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[test/scripts] Add odmlconvert basic conv test
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‎test/resources/scripts/odml_convert/conversion_example_A.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<?xml-stylesheet type="text/xsl" href="odmlTerms.xsl"?>
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<?xml-stylesheet type="text/xsl" href="odml.xsl"?>
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<odML version="1">
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<section>
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<property>
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<value>0.0<unit>um</unit></value>
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<name>Depth</name>
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</property>
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<property>
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<value>P-unit</value>
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<name>CellType</name>
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</property>
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<property>
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<value>Nerve</value>
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<name>Structure</name>
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</property>
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<property>
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<value>0.1</value>
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<name>CV</name>
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</property>
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<property>
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<value>12.8<unit>Hz</unit></value>
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<name>Baseline rate</name>
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</property>
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<name>Cell</name>
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<type>Cell</type>
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</section>
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<section>
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<property>
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<value>weak response</value>
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<name>Comment</name>
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</property>
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<property>
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<value>2020-06-24-ab</value>
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<name>Name</name>
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</property>
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<property>
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<value>Good</value>
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<name>Recording quality</name>
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</property>
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<property>
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<value>12.8.7 (20/06/24)</value>
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<name>Software version</name>
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</property>
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<property>
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<value>Ex Perimenter</value>
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<name>Experimenter</name>
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</property>
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<property>
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<value>Acquisition</value>
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<name>Mode</name>
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</property>
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<property>
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<value>conversion_example.xml</value>
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<name>File</name>
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</property>
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<property>
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<value>16:35:51</value>
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<name>Time</name>
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</property>
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<property>
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<value>2020-06-24</value>
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<name>Date</name>
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</property>
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<property>
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<value>100<unit>m</unit></value>
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<name>Recording duration</name>
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</property>
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<property>
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<value>./odml_convert</value>
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<name>Folder</name>
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</property>
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<property>
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<value>SomeEphysSoftware</value>
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<name>Software</name>
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</property>
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<name>Recording</name>
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<type>Recording</type>
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</section>
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<section>
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<property>
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<value>12.0<unit>Hz</unit></value>
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<name>Firing Rate1</name>
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</property>
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<property>
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<value>12.0<unit>Hz</unit></value>
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<name>EOD Frequency</name>
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</property>
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<property>
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<value>0.1</value>
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<name>P-Value1</name>
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</property>
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<name>Cell properties</name>
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<type>Cell properties</type>
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</section>
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<section>
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<property>
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<value>unknown</value>
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<name>Gender</name>
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</property>
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<property>
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<value>Xen Omorph</value>
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<name>Species</name>
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</property>
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<property>
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<value>10.0<unit>cm</unit></value>
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<name>Size</name>
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</property>
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<property>
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<value>1.0<unit>mV</unit></value>
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<name>Transdermal amplitude</name>
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</property>
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<property>
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<value>1.4<unit>Hz</unit></value>
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<name>EOD Frequency</name>
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</property>
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<name>Subject</name>
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<type>Subject</type>
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</section>
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<author>tester</author>
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</odML>

‎test/resources/scripts/odml_convert/conversion_example_B.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<?xml-stylesheet type="text/xsl" href="odmlTerms.xsl"?>
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<?xml-stylesheet type="text/xsl" href="odml.xsl"?>
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<odML version="1">
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<section>
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<property>
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<value>0.0<unit>um</unit></value>
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<name>Depth</name>
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</property>
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<property>
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<value>P-unit</value>
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<name>CellType</name>
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</property>
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<property>
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<value>Nerve</value>
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<name>Structure</name>
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</property>
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<property>
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<value>0.1</value>
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<name>CV</name>
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</property>
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<property>
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<value>12.8<unit>Hz</unit></value>
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<name>Baseline rate</name>
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</property>
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<name>Cell</name>
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<type>Cell</type>
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</section>
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<section>
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<property>
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<value>weak response</value>
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<name>Comment</name>
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</property>
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<property>
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<value>2020-06-24-ab</value>
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<name>Name</name>
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</property>
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<property>
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<value>Good</value>
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<name>Recording quality</name>
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</property>
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<property>
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<value>12.8.7 (20/06/24)</value>
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<name>Software version</name>
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</property>
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<property>
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<value>Ex Perimenter</value>
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<name>Experimenter</name>
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</property>
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<property>
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<value>Acquisition</value>
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<name>Mode</name>
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</property>
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<property>
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<value>conversion_example.xml</value>
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<name>File</name>
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</property>
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<property>
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<value>16:35:51</value>
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<name>Time</name>
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</property>
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<property>
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<value>2020-06-24</value>
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<name>Date</name>
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</property>
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<property>
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<value>100<unit>m</unit></value>
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<name>Recording duration</name>
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</property>
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<property>
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<value>./odml_convert</value>
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<name>Folder</name>
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</property>
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<property>
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<value>SomeEphysSoftware</value>
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<name>Software</name>
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</property>
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<name>Recording</name>
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<type>Recording</type>
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</section>
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<section>
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<property>
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<value>12.0<unit>Hz</unit></value>
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<name>Firing Rate1</name>
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</property>
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<property>
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<value>12.0<unit>Hz</unit></value>
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<name>EOD Frequency</name>
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</property>
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<property>
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<value>0.1</value>
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<name>P-Value1</name>
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</property>
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<name>Cell properties</name>
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<type>Cell properties</type>
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</section>
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<section>
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<property>
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<value>unknown</value>
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<name>Gender</name>
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</property>
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<property>
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<value>Xen Omorph</value>
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<name>Species</name>
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</property>
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<property>
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<value>10.0<unit>cm</unit></value>
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<name>Size</name>
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</property>
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<property>
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<value>1.0<unit>mV</unit></value>
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<name>Transdermal amplitude</name>
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</property>
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<property>
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<value>1.4<unit>Hz</unit></value>
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<name>EOD Frequency</name>
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</property>
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<name>Subject</name>
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<type>Subject</type>
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</section>
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<author>tester</author>
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</odML>

‎test/test_script_odml_convert.py‎

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from docopt import DocoptExit
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from odml import load as odml_load
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from odml.scripts import odml_convert
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from . import util
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def setUp(self):
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self.tmp_dir = util.create_test_dir(__file__)
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self.dir_files = os.path.join(util.TEST_RESOURCES_DIR, "scripts", "odml_convert")
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def tearDown(self):
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if self.tmp_dir and os.path.exists(self.tmp_dir):
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with self.assertRaises(SystemExit):
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odml_convert.main(["-h"])
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def test_valid_conversion(self):
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# make sure temp dir is empty
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self.assertListEqual(os.listdir(self.tmp_dir), [])
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# run converter on root directory containing two files
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odml_convert.main(["-o", self.tmp_dir, self.dir_files])
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# make sure an output directory has been created
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out_dir_lst = os.listdir(self.tmp_dir)
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self.assertEqual(len(out_dir_lst), 1)
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out_dir = os.path.join(self.tmp_dir, out_dir_lst[0])
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self.assertTrue(os.path.isdir(out_dir))
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# make sure two files have been created
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file_lst = os.listdir(out_dir)
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self.assertEqual(len(file_lst), 2)
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# make sure the files are valid odml files
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_ = odml_load(os.path.join(out_dir, file_lst[0]))
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_ = odml_load(os.path.join(out_dir, file_lst[1]))

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