package jalview.fts.threedbeacons;
+import static org.testng.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+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.threedbeacons.TDBeaconsFTSRestClient;
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(),
+ 13);
+ }
+
+ @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");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getAllFTSDataColumns()
+ {
+ Collection<FTSDataColumnI> allFields = ftsRestClient
+ .getAllFTSDataColumns();
+ Assert.assertNotNull(allFields);
+ // System.out.println(allFields.size());
+ Assert.assertEquals(allFields.size(), 19);
+ }
+
+ @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 mockRequest = "P38398.json";
+
+ private static String mockResponse = "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0h\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0k\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1n5o\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxc\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxd\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2u\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k15\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxe\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"613a3ff37621f8e40b0713bb\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-09\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"613a3ff37621f8e40b0713bf\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-09\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}";
+
+ public static void setMock()
+ {
+ FTSRestClient.createMockFTSRestClient(
+ (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
+ mockRequest, mockResponse);
+ }
+
+ private static String dev_url = "https://wwwdev.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
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Network", "Integration" })
+ public void verifyMockTDBRequest() throws Exception
+ {
+ URL tdb_req = new URL(dev_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