Mercurial > repos > ecology > taxo_cov_template

changeset 2:2af7401f13e0 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
author ecology
date Sat, 23 Dec 2023 20:41:42 +0000
parents 0cfc9b6da2ac
children a45fa46f8010
files entities_templates.R geo_cov_temp.R make_eml.R raster_templates.R taxo_cov_template.xml test-data/Present_Surface_pH.tif test-data/attributes_data_7.txt test-data/catvars_data_7.txt test-data/custom_units.txt test-data/data_7.GeoJSON test-data/entities.txt vector_templates.R
diffstat 12 files changed, 475 insertions(+), 36 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/entities_templates.R	Sat Dec 23 20:41:42 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)
+
+
--- a/geo_cov_temp.R	Mon Dec 04 21:48:41 2023 +0000
+++ b/geo_cov_temp.R	Sat Dec 23 20:41:42 2023 +0000
@@ -30,6 +30,7 @@
 }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)
--- a/make_eml.R	Mon Dec 04 21:48:41 2023 +0000
+++ b/make_eml.R	Sat Dec 23 20:41:42 2023 +0000
@@ -1,5 +1,5 @@
 ##07/06/2023 ##Genthon Tanguy
-##update 15/11/2023 ##Seguineau Pauline
+##update 15/11/2023 ## Seguineau Pauline
 
 ###make_eml
 
@@ -9,17 +9,27 @@
   start <- args[2]
   end <-args[3]
   data_table <- args[4]
-  data_other <- args[5]
-  destable <- args[6]
-  desother <- args[7]
-  quote <- args[8]
-  table_url <- args[9]
-  other_url <- args[10]
+  data_raster <- args[5]
+  data_vector <- args[6]
+  data_other <- args[7]
+  destable <- args[8]
+  desraster<- args[9]
+  desvector<- args[10]
+  desother <- args[11]
+  quote <- args[12]
+  table_url <- args[13]
+  other_url <- args[14]
+  raster_url <- args[15]
+  vector_url <- args[16]
 }
- 
+
+#Load package
+
+library(EMLassemblyline)
+sessionInfo()
+
 
 ###Format data###
-
 if (data_table == ""){
     table=NULL
 }else{
@@ -48,6 +58,22 @@
 }
 
   
+if (data_raster == ""){
+    raster=NULL
+}else{
+    raster =  strsplit(data_raster," ")
+    for (file in raster){
+         name_raster = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+    
+if (data_vector == ""){
+    vector=NULL
+}else{
+    vector =  strsplit(data_vector," ")
+    for (file in vector){
+         name_vector = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+
 if (data_other == ""){
     other=NULL
 }else{
@@ -63,6 +89,19 @@
        des_table =  strsplit(destable,",")}
 }
 
+if (data_raster !=""){
+   if (desraster == ""){
+       des_raster = name_raster
+   }else{
+       des_raster =  strsplit(desraster,",")}
+}
+
+if (data_vector !=""){ 
+   if (desvector == ""){
+       des_vector = name_vector
+   }else{
+       des_vector =  strsplit(desvector,",")}
+}
 
 if (data_other !=""){
    if (desother == ""){
@@ -71,7 +110,6 @@
        des_other =  strsplit(desother,",")}
 }
 
-
 if (data_table !=""){
    if (table_url == ""){
        urltable = ""
@@ -90,9 +128,79 @@
    }
 }
 
+if (data_raster !=""){
+   if (raster_url == ""){
+       urlraster = ""
+   }else{
+       raster_url = gsub("\\-" ,"", raster_url)
+       urlraster =  strsplit(raster_url,",")
+   }
+}
+
+if (data_vector !=""){
+   if (vector_url == ""){
+       urlvector = ""
+   }else{
+       vector_url = gsub("\\-" ,"", vector_url)
+       urlvector =  strsplit(vector_url,",")
+   }
+}
+
+
+
 ###Make EML###
    
-if (!is.null(table) && !is.null(other)){
+if (!is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end))
+   
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]]
+                      )
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
    
    EMLassemblyline::make_eml(
                       path="output_template",
@@ -105,22 +213,203 @@
                       data.table.description = des_table[[1]],
                       data.table.quote.character = tablequote,
                       data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (!is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                 
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
                       other.entity=other[[1]],
                       other.entity.name = name_other,
                       other.entity.description = des_other[[1]],
-                      other.entity.url= urlother[[1]]
-                      )
-                      
-}else if (is.null(table) && is.null(other)){
-  
+                      other.entity.url= urlother[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
+
    EMLassemblyline::make_eml(
                       path="output_template",
                       data.path="data_files",
                       eml.path=".", 
                       dataset.title = title,
-                      temporal.coverage = c(start,end))
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
    
-}else if (!is.null(table) && is.null(other)){
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
 
    EMLassemblyline::make_eml(
                       path="output_template",
@@ -132,26 +421,18 @@
                       data.table.name = name_table,
                       data.table.description = des_table[[1]],
                       data.table.quote.character = tablequote,
-                      data.table.url = urltable[[1]])
-                      
-
-}else if (is.null(table) && !is.null(other)){
-
-   EMLassemblyline::make_eml(
-                      path="output_template",
-                      data.path="data_files",
-                      eml.path=".", 
-                      dataset.title = title,
-                      temporal.coverage = c(start,end),
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
                       other.entity=other[[1]],
                       other.entity.name = name_other,
                       other.entity.description = des_other[[1]],
                       other.entity.url= urlother[[1]])}
-                      
 
-
+issues()
 old.names <- list.files(path=".", pattern=".xml")
-print(old.names)
 file.rename(from=old.names, to="eml.xml")
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raster_templates.R	Sat Dec 23 20:41:42 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")
+
+
--- a/taxo_cov_template.xml	Mon Dec 04 21:48:41 2023 +0000
+++ b/taxo_cov_template.xml	Sat Dec 23 20:41:42 2023 +0000
@@ -1,8 +1,7 @@
-<tool id="taxo_cov_template" name="Make taxonomic coverage template" version="0.1.0+galaxy0" profile="22.05">
+<tool id="taxo_cov_template" name="Make taxonomic coverage template" version="0.1.1+galaxy0" profile="22.05">
     <description>for EML metadata creation</description>
     <requirements>
-        <requirement type="package" version="4.3.1">r-base</requirement>
-        <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
+        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     
@@ -70,7 +69,7 @@
 --------------------
 
 This tool produce template for EML metadata. It produce templates for taxonomic coverage. 
-This tool can be used with the "Make templates for core features of a data package" tool before the "make eml" tool.
+After that, these files can be edited to add information about your data and then be used in the make eml tool to produce EML metadata.
 
 **How to use it?**
 --------------------
Binary file test-data/Present_Surface_pH.tif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_7.txt	Sat Dec 23 20:41:42 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	""	""	""	""
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_7.txt	Sat Dec 23 20:41:42 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_
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_units.txt	Sat Dec 23 20:41:42 2023 +0000
@@ -0,0 +1,1 @@
+id	unitType	parentSI	multiplierToSI	description
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_7.GeoJSON	Sat Dec 23 20:41:42 2023 +0000
@@ -0,0 +1,72 @@
+{
+"type": "FeatureCollection",
+"name": "shapefile",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+"features": [
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Haie de la Conch‚e", "X": -2.045717, "Y": 48.687067, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.045717, 48.687067 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Squ‚ouel", "X": -3.474583, "Y": 48.837417, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.474583, 48.837417 ] } },
+{ "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 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Roc'h Parou", "X": -3.620167, "Y": 48.715667, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.620167, 48.715667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Triagoz", "X": -3.6466, "Y": 48.871267, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -3.6466, 48.871267 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La BarriŠre", "X": -3.51345, "Y": 48.888767, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.51345, 48.888767 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Corbeau", "X": -3.888267, "Y": 48.6769, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.888267, 48.6769 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Penven", "X": -4.005867, "Y": 48.759633, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.005867, 48.759633 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Œles de la croix", "X": -4.603867, "Y": 48.615483, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.603867, 48.615483 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Liniou", "X": -4.8077, "Y": 48.490233, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.8077, 48.490233 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Morvan", "X": -4.585767, "Y": 48.638567, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -4.585767, 48.638567 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Fort de la Fraternit‚", "X": -4.577333, "Y": 48.3096, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.577333, 48.3096 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Gorle Vihan", "X": -5.043467, "Y": 48.47205, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -5.043467, 48.47205 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ile Ronde", "X": -4.4634, "Y": 48.32465, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.4634, 48.32465 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ar Forc'h Vihan", "X": -5.141717, "Y": 48.445367, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -5.141717, 48.445367 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ile de l'Aber", "X": -4.437717, "Y": 48.221833, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.437717, 48.221833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Van", "X": -4.717133, "Y": 48.066083, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.717133, 48.066083 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Bluiniers", "X": -4.063533, "Y": 47.722467, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.063533, 47.722467 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Linuen", "X": -3.96295, "Y": 47.844217, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.96295, 47.844217 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "les Poulains", "X": -4.056917, "Y": 47.793583, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.056917, 47.793583 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pen a Men", "X": -3.951233, "Y": 47.721667, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.951233, 47.721667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Trou d'Enfer", "X": -3.465867, "Y": 47.621317, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.465867, 47.621317 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Bastresse Sud", "X": -3.36735, "Y": 47.681817, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.36735, 47.681817 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Magou‰r Nord", "X": -3.210717, "Y": 47.661117, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.210717, 47.661117 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Tourelle de Gr‚gam", "X": -2.9167, "Y": 47.56565, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.9167, 47.56565 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Grand Guet", "X": -3.249933, "Y": 47.316767, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.249933, 47.316767 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Er Pondeux", "X": -3.074467, "Y": 47.452117, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.074467, 47.452117 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Wissant", "X": 1.676667, "Y": 50.912333, "PROGRAMME": "DCE", "OPERATEUR_": "Station de Wimer", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ 1.676667, 50.912333 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Audresselles", "X": 1.5845, "Y": 50.832833, "PROGRAMME": "DCE", "OPERATEUR_": "Station de Wimer", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ 1.5845, 50.832833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Saint Aubin", "X": -0.42885, "Y": 49.352833, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -0.42885, 49.352833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Tatihou", "X": -1.231933, "Y": 49.585867, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.231933, 49.585867 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Cap Levi", "X": -1.467817, "Y": 49.690883, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.467817, 49.690883 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Cap de Flamanville", "X": -1.894817, "Y": 49.529033, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.894817, 49.529033 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Ecrehou", "X": -1.937067, "Y": 49.2723, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.937067, 49.2723 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Chausey", "X": -1.85205, "Y": 48.865067, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.85205, 48.865067 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Guetary Sud", "X": -1.618, "Y": 43.428583, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.618, 43.428583 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Jumeaux", "X": -1.756583, "Y": 43.385567, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.756583, 43.385567 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } },
+{ "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 ] } }
+]
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/entities.txt	Sat Dec 23 20:41:42 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vector_templates.R	Sat Dec 23 20:41:42 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")
+
+