| Previous changeset 0:d4f168043757 (2023-12-04) Next changeset 2:debfa8a223c0 (2024-01-22) |
|
Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32 |
|
modified:
eal_templates.xml geo_cov_temp.R make_eml.R |
|
added:
entities_templates.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 |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e eal_templates.xml --- 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?** -------------------- |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e entities_templates.R --- /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) + + |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e geo_cov_temp.R --- 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 |
| b |
| @@ -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) |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e make_eml.R --- a/make_eml.R Mon Dec 04 21:48:55 2023 +0000 +++ b/make_eml.R Sat Dec 23 20:41:26 2023 +0000 |
| [ |
| b'@@ -1,5 +1,5 @@\n ##07/06/2023 ##Genthon Tanguy\r\n-##update 15/11/2023 ##Seguineau Pauline\r\n+##update 15/11/2023 ## Seguineau Pauline\r\n \r\n ###make_eml\r\n \r\n@@ -9,17 +9,27 @@\n start <- args[2]\r\n end <-args[3]\r\n data_table <- args[4]\r\n- data_other <- args[5]\r\n- destable <- args[6]\r\n- desother <- args[7]\r\n- quote <- args[8]\r\n- table_url <- args[9]\r\n- other_url <- args[10]\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+\r\n+#Load package\r\n+\r\n+library(EMLassemblyline)\r\n+sessionInfo()\r\n+\r\n \r\n ###Format data###\r\n-\r\n if (data_table == ""){\r\n table=NULL\r\n }else{\r\n@@ -48,6 +58,22 @@\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@@ -63,6 +89,19 @@\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@@ -71,7 +110,6 @@\n des_other = strsplit(desother,",")}\r\n }\r\n \r\n-\r\n if (data_table !=""){\r\n if (table_url == ""){\r\n urltable = ""\r\n@@ -90,9 +128,79 @@\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(other)){\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_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+ 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+ '..b'quote,\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- \r\n-}else if (is.null(table) && is.null(other)){\r\n- \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+ 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-}else if (!is.null(table) && is.null(other)){\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@@ -132,26 +421,18 @@\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- \r\n-\r\n-}else if (is.null(table) && !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.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 \r\n-\r\n+issues()\r\n old.names <- list.files(path=".", pattern=".xml")\r\n-print(old.names)\r\n file.rename(from=old.names, to="eml.xml")\r\n \r\n \r\n' |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e raster_templates.R --- /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") + + |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e test-data/Present_Surface_pH.tif |
| b |
| Binary file test-data/Present_Surface_pH.tif has changed |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e 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 20:41:26 2023 +0000 |
| b |
| @@ -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 "" "" "" "" |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e 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 20:41:26 2023 +0000 |
| b |
| @@ -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_ |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e test-data/custom_units.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_units.txt Sat Dec 23 20:41:26 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +id unitType parentSI multiplierToSI description |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e test-data/data_7.GeoJSON --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_7.GeoJSON Sat Dec 23 20:41:26 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' |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e test-data/entities.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/entities.txt Sat Dec 23 20:41:26 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +objectName variable value +data_7.GeoJSON geometry Point +data_7.GeoJSON geometricObjectCount 65 +data_7.GeoJSON spatialReference GCS_WGS_1984 |
| b |
| diff -r d4f168043757 -r 3b0fa963ae3e vector_templates.R --- /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") + + |