SE-147 data set is either the protXML file or a folder which contains a *prot.xml file

SVN: 12845

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLUploader.java

@@ -34,6 +34,7 @@ import ch.systemsx.cisd.etlserver.IDataSetUploader;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
 
 /**
  * @author Franz-Josef Elmer
@@ -83,14 +84,26 @@ public class ProtXMLUploader implements IDataSetUploader
     public void upload(File dataSet, DataSetInformation dataSetInformation)
     {
         long time = System.currentTimeMillis();
-        ProteinSummary summary = loader.readProtXML(dataSet);
+        File protXMLFile = getProtXMLFile(dataSet);
+        ProteinSummary summary = loader.readProtXML(protXMLFile);
         if (operationLog.isInfoEnabled())
         {
             operationLog.info(summary.getProteinGroups().size()
-                    + " protein groups are successfully read from '" + dataSet + "' in "
+                    + " protein groups are successfully read from '" + protXMLFile + "' in "
                     + (System.currentTimeMillis() - time) + " msec");
         }
         time = System.currentTimeMillis();
+        ResultDataSetUploader upLoader = createUploader();
+        upLoader.upload(dataSetInformation, summary);
+        if (operationLog.isInfoEnabled())
+        {
+            operationLog.info("Feeding result database took " + (System.currentTimeMillis() - time)
+                    + " msec.");
+        }
+    }
+
+    protected ResultDataSetUploader createUploader()
+    {
         Connection connection;
         try
         {
@@ -100,13 +113,24 @@ public class ProtXMLUploader implements IDataSetUploader
         {
             throw CheckedExceptionTunnel.wrapIfNecessary(ex);
         }
-        ResultDataSetUploader upLoader = new ResultDataSetUploader(connection, openbisService);
-        upLoader.upload(dataSetInformation, summary);
-        if (operationLog.isInfoEnabled())
+        return new ResultDataSetUploader(connection, openbisService);
+    }
+
+    private File getProtXMLFile(File dataSet)
+    {
+        if (dataSet.isDirectory() == false)
         {
-            operationLog.info("Feeding result database took " + (System.currentTimeMillis() - time)
-                    + " msec.");
+            return dataSet;
+        }
+        File[] files = dataSet.listFiles();
+        for (File file : files)
+        {
+            if (file.getName().endsWith("prot.xml"))
+            {
+                return file;
+            }
         }
+        throw new UserFailureException("No *prot.xml file found in data set '" + dataSet + "'.");
     }
 
 }

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLLoaderTest.java

@@ -21,7 +21,6 @@ import java.util.List;
 
 import org.testng.annotations.Test;
 
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
 import ch.systemsx.cisd.common.filesystem.FileUtilities;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein;
@@ -40,45 +39,8 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryHeader;
  *
  * @author Franz-Josef Elmer
  */
-public class ProtXMLLoaderTest extends AbstractFileSystemTestCase
+public class ProtXMLLoaderTest extends ProtXMLTestCase
 {
-    private static final String EXAMPLE = "<?xml version='1.0' encoding='UTF-8'?>\n"
-        + "<protein_summary xmlns='http://regis-web.systemsbiology.net/protXML' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v3.xsd'>\n"
-        + "<protein_summary_header reference_database='some/path/uniprot.HUMAN.v125.fasta'>\n"
-        + " <program_details>\n"
-        + " <proteinprophet_details >\n"
-        + " <protein_summary_data_filter min_probability='0.25' sensitivity='1' false_positive_error_rate='0.5' predicted_num_correct='9' predicted_num_incorrect='4'/>\n"
-        + " </proteinprophet_details >\n" 
-        + " </program_details>\n"
-        + "</protein_summary_header>\n"
-        + "<protein_group probability='1'>\n"
-        + " <protein probability='1'>\n"
-        + "  <parameter name='key1' value='value1' type='type1'/>\n"
-        + "  <parameter name='key2' value='value2' type='type2'/>\n"
-        + "  <annotation protein_description='P42'/>\n"
-        + "  <indistinguishable_protein><annotation protein_description='P43'/></indistinguishable_protein>\n"
-        + "  <indistinguishable_protein><annotation protein_description='P44'/></indistinguishable_protein>\n"
-        + "  <peptide peptide_sequence='VYQIDGNYSR'>\n"
-        + "   <modification_info mod_nterm_mass='42' mod_cterm_mass='24.25'>\n"
-        + "    <mod_aminoacid_mass position='1' mass='115.25'/>\n" 
-        + "    <mod_aminoacid_mass position='4' mass='31.75'/>\n" 
-        + "   </modification_info>\n"
-        + "  </peptide>\n"
-        + "  <peptide peptide_sequence='ITSN'/>\n"
-        + " </protein>\n"
-        + " <protein probability='0'>\n"
-        + "  <annotation protein_description='Q42'/>\n"
-        + "  <peptide peptide_sequence='YSR'/>\n"
-        + " </protein>\n"
-        + "</protein_group>\n"
-        + "<protein_group probability='0.75'>\n"
-        + " <protein probability='0.75'>\n"
-        + "  <annotation protein_description='R42'/>\n"
-        + "  <peptide peptide_sequence='IYSR'/>\n"
-        + " </protein>\n"
-        + "</protein_group>\n"
-        + "</protein_summary>\n";
-    
     @Test
     public void test()
     {

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLTestCase.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public abstract class ProtXMLTestCase extends AbstractFileSystemTestCase
+{
+
+    protected static final String EXAMPLE = "<?xml version='1.0' encoding='UTF-8'?>\n"
+            + "<protein_summary xmlns='http://regis-web.systemsbiology.net/protXML' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v3.xsd'>\n"
+            + "<protein_summary_header reference_database='some/path/uniprot.HUMAN.v125.fasta'>\n"
+            + " <program_details>\n"
+            + " <proteinprophet_details >\n"
+            + " <protein_summary_data_filter min_probability='0.25' sensitivity='1' false_positive_error_rate='0.5' predicted_num_correct='9' predicted_num_incorrect='4'/>\n"
+            + " </proteinprophet_details >\n" 
+            + " </program_details>\n"
+            + "</protein_summary_header>\n"
+            + "<protein_group probability='1'>\n"
+            + " <protein probability='1'>\n"
+            + "  <parameter name='key1' value='value1' type='type1'/>\n"
+            + "  <parameter name='key2' value='value2' type='type2'/>\n"
+            + "  <annotation protein_description='P42'/>\n"
+            + "  <indistinguishable_protein><annotation protein_description='P43'/></indistinguishable_protein>\n"
+            + "  <indistinguishable_protein><annotation protein_description='P44'/></indistinguishable_protein>\n"
+            + "  <peptide peptide_sequence='VYQIDGNYSR'>\n"
+            + "   <modification_info mod_nterm_mass='42' mod_cterm_mass='24.25'>\n"
+            + "    <mod_aminoacid_mass position='1' mass='115.25'/>\n" 
+            + "    <mod_aminoacid_mass position='4' mass='31.75'/>\n" 
+            + "   </modification_info>\n"
+            + "  </peptide>\n"
+            + "  <peptide peptide_sequence='ITSN'/>\n"
+            + " </protein>\n"
+            + " <protein probability='0'>\n"
+            + "  <annotation protein_description='Q42'/>\n"
+            + "  <peptide peptide_sequence='YSR'/>\n"
+            + " </protein>\n"
+            + "</protein_group>\n"
+            + "<protein_group probability='0.75'>\n"
+            + " <protein probability='0.75'>\n"
+            + "  <annotation protein_description='R42'/>\n"
+            + "  <peptide peptide_sequence='IYSR'/>\n"
+            + " </protein>\n"
+            + "</protein_group>\n"
+            + "</protein_summary>\n";
+
+    /**
+     *
+     *
+     */
+    public ProtXMLTestCase()
+    {
+        super();
+    }
+
+    /**
+     *
+     *
+     * @param cleanAfterMethod
+     */
+    public ProtXMLTestCase(boolean cleanAfterMethod)
+    {
+        super(cleanAfterMethod);
+    }
+
+}
\ No newline at end of file

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLUploaderTest.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import java.io.File;
+import java.util.Properties;
+
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryHeader;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProtXMLUploaderTest extends ProtXMLTestCase
+{
+    private static final class MockUploader extends ProtXMLUploader
+    {
+        private final IEncapsulatedOpenBISService openbisService;
+        private DataSetInformation dataSetInformation;
+        private ProteinSummary proteinSummary;
+        
+        public MockUploader(Properties properties, IEncapsulatedOpenBISService openbisService)
+        {
+            super(properties, openbisService);
+            this.openbisService = openbisService;
+        }
+
+        @Override
+        protected ResultDataSetUploader createUploader()
+        {
+            return new ResultDataSetUploader(null, null, null)
+                {
+                    @Override
+                    void upload(DataSetInformation dataSetInfo, ProteinSummary summary)
+                    {
+                        dataSetInformation = dataSetInfo;
+                        proteinSummary = summary;
+                    }
+                };
+        }
+
+        public IEncapsulatedOpenBISService getService()
+        {
+            return openbisService;
+        }
+        
+        public DataSetInformation getDataSetInformation()
+        {
+            return dataSetInformation;
+        }
+
+        public ProteinSummary getProteinSummary()
+        {
+            return proteinSummary;
+        }
+    }
+    
+    private Mockery context;
+    private IEncapsulatedOpenBISService service;
+    private MockUploader uploader;
+
+    @BeforeMethod
+    public void startUp()
+    {
+        context = new Mockery();
+        service = context.mock(IEncapsulatedOpenBISService.class);
+        Properties properties = new Properties();
+        properties.setProperty("database.kind", "test");
+        uploader = new MockUploader(properties, service);
+    }
+    @AfterMethod
+    public void afterMethod()
+    {
+        // To following line of code should also be called at the end of each test method.
+        // Otherwise one do not known which test failed.
+        context.assertIsSatisfied();
+    }
+
+    @Test
+    public void testDataSetIsProtXMLFile()
+    {
+        File file = new File(workingDirectory, "test.xml");
+        FileUtilities.writeToFile(file, EXAMPLE);
+        DataSetInformation dataSetInformation = new DataSetInformation();
+        
+        uploader.upload(file, dataSetInformation);
+        
+        assertSame(service, uploader.getService());
+        assertSame(dataSetInformation, uploader.getDataSetInformation());
+        ProteinSummaryHeader header = uploader.getProteinSummary().getSummaryHeader();
+        assertEquals("some/path/uniprot.HUMAN.v125.fasta", header.getReferenceDatabase());
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testDataSetIsFolderWithProtXMLFile()
+    {
+        File dataSet = new File(workingDirectory, "data-set");
+        dataSet.mkdir();
+        FileUtilities.writeToFile(new File(dataSet, "test-prot.xml"), EXAMPLE);
+        DataSetInformation dataSetInformation = new DataSetInformation();
+        
+        uploader.upload(dataSet, dataSetInformation);
+        
+        assertSame(service, uploader.getService());
+        assertSame(dataSetInformation, uploader.getDataSetInformation());
+        ProteinSummaryHeader header = uploader.getProteinSummary().getSummaryHeader();
+        assertEquals("some/path/uniprot.HUMAN.v125.fasta", header.getReferenceDatabase());
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testDataSetIsFolderWithoutProtXMLFile()
+    {
+        File dataSet = new File(workingDirectory, "data-set");
+        dataSet.mkdir();
+        FileUtilities.writeToFile(new File(dataSet, "pep.xml"), "peptides");
+        DataSetInformation dataSetInformation = new DataSetInformation();
+        
+        try
+        {
+            uploader.upload(dataSet, dataSetInformation);
+            fail("UserFailureException expected");
+        } catch (UserFailureException ex)
+        {
+            assertEquals(
+                    "No *prot.xml file found in data set "
+                            + "'targets/unit-test-wd/ch.systemsx.cisd.openbis.etlserver.phosphonetx.ProtXMLUploaderTest/data-set'.",
+                    ex.getMessage());
+        }
+        
+        context.assertIsSatisfied();
+    }
+}