Revision: 18659
http://sourceforge.net/p/jmol/code/18659
Author: hansonr
Date: 2013-09-17 14:29:00 +0000 (Tue, 17 Sep 2013)
Log Message:
-----------
abstraction of file writing for web
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v13_2/Jmol/src/org/jmol/api/ApiPlatform.java
branches/v13_2/Jmol/src/org/jmol/api/JmolFileAdapterInterface.java
branches/v13_2/Jmol/src/org/jmol/api/JmolStateCreator.java
branches/v13_2/Jmol/src/org/jmol/api/JmolViewer.java
branches/v13_2/Jmol/src/org/jmol/api/JmolZipUtility.java
branches/v13_2/Jmol/src/org/jmol/awt/JmolFileAdapter.java
branches/v13_2/Jmol/src/org/jmol/awt/Platform.java
branches/v13_2/Jmol/src/org/jmol/awtjs2d/JmolFileAdapter.java
branches/v13_2/Jmol/src/org/jmol/awtjs2d/Platform.java
branches/v13_2/Jmol/src/org/jmol/export/_ObjExporter.java
branches/v13_2/Jmol/src/org/jmol/export/___Exporter.java
branches/v13_2/Jmol/src/org/jmol/export/image/GenericImageCreator.java
branches/v13_2/Jmol/src/org/jmol/exportjs/Exporter.java
branches/v13_2/Jmol/src/org/jmol/io/JmolBinary.java
branches/v13_2/Jmol/src/org/jmol/io2/ZipUtil.java
branches/v13_2/Jmol/src/org/jmol/viewer/StateCreator.java
branches/v13_2/Jmol/src/org/jmol/viewer/StateManager.java
branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
branches/v13_2/Jmol/src/org/jmol/awtjs2d/WebPostOutputChannel.java
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-09-17 14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-09-17 14:29:00 UTC (rev 18659)
@@ -274,7 +274,7 @@
// just log and display some information here
- logging = (viewer.getLogFile().length() > 0);
+ logging = (viewer.getLogFileName().length() > 0);
JmolList<Object> names = getMapList(map, "names");
for (Map.Entry<String, Object> e : map.entrySet()) {
String name = e.getKey();
Modified: branches/v13_2/Jmol/src/org/jmol/api/ApiPlatform.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/ApiPlatform.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/api/ApiPlatform.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -8,7 +8,7 @@
public interface ApiPlatform {
- void setViewer(JmolViewer viewer, Object display);
+ void setViewer(Viewer viewer, Object display);
/////// Display
@@ -72,7 +72,7 @@
Object newOffScreenImage(int w, int h);
- void renderScreenImage(JmolViewer jmolViewer, Object g, Object currentSize);
+ void renderScreenImage(Object g, Object currentSize);
int[] getTextPixels(String text, JmolFont font3d, Object gObj,
Object image, int mapWidth, int height,
Modified: branches/v13_2/Jmol/src/org/jmol/api/JmolFileAdapterInterface.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/JmolFileAdapterInterface.java
2013-09-17 14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/api/JmolFileAdapterInterface.java
2013-09-17 14:29:00 UTC (rev 18659)
@@ -1,7 +1,12 @@
package org.jmol.api;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
import java.net.URL;
+import org.jmol.viewer.FileManager;
+
public interface JmolFileAdapterInterface {
public Object getBufferedURLInputStream(URL url, byte[] outputBytes,
@@ -9,4 +14,14 @@
public Object getBufferedFileInputStream(String name);
+ public Object openOutputChannel(double privateKey, FileManager fm, String
fileName, boolean asWriter) throws IOException;
+
+ public InputStream openFileInputStream(double privateKey, String fileName)
throws IOException;
+
+ public String getAbsolutePath(double privateKey, String fileName);
+
+ public long getFileLength(double privateKey, String fileName) throws
IOException;
+
+ public BufferedWriter openLogFile(double privateKey, String logFileName,
boolean asAppend) throws IOException ;
+
}
Modified: branches/v13_2/Jmol/src/org/jmol/api/JmolStateCreator.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/JmolStateCreator.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/api/JmolStateCreator.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -18,7 +18,7 @@
public interface JmolStateCreator {
- void setViewer(Viewer viewer);
+ void setViewer(Viewer viewer, double privateKey);
Object getWrappedState(String fileName, String[] scripts, boolean isImage,
boolean asJmolZip, int width, int height);
@@ -104,5 +104,9 @@
String getAtomDefs(Map<String, Object> names);
+ String getLogFileName();
+ String setLogFile(String name);
+
+
}
Modified: branches/v13_2/Jmol/src/org/jmol/api/JmolViewer.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/JmolViewer.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/api/JmolViewer.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -560,7 +560,7 @@
*/
public void renderScreenImage(Object g, Object currentSize,
Object rectClip) {
- apiPlatform.renderScreenImage(this, g, currentSize);
+ apiPlatform.renderScreenImage(g, currentSize);
}
public Object getJsObjectInfo(Object[] jsObject, String method, Object[]
args) {
Modified: branches/v13_2/Jmol/src/org/jmol/api/JmolZipUtility.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/JmolZipUtility.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/api/JmolZipUtility.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -37,13 +37,13 @@
String shortName,
Map<String, byte[]> pngjCache);
- public Object writeZipFile(FileManager fm, Viewer viewer, String outFileName,
+ public Object writeZipFile(double privateKey, FileManager fm, Viewer viewer,
String outFileName,
JmolList<Object> fileNamesAndByteArrays, String
msg);
public String getSceneScript(String[] scenes, Map<String, String> htScenes,
JmolList<Integer> list);
- public Object createZipSet(FileManager fm, Viewer viewer, String fileName,
+ public Object createZipSet(double privateKey, FileManager fm, Viewer viewer,
String fileName,
String script, String[] scripts,
boolean includeRemoteFiles);
Modified: branches/v13_2/Jmol/src/org/jmol/awt/JmolFileAdapter.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/awt/JmolFileAdapter.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/awt/JmolFileAdapter.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -1,18 +1,31 @@
package org.jmol.awt;
import java.io.BufferedInputStream;
+import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.net.URL;
import java.net.URLConnection;
import org.jmol.api.JmolFileAdapterInterface;
import org.jmol.api.JmolFileInterface;
+import org.jmol.viewer.FileManager;
+import org.jmol.viewer.Viewer;
public class JmolFileAdapter implements JmolFileAdapterInterface {
+ private Viewer viewer;
+
+ public JmolFileAdapter(Viewer viewer) {
+ this.viewer = viewer;
+ }
+
public Object getBufferedURLInputStream(URL url, byte[] outputBytes,
String post) {
try {
@@ -63,4 +76,30 @@
return new JmolFile(name);
}
+ public Object openOutputChannel(double privateKey, FileManager fm, String
fileName, boolean asWriter) throws IOException {
+ if (!viewer.checkPrivateKey(privateKey))
+ return null;
+ OutputStream os = new FileOutputStream(fileName);
+ return (asWriter ? new BufferedWriter(new OutputStreamWriter(os)) : os);
+ }
+
+ public InputStream openFileInputStream(double privateKey, String fileName)
+ throws IOException {
+ return (viewer.checkPrivateKey(privateKey) ? new FileInputStream(fileName)
: null);
+ }
+
+ public String getAbsolutePath(double privateKey, String fileName) {
+ return (viewer.isApplet() || !viewer.checkPrivateKey(privateKey) ? fileName
+ : (new File(fileName).getAbsolutePath()));
+ }
+
+ public long getFileLength(double privateKey, String fileName) {
+ return (new File(fileName)).length();
+ }
+
+ public BufferedWriter openLogFile(double privateKey, String logFileName,
boolean asAppend) throws IOException {
+ return (viewer.checkPrivateKey(privateKey) &&
logFileName.indexOf("JmolLog_") >= 0 ?
+ new BufferedWriter(new FileWriter(logFileName, asAppend)) : null);
+ }
+
}
Modified: branches/v13_2/Jmol/src/org/jmol/awt/Platform.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/awt/Platform.java 2013-09-17 14:28:46 UTC
(rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/awt/Platform.java 2013-09-17 14:29:00 UTC
(rev 18659)
@@ -17,7 +17,6 @@
import org.jmol.api.JmolFileInterface;
import org.jmol.api.JmolMouseInterface;
import org.jmol.api.JmolPopupInterface;
-import org.jmol.api.JmolViewer;
import org.jmol.api.JmolFileAdapterInterface;
import org.jmol.util.JmolFont;
import org.jmol.util.P3;
@@ -26,9 +25,9 @@
public class Platform implements ApiPlatform {
- JmolViewer viewer;
+ Viewer viewer;
- public void setViewer(JmolViewer viewer, Object display) {
+ public void setViewer(Viewer viewer, Object display) {
this.viewer = viewer;
}
@@ -62,11 +61,10 @@
/**
* legacy apps will use this
*
- * @param viewer
* @param g
* @param size
*/
- public void renderScreenImage(JmolViewer viewer, Object g, Object size) {
+ public void renderScreenImage(Object g, Object size) {
Display.renderScreenImage(viewer, g, size);
}
@@ -87,7 +85,7 @@
}
public JmolFileAdapterInterface getFileAdapter() {
- return new JmolFileAdapter();
+ return new JmolFileAdapter(viewer);
}
////// Mouse
@@ -246,5 +244,4 @@
.format(new Date());
}
-
}
Modified: branches/v13_2/Jmol/src/org/jmol/awtjs2d/JmolFileAdapter.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/awtjs2d/JmolFileAdapter.java
2013-09-17 14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/awtjs2d/JmolFileAdapter.java
2013-09-17 14:29:00 UTC (rev 18659)
@@ -1,10 +1,13 @@
package org.jmol.awtjs2d;
+import java.io.BufferedWriter;
import java.io.IOException;
+import java.io.InputStream;
import java.net.URL;
import java.net.UnknownServiceException;
import org.jmol.api.JmolFileAdapterInterface;
+import org.jmol.viewer.FileManager;
public class JmolFileAdapter implements JmolFileAdapterInterface {
@@ -31,5 +34,29 @@
}
}
+ public Object openOutputChannel(double privateKey, FileManager fm, String
fileName, boolean asWriter) {
+ return new WebPostOutputChannel(fm, fileName, asWriter);
+ }
+ public InputStream openFileInputStream(double privateKey, String fileName)
+ throws IOException {
+ // unused (to date) in JSmol/HTML5
+ return null;
+ }
+
+ public String getAbsolutePath(double privateKey, String fileName) {
+ return fileName;
+ }
+
+ public long getFileLength(double privateKey, String fileName)
+ throws IOException {
+ return 0;
+ }
+
+ public BufferedWriter openLogFile(double privateKey, String logFileName,
boolean asAppend) {
+ // could implement remote logging here
+ return null;
+ }
+
+
}
Modified: branches/v13_2/Jmol/src/org/jmol/awtjs2d/Platform.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/awtjs2d/Platform.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/awtjs2d/Platform.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -9,7 +9,6 @@
import org.jmol.api.JmolFileInterface;
import org.jmol.api.JmolMouseInterface;
import org.jmol.api.JmolPopupInterface;
-import org.jmol.api.JmolViewer;
import org.jmol.util.JmolFont;
import org.jmol.util.P3;
import org.jmol.viewer.ActionManager;
@@ -30,10 +29,10 @@
*/
public class Platform implements ApiPlatform {
Object canvas;
- JmolViewer viewer;
+ Viewer viewer;
Object context;
- public void setViewer(JmolViewer viewer, Object canvas) {
+ public void setViewer(Viewer viewer, Object canvas) {
/**
* @j2sNative
*
@@ -130,11 +129,10 @@
/**
* legacy apps will use this
*
- * @param viewer
* @param context
* @param size
*/
- public void renderScreenImage(JmolViewer viewer, Object context, Object
size) {
+ public void renderScreenImage(Object context, Object size) {
Display.renderScreenImage(viewer, context, size);
}
@@ -333,5 +331,4 @@
}
}
-
}
Added: branches/v13_2/Jmol/src/org/jmol/awtjs2d/WebPostOutputChannel.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/awtjs2d/WebPostOutputChannel.java
(rev 0)
+++ branches/v13_2/Jmol/src/org/jmol/awtjs2d/WebPostOutputChannel.java
2013-09-17 14:29:00 UTC (rev 18659)
@@ -0,0 +1,45 @@
+package org.jmol.awtjs2d;
+
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+
+import org.jmol.io.JmolBinary;
+import org.jmol.viewer.FileManager;
+
+public class WebPostOutputChannel extends ByteArrayOutputStream {
+
+ private String fileName;
+ private FileManager fm;
+ private BufferedWriter bw;
+
+ public WebPostOutputChannel(FileManager fm, String fileName, boolean
asWriter) {
+ this.fm = fm;
+ this.fileName = fileName;
+ if (asWriter)
+ bw = new BufferedWriter(new OutputStreamWriter(this));
+ }
+
+ // methods of BufferedWriter. These will be accessed by JavaScript, so no
type checking
+
+ public void write(String data) throws IOException {
+ bw.write(data);
+ }
+
+ @Override
+ public void flush() {
+ if (bw != null)
+ try {
+ bw.flush();
+ } catch (IOException e) {
+ }
+ else
+ flush();
+ }
+
+ @Override
+ public void close() {
+ JmolBinary.postByteArray(fm, fileName, toByteArray());
+ }
+}
Modified: branches/v13_2/Jmol/src/org/jmol/export/_ObjExporter.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/export/_ObjExporter.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/export/_ObjExporter.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -5,11 +5,7 @@
import java.awt.image.BufferedImage;
import java.io.BufferedWriter;
import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.io.IOException;
-//import java.io.OutputStream;
-import java.io.OutputStreamWriter;
import org.jmol.util.JmolList;
import java.util.HashSet;
@@ -75,8 +71,6 @@
private boolean normalizeUV = true;
/** BufferedWriter for the .mtl file. */
private BufferedWriter mtlbw;
- /** FileOutputStream for the .mtl file. */
- private FileOutputStream mtlos;
/** Path of the OBJ file without the extension. */
String objFileRootName;
/** File for the .mtl file. */
@@ -463,10 +457,9 @@
String mtlFileName = objFileRootName + ".mtl";
mtlFile = new File(mtlFileName);
System.out.println("_WavefrontObjExporter writing to "
- + mtlFile.getAbsolutePath());
- mtlos = new FileOutputStream(mtlFile);
- mtlbw = new BufferedWriter(new OutputStreamWriter(mtlos));
- } catch (FileNotFoundException ex) {
+ + viewer.getAbsolutePath(privateKey, mtlFileName));
+ mtlbw = (BufferedWriter) viewer.openOutputChannel(privateKey,
mtlFileName, true);
+ } catch (IOException ex) {
debugPrint("End initializeOutput (" + ex.getMessage() + "):");
return false;
}
@@ -492,7 +485,6 @@
try {
mtlbw.flush();
mtlbw.close();
- mtlos = null;
} catch (IOException ex) {
ex.printStackTrace();
if (retVal.startsWith("OK")) {
Modified: branches/v13_2/Jmol/src/org/jmol/export/___Exporter.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/export/___Exporter.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/export/___Exporter.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -29,10 +29,7 @@
import java.awt.Image;
import java.io.BufferedWriter;
import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.io.IOException;
-import java.io.OutputStreamWriter;
import java.text.SimpleDateFormat;
import org.jmol.util.JmolList;
@@ -150,7 +147,6 @@
protected JmolRendererInterface jmolRenderer;
protected SB output;
protected BufferedWriter bw;
- private FileOutputStream os;
protected String fileName;
protected String commandLineOptions;
@@ -244,9 +240,8 @@
try {
File f = new File(fileName);
System.out.println("__Exporter writing to " + f.getAbsolutePath());
- os = new FileOutputStream(fileName);
- bw = new BufferedWriter(new OutputStreamWriter(os));
- } catch (FileNotFoundException e) {
+ bw = (BufferedWriter)viewer.openOutputChannel(privateKey, fileName,
true);
+ } catch (IOException e) {
return false;
}
} else {
@@ -341,7 +336,6 @@
try {
bw.flush();
bw.close();
- os = null;
} catch (IOException e) {
System.out.println(e.getMessage());
return "ERROR EXPORTING FILE";
Modified: branches/v13_2/Jmol/src/org/jmol/export/image/GenericImageCreator.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/export/image/GenericImageCreator.java
2013-09-17 14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/export/image/GenericImageCreator.java
2013-09-17 14:29:00 UTC (rev 18659)
@@ -25,12 +25,8 @@
package org.jmol.export.image;
import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
-import java.io.OutputStreamWriter;
import org.jmol.api.JmolImageCreatorInterface;
import org.jmol.api.JmolViewer;
@@ -66,42 +62,43 @@
* @param quality
* @return null (canceled) or a message starting with OK or an error message
*/
- public Object createImage(String fileName, String type, String text, Object
bytes_or_image,
- String[] scripts, Object appendix, int quality) {
+ public Object createImage(String fileName, String type, String text,
+ Object bytes_or_image, String[] scripts,
+ Object appendix, int quality) {
// this method may not be accessed, though public, unless
// accessed via viewer, which provides its private key.
boolean isBytes = (bytes_or_image != null);
boolean isText = (!isBytes && quality == Integer.MIN_VALUE);
- FileOutputStream os = null;
+ OutputStream os = null;
long len = -1;
try {
if (!viewer.checkPrivateKey(privateKey))
return "NO SECURITY";
// returns message starting with OK or an error message
if ("OutputStream".equals(type))
- return (viewer.isJS ? new ByteArrayOutputStream() : new
FileOutputStream(fileName));
+ return viewer.openOutputChannel(privateKey, fileName, false);
if (isBytes) {
if (bytes_or_image instanceof byte[]) {
len = ((byte[]) bytes_or_image).length;
- os = new FileOutputStream(fileName);
+ os = (OutputStream) viewer.openOutputChannel(privateKey, fileName,
false);
byte[] b = (byte[]) bytes_or_image;
os.write(b, 0, b.length);
os.flush();
os.close();
+ os = null;
} else {
- getImageBytes(type, quality, fileName, scripts, bytes_or_image,
null, null);
+ getImageBytes(type, quality, fileName, scripts, bytes_or_image, null,
+ null);
return fileName;
}
} else if (isText) {
if (text == null)
return "NO DATA";
- os = new FileOutputStream(fileName);
- OutputStreamWriter osw = new OutputStreamWriter(os);
- BufferedWriter bw = new BufferedWriter(osw, 8192);
+ BufferedWriter bw = (BufferedWriter) viewer.openOutputChannel(
+ privateKey, fileName, true);
len = text.length();
bw.write(text);
bw.close();
- os = null;
} else {
len = 1;
Object bytesOrError = getImageBytes(type, quality, fileName, scripts,
@@ -111,7 +108,7 @@
byte[] bytes = (byte[]) bytesOrError;
if (bytes != null)
return (fileName == null ? bytes : new String(bytes));
- len = (new File(fileName)).length();
+ len = viewer.getFileLength(privateKey, fileName);
}
} catch (IOException exc) {
Logger.errorEx("IO Exception", exc);
@@ -126,8 +123,8 @@
}
}
return (len < 0 ? "Creation of " + fileName + " failed: "
- + viewer.getErrorMessageUn() : "OK " + type + " " + len + " "
- + fileName
+ + viewer.getErrorMessageUn() : "OK " + type + " "
+ + (len > 0 ? len + " " : "") + fileName
+ (quality == Integer.MIN_VALUE ? "" : "; quality=" + quality));
}
@@ -155,7 +152,7 @@
viewer.apiPlatform.getImageWidth(image), viewer.apiPlatform
.getImageHeight(image));
if (isOsTemp)
- os = new FileOutputStream(fileName);
+ os = (OutputStream) viewer.openOutputChannel(privateKey, fileName,
false);
if (type.equals("JPEG") || type.equals("JPG")) {
if (quality <= 0)
quality = 100; // high quality
Modified: branches/v13_2/Jmol/src/org/jmol/exportjs/Exporter.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/exportjs/Exporter.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/exportjs/Exporter.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -28,11 +28,7 @@
import java.awt.Image;
import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.io.IOException;
-import java.io.OutputStreamWriter;
import org.jmol.util.TextFormat;
@@ -142,7 +138,6 @@
protected JmolRendererInterface jmolRenderer;
protected SB output;
protected BufferedWriter bw;
- private FileOutputStream os;
protected String fileName;
protected String commandLineOptions;
@@ -226,11 +221,9 @@
}
//viewer.writeTextFile(fileName + ".spt",
viewer.getSavedState("_Export"));
try {
- File f = new File(fileName);
- System.out.println("__Exporter writing to " + f.getAbsolutePath());
- os = new FileOutputStream(fileName);
- bw = new BufferedWriter(new OutputStreamWriter(os));
- } catch (FileNotFoundException e) {
+ System.out.println("__Exporter writing to " +
viewer.getAbsolutePath(privateKey, fileName));
+ bw = (BufferedWriter) viewer.openOutputChannel(privateKey, fileName,
true);
+ } catch (IOException e) {
return false;
}
} else {
@@ -291,7 +284,6 @@
try {
bw.flush();
bw.close();
- os = null;
} catch (IOException e) {
System.out.println(e.toString());
return "ERROR EXPORTING FILE";
Modified: branches/v13_2/Jmol/src/org/jmol/io/JmolBinary.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/io/JmolBinary.java 2013-09-17 14:28:46 UTC
(rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/io/JmolBinary.java 2013-09-17 14:29:00 UTC
(rev 18659)
@@ -413,8 +413,8 @@
return getJzu().getZipFileContentsAsBytes(bis, subFileList, i);
}
- public static Object createZipSet(FileManager fm, Viewer viewer, String
fileName, String script, String[] scripts, boolean includeRemoteFiles) {
- return getJzu().createZipSet(fm, viewer, fileName, script, scripts,
includeRemoteFiles);
+ public static Object createZipSet(double privateKey, FileManager fm, Viewer
viewer, String fileName, String script, String[] scripts, boolean
includeRemoteFiles) {
+ return getJzu().createZipSet(privateKey, fm, viewer, fileName, script,
scripts, includeRemoteFiles);
}
public static Object getStreamAsBytes(BufferedInputStream bis,
@@ -443,6 +443,7 @@
/**
* generic method to create a zip file based on
* http://www.exampledepot.com/egs/java.util.zip/CreateZip.html
+ * @param privateKey
* @param fm
* @param viewer
*
@@ -453,10 +454,10 @@
* @param msg
* @return msg bytes filename or errorMessage or byte[]
*/
- public static Object writeZipFile(FileManager fm, Viewer viewer, String
outFileName,
+ public static Object writeZipFile(double privateKey, FileManager fm, Viewer
viewer, String outFileName,
JmolList<Object> fileNamesAndByteArrays,
String msg) {
- return getJzu().writeZipFile(fm, viewer, outFileName,
fileNamesAndByteArrays, msg);
+ return getJzu().writeZipFile(privateKey, fm, viewer, outFileName,
fileNamesAndByteArrays, msg);
}
Modified: branches/v13_2/Jmol/src/org/jmol/io2/ZipUtil.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/io2/ZipUtil.java 2013-09-17 14:28:46 UTC
(rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/io2/ZipUtil.java 2013-09-17 14:29:00 UTC
(rev 18659)
@@ -29,8 +29,6 @@
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
@@ -400,7 +398,8 @@
return newName;
}
- public Object writeZipFile(FileManager fm, Viewer viewer, String outFileName,
+ public Object writeZipFile(double privateKey, FileManager fm, Viewer viewer,
+ String outFileName,
JmolList<Object> fileNamesAndByteArrays, String
msg) {
byte[] buf = new byte[1024];
long nBytesOut = 0;
@@ -414,7 +413,8 @@
|| outFileName.startsWith("http://";) ? new ByteArrayOutputStream()
: null);
ZipOutputStream os = new ZipOutputStream(
- bos == null ? (OutputStream) new FileOutputStream(outFileName) :
bos);
+ bos == null ? (OutputStream) viewer.openOutputChannel(privateKey,
+ outFileName, false) : bos);
for (int i = 0; i < fileNamesAndByteArrays.size(); i += 3) {
String fname = (String) fileNamesAndByteArrays.get(i);
byte[] bytes = null;
@@ -446,7 +446,7 @@
int nOut = 0;
if (bytes == null) {
// get data from disk
- FileInputStream in = new FileInputStream(fname);
+ InputStream in = viewer.openFileInputStream(privateKey, fname);
int len;
while ((len = in.read(buf, 0, 1024)) > 0) {
os.write(buf, 0, len);
@@ -560,7 +560,7 @@
+ "\n}\n";
}
- public Object createZipSet(FileManager fm, Viewer viewer, String fileName,
+ public Object createZipSet(double privateKey, FileManager fm, Viewer viewer,
String fileName,
String script, String[] scripts,
boolean includeRemoteFiles) {
JmolList<Object> v = new JmolList<Object>();
@@ -660,7 +660,7 @@
v.addLast(bytes);
}
}
- return JmolBinary.writeZipFile(fm, viewer, fileName, v, "OK JMOL");
+ return JmolBinary.writeZipFile(privateKey, fm, viewer, fileName, v, "OK
JMOL");
}
public Object getAtomSetCollectionOrBufferedReaderFromZip(
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/StateCreator.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/StateCreator.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -25,7 +25,6 @@
import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
-import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStream;
import org.jmol.util.JmolList;
@@ -45,6 +44,7 @@
import org.jmol.constant.EnumStereoMode;
import org.jmol.constant.EnumStructure;
import org.jmol.constant.EnumVdw;
+import org.jmol.i18n.GT;
import org.jmol.io.Base64;
import org.jmol.io.JmolBinary;
import org.jmol.io.OutputStringBuilder;
@@ -103,11 +103,14 @@
}
private Viewer viewer;
+ private double privateKey;
- public void setViewer(Viewer viewer) {
+ public void setViewer(Viewer viewer, double privateKey) {
this.viewer = viewer;
+ this.privateKey = privateKey;
}
+
public Object getWrappedState(String fileName, String[] scripts,
boolean isImage, boolean asJmolZip, int width,
int height) {
@@ -120,7 +123,7 @@
viewer.fileManager.clearPngjCache(fileName);
// when writing a file, we need to make sure
// the pngj cache for that file is cleared
- return JmolBinary.createZipSet(viewer.fileManager, viewer, null, s,
+ return JmolBinary.createZipSet(privateKey, viewer.fileManager, viewer,
null, s,
scripts, true);
}
// we remove local file references in the embedded states for images
@@ -2037,7 +2040,7 @@
if (type.equals("ZIP") || type.equals("ZIPALL")) {
if (scripts != null && type.equals("ZIP"))
type = "ZIPALL";
- ret = JmolBinary.createZipSet(viewer.fileManager, viewer, localName,
+ ret = JmolBinary.createZipSet(privateKey, viewer.fileManager,
viewer, localName,
text, scripts, type.equals("ZIPALL"));
} else if (type.equals("SCENE")) {
ret = (viewer.isJS ? "ERROR: Not Available" : createSceneSet(
@@ -2248,11 +2251,13 @@
boolean useDialog = (fileName.indexOf("?") == 0);
if (useDialog)
fileName = fileName.substring(1);
- useDialog |= viewer.isApplet && (fileName.indexOf("http:") < 0);
+ useDialog |= viewer.isApplet() && (fileName.indexOf("http:") < 0);
fileName = FileManager.getLocalPathForWritingFile(viewer, fileName);
if (useDialog)
fileName = viewer.dialogAsk(quality == Integer.MIN_VALUE ? "save"
: "saveImage", fileName);
+ if (viewer.isJS && fileName.indexOf("http:") < 0)
+ fileName = "POST://" + fileName;
return fileName;
}
@@ -2393,7 +2398,7 @@
fileName = fileName.substring(1);
fileName = fileName.replace('\\', '/');
boolean isCached = fileName.startsWith("cache://");
- if (viewer.isApplet && fileName.indexOf("://") < 0)
+ if (viewer.isApplet() && fileName.indexOf("://") < 0)
fileName = "file://" + (fileName.startsWith("/") ? "" : "/") + fileName;
if (fileName.endsWith(".pse")) {
viewer.evalString((isCached ? "" : "zap;") + "load SYNC " +
Escape.eS(fileName)
@@ -2455,17 +2460,47 @@
scriptEditor.setVisible(true);
}
+ private String logFileName = null;
+
+ public String getLogFileName() {
+ return (logFileName == null ? "" : logFileName);
+ }
+
+ public String setLogFile(String value) {
+ String path = null;
+ String logFilePath = viewer.getLogFilePath();
+ if (logFilePath == null || value.indexOf("\\") >= 0
+ || value.indexOf("/") >= 0) {
+ value = null;
+ } else if (value.length() > 0) {
+ if (!value.startsWith("JmolLog_"))
+ value = "JmolLog_" + value;
+ path = viewer.getAbsolutePath(privateKey, logFilePath + value);
+ }
+ if (path == null)
+ value = null;
+ else
+ Logger.info(GT._("Setting log file to {0}", path));
+ if (value == null || !viewer.isRestricted(ACCESS.ALL)) {
+ Logger.info(GT._("Cannot set log file path."));
+ value = null;
+ } else {
+ logFileName = path;
+ viewer.global.setS("_logFile", viewer.isApplet() ? value : path);
+ }
+ return value;
+ }
+
public void logToFile(String data) {
try {
boolean doClear = (data.equals("$CLEAR$"));
if (data.indexOf("$NOW$") >= 0)
data = TextFormat.simpleReplace(data, "$NOW$", (new
Date()).toString());
- if (viewer.logFile == null) {
+ if (logFileName == null) {
System.out.println(data);
return;
}
- FileWriter fstream = new FileWriter(viewer.logFile, !doClear);
- BufferedWriter out = new BufferedWriter(fstream);
+ BufferedWriter out = (BufferedWriter) viewer.openLogFile(privateKey,
logFileName, !doClear);
if (!doClear) {
int ptEnd = data.indexOf('\0');
if (ptEnd >= 0)
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/StateManager.java 2013-09-17
14:28:46 UTC (rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/StateManager.java 2013-09-17
14:29:00 UTC (rev 18659)
@@ -719,7 +719,7 @@
setB("hideNotSelected", false); //maintained by the selectionManager
setS("hoverLabel", ""); // maintained by the Hover shape
setB("isKiosk", viewer.isKiosk()); // maintained by Viewer
- setS("logFile", viewer.getLogFile()); // maintained by Viewer
+ setS("logFile", viewer.getLogFileName()); // maintained by Viewer
setI("logLevel", Logger.getLogLevel());
setF("mouseWheelFactor", ActionManager.DEFAULT_MOUSE_WHEEL_FACTOR);
setF("mouseDragFactor", ActionManager.DEFAULT_MOUSE_DRAG_FACTOR);
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-09-17 14:28:46 UTC
(rev 18658)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-09-17 14:29:00 UTC
(rev 18659)
@@ -134,7 +134,8 @@
import java.net.URL;
import java.io.BufferedInputStream;
import java.io.BufferedReader;
-import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
import java.io.OutputStream;
import java.io.Reader;
import java.io.StringReader;
@@ -215,7 +216,12 @@
public ModelSet modelSet;
public FileManager fileManager;
- boolean isApplet;
+ private boolean isApplet;
+ @Override
+ public boolean isApplet() {
+ return isApplet;
+ }
+
boolean isSyntaxAndFileCheck = false;
boolean isSyntaxCheck = false;
boolean listCommands = false;
@@ -246,7 +252,10 @@
private String syncId = "";
private String logFilePath = "";
-
+ String getLogFilePath() {
+ return logFilePath;
+ }
+
private boolean allowScripting;
private boolean isPrintOnly = false;
private boolean isSignedApplet = false;
@@ -335,11 +344,6 @@
return statusManager;
}
- @Override
- public boolean isApplet() {
- return isApplet;
- }
-
public boolean isRestricted(ACCESS a) {
// disables WRITE, LOAD file:/, set logFile
// command line -g and -w options ARE available for final writing of image
@@ -3469,7 +3473,7 @@
public JmolStateCreator getStateCreator() {
if (sc == null)
(sc = (JmolStateCreator) Interface
- .getOptionInterface("viewer.StateCreator")).setViewer(this);
+ .getOptionInterface("viewer.StateCreator")).setViewer(this,
privateKey);
return sc;
}
@@ -5974,7 +5978,7 @@
global.defaultLoadFilter = value;
break;
case T.logfile:
- value = setLogFile(value);
+ value = getStateCreator().setLogFile(value);
if (value == null)
return;
break;
@@ -9066,43 +9070,6 @@
return (global.preserveState && scriptManager != null);
}
- String logFile = null;
-
- public String getLogFile() {
- return (logFile == null ? "" : logFile);
- }
-
- private String setLogFile(String value) {
- String path = null;
- if (logFilePath == null || value.indexOf("\\") >= 0
- || value.indexOf("/") >= 0) {
- value = null;
- } else if (value.length() > 0) {
- if (!value.startsWith("JmolLog_"))
- value = "JmolLog_" + value;
- try {
- path = (isApplet ? logFilePath + value : (new File(logFilePath + value)
- .getAbsolutePath()));
- } catch (Exception e) {
- value = null;
- }
- }
- if (value == null || !isRestricted(ACCESS.ALL)) {
- Logger.info(GT._("Cannot set log file path."));
- value = null;
- } else {
- if (path != null)
- Logger.info(GT._("Setting log file to {0}", path));
- logFile = path;
- }
- return value;
- }
-
- public void log(String data) {
- if (data != null)
- getStateCreator().logToFile(data);
- }
-
boolean isKiosk;
boolean isKiosk() {
@@ -10177,4 +10144,40 @@
}
}
+
+ // ///////////////////////////////////////////////////////////////
+ // delegated to JmolFileAdapter
+ // ///////////////////////////////////////////////////////////////
+
+ public Object openOutputChannel(double privateKey, String fileName, boolean
asWriter)
+ throws IOException {
+ return getFileAdapter().openOutputChannel(privateKey, fileManager,
fileName, asWriter);
+ }
+
+ public InputStream openFileInputStream(double privateKey, String fileName)
throws IOException {
+ return getFileAdapter().openFileInputStream(privateKey, fileName);
+ }
+
+ public String getAbsolutePath(double privateKey, String fileName) {
+ return getFileAdapter().getAbsolutePath(privateKey, fileName);
+ }
+
+ public long getFileLength(double privateKey, String fileName) throws
IOException {
+ return getFileAdapter().getFileLength(privateKey, fileName);
+ }
+
+ public Object openLogFile(double privateKey, String logFileName,
+ boolean asAppend) throws IOException {
+ return getFileAdapter().openLogFile(privateKey, logFileName, asAppend);
+ }
+
+ public void log(String data) {
+ if (data != null)
+ getStateCreator().logToFile(data);
+ }
+
+ public String getLogFileName() {
+ return getStateCreator().getLogFileName();
+ }
+
}
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