+/*
+ * 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 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;
.isEmpty());
Assert.assertEquals(
ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
- 13);
+ 15);
}
@Test(groups = { "Functional" })
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");
+ "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" })
.getAllFTSDataColumns();
Assert.assertNotNull(allFields);
// System.out.println(allFields.size());
- Assert.assertEquals(allFields.size(), 19);
+ Assert.assertEquals(allFields.size(), 20);
}
@Test(groups = { "Functional" })
}
}
- private static String[][] mocks = { { "P38398.json",
- "{\"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\":\"614057b7a2b5cc6a7fcb50bd\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-14\",\"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\":\"614057b7a2b5cc6a7fcb50c1\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-14\",\"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\"}]}" },
- { "P01308.json",
-"{\"uniprot_entry\":{\"sequence_length\":110,\"ac\":\"P01308\",\"id\":\"INS_HUMAN\"},\"structures\":[{\"model_identifier\":\"3w7y\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-11\",\"sequence_identity\":100.0,\"uniprot_start\":25,\"uniprot_end\":54,\"resolution\":0.92,\"coverage\":34.88,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3w7y_updated.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3w7y\"},{\"model_identifier\":\"3w7y\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-11\",\"sequence_identity\":100.0,\"uniprot_start\":90,\"uniprot_end\":110,\"resolution\":0.92,\"coverage\":24.42,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3w7y_updated.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3w7y\"},{\"model_identifier\":\"5e7w\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-10-13\",\"sequence_identity\":100.0,\"uniprot_start\":25,\"uniprot_end\":54,\"resolution\":0.9519,\"coverage\":34.88,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/5e7w_updated.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/5e7w\"},{\"model_identifier\":\"5e7w\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-10-13\",\"sequence_identity\":100.0,\"uniprot_start\":90,\"uniprot_end\":110,\"resolution\":0.9519,\"coverage\":24.42,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/5e7w_updated.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/5e7w\"},{\"model_identifier\":\"5hqi\",\"model_category\":\"EXPERIMENTALLY 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ENSEMBLE\",\"provider\":\"PED\",\"created\":\"2020-10-01\",\"uniprot_start\":90,\"uniprot_end\":110,\"model_url\":\"https://proteinensemble.org/api/ensemble/PED00095e000\",\"model_format\":\"PDB\",\"model_page_url\":\"https://proteinensemble.org/PED00095\",\"number_of_conformers\":25,\"ensemble_sample_url\":\"https://proteinensemble.org/api/ensemble_sample/PED00095e000\",\"ensemble_sample_format\":\"MMCIF\"},{\"model_identifier\":\"PED00101e000\",\"model_category\":\"CONFORMATIONAL ENSEMBLE\",\"provider\":\"PED\",\"created\":\"2020-10-01\",\"uniprot_start\":26,\"uniprot_end\":53,\"model_url\":\"https://proteinensemble.org/api/ensemble/PED00101e000\",\"model_format\":\"PDB\",\"model_page_url\":\"https://proteinensemble.org/PED00101\",\"number_of_conformers\":25,\"ensemble_sample_url\":\"https://proteinensemble.org/api/ensemble_sample/PED00101e000\",\"ensemble_sample_format\":\"MMCIF\"},{\"model_identifier\":\"PED00103e000\",\"model_category\":\"CONFORMATIONAL ENSEMBLE\",\"provider\":\"PED\",\"created\":\"2020-10-01\",\"uniprot_start\":25,\"uniprot_end\":54,\"model_url\":\"https://proteinensemble.org/api/ensemble/PED00103e000\",\"model_format\":\"PDB\",\"model_page_url\":\"https://proteinensemble.org/PED00103\",\"number_of_conformers\":30,\"ensemble_sample_url\":\"https://proteinensemble.org/api/ensemble_sample/PED00103e000\",\"ensemble_sample_format\":\"MMCIF\"},{\"model_identifier\":\"PED00102e000\",\"model_category\":\"CONFORMATIONAL ENSEMBLE\",\"provider\":\"PED\",\"created\":\"2020-10-01\",\"uniprot_start\":25,\"uniprot_end\":54,\"model_url\":\"https://proteinensemble.org/api/ensemble/PED00102e000\",\"model_format\":\"PDB\",\"model_page_url\":\"https://proteinensemble.org/PED00102\",\"number_of_conformers\":40,\"ensemble_sample_url\":\"https://proteinensemble.org/api/ensemble_sample/PED00102e000\",\"ensemble_sample_format\":\"MMCIF\"},{\"model_identifier\":\"61401d20ccef3f8332871ea3\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-14\",\"sequence_identity\":1.0,\"uniprot_start\":25,\"uniprot_end\":110,\"coverage\":0.782,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.526,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P01308.pdb?range=25-110&template=2lwz.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P01308-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":110,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P01308-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P01308\"},{\"model_identifier\":\"2400\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2018-11-11\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE25_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE25\"},{\"model_identifier\":\"2396\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2018-11-11\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE25_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE25\"},{\"model_identifier\":\"2452\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEV5\"},{\"model_identifier\":\"2453\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEV5\"},{\"model_identifier\":\"2456\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEW5\"},{\"model_identifier\":\"2457\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEW5\"},{\"model_identifier\":\"2459\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEX5\"},{\"model_identifier\":\"2460\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEX5\"},{\"model_identifier\":\"2462\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEY5\"},{\"model_identifier\":\"2463\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEY5\"},{\"model_identifier\":\"2465\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEZ5\"},{\"model_identifier\":\"2467\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEZ5\"},{\"model_identifier\":\"2469\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE26_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE26\"},{\"model_identifier\":\"2470\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE26_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE26\"},{\"model_identifier\":\"4420\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJY3\"},{\"model_identifier\":\"4421\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model2.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJY3\"},{\"model_identifier\":\"4422\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJZ3\"},{\"model_identifier\":\"4423\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model2.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJZ3\"}]}" } };
+ private static String[][] mocks = { { "P38398.json", null },
+ { "P01308.json", null },
+ { "P0DTD1.json", null },
+ { "P27787.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");
+
+ mocks[3][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p27787_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);
+ (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
{
- for (String[] otherMock:mocks)
+ setMockData();
+ for (String[] otherMock : mocks)
{
- verifyMockTDBRequest(otherMock[0],otherMock[1]);
+ verifyMockTDBRequest(otherMock[0], otherMock[1]);
}
}
- private void verifyMockTDBRequest(String mockRequest, String _mockResponse) throws Exception
+
+ private void verifyMockTDBRequest(String mockRequest,
+ String _mockResponse) throws Exception
{
- URL tdb_req = new URL(dev_url + mockRequest);
+ URL tdb_req = new URL(prod_url + mockRequest);
byte[] resp = tdb_req.openStream().readAllBytes();
String tresp = new String(resp, StandardCharsets.UTF_8);
+ // this simple test fails for responses containing multi-chain structures -
+ // since chain order in the json elements is arbitrary and varies between
+ // queries.
assertEquals(_mockResponse.trim(), tresp.trim());
}