R/ENVISIONQuery.R

Defines functions ENVISIONQuery ENVISIONQuery.chunk ENVISIONQuery.loop mergeFrameList toChunks progressMsg jgetOptions getMerger getFormatter getInputTypes getServiceClient getTool getToolNames getServiceOptions getService getServiceNames getServices

Documented in ENVISIONQuery ENVISIONQuery.chunk ENVISIONQuery.loop getFormatter getInputTypes getMerger getService getServiceClient getServiceNames getServiceOptions getServices getTool getToolNames jgetOptions mergeFrameList progressMsg toChunks

#' Get available services
#' 
#' @name getServices
#' @return The multi-level list of services and service attributes
#'
#' @examples
#' #get the handlers for all available services including utilities
#' services<-getServices();
#' names(services);
#'
#' @export getServices
#' @author  Alex Lisovich, Roger Day

getServices<-function(){
	if(is.null(ENVISIONServices))
		assignInNamespace("ENVISIONServices",registerServices(),"ENVISIONQuery");
	return(ENVISIONServices)
}


#' Get the names of available Envision services
#'
#' @name getServiceNames
#' @return Character vector representing the list of of available Envision service names.
#'
#' @examples
#'
#' #get the names of all available services
#' serviceNames<-getServiceNames();
#' print(serviceNames);
#'
#' @export getServiceNames
#' @author  Alex Lisovich, Roger Day

getServiceNames<-function(){
	return(names(getServices()));
}


#' Get the service handler using it's name
#'
#' @name getService
#' @param serviceName The name of Envision service which handler should be retrieved. If equal to "menu" (default)
#' menu is contructed allowing to choose one of the available services
#' @param graphicMenu If TRUE (default is FALSE), use a GUI window for the pick menus.
#' @return the Envision service handler.
#'
#' @examples
#'
#' #get an ID Conversion service handle
#'
#' service<-getService("ID Conversion");
#'
#' \dontrun{
#'
#' #get a handle to service selected interactively
#'
#' service<-getService("menu");
#' }
#'
#' @export getService
#' @author  Alex Lisovich, Roger Day

getService<-function(serviceName="menu",graphicMenu=getOption("menu.graphics")){
	serviceNames<-getServiceNames();
	if (serviceName=="menu"){
		item<-menu(graphics = graphicMenu, title = "Select Service", serviceNames[-1]);
		if(item==0)
			return(NULL);
		serviceName<-serviceNames[item+1];
	}

	if (!(serviceName %in% serviceNames)){
		warning("ENVISIONQuery: Invalid service name");
		return(NULL);
	}
	service<-getServices()[[serviceName]];
	attr(service,"serviceName")<-serviceName;

	return(service);
}

#' Get default service options.
#'
#' @name getServiceOptions
#' @param serviceName The name of Envision service which default options should be retrieved. 
#' @param graphicMenu If TRUE (default is FALSE), use a GUI window for the pick menus.
#' If equal to "menu" (default) menu is contructed allowing to choose one of the available services
#' @return The list where each item name and value corresponds to the particular option
#' name and default value correspondingly.
#'
#' @examples
#' #get options for 'Reactome' service
#' options<-getServiceOptions("Reactome");
#' print(options);
#'
#' \dontrun{
#' #get options for a service selected interactively
#' getServiceOptions("menu");
#' }
#'
#' @export getServiceOptions
#' @author  Alex Lisovich, Roger Day

getServiceOptions<-function(serviceName="menu",graphicMenu=getOption("menu.graphics")){
	service<-getService(serviceName,graphicMenu);
	if(is.null(service))
		return(NULL);

	s_options<-service$service$getDefaultOptions();
	
	options<-list();
	if(length(s_options)>1){
		for (i in seq(from=1,to=length(s_options),by=2))
			options[[s_options[i]]]<-c(options[[s_options[i]]],s_options[i+1]);
	}
	return(options);
}

#' Get the names of available tools for a given Envision service
#'
#' @name getToolNames
#' @param service The Envision service handler
#' @return Character vector representing the list of of available tool names for a given service.
#'
#' @examples
#'
#' #get the list of available tools for a given service
#'
#' service<-getService("ID Conversion");
#' toolNames<-getToolNames(service);
#' print(toolNames);
#'
#' @export getToolNames
#' @author  Alex Lisovich, Roger Day

getToolNames<-function(service){
	return(names(service$tools));
}


#' Get the tool handler of a given service using the tool name
#'
#' @name getTool
#' @param service Service handler
#' @param toolName The name of Envision service tool handler to be retrieved. If equal to "menu" (default)
#' and the number of tools is greater than 1 menu is contructed allowing to choose one of the available services.
#' @param selection.title The selection list title. Default is 'Select Tool'.
#' @param graphicMenu If TRUE (default is FALSE), use a GUI window for the pick menus.
#' @return the Envision service tool handler.
#' @usage getTool(service,toolName="menu",selection.title="Select Tool", graphicMenu=getOption("menu.graphics"))
#'
#' @examples
#' #get the tool handler for 'mapProteinsAdv' tool in 'Picr' service
#'
#' service<-getService("Picr");
#' getToolNames(service);
#' tool<-try({getTool(service,"FindPathAdv");
#' 		client<-getServiceClient(tool);
#' 		print(client);
#' })
#'
#' @export getTool
#' @author  Alex Lisovich, Roger Day

getTool<-function(service,toolName="menu",selection.title="Select Tool", graphicMenu=getOption("menu.graphics")){
	if(length(toolName)>1){
		toolNames<-toolName;
		toolName<-"menu";
	} else {
		toolNames<-getToolNames(service);
	}

	if (length(toolNames)>1) {
		if (toolName=="menu"){
			item<-menu(graphics = graphicMenu, title = selection.title, toolNames);
			if(item==0)
				return(NULL);
			toolName=toolNames[item];
		}
	}else{
		toolName<-toolNames[1];
	}

	if (!(toolName%in% toolNames)){
		warning("ENVISIONQuery: Invalid tool name");
		return(NULL);
	}

	tool<-service$tools[[toolName]];
	attr(tool,"toolName")<-toolName;
	return(tool);
}

#' Get the Web Service client finction handler for a given tool
#'
#' @name getServiceClient
#' @param tool The tool handler
#' @return the function which implements client functionality for a particular data retrieval service
#' 
#' @examples
#' #get Java Web Service client for 'FindPathAdv' tool of 'Reactome' service
#'
#' service<-getService("Reactome");
#' getToolNames(service);
#' try({tool<-getTool(service,"FindPathAdv");
#' 		client<-getServiceClient(tool);
#' 		print(client);
#' })
#' @export getServiceClient
#' @author  Alex Lisovich, Roger Day

getServiceClient<-function(tool){
	return(tool$client);
}

#' Get the list of available input types for a given tool.
#'
#' The input types could be subdivided into the following three groups:
#' 1. The list of IDs (types 'Uniprot ID', 'Affymetrix ID', 'Enquant ID' and 'Protein ID').
#' 2. The character string representing the enfinXML document ('Enfin XML') and
#' 3. The name of the file containing the enfinXML document.
#' The types belonging to the groups 2 and 3 can be used to construct a pipeline of queries, 
#' where the output of the given query can be used as an input for the next one
#'
#' @name getInputTypes
#' @param tool The tool handler
#' @param inputType Either 'menu' or a valid input type. Default is 'menu'.
#' @return If inputType is 'all', the character vector of all available input types. If inputType is 
#' valid input type, the inputType value returned, otherwise returns NULL.
#'
#' @examples
#'
#' #check available input type for a given tool
#'
#' service<-getService("Reactome");
#' try({tool<-getTool(service,"FindPathAdv");
#' 	print(getInputTypes(tool));
#' })
#'
#' @export getInputTypes
#' @author  Alex Lisovich, Roger Day

getInputTypes<-function(tool,inputType="menu"){
	if(inputType=="menu"){
		return(tool$input);
	} else if (inputType %in% tool$input){
		return(inputType);
	} else {
		warning("ENVISIONQuery: invalid input type");
		return(NULL);
	}
}


#' Get the formatting function for a given tool
#'
#' @name getFormatter
#' @param tool Tool handler
#' @return The formatting function for a given service.
#'
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

getFormatter<-function(tool) {
	return(tool$formatter);
}

#' Get the merging function for a given tool.
#'
#' If possible, meerging function merges the list of formatted query result chunks into a single formatted object (typically a data frame).
#'
#' @name getMerger
#' @param tool Tool handler
#' @return The merging function for a given service.
#' 
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

getMerger<-function(tool) {
	return(tool$merger);
}


#' Convert options list into the character vector.
#'
#' Convert options list into the character vector suitable for submission
#' to Java Web Services subsystem.
#'
#' @name jgetOptions
#' @param service Service handler
#' @param options Options list
#' @return Character vector containing set of <option name,value> pairs
#'
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

jgetOptions<-function(service,options){
	all_options<-getServiceOptions(attr(service,"serviceName"));
	option_names<-names(options) %in% names(all_options);
	options<-options[option_names];
	if(length(options)==0)
		return(character(0));

	res<-NULL;
	for (i in 1:length(options)){
		for (j in 1:length(options[[i]]))
			res<-c(res,c(names(options)[i],options[[i]][j]));
	}
	return(res);
}

#' Display the task progress message.
#'
#' Displays the percentage of task completeness accompanied by the custom message by repatedly updating the same output line.
#' @name progressMsg
#' @param msg Custom message to be displayed.
#' @param i Current task step.
#' @param total Total number of task steps.
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

progressMsg<-function(msg,i,total){
	msgFreq<-max(1,as.integer(total/100));
	if ((i %% msgFreq)==0){
		cat("                                                      \r");
		cat(msg,round(i*100/total),"%\r");
		flush.console();
	}
}

#' Convert the ID set into the list of ID subsets.
#'
#' Converts the ID set into the list of ID subsets according to the chunk size.
#' Used to subdivied a large query into the set of smaller queries to overcome a potential limitation
#' on a single query ID set size.
#'
#' @name toChunks
#' @param ids Character vector representing the input ID set.
#' @param chunk The maximium number of IDs retrieved during a single query session. Default is 1000.
#' @return A list of ID subsets according to the chunk size.
#'
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

toChunks<-function(ids,chunk=1000){
	sz<-length(ids);
	if(sz>chunk){
		start<-seq(from=1,to=sz,by=chunk);
		end<-seq(from=chunk,to=sz,by=chunk);
		if(length(end)<length(start))
			end<-c(end,sz);
	} else {
		start<-1;
		end<-sz;
	}

	chunks<-list();
	for(i in 1:length(start))
		chunks[[i]]<-ids[start[i]:end[i]];
	return(chunks);
}


#' Merges the data frames representing the partial query results into a single data frame.
#'
#' @name mergeFrameList
#' @param resList List of data frames.
#' @param verbose if TRUE enables diagnostic messages. Default is FALSE.
#' @return A single data frame representing the merged query results.
#'
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

mergeFrameList<-function(resList,verbose=FALSE){
	if(length(resList)==0)
		return(NULL);

	rows<-0;
	columns<-NULL;
	for(i in 1:length(resList)){
		if(!is.null(resList[[i]])){
			rows<-rows+nrow(resList[[i]]);
			if(is.null(columns))
				columns<-colnames(resList[[i]]);
		}
	}
	res<-array("",dim=c(rows,ncol(resList[[1]])));
	colnames(res)<-columns;
	res<-as.data.frame(res,stringsAsFactors=FALSE);

	row<-0;
	for(i in 1:length(resList)){
		if(!is.null(resList[[i]])){
			rows<-nrow(resList[[i]]);
			res[(row+1):(row+rows),]<-resList[[i]];
			row<-row+rows;
		}
	}
	return(res);
}

#' Perform queries in chunks to comply with potential limitations 
#' on the query size for Envision Web query system.
#'
#' @name ENVISIONQuery.loop
#' @param ids Character vector representing the input ID set.
#' @param chunk maximum size of the portion of the input ID list to be used in a single query Fun call.
#' @param queryFun a functions submitting the query to the Envision Web query system.
#' @param verbose if TRUE enables diagnostic messages. Default is FALSE.
#' @param ... additional arguments to be passed to queryFun.
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

ENVISIONQuery.loop<-function(ids,chunk,queryFun,verbose,...) {
	
	if(is.na(chunk))
		chunk=length(ids);

	idList<-toChunks(ids,chunk);

	res<-list();
	for (i in 1:length(idList)){
		if(verbose){
			if(verbose>1)
				cat("processing chunk",i,"out of",length(idList),"\n")
			else
				progressMsg("retrieved:",(i-1),length(idList));
		}
		nchunk=ifelse(length(idList)>1,i,-1);
		res[[i]]<-queryFun(idList[[i]],nchunk=nchunk,verbose=max(0,(verbose-1)),...);

	}
	if(verbose){
		progressMsg("retrieved:",length(idList),length(idList));
		cat("\n");

	}

	return(res);
}

#' Retrieves a set of unique matches for a given ID list.
#' 
#' @name ENVISIONQuery.chunk
#' @param ids Character vector representing the ID list.
#' @param utilityTool The tool used to convert the ID list into the input Enfin xml file.
#' @param service Service handler
#' @param tool The tool used to perform the conversion
#' @param formatIt If TRUE (default), try to interpret the returned character table and structure the result. 
#' If false, the character string representing the entire enfinXML file returned by ENVISION.
#' @param options The (optional)list each element of which represents the <name,value> pair used to apply
#' the additional constraints when sending a query to a particular service (maximum number of pathways
#' for Reactome service as an example)
#' @param filter The list where the name of each element represents an output data frame column
#' on which filetering is to be performed ('organism.species', 'Microarray.platform' etc.) and the element itself
#' containing a character vector defining the set of values on which the merging (intersection) for a given column
#' will be performed ('Homo sapiens' for 'organism.species', 'affy_hg_u133_plus_2' for 'Microarray.platform' etc.).
#' The filtering is performed if the list is not empty and the formatIt=TRUE. Default is an empty list.
#' @param compact If TRUE and the formatted output (formatIt = TRUE)is represented by a data frame, 
#' collapses the rows with duplicated match sets but different attributes into a single row with unique match set
#' and an attribute list separated by comma for each attribute column. Default is TRUE.
#' @param writeHTML If TRUE, write the received intermediate HTML to file. Default is FALSE.
#' @param nchunk Chunk number. If not NA and writeHTML is TRUE the input and output xml file names are appended 
#' with chunk number. Default is NA.
#' @param verbose If TRUE, enables diagnostic messages. Default is FALSE.
#' @param ... additional arguments.
#' @return The ENVISIONQueryResult structure
#' @keywords internal
#' @author  Alex Lisovich, Roger Day

ENVISIONQuery.chunk<-function(ids,utilityTool,service,tool,
		formatIt,options=list(),filter=list(),compact=TRUE,
		writeHTML=FALSE,nchunk=NA,verbose=FALSE,...){

	if(attr(utilityTool,"toolName") %in% c("Enfin XML","Enfine XML file")){
		jids<-.jarray(as.character(ids));
	} else {	
		jids<-.jarray(ids);
	}

	if(verbose)
		cat("Preparing input data...\n");
	inpXML<-utilityTool$client(jids);

	if (writeHTML)
		writeChar(inpXML,paste("input",ifelse(is.na(nchunk),"",nchunk),".xml",sep=""));


	if(verbose)
		cat("Retrieving query data...\n");
	outXML<-tool$client(inpXML,jgetOptions(service,options));

	if (writeHTML)
		writeChar(outXML,paste(attr(service,"serviceName"),"_",attr(tool,"toolName"),"_output",nchunk,".xml",sep=""));

	if(length(grep("Error",outXML,fixed=TRUE))){
		msg=paste("\n Web Service ***",attr(service,"serviceName"),"*** temporarily unavailable\n",
			"If the problem persists, contact EnCORE team ([email protected]) for technical support");
		stop(msg);
	}

	if (formatIt){
		formatter<-getFormatter(tool);
		if (!is.null(formatter)){
			res<-formatter(outXML,filter=filter,compact=compact,verbose=verbose,...);
			return(res);		
		}
	}
	return(outXML);
}

#' Launch a query against Envision, a web online query system
#' providing elaborated information for EnCORE services. 
#' Return the results into an R object.
#'
#' @name ENVISIONQuery
#' @param ids Depending on input type, IDs for desired objects as a character vector a character string containing
#' the entire Enfin xml document or a name of an Enfin xml file.
#' @param typeName Type of input ids. If 'menu' (default), a menu  is constructed allowing to choose one of the available types.
#' @param serviceName The Envision service name or a character vector of service names.
#' In a latter case system compbines requests into pipeline using the output of current service request as an input for a next one.
#' If 'menu' (default), the menu is contructed allowing to choose one of the available services. 
#' @param toolName The tool for a particular envision service. If 'menu' (default) and there is more than one tool available, 
#' a menu is contructed allowing to choose one of the available tools.
#' @param chunk The number of IDs retrieved during a single query session. In case the number of IDs exceeds the chunk size,
#' the whole ID set is retrieved during multiple query sessions overcoming the potential limitations on a single query session
#' ID set size. If NA, a single session is used. Default is 1000.
#' @param details If TRUE (default), a list of intermediate results is returned; otherwise, just the final query result.
#' Note: not implemented at this time
#' @param writeHTML If TRUE (default is FALSE), write the received intermediate HTML to files.
#' @param testMe If TRUE (default is FALSE), assign default values and run.
#' @param graphicMenu If TRUE (default is FALSE), use a GUI window for the pick menus.
#' @param formatIt If TRUE (default), try to interpret the returned character table and structure the result. 
#' If false, the character string representing the entire enfinXML file returned by ENVISION.
#' Note: formatting is implemented only for 'Probe2Uniprot' and 'ID conversion' services at this time.
#' If false, the character string representing the entire enfinXML file returned by ENVISION.
#' @param options The (optional)list each element of which represents the <name,value> pair used to apply
#' the additional constraints when sending a query to a particular service (maximum number of pathways
#' for Reactome service as an example)
#' @param filter The (optional)list where the name of each element represents the formatted output data frame column
#' on which filetering is to be performed ('organism.species', 'Microarray.platform' etc.) and the list element
#' containing a character vector defining the set of values on which the merging (intersection) for a given column
#' will be performed ('Homo sapiens' for 'organism.species', 'affy_hg_u133_plus_2' for 'Microarray.platform' etc.).
#' The filtering is performed if the list is not empty and the formatIt=TRUE. Default is an empty list.
#' @param compact If TRUE and the formatted output (formatIt = TRUE)is represented by a data frame, 
#' collapses the rows with duplicated match sets but different attributes into a single row with unique match set
#' and an attribute list separated by comma for each attribute column. Default is TRUE.
#' @param verbose If TRUE (default is FALSE), more debugging information is printed.
#' @return The ENVISIONQueryResult structure or NULL if no results were found.
#'
#' @note For a pipeline of services, only unformatted output supported at this time.
#'
#' @examples
#' #### basic ENVISIONQuery request
#'
#' #convert the Affy probeset IDs to UniProt IDs
#' res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),
#' 	serviceName="ID Conversion",toolName="Affy2Uniprot",typeName="Affymetrix ID");
#' print(res);
#' 
#' #retrieve the pathways for given Uniprot ID(s)
#' res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",typeName="Uniprot ID");
#' print(res[,-3]);
#' 
#' #retrieve protein-protein interactions
#' res<-ENVISIONQuery(ids="P38398",serviceName="Intact",typeName="Uniprot ID");
#' print(res[1:5,]);
#' 
#' #convert EnSembl IDs to Uniprot IDs
#' try({res<-ENVISIONQuery(ids=c("ENSP00000397145","ENSP00000269554"),serviceName="Picr",typeName="Protein ID");
#' print(res);
#' }) 
#'
#' #### ENVISIONQuery request using options and filters
#' 
#' #match Uniprot IDs to EnSembl and TrEMBL
#' options<-list("enfin-picr-search-database"=c("ENSEMBL_HUMAN","TREMBL"));
#' res<-try({ENVISIONQuery(ids="P38398",serviceName="Picr",options=options,typeName="Protein ID");
#' print(res);
#' })
#' 
#' #retrieve the pathways for given Uniprot ID(s)sorting them by coverage
#' #and calcultating the total protein count
#' options<-list("enfin-reactome-add-coverage"="true",
#' 	"enfin-reactome-sort-by-coverage"="true");
#' res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",options=options,typeName="Uniprot ID");
#' print(res[,-3]);
#' 
#' #convert the Affy probeset IDs to UniProt IDs restricting 
#' #output by micro array type and organism species
#' filter<-list(Microarray.Platform="affy_hg_u133_plus_2",
#' 	organism.species="Homo sapiens");
#' res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),filter=filter,
#' 	serviceName="ID Conversion",toolName="Affy2Uniprot",typeName="Affymetrix ID");
#' print(res);
#' 
#' #### pipeline of ENVISIONQuery requests. As of recent version, 
#' #### output formatting for a pipelined request is not supported yet.
#' 
#' #Intact-Reactome cascaded request for UniProt ID(s).   
#' IntactReactomeXML<-ENVISIONQuery(ids="P38398",
#' 	serviceName=c("Intact","Reactome"),typeName="Uniprot ID",verbose=TRUE);
#' #convert xml text into XMLDocument
#' #using XML package for further exploring
#' if(!is.null(IntactReactomeXML)){
#' xmlDoc<-xmlTreeParse(IntactReactomeXML,useInternalNodes = TRUE, asText=TRUE);
#' class(xmlDoc);
#' }
#' 
#' #### interactive ENVISIONQuery requests
#' \dontrun{
#' res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),filter=filter,
#' 	serviceName="menu",toolName="menu",typeName="menu");
#' print(res);
#' }
#' 
#' @export ENVISIONQuery
#' @author  Alex Lisovich, Roger Day

ENVISIONQuery<-function(ids=c("1553619_a_at","1553497_at"),typeName="menu",serviceName="menu",toolName="menu",chunk=1000,
	details=TRUE, writeHTML=FALSE, testMe=FALSE, graphicMenu=getOption("menu.graphics"), 
	formatIt=TRUE, options=list(),filter=list(), compact=TRUE, verbose=FALSE){

   if (testMe){
	typeName<-"Affymetrix ID";
	serviceName="ID Conversion";
	toolName<-"Affy2Uniprot";
	verbose=TRUE;
   }

   serviceNames<-serviceName;
   if(length(serviceNames)>1)
		formatIt<-FALSE;

  res<-tryCatch({ # catch any possible error
	for(i in 1:length(serviceNames)){
		serviceName<-serviceNames[i];
		if(i>1){
			ids<-res;
			typeName<-"Enfin XML";
		}

		# setup web service
		service<-getService(serviceName,graphicMenu=graphicMenu);
		if(is.null(service))
			return(NULL);

		# setup service tool
		tool<-getTool(service,toolName,graphicMenu=graphicMenu);
		if (is.null(tool))
			return(NULL);

		# setup utility service
		utilityTool<-getTool(getService("Utility"),getInputTypes(tool,typeName),
			selection.title="Select Input Type",graphicMenu=graphicMenu);
		if (is.null(utilityTool))
			return(NULL);

		#disable formatting for EnfinXML input
		if(attr(utilityTool,"toolName") %in% c("Enfin XML","Enfine XML file"))
			formatIt=FALSE;

		if(verbose)
			cat("Data retrieval started. It may take several minutes...\n");

		if(formatIt && is.null(getFormatter(tool))){
			warning(paste("No formatting implemented for",attr(tool,"toolName"),"tool"));
			formatIt<-FALSE;
		}

		res<-ENVISIONQuery.loop(ids,chunk,ENVISIONQuery.chunk,verbose=verbose,
				utilityTool,service,tool,formatIt,options,filter,compact,writeHTML);


		if(formatIt && !is.null(getMerger(tool))){
			if(verbose)
				cat("merging formatted output\n");
			merger<-getMerger(tool);	
			res<-merger(res,verbose=verbose);
		
		}

		if (!is.null(res)){
			attr(res,"options")<-options;
	   	 	attr(res, "filter") <- filter;
			attr(res, "type")<-attr(utilityTool,"toolName");
			attr(res, "service")<-attr(service,"serviceName");
			attr(res, "tool")<-attr(tool,"toolName");
		}
	}#for(serviceName in serviceNames)

	invisible(res);
    }, error=function(e){
      	cat("\n",as.character(e),"\n");
		res<-NULL;
   });
   if(is.null(res))
		cat("ENVISIONQuery: No results found\n");
   return(res);
}

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ENVISIONQuery documentation built on Nov. 1, 2018, 4:26 a.m.