From 0750766e222dcaba43f7f22081647a0b0ac7051d Mon Sep 17 00:00:00 2001 From: Lucio Lelii Date: Fri, 8 Sep 2017 14:17:24 +0000 Subject: [PATCH] git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@152921 82a268e6-3cf1-43bd-a215-b396298e98cf --- .classpath | 6 +- cfg/ALog.properties | 32 - cfg/DestinationDBHibernate.cfg.out.xml | 0 cfg/DestinationDBHibernate.cfg.xml | 18 - cfg/algorithms.properties | 11 - cfg/clusterers.properties | 3 - cfg/evaluators.properties | 3 - cfg/generators.properties | 6 - cfg/interpolateTacsat.r | 439 --- cfg/knitr_test_julien_wfs.zip | Bin 3114 -> 0 bytes cfg/modelers.properties | 1 - cfg/models.properties | 4 - cfg/nodealgorithms.properties | 13 - cfg/operators.xml | 2620 ----------------- cfg/transducerers.properties | 18 - cfg/userperspective.properties | 13 - .../StandardLocalInfraAlgorithm.java | 2 +- .../executor/util/InfraRetrieval.java | 7 +- 18 files changed, 5 insertions(+), 3191 deletions(-) delete mode 100644 cfg/ALog.properties delete mode 100644 cfg/DestinationDBHibernate.cfg.out.xml delete mode 100644 cfg/DestinationDBHibernate.cfg.xml delete mode 100644 cfg/algorithms.properties delete mode 100644 cfg/clusterers.properties delete mode 100644 cfg/evaluators.properties delete mode 100644 cfg/generators.properties delete mode 100644 cfg/interpolateTacsat.r delete mode 100644 cfg/knitr_test_julien_wfs.zip delete mode 100644 cfg/modelers.properties delete mode 100644 cfg/models.properties delete mode 100644 cfg/nodealgorithms.properties delete mode 100644 cfg/operators.xml delete mode 100644 cfg/transducerers.properties delete mode 100644 cfg/userperspective.properties diff --git a/.classpath b/.classpath index eed8a51..8f5c07e 100644 --- a/.classpath +++ b/.classpath @@ -22,10 +22,6 @@ - - - - - + diff --git a/cfg/ALog.properties b/cfg/ALog.properties deleted file mode 100644 index cd47834..0000000 --- a/cfg/ALog.properties +++ /dev/null @@ -1,32 +0,0 @@ -#### 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 - diff --git a/cfg/DestinationDBHibernate.cfg.out.xml b/cfg/DestinationDBHibernate.cfg.out.xml deleted file mode 100644 index e69de29..0000000 diff --git a/cfg/DestinationDBHibernate.cfg.xml b/cfg/DestinationDBHibernate.cfg.xml deleted file mode 100644 index 28b14d3..0000000 --- a/cfg/DestinationDBHibernate.cfg.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - org.postgresql.Driver - org.hibernate.connection.C3P0ConnectionProvider - jdbc:postgresql://localhost/testdb - gcube - d4science2 - - org.hibernate.dialect.PostgreSQLDialect - org.hibernate.transaction.JDBCTransactionFactory - 0 - 10 - 0 - 1 - thread - - \ No newline at end of file diff --git a/cfg/algorithms.properties b/cfg/algorithms.properties deleted file mode 100644 index edfd708..0000000 --- a/cfg/algorithms.properties +++ /dev/null @@ -1,11 +0,0 @@ -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 -FAOMSY=org.gcube.dataanalysis.executor.nodes.algorithms.FAOMSY -ICCAT_VPA=org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA \ No newline at end of file diff --git a/cfg/clusterers.properties b/cfg/clusterers.properties deleted file mode 100644 index c2801e9..0000000 --- a/cfg/clusterers.properties +++ /dev/null @@ -1,3 +0,0 @@ -DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan -KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans -XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper \ No newline at end of file diff --git a/cfg/evaluators.properties b/cfg/evaluators.properties deleted file mode 100644 index 1245533..0000000 --- a/cfg/evaluators.properties +++ /dev/null @@ -1,3 +0,0 @@ -DISCREPANCY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis -QUALITY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DistributionQualityAnalysis -HRS=org.gcube.dataanalysis.ecoengine.evaluation.HabitatRepresentativeness \ No newline at end of file diff --git a/cfg/generators.properties b/cfg/generators.properties deleted file mode 100644 index 3f13c9c..0000000 --- a/cfg/generators.properties +++ /dev/null @@ -1,6 +0,0 @@ -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 diff --git a/cfg/interpolateTacsat.r b/cfg/interpolateTacsat.r deleted file mode 100644 index a876861..0000000 --- a/cfg/interpolateTacsat.r +++ /dev/null @@ -1,439 +0,0 @@ -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") diff --git 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@@ -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 \ No newline at end of file diff --git a/cfg/nodealgorithms.properties b/cfg/nodealgorithms.properties deleted file mode 100644 index 742cbee..0000000 --- a/cfg/nodealgorithms.properties +++ /dev/null @@ -1,13 +0,0 @@ -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 -FAOMSY=org.gcube.dataanalysis.executor.nodes.algorithms.FAOMSY -ICCAT_VPA=org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA \ No newline at end of file diff --git a/cfg/operators.xml b/cfg/operators.xml deleted file mode 100644 index 93b465c..0000000 --- a/cfg/operators.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/cfg/transducerers.properties b/cfg/transducerers.properties deleted file mode 100644 index a7aad4d..0000000 --- a/cfg/transducerers.properties +++ /dev/null @@ -1,18 +0,0 @@ -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 -KNITR_COMPILER=org.gcube.dataanalysis.executor.rscripts.KnitrCompiler -WEB_APP_PUBLISHER= org.gcube.dataanalysis.executor.nodes.transducers.WebApplicationPublisher \ No newline at end of file diff --git a/cfg/userperspective.properties b/cfg/userperspective.properties deleted file mode 100644 index 66fc553..0000000 --- a/cfg/userperspective.properties +++ /dev/null @@ -1,13 +0,0 @@ -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 \ No newline at end of file diff --git a/src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java b/src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java index 02ef2d2..8e169bf 100644 --- a/src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java +++ b/src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java @@ -21,7 +21,7 @@ public abstract class StandardLocalInfraAlgorithm extends StandardLocalExternalA if (!serviceAddress.endsWith("/")) serviceAddress = serviceAddress+"/"; - String requestForMessage = serviceAddress + "messages/writeMessageToUsers" + "?gcube-token=" + config.getGcubeToken(); + String requestForMessage = serviceAddress + "2/messages/writeMessageToUsers" + "?gcube-token=" + config.getGcubeToken(); requestForMessage = requestForMessage.replace("http://", "https://").replace(":80", ""); // remove the port (or set it to 443) otherwise you get an SSL error LOGGER.debug("Emailing System->Request url is going to be " + requestForMessage); diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/InfraRetrieval.java b/src/main/java/org/gcube/dataanalysis/executor/util/InfraRetrieval.java index 62fb76e..55d5fe3 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/util/InfraRetrieval.java +++ b/src/main/java/org/gcube/dataanalysis/executor/util/InfraRetrieval.java @@ -59,9 +59,8 @@ public class InfraRetrieval { public static String findEmailingSystemAddress(String scope) throws Exception { String serviceName = "SocialNetworking"; - String serviceClass = "Portal"; - List endpoints = retrieveServiceAddress(serviceClass, serviceName,scope,"test"); + List endpoints = retrieveService(serviceName,scope); /* new code - deprecated @@ -83,10 +82,10 @@ public class InfraRetrieval { */ String resourceEntyName = endpoints.get(0); - if (endpoints == null || endpoints.isEmpty()) throw new Exception("Cannot retrieve the GCoreEndpoint serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+scope); + if (endpoints == null || endpoints.isEmpty()) throw new Exception("Cannot retrieve the GCoreEndpoint serviceName: "+serviceName +", in scope: "+scope); if(resourceEntyName==null) - throw new Exception("Endpoint:"+serviceName+", is null for serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+scope); + throw new Exception("Endpoint:"+serviceName+", is null for serviceName: "+serviceName +", in scope: "+scope); return resourceEntyName;