public Object getFileAsBytes(String name, OC out, boolean allowZip) {
// ?? used by eval of "WRITE FILE"
// will be full path name
if (name == null) return null;
String fullName = name;
String[] subFileList = null;
if (name.indexOf("|") >= 0) {
subFileList = PT.split(name, "|");
name = subFileList[0];
allowZip = true;
}
Object t =
getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false);
if (t instanceof String) return "Error:" + t;
try {
BufferedInputStream bis = (BufferedInputStream) t;
Object bytes =
(out != null
|| !allowZip
|| subFileList == null
|| subFileList.length <= 1
|| !JmolBinary.isZipS(bis) && !JmolBinary.isPngZipStream(bis)
? JmolBinary.getStreamAsBytes(bis, out)
: JmolBinary.getZipFileContentsAsBytes(bis, subFileList, 1));
bis.close();
return bytes;
} catch (Exception ioe) {
return ioe.toString();
}
}
Object createAtomSetCollectionFromString(
String strModel, Map<String, Object> htParams, boolean isAppend) {
setLoadState(htParams);
boolean isAddH = (strModel.indexOf(JC.ADD_HYDROGEN_TITLE) >= 0);
String[] fnames = (isAddH ? getFileInfo() : null);
FileReader fileReader =
new FileReader(
this,
viewer,
"string",
"string",
"string",
null,
JmolBinary.getBR(strModel),
htParams,
isAppend);
fileReader.run();
if (fnames != null) setFileInfo(fnames);
if (!isAppend && !(fileReader.getAtomSetCollection() instanceof String)) {
viewer.zap(false, true, false);
setFileInfo(
new String[] {strModel == JC.MODELKIT_ZAP_STRING ? JC.MODELKIT_ZAP_TITLE : "string"});
}
return fileReader.getAtomSetCollection();
}
@Override
public String postByteArray(String fileName, byte[] bytes) {
Object ret =
getBufferedInputStreamOrErrorMessageFromName(fileName, null, false, false, bytes, false);
if (ret instanceof String) return (String) ret;
try {
ret = JmolBinary.getStreamAsBytes((BufferedInputStream) ret, null);
} catch (IOException e) {
try {
((BufferedInputStream) ret).close();
} catch (IOException e1) {
// ignore
}
}
return (ret == null ? "" : JmolBinary.fixUTF((byte[]) ret));
}
public void clearPngjCache(String fileName) {
if (fileName != null
&& (pngjCache == null
|| !pngjCache.containsKey(getCanonicalName(JmolBinary.getZipRoot(fileName))))) return;
pngjCache = null;
Logger.info("PNGJ cache cleared");
}
/**
* Sets all local file references in a script file to point to files within dataPath. If a file
* reference contains dataPath, then the file reference is left with that RELATIVE path.
* Otherwise, it is changed to a relative file name within that dataPath.
*
* <p>Only file references starting with "file://" are changed.
*
* @param script
* @param dataPath
* @param isLocal
* @return revised script
*/
private static String setScriptFileRefs(String script, String dataPath, boolean isLocal) {
if (dataPath == null) return script;
boolean noPath = (dataPath.length() == 0);
List<String> fileNames = new List<String>();
JmolBinary.getFileReferences(script, fileNames);
List<String> oldFileNames = new List<String>();
List<String> newFileNames = new List<String>();
int nFiles = fileNames.size();
for (int iFile = 0; iFile < nFiles; iFile++) {
String name0 = fileNames.get(iFile);
String name = name0;
if (isLocal == isLocal(name)) {
int pt = (noPath ? -1 : name.indexOf("/" + dataPath + "/"));
if (pt >= 0) {
name = name.substring(pt + 1);
} else {
pt = name.lastIndexOf("/");
if (pt < 0 && !noPath) name = "/" + name;
if (pt < 0 || noPath) pt++;
name = dataPath + name.substring(pt);
}
}
Logger.info("FileManager substituting " + name0 + " --> " + name);
oldFileNames.addLast("\"" + name0 + "\"");
newFileNames.addLast("\1\"" + name + "\"");
}
return Txt.replaceStrings(script, oldFileNames, newFileNames);
}
void cachePut(String key, Object data) {
key = key.replace('\\', '/');
if (Logger.debugging) Logger.debug("cachePut " + key);
if (data == null || "".equals(data)) { // J2S error -- cannot implement Int32Array.equals
cache.remove(key);
return;
}
cache.put(key, data);
JmolBinary.getCachedPngjBytes(this, key);
}
/**
* just check for a file as being readable. Do not go into a zip file
*
* @param filename
* @return String[2] where [0] is fullpathname and [1] is error message or null
*/
String[] getFullPathNameOrError(String filename) {
String[] names = classifyName(filename, true);
if (names == null || names[0] == null || names.length < 2)
return new String[] {null, "cannot read file name: " + filename};
String name = names[0];
String fullPath = names[0].replace('\\', '/');
name = JmolBinary.getZipRoot(name);
Object errMsg =
getBufferedInputStreamOrErrorMessageFromName(name, fullPath, false, true, null, false);
return new String[] {fullPath, (errMsg instanceof String ? (String) errMsg : null)};
}
public String getEmbeddedFileState(String fileName) {
String[] dir = null;
dir = getZipDirectory(fileName, false);
if (dir.length == 0) {
String state = viewer.getFileAsString4(fileName, -1, false, true, false);
return (state.indexOf(JC.EMBEDDED_SCRIPT_TAG) < 0 ? "" : JmolBinary.getEmbeddedScript(state));
}
for (int i = 0; i < dir.length; i++)
if (dir[i].indexOf(".spt") >= 0) {
String[] data = new String[] {fileName + "|" + dir[i], null};
getFileDataOrErrorAsString(data, -1, false, false, false);
return data[1];
}
return "";
}
Object getBufferedReaderOrErrorMessageFromName(
String name, String[] fullPathNameReturn, boolean isBinary, boolean doSpecialLoad) {
Object data = cacheGet(name, false);
boolean isBytes = PT.isAB(data);
byte[] bytes = (isBytes ? (byte[]) data : null);
if (name.startsWith("cache://")) {
if (data == null) return "cannot read " + name;
if (isBytes) {
bytes = (byte[]) data;
} else {
return JmolBinary.getBR((String) data);
}
}
String[] names = classifyName(name, true);
if (names == null) return "cannot read file name: " + name;
if (fullPathNameReturn != null) fullPathNameReturn[0] = names[0].replace('\\', '/');
return getUnzippedReaderOrStreamFromName(
names[0], bytes, false, isBinary, false, doSpecialLoad, null);
}
/**
* @param data [0] initially path name, but returned as full path name; [1]file contents
* (directory listing for a ZIP/JAR file) or error string
* @param nBytesMax or -1
* @param doSpecialLoad
* @param allowBinary
* @param checkProtected TODO
* @return true if successful; false on error
*/
boolean getFileDataOrErrorAsString(
String[] data,
int nBytesMax,
boolean doSpecialLoad,
boolean allowBinary,
boolean checkProtected) {
data[1] = "";
String name = data[0];
if (name == null) return false;
Object t = getBufferedReaderOrErrorMessageFromName(name, data, false, doSpecialLoad);
if (t instanceof String) {
data[1] = (String) t;
return false;
}
if (checkProtected && !checkSecurity(data[0])) {
data[1] = "java.io. Security exception: cannot read file " + data[0];
return false;
}
try {
return JmolBinary.readAll((BufferedReader) t, nBytesMax, allowBinary, data, 1);
} catch (Exception e) {
return false;
}
}
/**
* @param fileName
* @param addManifest
* @return [] if not a zip file;
*/
public String[] getZipDirectory(String fileName, boolean addManifest) {
Object t =
getBufferedInputStreamOrErrorMessageFromName(fileName, fileName, false, false, null, false);
return JmolBinary.getZipDirectoryAndClose((BufferedInputStream) t, addManifest);
}
/**
* delivers file contents and directory listing for a ZIP/JAR file into sb
*
* @param name
* @param header
* @param fileData
* @return name of entry
*/
private String getObjectAsSections(String name, String header, Map<String, String> fileData) {
if (name == null) return null;
String[] subFileList = null;
boolean asBinaryString = false;
String name0 = name.replace('\\', '/');
if (name.indexOf(":asBinaryString") >= 0) {
asBinaryString = true;
name = name.substring(0, name.indexOf(":asBinaryString"));
}
SB sb = null;
if (fileData.containsKey(name0)) return name0;
if (name.indexOf("#JMOL_MODEL ") >= 0) {
fileData.put(name0, name0 + "\n");
return name0;
}
String fullName = name;
if (name.indexOf("|") >= 0) {
subFileList = PT.split(name, "|");
name = subFileList[0];
}
BufferedInputStream bis = null;
try {
Object t =
getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false);
if (t instanceof String) {
fileData.put(name0, (String) t + "\n");
return name0;
}
bis = (BufferedInputStream) t;
if (JmolBinary.isCompoundDocumentS(bis)) {
JmolDocument doc = (JmolDocument) Interface.getOptionInterface("io2.CompoundDocument");
doc.setStream(bis, true);
doc.getAllDataMapped(name.replace('\\', '/'), "Molecule", fileData);
} else if (JmolBinary.isZipS(bis)) {
JmolBinary.getAllZipData(bis, subFileList, name.replace('\\', '/'), "Molecule", fileData);
} else if (asBinaryString) {
// used for Spartan binary file reading
JmolDocument bd = (JmolDocument) Interface.getOptionInterface("io2.BinaryDocument");
bd.setStream(bis, false);
sb = new SB();
// note -- these headers must match those in ZipUtil.getAllData and
// CompoundDocument.getAllData
if (header != null) sb.append("BEGIN Directory Entry " + name0 + "\n");
try {
while (true) sb.append(Integer.toHexString(bd.readByte() & 0xFF)).appendC(' ');
} catch (Exception e1) {
sb.appendC('\n');
}
if (header != null) sb.append("\nEND Directory Entry " + name0 + "\n");
fileData.put(name0, sb.toString());
} else {
BufferedReader br =
JmolBinary.getBufferedReader(
JmolBinary.isGzipS(bis)
? new BufferedInputStream(JmolBinary.newGZIPInputStream(bis))
: bis,
null);
String line;
sb = new SB();
if (header != null) sb.append("BEGIN Directory Entry " + name0 + "\n");
while ((line = br.readLine()) != null) {
sb.append(line);
sb.appendC('\n');
}
br.close();
if (header != null) sb.append("\nEND Directory Entry " + name0 + "\n");
fileData.put(name0, sb.toString());
}
} catch (Exception ioe) {
fileData.put(name0, ioe.toString());
}
if (bis != null)
try {
bis.close();
} catch (Exception e) {
//
}
if (!fileData.containsKey(name0)) fileData.put(name0, "FILE NOT FOUND: " + name0 + "\n");
return name0;
}
public Object getUnzippedReaderOrStreamFromName(
String name,
byte[] bytes,
boolean allowZipStream,
boolean forceInputStream,
boolean isTypeCheckOnly,
boolean doSpecialLoad,
Map<String, Object> htParams) {
String[] subFileList = null;
String[] info = (bytes == null && doSpecialLoad ? getSpartanFileList(name) : null);
String name00 = name;
if (info != null) {
if (isTypeCheckOnly) return info;
if (info[2] != null) {
String header = info[1];
Map<String, String> fileData = new Hashtable<String, String>();
if (info.length == 3) {
// we need information from the output file, info[2]
String name0 = getObjectAsSections(info[2], header, fileData);
fileData.put("OUTPUT", name0);
info = JmolBinary.spartanFileList(name, fileData.get(name0));
if (info.length == 3) {
// might have a second option
name0 = getObjectAsSections(info[2], header, fileData);
fileData.put("OUTPUT", name0);
info = JmolBinary.spartanFileList(info[1], fileData.get(name0));
}
}
// load each file individually, but return files IN ORDER
SB sb = new SB();
if (fileData.get("OUTPUT") != null) sb.append(fileData.get(fileData.get("OUTPUT")));
String s;
for (int i = 2; i < info.length; i++) {
name = info[i];
name = getObjectAsSections(name, header, fileData);
Logger.info("reading " + name);
s = fileData.get(name);
sb.append(s);
}
s = sb.toString();
if (spardirCache == null) spardirCache = new Hashtable<String, byte[]>();
spardirCache.put(name00.replace('\\', '/'), s.getBytes());
return JmolBinary.getBR(s);
}
// continuing...
// here, for example, for an SPT file load that is not just a type check
// (type check is only for application file opening and drag-drop to
// determine if
// script or load command should be used)
}
if (bytes == null && pngjCache != null) {
bytes = JmolBinary.getCachedPngjBytes(this, name);
if (bytes != null && htParams != null) htParams.put("sourcePNGJ", Boolean.TRUE);
}
String fullName = name;
if (name.indexOf("|") >= 0) {
subFileList = PT.split(name, "|");
if (bytes == null) Logger.info("FileManager opening 3 " + name);
name = subFileList[0];
}
Object t =
(bytes == null
? getBufferedInputStreamOrErrorMessageFromName(
name, fullName, true, false, null, !forceInputStream)
: JmolBinary.getBIS(bytes));
try {
if (t instanceof String) return t;
if (t instanceof BufferedReader) return t;
BufferedInputStream bis = JmolBinary.getUnzippedInputStream((BufferedInputStream) t);
if (JmolBinary.isCompoundDocumentS(bis)) {
JmolDocument doc = (JmolDocument) Interface.getOptionInterface("io2.CompoundDocument");
doc.setStream(bis, true);
return JmolBinary.getBR(doc.getAllDataFiles("Molecule", "Input").toString());
}
if (JmolBinary.isPickleS(bis)) return bis;
bis = JmolBinary.checkPngZipStream(bis);
if (JmolBinary.isZipS(bis)) {
if (allowZipStream) return JmolBinary.newZipInputStream(bis);
Object o = JmolBinary.getZipFileContents(bis, subFileList, 1, forceInputStream);
return (o instanceof String ? JmolBinary.getBR((String) o) : o);
}
return (forceInputStream ? bis : JmolBinary.getBufferedReader(bis, null));
} catch (Exception ioe) {
return ioe.toString();
}
}
public Object getBufferedInputStreamOrErrorMessageFromName(
String name,
String fullName,
boolean showMsg,
boolean checkOnly,
byte[] outputBytes,
boolean allowReader) {
byte[] cacheBytes = null;
if (outputBytes == null) {
cacheBytes =
(fullName == null || pngjCache == null
? null
: JmolBinary.getCachedPngjBytes(this, fullName));
if (cacheBytes == null) cacheBytes = (byte[]) cacheGet(name, true);
}
BufferedInputStream bis = null;
Object ret = null;
String errorMessage = null;
try {
if (cacheBytes == null) {
boolean isPngjBinaryPost = (name.indexOf("?POST?_PNGJBIN_") >= 0);
boolean isPngjPost = (isPngjBinaryPost || name.indexOf("?POST?_PNGJ_") >= 0);
if (name.indexOf("?POST?_PNG_") > 0 || isPngjPost) {
String[] errMsg = new String[1];
byte[] bytes = viewer.getImageAsBytes(isPngjPost ? "PNGJ" : "PNG", 0, 0, -1, errMsg);
if (errMsg[0] != null) return errMsg[0];
if (isPngjBinaryPost) {
outputBytes = bytes;
name = PT.simpleReplace(name, "?_", "=_");
} else {
name = new SB().append(name).append("=").appendSB(Base64.getBase64(bytes)).toString();
}
}
int iurl = urlTypeIndex(name);
boolean isURL = (iurl >= 0);
String post = null;
if (isURL && (iurl = name.indexOf("?POST?")) >= 0) {
post = name.substring(iurl + 6);
name = name.substring(0, iurl);
}
boolean isApplet = (appletDocumentBaseURL != null);
if (name.indexOf(".png") >= 0 && pngjCache == null && viewer.cachePngFiles())
JmolBinary.cachePngjFile(this, null);
if (isApplet || isURL) {
if (isApplet && isURL && appletProxy != null)
name = appletProxy + "?url=" + urlEncode(name);
URL url =
(isApplet
? new URL(appletDocumentBaseURL, name, null)
: new URL((URL) null, name, null));
if (checkOnly) return null;
name = url.toString();
if (showMsg && name.toLowerCase().indexOf("password") < 0)
Logger.info("FileManager opening 1 " + name);
ret = viewer.apiPlatform.getBufferedURLInputStream(url, outputBytes, post);
byte[] bytes = null;
if (ret instanceof SB) {
SB sb = (SB) ret;
if (allowReader && !JmolBinary.isBase64(sb)) return JmolBinary.getBR(sb.toString());
bytes = JmolBinary.getBytesFromSB(sb);
} else if (PT.isAB(ret)) {
bytes = (byte[]) ret;
}
if (bytes != null) ret = JmolBinary.getBIS(bytes);
} else if ((cacheBytes = (byte[]) cacheGet(name, true)) == null) {
if (showMsg) Logger.info("FileManager opening 2 " + name);
ret = viewer.apiPlatform.getBufferedFileInputStream(name);
}
if (ret instanceof String) return ret;
}
bis = (cacheBytes == null ? (BufferedInputStream) ret : JmolBinary.getBIS(cacheBytes));
if (checkOnly) {
bis.close();
bis = null;
}
return bis;
} catch (Exception e) {
try {
if (bis != null) bis.close();
} catch (IOException e1) {
}
errorMessage = "" + e;
}
return errorMessage;
}
