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Changeset 0:9cbac7a9b1a3 (2023-09-13)

Next changeset 1:9d56f6480194 (2023-11-17)

Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d139641e5afb8c75b8aded37bdbd7aecae0fb83

added:
eml2eal.R
make_eml.R
make_eml.xml
test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml
test-data/annotations.tabular
test-data/annotations.txt
test-data/attributes_data_blary_al.tabular
test-data/attributes_data_blary_al.txt
test-data/catvars_data_blary_al.tabular
test-data/catvars_data_blary_al.txt
test-data/geographic_coverage.tabular
test-data/geographic_coverage.txt
test-data/keywords.tabular
test-data/keywords.txt
test-data/metadataoutput.xml
test-data/personnel.tabular
test-data/personnel.txt

diff -r 000000000000 -r 9cbac7a9b1a3 eml2eal.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eml2eal.R Wed Sep 13 19:56:16 2023 +0000

[

@@ -0,0 +1,15 @@
+##07/06/2023
+##Genthon Tanguy
+###eml2eal
+
+#load arguments
+args = commandArgs(trailingOnly=TRUE)
+if (length(args)==0)
+{
+ stop("This tool needs at least one argument")
+}else{
+ data <- args[1]
+}
+
+
+EMLassemblyline::eml2eal(data,path=".")

diff -r 000000000000 -r 9cbac7a9b1a3 make_eml.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_eml.R Wed Sep 13 19:56:16 2023 +0000

[

@@ -0,0 +1,13 @@
+##07/06/2023
+##Genthon Tanguy
+###make_eml
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+ title <- args[1]
+}
+
+EMLassemblyline::make_eml("output_template",eml.path=".", dataset.title = title)
+old.names <- list.files(path=".", pattern=".xml")
+print(old.names)
+file.rename(from=old.names, to="eml.xml")

diff -r 000000000000 -r 9cbac7a9b1a3 make_eml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_eml.xml Wed Sep 13 19:56:16 2023 +0000

[

@@ -0,0 +1,71 @@
+<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0">
+    <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>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir output_template &&
+    #for $input in $templates
+        ln -s '$input' 'output_template/${input.element_identifier}.txt';
+    #end for
+    Rscript
+ '$__tool_directory__/make_eml.R' 2> err.txt
+ 'title'
+    ]]></command>
+    <inputs>
+        <param name="templates" type="data_collection"  collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection." />
+ <param name="title" type="text" label="Title for your dataset." />
+    </inputs>
+    <outputs>
+ <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
+ <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="templates">
+                <collection type="list">
+ <element name="annotations" value="annotations.txt"/>
+                        <element name="keywords" value="keywords.txt" />
+                        <element name="attributes_data_blary_al" value="attributes_data_blary_al.txt"/>
+                        <element name="catvars_data_blary_al" value="catvars_data_blary_al.txt"/>
+                        <element name="geographic_coverage" value="geographic_coverage.txt" />
+                        <element name="personnel" value="personnel.txt" />
+                </collection>
+            </param>
+            <output name="metadataout" >
+ <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.
+
+**What it does?**
+--------------------
+
+This tool produce EML metadata from EAL templates.
+This tool can be used in the continuation of the eml2eal tool.
+
+**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 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*.
+
+ .. 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>

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Assessing_the_importance_of_field_margins_for_bat_species.xml Wed Sep 13 19:56:16 2023 +0000

b'@@ -0,0 +1,2074 @@\n+<?xml version="1.0" encoding="UTF-8"?><eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" packageId="doi:10.48502/hssh-5194" system="unknown" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://nis.lternet.edu/schemas/EML/eml-2.2.0/xsd/eml.xsd">\n+ <dataset id="dataset-02">\n+ <title>Assessing the importance of field margins for bat species and communities in intensive agricultural landscapes - Data</title>\n+ <creator>c\n+ <individualName>\n+ <givenName>Constance</givenName>\n+ <givenName/>\n+ <surName>Blary</surName>\n+ </individualName>\n+ <organizationName>CEFE</organizationName>\n+ <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-6204-9983</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>K\xc3\xa9vin</givenName>\n+ <givenName/>\n+ <surName>Barr\xc3\xa9</surName>\n+ </individualName>\n+ <organizationName>CESCO MNHN</organizationName>\n+ <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-5368-4053</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>Christian</givenName>\n+ <givenName/>\n+ <surName>Kerbiriou</surName>\n+ </individualName>\n+ <organizationName>CESCO</organizationName>\n+ <electronicMailAddress>christian.kerbiriou@mnhn.fr</electronicMailAddress>\n+ <userId directory="https://orcid.org">https://orcid.org/0000-0001-6080-4762</userId>\n+ </creator>\n+ <creator>\n+ <individualName>\n+ <givenName>Isabelle</givenName>\n+ <givenName/>\n+ <surName>Le Viol</surName>\n+ </individualName>\n+ <organizationName>CESCO</organizationName>\n+ <electronicMailAddress>isabelle.le-viol@mnhn.fr</electronicMailAddress>\n+ </creator>\n+ <pubDate>2021-05-25</pubDate>\n+ <abstract>\n+ <para>Landscape simplification and degradation through agricultural intensification is widely recognized as a main driver of biodiversity loss. In intensively used agricultural landscapes, patches of semi-natural habitats and particularly connections between them are of high importance for many taxa. Vegetated connections like hedgerows are especially important for foraging and commuting of mobile taxa such as bats. However, the interest of another treeless linear habitat \xe2\x80\x93 herbaceous field margins \xe2\x80\x93 remains unstudied for insectivorous bats. Field margins are nevertheless known as an important habitat for other taxa, including bat prey. Here we assessed the importance of field margins for bats compared to other landscape variables. We measured bat activity based on a repeated passive acoustic monitoring during 17 complete nights in summer on 112 study sites in an intensively used agricultural landscape. Each night, we sampled bat species activity and community metrics (i.e. species richness and community habitat specialization index) at different distances to field margins, and along a gradient of relative density of field margins. To compare field margin effects with other landscape variables, the sampled sites were selected by keeping a large variability in these other variables (land-cover Shannon diversity index, forests, hedgerows, water bodies, main roads, urban areas, grasslands, number of crops and rapeseed percentage). Only Myotis sp. were affected by herbaceous field margins. Specifically, the Myotis group activity decreased with the distance to herbaceous field margins (i.e. towards field crop cores), and positively correlated with relative density of herbaceous field margins, for which the effect size was comparable to other landscape variables. However, other landscape variables such as the proportion of and t'..b' </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Myo_ER05</attributeName>\n+ <attributeDefinition>Number of bat passes of Myo specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">42</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Myo_ER01</attributeName>\n+ <attributeDefinition>Number of bat passes of Myo specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">33</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Ple_ER05</attributeName>\n+ <attributeDefinition>Number of bat passes of Ple specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">8</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ <attribute>\n+ <attributeName>Ple_ER01</attributeName>\n+ <attributeDefinition>Number of bat passes of Ple specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold</attributeDefinition>\n+ <storageType>float</storageType>\n+ <measurementScale>\n+ <ratio>\n+ <unit>\n+ <standardUnit>number</standardUnit>\n+ </unit>\n+ <numericDomain>\n+ <numberType>whole</numberType>\n+ <bounds>\n+ <minimum exclusive="false">0</minimum>\n+ <maximum exclusive="false">5</maximum>\n+ </bounds>\n+ </numericDomain>\n+ </ratio>\n+ </measurementScale>\n+ <missingValueCode>\n+ <code>"NA"</code>\n+ <codeExplanation>"No information"</codeExplanation>\n+ </missingValueCode>\n+ </attribute>\n+ </attributeList>\n+ <numberOfRecords>112</numberOfRecords>\n+ </dataTable>\n+ </dataset>\n+</eml:eml>\n'

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/annotations.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.tabular Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,10 @@
+id element context subject predicate_label predicate_uri object_label object_uri
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 biodiversity http://aims.fao.org/aos/agrovoc/c_33949
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 mammals http://aims.fao.org/aos/agrovoc/c_4560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 chiroptera http://aims.fao.org/aos/agrovoc/c_1560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 bats http://aims.fao.org/aos/agrovoc/c_1560
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Landscape http://www.eionet.europa.eu/gemet/concept/4648
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Ecosystem http://www.eionet.europa.eu/gemet/concept/2519
+/dataset /dataset eml dataset is about http://purl.obolibrary.org/obo/IAO_0000136 Animal ecology http://www.eionet.europa.eu/gemet/concept/420
+/data_blary_al.txt/X /dataTable/attribute data_blary_al.txt X is a http://www.w3.org/1999/02/22-rdf-syntax-ns#type decimalLongitude http://rs.tdwg.org/dwc/terms/decimalLongitude
+/data_blary_al.txt/Y /dataTable/attribute data_blary_al.txt Y is a http://www.w3.org/1999/02/22-rdf-syntax-ns#type decimalLatitude http://rs.tdwg.org/dwc/terms/decimalLatitude

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/annotations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.txt Wed Sep 13 19:56:16 2023 +0000

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/attributes_data_blary_al.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_blary_al.tabular Wed Sep 13 19:56:16 2023 +0000

b'@@ -0,0 +1,81 @@\n+attributeName\tattributeDefinition\tclass\tunit\tdateTimeFormatString\tmissingValueCode\tmissingValueCodeExplanation\n+Id\tSampling site ID\tcharacter\t\t\t"NA"\t"No information"\n+dist_field_margin\tDistance to the nearest field margin element (in meters)\tnumeric\tmeter\t\tNA\tNo information\n+dist_hedgerow\tDistance to the nearest hedgerow element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_forest\tDistance to the nearest forest element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_road\tDistance to the nearest road element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_water\tDistance to the nearest water body element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+dist_urban\tDistance to the nearest urban element (in meters)\tnumeric\tmeter\t\t"NA"\t"No information"\n+density_field_margins_250m\tRelative density of field margins in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_500m\tRelative density of filed margins in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_750m\tRelative density of filed margins in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_1000m\tRelative density of filed margins in a 1000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_1500m\tRelative density of filed margins in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_2000m\tRelative density of filed margins in a 2000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_field_margins_4000m\tRelative density of filed margins in a 4000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_250m\tRelative density of roads in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_500m\tRelative density of roads in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_750m\tRelative density of roads in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_1000m\tDescription for density_roads_1000m\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_1500m\tRelative density of roads in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_2000m\tRelative density of roads in a 2000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_roads_4000m\tRelative density of roads in a 4000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_250m\tRelative density of hedgerows in a 250 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_500m\tRelative density of hedgerows in a 500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_750m\tRelative density of hedgerows in a 750 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_1000m\tRelative density of hedgerows in a 1000 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+density_hedgerows_1500m\tRelative density of hedgerows in a 1500 meters buffer around the sampling site (in meters per hectare)\tnumeric\tdimensionless\t\t"NA"\t"No informa'..b'eric\tpercent\t\t"NA"\t"No information"\n+forest_4000m\tPercentage of land covered by forest in different 4000 m buffer sizes\tnumeric\tpercent\t\t"NA"\t"No information"\n+urban_4000m\tPercentage of land covered by urban area in different 4000 m buffer sizes\tnumeric\tpercent\t\t"NA"\t"No information"\n+perc_rapeseed\tPercentage of rapeseed crops in a 100 m radius around each site at the sampling date\tnumeric\tpercent\t\t"NA"\t"No information"\n+nb_crops\tNumber of different crops in a 100 m radius around each site at the sampling date\tnumeric\tnumber\t\t"NA"\t"No information"\n+date\tDescription for date\tDate\t\tYYYY-MM-DD\t"NA"\t"No information"\n+X\tSampling site longitude\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+Y\tSampling site latitude\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+recorder\tRecorder ID used for data collection on the sampling site\tcategorical\t\t\t"NA"\t"No information"\n+min_t\tMinimum temperature recorded on the sampling area during the sampling night (in celsius)\tnumeric\tcelsius\t\t"NA"\t"No information"\n+max_wind\tMaximum wind speed recorded on the sampling area during the sampling night (in km/h)\tnumeric\tkilometerPerHour\t\t"NA"\t"No information"\n+CSI_ER05\tCommunity specialization index calculated from species level activity on the 0.5 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+CSI_ER01\tCommunity specialization index calculated from species level activity on the 0.1 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+richness_ER05\tSpecies richness calculated from species level activity on the 0.5 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+richness_ER01\tSpecies richness calculated from species level activity on the 0.1 maximum error rate tolerance threshold\tnumeric\tdimensionless\t\t"NA"\t"No information"\n+Nyclei_ER05\tNumber of bat passes of Nyclei specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nyclei_ER01\tNumber of bat passes of Nyclei specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Pippip_ER05\tNumber of bat passes of Pippip specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Pippip_ER01\tNumber of bat passes of Pippip specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Eptser_ER05\tNumber of bat passes of Epster specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Eptser_ER01\tNumber of bat passes of Epster specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nycnoc_ER05\tNumber of bat passes of Nycnoc specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Nycnoc_ER01\tNumber of bat passes of Nycnoc specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Myo_ER05\tNumber of bat passes of Myo specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Myo_ER01\tNumber of bat passes of Myo specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Ple_ER05\tNumber of bat passes of Ple specie or group recorded during the sampling night on the 0.5 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n+Ple_ER01\tNumber of bat passes of Ple specie or group recorded during the sampling night on the 0.1 maximum error rate tolerance threshold\tnumeric\tnumber\t\t"NA"\t"No information"\n'

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/attributes_data_blary_al.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_blary_al.txt Wed Sep 13 19:56:16 2023 +0000

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/catvars_data_blary_al.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_blary_al.tabular Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,16 @@
+attributeName code definition
+recorder 10250 Value: 10250 for attribute: recorder
+recorder 11693 Value: 11693 for attribute: recorder
+recorder 13289 Value: 13289 for attribute: recorder
+recorder 13676 Value: 13676 for attribute: recorder
+recorder 13733 Value: 13733 for attribute: recorder
+recorder 13740 Value: 13740 for attribute: recorder
+recorder 17232 Value: 17232 for attribute: recorder
+recorder 17329 Value: 17329 for attribute: recorder
+recorder 17573 Value: 17573 for attribute: recorder
+recorder 17578 Value: 17578 for attribute: recorder
+recorder 17598 Value: 17598 for attribute: recorder
+recorder 17601 Value: 17601 for attribute: recorder
+recorder 17607 Value: 17607 for attribute: recorder
+recorder 17608 Value: 17608 for attribute: recorder
+recorder 3760 Value: 3760 for attribute: recorder

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/catvars_data_blary_al.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_blary_al.txt Wed Sep 13 19:56:16 2023 +0000

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/geographic_coverage.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geographic_coverage.tabular Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,2 @@
+geographicDescription northBoundingCoordinate southBoundingCoordinate eastBoundingCoordinate westBoundingCoordinate
+Yvelines - Essonne - Seine et Marne 49.08428 48.12266 3.56409 1.60296

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/geographic_coverage.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geographic_coverage.txt Wed Sep 13 19:56:16 2023 +0000

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/keywords.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/keywords.tabular Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,7 @@
+keyword keywordThesaurus
+Acoustic monitoring Keywords
+Bat community Keywords
+Farmland biodiversity Keywords
+Field borders Keywords
+Habitat specialisation Keywords
+Landscape composition Keywords

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/keywords.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/keywords.txt Wed Sep 13 19:56:16 2023 +0000

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/metadataoutput.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadataoutput.xml Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,153 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="0a0472ad-2e8f-412f-8e95-ba84b7cc9996" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd" system="unknown">
+  <dataset id="dataset">
+    <creator>
+      <individualName>
+        <givenName>Constance</givenName>
+        <surName>Blary</surName>
+      </individualName>
+      <organizationName>CEFE</organizationName>
+      <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Kévin</givenName>
+        <surName>Barré</surName>
+      </individualName>
+      <organizationName>CESCO MNHN</organizationName>
+      <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Christian</givenName>
+        <surName>Kerbiriou</surName>
+      </individualName>
+      <organizationName>CESCO</organizationName>
+      <electronicMailAddress>christian.kerbiriou@mnhn.fr</electronicMailAddress>
+    </creator>
+    <creator>
+      <individualName>
+        <givenName>Isabelle</givenName>
+        <surName>Le Viol</surName>
+      </individualName>
+      <organizationName>CESCO</organizationName>
+      <electronicMailAddress>isabelle.le-viol@mnhn.fr</electronicMailAddress>
+    </creator>
+    <pubDate>2023-07-23</pubDate>
+    <keywordSet>
+      <keyword>Acoustic monitoring</keyword>
+      <keyword>Bat community</keyword>
+      <keyword>Farmland biodiversity</keyword>
+      <keyword>Field borders</keyword>
+      <keyword>Habitat specialisation</keyword>
+      <keyword>Landscape composition</keyword>
+      <keywordThesaurus>Keywords</keywordThesaurus>
+    </keywordSet>
+    <coverage>
+      <geographicCoverage>
+        <geographicDescription>Yvelines - Essonne - Seine et Marne</geographicDescription>
+        <boundingCoordinates>
+          <westBoundingCoordinate>1.60296</westBoundingCoordinate>
+          <eastBoundingCoordinate>3.56409</eastBoundingCoordinate>
+          <northBoundingCoordinate>49.08428</northBoundingCoordinate>
+          <southBoundingCoordinate>48.12266</southBoundingCoordinate>
+        </boundingCoordinates>
+      </geographicCoverage>
+    </coverage>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="biodiversity">http://aims.fao.org/aos/agrovoc/c_33949</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="mammals">http://aims.fao.org/aos/agrovoc/c_4560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="chiroptera">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="bats">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Landscape">http://www.eionet.europa.eu/gemet/concept/4648</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Ecosystem">http://www.eionet.europa.eu/gemet/concept/2519</valueURI>
+    </annotation>
+    <annotation>
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Animal ecology">http://www.eionet.europa.eu/gemet/concept/420</valueURI>
+    </annotation>
+    <contact>
+      <individualName>
+        <givenName>Constance</givenName>
+        <surName>Blary</surName>
+      </individualName>
+      <organizationName>CEFE</organizationName>
+      <electronicMailAddress>constance.blary@cefe.cnrs.fr</electronicMailAddress>
+    </contact>
+    <contact>
+      <individualName>
+        <givenName>Kévin</givenName>
+        <surName>Barré</surName>
+      </individualName>
+      <organizationName>CESCO MNHN</organizationName>
+      <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+    </contact>
+    <project>
+      <title>Effect of agricultural landscape features on bats</title>
+      <personnel>
+        <individualName>
+          <givenName>Kévin</givenName>
+          <surName>Barré</surName>
+        </individualName>
+        <organizationName>CESCO MNHN</organizationName>
+        <electronicMailAddress>kevin.barre@mnhn.fr</electronicMailAddress>
+        <role>Principal Investigator</role>
+      </personnel>
+      <funding>DIM ASTREA Région Ile-de-France, FRB</funding>
+    </project>
+  </dataset>
+  <annotations>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="biodiversity">http://aims.fao.org/aos/agrovoc/c_33949</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="mammals">http://aims.fao.org/aos/agrovoc/c_4560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="chiroptera">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="bats">http://aims.fao.org/aos/agrovoc/c_1560</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Landscape">http://www.eionet.europa.eu/gemet/concept/4648</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Ecosystem">http://www.eionet.europa.eu/gemet/concept/2519</valueURI>
+    </annotation>
+    <annotation references="dataset">
+      <propertyURI label="is about">http://purl.obolibrary.org/obo/IAO_0000136</propertyURI>
+      <valueURI label="Animal ecology">http://www.eionet.europa.eu/gemet/concept/420</valueURI>
+    </annotation>
+  </annotations>
+  <additionalMetadata>
+    <metadata>
+      <emlEditor>
+        <app>EMLassemblyline</app>
+        <release>3.5.5</release>
+      </emlEditor>
+    </metadata>
+  </additionalMetadata>
+</eml:eml>

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/personnel.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/personnel.tabular Wed Sep 13 19:56:16 2023 +0000

@@ -0,0 +1,8 @@
+givenName middleInitial surName organizationName electronicMailAddress userId role projectTitle fundingAgency fundingNumber
+Constance Blary CEFE constance.blary@cefe.cnrs.fr https://orcid.org/0000-0001-6204-9983 creator
+Kévin Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 creator
+Christian Kerbiriou CESCO christian.kerbiriou@mnhn.fr https://orcid.org/0000-0001-6080-4762 creator
+Isabelle Le Viol CESCO isabelle.le-viol@mnhn.fr creator
+Constance "" Blary CEFE constance.blary@cefe.cnrs.fr https://orcid.org/0000-0001-6204-9983 contact
+Kévin "" Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 contact
+Kévin "" Barré CESCO MNHN kevin.barre@mnhn.fr https://orcid.org/0000-0001-5368-4053 PI Effect of agricultural landscape features on bats DIM ASTREA Région Ile-de-France, FRB

diff -r 000000000000 -r 9cbac7a9b1a3 test-data/personnel.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/personnel.txt Wed Sep 13 19:56:16 2023 +0000