From 16b58dcceb63ffaf4a264f2f3d8bf8a406e8cb96 Mon Sep 17 00:00:00 2001 From: James Procter Date: Mon, 23 Oct 2023 18:29:33 +0100 Subject: [PATCH] JAL-4311 failing test case for 3d-beacons epas1_human including levyLab alphaFold2 pLDDT scored result --- .../fts/service/threedbeacons/TDB_FTSData.java | 9 + .../ThreeDBStructureChooserQuerySource.java | 2 +- .../fts/service/pdb/PDBFTSRestClientTest.java | 5 + .../threedbeacons/TDBeaconsFTSRestClientTest.java | 12 +- .../fts/threedbeacons/q99814_tdb_fts_query.txt | 1 + .../threedbeacons/q99814_tdb_fts_query_resp.txt | 1 + .../threedbeacons/q99814_tdb_pdbfts_query_resp.txt | 354 ++++++++++++++++++++ .../StructureChooserQuerySourceTest.java | 58 +++- 8 files changed, 437 insertions(+), 5 deletions(-) create mode 100644 test/jalview/fts/threedbeacons/q99814_tdb_fts_query.txt create mode 100644 test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt create mode 100644 test/jalview/fts/threedbeacons/q99814_tdb_pdbfts_query_resp.txt diff --git a/src/jalview/fts/service/threedbeacons/TDB_FTSData.java b/src/jalview/fts/service/threedbeacons/TDB_FTSData.java index 3045d3d..4e1b2b0 100644 --- a/src/jalview/fts/service/threedbeacons/TDB_FTSData.java +++ b/src/jalview/fts/service/threedbeacons/TDB_FTSData.java @@ -154,5 +154,14 @@ public class TDB_FTSData implements FTSData { return (String) getField(Model_id); } + + public String getConfidenceScoreType() + { + return (String) getField(Confidence_Score_Type); + } + public String getConfidenceScoreVersion() + { + return (String) getField(Confidence_Score_Version); + } } diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java index e32ba50..76ef85f 100644 --- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java +++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java @@ -310,7 +310,7 @@ public class ThreeDBStructureChooserQuerySource && tdBeaconsFilters.contains(fieldToFilterBy); } - private String remove_prefix(String fieldToFilterBy) + protected String remove_prefix(String fieldToFilterBy) { if (tdBeaconsFilters != null && tdBeaconsFilters.contains(fieldToFilterBy) diff --git a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java index 3839065..00e7b21 100644 --- a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java +++ b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java @@ -824,6 +824,11 @@ public class PDBFTSRestClientTest + " \"resolution\":2.2,\n" + " \"title\":\"Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal\"}]\n" + " }}" }); + mocks.add(new String[] { + "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4gs9+OR+6bvb+OR+8ck8+OR+8ck3+OR+6x3d+OR+8ck4+OR+6x28+OR+6i7r+OR+3h82+OR+6i7q+OR+6x21+OR+4xt2+OR+5kiz+OR+7q5v+OR+6x2h+OR+7q5x+OR+3f1n+OR+3f1o+OR+2a24+OR+3f1p+OR+1p97+OR+4ghi+OR+3h7w+OR+6d09+OR+6czw+OR+7ujv+OR+5tbm+OR+5ufp+OR+4pky+OR+6d0b+OR+6d0c+OR+6x37)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=" + , + readJsonStringFromFile( + "test/jalview/fts/threedbeacons/q99814_tdb_pdbfts_query_resp.txt")}); } catch (Throwable e) { Assert.fail("Couldn't read mock data.", e); diff --git a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java index c37058a..40e29d3 100644 --- a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java +++ b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java @@ -39,14 +39,20 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import jalview.datamodel.Sequence; +import jalview.fts.api.FTSData; 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.TDB_FTSData; import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient; import jalview.gui.JvOptionPane; +import jalview.gui.structurechooser.PDBStructureChooserQuerySource; +import jalview.gui.structurechooser.TDBResultAnalyser; +import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; public class TDBeaconsFTSRestClientTest { @@ -301,7 +307,8 @@ public class TDBeaconsFTSRestClientTest private static String[][] mocks = { { "P38398.json", null }, { "P01308.json", null }, { "P0DTD1.json", null }, - { "P27787.json", null } + { "P27787.json", null }, + { "Q99814.json", null } // , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body }; @@ -321,6 +328,8 @@ public class TDBeaconsFTSRestClientTest mocks[3][1] = PDBFTSRestClientTest.readJsonStringFromFile( "test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt"); + mocks[4][1] = PDBFTSRestClientTest.readJsonStringFromFile( + "test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt"); } catch (IOException e) { @@ -491,4 +500,5 @@ public class TDBeaconsFTSRestClientTest System.out.println("Search summary : \n" + response.getSearchSummary()); // System.out.println(response.getSearchSummary().size()); } + } diff --git a/test/jalview/fts/threedbeacons/q99814_tdb_fts_query.txt b/test/jalview/fts/threedbeacons/q99814_tdb_fts_query.txt new file mode 100644 index 0000000..774b719 --- /dev/null +++ b/test/jalview/fts/threedbeacons/q99814_tdb_fts_query.txt @@ -0,0 +1 @@ +https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/Q99814.json diff --git a/test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt b/test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt new file mode 100644 index 0000000..17ef5e2 --- /dev/null +++ b/test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt @@ -0,0 +1 @@ +{"uniprot_entry":{"ac":"Q99814","id":"EPAS1_HUMAN","uniprot_checksum":"4838989598234FC1","sequence_length":870,"segment_start":8,"segment_end":359},"structures":[{"summary":{"model_identifier":"3f1p","model_category":"EXPERIMENTALLY 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diffraction"], + "pdb_id":"6i7q", + "resolution":1.798, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7r", + "resolution":1.949, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"7ujv", + "resolution":1.8, + "title":"Structure of PHD2 in complex with HIF2a-CODD"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"7q5v", + "resolution":1.17, + "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"7q5x", + "resolution":1.21, + "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"7q5v", + "resolution":1.17, + "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6bvb", + "resolution":2.002, + "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"7q5x", + "resolution":1.21, + "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7r", + "resolution":1.949, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7q", + "resolution":1.798, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6bvb", + "resolution":2.002, + "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7r", + "resolution":1.949, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7q", + "resolution":1.798, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6bvb", + "resolution":2.002, + "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7q", + "resolution":1.798, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"}, + { + "experimental_method":["X-ray diffraction"], + "pdb_id":"6i7r", + "resolution":1.949, + "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"}] + }} diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java index c21add1..4579b9c 100644 --- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java +++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java @@ -22,7 +22,9 @@ package jalview.gui.structurechooser; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; +import static org.testng.Assert.fail; +import java.util.ArrayList; import java.util.List; import java.util.Vector; @@ -39,8 +41,13 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClientTest; +import jalview.fts.service.threedbeacons.TDB_FTSData; +import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient; import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest; import jalview.gui.JvOptionPane; import jalview.gui.StructureChooser; @@ -60,6 +67,8 @@ public class StructureChooserQuerySourceTest private Sequence upSeq_fer1_maize; + private Sequence upSeq_epas1_human; + // same set up as for structurechooser test @BeforeMethod(alwaysRun = true) @@ -237,7 +246,24 @@ public class StructureChooserQuerySourceTest upSeq_fer1_maize .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true)); upSeq_fer1_maize.createDatasetSequence(); - + + upSeq_epas1_human = new Sequence("EPAS1_HUMAN","MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n" + + "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n" + + "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n" + + "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n" + + "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n" + + "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n" + + "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n" + + "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n" + + "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n" + + "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n" + + "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n" + + "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n" + + "ALDQAT"); + upSeq_epas1_human.setDescription("Endothelial PAS domain-containing protein 1"); + upSeq_epas1_human + .addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true)); + upSeq_epas1_human.createDatasetSequence(); } @AfterMethod(alwaysRun = true) @@ -247,6 +273,7 @@ public class StructureChooserQuerySourceTest upSeq = null; upSeq_r1ab = null; upSeq_fer1_maize = null; + upSeq_epas1_human=null; } @SuppressWarnings("deprecation") @@ -438,6 +465,31 @@ public class StructureChooserQuerySourceTest pdbResponse); assertEquals(upResponse.getNumberOfItemsFound(), joinedResp.getNumberOfItemsFound()); + + // Special data test case + if (testUpSeq.getDisplayId(true) + .equals(upSeq_epas1_human.getDisplayId(true))) + { + + TDBResultAnalyser tDBResultAnalyz = new TDBResultAnalyser(testUpSeq, + joinedResp.getSearchSummary(), tdbquery.lastTdbRequest, + ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE, + tdbquery.remove_prefix( + ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE)); + List ordered = tDBResultAnalyz.getFilteredResponse(); + List selected = tDBResultAnalyz.selectStructures(ordered); + assertEquals(((TDB_FTSData) selected.get(0)).getProvider(), + "AlphaFold DB"); + // to be sufficient, should also + // test that adjacent ordered structure in ordered is levyLab + // TDB_FTSData first = (TDB_FTSData) ordered.get(0), + // second = (TDB_FTSData) ordered.get(1), + // third = (TDB_FTSData) ordered.get(2); + // Assert.assertEquals("pLDDT", first.getConfidenceScoreType()); + // Assert.assertTrue(first.getConfidenceScoreType() + // .equals(second.getConfidenceScoreType())); // pLDDT first and + // // second + } } catch ( @@ -458,7 +510,7 @@ public class StructureChooserQuerySourceTest { setUp(); return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab }, - { upSeq_fer1_maize } }; + { upSeq_fer1_maize },{upSeq_epas1_human} }; } @Test(groups = { "Functional" }) @@ -481,5 +533,5 @@ public class StructureChooserQuerySourceTest name = "abcde12[345a]fg"; AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name)); - } + } } -- 1.7.10.2