X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=ba72831c4f402de84217a42bdad948a8cfd59c5d;hb=refs%2Fheads%2Ffeature%2FJAL-4274_configurable_bitmap_export_preferences;hp=a3549aaaefe2098e66ef941408e1e472c1a48685;hpb=85fe704e3f4eeb6093f88f1d2f90f8e4db70b0d3;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index a3549aa..ba72831 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -14,6 +14,7 @@ import java.util.Map; import jalview.analysis.AlignmentUtils; import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Jalview.ExitCode; import jalview.bin.argparser.Arg; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.ArgParser.Position; @@ -66,10 +67,14 @@ public class Commands private Map afMap; + private Map> svMap; + private boolean commandArgsProvided = false; private boolean argsWereParsed = false; + private List errors = new ArrayList<>(); + public Commands(ArgParser argparser, boolean headless) { this(Desktop.instance, argparser, headless); @@ -81,16 +86,15 @@ public class Commands headless = h; desktop = d; afMap = new HashMap<>(); - if (argparser != null) - { - processArgs(argparser, headless); - } } - private boolean processArgs(ArgParser argparser, boolean h) + protected boolean processArgs() { - argParser = argparser; - headless = h; + if (argParser == null) + { + return true; + } + boolean theseArgsWereParsed = false; if (argParser != null && argParser.getLinkedIds() != null) @@ -99,9 +103,10 @@ public class Commands { ArgValuesMap avm = argParser.getLinkedArgs(id); theseArgsWereParsed = true; - theseArgsWereParsed &= processLinked(id); + boolean processLinkedOkay = processLinked(id); + theseArgsWereParsed &= processLinkedOkay; + processGroovyScript(id); - boolean processLinkedOkay = theseArgsWereParsed; // wait around until alignFrame isn't busy AlignFrame af = afMap.get(id); @@ -117,8 +122,11 @@ public class Commands } theseArgsWereParsed &= processImages(id); + if (processLinkedOkay) + { theseArgsWereParsed &= processOutput(id); + } // close ap if (avm.getBoolean(Arg.CLOSE)) @@ -133,9 +141,18 @@ public class Commands } } + + // report errors + Console.warn( + "The following errors and warnings occurred whilst processing files:\n" + + errorsToString()); + // gui errors reported in Jalview + if (argParser.getBoolean(Arg.QUIT)) { - Jalview.getInstance().quit(); + Jalview.getInstance().exit( + "Exiting due to " + Arg.QUIT.argString() + " argument.", + ExitCode.OK); return true; } // carry on with jalview.bin.Jalview @@ -153,17 +170,16 @@ public class Commands return argsWereParsed; } - protected boolean processUnlinked(String id) - { - return processLinked(id); - } - protected boolean processLinked(String id) { boolean theseArgsWereParsed = false; ArgValuesMap avm = argParser.getLinkedArgs(id); if (avm == null) + { return true; + } + + Boolean isError = Boolean.valueOf(false); // set wrap scope here so it can be applied after structures are opened boolean wrap = false; @@ -216,7 +232,9 @@ public class Commands { if (!(new File(openFile)).exists()) { - Console.warn("Can't find file '" + openFile + "'"); + addError("Can't find file '" + openFile + "'"); + isError = true; + continue; } } } @@ -230,7 +248,9 @@ public class Commands format = new IdentifyFile().identify(openFile, protocol); } catch (FileFormatException e1) { - Console.error("Unknown file format for '" + openFile + "'"); + addError("Unknown file format for '" + openFile + "'"); + isError = true; + continue; } af = afMap.get(id); @@ -247,9 +267,28 @@ public class Commands Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); - - af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, - format); + boolean xception = false; + try + { + af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, + format); + } catch (Throwable thr) + { + xception = true; + addError("Couldn't open '" + openFile + "' as " + format + " " + + thr.getLocalizedMessage() + + " (Enable debug for full stack trace)"); + isError = true; + Console.debug("Exception when opening '" + openFile + "'", thr); + } finally + { + if (af == null && !xception) + { + addInfo("Ignoring '" + openFile + + "' - no alignment data found."); + continue; + } + } // colour alignment? String colour = ArgParser.getFromSubValArgOrPref(avm, av, @@ -262,8 +301,7 @@ public class Commands if (cs == null && !"None".equals(colour)) { - Console.warn( - "Couldn't parse '" + colour + "' as a colourscheme."); + addWarn("Couldn't parse '" + colour + "' as a colourscheme."); } else { @@ -327,7 +365,8 @@ public class Commands "examples/testdata/uniref50_test_tree", treefile); } catch (IOException e) { - Console.warn("Couldn't add tree " + treefile, e); + addError("Couldn't add tree " + treefile, e); + isError = true; } } @@ -393,11 +432,12 @@ public class Commands { if (headless) { - Jalview.exit("Could not open any files in headless mode", 1); + Jalview.exit("Could not open any files in headless mode", + ExitCode.NO_FILES); } else { - Console.warn("No more files to open"); + Console.info("No more files to open"); } } if (progressBarSet && desktop != null) @@ -427,10 +467,8 @@ public class Commands if (seq == null) { - Console.warn("Could not find sequence for argument " + addWarn("Could not find sequence for argument " + Arg.STRUCTURE.argString() + "=" + val); - // you probably want to continue here, not break - // break; continue; } File structureFile = null; @@ -463,14 +501,14 @@ public class Commands if (structureFile == null) { - Console.warn("Not provided structure file with '" + val + "'"); + addWarn("Not provided structure file with '" + val + "'"); continue; } if (!structureFile.exists()) { - Console.warn("Structure file '" - + structureFile.getAbsoluteFile() + "' not found."); + addWarn("Structure file '" + structureFile.getAbsoluteFile() + + "' not found."); continue; } @@ -502,7 +540,7 @@ public class Commands } catch (IOException e) { paeFilepath = paeFile.getAbsolutePath(); - Console.warn("Problem with the PAE file path: '" + addWarn("Problem with the PAE file path: '" + paeFile.getPath() + "'"); } } @@ -545,7 +583,7 @@ public class Commands if (it.hasNext()) sb.append(", "); } - Console.warn(sb.toString()); + addWarn(sb.toString()); } } @@ -562,7 +600,8 @@ public class Commands if (sv == null) { - Console.error("Failed to import and open structure view."); + addError("Failed to import and open structure view for file '" + + structureFile + "'."); continue; } try @@ -580,14 +619,28 @@ public class Commands } if (tries == 0 && sv.isBusy()) { - Console.warn( - "Gave up waiting for structure viewer to load. Something may have gone wrong."); + addWarn("Gave up waiting for structure viewer to load file '" + + structureFile + + "'. Something may have gone wrong."); } } catch (Exception x) { - Console.warn("Exception whilst waiting for structure viewer " + addError("Exception whilst waiting for structure viewer " + structureFilepath, x); + isError = true; + } + + // add StructureViewer to svMap list + if (svMap == null) + { + svMap = new HashMap<>(); } + if (svMap.get(id) == null) + { + svMap.put(id, new ArrayList<>()); + } + svMap.get(id).add(sv); + Console.debug( "Successfully opened viewer for " + structureFilepath); String structureImageFilename = ArgParser.getValueFromSubValOrArg( @@ -623,7 +676,7 @@ public class Commands typeS.toUpperCase(Locale.ROOT)); } catch (IllegalArgumentException e) { - Console.warn("Do not know image format '" + typeS + addWarn("Do not know image format '" + typeS + "', using PNG"); imageType = TYPE.PNG; } @@ -633,14 +686,6 @@ public class Commands switch (StructureViewer.getViewerType()) { case JMOL: - try - { - Thread.sleep(1000); // WHY ??? - } catch (InterruptedException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } JalviewStructureDisplayI sview = sv .getJalviewStructureDisplay(); if (sview instanceof AppJmol) @@ -648,6 +693,14 @@ public class Commands AppJmol jmol = (AppJmol) sview; try { + boolean success = this.checksBeforeWritingToFile(avm, + subVals, false, structureImageFilename, + "structure image", isError); + if (!success) + { + continue; + } + Console.debug("Rendering image to " + structureImageFile); jmol.makePDBImage(structureImageFile, imageType, renderer, userBis); @@ -656,16 +709,18 @@ public class Commands } catch (ImageOutputException ioexc) { - Console.warn("Unexpected error whilst exporting image to " + addError("Unexpected error whilst exporting image to " + structureImageFile, ioexc); + isError = true; + continue; } } break; default: - Console.warn("Cannot export image for structure viewer " + addWarn("Cannot export image for structure viewer " + sv.getViewerType() + " yet"); - break; + continue; } } } @@ -698,7 +753,7 @@ public class Commands } */ - return theseArgsWereParsed; + return theseArgsWereParsed && !isError; } protected void processGroovyScript(String id) @@ -708,7 +763,7 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return; } @@ -732,10 +787,11 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return false; } + Boolean isError = Boolean.valueOf(false); if (avm.containsArg(Arg.IMAGE)) { for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) @@ -776,6 +832,14 @@ public class Commands Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); + + boolean success = checksBeforeWritingToFile(avm, subVal, false, + fileName, "image", isError); + if (!success) + { + continue; + } + try { switch (type) @@ -823,17 +887,19 @@ public class Commands break; default: - Console.warn(Arg.IMAGE.argString() + " type '" + type + addWarn(Arg.IMAGE.argString() + " type '" + type + "' not known. Ignoring"); break; } } catch (Exception ioex) { - Console.warn("Unexpected error during export", ioex); + addError("Unexpected error during export to '" + fileName + "'", + ioex); + isError = true; } } } - return true; + return !isError; } protected boolean processOutput(String id) @@ -843,10 +909,12 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return false; } + Boolean isError = Boolean.valueOf(false); + if (avm.containsArg(Arg.OUTPUT)) { for (ArgValue av : avm.getArgValueList(Arg.OUTPUT)) @@ -856,24 +924,6 @@ public class Commands String fileName = subVals.getContent(); boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName); File file = new File(fileName); - boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, - Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false); - // backups. Use the Arg.BACKUPS or subval "backups" setting first, - // otherwise if headless assume false, if not headless use the user - // preference with default true. - boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, - subVals, null, - Platform.isHeadless() ? null : BackupFiles.ENABLED, - !Platform.isHeadless()); - - // if backups is not true then --overwrite must be specified - if (file.exists() && !(overwrite || backups || stdout)) - { - Console.error("Won't overwrite file '" + fileName + "' without " - + Arg.OVERWRITE.argString() + " or " - + Arg.BACKUPS.argString() + " set"); - return false; - } String name = af.getName(); String format = ArgParser.getValueFromSubValOrArg(avm, av, @@ -923,41 +973,44 @@ public class Commands validSB.append(")"); } - Jalview.exit("No valid format specified for " + addError("No valid format specified for " + Arg.OUTPUT.argString() + ". Valid formats are " - + validSB.toString() + ".", 1); - // this return really shouldn't happen - return false; + + validSB.toString() + "."); + continue; } } - String savedBackupsPreference = Cache - .getDefault(BackupFiles.ENABLED, null); - Console.debug("Setting backups to " + backups); - Cache.applicationProperties.put(BackupFiles.ENABLED, - Boolean.toString(backups)); + boolean success = checksBeforeWritingToFile(avm, subVals, true, + fileName, ff.getName(), isError); + if (!success) + { + continue; + } + + boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, + subVals, null, + Platform.isHeadless() ? null : BackupFiles.ENABLED, + !Platform.isHeadless()); Console.info("Writing " + fileName); - af.saveAlignment(fileName, ff, stdout); - Console.debug("Returning backups to " + savedBackupsPreference); - if (savedBackupsPreference != null) - Cache.applicationProperties.put(BackupFiles.ENABLED, - savedBackupsPreference); + af.saveAlignment(fileName, ff, stdout, backups); if (af.isSaveAlignmentSuccessful()) { Console.debug("Written alignment '" + name + "' in " - + ff.getName() + " format to " + file); + + ff.getName() + " format to '" + file + "'"); } else { - Console.warn("Error writing file " + file + " in " + ff.getName() + addError("Error writing file '" + file + "' in " + ff.getName() + " format!"); + isError = true; + continue; } } } - return true; + return !isError; } private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm, @@ -989,10 +1042,125 @@ public class Commands seq = al.getSequenceAt(subVals.getIndex()); } } - else if (idAv != null) + if (seq == null && idAv != null) { seq = al.findName(idAv.getValue()); } return seq; } + + public AlignFrame[] getAlignFrames() + { + AlignFrame[] afs = null; + if (afMap != null) + { + afs = (AlignFrame[]) afMap.values().toArray(); + } + + return afs; + } + + public List getStructureViewers() + { + List svs = null; + if (svMap != null) + { + for (List svList : svMap.values()) + { + if (svs == null) + { + svs = new ArrayList<>(); + } + svs.addAll(svList); + } + } + return svs; + } + + private void addInfo(String errorMessage) + { + Console.info(errorMessage); + errors.add(errorMessage); + } + + private void addWarn(String errorMessage) + { + Console.warn(errorMessage); + errors.add(errorMessage); + } + + private void addError(String errorMessage) + { + addError(errorMessage, null); + } + + private void addError(String errorMessage, Exception e) + { + Console.error(errorMessage, e); + errors.add(errorMessage); + } + + private boolean checksBeforeWritingToFile(ArgValuesMap avm, + SubVals subVal, boolean includeBackups, String filename, + String adjective, Boolean isError) + { + File file = new File(filename); + + boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE, + subVal, null, "OVERWRITE_OUTPUT", false); + boolean stdout = false; + boolean backups = false; + if (includeBackups) + { + stdout = ArgParser.STDOUTFILENAME.equals(filename); + // backups. Use the Arg.BACKUPS or subval "backups" setting first, + // otherwise if headless assume false, if not headless use the user + // preference with default true. + backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal, + null, Platform.isHeadless() ? null : BackupFiles.ENABLED, + !Platform.isHeadless()); + } + + if (file.exists() && !(overwrite || backups || stdout)) + { + addWarn("Won't overwrite file '" + filename + "' without " + + Arg.OVERWRITE.argString() + + (includeBackups ? " or " + Arg.BACKUPS.argString() : "") + + " set"); + return false; + } + + boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS, + subVal, null, "MKDIRS_OUTPUT", false); + + if (!FileUtils.checkParentDir(file, mkdirs)) + { + addError("Directory '" + + FileUtils.getParentDir(file).getAbsolutePath() + + "' does not exist for " + adjective + " file '" + filename + + "'." + + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString())); + isError = true; + return false; + } + + return true; + } + + public List getErrors() + { + return errors; + } + + public String errorsToString() + { + StringBuilder sb = new StringBuilder(); + for (String error : errors) + { + if (sb.length() > 0) + sb.append("\n"); + sb.append("- " + error); + } + return sb.toString(); + } }