-package uk.ac.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.text.DateFormat;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-
-public class ArchiveWriter {
-
- /**
- * Test program for writing archive files.
- * form is ArchiveWriter new/modified argive command list
- */
-
- static Log log = LogFactory.getLog(ArchiveWriter.class);
-
- private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
- int i;
- for (i=0; i<svec1.length; i++)
- destvec[i] = svec1[i];
- for (int j=0; j<svec2.length; i++, j++)
- destvec[i] = svec2[j];
- }
- // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
- // Merge appDatas require eventually unique URNS
- // TODO: merging global appdata from different documents where same app has written them causes conflict
-
- public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
- if (ht==null)
- ht = new Hashtable();
- for (int i=0, j=appdatas.length; i<j; i++) {
- if (!ht.containsKey(appdatas[i].getUrn())) {
- Hashtable aphash = new Hashtable();
- ht.put(appdatas[i].getUrn(), aphash);
- aphash.put(appdatas[i], appdatas[i].getDataReference());
- } else {
- // ensure urns and references are unique
-
-
- }
-
- }
- return ht;
- }
- /**
- * safely copies an appData from one archive to another.
- * @param darc destination archive
- * @param dest destination document Vobject
- * @param sarc source archive reader
- * @param entry application data to be copied from source archive
- */
- public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, ApplicationData entry) {
- // TODO: fix instances
- // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn
- // check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
- // check uniqueness of entry.user
- // entry.getAppDataChoice().getData() or getDataReference is unique
- ApplicationData newo = new ApplicationData();
- for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- //String urn = entry.getUrn();
- int v = 1;
- //while (o.getUrn().equals(urn)) {
- // urn = entry.getUrn()+v++;
- // }
- // uniqueness of urn
- // check each user ApplicationData
- // uniqueness (again)
- // copy over valid objects
- //
- }
- }
- /**
- * Copy new datasets and appdatas from one vamsas document to another.
- * @param darc
- * @param dest
- * @param sarc
- * @param source
- * @return true if merge was successful.
- */
- public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, VamsasDocument source) {
- log.debug("mergeDocs entered.");
- // search for appDatas in cdoc
- VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount()+source.getVAMSASCount()];
- mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());
- dest.setVAMSAS(newr);
- /** TODO: LATER: should verify that all ids really are unique in newly merged document. If not then what ?
- * investigate possibility of having an id translation between appDatas and the core document -
- * the mapping is stored when an external application performs a merge, but when the owning
- * Application accesses the Vobject, the vorba_id is updated to the new one when it writes its
- * references in to its appdata again
- */
- if (source.getApplicationDataCount()>0) {
- ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
- ApplicationData[] sappd = source.getApplicationData();
- // check refs and update/modify if necessary
- for (int i=0; i<sappd.length; i++) {
- addAppDataEntry(darc, dest, sarc, sappd[i]);
- }
-
- }
-
- return true; // success
- }
-
- private static CommandProcessor cproc;
- static {
- cproc.addCommand("new", 0, "no args");
- cproc.addCommand("add", 1, "Need another vamsas document archive filename as argument.");
- cproc.addCommand("repair", 0, "no args");
- cproc.addCommand("list", 0, "no args");
- cproc.addCommand("monitor", 0, "no args");
- }
-
- public static void main(String argv[]) {
- /**
- * TODO: switches for setting user identities for writing to vamsas document
- */
- if (argv.length<1) {
- log.fatal("Usage : <archive to create> [(commands)]");
- return;
- }
- File newarch = new File(argv[0]);
- int argpos = 0;
- try {
- // test fully fledged doc construction
- VamsasArchive varc = new VamsasArchive(newarch, true);
- VamsasDocument docroot;
- docroot = new VamsasDocument();
- docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document"));
- while (++argpos<argv.length) {
- File archive = new File(argv[argpos]);
- InputStream istream;
- if (archive.exists()) {
- VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
- if (vdoc.isValid()) {
- istream = vdoc.getVamsasDocumentStream();
- if (istream!=null) {
- VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
- if (cdocroot!=null)
- mergeDocs(varc, docroot, vdoc, cdocroot);
- } else
- log.warn("Unexpectedly null document stream from existing document "+archive);
- } else {
- // updating an oldformat stream ?
- if ((istream = vdoc.getVamsasXmlStream())!=null) {
- // make a new vamsas document from the vamsas.xml entry
- VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
- docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user", "added vamsas.xml from "+argv[argpos-1]));
- docroot.addVAMSAS(root);
- }
- }
- } else {
- // Begin a new vamsas document
- PrintWriter docwriter = varc.getDocumentOutputStream();
- }
- }
- } catch (Exception e) {
- log.error("Whilst manipulating "+argv[0], e);
- }
- }
-}
+/*\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.test.simpleclient;\r
+\r
+import java.io.File;\r
+import java.io.InputStream;\r
+import java.io.InputStreamReader;\r
+import java.io.PrintWriter;\r
+import java.text.DateFormat;\r
+import java.util.Date;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+import org.apache.commons.logging.Log;\r
+import org.apache.commons.logging.LogFactory;\r
+import uk.ac.vamsas.objects.core.Alignment;\r
+import uk.ac.vamsas.objects.core.ApplicationData;\r
+import uk.ac.vamsas.objects.core.Entry;\r
+import uk.ac.vamsas.objects.core.Instance;\r
+import uk.ac.vamsas.objects.core.Provenance;\r
+import uk.ac.vamsas.objects.core.VAMSAS;\r
+import uk.ac.vamsas.objects.core.VamsasDocument;\r
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;\r
+\r
+public class ArchiveWriter {\r
+\r
+ /**\r
+ * Test program for writing archive files. form is ArchiveWriter new/modified\r
+ * argive command list\r
+ */\r
+\r
+ static Log log = LogFactory.getLog(ArchiveWriter.class);\r
+\r
+ private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {\r
+ int i;\r
+ for (i = 0; i < svec1.length; i++)\r
+ destvec[i] = svec1[i];\r
+ for (int j = 0; j < svec2.length; i++, j++)\r
+ destvec[i] = svec2[j];\r
+ }\r
+\r
+ // Merge appDataReferences require transfer of jar entries, perhaps with a\r
+ // renaming of the entry.\r
+ // Merge appDatas require eventually unique URNS\r
+ // TODO: merging global appdata from different documents where same app has\r
+ // written them causes conflict\r
+\r
+ public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {\r
+ if (ht == null)\r
+ ht = new Hashtable();\r
+ for (int i = 0, j = appdatas.length; i < j; i++) {\r
+ if (!ht.containsKey(appdatas[i].getUrn())) {\r
+ Hashtable aphash = new Hashtable();\r
+ ht.put(appdatas[i].getUrn(), aphash);\r
+ aphash.put(appdatas[i], appdatas[i].getDataReference());\r
+ } else {\r
+ // ensure urns and references are unique\r
+\r
+ }\r
+\r
+ }\r
+ return ht;\r
+ }\r
+\r
+ /**\r
+ * safely copies an appData from one archive to another.\r
+ * \r
+ * @param darc\r
+ * destination archive\r
+ * @param dest\r
+ * destination document Vobject\r
+ * @param sarc\r
+ * source archive reader\r
+ * @param entry\r
+ * application data to be copied from source archive\r
+ */\r
+ public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest,\r
+ VamsasArchiveReader sarc, ApplicationData entry) {\r
+ // TODO: fix instances\r
+ // check uniqueness of instance's[] entry.urn amongst\r
+ // dest.ApplicationData[].getInstances[].urn\r
+ // check uniqueness of entry.user[].urn amongst\r
+ // dest.ApplicationData[].user[].urn\r
+ // check uniqueness of entry.user\r
+ // entry.getAppDataChoice().getData() or getDataReference is unique\r
+ ApplicationData newo = new ApplicationData();\r
+ for (int i = 0, j = dest.getApplicationDataCount(); i < j; i++) {\r
+ ApplicationData o = dest.getApplicationData()[i];\r
+ // ensure new urn is really unique\r
+ // String urn = entry.getUrn();\r
+ int v = 1;\r
+ // while (o.getUrn().equals(urn)) {\r
+ // urn = entry.getUrn()+v++;\r
+ // }\r
+ // uniqueness of urn\r
+ // check each user ApplicationData\r
+ // uniqueness (again)\r
+ // copy over valid objects\r
+ // \r
+ }\r
+ }\r
+\r
+ /**\r
+ * Copy new datasets and appdatas from one vamsas document to another.\r
+ * \r
+ * @param darc\r
+ * @param dest\r
+ * @param sarc\r
+ * @param source\r
+ * @return true if merge was successful.\r
+ */\r
+ public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest,\r
+ VamsasArchiveReader sarc, VamsasDocument source) {\r
+ log.debug("mergeDocs entered.");\r
+ // search for appDatas in cdoc\r
+ VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount() + source.getVAMSASCount()];\r
+ mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());\r
+ dest.setVAMSAS(newr);\r
+ /**\r
+ * TODO: LATER: should verify that all ids really are unique in newly merged\r
+ * document. If not then what ? investigate possibility of having an id\r
+ * translation between appDatas and the core document - the mapping is\r
+ * stored when an external application performs a merge, but when the owning\r
+ * Application accesses the Vobject, the vorba_id is updated to the new one\r
+ * when it writes its references in to its appdata again\r
+ */\r
+ if (source.getApplicationDataCount() > 0) {\r
+ ApplicationData[] newdat = new ApplicationData[source\r
+ .getApplicationDataCount()\r
+ + dest.getApplicationDataCount()];\r
+ ApplicationData[] sappd = source.getApplicationData();\r
+ // check refs and update/modify if necessary\r
+ for (int i = 0; i < sappd.length; i++) {\r
+ addAppDataEntry(darc, dest, sarc, sappd[i]);\r
+ }\r
+\r
+ }\r
+\r
+ return true; // success\r
+ }\r
+\r
+ private static CommandProcessor cproc;\r
+ static {\r
+ cproc.addCommand("new", 0, "no args");\r
+ cproc.addCommand("add", 1,\r
+ "Need another vamsas document archive filename as argument.");\r
+ cproc.addCommand("repair", 0, "no args");\r
+ cproc.addCommand("list", 0, "no args");\r
+ cproc.addCommand("monitor", 0, "no args");\r
+ }\r
+\r
+ public static void main(String argv[]) {\r
+ /**\r
+ * TODO: switches for setting user identities for writing to vamsas document\r
+ */\r
+ if (argv.length < 1) {\r
+ log.fatal("Usage : <archive to create> [(commands)]");\r
+ return;\r
+ }\r
+ File newarch = new File(argv[0]);\r
+ int argpos = 0;\r
+ try {\r
+ // test fully fledged doc construction\r
+ VamsasArchive varc = new VamsasArchive(newarch, true);\r
+ VamsasDocument docroot;\r
+ docroot = new VamsasDocument();\r
+ docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter",\r
+ "user", "Created new Vamsas Document"));\r
+ while (++argpos < argv.length) {\r
+ File archive = new File(argv[argpos]);\r
+ InputStream istream;\r
+ if (archive.exists()) {\r
+ VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);\r
+ if (vdoc.isValid()) {\r
+ istream = vdoc.getVamsasDocumentStream();\r
+ if (istream != null) {\r
+ VamsasDocument cdocroot = VamsasDocument\r
+ .unmarshal(new InputStreamReader(istream));\r
+ if (cdocroot != null)\r
+ mergeDocs(varc, docroot, vdoc, cdocroot);\r
+ } else\r
+ log\r
+ .warn("Unexpectedly null document stream from existing document "\r
+ + archive);\r
+ } else {\r
+ // updating an oldformat stream ?\r
+ if ((istream = vdoc.getVamsasXmlStream()) != null) {\r
+ // make a new vamsas document from the vamsas.xml entry\r
+ VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO:\r
+ // verify\r
+ // only\r
+ // one\r
+ // VAMSAS\r
+ // element\r
+ // per\r
+ // vamsas.xml\r
+ // entry.\r
+ docroot.getProvenance().addEntry(\r
+ ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user",\r
+ "added vamsas.xml from " + argv[argpos - 1]));\r
+ docroot.addVAMSAS(root);\r
+ }\r
+ }\r
+ } else {\r
+ // Begin a new vamsas document\r
+ PrintWriter docwriter = varc.getDocumentOutputStream();\r
+ }\r
+ }\r
+ } catch (Exception e) {\r
+ log.error("Whilst manipulating " + argv[0], e);\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff