/** Tests expected behavior when an exception occurs during the search process. */
@Test
public void searchWithException() {
doThrow(Exception.class).when(bioDbNetRemoteService).db2db(any(Db2DbParams.class));
action.getSearchParameters().setSearchType(SearchType.PATHWAY);
action.getSearchParameters().setInputValues(PATHWAY_NAME);
assertEquals(Action.INPUT, action.search());
assertTrue(action.hasActionErrors());
assertEquals(1, action.getActionErrors().size());
assertEquals("bioDbNet.error", action.getActionErrors().iterator().next());
}
/** {@inheritDoc} */
@Before
@Override
public void setUp() throws Exception {
super.setUp();
BioDbNetSearchImpl bioDbNetSvc = new BioDbNetSearchImpl();
bioDbNetSvc.setBioDbNetRemoteService(bioDbNetRemoteService);
action = new BioDbNetSearchAction();
action.setBioDbNetService(bioDbNetSvc);
action.setWorkspaceService(workspaceService);
action.prepare();
}
/** Tests searching by gene id with case sensitivity enabled. */
@Test
public void searchGeneId() {
action.getSearchParameters().setSearchType(SearchType.GENE_ID);
action.getSearchParameters().setInputValues("1,2,3,4");
action.getSearchParameters().setCaseSensitiveSearch(true);
assertEquals(GENE_RESULT, action.search());
assertTrue(action.getGeneResults().size() > 0);
Db2DbParams expectedInput = new Db2DbParams();
expectedInput.setInputValues("1,2,3,4");
verify(bioDbNetRemoteService).db2db(refEq(expectedInput, ignoredParams));
}
/** Tests searching by gene pathways with case sensitivity disabled. */
@Test
public void searchPathwaysCaseInsensitive() {
action.getSearchParameters().setSearchType(SearchType.PATHWAY);
action.getSearchParameters().setInputValues(PATHWAY_NAME);
action.getSearchParameters().setCaseSensitiveSearch(false);
assertEquals(GENE_RESULT, action.search());
assertTrue(action.getGeneResults().size() > 0);
Db2DbParams expectedInput = new Db2DbParams();
expectedInput.setInputValues("H_BARD1PATHWAY,H_bard1Pathway,h_bard1Pathway,h_bard1pathway");
verify(bioDbNetRemoteService).db2db(refEq(expectedInput, ignoredParams));
}
/** Tests searching by gene alias with case sensitivity enabled. */
@Test
public void searchGeneSymbolCaseInsensitive() {
action.getSearchParameters().setSearchType(SearchType.GENE_SYMBOL);
action.getSearchParameters().setInputValues("BRCA1,BRCA2");
action.getSearchParameters().setCaseSensitiveSearch(false);
assertEquals(GENE_RESULT, action.search());
assertTrue(action.getGeneResults().size() > 0);
Db2DbParams expectedInput = new Db2DbParams();
expectedInput.setInputValues("BRCA1,BRCA2,brca1,brca2");
verify(bioDbNetRemoteService).db2db(refEq(expectedInput, ignoredParams));
}
/** Tests searching by gene alias with case sensitivity disabled. */
@Test
public void searchGeneAliasCaseInsensitive() {
action.getSearchParameters().setSearchType(SearchType.GENE_ALIAS);
action.getSearchParameters().setInputValues(GENE_ALIAS);
action.getSearchParameters().setCaseSensitiveSearch(false);
assertEquals(GENE_RESULT, action.search());
assertTrue(action.getGeneResults().size() > 0);
DbWalkParams expectedInput = new DbWalkParams();
expectedInput.setInputValues("BRCC1,Brcc1,brcc1");
verify(bioDbNetRemoteService).dbWalk(refEq(expectedInput, "dbPath", "taxonId"));
}
/** Tests action validation. */
@Test
public void validate() {
action.validate();
assertTrue(action.hasActionErrors());
assertEquals(1, action.getActionErrors().size());
assertEquals(
"struts.messages.error.must.enter.keywords", action.getActionErrors().iterator().next());
action.clearActionErrors();
action.prepare();
action.getSearchParameters().setInputValues("input");
action.validate();
assertFalse(action.hasActionErrors());
}
/** Tests expected behavior when no gene results are found. */
@Test
public void searchPathwayNoResults() {
bioDbNetRemoteService = mock(BioDbNetRemoteService.class);
when(bioDbNetRemoteService.db2db(any(Db2DbParams.class)))
.thenAnswer(
new Answer<String>() {
@Override
public String answer(InvocationOnMock invocation) throws Throwable {
return "Gene Symbol Biocarta Pathway Name";
}
});
BioDbNetSearchImpl bioDbNetSvc = new BioDbNetSearchImpl();
bioDbNetSvc.setBioDbNetRemoteService(bioDbNetRemoteService);
action.setBioDbNetService(bioDbNetSvc);
action.getSearchParameters().setSearchType(SearchType.PATHWAY_BY_GENE);
action.getSearchParameters().setInputValues(StringUtils.EMPTY);
assertEquals(PATHWAY_RESULTS, action.search());
assertTrue(action.getGeneResults().isEmpty());
assertTrue(action.hasActionErrors());
assertEquals(1, action.getActionErrors().size());
assertEquals("bioDbNet.noPathwayResultsFound", action.getActionErrors().iterator().next());
}
/** Tests expected behavior when no gene results are found. */
@Test
public void searchGenesNoResults() {
action.getSearchParameters().setSearchType(null);
action.getSearchParameters().setInputValues(StringUtils.EMPTY);
assertEquals(GENE_RESULT, action.search());
assertTrue(action.getGeneResults().isEmpty());
assertTrue(action.hasActionErrors());
assertEquals(1, action.getActionErrors().size());
assertEquals("bioDbNet.noGeneResultsFound", action.getActionErrors().iterator().next());
}
/** Tests search of pathways by genes with case sensitivity disabled. */
@Test
public void searchPathwaysByGeneCaseInsensitive() {
action.getSearchParameters().setSearchType(SearchType.PATHWAY_BY_GENE);
action.getSearchParameters().setInputValues("BRCA1");
action.getSearchParameters().setCaseSensitiveSearch(false);
assertEquals(PATHWAY_RESULTS, action.search());
assertTrue(action.getGeneResults().isEmpty());
assertFalse(action.getPathwayResults().isEmpty());
assertEquals(5, action.getPathwayResults().size());
Db2DbParams expectedInput = new Db2DbParams();
expectedInput.setInputValues("BRCA1,brca1");
verify(bioDbNetRemoteService).db2db(refEq(expectedInput, ignoredParams));
}
/** Tests input method. */
@Test
public void input() {
assertEquals(Action.SUCCESS, action.input());
}