From: Ben Soares Date: Wed, 5 Apr 2023 15:29:31 +0000 (+0100) Subject: JAL-629 Tests for FileUtils. Tidying counter substitutions. Fixing PAE opening. X-Git-Tag: Release_2_11_4_0~404 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=58827f5ad6ff27d76c20c1aba96cd3b4a200a691;p=jalview.git JAL-629 Tests for FileUtils. Tidying counter substitutions. Fixing PAE opening. --- diff --git a/examples/test_fab41.result/argfile.txt b/examples/test_fab41.result/argfile.txt index ed450dd..a3540cf 100644 --- a/examples/test_fab41.result/argfile.txt +++ b/examples/test_fab41.result/argfile.txt @@ -1,14 +1,16 @@ +--nonews +--nosplash --substitutions --open={argfiledirname}/sample.a2m --colour=gecos:flower ---structure={argfiledirname}/test_fab41_unrelaxed_rank_1_model_3.pdb ---paematrix=[label=pAE R1-M3]{argfiledirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json ---structure={argfiledirname}/test_fab41_unrelaxed_rank_2_model_4.pdb ---paematrix=[label=pAE R2-M4]{argfiledirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json ---structure={argfiledirname}/test_fab41_unrelaxed_rank_3_model_2.pdb ---paematrix=[label=pAE R3-M2]{argfiledirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json ---structure={argfiledirname}/test_fab41_unrelaxed_rank_4_model_5.pdb ---paematrix=[label=pAE R4-M5]{argfiledirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json ---structure={argfiledirname}/test_fab41_unrelaxed_rank_5_model_1.pdb ---paematrix=[label=pAE R5-M1]{argfiledirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json +--structure={dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb +--paematrix="[label=PAE R1-M3]{dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json" +--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb +--paematrix="[label=PAE R2-M4]{dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json" +--structure={dirname}/test_fab41_unrelaxed_rank_3_model_2.pdb +--paematrix="[label=PAE R3-M2]{dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json" +--structure={dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb +--paematrix="[label=PAE R4-M5]{dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json" +--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb +--paematrix="[label=PAE R5-M1]{dirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json" --image={dirname}/{basename}.html diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index e4be614..9ff95e3 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -403,6 +403,14 @@ public class Commands SequenceI seq = getSpecifiedSequence(af, subId); if (seq == null) { + // Could not find sequence from subId, let's assume the first + // sequence in the alignframe + AlignmentI al = af.getCurrentView().getAlignment(); + seq = al.getSequenceAt(0); + } + + if (seq == null) + { Console.warn("Could not find sequence for argument " + Arg.STRUCTURE.argString() + "=" + val); // you probably want to continue here, not break @@ -417,7 +425,6 @@ public class Commands Console.debug("Using structure file (from argument) '" + structureFile.getAbsolutePath() + "'"); } - // TRY THIS /* * PDBEntry fileEntry = new AssociatePdbFileWithSeq() @@ -428,7 +435,6 @@ public class Commands * SequenceI[] { selectedSequence }); * */ - /* THIS DOESN'T WORK */ else if (seq.getAllPDBEntries() != null && seq.getAllPDBEntries().size() > 0) @@ -479,7 +485,7 @@ public class Commands } } - // load a pAE file if given + // load a PAE file if given if (avm.containsArg(Arg.PAEMATRIX)) { AlignFrame af = afMap.get(id); @@ -503,7 +509,7 @@ public class Commands } String structid = null; String structfile = null; - String seqid = null; + int seqindex = SubVals.NOTSET; if (subVals.notSet()) { ArgValue likelyStructure = avm @@ -518,6 +524,9 @@ public class Commands else { structfile = likelyStructure.getValue(); + Console.debug( + "##### Using closest previous structure argument '" + + structfile + "'"); } } } @@ -532,27 +541,26 @@ public class Commands if (structfile != null) { Console.info("##### Attaching paeFile '" + paePath + "' to " - + "structfile=" + subVals.get("structfile")); + + "structfile=" + structfile); EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), subVals.get("structfile"), - true, false, paeLabel); + paeFile, seqindex, structfile, true, false, paeLabel); } else if (structid != null) { Console.info("##### Attaching paeFile '" + paePath + "' to " - + "structid=" + subVals.get("structid")); + + "structid=" + structid); EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), subVals.get("structid"), - true, true, paeLabel); + paeFile, seqindex, subVals.get("structid"), true, true, + paeLabel); } else { + seqindex = subVals.getIndex(); Console.debug("##### Attaching paeFile '" + paePath - + "' to sequence index " + subVals.getIndex()); + + "' to sequence index " + seqindex); EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), null, false, false, - paeLabel); - // required to readjust the height and position of the pAE + paeFile, seqindex, null, false, false, paeLabel); + // required to readjust the height and position of the PAE // annotation } for (AlignmentViewPanel ap : af.getAlignPanels()) @@ -646,15 +654,17 @@ public class Commands private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId) { + if (subId == null) + return null; AlignmentI al = af.getCurrentView().getAlignment(); - if (-1 < subId.getIndex() - && subId.getIndex() < al.getSequences().size()) + if (subId.has("seqid")) { - return al.getSequenceAt(subId.getIndex()); + return al.findName(subId.get("seqid")); } - else if (subId.has("seqid")) + else if (-1 < subId.getIndex() + && subId.getIndex() < al.getSequences().size()) { - return al.findName(subId.get("seqid")); + return al.getSequenceAt(subId.getIndex()); } return null; } diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java index ff238da..f3306d6 100644 --- a/src/jalview/bin/argparser/ArgParser.java +++ b/src/jalview/bin/argparser/ArgParser.java @@ -50,18 +50,24 @@ public class ArgParser // the counter added to the default linked id prefix private int defaultLinkedIdCounter = 0; - // the linked id prefix used for --opennew files - protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:"; + // the substitution string used to use the defaultLinkedIdCounter + private static final String DEFAULTLINKEDIDCOUNTER = "{}"; // the counter added to the default linked id prefix private int opennewLinkedIdCounter = 0; + // the linked id prefix used for --opennew files + protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:"; + + // the counter used for {n} substitutions + private int linkedIdAutoCounter = 0; + // the linked id substitution string used to increment the idCounter (and use // the incremented value) - private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}"; + private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}"; // the linked id substitution string used to use the idCounter - private static final String AUTOCOUNTERLINKEDID = "{n}"; + private static final String LINKEDIDAUTOCOUNTER = "{n}"; // the linked id substitution string used to use the base filename of --open // or --opennew @@ -82,8 +88,6 @@ public class ArgParser // --argfile name private static final String ARGFILEDIRNAME = "{argfiledirname}"; - private int linkedIdAutoCounter = 0; - // flag to say whether {n} subtitutions in output filenames should be made. // Turn on and off with --subs and --nosubs private boolean substitutions = false; @@ -369,21 +373,21 @@ public class ArgParser + arg); } } - else if (linkedId.contains(AUTOCOUNTERLINKEDID)) + else if (linkedId.contains(LINKEDIDAUTOCOUNTER)) { // turn {n} to the autoCounter autoCounterString = Integer.toString(linkedIdAutoCounter); - linkedId = linkedId.replace(AUTOCOUNTERLINKEDID, + linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER, autoCounterString); usingAutoCounterLinkedId = true; Console.debug( "Changing linkedId to '" + linkedId + "' from " + arg); } - else if (linkedId.contains(INCREMENTAUTOCOUNTERLINKEDID)) + else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER)) { // turn {++n} to the incremented autoCounter autoCounterString = Integer.toString(++linkedIdAutoCounter); - linkedId = linkedId.replace(INCREMENTAUTOCOUNTERLINKEDID, + linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER, autoCounterString); usingAutoCounterLinkedId = true; Console.debug( @@ -494,14 +498,15 @@ public class ArgParser subvals = ""; rest = val; } - if (rest.contains(AUTOCOUNTERLINKEDID)) - rest = rest.replace(AUTOCOUNTERLINKEDID, + if (rest.contains(LINKEDIDAUTOCOUNTER)) + rest = rest.replace(LINKEDIDAUTOCOUNTER, String.valueOf(linkedIdAutoCounter)); - if (rest.contains(INCREMENTAUTOCOUNTERLINKEDID)) - rest = rest.replace(INCREMENTAUTOCOUNTERLINKEDID, + if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER)) + rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER, String.valueOf(++linkedIdAutoCounter)); - if (rest.contains("{}")) - rest = rest.replace("{}", String.valueOf(defaultLinkedIdCounter)); + if (rest.contains(DEFAULTLINKEDIDCOUNTER)) + rest = rest.replace(DEFAULTLINKEDIDCOUNTER, + String.valueOf(defaultLinkedIdCounter)); ArgValuesMap avm = linkedArgs.get(linkedId); if (avm != null) { diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java index dd20ca6..3c7ba7c 100644 --- a/src/jalview/bin/argparser/SubVals.java +++ b/src/jalview/bin/argparser/SubVals.java @@ -15,7 +15,7 @@ import jalview.bin.Console; */ public class SubVals { - private static int NOTSET = -1; + public static int NOTSET = -1; private int index = NOTSET; diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 30c5e4e..cb4ac49 100644 --- a/test/jalview/bin/CommandsTest.java +++ b/test/jalview/bin/CommandsTest.java @@ -19,7 +19,7 @@ import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.util.ArrayUtils; -@Test(singleThreaded = true) +@Test public class CommandsTest { private static final String testfiles = "test/jalview/bin/argparser/testfiles"; diff --git a/test/jalview/util/FileUtilsTest.java b/test/jalview/util/FileUtilsTest.java new file mode 100644 index 0000000..8b52577 --- /dev/null +++ b/test/jalview/util/FileUtilsTest.java @@ -0,0 +1,104 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.util; + +import java.io.File; +import java.util.List; + +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +@Test +public class FileUtilsTest +{ + @Test(groups = "Functional", dataProvider = "patternsAndMinNumFiles") + public void testJavaFileGlob(String pattern, int atLeast, int atMost) + { + List files = FileUtils.getFilesFromGlob(pattern); + if (atLeast != -1) + { + Assert.assertTrue(files.size() > atLeast, + "Did not find more than " + atLeast + " files with " + pattern + + " (found " + files.size() + ")"); + } + if (atLeast != -1) + { + Assert.assertTrue(files.size() > atLeast, + "Did not find more than " + atLeast + " files with " + pattern + + " (found " + files.size() + ")"); + } + if (atMost != -1) + { + Assert.assertTrue(files.size() < atMost, + "Did not find fewer than " + atMost + " files with " + pattern + + " (found " + files.size() + ")"); + } + } + + @Test(groups = "Functional", dataProvider = "dirnamesAndBasenames") + public void testDirnamesAndBasenames(String filename, int where, + String dirname, String basename) + { + File file = new File(filename); + String d = FileUtils.getDirname(file); + String b = FileUtils.getBasename(file); + Assert.assertEquals(b, basename); + if (where == 0) + Assert.assertEquals(d, dirname); + else if (where < 0) + Assert.assertTrue(d.startsWith(dirname), + "getDirname(" + file.getPath() + ")=" + d + + " didn't start with '" + d + "'"); + else if (where > 0) + Assert.assertTrue(d.endsWith(dirname), "getDirname(" + file.getPath() + + ")=" + d + " didn't end with '" + d + "'"); + } + + @DataProvider(name = "patternsAndMinNumFiles") + public Object[][] patternsAndMinNumFiles() + { + return new Object[][] { { "src/**/*.java", 900, 100000 }, + { "src/**.java", 900, 100000 }, + { "test/**/*.java", 250, 2500 }, + { "test/**.java", 250, 2500 }, + { "help/**/*.html", 100, 1000 }, + { "test/**/F*.java", 15, 150 }, + { "test/jalview/*/F*.java", 10, 15 }, // 12 at time of writing + { "test/jalview/**/F*.java", 18, 30 }, // 20 at time of writing + { "test/jalview/util/F**.java", 1, 5 }, // 2 at time of writing + { "src/jalview/b*/*.java", 14, 19 }, // 15 at time of writing + { "src/jalview/b**/*.java", 20, 25 }, // 22 at time of writing + }; + } + + @DataProvider(name = "dirnamesAndBasenames") + public Object[][] dirnamesAndBasenames() + { + return new Object[][] { // -1=startsWith, 0=equals, 1=endsWith + { "~/hello/sailor", -1, System.getProperty("user.home"), "sailor" }, // + { "~/hello/sailor", 1, "/hello", "sailor" }, // + { "./examples/uniref50.fa", -1, "/", "uniref50" }, // + { "./examples/uniref50.fa", 1, "/examples", "uniref50" }, // + { "examples/uniref50.fa", 1, "/examples", "uniref50" }, // + }; + } +}