SpC, LWR, format(prior.Gen.BS[[Genus]]$mean_log10a, digits=3),
|
||||||
|
format(prior.Gen.BS[[Genus]]$sd_log10a, digits=3),
|
||||||
|
format(prior.Gen.BS[[Genus]]$mean_b, digits=3), format(prior.Gen.BS[[Genus]]$sd_b, digits=3),
|
||||||
|
paste("LWR estimates for this Genus-BS"))
|
||||||
|
write.table(out.SpC, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
} else {
|
||||||
|
# -----------------------------------------------
|
||||||
|
# assign Subfamily-BS priors to target species
|
||||||
|
cat("Assign Subfamily-BS prior for", TargetSpec,"\n")
|
||||||
|
out.SpC <- data.frame(Fam, SF, BS, SpC, LWR, format(prior.SFam.BS$mean_log10a, digits=3), format(prior.SFam.BS$sd_log10a, digits=3),
|
||||||
|
format(prior.SFam.BS$mean_b, digits=3), format(prior.SFam.BS$sd_b, digits=3), paste("LWR estimates for this Subfamily-BS"))
|
||||||
|
write.table(out.SpC, file=OutFile, append = T, sep=",", dec=".", row.names=F, col.names=F)
|
||||||
|
}
|
||||||
|
} # end of species loop for this Subfamily and body shape
|
||||||
|
|
||||||
|
} # end of section dealing with Subfamily - body shapes that contain LWR estimates
|
||||||
|
|
||||||
|
} # end of section that deals with Subfamily - body shapes that contain species
|
||||||
|
|
||||||
|
} # end of body shape section
|
||||||
|
|
||||||
|
} # end of Subfamily section
|
||||||
|
|
||||||
|
} # end of Family section
|
||||||
|
cat("End", date(),"\n")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
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|
|
@ -0,0 +1,17 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||||
|
<jardesc>
|
||||||
|
<jar path="EcologicalEngineExecutor/AQUAMAPS_SUITABLE/aquamapsnode.jar"/>
|
||||||
|
<options buildIfNeeded="true" compress="true" descriptionLocation="/EcologicalEngineExecutor/aquamapsjarcreator.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
|
||||||
|
<storedRefactorings deprecationInfo="true" structuralOnly="false"/>
|
||||||
|
<selectedProjects/>
|
||||||
|
<manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
|
||||||
|
<sealing sealJar="false">
|
||||||
|
<packagesToSeal/>
|
||||||
|
<packagesToUnSeal/>
|
||||||
|
</sealing>
|
||||||
|
</manifest>
|
||||||
|
<selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
|
||||||
|
<javaElement handleIdentifier="=EcologicalEngineExecutor/src\/main\/java<org.gcube.dataanalysis.executor.generators"/>
|
||||||
|
<javaElement handleIdentifier="=EcologicalEngineExecutor/src\/main\/java<org.gcube.dataanalysis.executor.nodes.algorithms"/>
|
||||||
|
</selectedElements>
|
||||||
|
</jardesc>
|
||||||
|
|
@ -0,0 +1,32 @@
|
||||||
|
#### Use two appenders, one to log to console, another to log to a file
|
||||||
|
log4j.rootCategory= R
|
||||||
|
|
||||||
|
#### First appender writes to console
|
||||||
|
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
|
||||||
|
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
|
||||||
|
log4j.appender.stdout.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n
|
||||||
|
#log4j.appender.stdout.layout.ConversionPattern=%m%n
|
||||||
|
#log4j.appender.stdout.File=Analysis.log
|
||||||
|
|
||||||
|
#### Second appender writes to a file
|
||||||
|
log4j.logger.AnalysisLogger=trace,stdout, R
|
||||||
|
log4j.appender.R=org.apache.log4j.RollingFileAppender
|
||||||
|
#log4j.appender.R=org.apache.log4j.AsyncAppender
|
||||||
|
#log4j.appender.R.Threshold=INFO
|
||||||
|
log4j.appender.R.File=Analysis.log
|
||||||
|
log4j.appender.R.MaxFileSize=50000KB
|
||||||
|
log4j.appender.R.MaxBackupIndex=2
|
||||||
|
log4j.appender.R.layout=org.apache.log4j.PatternLayout
|
||||||
|
log4j.appender.R.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n
|
||||||
|
#log4j.appender.R.layout.ConversionPattern=%m%n
|
||||||
|
|
||||||
|
#### Third appender writes to a file
|
||||||
|
log4j.logger.org.hibernate=H
|
||||||
|
#log4j.appender.H=org.apache.log4j.RollingFileAppender
|
||||||
|
log4j.appender.H=org.apache.log4j.AsyncAppender
|
||||||
|
#log4j.appender.H.File=HibernateLog.log
|
||||||
|
#log4j.appender.H.MaxFileSize=1024KB
|
||||||
|
#log4j.appender.H.MaxBackupIndex=2
|
||||||
|
log4j.appender.H.layout=org.apache.log4j.PatternLayout
|
||||||
|
log4j.appender.H.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n
|
||||||
|
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
<?xml version='1.0' encoding='UTF-8'?>
|
||||||
|
<hibernate-configuration>
|
||||||
|
<session-factory>
|
||||||
|
<property name="connection.driver_class">org.postgresql.Driver</property>
|
||||||
|
<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
|
||||||
|
<property name="connection.url">jdbc:postgresql://localhost/testdb</property>
|
||||||
|
<property name="connection.username">gcube</property>
|
||||||
|
<property name="connection.password">d4science2</property>
|
||||||
|
<!-- <property name="dialect">org.hibernatespatial.postgis.PostgisDialect</property>-->
|
||||||
|
<property name="dialect">org.hibernate.dialect.PostgreSQLDialect</property>
|
||||||
|
<property name="transaction.factory_class">org.hibernate.transaction.JDBCTransactionFactory</property>
|
||||||
|
<property name="c3p0.timeout">0</property>
|
||||||
|
<property name="c3p0.max_size">10</property>
|
||||||
|
<property name="c3p0.max_statements">0</property>
|
||||||
|
<property name="c3p0.min_size">1</property>
|
||||||
|
<property name="current_session_context_class">thread</property>
|
||||||
|
</session-factory>
|
||||||
|
</hibernate-configuration>
|
||||||
|
|
@ -0,0 +1,9 @@
|
||||||
|
AQUAMAPS_SUITABLE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable
|
||||||
|
AQUAMAPS_NATIVE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative
|
||||||
|
AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative2050
|
||||||
|
AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable2050
|
||||||
|
AQUAMAPS_NATIVE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNN
|
||||||
|
AQUAMAPS_SUITABLE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNNSuitable
|
||||||
|
FEED_FORWARD_A_N_N_DISTRIBUTION=org.gcube.dataanalysis.ecoengine.spatialdistributions.FeedForwardNeuralNetworkDistribution
|
||||||
|
LWR=org.gcube.dataanalysis.executor.nodes.algorithms.LWR
|
||||||
|
CMSY=org.gcube.dataanalysis.executor.nodes.algorithms.CMSY
|
||||||
|
|
@ -0,0 +1,3 @@
|
||||||
|
DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan
|
||||||
|
KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans
|
||||||
|
XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper
|
||||||
|
|
@ -0,0 +1,3 @@
|
||||||
|
DISCREPANCY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis
|
||||||
|
QUALITY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DistributionQualityAnalysis
|
||||||
|
HRS=org.gcube.dataanalysis.ecoengine.evaluation.HabitatRepresentativeness
|
||||||
|
|
@ -0,0 +1,6 @@
|
||||||
|
LOCAL_WITH_DATABASE=org.gcube.dataanalysis.ecoengine.processing.LocalSplitGenerator
|
||||||
|
SIMPLE_LOCAL=org.gcube.dataanalysis.ecoengine.processing.LocalSimpleSplitGenerator
|
||||||
|
D4SCIENCE=org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing
|
||||||
|
#OCCURRENCES_MERGER=org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing
|
||||||
|
OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing
|
||||||
|
#OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing
|
||||||
|
|
@ -0,0 +1,439 @@
|
||||||
|
cat("Retrieving Input Parameters\n")
|
||||||
|
inputFile<-'tacsat.csv'
|
||||||
|
outputFile<-'tacsat_interpolated.csv'
|
||||||
|
|
||||||
|
require(data.table)
|
||||||
|
print(Sys.time())
|
||||||
|
|
||||||
|
memory.size(max = TRUE)
|
||||||
|
memory.limit(size = 4000)
|
||||||
|
|
||||||
|
interCubicHermiteSpline <- function(spltx,spltCon,res,params,headingAdjustment){
|
||||||
|
|
||||||
|
#Formula of Cubic Hermite Spline
|
||||||
|
t <- seq(0,1,length.out=res)
|
||||||
|
F00 <- 2*t^3 -3*t^2 + 1
|
||||||
|
F10 <- t^3-2*t^2+t
|
||||||
|
F01 <- -2*t^3+3*t^2
|
||||||
|
F11 <- t^3-t^2
|
||||||
|
|
||||||
|
#Making tacsat dataset ready
|
||||||
|
spltx[spltCon[,1],"SI_HE"][which(is.na(spltx[spltCon[,1],"SI_HE"]))] <- 0
|
||||||
|
spltx[spltCon[,2],"SI_HE"][which(is.na(spltx[spltCon[,2],"SI_HE"]))] <- 0
|
||||||
|
|
||||||
|
#Heading at begin point in degrees
|
||||||
|
Hx0 <- sin(spltx[spltCon[,1],"SI_HE"]/(180/pi))
|
||||||
|
Hy0 <- cos(spltx[spltCon[,1],"SI_HE"]/(180/pi))
|
||||||
|
|
||||||
|
#Heading at end point in degrees
|
||||||
|
Hx1 <- sin(spltx[spltCon[,2]-headingAdjustment,"SI_HE"]/(180/pi))
|
||||||
|
Hy1 <- cos(spltx[spltCon[,2]-headingAdjustment,"SI_HE"]/(180/pi))
|
||||||
|
|
||||||
|
#Start and end positions
|
||||||
|
Mx0 <- spltx[spltCon[,1],"SI_LONG"]
|
||||||
|
Mx1 <- spltx[spltCon[,2],"SI_LONG"]
|
||||||
|
My0 <- spltx[spltCon[,1],"SI_LATI"]
|
||||||
|
My1 <- spltx[spltCon[,2],"SI_LATI"]
|
||||||
|
|
||||||
|
#Corrected for longitude lattitude effect
|
||||||
|
Hx0 <- Hx0 * params$fm * spltx[spltCon[,1],"SI_SP"] /((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hx1 <- Hx1 * params$fm * spltx[spltCon[,2],"SI_SP"] /((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hy0 <- Hy0 * params$fm * lonLatRatio(spltx[spltCon[,1],"SI_LONG"],spltx[spltCon[,1],"SI_LATI"]) * spltx[spltCon[,1],"SI_SP"]/((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hy1 <- Hy1 * params$fm * lonLatRatio(spltx[spltCon[,2],"SI_LONG"],spltx[spltCon[,2],"SI_LATI"]) * spltx[spltCon[,2],"SI_SP"]/((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
|
||||||
|
#Get the interpolation
|
||||||
|
fx <- outer(F00,Mx0,"*")+outer(F10,Hx0,"*")+outer(F01,Mx1,"*")+outer(F11,Hx1,"*")
|
||||||
|
fy <- outer(F00,My0,"*")+outer(F10,Hy0,"*")+outer(F01,My1,"*")+outer(F11,Hy1,"*")
|
||||||
|
|
||||||
|
#Create output format
|
||||||
|
intsx <- lapply(as.list(1:nrow(spltCon)),function(x){
|
||||||
|
matrix(rbind(spltx$ID[spltCon[x,]],cbind(fx[,x],fy[,x])),ncol=2,
|
||||||
|
dimnames=list(c("startendVMS",seq(1,res,1)),c("x","y")))})
|
||||||
|
return(intsx)}
|
||||||
|
|
||||||
|
rbindTacsat <- function(set1,set2){
|
||||||
|
cln1 <- colnames(set1)
|
||||||
|
cln2 <- colnames(set2)
|
||||||
|
if(any(duplicated(cln1)==TRUE) || any(duplicated(cln2)==TRUE)) stop("Duplicate column names in datasets")
|
||||||
|
idx1 <- which(is.na(pmatch(cln1,cln2))==TRUE)
|
||||||
|
idx2 <- which(is.na(pmatch(cln2,cln1))==TRUE)
|
||||||
|
|
||||||
|
if(length(idx1)>0){
|
||||||
|
for(i in idx1) set2 <- cbind(set2,NA)
|
||||||
|
colnames(set2) <- c(cln2,cln1[idx1])}
|
||||||
|
if(length(idx2)>0){
|
||||||
|
for(i in idx2) set1 <- cbind(set1,NA)
|
||||||
|
colnames(set1) <- c(cln1,cln2[idx2])}
|
||||||
|
cln1 <- colnames(set1)
|
||||||
|
cln2 <- colnames(set2)
|
||||||
|
mtch <- pmatch(cln1,cln2)
|
||||||
|
if(any(is.na(mtch))==TRUE) stop("Cannot find nor create all matching column names")
|
||||||
|
set3 <- rbind(set1,set2[,cln2[mtch]])
|
||||||
|
return(set3)}
|
||||||
|
|
||||||
|
bearing <- function(lon,lat,lonRef,latRef){
|
||||||
|
|
||||||
|
x1 <- lon
|
||||||
|
y1 <- lat
|
||||||
|
x2 <- lonRef
|
||||||
|
y2 <- latRef
|
||||||
|
|
||||||
|
y <- sin((x2-x1)*pi/180) * cos(y2*pi/180)
|
||||||
|
x <- cos(y1*pi/180) * sin(y2*pi/180) - sin(y1*pi/180) * cos(y2*pi/180) * cos((x2-x1)*pi/180)
|
||||||
|
bearing <- atan2(y,x)*180/pi
|
||||||
|
bearing <- (bearing + 360)%%360
|
||||||
|
return(bearing)}
|
||||||
|
|
||||||
|
`distance` <-
|
||||||
|
function(lon,lat,lonRef,latRef){
|
||||||
|
|
||||||
|
pd <- pi/180
|
||||||
|
|
||||||
|
a1<- sin(((latRef-lat)*pd)/2)
|
||||||
|
a2<- cos(lat*pd)
|
||||||
|
a3<- cos(latRef*pd)
|
||||||
|
a4<- sin(((lonRef-lon)*pd)/2)
|
||||||
|
a <- a1*a1+a2*a3*a4*a4
|
||||||
|
|
||||||
|
c <- 2*atan2(sqrt(a),sqrt(1-a));
|
||||||
|
return(6371*c)}
|
||||||
|
|
||||||
|
distanceInterpolation <- function(interpolation){
|
||||||
|
|
||||||
|
res <- unlist(lapply(interpolation,function(x){
|
||||||
|
dims <- dim(x)
|
||||||
|
res <- distance(x[3:dims[1],1],x[3:dims[1],2],x[2:(dims[1]-1),1],x[2:(dims[1]-1),2])
|
||||||
|
return(sum(res,na.rm=TRUE))}))
|
||||||
|
|
||||||
|
return(res)}
|
||||||
|
|
||||||
|
|
||||||
|
equalDistance <- function(interpolation,res=10){
|
||||||
|
|
||||||
|
#Calculate ditance of all interpolations at the same time
|
||||||
|
totDist <- distanceInterpolation(interpolation)
|
||||||
|
#Get dimensions of interpolations
|
||||||
|
lngInt <- lapply(interpolation,dim)
|
||||||
|
|
||||||
|
#Warn if resolution of equal distance is too high compared to original resolution of interpolation
|
||||||
|
if(min(unlist(lngInt)[seq(1,length(totDist),2)],na.rm=TRUE) < 9*res) warnings("Number of intermediate points in the interpolation might be too small for the equal distance pionts chosen")
|
||||||
|
|
||||||
|
#Get distance steps to get equal distance
|
||||||
|
eqStep <- totDist/(res-1)
|
||||||
|
|
||||||
|
#Get x-y values of all interpolations
|
||||||
|
intidx <- matrix(unlist(lapply(interpolation,function(x){return(x[1,])})),ncol=2,byrow=TRUE)
|
||||||
|
|
||||||
|
#Do the calculation
|
||||||
|
result <- lapply(interpolation,function(ind){
|
||||||
|
i <- which(intidx[,1] == ind[1,1] & intidx[,2] == ind[1,2])
|
||||||
|
idx <- apply(abs(outer(
|
||||||
|
cumsum(distance(ind[3:lngInt[[i]][1],1],ind[3:lngInt[[i]][1],2],ind[2:(lngInt[[i]][1]-1),1],ind[2:(lngInt[[i]][1]-1),2])),
|
||||||
|
seq(eqStep[i],totDist[i],eqStep[i]),
|
||||||
|
"-")),
|
||||||
|
2,which.min)+1
|
||||||
|
idx <- c(1,idx)
|
||||||
|
return(ind[c(1,idx+1),])})
|
||||||
|
#Return the equal distance interpolated set in the same format as the interpolated dataset (as a list)
|
||||||
|
return(result)}
|
||||||
|
|
||||||
|
interStraightLine <- function(spltx,spltCon,res){
|
||||||
|
|
||||||
|
fx <- mapply(seq,spltx[spltCon[,1],"SI_LONG"],spltx[spltCon[,2],"SI_LONG"],length.out=res)
|
||||||
|
fy <- mapply(seq,spltx[spltCon[,1],"SI_LATI"],spltx[spltCon[,2],"SI_LATI"],length.out=res)
|
||||||
|
|
||||||
|
#Create output format
|
||||||
|
intsx <- lapply(as.list(1:nrow(spltCon)),function(x){
|
||||||
|
matrix(rbind(spltx$ID[spltCon[x,]],cbind(fx[,x],fy[,x])),ncol=2,
|
||||||
|
dimnames=list(c("startendVMS",seq(1,res,1)),c("x","y")))})
|
||||||
|
return(intsx)}
|
||||||
|
|
||||||
|
interpolation2Tacsat <- function(interpolation,tacsat,npoints=10,equalDist=TRUE){
|
||||||
|
|
||||||
|
# This function takes the list of tracks output by interpolateTacsat and converts them back to tacsat format.
|
||||||
|
# The npoints argument is the optional number of points between each 'real' position.
|
||||||
|
tacsat <- sortTacsat(tacsat)
|
||||||
|
if(!"HL_ID" %in% colnames(tacsat)) tacsat$HL_ID <- 1:nrow(tacsat)
|
||||||
|
if(!"SI_DATIM" %in% colnames(tacsat)) tacsat$SI_DATIM <- as.POSIXct(paste(tacsat$SI_DATE, tacsat$SI_TIME, sep=" "), tz="GMT", format="%d/%m/%Y %H:%M")
|
||||||
|
if(equalDist){
|
||||||
|
interpolationEQ <- equalDistance(interpolation,npoints) #Divide points equally along interpolated track (default is 10).
|
||||||
|
} else {
|
||||||
|
interpolationEQ <- lapply(interpolation,function(x){idx <- round(seq(2,nrow(x),length.out=npoints)); return(x[c(1,idx),])})
|
||||||
|
}
|
||||||
|
res <- lapply(interpolationEQ,function(x){
|
||||||
|
idx <- unlist(x[1,1:2]@.Data); x <- data.frame(x)
|
||||||
|
colnames(x) <- c("SI_LONG","SI_LATI")
|
||||||
|
cls <- which(apply(tacsat[c(idx),],2,function(y){return(length(unique(y)))})==1)
|
||||||
|
for(i in cls){
|
||||||
|
x <- cbind(x,rep(tacsat[idx[1],i],nrow(x)));
|
||||||
|
colnames(x) <- c(colnames(x)[1:(ncol(x)-1)],colnames(tacsat)[i])
|
||||||
|
}
|
||||||
|
if(!"VE_COU" %in% colnames(x)) x$VE_COU <- rep(tacsat$VE_COU[idx[1]],nrow(x))
|
||||||
|
if(!"VE_REF" %in% colnames(x)) x$VE_REF <- rep(tacsat$VE_REF[idx[1]],nrow(x))
|
||||||
|
if(!"FT_REF" %in% colnames(x)) x$FT_REF <- rep(tacsat$FT_REF[idx[1]],nrow(x))
|
||||||
|
x$SI_DATIM <- tacsat$SI_DATIM[idx[1]]
|
||||||
|
x$SI_DATIM[-c(1:2)] <- as.POSIXct(cumsum(rep(difftime(tacsat$SI_DATIM[idx[2]],tacsat$SI_DATIM[idx[1]],units="secs")/(nrow(x)-2),nrow(x)-2))+tacsat$SI_DATIM[idx[1]],tz="GMT",format = "%d/%m/%Y %H:%M")
|
||||||
|
x$SI_DATE <- format(x$SI_DATIM,format="%d/%m/%Y")
|
||||||
|
timeNotation <- ifelse(length(unlist(strsplit(tacsat$SI_TIME[1],":")))>2,"secs","mins")
|
||||||
|
if(timeNotation == "secs") x$SI_TIME <- format(x$SI_DATIM,format="%H:%M:%S")
|
||||||
|
if(timeNotation == "mins") x$SI_TIME <- format(x$SI_DATIM,format="%H:%M")
|
||||||
|
x$SI_SP <- mean(c(tacsat$SI_SP[idx[1]],tacsat$SI_SP[idx[2]]),na.rm=TRUE)
|
||||||
|
x$SI_HE <- NA;
|
||||||
|
x$SI_HE[-c(1,nrow(x))] <- bearing(x$SI_LONG[2:(nrow(x)-1)],x$SI_LATI[2:(nrow(x)-1)],x$SI_LONG[3:nrow(x)],x$SI_LATI[3:nrow(x)])
|
||||||
|
x$HL_ID <- tacsat$HL_ID[idx[1]]
|
||||||
|
return(x[-c(1,2,nrow(x)),])})
|
||||||
|
|
||||||
|
#interpolationTot <- do.call(rbind,res)
|
||||||
|
interpolationTot <- res[[1]][,which(duplicated(colnames(res[[1]]))==FALSE)]
|
||||||
|
if(length(res)>1){
|
||||||
|
for(i in 2:length(res)){
|
||||||
|
if(nrow(res[[i]])>0)
|
||||||
|
interpolationTot <- rbindTacsat(interpolationTot,res[[i]][,which(duplicated(colnames(res[[i]]))==FALSE)])
|
||||||
|
}
|
||||||
|
}
|
||||||
|
#tacsatInt <- rbind(interpolationTot,tacsat[,colnames(interpolationTot)])
|
||||||
|
tacsatInt <- rbindTacsat(tacsat,interpolationTot)
|
||||||
|
tacsatInt <- sortTacsat(tacsatInt)
|
||||||
|
|
||||||
|
return(tacsatInt)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
`sortTacsat` <-
|
||||||
|
function(dat){
|
||||||
|
require(doBy)
|
||||||
|
|
||||||
|
if(!"SI_DATIM" %in% colnames(dat)) dat$SI_DATIM <- as.POSIXct(paste(dat$SI_DATE, dat$SI_TIME, sep=" "), tz="GMT", format="%d/%m/%Y %H:%M")
|
||||||
|
|
||||||
|
#Sort the tacsat data first by ship, then by date
|
||||||
|
if("VE_REF" %in% colnames(dat)) dat <- orderBy(~VE_REF+SI_DATIM,data=dat)
|
||||||
|
if("OB_REF" %in% colnames(dat)) dat <- orderBy(~OB_REF+SI_DATIM,data=dat)
|
||||||
|
|
||||||
|
return(dat)}
|
||||||
|
|
||||||
|
`lonLatRatio` <-
|
||||||
|
function(x1,lat){
|
||||||
|
#Based on the Haversine formula
|
||||||
|
#At the position, the y-position remains the same, hence, cos(lat)*cos(lat) instead of cos(lat) * cos(y2)
|
||||||
|
a <- cos(lat*pi/180)*cos(lat*pi/180)*sin((0.1*pi/180)/2)*sin((0.1*pi/180)/2);
|
||||||
|
c <- 2*atan2(sqrt(a),sqrt(1-a));
|
||||||
|
R <- 6371;
|
||||||
|
dx1 <- R*c
|
||||||
|
|
||||||
|
return(c(dx1/11.12))}
|
||||||
|
|
||||||
|
|
||||||
|
`an` <-
|
||||||
|
function(x){return(as.numeric(x))}
|
||||||
|
|
||||||
|
|
||||||
|
`findEndTacsat` <-
|
||||||
|
function(tacsat
|
||||||
|
,startTacsat #Starting point of VMS
|
||||||
|
,interval #Specify in minutes, NULL means use all points
|
||||||
|
,margin #Specify the margin in minutes it might deviate from the interval time, in minutes
|
||||||
|
){
|
||||||
|
VMS <- tacsat
|
||||||
|
if(!"SI_DATIM" %in% colnames(VMS)) VMS$SI_DATIM <- as.POSIXct(paste(tacsat$SI_DATE, tacsat$SI_TIME, sep=" "), tz="GMT", format="%d/%m/%Y %H:%M")
|
||||||
|
|
||||||
|
startVMS <- startTacsat
|
||||||
|
clStartVMS <- startVMS #Total VMS list starting point instead of subset use
|
||||||
|
iShip <- VMS$VE_REF[startVMS]
|
||||||
|
VMS. <- subset(VMS,VE_REF==iShip)
|
||||||
|
startVMS <- which(VMS$VE_REF[startVMS] == VMS.$VE_REF & VMS$SI_DATIM[startVMS] == VMS.$SI_DATIM)
|
||||||
|
if(clStartVMS != dim(VMS)[1]){
|
||||||
|
if(VMS$VE_REF[clStartVMS] != VMS$VE_REF[clStartVMS+1]){
|
||||||
|
#End of dataset reached
|
||||||
|
endDataSet <- 1
|
||||||
|
endVMS <- NA
|
||||||
|
} else {
|
||||||
|
#Calculate the difference in time between the starting VMS point and its succeeding points
|
||||||
|
diffTime <- difftime(VMS.$SI_DATIM[(startVMS+1):dim(VMS.)[1]],VMS.$SI_DATIM[startVMS],units=c("mins"))
|
||||||
|
if(length(which(diffTime >= (interval-margin) & diffTime <= (interval+margin)))==0){
|
||||||
|
warning("No succeeding point found, no interpolation possible")
|
||||||
|
endVMS <- NA
|
||||||
|
#Check if end of dataset has been reached
|
||||||
|
ifelse(all((diffTime < (interval-margin))==TRUE),endDataSet <- 1,endDataSet <- 0)
|
||||||
|
} else {
|
||||||
|
res <- which(diffTime >= (interval-margin) & diffTime <= (interval+margin))
|
||||||
|
if(length(res)>1){
|
||||||
|
res2 <- which.min(abs(interval-an(diffTime[res])))
|
||||||
|
endVMS <- startVMS + res[res2]
|
||||||
|
endDataSet <- 0
|
||||||
|
} else {
|
||||||
|
endVMS <- startVMS + res
|
||||||
|
endDataSet <- 0
|
||||||
|
}
|
||||||
|
}
|
||||||
|
#Build-in check
|
||||||
|
if(is.na(endVMS)==FALSE){
|
||||||
|
if(!an(difftime(VMS.$SI_DATIM[endVMS],VMS.$SI_DATIM[startVMS],units=c("mins"))) %in% seq((interval-margin),(interval+margin),1)) stop("found endVMS point not within interval range")
|
||||||
|
endVMS <- clStartVMS + (endVMS - startVMS)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
} else { endDataSet <- 1; endVMS <- NA}
|
||||||
|
|
||||||
|
return(c(endVMS,endDataSet))}
|
||||||
|
|
||||||
|
`interpolateTacsat` <-
|
||||||
|
function(tacsat #VMS datapoints
|
||||||
|
,interval=120 #Specify in minutes, NULL means use all points
|
||||||
|
,margin=12 #Specify the margin in minutes that the interval might deviate in a search for the next point
|
||||||
|
,res=100 #Resolution of interpolation method (default = 100)
|
||||||
|
,method="cHs" #Specify the method to be used: Straight line (SL) of cubic Hermite spline (cHs)
|
||||||
|
,params=list(fm=0.5,distscale=20,sigline=0.2,st=c(2,6)) #Specify the three parameters: fm, distscale, sigline, speedthreshold
|
||||||
|
,headingAdjustment=0
|
||||||
|
,fast=FALSE){
|
||||||
|
|
||||||
|
if(!"SI_DATIM" %in% colnames(tacsat)) tacsat$SI_DATIM <- as.POSIXct(paste(tacsat$SI_DATE, tacsat$SI_TIME, sep=" "), tz="GMT", format="%d/%m/%Y %H:%M")
|
||||||
|
|
||||||
|
#Start interpolating the data
|
||||||
|
if(!method %in% c("cHs","SL")) stop("method selected that does not exist")
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
#Fast method or not
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
if(fast){
|
||||||
|
#Interpolation only by vessel, so split tacsat up
|
||||||
|
tacsat$ID <- 1:nrow(tacsat)
|
||||||
|
splitTa <- split(tacsat,tacsat$VE_REF)
|
||||||
|
spltTaCon <- lapply(splitTa,function(spltx){
|
||||||
|
#Calculate time different between every record
|
||||||
|
dftimex <- outer(spltx$SI_DATIM,spltx$SI_DATIM,difftime,units="mins")
|
||||||
|
iStep <- 1
|
||||||
|
connect <- list()
|
||||||
|
counter <- 1
|
||||||
|
#Loop over all possible combinations and store if a connection can be made
|
||||||
|
while(iStep <= nrow(spltx)){
|
||||||
|
endp <- which(dftimex[,iStep] >= (interval - margin) & dftimex[,iStep] <= (interval + margin))
|
||||||
|
if(length(endp)>0){
|
||||||
|
if(length(endp)>1) endp <- endp[which.min(abs(interval - dftimex[endp,iStep]))][1]
|
||||||
|
connect[[counter]] <- c(iStep,endp)
|
||||||
|
counter <- counter + 1
|
||||||
|
iStep <- endp
|
||||||
|
} else { iStep <- iStep + 1}
|
||||||
|
}
|
||||||
|
#Return matrix of conenctions
|
||||||
|
return(do.call(rbind,connect))})
|
||||||
|
|
||||||
|
if(method=="cHs") returnInterpolations <- unlist(lapply(as.list(names(unlist(lapply(spltTaCon,nrow)))),function(y){
|
||||||
|
return(interCubicHermiteSpline(spltx=splitTa[[y]],spltCon=spltTaCon[[y]],res,params,headingAdjustment))}),recursive=FALSE)
|
||||||
|
if(method=="SL") returnInterpolations <- unlist(lapply(as.list(names(unlist(lapply(spltTaCon,nrow)))),function(y){
|
||||||
|
return(interStraightLine(splitTa[[y]],spltTaCon[[y]],res))}),recursive=FALSE)
|
||||||
|
|
||||||
|
} else {
|
||||||
|
|
||||||
|
|
||||||
|
#Initiate returning result object
|
||||||
|
returnInterpolations <- list()
|
||||||
|
|
||||||
|
#Start iterating over succeeding points
|
||||||
|
for(iStep in 1:(dim(tacsat)[1]-1)){
|
||||||
|
if(iStep == 1){
|
||||||
|
iSuccess <- 0
|
||||||
|
endDataSet <- 0
|
||||||
|
startVMS <- 1
|
||||||
|
ship <- tacsat$VE_REF[startVMS]
|
||||||
|
} else {
|
||||||
|
if(is.na(endVMS)==TRUE) endVMS <- startVMS + 1
|
||||||
|
startVMS <- endVMS
|
||||||
|
#-Check if the end of the dataset is reached
|
||||||
|
if(endDataSet == 1 & rev(unique(tacsat$VE_REF))[1] != ship){
|
||||||
|
startVMS <- which(tacsat$VE_REF == unique(tacsat$VE_REF)[which(unique(tacsat$VE_REF)==ship)+1])[1]
|
||||||
|
ship <- tacsat$VE_REF[startVMS]
|
||||||
|
endDataSet<- 0
|
||||||
|
}
|
||||||
|
if(endDataSet == 1 & rev(unique(tacsat$VE_REF))[1] == ship) endDataSet <- 2 #Final end of dataset
|
||||||
|
}
|
||||||
|
|
||||||
|
#if end of dataset is not reached, try to find succeeding point
|
||||||
|
if(endDataSet != 2){
|
||||||
|
result <- findEndTacsat(tacsat,startVMS,interval,margin)
|
||||||
|
endVMS <- result[1]
|
||||||
|
endDataSet <- result[2]
|
||||||
|
if(is.na(endVMS)==TRUE) int <- 0 #No interpolation possible
|
||||||
|
if(is.na(endVMS)==FALSE) int <- 1 #Interpolation possible
|
||||||
|
|
||||||
|
#Interpolate according to the Cubic Hermite Spline method
|
||||||
|
if(method == "cHs" & int == 1){
|
||||||
|
|
||||||
|
#Define the cHs formula
|
||||||
|
F00 <- numeric()
|
||||||
|
F10 <- numeric()
|
||||||
|
F01 <- numeric()
|
||||||
|
F11 <- numeric()
|
||||||
|
i <- 0
|
||||||
|
t <- seq(0,1,length.out=res)
|
||||||
|
F00 <- 2*t^3 -3*t^2 + 1
|
||||||
|
F10 <- t^3-2*t^2+t
|
||||||
|
F01 <- -2*t^3+3*t^2
|
||||||
|
F11 <- t^3-t^2
|
||||||
|
|
||||||
|
if (is.na(tacsat[startVMS,"SI_HE"])=="TRUE") tacsat[startVMS,"SI_HE"] <- 0
|
||||||
|
if (is.na(tacsat[endVMS, "SI_HE"])=="TRUE") tacsat[endVMS, "SI_HE"] <- 0
|
||||||
|
|
||||||
|
#Heading at begin point in degrees
|
||||||
|
Hx0 <- sin(tacsat[startVMS,"SI_HE"]/(180/pi))
|
||||||
|
Hy0 <- cos(tacsat[startVMS,"SI_HE"]/(180/pi))
|
||||||
|
#Heading at end point in degrees
|
||||||
|
Hx1 <- sin(tacsat[endVMS-headingAdjustment,"SI_HE"]/(180/pi))
|
||||||
|
Hy1 <- cos(tacsat[endVMS-headingAdjustment,"SI_HE"]/(180/pi))
|
||||||
|
|
||||||
|
Mx0 <- tacsat[startVMS, "SI_LONG"]
|
||||||
|
Mx1 <- tacsat[endVMS, "SI_LONG"]
|
||||||
|
My0 <- tacsat[startVMS, "SI_LATI"]
|
||||||
|
My1 <- tacsat[endVMS, "SI_LATI"]
|
||||||
|
|
||||||
|
#Corrected for longitude lattitude effect
|
||||||
|
Hx0 <- Hx0 * params$fm * tacsat[startVMS,"SI_SP"] /((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hx1 <- Hx1 * params$fm * tacsat[endVMS,"SI_SP"] /((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hy0 <- Hy0 * params$fm * lonLatRatio(tacsat[c(startVMS,endVMS),"SI_LONG"],tacsat[c(startVMS,endVMS),"SI_LATI"])[1] * tacsat[startVMS,"SI_SP"]/((params$st[2]-params$st[1])/2+params$st[1])
|
||||||
|
Hy1 <- Hy1 * params$fm * lonLatRatio(tacsat[c(startVMS,endVMS),"SI_LONG"],tacsat[c(startVMS,endVMS),"SI_LATI"])[2] * tacsat[endVMS,"SI_SP"]/((params$st[2]-params$st[1]) /2+params$st[1])
|
||||||
|
|
||||||
|
#Finalizing the interpolation based on cHs
|
||||||
|
fx <- numeric()
|
||||||
|
fy <- numeric()
|
||||||
|
fx <- F00*Mx0+F10*Hx0+F01*Mx1+F11*Hx1
|
||||||
|
fy <- F00*My0+F10*Hy0+F01*My1+F11*Hy1
|
||||||
|
|
||||||
|
#Add one to list of successful interpolations
|
||||||
|
iSuccess <- iSuccess + 1
|
||||||
|
returnInterpolations[[iSuccess]] <- matrix(rbind(c(startVMS,endVMS),cbind(fx,fy)),ncol=2,dimnames=list(c("startendVMS",seq(1,res,1)),c("x","y")))
|
||||||
|
}
|
||||||
|
|
||||||
|
#Interpolate according to a straight line
|
||||||
|
if(method == "SL" & int == 1){
|
||||||
|
fx <- seq(tacsat$SI_LONG[startVMS],tacsat$SI_LONG[endVMS],length.out=res)
|
||||||
|
fy <- seq(tacsat$SI_LATI[startVMS],tacsat$SI_LATI[endVMS],length.out=res)
|
||||||
|
|
||||||
|
#Add one to list of successful interpolations
|
||||||
|
iSuccess <- iSuccess + 1
|
||||||
|
returnInterpolations[[iSuccess]] <- matrix(rbind(c(startVMS,endVMS),cbind(fx,fy)),ncol=2,dimnames=list(c("startendVMS",seq(1,res,1)),c("x","y")))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return(returnInterpolations)}
|
||||||
|
|
||||||
|
|
||||||
|
cat("Loading Table\n")
|
||||||
|
tacsatX <-read.table(inputFile,sep=",",header=T)
|
||||||
|
cat("Adjusting Columns Types\n")
|
||||||
|
tacsatX<-transform(tacsatX, VE_COU= as.character(VE_COU), VE_REF= as.character(VE_REF), SI_LATI= as.numeric(SI_LATI), SI_LONG= as.numeric(SI_LONG), SI_DATE= as.character(SI_DATE),SI_TIME= as.character(SI_TIME),SI_SP= as.numeric(SI_SP),SI_HE= as.numeric(SI_HE))
|
||||||
|
tacsatX$SI_DATIM=NULL
|
||||||
|
cat("Sorting dataset\n")
|
||||||
|
tacsatS <- sortTacsat(tacsatX)
|
||||||
|
tacsatCut<-tacsatS
|
||||||
|
tacsatCut <- tacsatS[1:1000,]
|
||||||
|
|
||||||
|
cat("Interpolating\n")
|
||||||
|
interpolation <- interpolateTacsat(tacsatCut,interval=interval,margin=margin,res=res, method=method,params=list(fm=fm,distscale=distscale,sigline=sigline,st=st),headingAdjustment=headingAdjustment,fast=fast)
|
||||||
|
cat("Reconstructing Dataset\n")
|
||||||
|
tacsatInt <- interpolation2Tacsat(interpolation=interpolation,tacsat=tacsatCut,npoints=npoints,equalDist=equalDist)
|
||||||
|
tacsatInt <- sortTacsat(tacsatInt)
|
||||||
|
cat("Writing output file\n")
|
||||||
|
write.csv(tacsatInt, outputFile, row.names=T)
|
||||||
|
print(Sys.time())
|
||||||
|
cat("All Done.\n")
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler
|
||||||
|
|
@ -0,0 +1,4 @@
|
||||||
|
HSPEN=org.gcube.dataanalysis.ecoengine.models.ModelHSPEN
|
||||||
|
AQUAMAPSNN=org.gcube.dataanalysis.ecoengine.models.ModelAquamapsNN
|
||||||
|
FEED_FORWARD_ANN=org.gcube.dataanalysis.ecoengine.models.FeedForwardNN
|
||||||
|
FEED_FORWARD_ANN_FILE=org.gcube.dataanalysis.ecoengine.models.testing.FeedForwardNNFile
|
||||||
|
|
@ -0,0 +1,11 @@
|
||||||
|
AQUAMAPS_SUITABLE=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode
|
||||||
|
AQUAMAPS_NATIVE=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode
|
||||||
|
AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNative2050Node
|
||||||
|
AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitable2050Node
|
||||||
|
OCCURRENCES_MERGER=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode
|
||||||
|
OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceIntersectionNode
|
||||||
|
OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceSubtractionNode
|
||||||
|
LWR=org.gcube.dataanalysis.executor.nodes.algorithms.LWR
|
||||||
|
BIONYM=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer
|
||||||
|
BIONYM_BIODIV=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv
|
||||||
|
CMSY=org.gcube.dataanalysis.executor.nodes.algorithms.CMSY
|
||||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,16 @@
|
||||||
|
BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTransducer
|
||||||
|
BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer
|
||||||
|
BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer
|
||||||
|
HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer
|
||||||
|
HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter
|
||||||
|
HSPEN_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HspenFilter
|
||||||
|
ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution
|
||||||
|
PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints
|
||||||
|
OCCURRENCES_MERGER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger
|
||||||
|
OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsIntersector
|
||||||
|
OCCURRENCES_MARINE_TERRESTRIAL=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth
|
||||||
|
OCCURRENCES_DUPLICATES_DELETER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsDuplicatesDeleter
|
||||||
|
OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsSubtraction
|
||||||
|
BIONYM=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymTransducer
|
||||||
|
BIONYM_LOCAL=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer
|
||||||
|
SGVM_INTERPOLATION=org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation
|
||||||
|
|
@ -0,0 +1,13 @@
|
||||||
|
ANOMALIES_DETECTION=DBSCAN,KMEANS,XMEANS
|
||||||
|
CLASSIFICATION=FEED_FORWARD_A_N_N_DISTRIBUTION
|
||||||
|
CLIMATE=BIOCLIMATE_HSPEC,BIOCLIMATE_HCAF,BIOCLIMATE_HSPEN,HCAF_INTERPOLATION
|
||||||
|
CORRELATION_ANALYSIS=HRS
|
||||||
|
DATA_CLUSTERING=DBSCAN,KMEANS,XMEANS
|
||||||
|
FILTERING=HCAF_FILTER,HSPEN_FILTER
|
||||||
|
FUNCTION_SIMULATION=FEED_FORWARD_A_N_N_DISTRIBUTION
|
||||||
|
OCCURRENCES=ABSENCE_CELLS_FROM_AQUAMAPS,PRESENCE_CELLS_GENERATION,OCCURRENCES_MERGER,OCCURRENCES_INTERSECTOR,OCCURRENCES_MARINE_TERRESTRIAL,OCCURRENCES_DUPLICATES_DELETER,OCCURRENCES_SUBTRACTION
|
||||||
|
PERFORMANCES_EVALUATION=QUALITY_ANALYSIS,DISCREPANCY_ANALYSIS
|
||||||
|
SPECIES_SIMULATION=AQUAMAPS_SUITABLE,AQUAMAPS_NATIVE,AQUAMAPS_NATIVE_2050,AQUAMAPS_SUITABLE_2050,AQUAMAPS_NATIVE_NEURALNETWORK,AQUAMAPS_SUITABLE_NEURALNETWORK
|
||||||
|
TRAINING=HSPEN,AQUAMAPSNN,FEED_FORWARD_ANN
|
||||||
|
TIME_SERIES=HCAF_INTERPOLATION
|
||||||
|
VESSELS=SGVM_INTERPOLATION
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
|
||||||
|
<jardesc>
|
||||||
|
<jar path="ExecutorScriptFile/org.gcube.dataanalysis.executor.executorscriptplugin.jar"/>
|
||||||
|
<options buildIfNeeded="true" compress="true" descriptionLocation="/ExecutorScriptFile/createscript.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
|
||||||
|
<storedRefactorings deprecationInfo="true" structuralOnly="false"/>
|
||||||
|
<selectedProjects/>
|
||||||
|
<manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
|
||||||
|
<sealing sealJar="false">
|
||||||
|
<packagesToSeal/>
|
||||||
|
<packagesToUnSeal/>
|
||||||
|
</sealing>
|
||||||
|
</manifest>
|
||||||
|
<selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
|
||||||
|
<javaElement handleIdentifier="=ExecutorScriptFile/src<org.gcube.dataanalysis.executor.plugin.dummy"/>
|
||||||
|
<javaElement handleIdentifier="=ExecutorScriptFile/src<org.gcube.dataanalysis.executor.scripts"/>
|
||||||
|
<javaElement handleIdentifier="=ExecutorScriptFile/src<org.gcube.dataanalysis.executor.plugin"/>
|
||||||
|
</selectedElements>
|
||||||
|
</jardesc>
|
||||||
|
|
@ -0,0 +1,16 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||||
|
<jardesc>
|
||||||
|
<jar path="C:/Users/coro/Desktop/EcologicalEngineExecutor-1.4.0-SNAPSHOT.jar"/>
|
||||||
|
<options buildIfNeeded="true" compress="true" descriptionLocation="/EcologicalEngineExecutor/deployDesktop.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
|
||||||
|
<storedRefactorings deprecationInfo="true" structuralOnly="false"/>
|
||||||
|
<selectedProjects/>
|
||||||
|
<manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
|
||||||
|
<sealing sealJar="false">
|
||||||
|
<packagesToSeal/>
|
||||||
|
<packagesToUnSeal/>
|
||||||
|
</sealing>
|
||||||
|
</manifest>
|
||||||
|
<selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
|
||||||
|
<javaElement handleIdentifier="=EcologicalEngineExecutor/src\/main\/java"/>
|
||||||
|
</selectedElements>
|
||||||
|
</jardesc>
|
||||||
|
|
@ -0,0 +1,16 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||||
|
<jardesc>
|
||||||
|
<jar path="EcologicalEngineExecutor/PARALLEL_PROCESSING/EcologicalEngineExecutor-1.2.0-SNAPSHOT.jar"/>
|
||||||
|
<options buildIfNeeded="true" compress="true" descriptionLocation="/EcologicalEngineExecutor/deployParallelProcessing.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
|
||||||
|
<storedRefactorings deprecationInfo="true" structuralOnly="false"/>
|
||||||
|
<selectedProjects/>
|
||||||
|
<manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
|
||||||
|
<sealing sealJar="false">
|
||||||
|
<packagesToSeal/>
|
||||||
|
<packagesToUnSeal/>
|
||||||
|
</sealing>
|
||||||
|
</manifest>
|
||||||
|
<selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
|
||||||
|
<javaElement handleIdentifier="=EcologicalEngineExecutor/src\/main\/java"/>
|
||||||
|
</selectedElements>
|
||||||
|
</jardesc>
|
||||||
|
|
@ -0,0 +1,2 @@
|
||||||
|
v. 1.0.0 (20-04-2011)
|
||||||
|
* First release
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
Used as a library in the gCube Framework
|
||||||
|
|
@ -0,0 +1,8 @@
|
||||||
|
gCube System - License
|
||||||
|
------------------------------------------------------------
|
||||||
|
|
||||||
|
The gCube/gCore software is licensed as Free Open Source software conveying to
|
||||||
|
the EUPL (http://ec.europa.eu/idabc/eupl).
|
||||||
|
The software and documentation is provided by its authors/distributors "as is"
|
||||||
|
and no expressed or implied warranty is given for its use, quality or fitness
|
||||||
|
for a particular case.
|
||||||
|
|
@ -0,0 +1,2 @@
|
||||||
|
Gianpaolo Coro (gianpaolo.coro@isti.cnr.it), CNR Pisa,
|
||||||
|
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo"
|
||||||
|
|
@ -0,0 +1,42 @@
|
||||||
|
The gCube System - Ecological Engine Library
|
||||||
|
------------------------------------------------------------
|
||||||
|
|
||||||
|
This work is partially funded by the European Commission in the
|
||||||
|
context of the D4Science project (www.d4science.eu), under the
|
||||||
|
1st call of FP7 IST priority.
|
||||||
|
|
||||||
|
Authors
|
||||||
|
-------
|
||||||
|
|
||||||
|
* Gianpaolo Coro (gianpaolo.coro@isti.cnr.it), CNR Pisa,
|
||||||
|
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo"
|
||||||
|
|
||||||
|
Version and Release Date
|
||||||
|
------------------------
|
||||||
|
|
||||||
|
version 1.0.0 (22-06-2012)
|
||||||
|
|
||||||
|
Description
|
||||||
|
--------------------
|
||||||
|
|
||||||
|
Support library for statistics analysis on Time Series data.
|
||||||
|
|
||||||
|
|
||||||
|
Download information
|
||||||
|
--------------------
|
||||||
|
|
||||||
|
Source code is available from SVN:
|
||||||
|
http://svn.research-infrastructures.eu/d4science/gcube/trunk/content-management/EcologicalModelling
|
||||||
|
|
||||||
|
Binaries can be downloaded from:
|
||||||
|
http://software.d4science.research-infrastructures.eu/
|
||||||
|
|
||||||
|
Documentation
|
||||||
|
-------------
|
||||||
|
VREManager documentation is available on-line from the Projects Documentation Wiki:
|
||||||
|
https://gcube.wiki.gcube-system.org/gcube/index.php/Ecological_Modeling
|
||||||
|
|
||||||
|
Licensing
|
||||||
|
---------
|
||||||
|
|
||||||
|
This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
|
||||||
|
|
@ -0,0 +1,7 @@
|
||||||
|
<ReleaseNotes xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:noNamespaceSchemaLocation="xsd/changelog.xsd">
|
||||||
|
<Changeset component="org.gcube.data-analysis.ecological-engine-executor.1-0-0"
|
||||||
|
date="2012-02-23">
|
||||||
|
<Change>First Release</Change>
|
||||||
|
</Changeset>
|
||||||
|
</ReleaseNotes>
|
||||||
|
|
@ -0,0 +1,42 @@
|
||||||
|
<assembly
|
||||||
|
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
|
||||||
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
|
||||||
|
<id>servicearchive</id>
|
||||||
|
<formats>
|
||||||
|
<format>tar.gz</format>
|
||||||
|
</formats>
|
||||||
|
<baseDirectory>/</baseDirectory>
|
||||||
|
<fileSets>
|
||||||
|
<fileSet>
|
||||||
|
<directory>${distroDirectory}</directory>
|
||||||
|
<outputDirectory>/</outputDirectory>
|
||||||
|
<useDefaultExcludes>true</useDefaultExcludes>
|
||||||
|
<includes>
|
||||||
|
<include>README</include>
|
||||||
|
<include>LICENSE</include>
|
||||||
|
<include>INSTALL</include>
|
||||||
|
<include>MAINTAINERS</include>
|
||||||
|
<include>changelog.xml</include>
|
||||||
|
</includes>
|
||||||
|
<fileMode>755</fileMode>
|
||||||
|
<filtered>true</filtered>
|
||||||
|
</fileSet>
|
||||||
|
</fileSets>
|
||||||
|
<files>
|
||||||
|
<file>
|
||||||
|
<source>${distroDirectory}/profile.xml</source>
|
||||||
|
<outputDirectory>/</outputDirectory>
|
||||||
|
<filtered>true</filtered>
|
||||||
|
</file>
|
||||||
|
<file>
|
||||||
|
<source>target/${build.finalName}.jar</source>
|
||||||
|
<outputDirectory>/${artifactId}</outputDirectory>
|
||||||
|
</file>
|
||||||
|
<file>
|
||||||
|
<source>${distroDirectory}/svnpath.txt</source>
|
||||||
|
<outputDirectory>/${artifactId}</outputDirectory>
|
||||||
|
<filtered>true</filtered>
|
||||||
|
</file>
|
||||||
|
</files>
|
||||||
|
</assembly>
|
||||||
|
|
@ -0,0 +1,25 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||||
|
<ID></ID>
|
||||||
|
<Type>Library</Type>
|
||||||
|
<Profile>
|
||||||
|
<Description>Ecological Engine Executor Library</Description>
|
||||||
|
<Class>EcologicalEngineExecutor</Class>
|
||||||
|
<Name>${artifactId}</Name>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
<Packages>
|
||||||
|
<Software>
|
||||||
|
<Name>${artifactId}</Name>
|
||||||
|
<Version>${version}</Version>
|
||||||
|
<MavenCoordinates>
|
||||||
|
<groupId>${groupId}</groupId>
|
||||||
|
<artifactId>${artifactId}</artifactId>
|
||||||
|
<version>${version}</version>
|
||||||
|
</MavenCoordinates>
|
||||||
|
<Files>
|
||||||
|
<File>${build.finalName}.jar</File>
|
||||||
|
</Files>
|
||||||
|
</Software>
|
||||||
|
</Packages>
|
||||||
|
</Profile>
|
||||||
|
</Resource>
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine
|
||||||
|
|
@ -0,0 +1,28 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||||
|
<ID/>
|
||||||
|
<Type>Service</Type>
|
||||||
|
<Profile>
|
||||||
|
<Description>A Plugin Executing S.O. Scripts</Description>
|
||||||
|
<Class>ExecutorPlugins</Class>
|
||||||
|
<Name>ExecutorScript</Name>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
<Packages>
|
||||||
|
<Plugin>
|
||||||
|
<Name>plugin</Name>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
<TargetService>
|
||||||
|
<Service>
|
||||||
|
<Class>VREManagement</Class>
|
||||||
|
<Name>Executor</Name>
|
||||||
|
<Version>1.1.0</Version>
|
||||||
|
</Service>
|
||||||
|
<Package>main</Package>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
</TargetService>
|
||||||
|
<EntryPoint>org.gcube.dataanalysis.executor.plugin.ScriptPluginContext</EntryPoint>
|
||||||
|
<Files><File>org.gcube.dataanalysis.executor.executorscriptplugin.jar</File></Files>
|
||||||
|
</Plugin>
|
||||||
|
</Packages>
|
||||||
|
</Profile>
|
||||||
|
</Resource>
|
||||||
|
|
@ -0,0 +1,28 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||||
|
<ID/>
|
||||||
|
<Type>Service</Type>
|
||||||
|
<Profile>
|
||||||
|
<Description>A Plugin Executing S.O. Scripts</Description>
|
||||||
|
<Class>ExecutorPlugins</Class>
|
||||||
|
<Name>ExecutorScript</Name>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
<Packages>
|
||||||
|
<Plugin>
|
||||||
|
<Name>plugin</Name>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
<TargetService>
|
||||||
|
<Service>
|
||||||
|
<Class>VREManagement</Class>
|
||||||
|
<Name>Executor</Name>
|
||||||
|
<Version>1.1.0</Version>
|
||||||
|
</Service>
|
||||||
|
<Package>main</Package>
|
||||||
|
<Version>1.0.0</Version>
|
||||||
|
</TargetService>
|
||||||
|
<EntryPoint>org.gcube.dataanalysis.executor.plugin.ScriptPluginContext</EntryPoint>
|
||||||
|
<Files><File>org.gcube.dataanalysis.executor.executorscriptplugin.jar</File></Files>
|
||||||
|
</Plugin>
|
||||||
|
</Packages>
|
||||||
|
</Profile>
|
||||||
|
</Resource>
|
||||||
Binary file not shown.
|
|
@ -0,0 +1,138 @@
|
||||||
|
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||||
|
<modelVersion>4.0.0</modelVersion>
|
||||||
|
<parent>
|
||||||
|
<artifactId>maven-parent</artifactId>
|
||||||
|
<groupId>org.gcube.tools</groupId>
|
||||||
|
<version>1.0.0</version>
|
||||||
|
<relativePath />
|
||||||
|
</parent>
|
||||||
|
<groupId>org.gcube.dataanalysis</groupId>
|
||||||
|
<artifactId>EcologicalEngineExecutor</artifactId>
|
||||||
|
<version>1.6.4-SNAPSHOT</version>
|
||||||
|
<name>ecological-engine-executor</name>
|
||||||
|
<description>ecological-engine-executor</description>
|
||||||
|
<properties>
|
||||||
|
<distroDirectory>${project.basedir}/distro</distroDirectory>
|
||||||
|
</properties>
|
||||||
|
<dependencies>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.resourcemanagement</groupId>
|
||||||
|
<artifactId>executor-service</artifactId>
|
||||||
|
<version>[1.2.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.contentmanagement</groupId>
|
||||||
|
<artifactId>storage-manager-core</artifactId>
|
||||||
|
<version>[2.0.2-SNAPSHOT,4.0.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.contentmanagement</groupId>
|
||||||
|
<artifactId>storage-manager-wrapper</artifactId>
|
||||||
|
<version>[2.0.2-SNAPSHOT,4.0.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.apache.activemq</groupId>
|
||||||
|
<artifactId>activemq-core</artifactId>
|
||||||
|
<version>5.6.0</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.core</groupId>
|
||||||
|
<artifactId>gcf</artifactId>
|
||||||
|
<version>[1.4.1,2.0.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.dataanalysis</groupId>
|
||||||
|
<artifactId>ecological-engine</artifactId>
|
||||||
|
<version>[1.8.0-SNAPSHOT,2.0.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.informationsystem</groupId>
|
||||||
|
<artifactId>is-client</artifactId>
|
||||||
|
<version>[1.5.1,1.6.0]</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.informationsystem</groupId>
|
||||||
|
<artifactId>is-collector-stubs</artifactId>
|
||||||
|
<version>[3.0.0-SNAPSHOT, 3.1.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.gcube.core</groupId>
|
||||||
|
<artifactId>common-scope</artifactId>
|
||||||
|
<version>[1.2.0-SNAPSHOT,3.0.0)</version>
|
||||||
|
</dependency>
|
||||||
|
<!-- <dependency>
|
||||||
|
<groupId>org.apache.jcs</groupId>
|
||||||
|
<artifactId>jcs</artifactId>
|
||||||
|
<version>1.3</version>
|
||||||
|
</dependency>-->
|
||||||
|
<!-- <dependency> <groupId>org.gcube.dataanalysis</groupId> <artifactId>generic-worker</artifactId>
|
||||||
|
<version>1.2.0-SNAPSHOT</version> <type>jar</type> <scope>compile</scope>
|
||||||
|
<exclusions> <exclusion> <artifactId>common-scope</artifactId> <groupId>org.gcube.core</groupId>
|
||||||
|
</exclusion> </exclusions> </dependency> -->
|
||||||
|
</dependencies>
|
||||||
|
<build>
|
||||||
|
<plugins>
|
||||||
|
<plugin>
|
||||||
|
<artifactId>maven-compiler-plugin</artifactId>
|
||||||
|
<configuration>
|
||||||
|
<source>1.6</source>
|
||||||
|
<target>1.6</target>
|
||||||
|
</configuration>
|
||||||
|
</plugin>
|
||||||
|
<plugin>
|
||||||
|
<groupId>org.apache.maven.plugins</groupId>
|
||||||
|
<artifactId>maven-surefire-plugin</artifactId>
|
||||||
|
<version>2.12</version>
|
||||||
|
<configuration>
|
||||||
|
<skipTests>true</skipTests>
|
||||||
|
</configuration>
|
||||||
|
</plugin>
|
||||||
|
<plugin>
|
||||||
|
<groupId>org.apache.maven.plugins</groupId>
|
||||||
|
<artifactId>maven-resources-plugin</artifactId>
|
||||||
|
<version>2.5</version>
|
||||||
|
<executions>
|
||||||
|
<execution>
|
||||||
|
<id>copy-profile</id>
|
||||||
|
<phase>install</phase>
|
||||||
|
<goals>
|
||||||
|
<goal>copy-resources</goal>
|
||||||
|
</goals>
|
||||||
|
<configuration>
|
||||||
|
<outputDirectory>target</outputDirectory>
|
||||||
|
<resources>
|
||||||
|
<resource>
|
||||||
|
<directory>${distroDirectory}</directory>
|
||||||
|
<filtering>true</filtering>
|
||||||
|
<includes>
|
||||||
|
<include>profile.xml</include>
|
||||||
|
</includes>
|
||||||
|
</resource>
|
||||||
|
</resources>
|
||||||
|
</configuration>
|
||||||
|
</execution>
|
||||||
|
</executions>
|
||||||
|
</plugin>
|
||||||
|
<plugin>
|
||||||
|
<groupId>org.apache.maven.plugins</groupId>
|
||||||
|
<artifactId>maven-assembly-plugin</artifactId>
|
||||||
|
<version>2.2</version>
|
||||||
|
<configuration>
|
||||||
|
<descriptors>
|
||||||
|
<descriptor>${distroDirectory}/descriptor.xml</descriptor>
|
||||||
|
</descriptors>
|
||||||
|
</configuration>
|
||||||
|
<executions>
|
||||||
|
<execution>
|
||||||
|
<id>servicearchive</id>
|
||||||
|
<phase>install</phase>
|
||||||
|
<goals>
|
||||||
|
<goal>single</goal>
|
||||||
|
</goals>
|
||||||
|
</execution>
|
||||||
|
</executions>
|
||||||
|
</plugin>
|
||||||
|
</plugins>
|
||||||
|
</build>
|
||||||
|
</project>
|
||||||
|
|
@ -0,0 +1,148 @@
|
||||||
|
package org.gcube.dataanalysis.executor.generators;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Properties;
|
||||||
|
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
|
||||||
|
import org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent;
|
||||||
|
|
||||||
|
public class D4ScienceDistributedProcessing implements Generator {
|
||||||
|
public static int maxMessagesAllowedPerJob = 20;
|
||||||
|
public static boolean forceUpload = true;
|
||||||
|
public static String defaultContainerFolder = "PARALLEL_PROCESSING";
|
||||||
|
protected AlgorithmConfiguration config;
|
||||||
|
protected ActorNode distributedModel;
|
||||||
|
protected String mainclass;
|
||||||
|
DistributedProcessingAgent agent;
|
||||||
|
|
||||||
|
public D4ScienceDistributedProcessing(){
|
||||||
|
}
|
||||||
|
|
||||||
|
public D4ScienceDistributedProcessing(AlgorithmConfiguration config) {
|
||||||
|
this.config = config;
|
||||||
|
|
||||||
|
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void compute() throws Exception {
|
||||||
|
try {
|
||||||
|
agent.compute();
|
||||||
|
distributedModel.postProcess(agent.hasResentMessages(),false);
|
||||||
|
} catch (Exception e) {
|
||||||
|
distributedModel.postProcess(false,true);
|
||||||
|
AnalysisLogger.getLogger().error("ERROR: An Error occurred ", e);
|
||||||
|
throw e;
|
||||||
|
} finally {
|
||||||
|
shutdown();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public List<StatisticalType> getInputParameters() {
|
||||||
|
|
||||||
|
List<StatisticalType> distributionModelParams = new ArrayList<StatisticalType>();
|
||||||
|
distributionModelParams.add(new ServiceType(ServiceParameters.USERNAME,"ServiceUserName","The final user Name"));
|
||||||
|
|
||||||
|
return distributionModelParams;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getResources() {
|
||||||
|
return agent.getResources();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public float getStatus() {
|
||||||
|
return agent.getStatus();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public StatisticalType getOutput() {
|
||||||
|
return distributedModel.getOutput();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public ALG_PROPS[] getSupportedAlgorithms() {
|
||||||
|
ALG_PROPS[] p = { ALG_PROPS.PHENOMENON_VS_PARALLEL_PHENOMENON};
|
||||||
|
return p;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public INFRASTRUCTURE getInfrastructure() {
|
||||||
|
return INFRASTRUCTURE.D4SCIENCE;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void init() throws Exception {
|
||||||
|
|
||||||
|
Properties p = AlgorithmConfiguration.getProperties(config.getConfigPath() + AlgorithmConfiguration.nodeAlgorithmsFile);
|
||||||
|
String model = config.getModel();
|
||||||
|
String algorithm = null;
|
||||||
|
if ((model!=null) && (model.length()>0))
|
||||||
|
algorithm = model;
|
||||||
|
else
|
||||||
|
algorithm=config.getAgent();
|
||||||
|
|
||||||
|
mainclass = p.getProperty(algorithm);
|
||||||
|
distributedModel = (ActorNode) Class.forName(mainclass).newInstance();
|
||||||
|
distributedModel.setup(config);
|
||||||
|
String scope = config.getGcubeScope();
|
||||||
|
AnalysisLogger.getLogger().info("Using the following scope for the computation:"+scope);
|
||||||
|
String owner = config.getParam("ServiceUserName");
|
||||||
|
int leftNum = distributedModel.getNumberOfLeftElements();
|
||||||
|
int rightNum = distributedModel.getNumberOfRightElements();
|
||||||
|
agent = new DistributedProcessingAgent(config, scope, owner, mainclass, config.getPersistencePath(), algorithm, defaultContainerFolder, maxMessagesAllowedPerJob, forceUpload, leftNum, rightNum);
|
||||||
|
agent.setLogger(AnalysisLogger.getLogger());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void setConfiguration(AlgorithmConfiguration config) {
|
||||||
|
this.config = config;
|
||||||
|
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void shutdown() {
|
||||||
|
try {
|
||||||
|
agent.shutdown();
|
||||||
|
} catch (Exception e) {
|
||||||
|
}
|
||||||
|
try {
|
||||||
|
distributedModel.stop();
|
||||||
|
} catch (Exception e) {
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getLoad() {
|
||||||
|
return agent.getLoad();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getResourceLoad() {
|
||||||
|
return agent.getResourceLoad();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public GenericAlgorithm getAlgorithm() {
|
||||||
|
return distributedModel;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getDescription() {
|
||||||
|
return "A D4Science Cloud Processor for Species Distributions";
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,293 @@
|
||||||
|
package org.gcube.dataanalysis.executor.job.management;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
import org.apache.axis.message.addressing.Address;
|
||||||
|
import org.apache.axis.message.addressing.EndpointReferenceType;
|
||||||
|
import org.apache.log4j.Logger;
|
||||||
|
import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.utils.Operations;
|
||||||
|
|
||||||
|
import com.thoughtworks.xstream.XStream;
|
||||||
|
|
||||||
|
public class DistributedProcessingAgent {
|
||||||
|
|
||||||
|
protected QueueJobManager jobManager;
|
||||||
|
protected boolean deletefiles = true;
|
||||||
|
protected String mainclass;
|
||||||
|
public int maxElementsAllowedPerJob = 20;
|
||||||
|
protected boolean forceUpload = true;
|
||||||
|
protected boolean stop;
|
||||||
|
protected String gscope;
|
||||||
|
protected String userName;
|
||||||
|
protected String pathToLib;
|
||||||
|
protected String modelName;
|
||||||
|
protected String containerFolder;
|
||||||
|
protected Serializable configurationFile;
|
||||||
|
protected int rightSetNumberOfElements;
|
||||||
|
protected int leftSetNumberOfElements;
|
||||||
|
protected List<String> endpoints;
|
||||||
|
protected int subdivisiondiv;
|
||||||
|
|
||||||
|
protected static String defaultJobOutput = "execution.output";
|
||||||
|
protected static String defaultScriptFile = "script";
|
||||||
|
protected Logger logger;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* A distributed processing agent. Performs a distributed computation doing the MAP of the product of two sets: A and B
|
||||||
|
* Splits over B : A x B1 , A x B2, ... , A x Bn
|
||||||
|
* Prepares a script to be executed on remote nodes
|
||||||
|
* The computation is then sent to remote processors.
|
||||||
|
*/
|
||||||
|
public DistributedProcessingAgent(Serializable configurationFile,
|
||||||
|
String gCubeScope,
|
||||||
|
String computationOwner,
|
||||||
|
String mainClass,
|
||||||
|
String pathToLibFolder,
|
||||||
|
String modelName,
|
||||||
|
String containerFolder,
|
||||||
|
int maxElementsPerJob,
|
||||||
|
boolean forceReUploadofLibs,
|
||||||
|
int leftSetNumberOfElements,
|
||||||
|
int rightSetNumberOfElements
|
||||||
|
) {
|
||||||
|
this.stop = false;
|
||||||
|
this.deletefiles = true;
|
||||||
|
this.gscope=gCubeScope;
|
||||||
|
this.mainclass=mainClass;
|
||||||
|
this.maxElementsAllowedPerJob=maxElementsPerJob;
|
||||||
|
this.forceUpload=forceReUploadofLibs;
|
||||||
|
this.configurationFile=configurationFile;
|
||||||
|
this.rightSetNumberOfElements=rightSetNumberOfElements;
|
||||||
|
this.leftSetNumberOfElements=leftSetNumberOfElements;
|
||||||
|
this.userName=computationOwner;
|
||||||
|
this.pathToLib=pathToLibFolder;
|
||||||
|
this.modelName=modelName;
|
||||||
|
this.containerFolder=containerFolder;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setLogger(Logger logger){
|
||||||
|
this.logger=logger;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setEndPoints(List<String> endpoints){
|
||||||
|
this.endpoints=endpoints;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean hasResentMessages(){
|
||||||
|
return jobManager.hasResentMessages();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void compute() throws Exception {
|
||||||
|
try {
|
||||||
|
if (logger == null){
|
||||||
|
logger = AnalysisLogger.getLogger();
|
||||||
|
}
|
||||||
|
if (gscope == null)
|
||||||
|
throw new Exception("Null Scope");
|
||||||
|
AnalysisLogger.getLogger().debug("SCOPE: "+gscope);
|
||||||
|
if (endpoints != null) {
|
||||||
|
List<EndpointReferenceType> eprtList = new ArrayList<EndpointReferenceType>();
|
||||||
|
for (String ep : endpoints) {
|
||||||
|
eprtList.add(new EndpointReferenceType(new Address(ep)));
|
||||||
|
}
|
||||||
|
jobManager = new QueueJobManager(gscope, endpoints.size(), eprtList);
|
||||||
|
} else
|
||||||
|
jobManager = new QueueJobManager(gscope, 1);
|
||||||
|
|
||||||
|
int numberOfResources = jobManager.getNumberOfNodes();
|
||||||
|
// we split along right dimension so if elements are less than nodes, we should reduce the number of nodes
|
||||||
|
if (numberOfResources > 0) {
|
||||||
|
// chunkize the number of species in order to lower the computational effort of the workers
|
||||||
|
subdivisiondiv = rightSetNumberOfElements / (numberOfResources * maxElementsAllowedPerJob);
|
||||||
|
int rest = rightSetNumberOfElements % (numberOfResources * maxElementsAllowedPerJob);
|
||||||
|
if (rest > 0)
|
||||||
|
subdivisiondiv++;
|
||||||
|
if (subdivisiondiv == 0)
|
||||||
|
subdivisiondiv = 1;
|
||||||
|
|
||||||
|
executeWork(leftSetNumberOfElements, rightSetNumberOfElements, 0, subdivisiondiv, deletefiles, forceUpload);
|
||||||
|
|
||||||
|
if (jobManager.wasAborted()) {
|
||||||
|
logger.debug("Warning: Job was aborted");
|
||||||
|
// distributionModel.postProcess(false,true);
|
||||||
|
throw new Exception("Job System Error");
|
||||||
|
}
|
||||||
|
else{
|
||||||
|
//postprocess
|
||||||
|
// distributionModel.postProcess(jobManager.hasResentMessages(),false);
|
||||||
|
}
|
||||||
|
|
||||||
|
} else {
|
||||||
|
logger.debug("Warning: No Workers available");
|
||||||
|
throw new Exception("No Workers available");
|
||||||
|
}
|
||||||
|
|
||||||
|
} catch (Exception e) {
|
||||||
|
logger.error("ERROR: An Error occurred ", e);
|
||||||
|
e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
} finally {
|
||||||
|
shutdown();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void executeWork(int leftNum, int rightNum, int offset, int numberOfResources, boolean deletefiles, boolean forceUpload) throws Exception {
|
||||||
|
|
||||||
|
String owner = userName;
|
||||||
|
|
||||||
|
int[] chunkSizes = Operations.takeChunks(rightNum, numberOfResources);
|
||||||
|
List<String> arguments = new ArrayList<String>();
|
||||||
|
// chunkize respect to the cells: take a chunk of cells vs all species at each node!
|
||||||
|
|
||||||
|
for (int i = 0; i < chunkSizes.length; i++) {
|
||||||
|
String argumentString = "0 " + leftNum + " " + offset + " " + chunkSizes[i] + " ./ "+mainclass;
|
||||||
|
arguments.add(argumentString);
|
||||||
|
offset += chunkSizes[i];
|
||||||
|
logger.debug("Generator-> Argument " + i + ": " + argumentString);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (owner == null)
|
||||||
|
throw new Exception("Null Owner");
|
||||||
|
|
||||||
|
String pathToDir = new File (pathToLib, containerFolder).getAbsolutePath();
|
||||||
|
|
||||||
|
if (!(new File(pathToDir).exists()))
|
||||||
|
throw new Exception("No Implementation of node-model found for algorithm " + pathToDir);
|
||||||
|
|
||||||
|
if (mainclass == null)
|
||||||
|
throw new Exception("No mainClass found for algorithm " + pathToDir);
|
||||||
|
|
||||||
|
buildScriptFile(modelName, defaultJobOutput, pathToDir, mainclass);
|
||||||
|
|
||||||
|
jobManager.uploadAndExecuteChunkized(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, owner, pathToDir, "/" + modelName + "/", "./", getScriptName(mainclass), arguments, new XStream().toXML(configurationFile), deletefiles, forceUpload);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private String getScriptName(String fullMainClass){
|
||||||
|
String scriptName = defaultScriptFile+"_"+fullMainClass.substring(fullMainClass.lastIndexOf(".")+1)+".sh";
|
||||||
|
return scriptName;
|
||||||
|
}
|
||||||
|
// builds a job.sh
|
||||||
|
public void buildScriptFile(String jobName, String jobOutput, String jarsPath, String fullMainClass) throws Exception {
|
||||||
|
File expectedscript = new File(jarsPath,getScriptName(fullMainClass));
|
||||||
|
if (!expectedscript.exists()) {
|
||||||
|
StringBuffer sb = new StringBuffer();
|
||||||
|
sb.append("#!/bin/sh\n");
|
||||||
|
sb.append("# " + jobName + "\n");
|
||||||
|
sb.append("cd $1\n");
|
||||||
|
sb.append("\n");
|
||||||
|
sb.append("java -Xmx1024M -classpath ./:");
|
||||||
|
File jarsPathF = new File(jarsPath);
|
||||||
|
File[] files = jarsPathF.listFiles();
|
||||||
|
|
||||||
|
for (File jar : files) {
|
||||||
|
|
||||||
|
if (jar.getName().endsWith(".jar")) {
|
||||||
|
sb.append("./" + jar.getName());
|
||||||
|
sb.append(":");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
sb.deleteCharAt(sb.length() - 1);
|
||||||
|
sb.append(" " + fullMainClass + " $2 " + jobOutput);
|
||||||
|
sb.append("\n");
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().trace("D4ScienceGenerator->Generating script in " + expectedscript.getAbsolutePath());
|
||||||
|
FileTools.saveString(expectedscript.getAbsolutePath(), sb.toString(), true, "UTF-8");
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().trace("D4ScienceGenerator->Script " + expectedscript.getAbsolutePath()+" yet exists!");
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getResources() {
|
||||||
|
Resources res = new Resources();
|
||||||
|
try {
|
||||||
|
int activeNodes = jobManager.getActiveNodes();
|
||||||
|
for (int i = 0; i < activeNodes; i++) {
|
||||||
|
try {
|
||||||
|
res.addResource("Worker_" + (i + 1), 100);
|
||||||
|
} catch (Exception e1) {
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} catch (Exception e) {
|
||||||
|
AnalysisLogger.getLogger().debug("D4ScienceGenerator->active nodes not ready");
|
||||||
|
}
|
||||||
|
if ((res != null) && (res.list != null))
|
||||||
|
return HttpRequest.toJSon(res.list).replace("resId", "resID");
|
||||||
|
else
|
||||||
|
return "";
|
||||||
|
}
|
||||||
|
|
||||||
|
public float getStatus() {
|
||||||
|
try {
|
||||||
|
if (stop)
|
||||||
|
return 100f;
|
||||||
|
else
|
||||||
|
if (jobManager!=null)
|
||||||
|
return Math.max(0.5f, jobManager.getStatus() * 100f);
|
||||||
|
else
|
||||||
|
return 0;
|
||||||
|
} catch (Exception e) {
|
||||||
|
return 0f;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public ALG_PROPS[] getSupportedAlgorithms() {
|
||||||
|
ALG_PROPS[] p = { ALG_PROPS.PHENOMENON_VS_PARALLEL_PHENOMENON};
|
||||||
|
return p;
|
||||||
|
}
|
||||||
|
|
||||||
|
public INFRASTRUCTURE getInfrastructure() {
|
||||||
|
return INFRASTRUCTURE.D4SCIENCE;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void shutdown() {
|
||||||
|
|
||||||
|
try {
|
||||||
|
jobManager.stop();
|
||||||
|
} catch (Exception e) {
|
||||||
|
}
|
||||||
|
stop = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getLoad() {
|
||||||
|
long tk = System.currentTimeMillis();
|
||||||
|
ResourceLoad rs = null;
|
||||||
|
if (jobManager!=null)
|
||||||
|
rs = new ResourceLoad(tk, jobManager.currentNumberOfStages*subdivisiondiv);
|
||||||
|
else
|
||||||
|
rs = new ResourceLoad(tk, 0);
|
||||||
|
return rs.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
private long lastTime;
|
||||||
|
private int lastProcessed;
|
||||||
|
public String getResourceLoad() {
|
||||||
|
long thisTime = System.currentTimeMillis();
|
||||||
|
int processedRecords = 0;
|
||||||
|
if ((jobManager!=null) && (subdivisiondiv>0))
|
||||||
|
processedRecords = jobManager.currentNumberOfStages*subdivisiondiv;
|
||||||
|
|
||||||
|
int estimatedProcessedRecords = 0;
|
||||||
|
if (processedRecords == lastProcessed) {
|
||||||
|
estimatedProcessedRecords = Math.round(((float) thisTime * (float) lastProcessed) / (float) lastTime);
|
||||||
|
} else {
|
||||||
|
lastProcessed = processedRecords;
|
||||||
|
estimatedProcessedRecords = lastProcessed;
|
||||||
|
}
|
||||||
|
lastTime = thisTime;
|
||||||
|
ResourceLoad rs = new ResourceLoad(thisTime, estimatedProcessedRecords);
|
||||||
|
return rs.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,821 @@
|
||||||
|
package org.gcube.dataanalysis.executor.job.management;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Timer;
|
||||||
|
import java.util.TimerTask;
|
||||||
|
import java.util.UUID;
|
||||||
|
|
||||||
|
import javax.jms.ExceptionListener;
|
||||||
|
import javax.jms.JMSException;
|
||||||
|
import javax.jms.Message;
|
||||||
|
import javax.jms.MessageListener;
|
||||||
|
|
||||||
|
import org.apache.activemq.ActiveMQConnection;
|
||||||
|
import org.apache.axis.message.addressing.EndpointReferenceType;
|
||||||
|
import org.gcube.common.core.contexts.GHNContext;
|
||||||
|
import org.gcube.common.core.informationsystem.client.AtomicCondition;
|
||||||
|
import org.gcube.common.core.informationsystem.client.ISClient;
|
||||||
|
import org.gcube.common.core.informationsystem.client.RPDocument;
|
||||||
|
import org.gcube.common.core.informationsystem.client.queries.WSResourceQuery;
|
||||||
|
import org.gcube.common.core.scope.GCUBEScope;
|
||||||
|
import org.gcube.common.scope.api.ScopeProvider;
|
||||||
|
import org.gcube.contentmanagement.blobstorage.resource.StorageObject;
|
||||||
|
import org.gcube.contentmanagement.blobstorage.service.IClient;
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||||
|
import org.gcube.contentmanager.storageclient.wrapper.AccessType;
|
||||||
|
import org.gcube.contentmanager.storageclient.wrapper.MemoryType;
|
||||||
|
import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.utils.Operations;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.ATTRIBUTE;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.Consumer;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.Producer;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.QueueManager;
|
||||||
|
import org.gcube.dataanalysis.executor.scripts.ScriptIOWorker;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.ExecutorCall;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.TaskCall;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.TaskProxy;
|
||||||
|
|
||||||
|
public class QueueJobManager {
|
||||||
|
|
||||||
|
// broadcast message period
|
||||||
|
public static int broadcastTimePeriod = 120000;
|
||||||
|
// max silence before computation stops
|
||||||
|
public static int maxSilenceTimeBeforeComputationStop = 10800000;
|
||||||
|
// max number of retries per computation step
|
||||||
|
public static int maxNumberOfComputationRetries = 1;
|
||||||
|
// period for controlling a node activity
|
||||||
|
public static int computationWatcherTimerPeriod = 120000;
|
||||||
|
// max number of message to put in a queue
|
||||||
|
// protected static int maxNumberOfMessages = 20;
|
||||||
|
public static int maxNumberOfStages = Integer.MAX_VALUE;//10;
|
||||||
|
// timeout for resending a message
|
||||||
|
public static int queueWatcherMaxwaitingTime = QCONSTANTS.refreshStatusTime;// * 5;
|
||||||
|
|
||||||
|
protected int maxFailureTries;
|
||||||
|
private static String pluginName = "generic-worker";//"GenericWorker";
|
||||||
|
|
||||||
|
protected String scope;
|
||||||
|
protected GCUBEScope gscope;
|
||||||
|
protected String session;
|
||||||
|
|
||||||
|
protected boolean yetstopped;
|
||||||
|
protected boolean messagesresent;
|
||||||
|
protected float status;
|
||||||
|
protected boolean abort;
|
||||||
|
protected boolean shutdown;
|
||||||
|
|
||||||
|
protected List<EndpointReferenceType> eprs;
|
||||||
|
protected int activeNodes;
|
||||||
|
protected int computingNodes;
|
||||||
|
protected int numberOfMessages;
|
||||||
|
protected int totalNumberOfMessages;
|
||||||
|
protected int actualNumberOfNodes;
|
||||||
|
protected int totalNumberOfStages;
|
||||||
|
public int currentNumberOfStages;
|
||||||
|
|
||||||
|
// files management
|
||||||
|
protected List<String> filenames;
|
||||||
|
protected List<String> fileurls;
|
||||||
|
|
||||||
|
// queue parameters
|
||||||
|
protected String queueName;
|
||||||
|
protected String queueResponse;
|
||||||
|
protected String queueURL;
|
||||||
|
protected String queueUSER;
|
||||||
|
protected String queuePWD;
|
||||||
|
protected org.gcube.dataanalysis.executor.messagequeue.Consumer consumer;
|
||||||
|
protected Producer producer;
|
||||||
|
|
||||||
|
Timer broadcastTimer;
|
||||||
|
Timer computationWatcherTimer;
|
||||||
|
ComputationTimerWatcher computationWatcher;
|
||||||
|
String serviceClass;
|
||||||
|
String serviceName;
|
||||||
|
String owner;
|
||||||
|
String localDir;
|
||||||
|
String remoteDir;
|
||||||
|
String outputDir;
|
||||||
|
String script;
|
||||||
|
List<String> arguments;
|
||||||
|
String configuration;
|
||||||
|
boolean deletefiles;
|
||||||
|
StatusListener statuslistener;
|
||||||
|
|
||||||
|
private void resetAllVars() {
|
||||||
|
scope = null;
|
||||||
|
gscope = null;
|
||||||
|
|
||||||
|
yetstopped = false;
|
||||||
|
messagesresent = false;
|
||||||
|
status = 0;
|
||||||
|
abort = false;
|
||||||
|
shutdown = false;
|
||||||
|
|
||||||
|
eprs = null;
|
||||||
|
activeNodes = 0;
|
||||||
|
computingNodes = 0;
|
||||||
|
numberOfMessages = 0;
|
||||||
|
|
||||||
|
actualNumberOfNodes = 0;
|
||||||
|
filenames = null;
|
||||||
|
fileurls = null;
|
||||||
|
|
||||||
|
queueName = null;
|
||||||
|
queueResponse = null;
|
||||||
|
queueURL = null;
|
||||||
|
queueUSER = null;
|
||||||
|
queuePWD = null;
|
||||||
|
consumer = null;
|
||||||
|
producer = null;
|
||||||
|
broadcastTimer = null;
|
||||||
|
computationWatcherTimer = null;
|
||||||
|
computationWatcher = null;
|
||||||
|
serviceClass = null;
|
||||||
|
serviceName = null;
|
||||||
|
owner = null;
|
||||||
|
localDir = null;
|
||||||
|
remoteDir = null;
|
||||||
|
outputDir = null;
|
||||||
|
script = null;
|
||||||
|
arguments = null;
|
||||||
|
configuration = null;
|
||||||
|
deletefiles = false;
|
||||||
|
statuslistener = null;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getActiveNodes() {
|
||||||
|
return computingNodes;
|
||||||
|
}
|
||||||
|
|
||||||
|
public float getStatus() {
|
||||||
|
float innerStatus = 0;
|
||||||
|
if (totalNumberOfMessages != 0)
|
||||||
|
innerStatus = (1f - ((float) numberOfMessages / (float) totalNumberOfMessages));
|
||||||
|
if (totalNumberOfStages == 0)
|
||||||
|
return innerStatus;
|
||||||
|
else {
|
||||||
|
float offset = ((float) Math.max(currentNumberOfStages - 1, 0)) / (float) totalNumberOfStages;
|
||||||
|
float status = offset + (innerStatus / (float) totalNumberOfStages);
|
||||||
|
// AnalysisLogger.getLogger().info("stages: "+totalNumberOfStages+" inner status: "+innerStatus+" currentStage: "+currentNumberOfStages+" status: "+status);
|
||||||
|
return status;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// there is only one node from the client point of view
|
||||||
|
public int getNumberOfNodes() {
|
||||||
|
if (eprs.size() > 0)
|
||||||
|
return 1;
|
||||||
|
else
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setNumberOfNodes(int newNumberOfNodes) {
|
||||||
|
// ignore this setting in this case
|
||||||
|
}
|
||||||
|
|
||||||
|
private void init(String scope, int numberOfNodes) throws Exception {
|
||||||
|
resetAllVars();
|
||||||
|
// init scope variables
|
||||||
|
this.scope = scope;
|
||||||
|
gscope = GCUBEScope.getScope(scope);
|
||||||
|
// introduce a session
|
||||||
|
// initialize flags
|
||||||
|
shutdown = false;
|
||||||
|
yetstopped = false;
|
||||||
|
messagesresent = false;
|
||||||
|
abort = false;
|
||||||
|
// find all the nodes - initialize the eprs
|
||||||
|
findNodes(scope);
|
||||||
|
}
|
||||||
|
|
||||||
|
public QueueJobManager(String scope, int numberOfNodes) throws Exception {
|
||||||
|
init(scope, numberOfNodes);
|
||||||
|
}
|
||||||
|
|
||||||
|
public QueueJobManager(String scope, int numberOfNodes, List<EndpointReferenceType> eprs) throws Exception {
|
||||||
|
init(scope, numberOfNodes);
|
||||||
|
this.eprs = eprs;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void setGlobalVars(String serviceClass, String serviceName, String owner, String localDir, String remoteDir, String outputDir, String script, List<String> arguments, String configuration, boolean deletefiles) {
|
||||||
|
this.serviceClass = serviceClass;
|
||||||
|
this.serviceName = serviceName;
|
||||||
|
this.owner = owner;
|
||||||
|
this.localDir = localDir;
|
||||||
|
this.remoteDir = remoteDir;
|
||||||
|
this.outputDir = outputDir;
|
||||||
|
this.script = script;
|
||||||
|
this.arguments = arguments;
|
||||||
|
this.configuration = configuration;
|
||||||
|
this.deletefiles = deletefiles;
|
||||||
|
}
|
||||||
|
|
||||||
|
private int totalmessages = 0;
|
||||||
|
|
||||||
|
public boolean uploadAndExecuteChunkized(String serviceClass, String serviceName, String owner, String localDir, String remoteDir, String outputDir, String script, List<String> arguments, String configuration, boolean deletefiles, boolean forceUpload) throws Exception {
|
||||||
|
long t0 = System.currentTimeMillis();
|
||||||
|
|
||||||
|
int elements = arguments.size();
|
||||||
|
/*
|
||||||
|
* int div = elements / (maxNumberOfMessages); int rest = elements % (maxNumberOfMessages); if (rest > 0) div++; if (div == 0) { div = 1; }
|
||||||
|
*/
|
||||||
|
session = (("" + UUID.randomUUID()).replace("-", "") + Math.random()).replace(".", "");
|
||||||
|
int[] chunkSizes = null;
|
||||||
|
//up to 1120 species we don't make stages
|
||||||
|
if (elements>maxNumberOfStages)
|
||||||
|
chunkSizes = Operations.takeChunks(elements, maxNumberOfStages);
|
||||||
|
else {
|
||||||
|
chunkSizes = new int[1];
|
||||||
|
chunkSizes[0]=elements;
|
||||||
|
}
|
||||||
|
int allchunks = chunkSizes.length;
|
||||||
|
totalNumberOfStages = allchunks;
|
||||||
|
currentNumberOfStages = 0;
|
||||||
|
int start = 0;
|
||||||
|
totalmessages = 0;
|
||||||
|
AnalysisLogger.getLogger().info("Starting the computation in "+allchunks+" stages");
|
||||||
|
for (int i = 0; i < allchunks; i++) {
|
||||||
|
numberOfMessages = totalNumberOfMessages = 0;
|
||||||
|
currentNumberOfStages++;
|
||||||
|
int end = Math.min(elements, start + chunkSizes[i]);
|
||||||
|
AnalysisLogger.getLogger().info("Computing the chunk number " + (i + 1) + " of " + allchunks + " between " + start + " and " + (end - 1));
|
||||||
|
List<String> sublist = new ArrayList<String>();
|
||||||
|
for (int j = start; j < end; j++)
|
||||||
|
sublist.add(arguments.get(j));
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("size sub:" + sublist.size());
|
||||||
|
// totalmessages=totalmessages+sublist.size();
|
||||||
|
uploadAndExecute(serviceClass, serviceName, owner, localDir, remoteDir, outputDir, script, sublist, configuration, deletefiles, forceUpload);
|
||||||
|
if (abort)
|
||||||
|
break;
|
||||||
|
start = end;
|
||||||
|
AnalysisLogger.getLogger().info("Processed chunk number " + (i + 1));
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
currentNumberOfStages = totalNumberOfStages;
|
||||||
|
AnalysisLogger.getLogger().info("Finished computation on all chunks and messages " + totalmessages);
|
||||||
|
AnalysisLogger.getLogger().info("Whole Procedure done in " + (System.currentTimeMillis() - t0) + " ms");
|
||||||
|
return (!abort);
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean uploadAndExecute(String serviceClass, String serviceName, String owner, String localDir, String remoteDir, String outputDir, String script, List<String> arguments, String configuration, boolean deletefiles, boolean forceUpload) throws Exception {
|
||||||
|
int numberOfRetries = maxNumberOfComputationRetries;
|
||||||
|
boolean recompute = true;
|
||||||
|
|
||||||
|
while ((numberOfRetries > 0) && (recompute)) {
|
||||||
|
long t0 = System.currentTimeMillis();
|
||||||
|
// if (numberOfRetries<maxNumberOfComputationRetries)
|
||||||
|
init(scope, 1);
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Computation Try number " + (maxNumberOfComputationRetries + 1 - numberOfRetries));
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Contacting " + actualNumberOfNodes + " Nodes");
|
||||||
|
// set globals
|
||||||
|
setGlobalVars(serviceClass, serviceName, owner, localDir, remoteDir, outputDir, script, arguments, configuration, deletefiles);
|
||||||
|
// if not yet uploaded , upload required files
|
||||||
|
uploadFilesOnStorage(forceUpload);
|
||||||
|
|
||||||
|
// initializing queue
|
||||||
|
setQueueVariables();
|
||||||
|
// broadcast a message to all executors for purging previous queues
|
||||||
|
// purgeQueues();
|
||||||
|
createClientProducer();
|
||||||
|
broadcastListenCommandToExecutorNodes();
|
||||||
|
|
||||||
|
maxFailureTries = activeNodes * 1;
|
||||||
|
|
||||||
|
broadcastTimer = new Timer();
|
||||||
|
broadcastTimer.schedule(new Broadcaster(), broadcastTimePeriod, broadcastTimePeriod);
|
||||||
|
|
||||||
|
computationWatcherTimer = new Timer();
|
||||||
|
computationWatcher = new ComputationTimerWatcher(maxSilenceTimeBeforeComputationStop);
|
||||||
|
computationWatcherTimer.schedule(computationWatcher, computationWatcherTimerPeriod, computationWatcherTimerPeriod);
|
||||||
|
|
||||||
|
// send all messages
|
||||||
|
sendMessages();
|
||||||
|
createClientConsumer();
|
||||||
|
// wait for messages
|
||||||
|
waitForMessages();
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Wait for message finished - checking result");
|
||||||
|
if (numberOfMessages == 0) {
|
||||||
|
AnalysisLogger.getLogger().info("All tasks have correctly finished!");
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
* else{ AnalysisLogger.getLogger().info("Timeout - Warning Some Task is missing!"); for (int k=0;k<finishedChunks.length;k++){ if (finishedChunks[k]==0){ AnalysisLogger.getLogger().info("Sending Again message number " + k); Map<String, Object> inputs = generateInputMessage(filenames, fileurls, outputDir, script, arguments.get(k), k, scope, serviceClass, serviceName, owner, remoteDir, session, configuration, deletefiles); producer.sendMessage(inputs, 0); AnalysisLogger.getLogger().info("Sent Message " + k); } } waitForMessages(); if (numberOfMessages>0){ abort = true; } }
|
||||||
|
*/
|
||||||
|
|
||||||
|
// deleteRemoteFolder();
|
||||||
|
// summary
|
||||||
|
AnalysisLogger.getLogger().info("-SUMMARY-");
|
||||||
|
for (int i = 0; i < totalNumberOfMessages; i++) {
|
||||||
|
if (activeMessages[i])
|
||||||
|
AnalysisLogger.getLogger().info("Error : the Message Number " + i + " Was Never Processed!");
|
||||||
|
if (resentMessages[i] > 0) {
|
||||||
|
messagesresent = true;
|
||||||
|
AnalysisLogger.getLogger().info("Warning : the Message Number " + i + " Was resent " + resentMessages[i] + " Times");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("-SUMMARY END-");
|
||||||
|
|
||||||
|
stop();
|
||||||
|
AnalysisLogger.getLogger().info("Stopped");
|
||||||
|
AnalysisLogger.getLogger().info("Single Step Procedure done in " + (System.currentTimeMillis() - t0) + " ms");
|
||||||
|
activeNodes = 0;
|
||||||
|
numberOfRetries--;
|
||||||
|
if (abort) {
|
||||||
|
recompute = true;
|
||||||
|
if (numberOfRetries > 0)
|
||||||
|
Thread.sleep(10000);
|
||||||
|
} else
|
||||||
|
recompute = false;
|
||||||
|
}
|
||||||
|
|
||||||
|
return (!abort);
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean hasResentMessages() {
|
||||||
|
return messagesresent;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void waitForMessages() throws Exception {
|
||||||
|
AnalysisLogger.getLogger().info("Waiting...");
|
||||||
|
while ((numberOfMessages > 0) && (!abort)) {
|
||||||
|
Thread.sleep(2000);
|
||||||
|
|
||||||
|
// long tcurrent = System.currentTimeMillis();
|
||||||
|
// if ((tcurrent - waitTime) > maxwaitingTime) {
|
||||||
|
// break;
|
||||||
|
// }
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("...Stop - Abort?" + abort);
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean wasAborted() {
|
||||||
|
return abort;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void purgeQueues() throws Exception {
|
||||||
|
AnalysisLogger.getLogger().info("Purging Queue");
|
||||||
|
List<WorkerWatcher> tasksProxies = new ArrayList<WorkerWatcher>();
|
||||||
|
for (int j = 0; j < actualNumberOfNodes; j++) {
|
||||||
|
try {
|
||||||
|
contactNodes(tasksProxies, j, queueName, queueUSER, queuePWD, queueURL, queueResponse, session, "true");
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
AnalysisLogger.getLogger().info("Error in purgin queue on node " + j);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("Queue Purged");
|
||||||
|
}
|
||||||
|
|
||||||
|
public void stop() {
|
||||||
|
try {
|
||||||
|
if (!yetstopped) {
|
||||||
|
if (broadcastTimer != null) {
|
||||||
|
AnalysisLogger.getLogger().info("Stopping Broadcaster");
|
||||||
|
broadcastTimer.cancel();
|
||||||
|
broadcastTimer.purge();
|
||||||
|
}
|
||||||
|
|
||||||
|
if (computationWatcherTimer != null) {
|
||||||
|
AnalysisLogger.getLogger().info("Stopping Watcher");
|
||||||
|
computationWatcherTimer.cancel();
|
||||||
|
computationWatcherTimer.purge();
|
||||||
|
}
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Purging Status Listener");
|
||||||
|
|
||||||
|
if (statuslistener != null)
|
||||||
|
statuslistener.destroyAllWatchers();
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Stopping Producer and Consumer");
|
||||||
|
|
||||||
|
try{
|
||||||
|
producer.stop();
|
||||||
|
producer.closeSession();
|
||||||
|
}catch(Exception e1){}
|
||||||
|
try{
|
||||||
|
consumer.stop();
|
||||||
|
consumer.closeSession();
|
||||||
|
}catch(Exception e2){}
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Purging Remote Queues");
|
||||||
|
purgeQueues();
|
||||||
|
|
||||||
|
yetstopped = true;
|
||||||
|
}
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
AnalysisLogger.getLogger().info("Not completely stopped");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void contactNodes(List<WorkerWatcher> tasksProxies, int order, String queueName, String queueUSER, String queuePWD, String queueURL, String queueResponse, String session, String purgeQueue) throws Exception {
|
||||||
|
// generate the input map according to the arguments
|
||||||
|
Map<String, Object> inputs = generateWorkerInput(queueName, queueUSER, queuePWD, queueURL, queueResponse, session, purgeQueue);
|
||||||
|
AnalysisLogger.getLogger().info("Inputs " + inputs);
|
||||||
|
// take the i-th endpoint of the executor
|
||||||
|
EndpointReferenceType selectedEPR = eprs.get(order);
|
||||||
|
AnalysisLogger.getLogger().info("Broadcasting to node " + (order + 1) + " on " + selectedEPR.getAddress());
|
||||||
|
// run the executor script
|
||||||
|
ExecutorCall call = new ExecutorCall(pluginName, gscope);
|
||||||
|
call.setEndpointReference(selectedEPR);
|
||||||
|
TaskCall task = null;
|
||||||
|
AnalysisLogger.getLogger().info("EPR:" + selectedEPR);
|
||||||
|
task = call.launch(inputs);
|
||||||
|
// AnalysisLogger.getLogger().info("Task EPR:" + task.getEndpointReference());
|
||||||
|
TaskProxy proxy = task.getProxy();
|
||||||
|
tasksProxies.add(new WorkerWatcher(proxy, AnalysisLogger.getLogger()));
|
||||||
|
// AnalysisLogger.getLogger().info("Contacting node " + (order + 1) + " OK on " + selectedEPR);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private int findNodes(String scopeString) throws Exception {
|
||||||
|
AnalysisLogger.getLogger().debug("SCOPE:"+scopeString);
|
||||||
|
GCUBEScope scope = GCUBEScope.getScope(scopeString);
|
||||||
|
ISClient client = GHNContext.getImplementation(ISClient.class);
|
||||||
|
WSResourceQuery wsquery = client.getQuery(WSResourceQuery.class);
|
||||||
|
wsquery.addAtomicConditions(new AtomicCondition("//gc:ServiceName", "Executor"));
|
||||||
|
wsquery.addAtomicConditions(new AtomicCondition("/child::*[local-name()='Task']/name[text()='" + pluginName + "']", pluginName));
|
||||||
|
List<RPDocument> listdoc = client.execute(wsquery, scope);
|
||||||
|
EndpointReferenceType epr = null;
|
||||||
|
eprs = new ArrayList<EndpointReferenceType>();
|
||||||
|
int numberOfEP = 0;
|
||||||
|
for (RPDocument resource : listdoc) {
|
||||||
|
epr = resource.getEndpoint();
|
||||||
|
numberOfEP++;
|
||||||
|
eprs.add(epr);
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("Found " + numberOfEP + " endpoints");
|
||||||
|
// get current number of available nodes
|
||||||
|
actualNumberOfNodes = eprs.size();
|
||||||
|
return numberOfEP;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void setQueueVariables() throws Exception {
|
||||||
|
queueName = "D4ScienceJob"; // + session;
|
||||||
|
queueResponse = queueName + "Response"+session;
|
||||||
|
//general scope
|
||||||
|
queueURL = gscope.getServiceMap().getEndpoints(GHNContext.MSGBROKER).iterator().next().getAddress().toString();
|
||||||
|
//tests on ecosystem
|
||||||
|
//TODO: delete this!
|
||||||
|
// queueURL = "tcp://ui.grid.research-infrastructures.eu:6166";
|
||||||
|
// queueURL = "tcp://message-broker.d4science.research-infrastructures.eu:6166";
|
||||||
|
AnalysisLogger.getLogger().info("Queue for the scope: " + queueURL);
|
||||||
|
if (queueURL==null){
|
||||||
|
if (scope.startsWith("/gcube"))
|
||||||
|
queueURL = "tcp://ui.grid.research-infrastructures.eu:6166";
|
||||||
|
else
|
||||||
|
queueURL = "tcp://message-broker.d4science.research-infrastructures.eu:6166";
|
||||||
|
}
|
||||||
|
queueUSER = ActiveMQConnection.DEFAULT_USER;
|
||||||
|
queuePWD = ActiveMQConnection.DEFAULT_PASSWORD;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void deleteRemoteFolder() throws Exception {
|
||||||
|
ScopeProvider.instance.set(scope);
|
||||||
|
IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED,MemoryType.VOLATILE).getClient();
|
||||||
|
// IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, gscope).getClient();
|
||||||
|
AnalysisLogger.getLogger().info("Removing Remote Dir " + remoteDir);
|
||||||
|
client.removeDir().RDir(remoteDir);
|
||||||
|
AnalysisLogger.getLogger().info("Removed");
|
||||||
|
}
|
||||||
|
|
||||||
|
private void uploadFilesOnStorage(boolean forceupload) throws Exception {
|
||||||
|
ScopeProvider.instance.set(scope);
|
||||||
|
IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE).getClient();
|
||||||
|
// IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, gscope).getClient();
|
||||||
|
File dir = new File(localDir);
|
||||||
|
File[] files = dir.listFiles();
|
||||||
|
AnalysisLogger.getLogger().info("Start uploading");
|
||||||
|
filenames = new ArrayList<String>();
|
||||||
|
fileurls = new ArrayList<String>();
|
||||||
|
boolean uploadFiles = forceupload;
|
||||||
|
// if we do not force upload then check if the folder is yet there
|
||||||
|
if (!uploadFiles) {
|
||||||
|
List<StorageObject> remoteObjects = client.showDir().RDir(remoteDir);
|
||||||
|
// only upload files if they are not yet uploaded
|
||||||
|
if (remoteObjects.size() == 0)
|
||||||
|
uploadFiles = true;
|
||||||
|
}
|
||||||
|
if (!uploadFiles)
|
||||||
|
AnalysisLogger.getLogger().info("Unnecessary to Uploading Files");
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Loading files");
|
||||||
|
for (File sfile : files) {
|
||||||
|
if (sfile.getName().startsWith("."))
|
||||||
|
continue;
|
||||||
|
|
||||||
|
String localf = sfile.getAbsolutePath();
|
||||||
|
String filename = sfile.getName();
|
||||||
|
String remotef = remoteDir + sfile.getName();
|
||||||
|
if (uploadFiles) {
|
||||||
|
client.put(true).LFile(localf).RFile(remotef);
|
||||||
|
AnalysisLogger.getLogger().info("Uploading File "+localf+" as remote file "+remotef);
|
||||||
|
}
|
||||||
|
String url = client.getUrl().RFile(remotef);
|
||||||
|
// AnalysisLogger.getLogger().info("URL obtained: " + url);
|
||||||
|
filenames.add(filename);
|
||||||
|
fileurls.add(url);
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("Loading finished");
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private void broadcastListenCommandToExecutorNodes() throws Exception {
|
||||||
|
AnalysisLogger.getLogger().info("Submitting script to Remote Queue " + queueName);
|
||||||
|
List<WorkerWatcher> tasksProxies = new ArrayList<WorkerWatcher>();
|
||||||
|
try{
|
||||||
|
findNodes(scope);
|
||||||
|
}catch(Exception e){
|
||||||
|
AnalysisLogger.getLogger().info("Error in Finding nodes - using previous value");
|
||||||
|
}
|
||||||
|
activeNodes = actualNumberOfNodes;
|
||||||
|
// launch the tasks
|
||||||
|
for (int i = 0; i < actualNumberOfNodes; i++) {
|
||||||
|
try {
|
||||||
|
contactNodes(tasksProxies, i, queueName, queueUSER, queuePWD, queueURL, queueResponse, session, "false");
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
AnalysisLogger.getLogger().info("Error in Contacting nodes");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void createClientProducer() throws Exception {
|
||||||
|
AnalysisLogger.getLogger().info("Creating Message Queue and Producer");
|
||||||
|
// create the Producer
|
||||||
|
QueueManager qm = new QueueManager();
|
||||||
|
qm.createAndConnect(queueUSER, queuePWD, queueURL, queueName);
|
||||||
|
producer = new Producer(qm, queueName);
|
||||||
|
AnalysisLogger.getLogger().info("Producer OK");
|
||||||
|
}
|
||||||
|
|
||||||
|
private void createClientConsumer() throws Exception {
|
||||||
|
AnalysisLogger.getLogger().info("Creating Response Message Queue and Consumer");
|
||||||
|
// create the listener
|
||||||
|
statuslistener = new StatusListener();
|
||||||
|
QueueManager qm1 = new QueueManager();
|
||||||
|
qm1.createAndConnect(queueUSER, queuePWD, queueURL, queueResponse);
|
||||||
|
consumer = new Consumer(qm1, statuslistener, statuslistener, queueResponse);
|
||||||
|
AnalysisLogger.getLogger().info("Consumers OK");
|
||||||
|
}
|
||||||
|
|
||||||
|
boolean activeMessages[];
|
||||||
|
public int resentMessages[];
|
||||||
|
|
||||||
|
private void sendMessages() throws Exception {
|
||||||
|
int i = 0;
|
||||||
|
numberOfMessages = arguments.size();
|
||||||
|
totalNumberOfMessages = numberOfMessages;
|
||||||
|
AnalysisLogger.getLogger().info("Messages To Send " + numberOfMessages);
|
||||||
|
activeMessages = new boolean[numberOfMessages];
|
||||||
|
resentMessages = new int[numberOfMessages];
|
||||||
|
for (String argum : arguments) {
|
||||||
|
Map<String, Object> inputs = generateInputMessage(filenames, fileurls, outputDir, script, argum, i, scope, serviceClass, serviceName, owner, remoteDir, session, configuration, deletefiles, false);
|
||||||
|
producer.sendMessage(inputs, 0);
|
||||||
|
AnalysisLogger.getLogger().info("Send " + i);
|
||||||
|
activeMessages[i] = true;
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().info("Messages Sent " + numberOfMessages);
|
||||||
|
}
|
||||||
|
|
||||||
|
private Map<String, Object> generateInputMessage(Object filenames, Object fileurls, String outputDir, String script, String argum, int i, String scope, String serviceClass, String serviceName, String owner, String remoteDir, String session, String configuration, boolean deletefiles, boolean duplicateMessage) {
|
||||||
|
Map<String, Object> inputs = new HashMap<String, Object>();
|
||||||
|
|
||||||
|
inputs.put(ATTRIBUTE.FILE_NAMES.name(), filenames);
|
||||||
|
inputs.put(ATTRIBUTE.FILE_URLS.name(), fileurls);
|
||||||
|
inputs.put(ATTRIBUTE.OUTPUTDIR.name(), outputDir);
|
||||||
|
inputs.put(ATTRIBUTE.SCRIPT.name(), script);
|
||||||
|
inputs.put(ATTRIBUTE.ARGUMENTS.name(), argum + " " + duplicateMessage);
|
||||||
|
inputs.put(ATTRIBUTE.ORDER.name(), "" + i);
|
||||||
|
inputs.put(ATTRIBUTE.SCOPE.name(), scope);
|
||||||
|
inputs.put(ATTRIBUTE.SERVICE_CLASS.name(), serviceClass);
|
||||||
|
inputs.put(ATTRIBUTE.SERVICE_NAME.name(), serviceName);
|
||||||
|
inputs.put(ATTRIBUTE.OWNER.name(), owner);
|
||||||
|
inputs.put(ATTRIBUTE.REMOTEDIR.name(), remoteDir);
|
||||||
|
inputs.put(ATTRIBUTE.CLEAN_CACHE.name(), "" + deletefiles);
|
||||||
|
inputs.put(ATTRIBUTE.QSESSION.name(), session);
|
||||||
|
inputs.put(ATTRIBUTE.CONFIGURATION.name(), configuration);
|
||||||
|
inputs.put(ATTRIBUTE.TOPIC_RESPONSE_NAME.name(), queueResponse);
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_USER.name(), queueUSER);
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_PASSWORD.name(), queuePWD);
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_URL.name(), queueURL);
|
||||||
|
return inputs;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Map<String, Object> generateWorkerInput(String queueName, String queueUser, String queuePassword, String queueURL, String queueResponse, String session, String purge) {
|
||||||
|
|
||||||
|
Map<String, Object> inputs = new HashMap<String, Object>();
|
||||||
|
|
||||||
|
inputs.put(ATTRIBUTE.TOPIC_NAME.name(), ScriptIOWorker.toInputString(queueName));
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_USER.name(), ScriptIOWorker.toInputString(queueUser));
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_PASSWORD.name(), ScriptIOWorker.toInputString(queuePassword));
|
||||||
|
inputs.put(ATTRIBUTE.QUEUE_URL.name(), ScriptIOWorker.toInputString(queueURL));
|
||||||
|
inputs.put(ATTRIBUTE.TOPIC_RESPONSE_NAME.name(), ScriptIOWorker.toInputString(queueResponse));
|
||||||
|
inputs.put(ATTRIBUTE.QSESSION.name(), session);
|
||||||
|
inputs.put(ATTRIBUTE.ERASE.name(), purge);
|
||||||
|
return inputs;
|
||||||
|
}
|
||||||
|
|
||||||
|
public class Broadcaster extends TimerTask {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void run() {
|
||||||
|
try {
|
||||||
|
AnalysisLogger.getLogger().info("(((((((((((((((((((((((((((------Broadcasting Information To Watchers------)))))))))))))))))))))))))))");
|
||||||
|
broadcastListenCommandToExecutorNodes();
|
||||||
|
AnalysisLogger.getLogger().info("(((((((((((((((((((((((((((------END Broadcasting Information To Watchers------)))))))))))))))))))))))))))");
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
AnalysisLogger.getLogger().info("--------------------------------Broadcaster: Error Sending Listen Message to Executors------)))))))))))))))))))))))))))");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public class ComputationTimerWatcher extends TimerTask {
|
||||||
|
|
||||||
|
long maxTime;
|
||||||
|
long lastTimeClock;
|
||||||
|
|
||||||
|
public ComputationTimerWatcher(long maxtime) {
|
||||||
|
this.maxTime = maxtime;
|
||||||
|
this.lastTimeClock = System.currentTimeMillis();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void reset() {
|
||||||
|
lastTimeClock = System.currentTimeMillis();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setmaxTime(long maxTime) {
|
||||||
|
this.maxTime = maxTime;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void run() {
|
||||||
|
try {
|
||||||
|
long t0 = System.currentTimeMillis();
|
||||||
|
AnalysisLogger.getLogger().info("Computation Watcher Timing Is " + (t0 - lastTimeClock)+" max computation time is "+maxTime);
|
||||||
|
if ((t0 - lastTimeClock) > maxTime) {
|
||||||
|
AnalysisLogger.getLogger().info("Computation Watcher - Computation Timeout: Closing Queue Job Manager!!!");
|
||||||
|
abort();
|
||||||
|
}
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
AnalysisLogger.getLogger().info("Error Taking clock");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public synchronized void abort() {
|
||||||
|
AnalysisLogger.getLogger().info("Computation Aborted");
|
||||||
|
this.abort = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public class StatusListener implements MessageListener, ExceptionListener {
|
||||||
|
|
||||||
|
private QueueWorkerWatcher[] watchers;
|
||||||
|
|
||||||
|
synchronized public void onException(JMSException ex) {
|
||||||
|
abort();
|
||||||
|
AnalysisLogger.getLogger().info("JMS Exception occured. Shutting down client.");
|
||||||
|
}
|
||||||
|
|
||||||
|
private synchronized void addWatcher(int order) {
|
||||||
|
if (watchers == null)
|
||||||
|
watchers = new QueueWorkerWatcher[totalNumberOfMessages];
|
||||||
|
|
||||||
|
QueueWorkerWatcher watcher = watchers[order];
|
||||||
|
if (watcher != null) {
|
||||||
|
destroyWatcher(order);
|
||||||
|
}
|
||||||
|
|
||||||
|
Map<String, Object> message = generateInputMessage(filenames, fileurls, outputDir, script, arguments.get(order), order, scope, serviceClass, serviceName, owner, remoteDir, session, configuration, deletefiles, true);
|
||||||
|
watchers[order] = new QueueWorkerWatcher(producer, message, order);
|
||||||
|
}
|
||||||
|
|
||||||
|
private synchronized void resetWatcher(int order) {
|
||||||
|
if (watchers == null)
|
||||||
|
watchers = new QueueWorkerWatcher[totalNumberOfMessages];
|
||||||
|
else if (watchers[order] != null)
|
||||||
|
watchers[order].resetTime();
|
||||||
|
}
|
||||||
|
|
||||||
|
private synchronized void destroyWatcher(int order) {
|
||||||
|
if (watchers != null && watchers[order] != null) {
|
||||||
|
if (watchers[order].hasResent())
|
||||||
|
resentMessages[order] = resentMessages[order] + 1;
|
||||||
|
|
||||||
|
watchers[order].destroy();
|
||||||
|
watchers[order] = null;
|
||||||
|
AnalysisLogger.getLogger().info("Destroyed Watcher number " + order);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public synchronized void destroyAllWatchers() {
|
||||||
|
if (watchers != null) {
|
||||||
|
for (int i = 0; i < watchers.length; i++) {
|
||||||
|
destroyWatcher(i);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void onMessage(Message message) {
|
||||||
|
|
||||||
|
// get message
|
||||||
|
try {
|
||||||
|
|
||||||
|
HashMap<String, Object> details = (HashMap<String, Object>) (HashMap<String, Object>) message.getObjectProperty(ATTRIBUTE.CONTENT.name());
|
||||||
|
String status = (String) details.get(ATTRIBUTE.STATUS.name());
|
||||||
|
String order = "" + details.get(ATTRIBUTE.ORDER.name());
|
||||||
|
String nodeaddress = (String) details.get(ATTRIBUTE.NODE.name());
|
||||||
|
String msession = (String) details.get(ATTRIBUTE.QSESSION.name());
|
||||||
|
Object error = details.get(ATTRIBUTE.ERROR.name());
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Current session " + session);
|
||||||
|
if ((msession != null) && (msession.equals(session))) {
|
||||||
|
AnalysisLogger.getLogger().info("Session " + session + " is right - acknowledge");
|
||||||
|
message.acknowledge();
|
||||||
|
AnalysisLogger.getLogger().info("Session " + session + " acknowledged");
|
||||||
|
int orderInt = -1;
|
||||||
|
try {
|
||||||
|
orderInt = Integer.parseInt(order);
|
||||||
|
} catch (Exception e3) {
|
||||||
|
e3.printStackTrace();
|
||||||
|
}
|
||||||
|
if (orderInt > -1) {
|
||||||
|
|
||||||
|
// reset the watcher
|
||||||
|
if (computationWatcher!=null)
|
||||||
|
computationWatcher.reset();
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Task number " + order + " is " + status + " on node " + nodeaddress + " and session " + session);
|
||||||
|
|
||||||
|
if (status.equals(ATTRIBUTE.STARTED.name())) {
|
||||||
|
computingNodes++;
|
||||||
|
addWatcher(orderInt);
|
||||||
|
}
|
||||||
|
if (status.equals(ATTRIBUTE.PROCESSING.name())) {
|
||||||
|
|
||||||
|
resetWatcher(orderInt);
|
||||||
|
} else if (status.equals(ATTRIBUTE.FINISHED.name())) {
|
||||||
|
|
||||||
|
totalmessages++;
|
||||||
|
computingNodes--;
|
||||||
|
destroyWatcher(orderInt);
|
||||||
|
if (numberOfMessages > 0)
|
||||||
|
numberOfMessages--;
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Remaining " + numberOfMessages + " messages to manage");
|
||||||
|
activeMessages[orderInt] = false;
|
||||||
|
|
||||||
|
} else if (status.equals(ATTRIBUTE.FATAL_ERROR.name())) {
|
||||||
|
if (error!=null)
|
||||||
|
AnalysisLogger.getLogger().info("REPORTED FATAL_ERROR on " +nodeaddress+" : ");
|
||||||
|
AnalysisLogger.getLogger().info(error);
|
||||||
|
|
||||||
|
computingNodes--;
|
||||||
|
if (maxFailureTries <= 0) {
|
||||||
|
AnalysisLogger.getLogger().info("Too much Failures - Aborting");
|
||||||
|
destroyAllWatchers();
|
||||||
|
abort();
|
||||||
|
} else {
|
||||||
|
AnalysisLogger.getLogger().info("Failure Occurred - Now Resending Message " + orderInt);
|
||||||
|
resentMessages[orderInt] = resentMessages[orderInt] + 1;
|
||||||
|
maxFailureTries--;
|
||||||
|
// resend message
|
||||||
|
Map<String, Object> retrymessage = generateInputMessage(filenames, fileurls, outputDir, script, arguments.get(orderInt), orderInt, scope, serviceClass, serviceName, owner, remoteDir, session, configuration, deletefiles, true);
|
||||||
|
producer.sendMessage(retrymessage, QCONSTANTS.timeToLive);
|
||||||
|
AnalysisLogger.getLogger().info("Failure Occurred - Resent Message " + orderInt);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
} else
|
||||||
|
AnalysisLogger.getLogger().info("Ignoring message " + order + " with status " + status);
|
||||||
|
} else {
|
||||||
|
AnalysisLogger.getLogger().info("wrong session " + msession + " ignoring message");
|
||||||
|
// consumer.manager.session.recover();
|
||||||
|
}
|
||||||
|
} catch (Exception e) {
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Error reading details ", e);
|
||||||
|
AnalysisLogger.getLogger().info("...Aborting Job...");
|
||||||
|
abort();
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,76 @@
|
||||||
|
package org.gcube.dataanalysis.executor.job.management;
|
||||||
|
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Timer;
|
||||||
|
import java.util.TimerTask;
|
||||||
|
|
||||||
|
import javax.jms.Message;
|
||||||
|
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.ATTRIBUTE;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.Producer;
|
||||||
|
import org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS;
|
||||||
|
|
||||||
|
public class QueueWorkerWatcher {
|
||||||
|
|
||||||
|
protected int maxwaitingTime = 2*QueueJobManager.queueWatcherMaxwaitingTime;
|
||||||
|
private long lastTimeClock;
|
||||||
|
Timer watcher;
|
||||||
|
Producer producer;
|
||||||
|
Map<String, Object> message;
|
||||||
|
public boolean resent=false;
|
||||||
|
int order;
|
||||||
|
|
||||||
|
public QueueWorkerWatcher(Producer producer, Map<String, Object> message, int order) {
|
||||||
|
this.producer = producer;
|
||||||
|
this.message = message;
|
||||||
|
resent=false;
|
||||||
|
this.order = order;
|
||||||
|
|
||||||
|
watcher = new Timer();
|
||||||
|
watcher.schedule(new Controller(), 0, QCONSTANTS.refreshStatusTime);
|
||||||
|
resetTime();
|
||||||
|
}
|
||||||
|
|
||||||
|
public synchronized void resetTime() {
|
||||||
|
lastTimeClock = System.currentTimeMillis();
|
||||||
|
}
|
||||||
|
|
||||||
|
public synchronized void destroy() {
|
||||||
|
if (watcher != null) {
|
||||||
|
watcher.cancel();
|
||||||
|
watcher.purge();
|
||||||
|
watcher = null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean hasResent(){
|
||||||
|
return resent;
|
||||||
|
}
|
||||||
|
|
||||||
|
private class Controller extends TimerTask {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void run() {
|
||||||
|
try {
|
||||||
|
long t0 = System.currentTimeMillis();
|
||||||
|
AnalysisLogger.getLogger().debug("Watcher "+order+" Timing Is "+(t0 - lastTimeClock)+ " max waiting time: "+maxwaitingTime);
|
||||||
|
if ((t0 - lastTimeClock) > maxwaitingTime) {
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Watcher "+order+" Time Is Over "+(t0 - lastTimeClock));
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().info("Watcher "+order+" Re-Sending Message "+message);
|
||||||
|
producer.sendMessage(message, QCONSTANTS.timeToLive);
|
||||||
|
// QueueJobManager.resentMessages[Integer.parseInt(""+message.get(ATTRIBUTE.ORDER.name()))]=QueueJobManager.resentMessages[Integer.parseInt(""+message.get(ATTRIBUTE.ORDER.name()))]+1;
|
||||||
|
resent = true;
|
||||||
|
AnalysisLogger.getLogger().info("Watcher "+order+" Destroying watcher");
|
||||||
|
destroy();
|
||||||
|
|
||||||
|
}
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,248 @@
|
||||||
|
package org.gcube.dataanalysis.executor.job.management;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.UUID;
|
||||||
|
|
||||||
|
import org.apache.axis.message.addressing.EndpointReferenceType;
|
||||||
|
import org.gcube.common.core.contexts.GHNContext;
|
||||||
|
import org.gcube.common.core.informationsystem.client.AtomicCondition;
|
||||||
|
import org.gcube.common.core.informationsystem.client.ISClient;
|
||||||
|
import org.gcube.common.core.informationsystem.client.RPDocument;
|
||||||
|
import org.gcube.common.core.informationsystem.client.queries.WSResourceQuery;
|
||||||
|
import org.gcube.common.core.scope.GCUBEScope;
|
||||||
|
import org.gcube.common.scope.api.ScopeProvider;
|
||||||
|
import org.gcube.contentmanagement.blobstorage.service.IClient;
|
||||||
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||||
|
import org.gcube.contentmanager.storageclient.wrapper.AccessType;
|
||||||
|
import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
|
||||||
|
import org.gcube.dataanalysis.executor.scripts.ScriptIOWorker;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.ExecutorCall;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.TaskCall;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.TaskProxy;
|
||||||
|
|
||||||
|
public class RemoteJobManager {
|
||||||
|
|
||||||
|
private static String pluginName = "ExecutorScript";
|
||||||
|
private int actualNumberOfNodes;
|
||||||
|
private GCUBEScope gscope;
|
||||||
|
private List<EndpointReferenceType> eprs;
|
||||||
|
float status;
|
||||||
|
boolean abort;
|
||||||
|
boolean shutdown;
|
||||||
|
protected int activeNodes;
|
||||||
|
String scope;
|
||||||
|
|
||||||
|
public int getActiveNodes() {
|
||||||
|
return activeNodes;
|
||||||
|
}
|
||||||
|
|
||||||
|
public float getStatus() {
|
||||||
|
return status;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getNumberOfNodes() {
|
||||||
|
return actualNumberOfNodes;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setNumberOfNodes(int newNumberOfNodes) {
|
||||||
|
actualNumberOfNodes = newNumberOfNodes;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void init(String scope, int numberOfNodes) throws Exception {
|
||||||
|
this.scope = scope;
|
||||||
|
gscope = GCUBEScope.getScope(scope);
|
||||||
|
AnalysisLogger.getLogger().debug("Using the following scope for this computation:"+gscope);
|
||||||
|
shutdown = false;
|
||||||
|
yetuploaded = false;
|
||||||
|
if (eprs == null)
|
||||||
|
actualNumberOfNodes = findNodes(scope);
|
||||||
|
else
|
||||||
|
actualNumberOfNodes = eprs.size();
|
||||||
|
|
||||||
|
if (numberOfNodes < actualNumberOfNodes)
|
||||||
|
actualNumberOfNodes = numberOfNodes;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public RemoteJobManager(String scope, int numberOfNodes) throws Exception {
|
||||||
|
init(scope, numberOfNodes);
|
||||||
|
}
|
||||||
|
|
||||||
|
public RemoteJobManager(String scope, int numberOfNodes, List<EndpointReferenceType> eprs) throws Exception {
|
||||||
|
this.eprs = eprs;
|
||||||
|
init(scope, numberOfNodes);
|
||||||
|
}
|
||||||
|
|
||||||
|
List<String> filenames;
|
||||||
|
List<String> fileurls;
|
||||||
|
boolean yetuploaded;
|
||||||
|
String session;
|
||||||
|
|
||||||
|
public boolean uploadAndExecute(String serviceClass, String serviceName, String owner, String localDir, String remoteDir, String outputDir, String script, List<String> arguments, boolean deletefiles) throws Exception {
|
||||||
|
boolean executeAll = false;
|
||||||
|
long t0 = System.currentTimeMillis();
|
||||||
|
//if not yet uploaded , upload required files
|
||||||
|
if (!yetuploaded) {
|
||||||
|
ScopeProvider.instance.set(scope);
|
||||||
|
IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED).getClient();
|
||||||
|
// IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, gscope).getClient();
|
||||||
|
File dir = new File(localDir);
|
||||||
|
File[] files = dir.listFiles();
|
||||||
|
AnalysisLogger.getLogger().debug("Start uploading");
|
||||||
|
filenames = new ArrayList<String>();
|
||||||
|
fileurls = new ArrayList<String>();
|
||||||
|
for (File sfile : files) {
|
||||||
|
String localf = sfile.getAbsolutePath();
|
||||||
|
String filename = sfile.getName();
|
||||||
|
String remotef = remoteDir + sfile.getName();
|
||||||
|
client.put(true).LFile(localf).RFile(remotef);
|
||||||
|
String url = client.getUrl().RFile(remotef);
|
||||||
|
AnalysisLogger.getLogger().debug("URL created: " + url);
|
||||||
|
filenames.add(filename);
|
||||||
|
fileurls.add(url);
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().debug("Upload end");
|
||||||
|
yetuploaded = true;
|
||||||
|
session = (""+UUID.randomUUID()).replace("-", "");
|
||||||
|
}
|
||||||
|
|
||||||
|
//if the number of available nodes is higher than zero launch the tasks
|
||||||
|
if (actualNumberOfNodes > 0) {
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().debug("Executing script on " + actualNumberOfNodes + " nodes");
|
||||||
|
int len = arguments.size();
|
||||||
|
List<WorkerWatcher> tasksProxies = new ArrayList<WorkerWatcher>();
|
||||||
|
activeNodes = 0;
|
||||||
|
//launch the tasks
|
||||||
|
for (int i = 0; i < actualNumberOfNodes; i++) {
|
||||||
|
String argum = "";
|
||||||
|
//supply the arguments if they are available
|
||||||
|
if (i < len)
|
||||||
|
argum = arguments.get(i);
|
||||||
|
//generate the input map according to the arguments
|
||||||
|
Map<String, Object> inputs = generateInput(filenames, fileurls, outputDir, script, argum, i, scope, serviceClass, serviceName, owner, remoteDir,session,deletefiles);
|
||||||
|
AnalysisLogger.getLogger().debug("-> Owner: " + owner + " ServiceClass: " + serviceClass + " ServiceName:" + serviceName + " remoteDir:" + remoteDir);
|
||||||
|
//take the i-th endpoint of the executor
|
||||||
|
EndpointReferenceType selectedEPR = eprs.get(i);
|
||||||
|
AnalysisLogger.getLogger().debug("Launching node " + (i + 1) + " on " + selectedEPR);
|
||||||
|
//run the executor script
|
||||||
|
ExecutorCall call = new ExecutorCall(pluginName, gscope);
|
||||||
|
call.setEndpointReference(selectedEPR);
|
||||||
|
TaskCall task = null;
|
||||||
|
task = call.launch(inputs);
|
||||||
|
TaskProxy proxy = task.getProxy();
|
||||||
|
tasksProxies.add(new WorkerWatcher(proxy, AnalysisLogger.getLogger()));
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().debug("Launching node " + (i + 1) + " OK on " + selectedEPR);
|
||||||
|
//add the task to the list in order to reuse it
|
||||||
|
}
|
||||||
|
|
||||||
|
activeNodes = actualNumberOfNodes;
|
||||||
|
AnalysisLogger.getLogger().debug("Launch Finished - Controlling Status");
|
||||||
|
int allstatus = 0;
|
||||||
|
abort = false;
|
||||||
|
//control the execution: go until there are active nodes or the process must stop
|
||||||
|
while ((activeNodes != 0) && (!abort) && (!shutdown)) {
|
||||||
|
//for each node get the task state
|
||||||
|
int nworkers = tasksProxies.size();
|
||||||
|
int i=0;
|
||||||
|
while (i < nworkers) {
|
||||||
|
WorkerWatcher proxy = tasksProxies.get(i);
|
||||||
|
String state = proxy.getState();
|
||||||
|
AnalysisLogger.getLogger().debug("REMOTE JOB MANAGER-> STATE " + state );
|
||||||
|
//control for aborted computation
|
||||||
|
abort = ((state == null) || state.equals("FAILED") || (!state.equals("DONE") && !state.equals("RUNNING")));
|
||||||
|
//control for finished computation
|
||||||
|
boolean finished = false;
|
||||||
|
if (state != null)
|
||||||
|
finished = state.equals("DONE");
|
||||||
|
//if finished update the active nodes
|
||||||
|
if (finished) {
|
||||||
|
tasksProxies.remove(i);
|
||||||
|
allstatus++;
|
||||||
|
activeNodes--;
|
||||||
|
nworkers--;
|
||||||
|
if (activeNodes == 0)
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
else
|
||||||
|
i++;
|
||||||
|
|
||||||
|
status = Math.min(((float) allstatus / (float) actualNumberOfNodes) * 100f, 95f);
|
||||||
|
if (abort)
|
||||||
|
break;
|
||||||
|
if (shutdown)
|
||||||
|
break;
|
||||||
|
// AnalysisLogger.getLogger().debug(String.format("Task " + i + "executed started at %Tc with %s state ", proxy.getStartTime(), state));
|
||||||
|
//sleep before polling again
|
||||||
|
Thread.sleep(2000);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
activeNodes = 0;
|
||||||
|
|
||||||
|
AnalysisLogger.getLogger().debug("All Tasks have Finished");
|
||||||
|
if (!abort) {
|
||||||
|
AnalysisLogger.getLogger().debug("All Task were successful");
|
||||||
|
/*
|
||||||
|
* List<StorageObject> listElements = client.showDir().RDir(remoteDir); for (StorageObject obj : listElements) { AnalysisLogger.getLogger().debug("obj stored in directory " + remoteDir + ": " + obj.getName()); }
|
||||||
|
*/
|
||||||
|
} else
|
||||||
|
AnalysisLogger.getLogger().debug("Tasks were NOT successful");
|
||||||
|
} else
|
||||||
|
AnalysisLogger.getLogger().debug("Warning: could not execute tasks: No Nodes Available!");
|
||||||
|
AnalysisLogger.getLogger().debug("Whole procedure done in " + (System.currentTimeMillis() - t0) + " ms");
|
||||||
|
status = 100f;
|
||||||
|
return executeAll;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean wasAborted() {
|
||||||
|
return abort;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void stop() {
|
||||||
|
shutdown = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
private int findNodes(String scopeString) throws Exception {
|
||||||
|
GCUBEScope scope = GCUBEScope.getScope(scopeString);
|
||||||
|
ISClient client = GHNContext.getImplementation(ISClient.class);
|
||||||
|
WSResourceQuery wsquery = client.getQuery(WSResourceQuery.class);
|
||||||
|
wsquery.addAtomicConditions(new AtomicCondition("//gc:ServiceName", "Executor"));
|
||||||
|
wsquery.addAtomicConditions(new AtomicCondition("/child::*[local-name()='Task']/name[text()='"+pluginName+"']", pluginName));
|
||||||
|
List<RPDocument> listdoc = client.execute(wsquery, scope);
|
||||||
|
EndpointReferenceType epr = null;
|
||||||
|
eprs = new ArrayList<EndpointReferenceType>();
|
||||||
|
int numberOfEP = 0;
|
||||||
|
for (RPDocument resource : listdoc) {
|
||||||
|
epr = resource.getEndpoint();
|
||||||
|
numberOfEP++;
|
||||||
|
eprs.add(epr);
|
||||||
|
}
|
||||||
|
AnalysisLogger.getLogger().debug("Found " + numberOfEP + " endpoints");
|
||||||
|
|
||||||
|
return numberOfEP;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Map<String, Object> generateInput(Object filenames, Object fileurls, String outputDir, String script, String argum, int i, String scope, String serviceClass, String serviceName, String owner, String remoteDir,String session,boolean deletefiles) {
|
||||||
|
Map<String, Object> inputs = new HashMap<String, Object>();
|
||||||
|
inputs.put("FILE_NAMES", filenames);
|
||||||
|
inputs.put("FILE_URLS", fileurls);
|
||||||
|
inputs.put("OUTPUTDIR", ScriptIOWorker.toInputString(outputDir));
|
||||||
|
inputs.put("SCRIPT", ScriptIOWorker.toInputString(script));
|
||||||
|
inputs.put("ARGUMENTS", ScriptIOWorker.toInputString(argum));
|
||||||
|
inputs.put("NODE_IDENTIFIER", "" + i);
|
||||||
|
inputs.put("SCOPE", ScriptIOWorker.toInputString(scope));
|
||||||
|
inputs.put("SERVICE_CLASS", ScriptIOWorker.toInputString(serviceClass));
|
||||||
|
inputs.put("SERVICE_NAME", ScriptIOWorker.toInputString(serviceName));
|
||||||
|
inputs.put("OWNER", ScriptIOWorker.toInputString(owner));
|
||||||
|
inputs.put("REMOTEDIR", ScriptIOWorker.toInputString(remoteDir));
|
||||||
|
inputs.put("CLEAN_CACHE",""+deletefiles);
|
||||||
|
// inputs.put("SESSION", ScriptIO.toInputString(session));
|
||||||
|
return inputs;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,37 @@
|
||||||
|
package org.gcube.dataanalysis.executor.job.management;
|
||||||
|
|
||||||
|
import org.apache.log4j.Logger;
|
||||||
|
import org.gcube.vremanagement.executor.stubs.TaskProxy;
|
||||||
|
|
||||||
|
public class WorkerWatcher {
|
||||||
|
private static int maxTries = 15;
|
||||||
|
private int currentTries;
|
||||||
|
private static String runningState = "RUNNING";
|
||||||
|
private static String failedState = "FAILED";
|
||||||
|
Logger logger;
|
||||||
|
|
||||||
|
TaskProxy proxy;
|
||||||
|
public WorkerWatcher(TaskProxy proxy, Logger logger){
|
||||||
|
this.proxy = proxy;
|
||||||
|
this.logger = logger;
|
||||||
|
currentTries = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getState(){
|
||||||
|
String state ="";
|
||||||
|
try{
|
||||||
|
proxy.synchronize();
|
||||||
|
state = proxy.getState();
|
||||||
|
return state;
|
||||||
|
}catch(Exception e){
|
||||||
|
logger.error("Error in getting state: recover try number "+currentTries,e);
|
||||||
|
currentTries++;
|
||||||
|
if (currentTries>maxTries){
|
||||||
|
return failedState;
|
||||||
|
}
|
||||||
|
else return runningState;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,34 @@
|
||||||
|
package org.gcube.dataanalysis.executor.messagequeue;
|
||||||
|
|
||||||
|
public enum ATTRIBUTE {
|
||||||
|
STATUS,
|
||||||
|
DONE,
|
||||||
|
STARTED,
|
||||||
|
FINISHED,
|
||||||
|
PROCESSING,
|
||||||
|
FATAL_ERROR,
|
||||||
|
TRIVIAL_ERROR,
|
||||||
|
ORDER,
|
||||||
|
NODE,
|
||||||
|
CONTENT,
|
||||||
|
QSESSION,
|
||||||
|
TOPIC_NAME,
|
||||||
|
QUEUE_USER,
|
||||||
|
QUEUE_PASSWORD,
|
||||||
|
QUEUE_URL,
|
||||||
|
TOPIC_RESPONSE_NAME,
|
||||||
|
ERASE,
|
||||||
|
FILE_NAMES,
|
||||||
|
FILE_URLS,
|
||||||
|
CONFIGURATION,
|
||||||
|
OUTPUTDIR,
|
||||||
|
OWNER,
|
||||||
|
REMOTEDIR,
|
||||||
|
SERVICE_CLASS,
|
||||||
|
SERVICE_NAME,
|
||||||
|
SCOPE,
|
||||||
|
SCRIPT,
|
||||||
|
ARGUMENTS,
|
||||||
|
CLEAN_CACHE,
|
||||||
|
ERROR
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,62 @@
|
||||||
|
package org.gcube.dataanalysis.executor.messagequeue;
|
||||||
|
|
||||||
|
import javax.jms.ExceptionListener;
|
||||||
|
import javax.jms.JMSException;
|
||||||
|
import javax.jms.MessageConsumer;
|
||||||
|
import javax.jms.MessageListener;
|
||||||
|
|
||||||
|
public class Consumer {
|
||||||
|
public QueueManager manager;
|
||||||
|
public MessageConsumer consumer;
|
||||||
|
private MessageListener consumerCallback;
|
||||||
|
private ExceptionListener errorCallback;
|
||||||
|
private String topic;
|
||||||
|
|
||||||
|
|
||||||
|
public Consumer(QueueManager manager, MessageListener consumerCallback, ExceptionListener errorCallback, String topic) throws JMSException, InterruptedException {
|
||||||
|
this.manager = manager;
|
||||||
|
this.consumerCallback = consumerCallback;
|
||||||
|
this.errorCallback = errorCallback;
|
||||||
|
this.topic = topic;
|
||||||
|
|
||||||
|
create();
|
||||||
|
}
|
||||||
|
|
||||||
|
private void create() throws JMSException, InterruptedException {
|
||||||
|
|
||||||
|
// Topic ConsumerTopic = manager.session.createTopic(topic);
|
||||||
|
|
||||||
|
MessageConsumer consumer = manager.session.createConsumer(manager.destination);
|
||||||
|
// MessageConsumer consumer = manager.session.createDurableSubscriber(ConsumerTopic, "Consumer."+topic);
|
||||||
|
// MessageConsumer consumer = manager.session.createConsumer(ConsumerTopic);
|
||||||
|
manager.connection.setExceptionListener(errorCallback);
|
||||||
|
consumer.setMessageListener(consumerCallback);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public void standBy() throws JMSException {
|
||||||
|
if (consumer != null)
|
||||||
|
consumer.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void wake() throws Exception {
|
||||||
|
this.create();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void stop() throws JMSException {
|
||||||
|
if (consumer != null) {
|
||||||
|
consumer.close();
|
||||||
|
|
||||||
|
}
|
||||||
|
// closeSession();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void closeSession() throws JMSException {
|
||||||
|
try {
|
||||||
|
manager.closeSession();
|
||||||
|
manager.connection.close();
|
||||||
|
} catch (Exception e) {
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,70 @@
|
||||||
|
package org.gcube.dataanalysis.executor.messagequeue;
|
||||||
|
|
||||||
|
import java.util.UUID;
|
||||||
|
|
||||||
|
import javax.jms.DeliveryMode;
|
||||||
|
import javax.jms.JMSException;
|
||||||
|
import javax.jms.Message;
|
||||||
|
import javax.jms.MessageProducer;
|
||||||
|
import javax.jms.TextMessage;
|
||||||
|
import javax.jms.Topic;
|
||||||
|
|
||||||
|
public class Producer {
|
||||||
|
|
||||||
|
public MessageProducer producer;
|
||||||
|
public QueueManager manager;
|
||||||
|
public String topic;
|
||||||
|
public String identifier;
|
||||||
|
public Producer(QueueManager manager,String topic) throws JMSException {
|
||||||
|
this.manager = manager;
|
||||||
|
this.topic = topic;
|
||||||
|
this.identifier = "" + UUID.randomUUID();
|
||||||
|
create();
|
||||||
|
}
|
||||||
|
|
||||||
|
private void create() throws JMSException {
|
||||||
|
// Topic ProducerTopic = manager.session.createTopic(topic);
|
||||||
|
producer = manager.session.createProducer(manager.destination);
|
||||||
|
// producer = manager.session.createProducer(ProducerTopic);
|
||||||
|
producer.setDeliveryMode(DeliveryMode.PERSISTENT);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void sendTextMessage(String text, long timeToLive) throws JMSException {
|
||||||
|
TextMessage message = manager.session.createTextMessage(text);
|
||||||
|
producer.setTimeToLive(timeToLive);
|
||||||
|
producer.send(message);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void sendMessage(Object toSend, long timeToLive) throws JMSException {
|
||||||
|
Message message = manager.session.createMessage();
|
||||||
|
message.setObjectProperty(ATTRIBUTE.CONTENT.name(), toSend);
|
||||||
|
producer.setTimeToLive(timeToLive);
|
||||||
|
producer.send(message);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void standBy() throws JMSException {
|
||||||
|
producer.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void wake() throws Exception {
|
||||||
|
this.create();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void stop() throws JMSException {
|
||||||
|
if (producer != null){
|
||||||
|
producer.close();
|
||||||
|
|
||||||
|
}
|
||||||
|
// closeSession();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public void closeSession() throws JMSException {
|
||||||
|
try {
|
||||||
|
manager.closeSession();
|
||||||
|
manager.connection.close();
|
||||||
|
} catch (Exception e) {
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,8 @@
|
||||||
|
package org.gcube.dataanalysis.executor.messagequeue;
|
||||||
|
|
||||||
|
public class QCONSTANTS {
|
||||||
|
|
||||||
|
public static int refreshStatusTime = 60000;
|
||||||
|
public static int QueueLifeTime = 60000;//3600000;
|
||||||
|
public static long timeToLive = 0;
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,77 @@
|
||||||
|
package org.gcube.dataanalysis.executor.messagequeue;
|
||||||
|
|
||||||
|
import java.util.Hashtable;
|
||||||
|
import java.util.Properties;
|
||||||
|
import java.util.UUID;
|
||||||
|
|
||||||
|
import javax.jms.Connection;
|
||||||
|
import javax.jms.ConnectionFactory;
|
||||||
|
import javax.jms.Destination;
|
||||||
|
import javax.jms.JMSException;
|
||||||
|
import javax.jms.Session;
|
||||||
|
import javax.management.ObjectName;
|
||||||
|
import javax.management.remote.JMXConnector;
|
||||||
|
import javax.management.remote.JMXConnectorFactory;
|
||||||
|
import javax.management.remote.JMXServiceURL;
|
||||||
|
import javax.naming.Context;
|
||||||
|
import javax.naming.InitialContext;
|
||||||
|
|
||||||
|
import org.apache.activemq.ActiveMQConnectionFactory;
|
||||||
|
import org.apache.activemq.broker.BrokerService;
|
||||||
|
import org.apache.activemq.broker.jmx.QueueViewMBean;
|
||||||
|
|
||||||
|
public class QueueManager {
|
||||||
|
|
||||||
|
public ActiveMQConnectionFactory connectionFactory;
|
||||||
|
public Connection connection;
|
||||||
|
public Session session;
|
||||||
|
public Destination destination;
|
||||||
|
boolean transacted = false;
|
||||||
|
public String mqurl;
|
||||||
|
private String identifier;
|
||||||
|
|
||||||
|
public void createAndConnect(String user,String password, String mqurl, String queueName) throws JMSException {
|
||||||
|
this.mqurl=mqurl;
|
||||||
|
connect(user,password,mqurl);
|
||||||
|
session = connection.createSession(transacted, Session.CLIENT_ACKNOWLEDGE);
|
||||||
|
this.identifier = ""+UUID.randomUUID();
|
||||||
|
/*
|
||||||
|
Hashtable properties = new Hashtable();
|
||||||
|
properties.put(Context.INITIAL_CONTEXT_FACTORY, "org.apache.activemq.jndi.ActiveMQInitialContextFactory");
|
||||||
|
properties.put(Context.PROVIDER_URL, mqurl);
|
||||||
|
InitialContext context = new InitialContext(properties);
|
||||||
|
ConnectionFactory factory = (ConnectionFactory) context.lookup("ConnectionFactory");
|
||||||
|
|
||||||
|
destination = (Destination) context.lookup(queueName);
|
||||||
|
*/
|
||||||
|
// destination = session.createQueue(queueName+"?consumer.prefetchSize=3");
|
||||||
|
destination = session.createQueue(queueName+"?wireFormat.maxInactivityDurationInitalDelay=3600000&requestTimeout=240000&wireFormat.maxInactivityDuration=3600000");
|
||||||
|
}
|
||||||
|
|
||||||
|
public void destroy(){
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private void connect(String user,String password, String mqurl) throws JMSException{
|
||||||
|
connectionFactory = new ActiveMQConnectionFactory(user, password, mqurl);
|
||||||
|
connectionFactory.getPrefetchPolicy().setQueuePrefetch(1);
|
||||||
|
|
||||||
|
// Properties p = new Properties();
|
||||||
|
// p.put("persistent", "false");
|
||||||
|
// p.put("consumer.prefetchSize", "3");
|
||||||
|
// p.put("ms.prefetchPolicy.all", "3");
|
||||||
|
// p.put("cms.PrefetchPolicy.queuePrefetch", "3");
|
||||||
|
|
||||||
|
// connectionFactory.setProperties(p);
|
||||||
|
connection = connectionFactory.createConnection();
|
||||||
|
connection.setClientID(identifier);
|
||||||
|
connection.start();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void closeSession() throws Exception{
|
||||||
|
// session.unsubscribe(identifier);
|
||||||
|
|
||||||
|
session.close();
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,19 @@
|
||||||
|
package org.gcube.dataanalysis.executor.nodes.algorithms;
|
||||||
|
|
||||||
|
|
||||||
|
public class AquamapsNative2050Node extends AquamapsNativeNode{
|
||||||
|
|
||||||
|
public AquamapsNative2050Node(){
|
||||||
|
super();
|
||||||
|
type = "2050";
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getName() {
|
||||||
|
return "AQUAMAPS_NATIVE_2050";
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getDescription() {
|
||||||
|
return "Algorithm for Native Range in 2050 by Aquamaps on a single node";
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,70 @@
|
||||||
|
package org.gcube.dataanalysis.executor.nodes.algorithms;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Queue;
|
||||||
|
import java.util.concurrent.ConcurrentLinkedQueue;
|
||||||
|
|
||||||
|
import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative;
|
||||||
|
|
||||||
|
public class AquamapsNativeNode extends AquamapsSuitableNode{
|
||||||
|
|
||||||
|
public AquamapsNativeNode(){
|
||||||
|
super();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getName() {
|
||||||
|
return "AQUAMAPS_NATIVE";
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getDescription() {
|
||||||
|
return "Algorithm for Native Range by Aquamaps on a single node";
|
||||||
|
}
|
||||||
|
|
||||||
|
// writes the distribution model on the DB: input species vector + list of areas vectors to report
|
||||||
|
public void singleStepPostprocess(Object species) {
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Analyzing Species distribution");
|
||||||
|
// write info on DB
|
||||||
|
Queue<String> rows = new ConcurrentLinkedQueue<String>();
|
||||||
|
String speciesID = AquamapsSuitableFunctions.getMainInfoID(species);
|
||||||
|
Map<String, Float> csquaresMap = operations.completeDistribution.get(speciesID);
|
||||||
|
|
||||||
|
if (csquaresMap != null) {
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Getting csquare probabilites");
|
||||||
|
// write only processed areas
|
||||||
|
for (String singleCsquare : csquaresMap.keySet()) {
|
||||||
|
String additionalInformation = operations.getAdditionalInformation(species, operations.processedAreas.get(singleCsquare));
|
||||||
|
if (additionalInformation == null)
|
||||||
|
additionalInformation = "";
|
||||||
|
else if (additionalInformation.length() > 0)
|
||||||
|
additionalInformation = "," + additionalInformation.trim();
|
||||||
|
|
||||||
|
float prob = 0f;
|
||||||
|
try {
|
||||||
|
prob = csquaresMap.get(singleCsquare);
|
||||||
|
} catch (Exception e) {
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess ->Error in getting probability value at " + speciesID + " , " + singleCsquare);
|
||||||
|
}
|
||||||
|
if (prob > 0)
|
||||||
|
rows.offer("'" + speciesID + "','" + singleCsquare + "','" + MathFunctions.roundDecimal(prob, 3) + "'" + additionalInformation);
|
||||||
|
}
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Filtering probabilities. Size:"+rows.size());
|
||||||
|
Queue<String> newrows = new AquamapsNative().filterProbabilitySet(rows);
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Filtered probabilities. Size:"+newrows.size());
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Writing rows on DB");
|
||||||
|
List<String> toWrite = new ArrayList<String>();
|
||||||
|
for (String row:newrows){
|
||||||
|
toWrite.add(row);
|
||||||
|
// System.out.println("Added row: "+row);
|
||||||
|
}
|
||||||
|
AquamapsSuitableFunctions.writeOnDB(toWrite, currentconfig.getParam("DistributionTable"), dbHibConnection);
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Rows written on DB");
|
||||||
|
}
|
||||||
|
else
|
||||||
|
System.out.println("Aquamaps Algorithm Single Step PostProcess-> Probability distribution is void");
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,19 @@
|
||||||
|
package org.gcube.dataanalysis.executor.nodes.algorithms;
|
||||||
|
|
||||||
|
|
||||||
|
public class AquamapsSuitable2050Node extends AquamapsSuitableNode{
|
||||||
|
|
||||||
|
public AquamapsSuitable2050Node(){
|
||||||
|
super();
|
||||||
|
type = "2050";
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getName() {
|
||||||
|
return "AQUAMAPS_SUITABLE_2050";
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getDescription() {
|
||||||
|
return "Algorithm for Suitable Range in 2050 by Aquamaps on a single node";
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,200 @@
|
||||||
|
package org.gcube.dataanalysis.executor.nodes.algorithms;
|
||||||
|
|
||||||
|
import java.io.BufferedWriter;
|
||||||
|
import java.io.File;
|
||||||
|
import java.io.FileInputStream;
|
||||||
|
import java.io.ObjectInputStream;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.concurrent.ConcurrentHashMap;
|
||||||
|
|
||||||
|
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsAlgorithmCore;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
|
||||||
|
import org.gcube.dataanalysis.ecoengine.utils.Transformations;
|
||||||
|
import org.hibernate.SessionFactory;
|
||||||
|
|
||||||
|
import com.thoughtworks.xstream.XStream;
|
||||||
|
|
||||||
|
public class AquamapsSuitableFunctions {
|
||||||
|
|
||||||
|
public static String countAllSpeciesQuery = "select count(*) from %1$s;";
|
||||||
|
// public static String countAll = "select count(*) from %1$s;";
|
||||||
|
public static String countAll = "EXPLAIN SELECT * FROM %1$s;";
|
||||||
|
public static String countCsquareCodeQuery = "select count (*) from %1$s d where oceanarea>0";
|
||||||
|
public static String selectAllSpeciesQuery = "select depthmin,meandepth,depthprefmin,pelagic,depthprefmax,depthmax,tempmin,layer,tempprefmin,tempprefmax,tempmax,salinitymin,salinityprefmin,salinityprefmax,salinitymax,primprodmin,primprodprefmin,primprodprefmax,primprodmax,iceconmin,iceconprefmin,iceconprefmax,iceconmax,landdistyn,landdistmin,landdistprefmin,landdistprefmax,landdistmax,nmostlat,smostlat,wmostlong,emostlong,faoareas,speciesid from %1$s order by speciesid limit %2$s offset %3$s;";
|
||||||
|
public static String csquareCodeQuery = "select csquarecode,depthmean,depthmax,depthmin, sstanmean,sbtanmean,salinitymean,salinitybmean, primprodmean,iceconann,landdist,oceanarea,centerlat,centerlong,faoaream,eezall,lme from %1$s d where oceanarea>0 order by csquarecode limit %2$s offset %3$s";
|
||||||
|
public static String createTableStatement = "CREATE TABLE %1$s ( speciesid character varying, csquarecode character varying, probability real, boundboxyn smallint, faoareayn smallint, faoaream integer, eezall character varying, lme integer) WITH (OIDS=FALSE ) #TABLESPACE#; CREATE INDEX CONCURRENTLY %1$s_idx ON %1$s USING btree (speciesid, csquarecode, faoaream, eezall, lme);";
|
||||||
|
public static String metainfo = "boundboxyn, faoareayn, faoaream, eezall, lme";
|
||||||
|
public static String selectAllSpeciesObservationQuery = "SELECT speciesid,maxclat,minclat from %1$s;";
|
||||||
|
public static String probabilityInsertionStatement = "insert into %1$s (speciesid,csquarecode,probability %ADDEDINFORMATION%) VALUES %2$s";
|
||||||
|
public static String deleteDuplicates = "delete from %1$s where speciesid='%2$s'";
|
||||||
|
|
||||||
|
|
||||||
|
// Default Files
|
||||||
|
private static String speciesFile = "species.dat";
|
||||||
|
private static String csquaresFile = "csquares.dat";
|
||||||
|
private static String maxminlatFile = "maxminlat.dat";
|
||||||
|
private static String configFile = "config.dat";
|
||||||
|
|
||||||
|
// file1
|
||||||
|
public HashMap<String, List<Object>> allSpeciesObservations;
|
||||||
|
// file2
|
||||||
|
public List<Object> speciesVectors;
|
||||||
|
// file3
|
||||||
|
public List<Object> environmentVectors;
|
||||||
|
public int numberOfSpecies;
|
||||||
|
public int numberOfCells;
|
||||||
|
|
||||||
|
|
||||||
|
//processing variables
|
||||||
|
public AlgorithmConfiguration currentconfig;
|
||||||
|
public HashMap<String, String> currentSpeciesBoundingBoxInfo;
|
||||||
|
public String currentFAOAreas;
|
||||||
|
public AquamapsAlgorithmCore core;
|
||||||
|
public String type;
|
||||||
|
public HashMap<String, Object> processedAreas;
|
||||||
|
public ConcurrentHashMap<String, Map<String, Float>> completeDistribution;
|
||||||
|
|
||||||
|
public AquamapsSuitableFunctions(AquamapsAlgorithmCore core, String type, AlgorithmConfiguration config) {
|
||||||
|
this.core = core;
|
||||||
|
this.type = type;
|
||||||
|
this.currentconfig = config;
|
||||||
|
}
|
||||||
|
|
||||||
|
//PROBABILITY CALCULATION
|
||||||
|
// calculates probability and takes into account the processes areas by this node
|
||||||
|
public float calcProb(Object species, Object area) {
|
||||||
|
float prob = (float) core.getSpeciesProb((Object[]) species, (Object[]) area);
|
||||||
|
|
||||||
|
String speciesID = getMainInfoID(species);
|
||||||
|
String csquareCode = getGeographicalID(area);
|
||||||
|
if (completeDistribution == null)
|
||||||
|
completeDistribution = new ConcurrentHashMap<String, Map<String, Float>>();
|
||||||
|
|
||||||
|
Map<String, Float> geoDistrib = completeDistribution.get(speciesID);
|
||||||
|
// if the map is null then generate a new map, otherwise update it
|
||||||
|
if (geoDistrib == null) {
|
||||||
|
geoDistrib = new ConcurrentHashMap<String, Float>();
|
||||||
|
completeDistribution.put(speciesID, geoDistrib);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (prob > 0.1) {
|
||||||
|
// record the overall probability distribution
|
||||||
|
geoDistrib.put(csquareCode, prob);
|
||||||
|
if (processedAreas == null)
|
||||||
|
processedAreas = new HashMap<String, Object>();
|
||||||
|
processedAreas.put(csquareCode, area);
|
||||||
|
}
|
||||||
|
|
||||||
|
return prob;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
//BOUNDING BOX CALCULATION
|
||||||
|
// calculates the bounding box information
|
||||||
|
public HashMap<String, Integer> calculateBoundingBox(Object[] csquarecode) {
|
||||||
|
HashMap<String, Integer> boundingInfo = core.calculateBoundingBox("" + csquarecode[0], currentSpeciesBoundingBoxInfo.get("$pass_NS"), currentSpeciesBoundingBoxInfo.get("$pass_N"), currentSpeciesBoundingBoxInfo.get("$pass_S"), AquamapsAlgorithmCore.getElement(csquarecode, 12),// centerlat
|
||||||
|
AquamapsAlgorithmCore.getElement(csquarecode, 13),// centerlong
|
||||||
|
AquamapsAlgorithmCore.getElement(csquarecode, 14),// faoaream
|
||||||
|
currentSpeciesBoundingBoxInfo.get("$paramData_NMostLat"), currentSpeciesBoundingBoxInfo.get("$paramData_SMostLat"), currentSpeciesBoundingBoxInfo.get("$paramData_WMostLong"), currentSpeciesBoundingBoxInfo.get("$paramData_EMostLong"), currentFAOAreas, currentSpeciesBoundingBoxInfo.get("$northern_hemisphere_adjusted"), currentSpeciesBoundingBoxInfo.get("$southern_hemisphere_adjusted"));
|
||||||
|
|
||||||
|
return boundingInfo;
|
||||||
|
}
|
||||||
|
|
||||||
|
// initializes currentFAOAreas and currentSpeciesBoundingBoxInfo
|
||||||
|
public void getBoundingBoxInformation(Object[] speciesInfoRow, Object[] speciesObservations) {
|
||||||
|
Object[] row = speciesInfoRow;
|
||||||
|
String $paramData_NMostLat = AquamapsAlgorithmCore.getElement(row, 28);
|
||||||
|
String $paramData_SMostLat = AquamapsAlgorithmCore.getElement(row, 29);
|
||||||
|
String $paramData_WMostLong = AquamapsAlgorithmCore.getElement(row, 30);
|
||||||
|
String $paramData_EMostLong = AquamapsAlgorithmCore.getElement(row, 31);
|
||||||
|
currentFAOAreas = AquamapsAlgorithmCore.getElement(row, 32);
|
||||||
|
// adjust FAO areas
|
||||||
|
currentFAOAreas = core.procFAO_2050(currentFAOAreas);
|
||||||
|
// get Bounding Box Information
|
||||||
|
// System.out.println("TYPE:"+type);
|
||||||
|
currentSpeciesBoundingBoxInfo = core.getBoundingBoxInfo($paramData_NMostLat, $paramData_SMostLat, $paramData_WMostLong, $paramData_EMostLong, speciesObservations, type);
|
||||||
|
// end of get BoundingBoxInformation
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
// DATABASE INTERACTION
|
||||||
|
public static void writeOnDB(List<String> buffer, String destinationTable, SessionFactory dbHibConnection) {
|
||||||
|
|
||||||
|
int endIndex = buffer.size();
|
||||||
|
if (endIndex > 0) {
|
||||||
|
System.out.println("\tWriting Buffer is not empty: "+endIndex);
|
||||||
|
String $probabilityInsertionStatement = AquamapsSuitableFunctions.probabilityInsertionStatement.replace("%ADDEDINFORMATION%", ","+metainfo);
|
||||||
|
|
||||||
|
StringBuffer sb = new StringBuffer();
|
||||||
|
// System.out.println("writeOnDB()->PROBABILITIES BUFFER SIZE DELETION");
|
||||||
|
for (int i = 0; i < endIndex; i++) {
|
||||||
|
sb.append("(" + buffer.get(i) + ")");
|
||||||
|
if (i < endIndex - 1) {
|
||||||
|
sb.append(",");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
String insertionString = String.format($probabilityInsertionStatement, destinationTable, sb.toString());
|
||||||
|
|
||||||
|
try {
|
||||||
|
// System.out.println(insertionString);
|
||||||
|
DatabaseFactory.executeSQLUpdate(insertionString, dbHibConnection);
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
else
|
||||||
|
System.out.println("\tWarning : writing buffer is empty!");
|
||||||
|
System.out.println("\tWriting on DB FINISHED");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
//FILES MANAGEMENT
|
||||||
|
public void dumpAll(String path) throws Exception {
|
||||||
|
Transformations.dumpObjectToFile(path + configFile, currentconfig);
|
||||||
|
// Transformations.dumpObjectToFile(path + csquaresFile, environmentVectors);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void rebuildConfig(String configFile) throws Exception{
|
||||||
|
FileInputStream fis = new FileInputStream(new File(configFile));
|
||||||
|
currentconfig = (AlgorithmConfiguration) new XStream().fromXML(fis);
|
||||||
|
fis.close();
|
||||||
|
}
|
||||||
|
// when uploaded the files will be local
|
||||||
|
public void rebuildAll(int cellOrdinal, int chunksize, int speciesOrdinal, int speciesChunkSize, String pathToFiles) throws Exception {
|
||||||
|
// currentconfig = (AlgorithmConfiguration) Transformations.getObjectFromFile(pathToFiles+configFile);
|
||||||
|
|
||||||
|
/*
|
||||||
|
try{
|
||||||
|
environmentVectors = (List<Object>) Transformations.getObjectFromFile(pathToFiles+csquaresFile);
|
||||||
|
}catch(Exception e){
|
||||||
|
System.out.println("\tError in retrieving environmental vectors");
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getAdditionalInformation(Object species, Object area) {
|
||||||
|
Object[] arearray = (Object[]) area;
|
||||||
|
HashMap<String, Integer> boundingInfo = calculateBoundingBox(arearray);
|
||||||
|
String addedInformation = "'" + boundingInfo.get("$InBox") + "','" + boundingInfo.get("$InFAO") + "','" + arearray[14] + "','" + arearray[15] + "','" + arearray[16] + "'";
|
||||||
|
return addedInformation;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
//AUXILIARY FUNCTIONS
|
||||||
|
public static String getMainInfoID(Object speciesInfo) {
|
||||||
|
String s = "" + ((Object[]) speciesInfo)[33];
|
||||||
|
return s;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String getGeographicalID(Object geoInfo) {
|
||||||
|
String s = "" + ((Object[]) geoInfo)[0];
|
||||||
|
return s;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
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Reference in New Issue