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;
private boolean argsWereParsed = false;
+ private List<String> errors = new ArrayList<>();
+
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
}
}
+
+ // report errors
+ StringBuilder sb = new StringBuilder();
+ for (String error : errors)
+ {
+ sb.append("- " + error);
+ sb.append("\n");
+ }
+ if (Platform.isHeadless())
+ {
+ Console.debug("All errors from command line argument commands:\n"
+ + sb.toString());
+ }
+ else
+ {
+ // scrollable dialog box
+
+ }
+
if (argParser.getBoolean(Arg.QUIT))
{
- Jalview.exit("Exiting due to " + Arg.QUIT.argString(), 0);
+ Jalview.getInstance().exit(
+ "Exiting due to " + Arg.QUIT.argString() + " argument.",
+ ExitCode.OK);
return true;
}
// carry on with jalview.bin.Jalview
boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
+ {
return true;
+ }
+
+ boolean isError = false;
// set wrap scope here so it can be applied after structures are opened
boolean wrap = false;
{
if (!(new File(openFile)).exists())
{
- Console.warn("Can't find file '" + openFile + "'");
+ addError("Can't find file '" + openFile + "'");
+ isError = true;
continue;
}
}
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;
}
} catch (Throwable thr)
{
xception = true;
- Console.error("Couldn't open '" + openFile + "' as " + format
- + " " + thr.getLocalizedMessage()
+ 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)
{
- Console.info("Ignoring '" + openFile
+ addInfo("Ignoring '" + openFile
+ "' - no alignment data found.");
continue;
}
if (cs == null && !"None".equals(colour))
{
- Console.warn(
- "Couldn't parse '" + colour + "' as a colourscheme.");
+ addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
}
else
{
"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;
}
}
{
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)
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;
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;
}
} catch (IOException e)
{
paeFilepath = paeFile.getAbsolutePath();
- Console.warn("Problem with the PAE file path: '"
+ addWarn("Problem with the PAE file path: '"
+ paeFile.getPath() + "'");
}
}
if (it.hasNext())
sb.append(", ");
}
- Console.warn(sb.toString());
+ addWarn(sb.toString());
}
}
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
}
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
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;
}
AppJmol jmol = (AppJmol) sview;
try
{
+ whatNext wn = this.checksBeforeWritingToFile(avm, subVals,
+ false, structureImageFilename, "structure image");
+ if (wn == whatNext.ERROR)
+ {
+ isError = true;
+ continue;
+ }
+ else if (wn == whatNext.CONTINUE)
+ {
+ continue;
+ }
+
Console.debug("Rendering image to " + structureImageFile);
jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
} 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;
}
}
}
}
*/
- return theseArgsWereParsed;
+ return theseArgsWereParsed && !isError;
}
protected void processGroovyScript(String id)
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;
}
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 = false;
if (avm.containsArg(Arg.IMAGE))
{
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
+
+ whatNext wn = this.checksBeforeWritingToFile(avm, subVal, false,
+ fileName, "image");
+ if (wn == whatNext.ERROR)
+ {
+ isError = true;
+ continue;
+ }
+ else if (wn == whatNext.CONTINUE)
+ {
+ continue;
+ }
+
try
{
switch (type)
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)
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 = false;
+
if (avm.containsArg(Arg.OUTPUT))
{
for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
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,
validSB.append(")");
}
- Jalview.exit("No valid format specified for "
+ addError("No valid format specified for "
+ Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", ExitCode.INVALID_FORMAT);
- // 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));
+ whatNext wn = this.checksBeforeWritingToFile(avm, subVals, true,
+ fileName, ff.getName());
+ if (wn == whatNext.ERROR)
+ {
+ isError = true;
+ continue;
+ }
+ else if (wn == whatNext.CONTINUE)
+ {
+ 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,
}
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 enum whatNext
+ {
+ OKAY, CONTINUE, ERROR;
+ }
+
+ private whatNext checksBeforeWritingToFile(ArgValuesMap avm,
+ SubVals subVal, boolean includeBackups, String filename,
+ String adjective)
+ {
+ 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 whatNext.CONTINUE;
+ }
+
+ 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()));
+ return whatNext.ERROR;
+ }
+
+ return whatNext.OKAY;
+ }
}
git://source.jalview.org / jalview.git / commitdiff