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schemaListallSchemasRegistered eresolverLorg/xml/sax/EntityResolver; dtdhandlerLorg/xml/sax/DTDHandler; parserName>Ljava/util/Vector;S {T(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;Ljava/lang/String;Ljava/io/Reader;Ljava/lang/String;Ljava/lang/String;[Ljava/lang/String;Ljava/lang/String;ILjava/io/Reader;Ljava/lang/String;ZZLjava/util/Date;Ljava/util/Date;Ljava/lang/String;ZLjava/util/Vector;Ljava/lang/String;)Lorg/xml/sax/XMLReader;archiveDocAndNodesRevisionz(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;Ljava/lang/String;Ledu/ucsb/nceas/metacat/DocumentImpl;)VarchiveDocAndNodesRevisonV(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;Ljava/lang/String;J)VupdateNodeValuesC(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;)V dataNumeric dataDateValueLjava/util/Calendar; dataTimestamp sqlStatementrsetcountmoveNodesToNodesRevision2(Ledu/ucsb/nceas/metacat/database/DBConnection;J)VarchiveDocRevisionU(Ljava/lang/String;Ljava/lang/String;Ledu/ucsb/nceas/metacat/database/DBConnection;)VdeleteXMLDocumentspStmtgetServerLocationNumber(Ljava/lang/String;)IhasRow getServerCode serverName insertServerIntoReplicationTablecal replicate dataReplicatehubmain([Ljava/lang/String;)Vxmldocfilename dtdfilename showRuntimeuseOldReadAlgorithm argsAreValid startTimeconnTimestopTime dbOpenTime insertTime executionTimemeane1Ledu/ucsb/nceas/metacat/AccessionNumberException;args BwriteDocumentToRevisionTable(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;IJLjava/util/Date;Ljava/util/Date;)VconregisterDeletedDataFiledeleteXMLNodesgetRevisionRootNodeIdD(Ledu/ucsb/nceas/metacat/database/DBConnection;Ljava/lang/String;I)Jeml200NameSpaceeml201NameSpaceeml210NameSpaceeml211NameSpace rdfNameSpace SourceFileDocumentImpl.java               | } ~   ,-  34$edu/ucsb/nceas/metacat/McdbExceptionjava/lang/Throwablejava/lang/StringBuilderError reading document: [J  java/lang/Integer V AB  java/lang/Exception*DocumentImpl.registerDocumentInreplication  m V 56 after check rev, the action is  UPDATE  document.accNumSeparator  User 0 does not have permission to update the document  [ #edu/ucsb/nceas/metacat/DocumentImpl xml_documents     xml_revisions 86 Couldn't handle this table name   Jjava/util/Date N  java/lang/StringBufferINSERT insert into  (docid, docname, doctype, >user_owner, user_updated, server_location, rev, date_created, %date_updated, public_access) values (?, '0')  n java/sql/Timestamp N %update xml_documents set docname = ?,user_updated = ?, server_location= ?,  rev = ?, date_updated = ? where docid = ? 8DocumentImpl.modifyRecordsInGivenTable - executing SQL: Caught a general exception: J5Please specify the directory where file will be store#Please specify the stored file name   java/io/File  java/io/FileOutputStream  java/io/BufferedOutputStream  java/io/BufferedInputStream  J    :edu/ucsb/nceas/metacat/replication/ForceReplicationHandler  !ForceReplicationHandler created: The docid without rev is The user specifyRev: The rev in data base: Local server: J has newer revision of doc: .. Please notify it. The docid's revision number couldn't be java/sql/SQLExceptionLocal rev for docid  could not be found because Docid G could not be written because error happend to find it's local revision)rev list in xml_revision table for docid  is  2The docid and rev is already in xml_revision table ?A   attempting to lock  java/net/URLhttps://?server= J&action=getlock&updaterev=&docid= >   lock granted for  from  lock denied for  on  reason: file already lockedThe file specified is already locked by another user. Please wait 30 seconds, checkout the newer document, merge your changes and try again. reason: local file outdatedThe file you are trying to update is an outdated version. Please checkout the newest document, merge your changes and try again.   java/io/ByteArrayOutputStream mn+org/apache/commons/io/input/XmlStreamReaderjava/io/ByteArrayInputStream j  J ['Could not convert documentImpl to xml: "edu/ucsb/nceas/metacat/ElementNode    > application.documentfilepath   {| 2edu/ucsb/nceas/utilities/PropertyNotFoundExceptionCould not write file:  : java/io/IOException5Attempting to read a zero length document from disk:     UTF-8java/io/OutputStreamWriter  java/util/Stack  r !edu/ucsb/nceas/metacat/NodeRecord[Got Node ID: N  ( N, N J J J)]  POPPED:  q J JELEMENT">  PUSHED: <'edu/ucsb/nceas/metacat/Eml200SAXHandlerinline ATTRIBUTE ="" NAMESPACE xmlns: J xmlnsTEXT  t  s java/lang/String  COMMENTPIpublicidsystemid V  ij   u @   java/io/FileInputStream &edu/ucsb/nceas/utilities/UtilException0Attempting to write a file with no xml content: ?Could not write document file. Accession Number number is null `The file you are trying to write already exists in metacat. Please update your version number. v JKDocumentImple.writeToFileSystem - the checksum from the system metadata is hDocumentImple.writeToFileSystem - the checksum value from the system metadata shouldn't be null or blank4org/dataone/service/exceptions/InvalidSystemMetadata1180GThe checksum value from the system metadata shouldn't be null or blank. l JfDocumentImple.writeToFileSystem - the algorithm to calculate the checksum from the system metadata is }DocumentImple.writeToFileSystem - the algorithm to calculate the checksum from the system metadata shouldn't be null or blank\The algorithm to calculate the checksum from the system metadata shouldn't be null or blank. w &java/security/NoSuchAlgorithmExceptionADocumentImple.writeToFileSystem - we don't support the algorithm  to calculate the checksum. The algorithm - to calculate the checksum is not supported: ^DocumentImple.writeToFileSystem - we need to compute the checksum since it is from DataONE API java/security/DigestOutputStream  dDocumentImple.writeToFileSystem - we don't need to compute the checksum since it is from Metacat API J  p j XDocumentImple.writeToFileSystem - the check sum calculated from the saved local file is @:. But it doesn't match the value from the system metadata Delete the file J sucessfully? 5The checksum calculated from the saved local file is 7Could not delete file. Accession Number number is null  Could not delete file: ECould not get the file path since the Accession Number number is nullapplication.datafilepath    J!: Could not delete file because:  id="  .*   x  CV  'Could not find end tag for distribution V   3Could not find an inline element for distribution:  #Could not find distribution number  !7edu/ucsb/nceas/metacat/common/query/EnabledQueryEngines pathquery "@3DocumentImpl.buildIndex - building index for docid  # $Njava/util/HashMapjava/lang/Long % &>DocumentImpl.buildIndex - The time to put node id into map is 'DocumentImpl.buildIndex    ( ))DocumentImpl.buildIndex - Converted node  to type * + -DocumentImpl.buildIndex - updating path index   ,@DocumentImpl.buildIndex - SQL Exception while indexing document 4DocumentImpl.buildIndex - Error while rolling back: SQL error when building Index: 4DocumentImpl.buildIndex - The time for inserting is 8DocumentImpl.buildIndex - BuildIndex complete for docid spatial.runSpatialOptiontrue/edu/ucsb/nceas/metacat/spatial/SpatialHarvesterLDocumentImpl.buildIndex - Attempting to update the spatial cache for docid - .HDocumentImpl.buildIndex - Finished updating the spatial cache for docid gDocumentImpl.buildIndex - Could not get 'runSpatialOption' property. Spatial cache not run for docid: )java/lang/StringIndexOutOfBoundsExceptionVDocumentImpl.buildIndex - String indexing problem. Spatial cache not run for docid: / 0 1 2@"DocumentImpl.traverseParents - A:  %edu/ucsb/nceas/metacat/PathIndexEntry  3 V9DocumentImpl.traverseParents - paths found for indexing:  4/"DocumentImpl.traverseParents - B: "DocumentImpl.traverseParents - C: %DELETE FROM xml_index WHERE docid = ? 5 .DocumentImpl.deleteNodeIndex - executing SQL: 6V'DocumentImpl.deleteNodeIndex - Deleted " rows from xml_index for document 8DocumentImpl.deleteNodeIndex - The delete index time is +edu/ucsb/nceas/metacat/XMLQueryresultAccess 7-edu/ucsb/nceas/metacat/shared/AccessException,Problem deleting xml query result for docid ( rows from xml_queryresult for document ?DocumentImpl.deleteNodeIndex - The delete query result time is *DELETE FROM xml_path_index WHERE docid = ?=DocumentImpl.deleteNodeIndex - The delete path index time is ' rows from xml_path_index for document YINSERT INTO xml_index (nodeid, path, docid, doctype, parentnodeid) VALUES (?, ?, ?, ?, ?) 8 9 :  ; <  .DocumentImpl.updateNodeIndex - executing SQL: {INSERT INTO xml_path_index (docid, path, nodedata, nodedatanumerical, nodedatadate, parentnodeid) VALUES (?, ?, ?, ?, ?, ?)3DocumentImpl.updatePathIndex - the path for doc id E is too long and will db break indexing. This path was not indexed: =8DocumentImpl.updatePathIndex - the node data for doc id E is too long and will break db indexing. This path was not indexed: > ? @ A .DocumentImpl.updatePathIndex - executing SQL: DocumentImpl.isRevisionOnly0select rev from xml_documents where docid like ?-DocumentImpl.isRevisionOnly - executing SQL: B C y D EErequested revision cannot be greater than the latest revision number./edu/ucsb/nceas/metacat/McdbDocNotFoundExceptionthe requested docid '' does not exist  F "A.DocumentImpl.getDocumentInfo - general error: DocumentImpl.getDocumentInfo%SELECT docname, doctype, rootnodeid, 5date_created, date_updated, user_owner, user_updated,$ server_location, public_access, rev FROM  WHERE docid LIKE ?  and rev = ? .DocumentImpl.getDocumentInfo - executing SQL: G H I J K5select server from xml_replication where serverid = ? localhost'DocumentImpl.getDocumentInfo - server: ASELECT system_id, entry_type FROM xml_catalog WHERE public_id = ?http:// LJ,DocumentImpl.getDocumentInfo - General errorFDocumentImpl.getDocumentInfo - Error in DocumentImpl.getDocumentInfo: a M N ODDocumentImpl.getDocumentInfo - Error accessing database connection:  PDocument not found: java/util/TreeSet%edu/ucsb/nceas/metacat/NodeComparator  Q xml_nodesxml_nodes_revisions0DocumentImpl.getNodeRecordList - General error: DocumentImpl.getNodeRecordListrSELECT nodeid,parentnodeid,nodeindex, nodetype,nodename,nodeprefix,nodedata, nodedatanumerical, nodedatadate FROM  WHERE rootnodeid = ?0DocumentImpl.getNodeRecordList - executing SQL: ODocumentImpl.getNodeRecordList - Node data in read process before normalize=== RODocumentImpl.getNodeRecordList - Node data in read process after normalize==== jDocumentImpl.getNodeRecordList - StringIndexOutOfBoundsException in normalize() while reading the document S T  U V (Error in DocumentImpl.getNodeRecordList PINSERT INTO xml_documents (docid, rootnodeid, docname, doctype, user_owner, user_updated, date_created, date_updated, public_access, server_location, rev, catalog_id) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)INSERT INTO xml_documents (docid, rootnodeid, docname, doctype, user_owner, user_updated, date_created, date_updated, public_access, server_location, rev) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)3DocumentImpl.writeDocumentToDB - this revision is: 4Next revision number couldn't be less than or equal 4DocumentImpl.writeDocumentToDB - final revision is: java/lang/Booleandatabase.usexmlindex W  ml#DELETE FROM xml_index WHERE docid=''0DocumentImpl.writeDocumentToDB - executing SQL: HDocumentImpl.writeDocumentToDB - Time for delete xml_index in UPDATE is UPDATE xml_documents SET rootnodeid = ?, docname = ?, doctype = ?, user_updated = ?, date_updated = ?, server_location = ?, rev = ?, public_access = ?, catalog_id = ? WHERE docid = ?UPDATE xml_documents SET rootnodeid = ?, docname = ?, doctype = ?, user_updated = ?, date_updated = ?, server_location = ?, rev = ?, public_access = ? WHERE docid = ?7DocumentImpl.writeDocumentToDB - Action not supported: ?DocumentImpl.writeDocumentToDB - Deleting xml nodes for docid: RJ using root node ID: MN ,DocumentImpl.writeDocumentToDB - SQL error: N0DocumentImpl.writeDocumentToDB - General error: JSjava/io/StringReader i X6DocumentImpl.write - conn usage count before writing: YV&edu/ucsb/nceas/metacat/AccessionNumber ZJ YJDocumentImpl.write - action:  servercode:  override: [2 does not have permission to update XML Document #0Error during replication lock request on server=  \java/util/Vector(DocumentImpl.write - initializing parser  DocumentImpl.write - parsing xmlorg/xml/sax/InputSource  ] z ^ _ /DocumentImpl.write - Writing xml to file system  kl/edu/ucsb/nceas/metacat/dataone/SyncAccessPolicy ` a'Error syncing pids with CN: Exception +DocumentImpl.write - Problem with parsing: b c d vw6DocumentImpl.write - ForceReplicationHandler created: %DocumentImpl.write - lock denied for  e f gTDocumentImpl.write - Error in deleting enteries from xml_queryresult where docid is  in DBQuery.write:  hdatabase.queryCacheOn i j5DocumentImpl.write - Conn Usage count after writing:  k l Vl ml3DocumentImpl.writeReplication - user in replication9DocumentImpl.writeReplication - The docid without rev is 5DocumentImpl.writeReplication - The user specifyRev: 6DocumentImpl.writeReplication - The rev in data base: The table name is not support )DocumentImpl.writeReplication - Document % into local metacat with servercode: #edu/ucsb/nceas/metacat/DBSAXHandler nN oJ pJ qJ6DocumentImpl.writeReplication - Problem with parsing:  JDocumentImpl.writeReplication - Failed to create access rule for package:  because KDocumentImpl.writeReplication - Failed to create access rule for package: ADocumentImpl.writeReplication - ForceReplicationHandler created: xml.packagedoctype r )DocumentImpl.runRelationAndAccessHandeler s t xml.accessdoctype^DocumentImpl.runRelationAndAccessHandler - Error in DocumentImple.runRelationAndAccessHandler 6edu/ucsb/nceas/metacat/accesscontrol/AccessControlList 1SELECT doctype FROM xml_documents where docid = ?*DocumentImpl.getDocTypeFromDBForCurrentDocADocumentImpl.getDocTypeFromDBForCurrentDocument - executing SQL: =DocumentImpl.getDocTypeFromDBForCurrentDocument - SQL error: RDocumentImpl.getDocTypeFromDBForCurrentDocument - The current doctype from db is: DocumentImpl.delete*DocumentImp.delete - archive the document 4SELECT rev, docid FROM xml_documents WHERE docid = ?%DocumentImpl.delete - executing SQL: _ does not exist. Please check that you have also specified the revision number of the document.>DocumentImpl.delete - in the archive the user specified rev - 1is less than the version in xml_document table - !. We will use the one from table.2DocumentImp.delete - complete delete the document 7SELECT * FROM xml_documents WHERE docid = ? and rev = ?(DocumentImpl.delete - look at the docid  in the xml_revision table7SELECT * FROM xml_revisions WHERE docid = ? AND rev = ?9 does not exist. Please check and try to delete it again. /DocumentImpl.delete - the deleting doc type is ...BIN)DocumentImpl.delete - Start deleting doc 8edu/ucsb/nceas/metacat/client/InsufficientKarmaException2 does not have permission to delete XML Document #8DocumentImpl.delete - calling archiveDocAndNodesRevisionADocumentImpl.delete - The time for archiveDocAndNodesRevision is 5DocumentImpl.delete - The deleting xml_index time is ;DocumentImpl.delete - The deleting xml_queryresult time is (DELETE FROM xml_relation WHERE docid = ?#DocumentImpl.delete - running sql: 5DocumentImpl.delete - The deleting time relation is 2DocumentImpl.delete - deleting from xml_path_index5DocumentImpl.delete - deleting from xml_accesssubtree-DELETE FROM xml_accesssubtree WHERE docid = ?1DocumentImpl.delete - deleting from xml_documents)DELETE FROM xml_documents WHERE docid = ?dDocumentImpl.delete - the time to delete xml_path_index, xml_accesssubtree, xml_documents time is %DELETE FROM xml_nodes WHERE docid = ?1DocumentImpl.delete - Deleting xml_nodes time is 1DocumentImpl.delete - deleting from xml_revisions5DELETE FROM xml_revisions WHERE docid = ? AND rev = ?7DocumentImpl.delete - deleting from xml_nodes_revisions4DELETE FROM xml_nodes_revisions WHERE rootnodeid = ? u v w6'org/dataone/service/types/v1/Identifier x y z { | }+org/dataone/service/types/v2/SystemMetadata ~  V   ,the system metadata contains the key - guid  before removing is m &the system metadata contains the guid  after removing is java/lang/RuntimeExceptionhttp://apache.org/xml/features/validation/schema-full-checkingADocumentImpl.initalizeParser - Generic external schema location: The schema for the document NoNamespaceSchemaNDocumentImpl.initalizeParser - Generic external no-namespace schema location: Jhttp://apache.org/xml/properties/schema/external-noNamespaceSchemaLocation/DocumentImpl.initalizeParser - Using dtd parser'edu/ucsb/nceas/metacat/DBEntityResolver  #edu/ucsb/nceas/metacat/DBDTDHandler  1DocumentImpl.initalizeParser - Using other parser UDocumentImpl.archiveDocAndNodesRevision - Error in DocumentImpl.archiveDocRevision : LINSERT INTO xml_revisions (docid, rootnodeid, docname, doctype, user_owner, user_updated, date_created, date_updated, server_location, rev, public_access, catalog_id) SELECT ?, rootnodeid, docname, doctype, user_owner, ?, date_created, date_updated, server_location, rev, public_access, catalog_id FROM xml_documents WHERE docid = ?8DocumentImpl.archiveDocAndNodesRevison - executing SQL: _DocumentImpl.archiveDocAndNodesRevision - moving docs from xml_documents to xml_revision takes UDocumentImpl.archiveDocAndNodesRevision - SQL error when closing prepared statement: 5DocumentImpl.archiveDocAndNodesRevision - SQL error: 9DocumentImpl.archiveDocAndNodesRevision - General error: XSELECT DISTINCT NODEID, NODEDATA FROM xml_nodes WHERE nodedata IS NOT NULL AND docid = ? ;UPDATE xml_nodes SET nodedatanumerical = ? WHERE nodeid = 6UPDATE xml_nodes SET nodedatadate = ? WHERE nodeid =  [-d docid] <-f filename> [-r dtdfilename]O OR: java DocumentImpl [-t] <-a UPDATE -d docid -f filename> [-r dtdfilename]2 OR: java DocumentImpl [-t] <-a DELETE -d docid>7 OR: java DocumentImpl [-t] [-old] <-a READ -d docid>DocumentImpl.mainDocumentImpl.main - kJ .DocumentImpl.main - Total Execution time was:  seconds.4DocumentImpl.main - Time to open DB connection was: 1DocumentImpl.main - Time to insert document was: m /edu/ucsb/nceas/metacat/AccessionNumberExceptionEXCEPTION HANDLING REQUIRED?DocumentImpl.writeDocumentToRevisionTable - the create date is ?DocumentImpl.writeDocumentToRevisionTable - the update date is @DocumentImpl.writeDocumentToRevisionTable - the root node id is INSERT INTO xml_revisions (docid, docname, doctype, user_owner, user_updated, date_created, date_updated, public_access, server_location, rev) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)INSERT INTO xml_revisions (docid, docname, doctype, user_owner, user_updated, date_created, date_updated, public_access, server_location, rev, catalog_id, rootnodeid ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)INSERT INTO xml_revisions (docid, docname, doctype, user_owner, user_updated, date_created, date_updated, public_access, server_location, rev, rootnodeid ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)5DocumentImpl.writeDocumentToRevisionTable - docid is 7DocumentImpl.writeDocumentToRevisionTable - docname is 7DocumentImpl.writeDocumentToRevisionTable - docType is 5DocumentImpl.writeDocumentToRevisionTable - onwer is ;DocumentImpl.writeDocumentToRevisionTable - update user is ;DocumentImpl.writeDocumentToRevisionTable - server code is 3DocumentImpl.writeDocumentToRevisionTable - rev is :DocumentImpl.writeDocumentToRevisionTable - catalog id is 7DocumentImpl.writeDocumentToRevisionTable - root id is ;DocumentImpl.writeDocumentToRevisionTable - executing SQL: FDocumentImpl.writeDocumentToRevisionTable - end of write into revisons7DocumentImpl.writeDocumentToRevisionTable - SQL error: ;DocumentImpl.writeDocumentToRevisionTable - General error: +DeletedDocumentImpl.registerDeletedDataFile +DocumentImpl.deleteXMLNodes - for root Id: +DELETE FROM xml_nodes WHERE rootnodeid = ? -DocumentImpl.deleteXMLNodes - executing SQL: HDocumentImpl.deleteXMLNodes - The time to delete xml_nodes in UPDATE is @SELECT rootnodeid FROM xml_revisions WHERE docid = ? and rev = ??DocumentImpl.getRevisionRootNodeId - The root node id of docid xml.eml2_0_0namespacexml.eml2_0_1namespacexml.eml2_1_0namespacexml.eml2_1_1namespacexml.rdf_syntax_namespace(Could not get property in static block:  ReplicationLogging java/lang/Object.http://xml.org/sax/features/namespace-prefixes,edu/ucsb/nceas/metacat/database/DBConnectionjava/sql/PreparedStatementjava/io/InputStreamjava/io/OutputStreamjava/io/Writerjava/util/Iteratorjava/io/Readerjava/util/Hashtable java/util/Set%org/dataone/service/types/v1/Checksumjava/security/MessageDigestjava/util/regex/Matcherjava/sql/ResultSetorg/xml/sax/XMLReader/edu/ucsb/nceas/metacat/service/XMLSchemaService(edu/ucsb/nceas/metacat/util/DocumentUtilgetDocIdFromAccessionNumbergetRevisionFromAccessionNumber&edu/ucsb/nceas/metacat/util/SystemUtilgetPathsForIndexing()Ljava/util/Vector;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;intValue0edu/ucsb/nceas/metacat/database/DBConnectionPoolgetDBConnectionB(Ljava/lang/String;)Ledu/ucsb/nceas/metacat/database/DBConnection;getCheckOutSerialNumber setAutoCommit(Z)Vorg/apache/log4j/Loggerdebug(Ljava/lang/Object;)Vequals(Ljava/lang/Object;)Zedu/ucsb/nceas/metacat/DBUtil getLatestRevisionInDocumentTable1edu/ucsb/nceas/metacat/properties/PropertyService getProperty(I)Ljava/lang/StringBuilder;(I)Ljava/lang/String;commitreturnDBConnection2(Ledu/ucsb/nceas/metacat/database/DBConnection;I)Vrollback/edu/ucsb/nceas/metacat/database/DatabaseService getInstance3()Ledu/ucsb/nceas/metacat/database/DatabaseService; 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