import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
theseArgsWereParsed &= processLinked(id);
+ processGroovyScript(id);
boolean processLinkedOkay = theseArgsWereParsed;
theseArgsWereParsed &= processImages(id);
if (processLinkedOkay)
}
}
- if (argParser.getBool(Arg.QUIT))
+ if (argParser.getBoolean(Arg.QUIT))
{
Jalview.getInstance().quit();
return true;
if (af == null || "true".equals(av.getSubVal("new"))
|| a == Arg.OPEN || format == FileFormat.Jalview)
{
- /*
- * this approach isn't working yet // get default annotations before opening
- * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
- * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
- * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
- * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
- * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
- * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
- * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
- * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
- * StructureSelectionManager ssm = StructureSelectionManager
- * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
- * ssm.setAddTempFacAnnot(showTemperatureFactor);
- * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
- */
+ if (a == Arg.OPEN)
+ {
+ Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+ openFile);
+ }
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
- boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.ANNOTATIONS, av.getSubVals(), null,
- "SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
null, "WRAP_ALIGNMENT", false);
af.getCurrentView().setWrapAlignment(wrap);
- // colour aligment?
+ // colour alignment?
String colour = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
-
if ("" != colour)
{
af.changeColour_actionPerformed(colour);
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
- // change alignment frame title
+ // Change alignment frame title
String title = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.TITLE, sv, null, null, null);
if (title != null)
+ {
af.setTitle(title);
+ Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
+ }
+
+ // Add features
+ String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FEATURES, sv);
+ if (featuresfile != null)
+ {
+ af.parseFeaturesFile(featuresfile,
+ AppletFormatAdapter.checkProtocol(featuresfile));
+ Jalview.testoutput(argParser, Arg.FEATURES,
+ "examples/testdata/plantfdx.features", featuresfile);
+ }
- // show secondary structure annotations?
+ // Add annotations from file
+ String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
+ av, Arg.ANNOTATIONS, sv);
+ if (annotationsfile != null)
+ {
+ af.loadJalviewDataFile(annotationsfile, null, null, null);
+ Jalview.testoutput(argParser, Arg.ANNOTATIONS,
+ "examples/testdata/plantfdx.annotations",
+ annotationsfile);
+ }
+
+ // Set or clear the sortbytree flag
+ boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
+ Arg.SORTBYTREE, sv);
+ if (sortbytree)
+ {
+ af.getViewport().setSortByTree(true);
+ Jalview.testoutput(argParser, Arg.SORTBYTREE);
+ }
+
+ // Load tree from file
+ String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TREE, sv);
+ if (treefile != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(treefile,
+ AppletFormatAdapter.checkProtocol(treefile));
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, treefile).getTree());
+ Jalview.testoutput(argParser, Arg.TREE,
+ "examples/testdata/uniref50_test_tree", treefile);
+ } catch (IOException e)
+ {
+ Console.warn("Couldn't add tree " + treefile, e);
+ }
+ }
+
+ // Show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
Arg.SSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
- if (avm.getBoolean(Arg.SSANNOTATIONS))
- {
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
- /*
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Secondary Structure"), null,
- false, false);
- */
- }
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+ // Show sequence annotations?
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
// show temperature factor annotations?
if (avm.getBoolean(Arg.NOTEMPFAC))
}
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
- Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
- "viewer", null, "jmol");
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
+ null, "jmol");
ViewerType viewerType = null;
if (!"none".equals(sViewer))
{
return theseArgsWereParsed;
}
+ protected void processGroovyScript(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return;
+ }
+
+ if (avm.containsArg(Arg.GROOVY))
+ {
+ String groovyscript = avm.getValue(Arg.GROOVY);
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ Console.info("Executing script " + groovyscript);
+ Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ }
+ }
+ }
+
protected boolean processImages(String id)
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.Arg.Opt;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.BootstrapArgs;
import jalview.ext.so.SequenceOntology;
{
System.out.println(
"CMD [-props " + usrPropsFile + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.PROPS,
+ "test/jalview/bin/testProps.jvprops", usrPropsFile);
}
// new ArgParser
{
argparser = ArgParser.parseArgFiles(
bootstrapArgs.getList(Arg.ARGFILE),
- bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
}
else
{
argparser = new ArgParser(args,
- bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
}
if (!Platform.isJS())
// allow https handshakes to download intermediate certs if necessary
System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
- final String jabawsUrl = aparser.getValue("jabaws");
+ String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+ if (jabawsUrl == null)
+ jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
try
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.JABAWS,
+ "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
} catch (MalformedURLException e)
{
System.err.println(
}
}
- boolean doWebServiceDiscovery = !aparser
- .contains("nowebservicediscovery");
- if (bootstrapArgs.contains(Arg.WEBSERVICEDISCOVERY))
- doWebServiceDiscovery = bootstrapArgs
- .getBoolean(Arg.WEBSERVICEDISCOVERY);
- if (doWebServiceDiscovery)
+ boolean webservicediscovery = bootstrapArgs
+ .getBoolean(Arg.WEBSERVICEDISCOVERY);
+ if (aparser.contains("nowebservicediscovery"))
+ webservicediscovery = false;
+ if (webservicediscovery)
{
desktop.startServiceDiscovery();
}
- if (!aparser.contains("nousagestats"))
+ else
+ {
+ testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
+ }
+
+ boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+ if (aparser.contains("nousagestats"))
+ usagestats = false;
+ if (usagestats)
{
startUsageStats(desktop);
+ testoutput(argparser, Arg.USAGESTATS);
}
else
{
- System.err.println("CMD [-nousagestats] executed successfully!");
+ System.out.println("CMD [-nousagestats] executed successfully!");
+ testoutput(argparser, Arg.USAGESTATS);
}
- if (!aparser.contains("noquestionnaire"))
+ boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+ if (aparser.contains("noquestionnaire"))
+ questionnaire = false;
+ if (questionnaire)
{
String url = aparser.getValue("questionnaire");
if (url != null)
}
else
{
- System.err
+ System.out
.println("CMD [-noquestionnaire] executed successfully!");
+ testoutput(argparser, Arg.QUESTIONNAIRE);
}
if ((!aparser.contains("nonews")
* the Jalview Desktop object passed in to the groovy binding as the
* 'Jalview' object.
*/
- private void executeGroovyScript(String groovyscript, AlignFrame af)
+ protected void executeGroovyScript(String groovyscript, AlignFrame af)
{
/**
* for scripts contained in files
if (exitcode > -1)
System.exit(exitcode);
}
+
+ /*
+ * testoutput for string values
+ */
+ protected static void testoutput(ArgParser ap, Arg a, String s1,
+ String s2)
+ {
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+ {
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
+ }
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(true, a, s1, s2);
+ }
+
+ protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+ String s2)
+ {
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+ {
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
+ }
+ if (!a.hasOption(Opt.BOOTSTRAP))
+ {
+ Console.error("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(true, a, s1, s2);
+ }
+
+ private static void testoutput(boolean yes, Arg a, String s1, String s2)
+ {
+ if (yes && ((s1 == null && s2 == null)
+ || (s1 != null && s1.equals(s2))))
+ {
+ System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ + "' was set");
+ }
+ }
+
+ /*
+ * testoutput for boolean values
+ */
+ protected static void testoutput(ArgParser ap, Arg a)
+ {
+ if (ap == null)
+ return;
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (bsa == null)
+ return;
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+ : ap.getBoolean(a);
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(val, a);
+ }
+
+ protected static void testoutput(BootstrapArgs bsa, Arg a)
+ {
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!a.hasOption(Opt.BOOTSTRAP))
+ {
+ Console.warn("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
+
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(bsa.getBoolean(a), a);
+ }
+
+ private static void testoutput(boolean yes, Arg a)
+ {
+ System.out.println("[TESTOUTPUT] arg "
+ + (yes ? a.argString() : a.negateArgString()) + " was set");
+ }
}
public enum Arg
{
- HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
- COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
- SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
- VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE, PAEMATRIX,
- WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, TYPE, FORMAT,
- OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE, QUIET("q"), ARGFILE,
- NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH,
- SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS;
-
- protected static enum Opt
+ HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, SHOWANNOTATIONS,
+ COLOUR("color"), FEATURES, ANNOTATIONS, GROOVY, GROUPS, HEADLESS, JABAWS,
+ DISPLAY, NEWS, SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE,
+ SETPROP, TREE, VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+ TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
+ TYPE, FORMAT, OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE,
+ QUIET("q"), ARGFILE, NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS,
+ NIL, SPLASH, SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS,
+ TESTOUTPUT;
+
+ public static enum Opt
{
BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or
// false. A default can be given with setOptions(bool, Opt....).
MENUBAR.setOptions(true, Opt.BOOLEAN);
STATUS.setOptions(true, Opt.BOOLEAN);
SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ SHOWANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
COLOUR.setOptions(Opt.STRING, Opt.LINKED);
FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
+ ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ TREE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
GROUPS.setOptions(Opt.STRING, Opt.LINKED);
HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
- JABAWS.setOptions(Opt.STRING);
+ TESTOUTPUT.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
+ JABAWS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
DISPLAY.setOptions(true, Opt.BOOLEAN);
- GUI.setOptions(true, Opt.BOOLEAN);
NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- // expects a string value
- SORTBYTREE.setOptions(true, Opt.BOOLEAN);
- USAGESTATS.setOptions(true, Opt.BOOLEAN);
+ SORTBYTREE.setOptions(true, Opt.LINKED, Opt.BOOLEAN);
+ QUESTIONNAIRE.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ USAGESTATS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ WEBSERVICEDISCOVERY.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
Opt.MULTI, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
- QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
- TREE.setOptions(Opt.STRING);
VDOC.setOptions(Opt.UNARY);
VSESS.setOptions(Opt.UNARY);
NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
- WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
}
private int argIndex = 0;
+ private BootstrapArgs bootstrapArgs = null;
+
static
{
argMap = new HashMap<>();
public ArgParser(String[] args)
{
- this(args, false);
+ this(args, false, null);
}
- public ArgParser(String[] args, boolean initsubstitutions)
+ public ArgParser(String[] args, boolean initsubstitutions,
+ BootstrapArgs bsa)
{
// Make a mutable new ArrayList so that shell globbing parser works.
// (When shell file globbing is used, there are a sequence of non-Arg
// consumed by the --append/--argfile/etc Arg which is most easily done by
// removing these filenames from the list one at a time. This can't be done
// with an ArrayList made with only Arrays.asList(String[] args). )
- this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
+ this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
+ bsa);
}
public ArgParser(List<String> args, boolean initsubstitutions)
{
- this(args, initsubstitutions, false);
+ this(args, initsubstitutions, false, null);
}
public ArgParser(List<String> args, boolean initsubstitutions,
- boolean allowPrivate)
+ boolean allowPrivate, BootstrapArgs bsa)
{
// do nothing if there are no "--" args and (some "-" args || >0 arg is
// "open")
parse(new ArrayList<String>(), false, false);
return;
}
+ if (bsa != null)
+ this.bootstrapArgs = bsa;
+ else
+ this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
parse(args, initsubstitutions, allowPrivate);
}
return vals;
}
+ public BootstrapArgs getBootstrapArgs()
+ {
+ return bootstrapArgs;
+ }
+
public boolean isSet(Arg a)
{
- return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
+ return a.hasOption(Opt.LINKED) ? isSetAtAll(a) : isSet(null, a);
+ }
+
+ public boolean isSetAtAll(Arg a)
+ {
+ for (String linkedId : linkedOrder)
+ {
+ if (isSet(linkedId, a))
+ return true;
+ }
+ return false;
}
public boolean isSet(String linkedId, Arg a)
return avm == null ? false : avm.containsArg(a);
}
- public boolean getBool(Arg a)
+ public boolean getBoolean(Arg a)
{
if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
{
}
public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<File> argFiles = new ArrayList<>();
argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
}
- return parseArgFileList(argFiles, initsubstitutions);
+ return parseArgFileList(argFiles, initsubstitutions, bsa);
}
public static ArgParser parseArgFileList(List<File> argFiles,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<String> argsList = new ArrayList<>();
for (File argFile : argFiles)
}
// Third param "true" uses Opt.PRIVATE args --setargile=argfile and
// --unsetargfile
- return new ArgParser(argsList, initsubstitutions, true);
+ return new ArgParser(argsList, initsubstitutions, true, bsa);
}
protected static List<String> readArgFile(File argFile)
return new BootstrapArgs(argList);
}
+ public static BootstrapArgs getBootstrapArgs(List<String> args)
+ {
+ return new BootstrapArgs(args);
+ }
+
private BootstrapArgs(List<String> args)
{
parse(args, null);
public enum FileFormat implements FileFormatI
{
- Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
+ Fasta("Fasta", "fa,fasta,mfa,fastq", true, true)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
return new PIRFile();
}
},
- BLC("BLC", "BLC", true, true)
+ BLC("BLC", "blc", true, true)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
return new PhylipFile();
}
},
- GenBank("GenBank Flatfile", "gb, gbk", true, false)
+ GenBank("GenBank Flatfile", "gb,gbk", true, false)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
return true;
}
},
- Jalview("Jalview", "jvp, jar", true, true)
+ Jalview("Jalview", "jvp,jar", true, true)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
}
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
}
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
int count = 0;
try
{
- while ((ln = worker.getErrorReader().readLine()) != null)
+ while ((ln = worker.getOutputReader().readLine()) != null)
{
System.out.println(ln);
successfulCMDs.add(ln);
--- /dev/null
+/*
+ * 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.bin;
+
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import jalview.gui.JvOptionPane;
+
+public class CommandLineOperationsNG
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ // Note longer timeout needed on full test run than on individual tests
+ private static final int TEST_TIMEOUT = 13000;
+
+ private static final int SETUP_TIMEOUT = 9500;
+
+ private static final int MINFILESIZE_SMALL = 2096;
+
+ private static final int MINFILESIZE_BIG = 4096;
+
+ private List<String> successfulCMDs = new ArrayList<>();
+
+ /***
+ * from
+ * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+ * -using-javas-runtime-exec
+ *
+ * @author jimp
+ *
+ */
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private BufferedReader outputReader;
+
+ private BufferedReader errorReader;
+
+ private Integer exit;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ exit = process.waitFor();
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
+ }
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
+ }
+
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ private static String modules = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ // if (scanner == null)
+ // {
+ // scanner = new ClassGraph();
+ // ScanResult scan = scanner.scan();
+ // classpath = scan.getClasspath();
+ modules = "";
+ // for (ModuleRef mr : scan.getModules())
+ // {
+ // modules.concat(mr.getName());
+ // }
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ // }
+
+ // while (classpath == null)
+ // {
+ // try
+ // {
+ // Thread.sleep(10);
+ // } catch (InterruptedException x)
+ // {
+ //
+ // }
+ // }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout)
+ {
+ // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
+ // not expanded by the shell
+ // String classpath = getClassPath();
+ getClassPath();
+ boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
+ String pwd = "";
+ try
+ {
+ Path currentRelativePath = Paths.get("");
+ pwd = currentRelativePath.toAbsolutePath().toString();
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ if (pwd == null || pwd.length() == 0)
+ pwd = ".";
+ String[] classpaths = new String[] { pwd + "/bin/main",
+ pwd + "/j11lib/*", pwd + "/resources", pwd + "/help" };
+ String classpath = String.join(win ? ";" : ":", classpaths);
+ String _cmd = java_exe + " "
+ + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+ + classpath
+ + ((modules != null && modules.length() > 2)
+ ? "--add-modules=\"" + modules + "\""
+ : "")
+ + " jalview.bin.Jalview ";
+ Process ls2_proc = null;
+ Worker worker = null;
+ try
+ {
+ cmd = " --testoutput " + cmd;
+ System.out.println("Running '" + _cmd + cmd + "'");
+ ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+ } catch (Throwable e1)
+ {
+ e1.printStackTrace();
+ }
+ if (ls2_proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getErrorStream()));
+ worker = new Worker(ls2_proc);
+ worker.start();
+ try
+ {
+ worker.join(timeout);
+ } catch (InterruptedException e)
+ {
+ System.err.println("Thread interrupted");
+ }
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @Test(groups = { "Functional" })
+ public void reportCurrentWorkingDirectory()
+ {
+ try
+ {
+ Path currentRelativePath = Paths.get("");
+ String s = currentRelativePath.toAbsolutePath().toString();
+ System.out.println("Test CWD is " + s);
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void initialize()
+ {
+ new CommandLineOperationsNG();
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpForHeadlessCommandLineInputOperations()
+ throws IOException
+ {
+ String cmds = "--headless " + "--open examples/uniref50.fa "
+ + "--sortbytree "
+ + "--props test/jalview/bin/testProps.jvprops "
+ + "--colour zappo "
+ + "--jabaws http://www.compbio.dundee.ac.uk/jabaws "
+ + "--features examples/testdata/plantfdx.features "
+ + "--annotations examples/testdata/plantfdx.annotations "
+ + "--tree examples/testdata/uniref50_test_tree "
+ + "--nousagestats ";
+ Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+ String ln = null;
+ while ((ln = worker.getOutputReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ }
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ System.err.println(ln);
+ }
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpForCommandLineInputOperations() throws IOException
+ {
+ String cmds = "--open examples/uniref50.fa --noquestionnaire --nousagestats";
+ final Worker worker = getJalviewDesktopRunner(false, cmds,
+ SETUP_TIMEOUT);
+
+ // number of lines expected on STDERR when Jalview starts up normally
+ // may need to adjust this if Jalview is excessively noisy ?
+ final int STDERR_SETUPLINES = 50;
+
+ // thread monitors stderr - bails after SETUP_TIMEOUT or when
+ // STDERR_SETUPLINES have been read
+ Thread runner = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ String ln = null;
+ int count = 0;
+ try
+ {
+ while ((ln = worker.getOutputReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > STDERR_SETUPLINES)
+ {
+ break;
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Unexpected Exception reading stderr from the Jalview process");
+ e.printStackTrace();
+ }
+ }
+ });
+ long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+ runner.start();
+ while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ runner.interrupt();
+ if (worker != null && worker.exit == null)
+ {
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
+ }
+ }
+
+ @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
+ public void testAllInputOperations(String expectedString,
+ String failureMsg)
+ {
+ if ("[TESTOUTPUT] arg --nousagestats was set".equals(expectedString))
+ Assert.assertTrue(successfulCMDs.contains(expectedString),
+ failureMsg);
+ }
+
+ @Test(
+ groups =
+ { "Functional" },
+ dataProvider = "headlessModeOutputOperationsData")
+ public void testHeadlessModeOutputOperations(String harg, String type,
+ String fileName, boolean withAWT, int expectedMinFileSize,
+ int timeout)
+ {
+ String cmd = harg + type + " " + fileName;
+ // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+ File file = new File(fileName);
+ file.deleteOnExit();
+ Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
+ assertNotNull(worker, "worker is null");
+ String msg = "Didn't create an output" + type + " file.[" + cmd + "]";
+ assertTrue(file.exists(), msg);
+ FileAssert.assertFile(file, msg);
+ FileAssert.assertMinLength(file, expectedMinFileSize);
+ if (worker != null && worker.exit == null)
+ {
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
+ Assert.fail("Jalview did not exit after " + type
+ + " generation (try running test again to verify - timeout at "
+ + timeout + "ms). [" + harg + "]");
+ }
+ file.delete();
+ }
+
+ @DataProvider(name = "allInputOperationsData")
+ public Object[][] getHeadlessModeInputParams()
+ {
+ return new Object[][] {
+ // headless mode input operations
+ { "[TESTOUTPUT] arg --colour='zappo' was set",
+ "Failed setting arg --colour" },
+ { "[TESTOUTPUT] arg --props='test/jalview/bin/testProps.jvprops' was set",
+ "Failed setting arg --props" },
+ { "[TESTOUTPUT] arg --sortbytree was set",
+ "Failed setting arg --sortbytree" },
+ { "[TESTOUTPUT] arg --jabaws='http://www.compbio.dundee.ac.uk/jabaws' was set",
+ "Failed setting arg --jabaws" },
+ { "[TESTOUTPUT] arg --open='examples/uniref50.fa' was set",
+ "Failed setting arg --open" },
+ { "[TESTOUTPUT] arg --features='examples/testdata/plantfdx.features' was set",
+ "Failed setting arg --features" },
+ { "[TESTOUTPUT] arg --annotations='examples/testdata/plantfdx.annotations' was set",
+ "Failed setting arg --annotations" },
+ { "[TESTOUTPUT] arg --tree='examples/testdata/uniref50_test_tree' was set",
+ "Failed setting arg --tree" },
+ // non headless mode input operations
+ { "[TESTOUTPUT] arg --nousagestats was set",
+ "Failed setting arg --nousagestats" },
+ { "[TESTOUTPUT] arg --noquestionnaire was set",
+ "Failed setting arg --noquestionnaire" }
+ //
+ };
+ }
+
+ @DataProvider(name = "headlessModeOutputOperationsData")
+ public static Object[][] getHeadlessModeOutputParams()
+ {
+ // JBPNote: I'm not clear why need to specify full path for output file
+ // when running tests on build server, but we will keep this patch for now
+ // since it works.
+ // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
+ String workingDir = "test/jalview/bin/";
+ return new Object[][] {
+ //
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ //
+ };
+ }
+}
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--noannotations "
+ + "--noshowannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 3, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--noannotations " + "--nossannotations "
+ + "--noshowannotations " + "--nossannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 0, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--noannotations " + "--nossannotations "
+ + "--noshowannotations " + "--nossannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 0, 1 },
{ "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
--substitutions
--append=examples/test_fab41.result/sample.a2m
---annotations
+--showannotations
--ssannotations
--colour=gecos-flower
--structure=[viewer=jmol,tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--nosplash
--substitutions
--append=examples/test_fab41.result/sample.a2m
---noannotations
+--noshowannotations
--nossannotations
--colour=gecos-flower
--structure=[tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structureviewer=jmol
--paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
--tempfac=plddt
---structure=[viewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--structure=[structureviewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
--paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
--tempfac=plddt
--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
git://source.jalview.org / jalview.git / commitdiff