Mercurial > repos > ecology > eal_templates
changeset 1:3b0fa963ae3e draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
| author | ecology |
|---|---|
| date | Sat, 23 Dec 2023 20:41:26 +0000 |
| parents | d4f168043757 |
| children | debfa8a223c0 |
| files | eal_templates.xml entities_templates.R geo_cov_temp.R make_eml.R raster_templates.R 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, 487 insertions(+), 39 deletions(-) [+] |
line wrap: on
line diff
--- a/eal_templates.xml Mon Dec 04 21:48:55 2023 +0000 +++ b/eal_templates.xml Sat Dec 23 20:41:26 2023 +0000 @@ -1,8 +1,7 @@ -<tool id="eal_templates" name="Make templates" version="0.1.0+galaxy0" profile="22.05"> +<tool id="eal_templates" name="Make templates" version="0.1.1+galaxy0" profile="22.05"> <description>for core features of a data package 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[ @@ -25,8 +24,10 @@ </inputs> <outputs> - <collection name="output" type="list" label="Templates"> - <discover_datasets pattern="__name_and_ext__"/> + <collection name="output" type="list" label="Core features templates"> + <discover_datasets pattern="(?P<designation>.+\.txt)" format="txt"/> + <discover_datasets pattern="(?P<designation>.+\.docx)" format="docx"/> + <discover_datasets pattern="(?P<designation>.+\.md)" format="markdown"/> </collection> </outputs> <tests> @@ -40,9 +41,16 @@ **What it does?** -------------------- +This tool produce templates for core features of a data package used to build EML metadata. It produces the following eal files: -This tool produce templates for core features of a data package for EML metadata. -This tool can be used before of the make eml tool. +- abstract.txt +- keywords.txt +- methods.txt +- personnel.txt +- intellectual_rights.txt +- additional_info.txt + +After that, these files can be edited to add informations about your data and then be used in the make EML tool to produce EML metadata. **How to use it?** --------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/entities_templates.R Sat Dec 23 20:41:26 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 21:48:55 2023 +0000 +++ b/geo_cov_temp.R Sat Dec 23 20:41:26 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 21:48:55 2023 +0000 +++ b/make_eml.R Sat Dec 23 20:41:26 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 20:41:26 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") + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/attributes_data_7.txt Sat Dec 23 20:41:26 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 20:41:26 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 20:41:26 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 20:41:26 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 Conche", "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": "Squouel", "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 Barrire", "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 les 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": "Magour 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 Grgam", "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 20:41:26 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 20:41:26 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") + +