lcmsmatching: search-mz comparison

comparison search-mz @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

author	prog
date	Sat, 03 Sep 2016 17:02:01 -0400
parents	e66bb061af06
children	20d69a062da3

comparison

equal deleted inserted replaced

-:e66bb061af06
+:253d531a0193
 source(file.path(dirname(script.path), 'strhlp.R'), chdir = TRUE)
 source(file.path(dirname(script.path), 'fshlp.R'), chdir = TRUE)
 source(file.path(dirname(script.path), 'biodb-common.R'), chdir = TRUE)
 source(file.path(dirname(script.path), 'nethlp.R'), chdir = TRUE)
+# Missing paste0() function in R 2.14.1
+if (as.integer(R.Version()$major) == 2 && as.numeric(R.Version()$minor) < 15)
+	paste0 <- function(...) paste(..., sep = '')
 #############
 # CONSTANTS #
 #############
 PROG <- sub('^.*/([^/]+)$', '\\1', commandArgs()[4], perl = TRUE)
+USERAGENT <- 'search-mz ; pierrick.roger@gmail.com'
 # Authorized database types
 MSDB.XLS <- 'xls'
 MSDB.4TABSQL <- '4tabsql'
 MSDB.FILE <- 'file'
 		'first-val',        NA_character_,  0,  'logical',      'Keep only the first value in multi-value fields. Unset by default.',
 		'excel2011comp',            NA_character_,  0,  'logical',      'Excel 2011 compatiblity mode. Output ASCII text files instead of UTF-8 files, where greek letters are replaced with their latin names, plusminus sign is replaced with +- and apostrophe is replaced with \"prime\". All other non-ASCII characters are repladed with underscore.',
 		'database',         'd',            1,  'character',    paste0('Set database to use: "xls" for an Excel database, "file" for a single file database, "4tabsql" for a 4Tab SQL database, and "peakforest" for a connection to PeakForest database.'),
 		'url',              NA_character_,  1,  'character',    'URL of database. For "peakforest" database it is the HTTP URL, for the "xls" database it is the path to the directory containing the Excel files, for the "file" database it is the path to the file database and for the "4tabsql" database it is the IP address of the server.',
 		'cache-dir',        NA_character_,  1,  'character',    'Path to directory where to store cache files. Only used when database flag is set to "xls".',
-		'useragent',        NA_character_,  1,  'character',    'User agent. Used by the "Peakforest" database.',
 		'db-name',          NA_character_,  1,  'character',    'Name of the database. Used by the "4tabsql" database.',
-		'db-user',          NA_character_,  1,  'character',    'Name of the database. Used by the "4tabsql" database.',
+		'db-user',          NA_character_,  1,  'character',    'User of the database. Used by the "4tabsql" database.',
-		'db-password',      NA_character_,  1,  'character',    'Name of the database. Used by the "4tabsql" database.',
+		'db-password',      NA_character_,  1,  'character',    'Password of the database user. Used by the "4tabsql" database.',
 		'db-fields',        NA_character_,  1,  'character',    paste0('Comma separated key/value list giving the field names to be used in the single file database (option --db-file). Default is "', MSDB.DFT[['db-fields']], '".'),
 		'db-ms-modes',      NA_character_,  1,  'character',    paste0('Comma separated key/value list giving the MS modes to be used in the single file database (option --db-file). Default is "', MSDB.DFT[['db-ms-modes']], '".'),
+		'db-token',         NA_character_,  1,  'character',    'Database token. Used by Peakforest database.',
 		'debug',            NA_character_,  0,  'logical',      'Set debug mode.'
 		)
 	spec <- c(spec, make.getopt.spec.print.dft())
 	opt <- set.dft.arg.val(opt) # Set default values
 	opt <- parse.arg.val(opt) # Parse list values
 	# Check values
 	error <- .check.db.conn.opts(opt)
-	if (is.null(opt[['output-file']])) {
+	if (is.null(opt[['output-file']]) && is.null(opt[['list-cols']])) {
 		warning("You must set a path for the output file.")
 		error <- TRUE
 	}
 	if (is.null(opt[['list-cols']])) {
 		if (is.null(opt[['input-file']])) {
 			}
 		}
 		if (opt$database == MSDB.PEAKFOREST) {
 			if (is.null(opt$url)) {
 				warning("When using PeakForest database, you must specify the URL of the PeakForest server with option --url.")
-				error <- TRUE
-			}
-			if (is.null(opt$useragent)) {
-				warning("When using PeakForest database, you must specify a user agent with option --useragent.")
 				error <- TRUE
 			}
 		}
 		return(error)
 			precursors[[MSDB.TAG.POS]] <- opt[['pos-prec']]
 			precursors[[MSDB.TAG.NEG]] <- opt[['neg-prec']]
 		}
 		db <- switch(opt$database,
-		             peakforest = MsPeakForestDb$new(url = opt$url, useragent = opt$useragent),
+		             peakforest = MsPeakForestDb$new(url = opt$url, useragent = USERAGENT, token = opt[['db-token']]),
-		             xls = MsXlsDb(db_dir = opt$url, cache_dir = opt[['cache-dir']]),
+		             xls = MsXlsDb$new(db_dir = opt$url, cache_dir = opt[['cache-dir']]),
-		             '4tabsql' = Ms4TabSqlDb(host = extract.address(opt$url), port = extract.port(opt$url), dbname = opt[['db-name']], user = opt[['db-user']], password = opt[['db-password']]),
+		             '4tabsql' = Ms4TabSqlDb$new(host = extract.address(opt$url), port = extract.port(opt$url), dbname = opt[['db-name']], user = opt[['db-user']], password = opt[['db-password']]),
-		             file = MsFileDb(file = opt$url),
+		             file = MsFileDb$new(file = opt$url),
 		             NULL)
 		db$setPrecursors(precursors)
 		if (db$areDbFieldsSettable())
 			db$setDbFields(opt[['db-fields']])
 		if (db$areDbMsModesSettable())
 	# Replace public database IDs by URLs
 	if ( ! is.null(peaks))
 		for (extdb in c(MSDB.TAG.KEGG, MSDB.TAG.HMDB, MSDB.TAG.CHEBI, MSDB.TAG.PUBCHEM)) {
 			field <- output.fields[[extdb]]
 			if (field %in% colnames(peaks))
-				peaks[[field]] <- vapply(peaks[[field]], function(id) paste0('<a href="', get.entry.url(class = extdb, accession = id, content.type = RBIODB.HTML), '">', id, '</a>'), FUN.VALUE = '')
+				peaks[[field]] <- vapply(peaks[[field]], function(id) paste0('<a href="', get.entry.url(class = extdb, accession = id, content.type = BIODB.HTML), '">', id, '</a>'), FUN.VALUE = '')
 		}
 	# Write HTML
 	html <- HtmlWriter(file = file)
 	html$writeBegTag('html')
 db <- .load.db(opt)
 # Print columns
 if ( ! is.null(opt[['list-cols']])) {
 	cols <- db$getChromCol()
-	df.write.tsv(cols, file = opt[['output-file']])
+	df.write.tsv(cols, file = if (is.null(opt[['output-file']])) stdout() else opt[['output-file']])
 	q(status = 0)
 }
 # Read input
 if ( ! is.null(opt[['input-file']]) && ! file.exists(opt[['input-file']]))
 if ( ! is.null(opt[['all-cols']]))
 	opt$rtcol <- db$getChromCol()
 # Check chrom columns
 if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) {
-	dbcols <- db$getChromCol()
+	dbcols <- db$getChromCol()[['id']]
 	unknown.cols <- opt$rtcol[ ! opt$rtcol %in% dbcols]
 	if (length(unknown.cols) > 0) {
 		stop(paste0("Unknown chromatographic column", (if (length(unknown.cols) > 1) 's' else ''), ': ', paste(unknown.cols, collapse = ', '), ".\nAllowed chromatographic column names are:\n", paste(dbcols, collapse = "\n")))
 	}
 }

Mercurial > repos > prog > lcmsmatching

comparison search-mz @ 1:253d531a0193 draft