Mercurial > repos > ecology > makeeml
changeset 4:59349973537f draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
| author | ecology |
|---|---|
| date | Sat, 23 Dec 2023 20:41:10 +0000 |
| parents | 642e31c435c9 |
| children | 34dcb86a9351 |
| files | entities_templates.R geo_cov_temp.R make_eml.R make_eml.xml 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, 517 insertions(+), 72 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/entities_templates.R Sat Dec 23 20:41:10 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 21:49:43 2023 +0000 +++ b/geo_cov_temp.R Sat Dec 23 20:41:10 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 21:49:43 2023 +0000 +++ b/make_eml.R Sat Dec 23 20:41:10 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")
--- a/make_eml.xml Mon Dec 04 21:49:43 2023 +0000 +++ b/make_eml.xml Sat Dec 23 20:41:10 2023 +0000 @@ -1,8 +1,7 @@ -<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0" profile="22.05"> +<tool id="makeeml" name="Make EML" version="0.1.1+galaxy1" profile="22.05"> <description> Create EML from EAL templates</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[ @@ -18,6 +17,18 @@ #set $table += $indata.element_identifier + " "; #end for + #set $raster = "" + #for $data_raster in $dataraster + ln -s '$data_raster' 'data_files/${data_raster.element_identifier}'; + #set $raster += $data_raster.element_identifier + " "; + #end for + + #set $vector = "" + #for $data_vector in $datavector + ln -s '$data_vector' 'data_files/${data_vector.element_identifier}'; + #set $vector += $data_vector.element_identifier + " "; + #end for + #set $other = "" #for $data_other in $dataother ln -s '$data_other' 'data_files/${data_other.element_identifier}'; @@ -29,22 +40,34 @@ #set $quotetable += $q.quote + ","; #end for + Rscript '$__tool_directory__/make_eml.R' 2> err.txt '$title' '$temporal_coverage.start' '$temporal_coverage.end' '$table' + '$raster' + '$vector' '$other' '$destable' + '$desraster' + '$desvector' '$desother' '$quotetable' '$table_url' '$other_url' + '$raster_url' + '$vector_url' ]]></command> <inputs> - <param name="templates" type="data_collection" collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection with only tabular files." /> + <param name="templates" type="data" multiple="True" label="Upload all EAL templates" help="You can upload dataset collection or upload templates one by one (especially if there are multiple format)."/> + <param name="title" type="text" label="Title for your dataset." /> + <section name="temporal_coverage" title="Temporal coverage" expanded="true"> + <param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" optional="false"/> + <param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" optional="false"/> + </section> <section name="data_table" title="Do you have data table ? " > <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are data table" help= "Input a data collection." optional = "true"/> <param name="destable" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/> @@ -57,16 +80,21 @@ </repeat> <param name="table_url" type="text" label="Give the publicly accessible URL from which your data table can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/> </section> + <section name="data_raster" title="Do you have raster data ? " > + <param name="dataraster" type="data_collection" collection_type="list" label="Upload all data files wich are spatial raster" help= "Input a data collection." optional = "true"/> + <param name="desraster" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/> + <param name="raster_url" type="text" label="Give the publicly accessible URL from which your raster data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/> + </section> + <section name="data_vector" title="Do you have vector data ? " > + <param name="datavector" type="data_collection" collection_type="list" label="Upload all data files wich are spatial vector" help= "Input a data collection." optional = "true"/> + <param name="desvector" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/> + <param name="vector_url" type="text" label="Give the publicly accessible URL from which your vector data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/> + </section> <section name="data_other" title="Do you have other data entity ? " > <param name="dataother" type="data_collection" collection_type="list" label="Upload all data files wich are other entity" help= "Input a data collection." optional = "true"/> - <param name="desother" type="text" label="Give a short description of your data file. If there are multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/> + <param name="desother" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/> <param name="other_url" type="text" label="Give the publicly accessible URL from which your other data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/> </section> - <param name="title" type="text" label="Title for your dataset." /> - <section name="temporal_coverage" title="Temporal coverage" > - <param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" /> - <param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" /> - </section> </inputs> <outputs> <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/> @@ -74,28 +102,18 @@ </outputs> <tests> <test expect_num_outputs="2"> - <param name="templates"> - <collection type="list"> - <element name="annotations.txt" value="annotations.txt"/> - <element name="keywords.txt" value="keywords.txt" /> - <element name="attributes_data_blary_al.txt" value="attributes_data_blary_al.txt"/> - <element name="catvars_data_blary_al.txt" value="catvars_data_blary_al.txt"/> - <element name="geographic_coverage.txt" value="geographic_coverage.txt" /> - <element name="personnel.txt" value="personnel.txt" /> - </collection> + <param name="templates" value="annotations.txt,keywords.txt,attributes_data_blary_al.txt,catvars_data_blary_al.txt,geographic_coverage.tabular,personnel.txt" > </param> <output name="metadataout" > - <assert_contents> - <is_valid_xml /> - <xml_element path="./dataset"/> - </assert_contents> + <assert_contents> + <is_valid_xml /> + <xml_element path="./dataset"/> + </assert_contents> </output> </test> </tests> <help><![CDATA[ -.. class:: warningmark -'''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates in tabular format. **What it does?** -------------------- @@ -105,30 +123,17 @@ **How to use it?** -------------------- -To use this tool, you can select, in your history a data collection with EAL templates made by the eml2eal tool. -You can also select your own templates that you have to integrate into a Galaxy collection. +To use this tool, you can select, in your history a data collection with EAL templates or select templates one by one. To do so you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*. -**Recommended optional input:** - -Data files : If you have data files you can input them to give more information in your metadata file. There are two parameters to do to so. The first is "Do you have data table ?" that provide you to import a collection with all your data table. The second is "Do you have other data entity ?" is for all your data file that not data table. - -Description : You can add a short description of each data files you input. If there are multiple data files, please separate your descriptions with a comma (,) in the same order of your data input - -Quote : If you have import data table files, you can specify if there are quotes and what type of quote is it. Repeat this parameter as many times as the number of data tables you've input and in the same order - -Title : You can give a title for your dataset. - -Temporal coverage : You can specify the temporal coverage of your data. - .. class:: infomark Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.) -You then have to select your collection in the upload box of the tool and click **Execute** to get your EML metadata. + ]]></help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raster_templates.R Sat Dec 23 20:41:10 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 20:41:10 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 20:41:10 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 20:41:10 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 20:41:10 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 ] } }, 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"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 20:41:10 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 20:41:10 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") + +