import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
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 Map<String, AlignFrame> afMap;
+ private Map<String, List<StructureViewer>> svMap;
+
private boolean commandArgsProvided = false;
private boolean argsWereParsed = false;
+ private List<String> errors = new ArrayList<>();
+
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
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)
{
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);
}
theseArgsWereParsed &= processImages(id);
+
if (processLinkedOkay)
+ {
theseArgsWereParsed &= processOutput(id);
+ }
// close ap
if (avm.getBoolean(Arg.CLOSE))
}
}
+
+ // 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
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;
- /*
- * // script to execute after all loading is completed one way or another String
- * groovyscript = m.get(Arg.GROOVY) == null ? null :
- * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
- * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
- * DataSourceType protocol = null;
- */
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
{
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;
}
af = afMap.get(id);
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
-
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
- format);
-
- // wrap alignment?
- boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
- null, "WRAP_ALIGNMENT", false);
- af.getCurrentView().setWrapAlignment(wrap);
+ 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,
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;
}
}
false, false);
}
+ // wrap alignment? do this last for formatting reasons
+ wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+ "WRAP_ALIGNMENT", false);
+ // af.setWrapFormat(wrap) is applied after structures are opened for
+ // annotation reasons
+
// store the AlignFrame for this id
afMap.put(id, af);
{
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());
}
}
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
- {
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
- {
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
- {
- viewerType = v;
- break;
- }
- }
- }
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
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
+ 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(
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;
}
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)
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);
} 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;
}
}
}
}
}
+ if (wrap)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.setWrapFormat(wrap, true);
+ }
+ }
+
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
}
*/
- 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 = Boolean.valueOf(false);
if (avm.containsArg(Arg.IMAGE))
{
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
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)
case "biojs":
Console.debug(
- "Creating BioJS MSA Viwer HTML file: " + fileName);
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
break;
case "eps":
- Console.debug("Creating EPS file: " + fileName);
- af.createEPS(file, name);
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
break;
case "imagemap":
- Console.debug("Creating ImageMap file: " + fileName);
+ Console.debug("Outputting ImageMap file: " + fileName);
af.createImageMap(file, name);
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 = Boolean.valueOf(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() + ".", 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,
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<StructureViewer> getStructureViewers()
+ {
+ List<StructureViewer> svs = null;
+ if (svMap != null)
+ {
+ for (List<StructureViewer> 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<String> 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();
+ }
}
git://source.jalview.org / jalview.git / blobdiff