/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.bin;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.Constructor;
+import java.net.URL;
import java.util.*;
import javax.swing.*;
+ "-noquestionnaire\tTurn off questionnaire check."
+ "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
+ + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
+ "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
Vector getFeatures = null; // vector of das source nicknames to fetch features from
// loading is done.
+ String groovyscript = null; // script to execute after all loading is completed one way or another
+ // extract groovy argument and execute if necessary
+ groovyscript = aparser.getValue("groovy");
file = aparser.getValue("open");
if (file == null && desktop == null)
}
}
}
+ if (groovyscript!=null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script "+groovyscript);
+ executeGroovyScript(groovyscript, desktop);
+ } else {
+ System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ }
+ groovyscript = null;
+ }
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
getFeatures = checkDasArguments(aparser);
+ // extract groovy arguments before anything else.
}
// Once all loading is done. Retrieve features.
if (getFeatures!=null)
startFeatureFetching(getFeatures);
}
}
+ if (groovyscript!=null)
+ {
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script "+groovyscript);
+ executeGroovyScript(groovyscript, desktop);
+ } else {
+ System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ }
+ }
+
+ // Once all other stuff is done, execute any groovy scripts (in order)
+ }
+ /**
+ * Locate the given string as a file and pass it to the groovy interpreter.
+ * @param groovyscript the script to execute
+ * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+ */
+ private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+ {
+ if (jalviewContext==null)
+ {
+ System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+ }
+ File sfile = null;
+ if (groovyscript.trim().equals("STDIN"))
+ {
+ // read from stdin into a tempfile and execute it
+ try {
+ sfile = File.createTempFile("jalview", "groovy");
+ PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
+ BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
+ String line=null;
+ while ((line=br.readLine())!=null)
+ {
+ outfile.write(line+"\n");
+ }
+ br.close();
+ outfile.flush();
+ outfile.close();
+
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+ ex.printStackTrace();
+ return;
+ }
+ } else {
+ sfile = new File(groovyscript);
+ }
+ if (!sfile.exists())
+ {
+ System.err.println("File '"+groovyscript+"' does not exist.");
+ return;
+ }
+ if (!sfile.canRead())
+ {
+ System.err.println("File '"+groovyscript+"' cannot be read.");
+ return;
+ }
+ if (sfile.length()<1)
+ {
+ System.err.println("File '"+groovyscript+"' is empty.");
+ return;
+ }
+ boolean success = false;
+ try {
+ /* The following code performs the GroovyScriptEngine invocation using reflection,
+ * and is equivalent to this fragment from the embedding groovy documentation on
+ * the groovy site:
+ * <code>
+ import groovy.lang.Binding;
+ import groovy.util.GroovyScriptEngine;
+
+ String[] roots = new String[] { "/my/groovy/script/path" };
+ GroovyScriptEngine gse = new GroovyScriptEngine(roots);
+ Binding binding = new Binding();
+ binding.setVariable("input", "world");
+ gse.run("hello.groovy", binding);
+ * </code>
+ */
+ ClassLoader cl = jalviewContext.getClass().getClassLoader();
+ Class gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor gbcons = gbindingc.getConstructor(null);
+ Object gbinding = gbcons.newInstance(null);
+ java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
+ setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
+ Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
+ Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+ success = true;
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+ e.printStackTrace(System.err);
+
+ }
+ if (success && groovyscript.equals("STDIN"))
+ {
+ // delete temp file that we made - but only if it was successfully executed
+ sfile.delete();
+ }
}
/**
* Check commandline for any das server definitions or any fetchfrom switches
git://source.jalview.org / jalview.git / blobdiff