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fix bug 3073, HandlerTest method -> manager test
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Moved the HandlerTest method in the manager test cause it actually only tested if the SMILES file was loaded with properties and it's better to do that in CDKManager test.
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@jonalv
jonalv committed Sep 1, 2011
1 parent f336398 commit 9a4fa83
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Showing 3 changed files with 41 additions and 43 deletions.
32 changes: 32 additions & 0 deletions ...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java
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Expand Up @@ -62,6 +62,7 @@
import org.eclipse.core.runtime.FileLocator;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.NullProgressMonitor;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.Status;
import org.eclipse.core.runtime.content.IContentType;
Expand Down Expand Up @@ -267,6 +268,37 @@ public void testBug3055_SmilesProperties() throws Exception {
List<ICDKMolecule> mols = cdk.loadSMILESFile(path);
assertNotNull( mols.get( 0 ).getProperty("name",
Property.USE_CACHED) );

String csvfile = "/testFiles/testsmi2sdf.smi";
InputStream stream = getClass().getResourceAsStream(csvfile);
MockIFile ifile=new MockIFile(stream).extension("smi");

mols = cdk.loadSMILESFile( ifile, new NullProgressMonitor() );

//Confirm all molecules are read
assertEquals(8, mols.size());

//Confirm properties are stored on first mol
assertEquals("842267", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_SID"));
assertEquals("", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_EXT_DATASOURCE_REGID"));
assertEquals("644526", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_CID"));
assertEquals("2", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_ACTIVITY_OUTCOME"));
assertEquals("26", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_ACTIVITY_SCORE"));
assertEquals("\"\"", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_ACTIVITY_URL"));
assertEquals("20100519", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_ASSAYDATA_COMMENT"));
assertEquals("\"\"", mols.get(0).getAtomContainer()
.getProperty("PUBCHEM_ASSAYDATA_REVOKE"));
assertEquals("123.22", mols.get(0).getAtomContainer()
.getProperty("1"));
assertEquals("10.2743", mols.get(0).getAtomContainer()
.getProperty("2"));
}

@Test
Expand Down
9 changes: 9 additions & 0 deletions plugins/net.bioclipse.cdk.business.test/src/testFiles/testsmi2sdf.smi
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@@ -0,0 +1,9 @@
SMILES,"PUBCHEM_SID","PUBCHEM_EXT_DATASOURCE_REGID","PUBCHEM_CID","PUBCHEM_ACTIVITY_OUTCOME","PUBCHEM_ACTIVITY_SCORE","PUBCHEM_ACTIVITY_URL","PUBCHEM_ASSAYDATA_COMMENT","PUBCHEM_ASSAYDATA_REVOKE",1,2
C1=CC=C(C=C1)OCCN2C3=CC=CC=C3SC2=O,842267,,644526,2,26,"",20100519,"",123.22,10.2743
CN\1C2=CC=CC=C2S/C1=C\C(=O)C3CCC3,842317,,5409720,2,30,"",20100519,"",137.55,10.0768
C1OC2=C(O1)C=C(C=C2)NC(=O)CSC3=NN=NN3CC4=CC=CC=C4,842386,,644654,2,18,"",20100519,"",84.67,3.7112
C1=CC=C(C=C1)NC(=O)C2=CC3=C(C=C2)N=C(S3)N,842516,,644786,2,29,"",20100519,"",137.13,5.14689
C1=CC=C(C=C1)OCC2=NN=C3N2N=C(S3)C4=CC=CS4,842734,,645009,2,17,"",20100519,"",80.71,14.5673
C1=CC=C(C=C1)C2=NC3=CC=CC=C3C4=NN=CN24,843032,,645307,2,26,"",20100519,"",123.13,7.53848
CC(=O)NC1=NC2=C(S1)C=C(C=C2)C(=O)NC,843041,,645316,1,4,"",20100519,"",22.68,0.948018
CC1=NN=C(C2=CC=CC=C12)NC3=CC=CC=N3,843042,,645317,2,31,"",20100519,"",142.71,3.81868
43 changes: 0 additions & 43 deletions plugins/net.bioclipse.cdk.ui.tests/src/net/bioclipse/cdk/ui/tests/HandlerTests.java
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Expand Up @@ -44,40 +44,6 @@
*/
public class HandlerTests {

/**
* Test converting a comma-separated SMIELS file into an SDF.
* @throws CoreException
* @throws IOException
* @throws URISyntaxException
* @throws BioclipseException
* @throws InvocationTargetException
* @throws InterruptedException
*/
@Test
public void testConvertSMILEStoSDF() throws CoreException, IOException, URISyntaxException, BioclipseException, InvocationTargetException, InterruptedException {
String csvfile = "/testFiles/testsmi2sdf.smi";
InputStream stream = getClass().getResourceAsStream(csvfile);
MockIFile ifile=new MockIFile(stream);

List<ICDKMolecule> mols = ConvertSMILEStoSDF.readFileIntoMoleculeList(ifile, new NullProgressMonitor());

//Confirm all molecules are read
assertEquals(8, mols.size());

//Confirm properties are stored on first mol
assertEquals("842267", mols.get(0).getAtomContainer().getProperty("PUBCHEM_SID"));
assertEquals("", mols.get(0).getAtomContainer().getProperty("PUBCHEM_EXT_DATASOURCE_REGID"));
assertEquals("644526", mols.get(0).getAtomContainer().getProperty("PUBCHEM_CID"));
assertEquals("2", mols.get(0).getAtomContainer().getProperty("PUBCHEM_ACTIVITY_OUTCOME"));
assertEquals("26", mols.get(0).getAtomContainer().getProperty("PUBCHEM_ACTIVITY_SCORE"));
assertEquals("\"\"", mols.get(0).getAtomContainer().getProperty("PUBCHEM_ACTIVITY_URL"));
assertEquals("20100519", mols.get(0).getAtomContainer().getProperty("PUBCHEM_ASSAYDATA_COMMENT"));
assertEquals("\"\"", mols.get(0).getAtomContainer().getProperty("PUBCHEM_ASSAYDATA_REVOKE"));
assertEquals("123.22", mols.get(0).getAtomContainer().getProperty("1"));
assertEquals("10.2743", mols.get(0).getAtomContainer().getProperty("2"));

}

@Test
public void testFilterOutSalts() throws MalformedURLException, IOException, BioclipseException, CoreException, URISyntaxException{

Expand All @@ -104,13 +70,4 @@ public void testFilterOutSalts() throws MalformedURLException, IOException, Bioc
}

}


private String sourcePathtoAbsolutePath(String sourcepath)
throws URISyntaxException, MalformedURLException, IOException{
URI uri = getClass().getResource(sourcepath).toURI();
URL url = FileLocator.toFileURL(uri.toURL());
return url.getFile();
}

}

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