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Add duplicate test
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@ridderl
ridderl committed Aug 15, 2016
1 parent 9a1b0f0 commit 2d53fb9
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Showing 45 changed files with 1,684 additions and 1 deletion.
9 changes: 8 additions & 1 deletion tests/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesWorkflowTest.java
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Expand Up @@ -42,7 +42,14 @@ public static void setUpPythonUtils() throws MalformedURLException, IOException
@Test
public void test_simple() throws IOException, InvalidSettingsException, CanceledExecutionException,
UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {
File workflowDir = new File("src/knime/SyGMA-test");
File workflowDir = new File("src/knime/SyGMa-test");
runner.runTestWorkflow(workflowDir);
}

@Test
public void test_duplicate() throws IOException, InvalidSettingsException, CanceledExecutionException,
UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {
File workflowDir = new File("src/knime/SyGMa-duplicate-test");
runner.runTestWorkflow(workflowDir);
}
}
4 changes: 4 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/.savedWithData
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Do not delete this file!
This file serves to indicate that the workflow was written as part of the usual save routine (not exported).

Workflow was last saved by user vagrant on Mon Aug 15 09:53:05 UTC 2016
65 changes: 65 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#15)/settings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="settings.xml">
<entry key="node_file" type="xstring" value="settings.xml"/>
<config key="flow_stack"/>
<config key="internal_node_subsettings">
<entry key="memory_policy" type="xstring" value="CacheSmallInMemory"/>
</config>
<config key="model">
<config key="phase1_cycles_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_integer"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="phase1_cycles" type="xint" value="1"/>
<config key="phase2_cycles_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_integer"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="phase2_cycles" type="xint" value="1"/>
<config key="parents_column_name_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_string"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="parents_column_name" type="xstring" value="RDKit Mol"/>
</config>
<config key="nodeAnnotation">
<entry key="text" type="xstring" value="Phase 1"/>
<entry key="bgcolor" type="xint" value="16777215"/>
<entry key="x-coordinate" type="xint" value="345"/>
<entry key="y-coordinate" type="xint" value="224"/>
<entry key="width" type="xint" value="134"/>
<entry key="height" type="xint" value="20"/>
<entry key="alignment" type="xstring" value="CENTER"/>
<entry key="borderSize" type="xint" value="0"/>
<entry key="borderColor" type="xint" value="16777215"/>
<entry key="defFontSize" type="xint" value="11"/>
<entry key="annotation-version" type="xint" value="20151123"/>
<config key="styles"/>
</config>
<entry key="customDescription" type="xstring" isnull="true" value=""/>
<entry key="state" type="xstring" value="CONFIGURED"/>
<entry key="factory" type="xstring" value="nl.esciencecenter.e3dchem.sygma.PredictMetabolitesFactory"/>
<entry key="node-name" type="xstring" value="Predict metabolites"/>
<entry key="node-bundle-name" type="xstring" value="Sygma KNIME nodes"/>
<entry key="node-bundle-symbolic-name" type="xstring" value="nl.esciencecenter.e3dchem.sygma.plugin"/>
<entry key="node-bundle-vendor" type="xstring" value="Netherlands eScience Center"/>
<entry key="node-bundle-version" type="xstring" value="1.0.2"/>
<entry key="node-feature-name" type="xstring" value="Sygma KNIME nodes"/>
<entry key="node-feature-symbolic-name" type="xstring" value="nl.esciencecenter.e3dchem.sygma.feature.feature.group"/>
<entry key="node-feature-vendor" type="xstring" value="Netherlands eScience Center"/>
<entry key="node-feature-version" type="xstring" value="1.0.2"/>
<config key="factory_settings"/>
<entry key="name" type="xstring" value="Predict metabolites"/>
<entry key="hasContent" type="xboolean" value="false"/>
<entry key="isInactive" type="xboolean" value="false"/>
<config key="ports">
<config key="port_1">
<entry key="index" type="xint" value="1"/>
<entry key="port_dir_location" type="xstring" isnull="true" value=""/>
</config>
</config>
<config key="filestores">
<entry key="file_store_location" type="xstring" isnull="true" value=""/>
<entry key="file_store_id" type="xstring" isnull="true" value=""/>
</config>
</config>
1 change: 1 addition & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/internal/execErrout
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1 change: 1 addition & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/internal/execOutput
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6 changes: 6 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/data.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="table_meta_info">
<entry key="table_ID" type="xint" value="123"/>
<entry key="table_type" type="xstring" value="container_table"/>
<entry key="table_file_name" type="xstring" value="data.zip"/>
</config>
Binary file added tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/data.zip
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186 changes: 186 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/spec.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="spec.xml">
<entry key="spec_name" type="xstring" value="default"/>
<entry key="number_columns" type="xint" value="6"/>
<config key="column_spec_0">
<entry key="column_name" type="xstring" value="Drug"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.knime.core.data.def.StringCell"/>
</config>
<config key="column_domain">
<config key="possible_values">
<entry key="array-size" type="xint" value="2"/>
<config key="0">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="Phenol"/>
</config>
</config>
<config key="1">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="Hydroxybenzene"/>
</config>
</config>
</config>
</config>
<config key="column_properties"/>
</config>
<config key="column_spec_1">
<entry key="column_name" type="xstring" value="smiles"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.knime.core.data.def.StringCell"/>
</config>
<config key="column_domain">
<config key="possible_values">
<entry key="array-size" type="xint" value="1"/>
<config key="0">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="c1ccccc1O"/>
</config>
</config>
</config>
</config>
<config key="column_properties"/>
</config>
<config key="column_spec_2">
<entry key="column_name" type="xstring" value="RDKit Mol"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.rdkit.knime.types.RDKitMolCell2"/>
</config>
<config key="column_domain"/>
<config key="column_properties"/>
</config>
<config key="column_spec_3">
<entry key="column_name" type="xstring" value="SyGMa_metabolite"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.rdkit.knime.types.RDKitMolCell2"/>
</config>
<config key="column_domain"/>
<config key="column_properties"/>
</config>
<config key="column_spec_4">
<entry key="column_name" type="xstring" value="SyGMa_pathway"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.knime.core.data.def.StringCell"/>
</config>
<config key="column_domain">
<config key="possible_values">
<entry key="array-size" type="xint" value="12"/>
<config key="0">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="parent;"/>
</config>
</config>
<config key="1">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="O-glucuronidation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="2">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="sulfation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="3">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(para_to_oxygen); %%00010"/>
</config>
</config>
<config key="4">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="methylation_(aromatic_OH); %%00010"/>
</config>
</config>
<config key="5">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(ortho_to_oxygen); %%00010"/>
</config>
</config>
<config key="6">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(para_to_oxygen); %%00010O-glucuronidation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="7">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(ortho_to_oxygen); %%00010O-glucuronidation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="8">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(para_to_oxygen); %%00010sulfation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="9">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(ortho_to_oxygen); %%00010sulfation_(aromatic_hydroxyl); %%00010"/>
</config>
</config>
<config key="10">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(para_to_oxygen); %%00010methylation_(aromatic_OH); %%00010"/>
</config>
</config>
<config key="11">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.StringCell"/>
<config key="org.knime.core.data.def.StringCell">
<entry key="StringCell" type="xstring" value="aromatic_hydroxylation_(ortho_to_oxygen); %%00010methylation_(aromatic_OH); %%00010"/>
</config>
</config>
</config>
</config>
<config key="column_properties"/>
</config>
<config key="column_spec_5">
<entry key="column_name" type="xstring" value="SyGMa_score"/>
<config key="element_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="column_type">
<entry key="cell_class" type="xstring" value="org.knime.core.data.def.DoubleCell"/>
</config>
<config key="column_domain">
<config key="lower_bound">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.DoubleCell"/>
<config key="org.knime.core.data.def.DoubleCell">
<entry key="DoubleCell" type="xdouble" value="0.001728"/>
</config>
</config>
<config key="upper_bound">
<entry key="datacell" type="xstring" value="org.knime.core.data.def.DoubleCell"/>
<config key="org.knime.core.data.def.DoubleCell">
<entry key="DoubleCell" type="xdouble" value="1.0"/>
</config>
</config>
</config>
<config key="column_properties"/>
</config>
</config>
68 changes: 68 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/settings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="settings.xml">
<entry key="node_file" type="xstring" value="settings.xml"/>
<config key="flow_stack"/>
<config key="internal_node_subsettings">
<entry key="memory_policy" type="xstring" value="CacheSmallInMemory"/>
</config>
<config key="model">
<config key="phase1_cycles_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_integer"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="phase1_cycles" type="xint" value="1"/>
<config key="phase2_cycles_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_integer"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="phase2_cycles" type="xint" value="1"/>
<config key="parents_column_name_Internals">
<entry key="SettingsModelID" type="xstring" value="SMID_string"/>
<entry key="EnabledStatus" type="xboolean" value="true"/>
</config>
<entry key="parents_column_name" type="xstring" value="RDKit Mol"/>
</config>
<config key="nodeAnnotation">
<entry key="text" type="xstring" value="Phase 1"/>
<entry key="bgcolor" type="xint" value="16777215"/>
<entry key="x-coordinate" type="xint" value="353"/>
<entry key="y-coordinate" type="xint" value="399"/>
<entry key="width" type="xint" value="134"/>
<entry key="height" type="xint" value="20"/>
<entry key="alignment" type="xstring" value="CENTER"/>
<entry key="borderSize" type="xint" value="0"/>
<entry key="borderColor" type="xint" value="16777215"/>
<entry key="defFontSize" type="xint" value="11"/>
<entry key="annotation-version" type="xint" value="20151123"/>
<config key="styles"/>
</config>
<entry key="customDescription" type="xstring" isnull="true" value=""/>
<entry key="state" type="xstring" value="EXECUTED"/>
<entry key="factory" type="xstring" value="nl.esciencecenter.e3dchem.sygma.PredictMetabolitesFactory"/>
<entry key="node-name" type="xstring" value="Predict metabolites"/>
<entry key="node-bundle-name" type="xstring" value="Sygma KNIME nodes"/>
<entry key="node-bundle-symbolic-name" type="xstring" value="nl.esciencecenter.e3dchem.sygma.plugin"/>
<entry key="node-bundle-vendor" type="xstring" value="Netherlands eScience Center"/>
<entry key="node-bundle-version" type="xstring" value="1.0.2"/>
<entry key="node-feature-name" type="xstring" value="Sygma KNIME nodes"/>
<entry key="node-feature-symbolic-name" type="xstring" value="nl.esciencecenter.e3dchem.sygma.feature.feature.group"/>
<entry key="node-feature-vendor" type="xstring" value="Netherlands eScience Center"/>
<entry key="node-feature-version" type="xstring" value="1.0.2"/>
<config key="factory_settings"/>
<entry key="name" type="xstring" value="Predict metabolites"/>
<entry key="hasContent" type="xboolean" value="true"/>
<entry key="isInactive" type="xboolean" value="false"/>
<config key="ports">
<config key="port_1">
<entry key="index" type="xint" value="1"/>
<entry key="port_spec_class" type="xstring" value="org.knime.core.data.DataTableSpec"/>
<entry key="port_object_class" type="xstring" value="org.knime.core.node.BufferedDataTable"/>
<entry key="port_object_summary" type="xstring" value="Rows: 24, Cols: 6"/>
<entry key="port_dir_location" type="xstring" value="port_1"/>
</config>
</config>
<config key="filestores">
<entry key="file_store_location" type="xstring" isnull="true" value=""/>
<entry key="file_store_id" type="xstring" value="1af2adcc-0f66-45c9-b1d8-8bbfefcff73a"/>
</config>
</config>
6 changes: 6 additions & 0 deletions tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_1/data.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="table_meta_info">
<entry key="table_ID" type="xint" value="120"/>
<entry key="table_type" type="xstring" value="container_table"/>
<entry key="table_file_name" type="xstring" value="data.zip"/>
</config>
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