X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Ffts%2Fthreedbeacons%2FTDBeaconsFTSRestClientTest.java;h=00adf063795512be9b3ddd475855c1db2552e545;hb=8498532d3613b633e6a63e7cdbfecd9add16f43b;hp=b144aa56e57121b88af1a003e414aca46ccb98a9;hpb=a848ed8eb380e5f9d915b0d7a062feec4f9d3dad;p=jalview.git diff --git a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java index b144aa5..00adf06 100644 --- a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java +++ b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java @@ -1,8 +1,11 @@ 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; @@ -20,7 +23,6 @@ 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.PDBFTSRestClient; import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient; import jalview.gui.JvOptionPane; @@ -32,7 +34,7 @@ public class TDBeaconsFTSRestClientTest JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - + private FTSRestClient ftsRestClient; @BeforeMethod(alwaysRun = true) @@ -60,20 +62,22 @@ public class TDBeaconsFTSRestClientTest public void tearDown() throws Exception { } - + @Test public void getAllDefaulDisplayedDataColumns() { - Assert.assertNotNull(ftsRestClient - .getAllDefaultDisplayedFTSDataColumns()); - System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns()); + // 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(), 3); - // currently 3, may change -> change this test and the nexts accordingly + Assert.assertEquals( + ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(), + 13); } - + @Test(groups = { "Functional" }) public void getPrimaryKeyColumIndexTest() { @@ -85,56 +89,60 @@ public class TDBeaconsFTSRestClientTest Assert.assertEquals(foundIndex, -1); foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields, false); - Assert.assertEquals(foundIndex, 0); - foundIndex = ftsRestClient - .getPrimaryKeyColumIndex(wantedFields, true); - Assert.assertEquals(foundIndex, 1); + 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 wantedFields = ftsRestClient .getAllDefaultDisplayedFTSDataColumns(); String actual = ftsRestClient .getDataColumnsFieldsAsCommaDelimitedString(wantedFields); Assert.assertEquals(actual, - "id,uniprot_accession,entry name"); + "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 allFields = ftsRestClient .getAllFTSDataColumns(); Assert.assertNotNull(allFields); - //System.out.println(allFields.size()); - Assert.assertEquals(allFields.size(), 3); + // 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 searchableFields = ftsRestClient .getSearchableDataColumns(); Assert.assertNotNull(searchableFields); - //System.out.println(searchableFields.size()); - Assert.assertEquals(searchableFields.size(), 1); //only 1, as of first 3DB test + // 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("Uniprot Id"); + expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url"); Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn()); Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(), expectedPKColumn); @@ -144,7 +152,7 @@ public class TDBeaconsFTSRestClientTest Assert.fail("Exception thrown while testing..."); } } - + @Test(groups = { "Functional" }) public void getDataColumnByNameOrCode() { @@ -160,7 +168,7 @@ public class TDBeaconsFTSRestClientTest Assert.fail("Exception thrown while testing..."); } } - + @Test(groups = { "Functional" }) public void getDataColumnGroupById() { @@ -169,20 +177,21 @@ public class TDBeaconsFTSRestClientTest { foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2"); Assert.assertNotNull(foundDataColGroup); - Assert.assertEquals(foundDataColGroup.getName(), "Name"); + 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 + Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100, + // uniprot 500 } - + @Test(groups = { "Functional" }) public void getColumnMinWidthTest() { @@ -200,7 +209,7 @@ public class TDBeaconsFTSRestClientTest } } // could add test for MaxWidth & PreferedWith - + @Test(groups = { "Functional" }) public void getColumnClassTest() { @@ -221,7 +230,7 @@ public class TDBeaconsFTSRestClientTest Assert.fail("Exception thrown while testing..."); } } - + @Test(groups = { "Functional" }) public void coverageForEqualsAndHashFunction() { @@ -236,9 +245,9 @@ public class TDBeaconsFTSRestClientTest uniqueSet.add(foundCol); } Assert.assertTrue(!uniqueSet.isEmpty()); - //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB + // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB } - + @Test(groups = { "Functional" }) public void getTDBIdColumIndexTest() { @@ -250,38 +259,142 @@ public class TDBeaconsFTSRestClientTest wantedFields.add(TDBeaconsFTSRestClient.getInstance() .getDataColumnByNameOrCode("uniprot_accession")); wantedFields.add(TDBeaconsFTSRestClient.getInstance() - .getDataColumnByNameOrCode("entry name")); + .getDataColumnByNameOrCode("Title")); } catch (Exception e) { e.printStackTrace(); } try { - assertEquals(1, TDBeaconsFTSRestClient.getInstance() + assertEquals(4, TDBeaconsFTSRestClient.getInstance() .getPrimaryKeyColumIndex(wantedFields, true)); -// assertEquals(3, TDBeaconsFTSRestClient.getInstance() -// .getPrimaryKeyColumIndex(wantedFields, true)); + // assertEquals(3, TDBeaconsFTSRestClient.getInstance() + // .getPrimaryKeyColumIndex(wantedFields, true)); } catch (Exception e) { e.printStackTrace(); } } - - @Test(groups = { "External", "Network" }) - public void executeRequestTest() + 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 wantedFields = new ArrayList(); try { wantedFields.add(TDBeaconsFTSRestClient.getInstance() - .getDataColumnByNameOrCode("Model id")); + .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 wantedFields = new ArrayList(); + 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("confidence_avg_local_score")); + wantedFields.add(TDBeaconsFTSRestClient.getInstance() + .getDataColumnByNameOrCode("uniprot_start")); + wantedFields.add(TDBeaconsFTSRestClient.getInstance() + .getDataColumnByNameOrCode("uniprot_end")); } catch (Exception e1) { e1.printStackTrace(); @@ -290,16 +403,17 @@ public class TDBeaconsFTSRestClientTest FTSRestRequest request = new FTSRestRequest(); request.setResponseSize(100); - request.setFieldToSearchBy("P"); - request.setSearchTerm("01318.json"); + request.setFieldToSearchBy(""); + request.setSearchTerm("P01318.json"); request.setWantedFields(wantedFields); System.out.println("request : " + request.getFieldToSearchBy()); - //System.out.println(request.toString()); + // System.out.println(request.toString()); FTSRestResponse response; try { - response = TDBeaconsFTSRestClient.getInstance().executeRequest(request); + response = TDBeaconsFTSRestClient.getInstance() + .executeRequest(request); } catch (Exception e) { e.printStackTrace(); @@ -307,8 +421,8 @@ public class TDBeaconsFTSRestClientTest return; } assertTrue(response.getSearchSummary() != null); - assertTrue(response.getNumberOfItemsFound() > 3); //4 atm + assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm System.out.println("Search summary : \n" + response.getSearchSummary()); - //System.out.println(response.getSearchSummary().size()); + // System.out.println(response.getSearchSummary().size()); } }