-package uk.ac.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.BufferedInputStream;
-import java.io.FileInputStream;
-import java.io.RandomAccessFile;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import org.apache.tools.zip.*;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.AppDataInputStream;
-import uk.ac.vamsas.objects.utils.document.VersionEntries;
-/**
- * Basic methods for accessing an existing Vamsas Archive,
- * and Jar entry names for creating new vamsas archives.
- *
- * @author jimp
- *
- */
-public class VamsasArchiveReader {
- private static final int JARFILE_OPEN_RETRIES = 50;
- private static final int JARFILE_OPEN_RETRYWAIT = 1;
- private static Log log = LogFactory.getLog(VamsasArchiveReader.class);
- ZipFile jfile=null;
- String jfileName="randomAccessFile";
- boolean stream=false; // true if we are seeking on the stream.
- RandomAccessFile rfile;
- // ZipInputStream jstream=null;
- Hashtable strmentries = null;
- private void streamInit() {
- //throw new Error("VamsasArchiveReader(Stream) Not implemented!");
- if (!stream) {
- log.debug("Skipping init for Jar Stream input.");
- return;
- } else {
- throw new Error("Implementation error - we don't do streams - only files or RA files");
- }
- /*strmentries = new Hashtable();
- log.debug("Jar Stream input Initialisation");
- try {
- rfile.seek(0);
- // no buffering - we need to be able to move around the random access stream.
- jstream = new ZipInputStream(new FileInputStream(rfile.getFD())); // no manifest (probably)
- if (jstream.available()==0)
- log.warn("Can't read from JarInputStream (Locked stream!)");
- ZipEntry entry=null;
- long pos=0;
- do {
- if ((entry=jstream.getNextEntry())!=null) {
- if (strmentries.containsKey(entry.getName())) {
- log.info("Only recording last of duplicate entries '"+entry.getName()+"'");
- }
- strmentries.put(entry.getName(), new Long(pos++));
- jstream.closeEntry();
- }
- } while (entry!=null);
- }
- catch (Exception e) {
- log.warn("Exceptions during init!",e);
- jstream=null;
- } */
- }
-
- public VamsasArchiveReader(File vamsasfile) {
- jfile=null;
- int retries=JARFILE_OPEN_RETRIES;
- Exception ex=null;
- if (vamsasfile.exists()) {
- while (jfile==null && --retries>0)
- {
- try {
- jfile=new ZipFile(vamsasfile);
- jfileName = vamsasfile.toString();
- }
- catch (Exception e) {
- ex = e;
- jfile=null;
- try {
- Thread.sleep(JARFILE_OPEN_RETRYWAIT);
- } catch (Exception w) {};
- }
- }
- if (jfile==null && ex!=null)
- {
- log.debug("non-serious? Exceptions when opening JarFile at "+vamsasfile,ex);
- }
- }
- }
- /**
- * in an ideal world - this constructor will create a reader object
- * for the locked file's random access stream.
- *
- * @param vamsaslock
- */
- public VamsasArchiveReader(Lock vamsaslock) {
- jfile = null;
- if (vamsaslock==null || !vamsaslock.isLocked())
- throw new Error("IMPLEMENTATION ERROR: Cannot create a VamsasArchiveReader without a valid lock.");
- // throw new Error("VamsasArchiveReading from locked IO stream not yet implemented.");
- try {
- rfile = vamsaslock.getRaFile();
- jfile = new ZipFile(rfile);
- if (vamsaslock.target!=null)
- jfileName = vamsaslock.target.toString();
- } catch (Exception e) {
- rfile = null;
- jfile = null;
- log.warn("Unexpected IO Exception when accessing locked vamsas archive stream "+vamsaslock.target,e);
- }
- /*stream = true;
- streamInit();
- if (jstream==null)
- throw new Error("Failed to open archive from Locked random access stream.");
- */
- }
-
- /**
- * the vamsas document version(s) handled by this Reader
- */
- final public static String DOCUMENT_VERSION=VersionEntries.BETA_VERSION;
- /**
- * name of the jarEntry containing a well formatted vamsas XML Document
- */
-
- final public static String VAMSASDOC="vamsasDocument.xml";
-
- /**
- * name of the jarEntry containing a root VAMSAS element, and containing a
- * random sequence of VAMSAS DataSet elements
- */
-
- final public static String VAMSASXML="vamsas.xml";
- /**
- * seeks jstream to the given entry name and reads it.
- * @param entryname
- * @return
- private JarEntry seekEntry(String entryname) {
- if (jstream==null)
- return null;
- if (!strmentries.containsKey(entryname))
- return null;
- Long entrypos = (Long) strmentries.get(entryname);
- if (entrypos==null) {
- log.error("Null entry position for "+entryname);
- return null;
- }
- try {
- jstream=null;
- rfile.seek(0);
- jstream = new ZipInputStream(new FileInputStream(rfile.getFD()));
- ZipEntry entry = null;
- long epos = entrypos.longValue();
- do {
- entry = jstream.getNextEntry();
- } while (entry!=null && --epos>=0);
- // rfile.seek(entrypos.longValue());
- // make a Jar entry from a zip entry.
- return new JarEntry(entry);
- }
- catch (Exception e) {
- log.warn("Whilst seeking for "+entryname, e);
- }
- return null;
- }
- */
- /**
- *
- * @return JarEntry for VamsasArchiveReader.VAMSASDOC
- */
- protected ZipEntry getVamsasDocumentEntry() {
- return getJarEntry(VAMSASDOC);
- }
- /**
- *
- * @return JarEntry for VamsasArchiveReader.VAMSASXML
- */
- protected ZipEntry getVamsasXmlEntry() {
- return getJarEntry(VAMSASXML);
- }
- /**
- * Test for valid vamsas document archive
- * @return true if getVamsasDocumentStream will return a stream likely to contain valid XML
- */
- public boolean isValid() {
- // TODO: check if VAMSASDOC is well formed (follows www.vamsas.ac.uk/schemas/vamsasDocument.xsd) and all appData references are resolvable - preferably as jar entries
- if (jfile!=null) // || jstream!=null)
- return (getVamsasDocumentEntry()!=null);
- return false;
- }
-
-
- protected ZipEntry getAppdataEntry(String AppdataRef) {
- ZipEntry entry;
- if (jfile==null || !isValid() || (entry=getJarEntry(AppdataRef))==null)
- return null;
-
- return entry;
- }
-
- public InputStream getAppdataStream(String AppdataRef) {
- ZipEntry entry=getAppdataEntry(AppdataRef);
- try {
- if (entry!=null)
- return getInputStream(entry);
- } catch (IOException e) {
- log.error("Failed when opening AppdataStream for "+AppdataRef, e);
- }
- return null;
- }
- /**
- * get the VamsasDocument input stream, if it exists.
- * @return null or valid input stream
- */
- public InputStream getVamsasDocumentStream() {
- InputStream vdoc;
- if (jfile==null || !isValid())
- return null;
- try {
- vdoc = getInputStream(getVamsasDocumentEntry());
- } catch (IOException e) {
- log.error("Whilst geting document stream",e);
- vdoc=null;
- }
- return vdoc;
- }
-
- /**
- * get the VamsasXML input stream, if it exists.
- * Note: Deprecated beyond our prealpha testing.
- * @return null or valid input stream.
- */
-
- public InputStream getVamsasXmlStream() {
- // log.warn("Deprecated call");
- ZipEntry xmle=getVamsasXmlEntry();
- InputStream vdoc;
- if (xmle==null)
- return null;
- try {
- vdoc = getInputStream(xmle);
- } catch (IOException e) {
- log.error("Whilst getting VamsasXmlStream",e);
- vdoc=null;
- }
- return vdoc;
- }
-
- /**
- * silently close the jar file.
- *
- */
- public void close() {
- if (jfile!=null) {
- try {
- jfile.close();
- rfile=null;
- }
- catch (Exception e) {
- log.error("Whilst closing JarFile "+jfileName, e);
- }
- }
- }
-
- /**
- * returns all entries not matching the filespec of a vamsas xml entry
- * @return array of entries.
- */
- public Vector getExtraEntries() {
- if (jfile==null || !isValid())
- return null;
- Vector e = new Vector();
- /*if (jstream!=null) {
- Enumeration entries = strmentries.keys();
- if (entries!=null && entries.hasMoreElements()) {
- do {
- JarEntry el = (JarEntry) entries.nextElement();
- if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML))
- e.add(new String(el.getName())); // avoid references
- } while (entries.hasMoreElements());
- }
- } else */
- Enumeration entries = jfile.getEntries();
- if (entries!=null && entries.hasMoreElements()) {
- do {
- ZipEntry el = (ZipEntry) entries.nextElement();
- if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML))
- e.add(new String(el.getName())); // avoid references
- } while (entries.hasMoreElements());
- }
- return e;
- }
-
- /* (non-Javadoc)
- * @see java.util.jar.JarFile#getInputStream(java.util.zip.ZipEntry)
- */
- private InputStream getInputStream(ZipEntry ze) throws IOException {
- if (jfile!=null)
- return jfile.getInputStream(ze);
- return null;
- }
-
- /* (non-Javadoc)
- * @see java.util.jar.JarFile#getJarEntry(java.lang.String)
- */
- private ZipEntry getJarEntry(String name) {
- if (jfile!=null)
- return jfile.getEntry(name);
- return null;
- }
- }
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.client.simpleclient;\r
+\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.io.BufferedInputStream;\r
+import java.io.FileInputStream;\r
+import java.io.RandomAccessFile;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Iterator;\r
+import java.util.Vector;\r
+import org.apache.tools.zip.*;\r
+import org.apache.commons.logging.Log;\r
+import org.apache.commons.logging.LogFactory;\r
+\r
+import uk.ac.vamsas.client.AppDataInputStream;\r
+import uk.ac.vamsas.objects.utils.document.VersionEntries;\r
+\r
+/**\r
+ * Basic methods for accessing an existing Vamsas Archive, and Jar entry names\r
+ * for creating new vamsas archives.\r
+ * \r
+ * @author jimp\r
+ * \r
+ */\r
+public class VamsasArchiveReader {\r
+ private static final int JARFILE_OPEN_RETRIES = 50;\r
+\r
+ private static final int JARFILE_OPEN_RETRYWAIT = 1;\r
+\r
+ private static Log log = LogFactory.getLog(VamsasArchiveReader.class);\r
+\r
+ ZipFile jfile = null;\r
+\r
+ String jfileName = "randomAccessFile";\r
+\r
+ boolean stream = false; // true if we are seeking on the stream.\r
+\r
+ RandomAccessFile rfile;\r
+\r
+ // ZipInputStream jstream=null;\r
+ Hashtable strmentries = null;\r
+\r
+ private void streamInit() {\r
+ // throw new Error("VamsasArchiveReader(Stream) Not implemented!");\r
+ if (!stream) {\r
+ log.debug("Skipping init for Jar Stream input.");\r
+ return;\r
+ } else {\r
+ throw new Error(\r
+ "Implementation error - we don't do streams - only files or RA files");\r
+ }\r
+ /*\r
+ * strmentries = new Hashtable();\r
+ * log.debug("Jar Stream input Initialisation"); try { rfile.seek(0); // no\r
+ * buffering - we need to be able to move around the random access stream.\r
+ * jstream = new ZipInputStream(new FileInputStream(rfile.getFD())); // no\r
+ * manifest (probably) if (jstream.available()==0)\r
+ * log.warn("Can't read from JarInputStream (Locked stream!)"); ZipEntry\r
+ * entry=null; long pos=0; do { if ((entry=jstream.getNextEntry())!=null) {\r
+ * if (strmentries.containsKey(entry.getName())) {\r
+ * log.info("Only recording last of duplicate entries '"\r
+ * +entry.getName()+"'"); } strmentries.put(entry.getName(), new\r
+ * Long(pos++)); jstream.closeEntry(); } } while (entry!=null); } catch\r
+ * (Exception e) { log.warn("Exceptions during init!",e); jstream=null; }\r
+ */\r
+ }\r
+\r
+ public VamsasArchiveReader(File vamsasfile) {\r
+ jfile = null;\r
+ int retries = JARFILE_OPEN_RETRIES;\r
+ Exception ex = null;\r
+ if (vamsasfile.exists()) {\r
+ while (jfile == null && --retries > 0) {\r
+ try {\r
+ jfile = new ZipFile(vamsasfile);\r
+ jfileName = vamsasfile.toString();\r
+ } catch (Exception e) {\r
+ ex = e;\r
+ jfile = null;\r
+ try {\r
+ Thread.sleep(JARFILE_OPEN_RETRYWAIT);\r
+ } catch (Exception w) {\r
+ }\r
+ ;\r
+ }\r
+ }\r
+ if (jfile == null && ex != null) {\r
+ log.debug("non-serious? Exceptions when opening JarFile at "\r
+ + vamsasfile, ex);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * in an ideal world - this constructor will create a reader object for the\r
+ * locked file's random access stream.\r
+ * \r
+ * @param vamsaslock\r
+ */\r
+ public VamsasArchiveReader(Lock vamsaslock) {\r
+ jfile = null;\r
+ if (vamsaslock == null || !vamsaslock.isLocked())\r
+ throw new Error(\r
+ "IMPLEMENTATION ERROR: Cannot create a VamsasArchiveReader without a valid lock.");\r
+ // throw new\r
+ // Error("VamsasArchiveReading from locked IO stream not yet implemented.");\r
+ try {\r
+ rfile = vamsaslock.getRaFile();\r
+ jfile = new ZipFile(rfile);\r
+ if (vamsaslock.target != null)\r
+ jfileName = vamsaslock.target.toString();\r
+ } catch (Exception e) {\r
+ rfile = null;\r
+ jfile = null;\r
+ log.warn(\r
+ "Unexpected IO Exception when accessing locked vamsas archive stream "\r
+ + vamsaslock.target, e);\r
+ }\r
+ /*\r
+ * stream = true; streamInit(); if (jstream==null) throw new\r
+ * Error("Failed to open archive from Locked random access stream.");\r
+ */\r
+ }\r
+\r
+ /**\r
+ * the vamsas document version(s) handled by this Reader\r
+ */\r
+ final public static String DOCUMENT_VERSION = VersionEntries.BETA_VERSION;\r
+\r
+ /**\r
+ * name of the jarEntry containing a well formatted vamsas XML Document\r
+ */\r
+\r
+ final public static String VAMSASDOC = "vamsasDocument.xml";\r
+\r
+ /**\r
+ * name of the jarEntry containing a root VAMSAS element, and containing a\r
+ * random sequence of VAMSAS DataSet elements\r
+ */\r
+\r
+ final public static String VAMSASXML = "vamsas.xml";\r
+\r
+ /**\r
+ * seeks jstream to the given entry name and reads it.\r
+ * \r
+ * @param entryname\r
+ * @return private JarEntry seekEntry(String entryname) { if (jstream==null)\r
+ * return null; if (!strmentries.containsKey(entryname)) return null;\r
+ * Long entrypos = (Long) strmentries.get(entryname); if\r
+ * (entrypos==null) { log.error("Null entry position for "+entryname);\r
+ * return null; } try { jstream=null; rfile.seek(0); jstream = new\r
+ * ZipInputStream(new FileInputStream(rfile.getFD())); ZipEntry entry\r
+ * = null; long epos = entrypos.longValue(); do { entry =\r
+ * jstream.getNextEntry(); } while (entry!=null && --epos>=0); //\r
+ * rfile.seek(entrypos.longValue()); // make a Jar entry from a zip\r
+ * entry. return new JarEntry(entry); } catch (Exception e) {\r
+ * log.warn("Whilst seeking for "+entryname, e); } return null; }\r
+ */\r
+ /**\r
+ * \r
+ * @return JarEntry for VamsasArchiveReader.VAMSASDOC\r
+ */\r
+ protected ZipEntry getVamsasDocumentEntry() {\r
+ return getJarEntry(VAMSASDOC);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return JarEntry for VamsasArchiveReader.VAMSASXML\r
+ */\r
+ protected ZipEntry getVamsasXmlEntry() {\r
+ return getJarEntry(VAMSASXML);\r
+ }\r
+\r
+ /**\r
+ * Test for valid vamsas document archive\r
+ * \r
+ * @return true if getVamsasDocumentStream will return a stream likely to\r
+ * contain valid XML\r
+ */\r
+ public boolean isValid() {\r
+ // TODO: check if VAMSASDOC is well formed (follows\r
+ // www.vamsas.ac.uk/schemas/vamsasDocument.xsd) and all appData references\r
+ // are resolvable - preferably as jar entries\r
+ if (jfile != null) // || jstream!=null)\r
+ return (getVamsasDocumentEntry() != null);\r
+ return false;\r
+ }\r
+\r
+ protected ZipEntry getAppdataEntry(String AppdataRef) {\r
+ ZipEntry entry;\r
+ if (jfile == null || !isValid()\r
+ || (entry = getJarEntry(AppdataRef)) == null)\r
+ return null;\r
+\r
+ return entry;\r
+ }\r
+\r
+ public InputStream getAppdataStream(String AppdataRef) {\r
+ ZipEntry entry = getAppdataEntry(AppdataRef);\r
+ try {\r
+ if (entry != null)\r
+ return getInputStream(entry);\r
+ } catch (IOException e) {\r
+ log.error("Failed when opening AppdataStream for " + AppdataRef, e);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get the VamsasDocument input stream, if it exists.\r
+ * \r
+ * @return null or valid input stream\r
+ */\r
+ public InputStream getVamsasDocumentStream() {\r
+ InputStream vdoc;\r
+ if (jfile == null || !isValid())\r
+ return null;\r
+ try {\r
+ vdoc = getInputStream(getVamsasDocumentEntry());\r
+ } catch (IOException e) {\r
+ log.error("Whilst geting document stream", e);\r
+ vdoc = null;\r
+ }\r
+ return vdoc;\r
+ }\r
+\r
+ /**\r
+ * get the VamsasXML input stream, if it exists. Note: Deprecated beyond our\r
+ * prealpha testing.\r
+ * \r
+ * @return null or valid input stream.\r
+ */\r
+\r
+ public InputStream getVamsasXmlStream() {\r
+ // log.warn("Deprecated call");\r
+ ZipEntry xmle = getVamsasXmlEntry();\r
+ InputStream vdoc;\r
+ if (xmle == null)\r
+ return null;\r
+ try {\r
+ vdoc = getInputStream(xmle);\r
+ } catch (IOException e) {\r
+ log.error("Whilst getting VamsasXmlStream", e);\r
+ vdoc = null;\r
+ }\r
+ return vdoc;\r
+ }\r
+\r
+ /**\r
+ * silently close the jar file.\r
+ * \r
+ */\r
+ public void close() {\r
+ if (jfile != null) {\r
+ try {\r
+ jfile.close();\r
+ rfile = null;\r
+ } catch (Exception e) {\r
+ log.error("Whilst closing JarFile " + jfileName, e);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * returns all entries not matching the filespec of a vamsas xml entry\r
+ * \r
+ * @return array of entries.\r
+ */\r
+ public Vector getExtraEntries() {\r
+ if (jfile == null || !isValid())\r
+ return null;\r
+ Vector e = new Vector();\r
+ /*\r
+ * if (jstream!=null) { Enumeration entries = strmentries.keys(); if\r
+ * (entries!=null && entries.hasMoreElements()) { do { JarEntry el =\r
+ * (JarEntry) entries.nextElement(); if (!el.getName().equals(VAMSASDOC) &&\r
+ * !el.getName().equals(VAMSASXML)) e.add(new String(el.getName())); //\r
+ * avoid references } while (entries.hasMoreElements()); } } else\r
+ */\r
+ Enumeration entries = jfile.getEntries();\r
+ if (entries != null && entries.hasMoreElements()) {\r
+ do {\r
+ ZipEntry el = (ZipEntry) entries.nextElement();\r
+ if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML))\r
+ e.add(new String(el.getName())); // avoid references\r
+ } while (entries.hasMoreElements());\r
+ }\r
+ return e;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see java.util.jar.JarFile#getInputStream(java.util.zip.ZipEntry)\r
+ */\r
+ private InputStream getInputStream(ZipEntry ze) throws IOException {\r
+ if (jfile != null)\r
+ return jfile.getInputStream(ze);\r
+ return null;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see java.util.jar.JarFile#getJarEntry(java.lang.String)\r
+ */\r
+ private ZipEntry getJarEntry(String name) {\r
+ if (jfile != null)\r
+ return jfile.getEntry(name);\r
+ return null;\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff