+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.fts.threedbeacons;
+import static org.testng.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import org.testng.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.Test;
import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.gui.JvOptionPane;
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ private FTSRestClient ftsRestClient;
+
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
+ ftsRestClient = new FTSRestClient()
+ {
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return "/fts/tdbeacons_data_columns.txt";
+ }
+
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
+ throws Exception
+ {
+ return null;
+ }
+ };
}
@AfterMethod(alwaysRun = true)
{
}
+ @Test
+ public void getAllDefaulDisplayedDataColumns()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Assert.assertNotNull(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ System.out
+ .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
+ .isEmpty());
+ Assert.assertEquals(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
+ 15);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumIndexTest()
+ {
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns();
+ int foundIndex = -1;
+ try
+ {
+ Assert.assertEquals(foundIndex, -1);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ false);
+ Assert.assertEquals(foundIndex, 12);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ true);
+ // 1+primary key index
+ Assert.assertEquals(foundIndex, 13);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnsFieldsAsCommaDelimitedString()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns();
+ String actual = ftsRestClient
+ .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
+ Assert.assertEquals(actual,
+ "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getAllFTSDataColumns()
+ {
+ Collection<FTSDataColumnI> allFields = ftsRestClient
+ .getAllFTSDataColumns();
+ Assert.assertNotNull(allFields);
+ // System.out.println(allFields.size());
+ Assert.assertEquals(allFields.size(), 20);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getSearchableDataColumns()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Collection<FTSDataColumnI> searchableFields = ftsRestClient
+ .getSearchableDataColumns();
+ Assert.assertNotNull(searchableFields);
+ // System.out.println(searchableFields.size());
+ Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
+ // accession
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumn()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ FTSDataColumnI expectedPKColumn;
+ try
+ {
+ expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
+ Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
+ Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
+ expectedPKColumn);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnByNameOrCode()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnGroupById()
+ {
+ FTSDataColumnGroupI foundDataColGroup;
+ try
+ {
+ foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
+ Assert.assertNotNull(foundDataColGroup);
+ Assert.assertEquals(foundDataColGroup.getName(), "Quality");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDefaultResponsePageSize()
+ {
+ int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
+ Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
+ // uniprot 500
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnMinWidthTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ int actualColMinWidth = foundDataCol.getMinWidth();
+ Assert.assertEquals(actualColMinWidth, 50);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+ // could add test for MaxWidth & PreferedWith
+
+ @Test(groups = { "Functional" })
+ public void getColumnClassTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ String.class);
+ foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ String.class);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void coverageForEqualsAndHashFunction()
+ {
+ Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
+ Collection<FTSDataColumnI> searchableCols = ftsRestClient
+ .getSearchableDataColumns();
+ System.out.println(searchableCols);
+ for (FTSDataColumnI foundCol : searchableCols)
+ {
+ System.out.println(foundCol.toString());
+ uniqueSet.add(foundCol);
+ uniqueSet.add(foundCol);
+ }
+ Assert.assertTrue(!uniqueSet.isEmpty());
+ // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
+ }
+
+ @Test(groups = { "Functional" })
+ public void getTDBIdColumIndexTest()
+ {
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Model id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_accession"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Title"));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ try
+ {
+ assertEquals(4, TDBeaconsFTSRestClient.getInstance()
+ .getPrimaryKeyColumIndex(wantedFields, true));
+ // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
+ // .getPrimaryKeyColumIndex(wantedFields, true));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ private static String[][] mocks = { { "P38398.json", null },
+ { "P01308.json", null },
+ { "P0DTD1.json", null }
+
+ // , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body
+ };
+
+ private static void setMockData()
+ {
+ try
+ {
+ mocks[0][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt");
+
+ mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt");
+
+ mocks[2][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt");
+
+ } catch (IOException e)
+ {
+ Assert.fail("Couldn't read mock response data", e);
+ }
+ }
+
+ public static void setMock()
+ {
+ setMockData();
+ FTSRestClient.createMockFTSRestClient(
+ (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
+ }
+
+ private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ /**
+ * check that the mock request and response are the same as the response from
+ * a live 3D-beacons endpoint
+ *
+ * Note - servers often have rapidly changing ids / URIs so this might fail,
+ * but the overall structure will remain.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Network", "Integration" })
+ public void verifyMockTDBRequest() throws Exception
+ {
+ setMockData();
+ for (String[] otherMock : mocks)
+ {
+ verifyMockTDBRequest(otherMock[0], otherMock[1]);
+ }
+ }
+
+ private void verifyMockTDBRequest(String mockRequest,
+ String _mockResponse) throws Exception
+ {
+ URL tdb_req = new URL(prod_url + mockRequest);
+ byte[] resp = tdb_req.openStream().readAllBytes();
+ String tresp = new String(resp, StandardCharsets.UTF_8);
+ assertEquals(_mockResponse.trim(), tresp.trim());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMockTDBRequest()
+ {
+
+ setMock();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Model Id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_url"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("provider"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_category"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("qmean_avg_local_score"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_start"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_end"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+ System.out.println("wantedFields >>" + wantedFields);
+
+ FTSRestRequest request = new FTSRestRequest();
+ FTSRestResponse response;
+
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("");
+ request.setWantedFields(wantedFields);
+ // check 404 behaviour
+ request.setSearchTerm("P00000.json");
+
+ try
+ {
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
+
+ assertNull(response);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
+ }
+
+ // check 200 behaviour
+ request.setSearchTerm("P38398.json");
+ System.out.println("request : " + request.getFieldToSearchBy());
+ // System.out.println(request.toString());
+
+ try
+ {
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Couldn't execute webservice call!");
+ return;
+ }
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
+ System.out.println("Search summary : \n" + response.getSearchSummary());
+
+ // System.out.println(response.getSearchSummary().size());
+ }
+
@Test(groups = { "External", "Network" })
-
public void executeRequestTest()
{
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
try
{
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
- .getDataColumnByNameOrCode("uniprot_entry"));
+ .getDataColumnByNameOrCode("Model Id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_url"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("provider"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_category"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("confidence_avg_local_score"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_start"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_end"));
} catch (Exception e1)
{
e1.printStackTrace();
}
- System.out.println(wantedFields);
+ System.out.println("wantedFields >>" + wantedFields);
FTSRestRequest request = new FTSRestRequest();
- //request.setAllowEmptySeq(false);
- //request.setResponseSize(100);
- request.setSearchTerm("01308.json");
- //request.setWantedFields(wantedFields);
- System.out.println(request.toString());
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("");
+ request.setSearchTerm("P01318.json");
+ request.setWantedFields(wantedFields);
+ System.out.println("request : " + request.getFieldToSearchBy());
+ // System.out.println(request.toString());
FTSRestResponse response;
try
{
- response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
} catch (Exception e)
{
e.printStackTrace();
Assert.fail("Couldn't execute webservice call!");
return;
}
- //assertTrue(response.getNumberOfItemsFound() > 99);
assertTrue(response.getSearchSummary() != null);
- assertTrue(response.getSearchSummary().size() > 99);
+ assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
+ System.out.println("Search summary : \n" + response.getSearchSummary());
+ // System.out.println(response.getSearchSummary().size());
}
-
}
git://source.jalview.org / jalview.git / blobdiff