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Alexander OSTROVSKY
2641c692e2
accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files
78 lines
2.6 KiB
XML
78 lines
2.6 KiB
XML
<tool id="interactive_tool_openrefine" tool_type="interactive" name="OpenRefine" version="0.1">
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<description>Working with messy data</description>
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<requirements>
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<container type="docker">ylebras/openrefine-docker</container>
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</requirements>
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<entry_points>
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<entry_point name="Openrefine visualisation" requires_domain="True">
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<port>3333</port>
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</entry_point>
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</entry_points>
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<environment_variables>
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<environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
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<environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
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<environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="API_KEY" inject="api_key" />
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</environment_variables>
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<configfiles>
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<configfile name="start_openrefine"><![CDATA[
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exec /OpenRefine/refine -i 0.0.0.0 -m \$GALAXY_MEMORY_MB &
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##Check if openrefine is up to work
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STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
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while [[ \${STATUS} =~ "refused" ]]
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do
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echo "Waiting for openrefine: \$STATUS \n"
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STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
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sleep 4
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done
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]]>
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</configfile>
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</configfiles>
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<command detect_errors="aggressive"><![CDATA[
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cp '$infile' /import/input.tabular &&
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cat '$start_openrefine' &&
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bash '$start_openrefine' &&
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## Createnew project with the dataset
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cd /refine-python &&
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python openrefine_create_project_API.py '/import/input.tabular' &&
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tail -f /dev/null
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" format="tabular" label="tabular file"/>
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</inputs>
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<outputs>
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<data name="outfile" format="tabular" />
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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</test>
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</tests>
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<help><![CDATA[
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`Openrefine <https://openrefine.org/>`_ (previously Google Refine) is a powerful tool for working with messy data:
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cleaning it; transforming it from one format into another; and extending it with web services and external data.
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.. class:: infomark
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Example input file (TAB separated)::
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"name" "longitude" "latitude" "countryCode"
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Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA
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Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US
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Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US
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Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA
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Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US
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Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US
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Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US
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]]>
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</help>
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</tool>
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