Mercurial > repos > ecology > geo_cov_template
changeset 2:0fe3b8bd9d8b draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
| author | ecology |
|---|---|
| date | Sat, 23 Dec 2023 20:39:46 +0000 |
| parents | 4f5816b57c13 |
| children | a5f887cfcf94 |
| files | entities_templates.R geo_cov_temp.R geo_cov_template.xml 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, 476 insertions(+), 36 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/entities_templates.R Sat Dec 23 20:39:46 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 21:48:29 2023 +0000 +++ b/geo_cov_temp.R Sat Dec 23 20:39:46 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/geo_cov_template.xml Mon Dec 04 21:48:29 2023 +0000 +++ b/geo_cov_template.xml Sat Dec 23 20:39:46 2023 +0000 @@ -1,6 +1,6 @@ <tool id="geo_cov_template" name="Make geographic coverage template" version="0.1.0+galaxy0" profile="22.05"> <description>for EML metadata creation</description> - <requirements> + <requirements> <requirement type="package" version="4.3.1">r-base</requirement> <requirement type="package" version="3.5.5">r-emlassemblyline</requirement> </requirements> @@ -28,7 +28,7 @@ <param name="empty" type="boolean" label="Write an empty template file ?" /> </inputs> <outputs> - <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic coverage template"/> + <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic_coverage.txt"/> </outputs> <tests> <test> @@ -45,8 +45,8 @@ **What it does?** -------------------- -This tool produce template for EML metadata. It produce templates for geographic coverage. -This tool can be used with the "Make templates for core features of a data package" tool before the "make eml" tool. +This tool produce template for EML metadata. It produce template for geographic coverage. +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?** --------------------
--- a/make_eml.R Mon Dec 04 21:48:29 2023 +0000 +++ b/make_eml.R Sat Dec 23 20:39:46 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 20:39:46 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 20:39:46 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 20:39:46 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 20:39:46 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 20:39:46 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", 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"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 20:39:46 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 20:39:46 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") + +