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Changeset 0:330f15f2ad3f (2023-12-23)

Next changeset 1:559744b4c50c (2024-01-22)

Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32

added:
eal_table_templates.R
eal_templates.R
eml2eal.R
entities_templates.R
geo_cov_temp.R
make_eml.R
raster_templates.R
taxo_cov_template.R
test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml
test-data/Present_Surface_pH.tif
test-data/annotations.tabular
test-data/annotations.txt
test-data/attributes_data_7.txt
test-data/attributes_data_blary_al.tabular
test-data/attributes_data_blary_al.txt
test-data/catvars_data_7.txt
test-data/catvars_data_blary_al.tabular
test-data/catvars_data_blary_al.txt
test-data/custom_units.txt
test-data/data_7.GeoJSON
test-data/datafile_1.tsv
test-data/entities.txt
test-data/geographic_coverage.tabular
test-data/geographic_coverage.txt
test-data/keywords.tabular
test-data/keywords.txt
test-data/metadataoutput.xml
test-data/personnel.tabular
test-data/personnel.txt
test-data/taxa.tsv
test-data/taxonomic_coverage.txt
test-data/test-geocov.tabular
vector_template.xml
vector_templates.R

diff -r 000000000000 -r 330f15f2ad3f eal_table_templates.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eal_table_templates.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,21 @@
+#28/11/2023 #SEGUINEAU Pauline
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+ data_table <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+table = strsplit(data_table," ")
+
+#Make templates to describe data tables : Describes columns of a data table (classes, units, datetime formats, missing value codes) + catégorical variables.
+
+template_table_attributes(path = ".",data.path= "data_files", data.table = table[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+

diff -r 000000000000 -r 330f15f2ad3f eal_templates.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eal_templates.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,23 @@
+#22/11/2023 #SEGUINEAU Pauline
+
+###First tool of EML Workflow
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+
+  license <- args[1]
+  file_type <- args[2]
+}
+
+#Make templates to describe core features of a data package (abstract, methods, keywords, personnel, license).
+
+template_core_metadata(path=".",license = license, file.type = file_type)
+
+
+

diff -r 000000000000 -r 330f15f2ad3f eml2eal.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eml2eal.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,15 @@
+##07/06/2023
+##Genthon Tanguy
+###eml2eal
+
+#load arguments
+args = commandArgs(trailingOnly=TRUE)
+if (length(args)==0)
+{
+ stop("This tool needs at least one argument")
+}else{
+ data <- args[1]
+}
+
+
+EMLassemblyline::eml2eal(data,path=".")

diff -r 000000000000 -r 330f15f2ad3f entities_templates.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/entities_templates.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,17 @@
+#19/12/2023 #SEGUINEAU Pauline
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+ data_objects <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+data = strsplit(data_objects," ")[[1]]
+
+#Make entities templates for raster and/or vector and/or other entities data
+
+EMLassemblyline::template_entities(path="output_template",data.path="data_files",data.objects=data)
+
+

diff -r 000000000000 -r 330f15f2ad3f geo_cov_temp.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/geo_cov_temp.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,38 @@
+#27/11/2023
+#Seguineau Pauline
+#Make geographic coverage template
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+
+  data_table <- args[1]
+  tablename <- args[2]
+  lat_col <- as.numeric(args[3])
+  long_col <- as.numeric(args[4])
+  site_col <- as.numeric(args[5])
+  empty <- args[6]
+}
+
+datatable = read.table(data_table,header=T)
+
+latcol = names(datatable[lat_col])
+longcol = names(datatable[long_col])
+sitecol = names(datatable[site_col])
+
+if (empty == "false"){
+   empty = FALSE
+}else if (empty=="true"){
+   empty=TRUE}
+
+
+#Make template
+
+template_geographic_coverage(path =".", data.path = "data_files", data.table = tablename, lat.col = latcol, lon.col = longcol, site.col = sitecol, empty = empty)
+
+

diff -r 000000000000 -r 330f15f2ad3f make_eml.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_eml.R Sat Dec 23 20:40:29 2023 +0000

[

b'@@ -0,0 +1,442 @@\n+##07/06/2023 ##Genthon Tanguy\r\n+##update 15/11/2023 ## Seguineau Pauline\r\n+\r\n+###make_eml\r\n+\r\n+args = commandArgs(trailingOnly=TRUE)\r\n+if(length(args)>0){\r\n+ title <- args[1]\r\n+ start <- args[2]\r\n+ end <-args[3]\r\n+ data_table <- args[4]\r\n+ data_raster <- args[5]\r\n+ data_vector <- args[6]\r\n+ data_other <- args[7]\r\n+ destable <- args[8]\r\n+ desraster<- args[9]\r\n+ desvector<- args[10]\r\n+ desother <- args[11]\r\n+ quote <- args[12]\r\n+ table_url <- args[13]\r\n+ other_url <- args[14]\r\n+ raster_url <- args[15]\r\n+ vector_url <- args[16]\r\n+}\r\n+\r\n+#Load package\r\n+\r\n+library(EMLassemblyline)\r\n+sessionInfo()\r\n+\r\n+\r\n+###Format data###\r\n+if (data_table == ""){\r\n+ table=NULL\r\n+}else{\r\n+ table = strsplit(data_table," ")\r\n+ for (file in table){\r\n+ name_table = gsub("\\\\.[a-zA-Z]*", "", file)}\r\n+ }\r\n+ \r\n+ \r\n+if (quote != ""){\r\n+ quote = strsplit(quote,",")\r\n+ if (length(quote[[1]]) != length(table[[1]])){\r\n+ stop("Your number of quote(s) isn\'t equal to your number of data table file(s). Please enter the quote parameter as many time as the number of data tables you\'ve input")}\r\n+}\r\n+\r\n+\r\n+tablequote=NULL\r\n+for (quote_table in quote[[1]]){\r\n+ if (quote_table=="quote"){\r\n+ quote_table = sub("quote",\'"\', quote_table)}\r\n+ else if (quote_table=="apostrophe"){\r\n+ quote_table = gsub("apostrophe","\'",quote_table)}\r\n+ else if (quote_table=="none"){\r\n+ quote_table = gsub("none","",quote_table)}\r\n+ tablequote = c(tablequote, quote_table)\r\n+}\r\n+\r\n+ \r\n+if (data_raster == ""){\r\n+ raster=NULL\r\n+}else{\r\n+ raster = strsplit(data_raster," ")\r\n+ for (file in raster){\r\n+ name_raster = gsub("\\\\.[a-zA-Z]*", "", file)}\r\n+ }\r\n+ \r\n+if (data_vector == ""){\r\n+ vector=NULL\r\n+}else{\r\n+ vector = strsplit(data_vector," ")\r\n+ for (file in vector){\r\n+ name_vector = gsub("\\\\.[a-zA-Z]*", "", file)}\r\n+ }\r\n+\r\n+if (data_other == ""){\r\n+ other=NULL\r\n+}else{\r\n+ other = strsplit(data_other," ")\r\n+ for (file in other){\r\n+ name_other = gsub("\\\\.[a-zA-Z]*", "", file)}\r\n+ }\r\n+\r\n+if (data_table !=""){\r\n+ if (destable == ""){\r\n+ des_table = name_table\r\n+ }else{\r\n+ des_table = strsplit(destable,",")}\r\n+}\r\n+\r\n+if (data_raster !=""){\r\n+ if (desraster == ""){\r\n+ des_raster = name_raster\r\n+ }else{\r\n+ des_raster = strsplit(desraster,",")}\r\n+}\r\n+\r\n+if (data_vector !=""){ \r\n+ if (desvector == ""){\r\n+ des_vector = name_vector\r\n+ }else{\r\n+ des_vector = strsplit(desvector,",")}\r\n+}\r\n+\r\n+if (data_other !=""){\r\n+ if (desother == ""){\r\n+ des_other = name_other\r\n+ }else{\r\n+ des_other = strsplit(desother,",")}\r\n+}\r\n+\r\n+if (data_table !=""){\r\n+ if (table_url == ""){\r\n+ urltable = ""\r\n+ }else{\r\n+ table_url = gsub("\\\\-" ,"", table_url)\r\n+ urltable = strsplit(table_url,",")\r\n+ }\r\n+}\r\n+\r\n+if (data_other !=""){\r\n+ if (other_url == ""){\r\n+ urlother = ""\r\n+ }else{\r\n+ other_url = gsub("\\\\-" ,"", other_url)\r\n+ urlother = strsplit(other_url,",")\r\n+ }\r\n+}\r\n+\r\n+if (data_raster !=""){\r\n+ if (raster_url == ""){\r\n+ urlraster = ""\r\n+ }else{\r\n+ raster_url = gsub("\\\\-" ,"", raster_url)\r\n+ urlraster = strsplit(raster_url,",")\r\n+ }\r\n+}\r\n+\r\n+if (data_vector !=""){\r\n+ if (vector_url == ""){\r\n+ urlvector = ""\r\n+ }else{\r\n+ vector_url = gsub("\\\\-" ,"", vector_url)\r\n+ urlvector = strsplit(vector_url,",")\r\n+ }\r\n+}\r\n+\r\n+\r\n+\r\n+###Make EML###\r\n+ \r\n+if (!is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){\r\n+ \r\n+ EMLassemblyline::make_eml(\r\n+ path="output_template",\r\n+ data.path="data_files",\r\n+ eml.path=".", \r\n+ dataset.title = title,\r\n+ temporal.coverage = c(start,end),\r\n+ data.table=table[[1]],\r\n+ data.table.name = name_ta'..b'MLassemblyline::make_eml(\r\n+ path="output_template",\r\n+ data.path="data_files",\r\n+ eml.path=".", \r\n+ dataset.title = title,\r\n+ temporal.coverage = c(start,end),\r\n+ data.table=table[[1]],\r\n+ data.table.name = name_table,\r\n+ data.table.description = des_table[[1]],\r\n+ data.table.quote.character = tablequote,\r\n+ data.table.url = urltable[[1]],\r\n+ other.entity=other[[1]],\r\n+ other.entity.name = name_other,\r\n+ other.entity.description = des_other[[1]],\r\n+ other.entity.url= urlother[[1]])\r\n+\r\n+}else if (is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){\r\n+\r\n+ EMLassemblyline::make_eml(\r\n+ path="output_template",\r\n+ data.path="data_files",\r\n+ eml.path=".", \r\n+ dataset.title = title,\r\n+ temporal.coverage = c(start,end),\r\n+ spatial.raster=raster[[1]],\r\n+ spatial.raster.name = name_raster,\r\n+ spatial.raster.description = des_raster[[1]],\r\n+ spatial.raster.url = urlraster[[1]],\r\n+ other.entity=other[[1]],\r\n+ other.entity.name = name_other,\r\n+ other.entity.description = des_other[[1]],\r\n+ other.entity.url= urlother[[1]])\r\n+\r\n+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){\r\n+ \r\n+ EMLassemblyline::make_eml(\r\n+ path="output_template",\r\n+ data.path="data_files",\r\n+ eml.path=".", \r\n+ dataset.title = title,\r\n+ temporal.coverage = c(start,end),\r\n+ data.table=table[[1]],\r\n+ data.table.name = name_table,\r\n+ data.table.description = des_table[[1]],\r\n+ data.table.quote.character = tablequote,\r\n+ data.table.url = urltable[[1]],\r\n+ spatial.vector=vector[[1]],\r\n+ spatial.vector.name = name_vector,\r\n+ spatial.vector.description = des_vector[[1]],\r\n+ spatial.vector.url = urlvector[[1]],\r\n+ other.entity=other[[1]],\r\n+ other.entity.name = name_other,\r\n+ other.entity.description = des_other[[1]],\r\n+ other.entity.url= urlother[[1]])\r\n+\r\n+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){\r\n+\r\n+ EMLassemblyline::make_eml(\r\n+ path="output_template",\r\n+ data.path="data_files",\r\n+ eml.path=".", \r\n+ dataset.title = title,\r\n+ temporal.coverage = c(start,end),\r\n+ data.table=table[[1]],\r\n+ data.table.name = name_table,\r\n+ data.table.description = des_table[[1]],\r\n+ data.table.quote.character = tablequote,\r\n+ data.table.url = urltable[[1]],\r\n+ spatial.raster=raster[[1]],\r\n+ spatial.raster.name = name_raster,\r\n+ spatial.raster.description = des_raster[[1]],\r\n+ spatial.raster.url = urlraster[[1]],\r\n+ other.entity=other[[1]],\r\n+ other.entity.name = name_other,\r\n+ other.entity.description = des_other[[1]],\r\n+ other.entity.url= urlother[[1]])}\r\n+\r\n+issues()\r\n+old.names <- list.files(path=".", pattern=".xml")\r\n+file.rename(from=old.names, to="eml.xml")\r\n+\r\n+\r\n+\r\n+\r\n+\r\n+\r\n'

diff -r 000000000000 -r 330f15f2ad3f raster_templates.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/raster_templates.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,22 @@
+#15/12/2023 #SEGUINEAU Pauline
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+ data_raster <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+raster = strsplit(data_raster," ")
+
+#Make templates to describe data raster
+
+template_raster_attributes(path = ".",data.path= "data_files", raster.file = raster[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+
+

diff -r 000000000000 -r 330f15f2ad3f taxo_cov_template.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/taxo_cov_template.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,47 @@
+#28/11/2023
+#Seguineau Pauline
+#Make taxonomic coverage template
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  data_taxa <- args[1]
+  taxa_table <- args[2]
+  taxa_col <- as.numeric(args[3])
+  taxa_name_type <- args[4]
+  authority <- as.numeric(args[5])
+  authority2 <- as.numeric(args[6])
+  authority3 <- as.numeric(args[7])
+  empty <- args[8]
+}
+
+#transfom arguments
+taxatable = read.table(data_taxa,header=T,sep="\t")
+taxacol = names(taxatable[taxa_col])
+
+if (authority2 == 0 && authority3==0){
+   authority_f = authority}
+
+if(authority2 == 0 && authority3 != 0){
+   authority_f = c(authority,authority3)}
+
+if (authority2 !=0 && authority3==0){
+   authority_f = c(authority,authority2)}
+
+if (authority3 !=0 && authority2 !=0){
+   authority_f = c(authority,authority2,authority3)}
+
+if (empty == "false"){
+   empty = FALSE
+}else if (empty=="true"){
+   empty=TRUE}
+
+
+#Make template
+
+template_taxonomic_coverage(path =".", data.path = "data_files", taxa.table = taxa_table, taxa.col = taxacol, taxa.name.type = taxa_name_type , taxa.authority = authority_f, empty = empty)

diff -r 000000000000 -r 330f15f2ad3f test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml Sat Dec 23 20:40:29 2023 +0000

b'@@ -0,0 +1,2074 @@\n+<?xml version="1.0" encoding="UTF-8"?><eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" packageId="doi:10.48502/hssh-5194" system="unknown" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://nis.lternet.edu/schemas/EML/eml-2.2.0/xsd/eml.xsd">\n+ <dataset id="dataset-02">\n+ <title>Assessing the importance of field margins for bat species and communities in intensive agricultural landscapes - Data</title>\n+ <creator>c\n+ <individualName>\n+ <givenName>Constance</givenName>\n+ <givenName/>\n+ <surName>Blary</surName>\n+ </individualName>\n+ <organizationName>CEFE</organizationName>\n+ <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-6204-9983</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>K\xc3\xa9vin</givenName>\n+ <givenName/>\n+ <surName>Barr\xc3\xa9</surName>\n+ </individualName>\n+ <organizationName>CESCO MNHN</organizationName>\n+ <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-5368-4053</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>Christian</givenName>\n+ <givenName/>\n+ <surName>Kerbiriou</surName>\n+ </individualName>\n+ <organizationName>CESCO</organizationName>\n+ <electronicMailAddress>christian.kerbiriou@mnhn.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-6080-4762</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>Isabelle</givenName>\n+ <givenName/>\n+ <surName>Le Viol</surName>\n+ </individualName>\n+ <organizationName>CESCO</organizationName>\n+ <electronicMailAddress>isabelle.le-viol@mnhn.fr</electronicMailAddress>\n+ </creator>\n+ <pubDate>2021-05-25</pubDate>\n+ <abstract>\n+ <para>Landscape simplification and degradation through agricultural intensification is widely recognized as a main driver of biodiversity loss. In intensively used agricultural landscapes, patches of semi-natural habitats and particularly connections between them are of high importance for many taxa. Vegetated connections like hedgerows are especially important for foraging and commuting of mobile taxa such as bats. However, the interest of another treeless linear habitat \xe2\x80\x93 herbaceous field margins \xe2\x80\x93 remains unstudied for insectivorous bats. Field margins are nevertheless known as an important habitat for other taxa, including bat prey. Here we assessed the importance of field margins for bats compared to other landscape variables. We measured bat activity based on a repeated passive acoustic monitoring during 17 complete nights in summer on 112 study sites in an intensively used agricultural landscape. Each night, we sampled bat species activity and community metrics (i.e. species richness and community habitat specialization index) at different distances to field margins, and along a gradient of relative density of field margins. To compare field margin effects with other landscape variables, the sampled sites were selected by keeping a large variability in these other variables (land-cover Shannon diversity index, forests, hedgerows, water bodies, main roads, urban areas, grasslands, number of crops and rapeseed percentage). Only Myotis sp. were affected by herbaceous field margins. Specifically, the Myotis group activity decreased with the distance to herbaceous field margins (i.e. towards field crop cores), and positively correlated with relative density of herbaceous field margins, for which the effect size was comparable to other landscape variables. However, other landscape variables such as the proportion of and t'..b' </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Myo_ER05</attributeName>\n+ <attributeDefinition>Number of bat passes of Myo specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">42</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Myo_ER01</attributeName>\n+ <attributeDefinition>Number of bat passes of Myo specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">33</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Ple_ER05</attributeName>\n+ <attributeDefinition>Number of bat passes of Ple specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">8</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Ple_ER01</attributeName>\n+ <attributeDefinition>Number of bat passes of Ple specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">5</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ </attributeList>\n+ <numberOfRecords>112</numberOfRecords>\n+ </dataTable>\n+ </dataset>\n+</eml:eml>\n'

diff -r 000000000000 -r 330f15f2ad3f test-data/Present_Surface_pH.tif

Binary file test-data/Present_Surface_pH.tif has changed

diff -r 000000000000 -r 330f15f2ad3f test-data/annotations.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,10 @@
+id element context subject predicate_label predicate_uri object_label object_uri
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 biodiversity http://aims.fao.org/aos/agrovoc/c_33949
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 mammals http://aims.fao.org/aos/agrovoc/c_4560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 chiroptera http://aims.fao.org/aos/agrovoc/c_1560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 bats http://aims.fao.org/aos/agrovoc/c_1560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Landscape http://www.eionet.europa.eu/gemet/concept/4648
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Ecosystem http://www.eionet.europa.eu/gemet/concept/2519
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Animal ecology http://www.eionet.europa.eu/gemet/concept/420
+/data_blary_al.txt/X /dataTable/attribute data_blary_al.txt X is a http://www.w3.org/1999/02/22-rdf-syntax-ns#type decimalLongitude http://rs.tdwg.org/dwc/terms/decimalLongitude
+/data_blary_al.txt/Y /dataTable/attribute data_blary_al.txt Y is a http://www.w3.org/1999/02/22-rdf-syntax-ns#type decimalLatitude http://rs.tdwg.org/dwc/terms/decimalLatitude

diff -r 000000000000 -r 330f15f2ad3f test-data/annotations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.txt Sat Dec 23 20:40:29 2023 +0000

diff -r 000000000000 -r 330f15f2ad3f test-data/attributes_data_7.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_7.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,7 @@
+attributeName attributeDefinition class unit dateTimeFormatString missingValueCode missingValueCodeExplanation
+LIB_SITE Description for: LIB_SITE character "" "" "" ""
+X Description for: X numeric dimensionless "" "" ""
+Y Description for: Y numeric dimensionless "" "" ""
+PROGRAMME Description for: PROGRAMME categorical "" "" "" ""
+OPERATEUR_ Description for: OPERATEUR_ categorical "" "" "" ""
+STATUT_DU_ Description for: STATUT_DU_ categorical "" "" "" ""

diff -r 000000000000 -r 330f15f2ad3f test-data/attributes_data_blary_al.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_blary_al.tabular Sat Dec 23 20:40:29 2023 +0000

b'@@ -0,0 +1,81 @@\n+attributeName\tattributeDefinition\tclass\tunit\tdateTimeFormatString\tmissingValueCode\tmissingValueCodeExplanation\n+Id\tSampling site ID\tcharacter\t\t\t"NA"\t"No information"\n+dist_field_margin\tDistance to the nearest field margin element (in meters)\tnumeric\tmeter\t\tNA\tNo information\n+dist_hedgerow\tDistance to the nearest hedgerow element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_forest\tDistance to the nearest forest element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_road\tDistance to the nearest road element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_water\tDistance to the nearest water body element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_urban\tDistance to the nearest urban element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+density_field_margins_250m\tRelative density of field margins in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_500m\tRelative density of filed margins in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_750m\tRelative density of filed margins in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_1000m\tRelative density of filed margins in a 1000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_1500m\tRelative density of filed margins in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_2000m\tRelative density of filed margins in a 2000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_4000m\tRelative density of filed margins in a 4000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_250m\tRelative density of roads in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_500m\tRelative density of roads in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_750m\tRelative density of roads in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_1000m\tDescription for density_roads_1000m\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_1500m\tRelative density of roads in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_2000m\tRelative density of roads in a 2000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_4000m\tRelative density of roads in a 4000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_250m\tRelative density of hedgerows in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_500m\tRelative density of hedgerows in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_750m\tRelative density of hedgerows in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_1000m\tRelative density of hedgerows in a 1000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_1500m\tRelative density of hedgerows in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No informa'..b'eric\tpercent\t\t"NA"\t"No information"\n+forest_4000m\tPercentage of land covered by forest in different 4000 m buffer sizes\tnumeric\tpercent\t\t"NA"\t"No information"\n+urban_4000m\tPercentage of land covered by urban area in different 4000 m buffer sizes\tnumeric\tpercent\t\t"NA"\t"No information"\n+perc_rapeseed\tPercentage of rapeseed crops in a 100 m radius around each site at the sampling date\tnumeric\tpercent\t\t"NA"\t"No information"\n+nb_crops\tNumber of different crops in a 100 m radius around each site at the sampling date\tnumeric\tnumber\t\t"NA"\t"No information"\n+date\tDescription for date\tDate\t\tYYYY-MM-DD\t"NA"\t"No information"\n+X\tSampling site longitude\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+Y\tSampling site latitude\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+recorder\tRecorder ID used for data collection on the sampling site\tcategorical\t\t\t"NA"\t"No information"\n+min_t\tMinimum temperature recorded on the sampling area during the sampling night (in celsius)\tnumeric\tcelsius\t\t"NA"\t"No information"\n+max_wind\tMaximum wind speed recorded on the sampling area during the sampling night (in km/h)\tnumeric\tkilometerPerHour\t\t"NA"\t"No information"\n+CSI_ER05\tCommunity specialization index calculated from species level activity on the 0.5 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+CSI_ER01\tCommunity specialization index calculated from species level activity on the 0.1 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+richness_ER05\tSpecies richness calculated from species level activity on the 0.5 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+richness_ER01\tSpecies richness calculated from species level activity on the 0.1 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+Nyclei_ER05\tNumber of bat passes of Nyclei specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nyclei_ER01\tNumber of bat passes of Nyclei specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Pippip_ER05\tNumber of bat passes of Pippip specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Pippip_ER01\tNumber of bat passes of Pippip specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Eptser_ER05\tNumber of bat passes of Epster specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Eptser_ER01\tNumber of bat passes of Epster specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nycnoc_ER05\tNumber of bat passes of Nycnoc specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nycnoc_ER01\tNumber of bat passes of Nycnoc specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Myo_ER05\tNumber of bat passes of Myo specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Myo_ER01\tNumber of bat passes of Myo specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Ple_ER05\tNumber of bat passes of Ple specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Ple_ER01\tNumber of bat passes of Ple specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n'

diff -r 000000000000 -r 330f15f2ad3f test-data/attributes_data_blary_al.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_blary_al.txt Sat Dec 23 20:40:29 2023 +0000

diff -r 000000000000 -r 330f15f2ad3f test-data/catvars_data_7.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_7.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,13 @@
+attributeName code definition
+PROGRAMME DCE Value: DCE for attribute: PROGRAMME
+PROGRAMME ELV Value: ELV for attribute: PROGRAMME
+PROGRAMME DCE/ELV Value: DCE/ELV for attribute: PROGRAMME
+PROGRAMME REBENT Value: REBENT for attribute: PROGRAMME
+PROGRAMME REBENT/DCE Value: REBENT/DCE for attribute: PROGRAMME
+OPERATEUR_ MNHN CC Value: MNHN CC for attribute: OPERATEUR_
+OPERATEUR_ Station de Wimer Value: Station de Wimer for attribute: OPERATEUR_
+OPERATEUR_ Ifremer Anglet Value: Ifremer Anglet for attribute: OPERATEUR_
+OPERATEUR_ Bio-Littoral Value: Bio-Littoral for attribute: OPERATEUR_
+OPERATEUR_ Ecosub Value: Ecosub for attribute: OPERATEUR_
+STATUT_DU_ actif Value: actif for attribute: STATUT_DU_
+STATUT_DU_ inactif Value: inactif for attribute: STATUT_DU_

diff -r 000000000000 -r 330f15f2ad3f test-data/catvars_data_blary_al.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_blary_al.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,16 @@
+attributeName code definition
+recorder 10250 Value: 10250 for attribute: recorder
+recorder 11693 Value: 11693 for attribute: recorder
+recorder 13289 Value: 13289 for attribute: recorder
+recorder 13676 Value: 13676 for attribute: recorder
+recorder 13733 Value: 13733 for attribute: recorder
+recorder 13740 Value: 13740 for attribute: recorder
+recorder 17232 Value: 17232 for attribute: recorder
+recorder 17329 Value: 17329 for attribute: recorder
+recorder 17573 Value: 17573 for attribute: recorder
+recorder 17578 Value: 17578 for attribute: recorder
+recorder 17598 Value: 17598 for attribute: recorder
+recorder 17601 Value: 17601 for attribute: recorder
+recorder 17607 Value: 17607 for attribute: recorder
+recorder 17608 Value: 17608 for attribute: recorder
+recorder 3760 Value: 3760 for attribute: recorder

diff -r 000000000000 -r 330f15f2ad3f test-data/catvars_data_blary_al.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_blary_al.txt Sat Dec 23 20:40:29 2023 +0000

diff -r 000000000000 -r 330f15f2ad3f test-data/custom_units.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_units.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,1 @@
+id unitType parentSI multiplierToSI description

diff -r 000000000000 -r 330f15f2ad3f test-data/data_7.GeoJSON
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_7.GeoJSON Sat Dec 23 20:40:29 2023 +0000

[

b'@@ -0,0 +1,72 @@\n+{\n+"type": "FeatureCollection",\n+"name": "shapefile",\n+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },\n+"features": [\n+{ "type": "Feature", "properties": { "LIB_SITE": "Rohein", "X": -2.630417, "Y": 48.64695, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.630417, 48.64695 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Goue Vas", "X": -2.636567, "Y": 47.253417, "PROGRAMME": "ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -2.636567, 47.253417 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Grand Coin", "X": -3.004233, "Y": 47.407783, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.004233, 47.407783 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Gaouac\'h", "X": -4.398067, "Y": 47.807367, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.398067, 47.807367 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Pierres Noires", "X": -3.2159, "Y": 47.598067, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.2159, 47.598067 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Ile Dumet", "X": -2.623133, "Y": 47.408667, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.623133, 47.408667 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Bonen", "X": -2.65305, "Y": 47.303917, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.65305, 47.303917 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Cancavale", "X": -2.018067, "Y": 48.604633, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.018067, 48.604633 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Haie de la Conch\xc2\x82e", "X": -2.045717, "Y": 48.687067, "PROGRAMME": "REBENT\\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.045717, 48.687067 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Vieux Banc", "X": -2.167383, "Y": 48.699133, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.167383, 48.699133 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Kein an duono", "X": -3.145533, "Y": 48.889183, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -3.145533, 48.889183 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Moguedhier", "X": -3.056567, "Y": 48.838983, "PROGRAMME": "REBENT\\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.056567, 48.838983 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Paon", "X": -2.984967, "Y": 48.866383, "PROGRAMME": "REBENT\\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.984967, 48.866383 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Squ\xc2\x82ouel", "X": -3.474583, "Y": 48.837417, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.474583, 48.837417 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Roc\'h Mignon", "X": -3.5768, "Y": 48.756183, "PROGRAMME": "REBENT\\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.5768, 48.756183 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Roc\'h Parou", "X": -3.620167, "Y": 48.715667, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "'..b'"type": "Feature", "properties": { "LIB_SITE": "Soccoa", "X": -1.689, "Y": 43.396667, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.689, 43.396667 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Le Pilier", "X": -2.377417, "Y": 47.045083, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.377417, 47.045083 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Yeu Basse Flore", "X": -2.40571, "Y": 46.7322, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.40571, 46.7322 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "La Vigie", "X": -2.01735, "Y": 46.721367, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.01735, 46.721367 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Phare des baleines", "X": -1.592167, "Y": 46.2476, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.592167, 46.2476 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Guetary Nord", "X": -1.60625, "Y": 43.4289, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.60625, 43.4289 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Viviers Basques", "X": -1.712017, "Y": 43.389367, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.712017, 43.389367 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Port Vieux", "X": -1.5717, "Y": 43.483133, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.5717, 43.483133 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Dielette", "X": -1.869833, "Y": 49.550517, "PROGRAMME": "DCE", "OPERATEUR_": "Ecosub", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.869833, 49.550517 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Gouville", "X": -1.648583, "Y": 49.107267, "PROGRAMME": "DCE", "OPERATEUR_": "Ecosub", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.648583, 49.107267 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Le Croisic SR", "X": -2.559867, "Y": 47.30305, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.559867, 47.30305 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Penchateau SR", "X": -2.412467, "Y": 47.256833, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.412467, 47.256833 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "Baguenaud SR", "X": -2.35355, "Y": 47.232017, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.35355, 47.232017 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "La Banche Nord SR", "X": -2.4672, "Y": 47.184617, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.4672, 47.184617 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "La Pointe Saint Gildas", "X": -2.253433, "Y": 47.134083, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.253433, 47.134083 ] } },\n+{ "type": "Feature", "properties": { "LIB_SITE": "La Banche Sud SR", "X": -2.467883, "Y": 47.17335, "PROGRAMME": "DCE\\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.467883, 47.17335 ] } }\n+]\n+}\n'

diff -r 000000000000 -r 330f15f2ad3f test-data/datafile_1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datafile_1.tsv Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,113 @@
+Id density_boats distance_coast percentage_turbidity nb_individual recorder min_t max_wind
+ID1 0 7.083851986 1 1 13740 9 13
+ID2 0 5.057419245 1 1 3760 11.7 15
+ID3 0 14.81271925 1 1 17598 9 13
+ID4 23.38130966 17.39474876 0 1 17607 12.8 24
+ID5 0 13.8788222 1 1 17608 14.3 17
+ID6 0 20.55593297 1 1 13733 20 17
+ID7 0 5.228906117 1 1 10250 14.3 30
+ID8 0 8.18336163 0.963336783 2 13740 11.7 15
+ID9 0 14.77478497 1 1 13733 11.7 15
+ID10 0 18.23789045 1 1 17573 9 13
+ID11 0 30.97770737 0.934057759 2 17608 8.1 13
+ID12 0 14.72135785 0 2 13733 8.1 13
+ID13 0 26.97792869 1 1 17578 8.1 13
+ID14 0 8.63834361 1 1 17329 11.7 15
+ID15 23.42372625 2.371250707 0.611485317 2 17232 14.3 30
+ID16 0 2.058590657 1 1 NA 11.7 15
+ID17 0 14.5557442 1 1 11693 14.3 17
+ID18 0 15.31628381 0.484376584 2 10250 14.2 9
+ID19 22.68310089 18.12266606 1 1 13733 16.9 13
+ID20 0 10.71630644 0.946424061 2 17608 NA NA
+ID21 0 7.492501839 1 1 17608 14.3 30
+ID22 0 2.455167732 1 1 17578 8.1 13
+ID23 0 0.215005092 0.619357094 2 17608 13.3 0
+ID24 0 20.5942275 0.530977409 2 17573 12.8 24
+ID25 0 0.00565931 1 1 10250 9 13
+ID26 0 4.61669024 1 1 3760 8.1 13
+ID27 0 0.650746944 1 1 13289 NA NA
+ID28 11.55094443 4.256523462 0.534748923 2 17608 17.4 15
+ID29 25.29249263 0.333785924 0 3 11693 16.9 13
+ID30 5.659985665 3.927116342 1 1 17578 16.9 13
+ID31 0 0.011314137 0 2 13740 20 17
+ID32 0 6.724401426 0.262229612 3 17578 8.5 7
+ID33 0 10.20546782 0.456408314 2 13676 17.8 13
+ID34 0 0.005662514 1 1 13289 9 13
+ID35 0 12.50424544 1 1 13733 13.3 0
+ID36 41.24173899 0.028288543 0 2 17607 NA NA
+ID37 0 0.707453733 0 2 13733 17.8 13
+ID38 7.278017273 8.411585021 0.521433594 2 17601 17.4 15
+ID39 26.46665163 3.174693 1 1 17598 11.7 15
+ID40 21.65723654 8.846001472 0.672489759 2 17232 9 13
+ID41 0 7.296088753 0.033790965 2 17601 9 13
+ID42 0 0.848848396 0 3 17608 17.4 14
+ID43 0 17.47693701 1 1 NA 8.1 13
+ID44 0 8.040770102 1 1 17329 8.1 13
+ID45 0 9.227200724 1 1 17607 8.1 13
+ID46 0 4.089829166 0 1 17607 17.4 15
+ID47 16.24258106 12.9081546 0.519677866 2 17232 14.3 17
+ID48 0 28.17682685 0 3 13733 14.2 9
+ID49 0 11.13752122 0.568145458 2 17329 12.8 24
+ID50 0 12.15482119 0.744442086 2 13676 17.4 14
+ID51 0 1.075147125 0.126547756 2 17329 17.8 13
+ID52 0 0.639429606 0.318501019 3 17573 17.8 13
+ID53 0 11.34563151 1 1 13289 9 13
+ID54 0 6.070721358 1 1 11693 8.1 13
+ID55 0 2.534940304 1 1 3760 NA NA
+ID56 0 0 1 1 17608 14.9 13
+ID57 23.6734518 9.73526417 1 1 13733 14.9 13
+ID58 22.77461434 2.30834512 0 2 3760 17.4 15
+ID59 0 9.034849513 1 1 NA 14.3 30
+ID60 0 1.61299451 1 1 17598 8.1 13
+ID61 0 1.550212164 1 1 17601 8.1 13
+ID62 16.6417688 0.198064626 1 1 13676 13.3 0
+ID63 0 0.147167035 0.503759276 2 13740 14.9 13
+ID64 0 1.126075147 1 1 17329 14.2 9
+ID65 0 1.166213768 0.486555056 2 10250 17.4 14
+ID66 0 37.17890687 0.241246715 3 11693 12.3 11
+ID67 0 1.01318843 1 1 NA 11.7 15
+ID68 0 14.97426034 0.513275979 3 17578 8.5 7
+ID69 0 0.050933786 1 1 10250 13.3 0
+ID70 0 1.60733488 1 1 11693 13.3 0
+ID71 0 0.15274085 0.616607437 2 11693 14.9 13
+ID72 0 4.745186863 0.427826338 3 17578 14.9 13
+ID73 0 0.005658029 1 1 13289 17.4 15
+ID74 20.10097018 1.120479882 1 1 17329 9 13
+ID75 0 1.833512535 1 1 11693 9 13
+ID76 0 1.964892412 1 1 3760 14.9 13
+ID77 0 1.024508972 1 1 17598 13.3 0
+ID78 13.02008677 2.446206116 0 2 17601 17.8 13
+ID79 0 5.849408836 0.506514891 2 17601 12.3 11
+ID80 0 0.82602546 1 1 17607 20 17
+ID81 0 6.632335465 1 1 13733 17.8 13
+ID82 9.774097667 2.083923212 0.147137616 2 17329 17.4 14
+ID83 0 0.843046283 1 1 17598 11.7 15
+ID84 0 17.16743054 1 1 3760 9 13
+ID85 0 2.347816248 1 1 17607 13.3 0
+ID86 0 2.089467724 1 1 17608 8.1 13
+ID87 14.70497236 1.782279054 1 1 17329 8.1 13
+ID88 0 1.828267391 1 1 10250 8.1 13
+ID89 19.54258479 2.829334541 1 1 3760 14.3 30
+ID90 22.89867383 0.50376408 1 1 17573 14.3 30
+ID91 0 7.486419194 1 1 13676 14.2 9
+ID92 0 4.612337295 1 1 17601 11.7 15
+ID93 0 20.34521788 1 1 17232 11.7 15
+ID94 0 13.69731259 0.558754442 2 13289 14.3 17
+ID95 0 0.481041313 0.601822162 2 17607 14.3 17
+ID96 0 19.55721647 0.856473518 3 17232 16.9 13
+ID97 0 9.467489106 1 1 10250 17.4 15
+ID98 0 22.78746039 0.460271388 3 11693 14.3 30
+ID99 0 8.380520951 0.769578171 2 17607 9 13
+ID100 32.43763517 0.486507892 0.297384797 4 17573 12.3 11
+ID101 39.87341993 18.47598574 0.377696294 3 17329 NA NA
+ID102 0 1.482655198 0.420523151 2 17598 NA NA
+ID103 0 1.188455008 1 1 13289 8.1 13
+ID104 0 2.981949867 1 1 17232 13.3 0
+ID105 6.048310547 0.06224536 1 1 17578 17.4 14
+ID106 0 0.067957866 1 1 17232 17.4 14
+ID107 0 0.305516266 0 1 17598 17.4 14
+ID108 0 1.375212224 0.512278187 2 17601 20 17
+ID109 23.18323585 0.045282164 0.355925541 2 13676 17.4 14
+ID110 0 0 0.599181014 2 17232 13.3 0
+ID111 0 0.050922259 1 1 17329 14.9 13
+ID112 0 0.763920326 1 1 13740 13.3 0

diff -r 000000000000 -r 330f15f2ad3f test-data/entities.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/entities.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,4 @@
+objectName variable value
+data_7.GeoJSON geometry Point
+data_7.GeoJSON geometricObjectCount 65
+data_7.GeoJSON spatialReference GCS_WGS_1984

diff -r 000000000000 -r 330f15f2ad3f test-data/geographic_coverage.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geographic_coverage.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,2 @@
+geographicDescription northBoundingCoordinate southBoundingCoordinate eastBoundingCoordinate westBoundingCoordinate
+Yvelines - Essonne - Seine et Marne 49.08428 48.12266 3.56409 1.60296

diff -r 000000000000 -r 330f15f2ad3f test-data/geographic_coverage.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geographic_coverage.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,5 @@
+geographicDescription northBoundingCoordinate southBoundingCoordinate eastBoundingCoordinate westBoundingCoordinate
+1 -65.999946 -65.999946 142.3360535 142.3360535
+2 -66.394359 -66.394359 140.4840125 140.4840125
+3 -66.023545 -66.023545 142.745584 142.745584
+4 -66.3379125 -66.3379125 144.011634 144.011634

diff -r 000000000000 -r 330f15f2ad3f test-data/keywords.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/keywords.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,7 @@
+keyword keywordThesaurus
+Acoustic monitoring Keywords
+Bat community Keywords
+Farmland biodiversity Keywords
+Field borders Keywords
+Habitat specialisation Keywords
+Landscape composition Keywords

diff -r 000000000000 -r 330f15f2ad3f test-data/keywords.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/keywords.txt Sat Dec 23 20:40:29 2023 +0000

diff -r 000000000000 -r 330f15f2ad3f test-data/metadataoutput.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadataoutput.xml Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,153 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="0a0472ad-2e8f-412f-8e95-ba84b7cc9996" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd" system="unknown">
+  <dataset id="dataset">
+    <creator>
+      <individualName>
+        <givenName>Constance</givenName>
+        <surName>Blary</surName>
+      </individualName>
+      <organizationName>CEFE</organizationName>
+      <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Kévin</givenName>
+        <surName>Barré</surName>
+      </individualName>
+      <organizationName>CESCO MNHN</organizationName>
+      <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Christian</givenName>
+        <surName>Kerbiriou</surName>
+      </individualName>
+      <organizationName>CESCO</organizationName>
+      <electronicMailAddress>christian.kerbiriou@mnhn.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Isabelle</givenName>
+        <surName>Le Viol</surName>
+      </individualName>
+      <organizationName>CESCO</organizationName>
+      <electronicMailAddress>isabelle.le-viol@mnhn.fr</electronicMailAddress>
+    </creator>
+    <pubDate>2023-07-23</pubDate>
+    <keywordSet>
+      <keyword>Acoustic monitoring</keyword>
+      <keyword>Bat community</keyword>
+      <keyword>Farmland biodiversity</keyword>
+      <keyword>Field borders</keyword>
+      <keyword>Habitat specialisation</keyword>
+      <keyword>Landscape composition</keyword>
+      <keywordThesaurus>Keywords</keywordThesaurus>
+    </keywordSet>
+    <coverage>
+      <geographicCoverage>
+        <geographicDescription>Yvelines - Essonne - Seine et Marne</geographicDescription>
+        <boundingCoordinates>
+          <westBoundingCoordinate>1.60296</westBoundingCoordinate>
+          <eastBoundingCoordinate>3.56409</eastBoundingCoordinate>
+          <northBoundingCoordinate>49.08428</northBoundingCoordinate>
+          <southBoundingCoordinate>48.12266</southBoundingCoordinate>
+        </boundingCoordinates>
+      </geographicCoverage>
+    </coverage>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="biodiversity">http://aims.fao.org/aos/agrovoc/c_33949</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="mammals">http://aims.fao.org/aos/agrovoc/c_4560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="chiroptera">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="bats">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Landscape">http://www.eionet.europa.eu/gemet/concept/4648</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Ecosystem">http://www.eionet.europa.eu/gemet/concept/2519</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Animal ecology">http://www.eionet.europa.eu/gemet/concept/420</valueURI>
+    </annotation>
+    <contact>
+      <individualName>
+        <givenName>Constance</givenName>
+        <surName>Blary</surName>
+      </individualName>
+      <organizationName>CEFE</organizationName>
+      <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>
+    </contact>
+    <contact>
+      <individualName>
+        <givenName>Kévin</givenName>
+        <surName>Barré</surName>
+      </individualName>
+      <organizationName>CESCO MNHN</organizationName>
+      <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+    </contact>
+    <project>
+      <title>Effect of agricultural landscape features on bats</title>
+      <personnel>
+        <individualName>
+          <givenName>Kévin</givenName>
+          <surName>Barré</surName>
+        </individualName>
+        <organizationName>CESCO MNHN</organizationName>
+        <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+        <role>Principal Investigator</role>
+      </personnel>
+      <funding>DIM ASTREA Région Ile-de-France, FRB</funding>
+    </project>
+  </dataset>
+  <annotations>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="biodiversity">http://aims.fao.org/aos/agrovoc/c_33949</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="mammals">http://aims.fao.org/aos/agrovoc/c_4560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="chiroptera">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="bats">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Landscape">http://www.eionet.europa.eu/gemet/concept/4648</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Ecosystem">http://www.eionet.europa.eu/gemet/concept/2519</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Animal ecology">http://www.eionet.europa.eu/gemet/concept/420</valueURI>
+    </annotation>
+  </annotations>
+  <additionalMetadata>
+    <metadata>
+      <emlEditor>
+        <app>EMLassemblyline</app>
+        <release>3.5.5</release>
+      </emlEditor>
+    </metadata>
+  </additionalMetadata>
+</eml:eml>

diff -r 000000000000 -r 330f15f2ad3f test-data/personnel.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/personnel.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,8 @@
+givenName middleInitial surName organizationName electronicMailAddress userId role projectTitle fundingAgency fundingNumber
+Constance Blary CEFE constance.blary@cefe.cnrs.fr https://orcid.org/0000-0001-6204-9983 creator
+Kévin Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 creator
+Christian Kerbiriou CESCO christian.kerbiriou@mnhn.fr https://orcid.org/0000-0001-6080-4762 creator
+Isabelle Le Viol CESCO isabelle.le-viol@mnhn.fr creator
+Constance "" Blary CEFE constance.blary@cefe.cnrs.fr https://orcid.org/0000-0001-6204-9983 contact
+Kévin "" Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 contact
+Kévin "" Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 PI Effect of agricultural landscape features on bats DIM ASTREA Région Ile-de-France, FRB

diff -r 000000000000 -r 330f15f2ad3f test-data/personnel.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/personnel.txt Sat Dec 23 20:40:29 2023 +0000

diff -r 000000000000 -r 330f15f2ad3f test-data/taxa.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxa.tsv Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,5 @@
+taxa site
+Achelia_sp 1
+Achelia_spicata 2
+Achelia_suflata 2
+Ammothea_adunca 3

diff -r 000000000000 -r 330f15f2ad3f test-data/taxonomic_coverage.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomic_coverage.txt Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,5 @@
+name name_type name_resolved authority_system authority_id
+Achelia_sp scientific Achelia GBIF Backbone Taxonomy 2118396
+Achelia_spicata scientific Achelia spicata GBIF Backbone Taxonomy 4338694
+Achelia_suflata scientific Achelia suflata GBIF Backbone Taxonomy NA
+Ammothea_adunca scientific Ammothea adunca GBIF Backbone Taxonomy 5720487

diff -r 000000000000 -r 330f15f2ad3f test-data/test-geocov.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-geocov.tabular Sat Dec 23 20:40:29 2023 +0000

@@ -0,0 +1,5 @@
+site lat long
+1 -65.999946 142.3360535
+2 -66.394359 140.4840125
+3 -66.023545 142.745584
+4 -66.3379125 144.011634

diff -r 000000000000 -r 330f15f2ad3f vector_template.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vector_template.xml Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,61 @@
+<tool id="vector_template" name="Make templates for vector files" version="0.1.0+galaxy0" profile="22.05">
+    <description>attributes for EML metadata creation</description>
+    <requirements>
+        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+    #set $table = ""
+    mkdir data_files &&
+
+    #for $indata in $inputdata
+        ln -s '$indata' 'data_files/${indata.element_identifier}';
+        #set $table += $indata.element_identifier + " ";
+    #end for
+
+    Rscript
+         '$__tool_directory__/vector_templates.R'
+         '$table'
+
+
+    ]]></command>
+    <inputs>
+         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are vector files" help= "Input a data collection."/>
+    </inputs>
+    <outputs>
+       <collection name="templates" type="list" label="Templates for vector data">
+             <discover_datasets pattern="(?P<designation>.+\.txt)" format="txt"/>
+       </collection>
+    </outputs>
+    <tests>
+        <test>
+           <param name="inputdata">
+              <collection type="list">
+                 <element name="data_7.GeoJSON" value="data_7.GeoJSON"/>
+              </collection>
+           </param>
+           <output_collection name='templates' type = "list" count="3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does?**
+--------------------
+
+This tool is used to produce EAL templates for data table used to build EML metadata. It produces the following eal files:
+
+- attibutes_my_vector.txt (describe the attributes of your vector file)
+- catvars_my_vector.txt (only if there are one or more catégorical variable in your vector file)
+- custom_units.txt (made to describe custom units if there are any)
+
+After that, these files can be edited to add information about your vector file and then be used in the make eml tool to produce EML metadata.
+
+**How to use it?**
+--------------------
+To use this tool, you need to select, in your history a data collection with your vector data file(s) (format GeoJSON). To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*. To upload shapefile you need to create a composite data.
+
+.. class:: warningmark
+'''TIP''' This tool dont accept as inputs composite data like shapefile at the moment.
+
+    ]]></help>
+</tool>

diff -r 000000000000 -r 330f15f2ad3f vector_templates.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vector_templates.R Sat Dec 23 20:40:29 2023 +0000

[

@@ -0,0 +1,22 @@
+#15/12/2023 #SEGUINEAU Pauline
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+ data_vector <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+vector = strsplit(data_vector," ")
+
+#Make templates to describe data raster
+
+template_vector_attributes(path = ".",data.path= "data_files", vector.file = vector[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+
+