Merge pull request #417 from StoXProject/develop

Develop

Author: arnejohannesholmin

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxData
-Version: 2.1.2
-Date: 2025-01-20
+Version: 2.1.3-9001
+Date: 2025-03-17
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(
   person(given = "Edvin", 

NEWS.md

@@ -39,7 +39,7 @@
 * Temporarily hiding Prey tables in StoxBiotic().
 
 # RstoxData v2.0.1-9004  (2024-10-08)
-* Fixed a bug where certain values of BiologyLengthCode were shifted one integer value down in ICESBiotic(). The bug is related to floating point precision which causes some values to be slightly lower than the corresponding integer after calculations. In R one example is format(29 / 100 * 100, digits = 20) = "28.999999999999996447", which results in 28 when converted to integer. The following values are affected:
+* Fixed a bug where certain values of BiologyLengthClass were shifted one integer value down in ICESBiotic(). The bug is related to floating point precision which causes some values to be slightly lower than the corresponding integer after calculations. In R one example is format(29 / 100 * 100, digits = 20) = "28.999999999999996447", which results in 28 when converted to integer. The following values are affected:
 	* 29, 57, 58, 113, 114, 115, 116 when BiologyLengthCode is "cm" (lengthresolution "3")
 	* 1001, 1003, 1005, 1007, 1009, 1011, 1013, 1015, 1017, 1019, 1021 and 1023 when BiologyLengthCode is "mm"  (lengthresolution "1")
 	* 1005 and 1015 (a subset of the values for "mm") when BiologyLengthCode is "halfcm" (lengthresolution "2")

R/readXmlFile.R

@@ -93,7 +93,7 @@ readXmlFile <- function(xmlFilePath, stream = TRUE, useXsd = NULL, usePrefix = N
 	#	close(fileConn)
 	#	xmlFilePath <- tempXml
 	#}
-
+	
 	# Apply preprocess for ICES XSDs. This must happen on the xsdObjects, and not e.g. on a copy, as the zip reading fails in that case:
 	if(!is.null(useXsd) && useXsd == "icesAcoustic") {
 		xsdObjects$icesAcoustic.xsd <- icesAcousticPreprocess(xsdObjects$icesAcoustic.xsd)

R/writeXmlFile.R

@@ -1142,7 +1142,67 @@ MergeNMDEchosounderOne <- function(NMDEchosounderOne) {
 }
 
 MergeICESAcousticOne <- function(ICESAcousticOne) {
-	stop("Not yet implemented.")
+	
+	stop("Not finished!")
+	
+	# The following code is an attempt to merge ICESAcoustic data. The problem that remains unsolved is that when reading the ICESAcoustic XML there is a table named "Survey" and a column named Survey in the Cruise table. The reader misinterprets this so that the Survey column of the Cruise table is appended as an additional row in the Survey table:
+	
+	# Make a copy, as we are translating by reference:
+	ICESAcousticOne <- data.table::copy(ICESAcousticOne)
+	
+	
+	tablesToMerge <- c("Cruise", "Log", "Sample", "Data")
+	
+	# Apply translations defined in the table 'vocabulary':
+	if(length(ICESAcousticOne$vocabulary)) {
+		vocabulary <- findVariablesMathcinigVocabulary(
+			vocabulary = ICESAcousticOne$vocabulary, 
+			data = ICESAcousticOne[tablesToMerge]
+		)
+		# Uniqueify since some columns (keys) are present in several tables:
+		vocabulary <- unique(vocabulary)
+		
+		translateVariables(
+			data = ICESAcousticOne[tablesToMerge], 
+			TranslationDefinition = "FunctionInput",
+			Translation = vocabulary, 
+			translate.keys = TRUE
+		)
+	}
+	
+	
+	
+	merged <- RstoxData::mergeDataTables(ICESAcousticOne[tablesToMerge], output.only.last = TRUE, all = TRUE)
+	
+	# Add the echosounder_dataset:
+	merged <- cbind(
+		ICESAcousticOne$Survey,
+		merged, 
+		ICESAcousticOne$Instrument, 
+		ICESAcousticOne$Calibration, 
+		ICESAcousticOne$DataAcquisition, 
+		ICESAcousticOne$DataProcessing
+	)
+	
+	
+	# # Apply translations defined in the table 'vocabulary':
+	# if(length(ICESAcousticOne$vocabulary)) {
+	# 	vocabulary <- findVariablesMathcinigVocabulary(
+	# 		vocabulary = ICESAcousticOne$vocabulary, 
+	# 		data = merged
+	# 	)
+	# 	# Uniqueify since some columns (keys) are present in several tables:
+	# 	vocabulary <- unique(vocabulary)
+	# 	
+	# 	translateVariables(
+	# 		data = merged, 
+	# 		TranslationDefinition = "FunctionInput",
+	# 		Translation = vocabulary, 
+	# 		translate.keys = TRUE
+	# 	)
+	# }
+	
+	return(merged)
 }
 
 

R/xsdUtils.R

@@ -363,17 +363,26 @@ autodetectXml <- function(xmlFile, xsdObjects, verbose) {
 }
 
 readCharZip <- function(x, ...) {
+	
 	if(tolower(tools::file_ext(x)) == "zip") {
 		file <- utils::unzip(zipfile = x, list = TRUE)[, "Name"]
 		file <- file[!grepl("__MACOSX", file)]
 		if(length(file) > 1) {
 			stop("Input data can be zipped, but then each file must be zipped individually, so that each zipfile contains only one file (and this file must have the same name as the zip, excluding file extension).")
 		}
-		readChar(unz(x, file), ...)
+		output <- readChar(unz(x, file), ...)
 	}
 	else {
-		readChar(x, ...)
+		output <- readChar(x, ...)
+	}
+	
+	# Make sure the output is a complete xml (ending with ">"):
+	last <- utils::tail(gregexpr(">", output)[[1]], 1)
+	if(is.finite(last)) {
+		output <- substr(output, 1, last)
 	}
+	
+	return(output)
 }
 
 checkFileNameInZip <- function(x) {

data-raw/prepUnits.R

@@ -44,6 +44,7 @@ StoxUnits <- rbind(StoxUnits, list("cardinality-TN", "cardinality", "TN", "10^12
 StoxUnits <- rbind(StoxUnits, list("area_number_density-N/nmi^2", "area_number_density", "N/nmi^2", "individuals/nmi^2", "individuals per square nautical mile", 1))
 StoxUnits <- rbind(StoxUnits, list("area_number_density-kN/nmi^2", "area_number_density", "kN/nmi^2", "10^3 individuals/nmi^2", "thousand individuals per square nautical mile", 1e3))
 StoxUnits <- rbind(StoxUnits, list("area_number_density-MN/nmi^2", "area_number_density", "MN/nmi^2", "10^6 individuals/nmi^2", "million individuals per square nautical mile", 1e6))
+StoxUnits <- rbind(StoxUnits, list("area_number_density-GN/nmi^2", "area_number_density", "GN/nmi^2", "10^9 individuals/nmi^2", "billion individuals per square nautical mile", 1e9))
 
 StoxUnits <- rbind(StoxUnits, list("NASC-m^2/nmi^2", "NASC", "m^2/nmi^2", "m^2/nmi^2", "square meter backscattering cross-section per square nautical mile surveyed area", 1))