BaseX-Talk

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13 participants
5244 discussions

Exhausting PermGen space when using xar extensions w/ Java modules?
by Charles Duffy 05 Apr '12

05 Apr '12

Howdy -- I'm occasionally getting the following after a BaseX instance has been up and accepting queries for some time: [XPST0017] Class cannot be initialized: PermGen space. As I understand it, PermGen space is used during classloading. I'm using a Java extension (packaged in a xar); as BaseX has a fair bit of custom code around classloading, this seems the obvious first place to start looking. That said -- has anyone already seen this? (By the way -- without looking at the code, I would expect new classloading to only happen if the repo holding this plugin is being uninstalled and reinstalled; is this expectation accurate, or are plugins reloaded within a running instance more frequently?)

2 3

Shouldn't condition and true be a no-op?
by Meredith Gregory 05 Apr '12

05 Apr '12

Dear BaseXer's, The following query for $xqV1 in collection( 'localex' )//kRecord let $xqV2 := $xqV1/*[1] , $xqV7 := $xqV1/*[2] where ( count($xqV1/*) = 2 ) and ( for $xqV3 in $xqV1/node let $xqV4 := $xqV3/*[1] where ( count($xqV3/*) = 1 ) and ( for $xqV5 in $xqV3/uid let $xqV6 := $xqV5/*[1] where ( count($xqV5/*) = 1 ) and ( ( ( $xqV6 = <string>uid.value</string> ) or ( fn:string( fn:node-name( $xqV6 ) ) = "var" ) ) ) and ( $xqV4 = $xqV5 ) return $xqV5 ) and ( $xqV2 = $xqV3 ) return $xqV3 ) return $xqV1 returns our expected result, while for $xqV1 in collection( 'localex' )//kRecord let $xqV2 := $xqV1/*[1] , $xqV7 := $xqV1/*[2] where ( count($xqV1/*) = 2 ) and ( for $xqV3 in $xqV1/node let $xqV4 := $xqV3/*[1] where ( count($xqV3/*) = 1 ) and ( for $xqV5 in $xqV3/uid let $xqV6 := $xqV5/*[1] where ( count($xqV5/*) = 1 ) and ( ( ( $xqV6 = <string>uid.value</string> ) or ( fn:string( fn:node-name( $xqV6 ) ) = "var" ) ) ) and ( $xqV4 = $xqV5 ) return $xqV5 ) and ( $xqV2 = $xqV3 ) return $xqV3 ) and ( true ) return $xqV1 which is the same query with an 'and ( true )' added to the outer where-clause returns no results. Should we expect that for ... let ... where C return ... == for ... let ... where C and ( true ) return ... ? Best wishes, --greg -- L.G. Meredith Managing Partner Biosimilarity LLC 7329 39th Ave SW Seattle, WA 98136 +1 206.650.3740 http://biosimilarity.blogspot.com

2 3

Problem with BaseX inserting a namespace … how do I stop it
by Mike Hawkes 05 Apr '12

05 Apr '12

Hi I have a weird problem ... I'm running a query via the PHP interface and run the following query: declare variable $DB external; insert node <audit QID='C54B14ED-C748-4DF0-87F2-91F505BE207B' UID='i1' guid='CC9D4D2B-B380-494B-B0F6-4D72471557B0' sessionID='48090b7f0e3a62a42a0457a3e88301ca' mode='active' date='2012-04-02T12:21:05+00:00'/> into doc($DB)/root/auditlog -- BaseX log shows that it gets the query as-is. When I look at the data within the database by running the XQuery /root/auditlog I find that BaseX has inserted a namespace attribute as follows: <audit xmlns="http://www.w3.org/1999/xhtml" QID="C54B14ED-C748-4DF0-87F2-91F505BE207B" UID="i1" guid="CC9D4D2B-B380-494B-B0F6-4D72471557B0" sessionID="48090b7f0e3a62a42a0457a3e88301ca" mode="active" date="2012-04-02T12:21:05+00:00"/> How do I stop this occurring? It only does it on the audit components, not on anything else inserted by the PHP script. So, if I run two insert node queries, the first will run normally, the audit update causes the xmlns attribute to appear, effectively putting it in a different namespace to the other data inserted by the PHP. The PHP script is as follows: $audit = "declare variable \$DB external; " . "insert node <audit QID='$queryID' UID='$userID' " . "guid='$guid' sessionID='" . session_id() . "' " . "mode='active' " . "date='$dateTime'/> into doc(\$DB)/root/auditlog"; $query = $session->query( $audit ); $query->bind( 'DB', $DB); $query->bind( 'SYSDATA', $SYSDATA ); $query->execute(); $query->close(); Thanks in advance for any suggestions. Mike

4 16

Moving to log4j, java.util.logging, Apache Commons Logging, etc?
by Charles Duffy 04 Apr '12

04 Apr '12

Howdy -- Right now, logging in BaseX is managed through org.basex.server.Log, allocated within each BaseXServer instance and passed to classes such as ClientListener with a known need to do logging. Compared to common logging approaches, this is somewhat unfortunate -- any class not passed a reference to the Log instance is unable to perform logging, and functionality common to log4j-derived logging frameworks (such as fine-grained log level and destination control) is unavailable. Is the decision to use an in-house logging framework open to reconsideration? I'd be willing to do a first-draft cut on a transition to log4j, Sun's java.util.logging, or Apache Commons Logging (a thin indirection layer which can use either of those as an underlying backend) if there's agreement to do so.

5 15

Losing username/password info
by Charles Duffy 03 Apr '12

03 Apr '12

Howdy -- I have a number of different installed instances of BaseX (7.2 release, current snapshot, local build, etc), each with a .basex file pointing against the same DBPATH. I've frequently noticed when switching between trees that "admin" account switches back to its default password, and my more limited user accounts disappear and need to be recreated. Are these stored somewhere other than DBPATH?

2 3

Locking and long-running update operations
by Charles Duffy 03 Apr '12

03 Apr '12

I have a set of expensive cached data which requires about ~20 minutes to refresh/recalculate. However -- while this recalculation is running (via a single XQUF operation), read queries against the same database are unable to operate. My expectation is that the old, pre-update data will remain continually available until the update commits. If this expectation is incorrect, what is the suggested mechanism for running such expensive updates without impacting availability?

2 2

Problem with XQJ-Implementation (method XQResultSequence.getSequenceAsStream)
by Isidre Guixà 03 Apr '12

03 Apr '12

Hi I am experiencing the BaseX API XQJ and I compare to other XQJ NXD and I find the following problem. Suppose we have the next XML file in database "test": <?xml version="1.0" encoding="ISO-8859-1"?> <bookstore param="hao"> <book> <title>Book01</title> </book> <book> <title>Book02</title> </book> </bookstore> If I execute: XQDataSource xqs = ... XQConnection conn = xqs.getConnection(); XQExpression xqe = conn.createExpression(); String cad= "collection('test')//title"; XQResultSequence xqrs = xqe.executeQuery(cad); XMLStreamReader result = xqrs.getSequenceAsStream(); System.out.println("Iteration on XMLStreamReader..."); for(; result.hasNext(); result.next()) System.out.println(getEventString(result)); xqrs = xqe.executeQuery(cad); System.out.println("Using a Transformer..."); Source resultXML = new StAXSource(xqrs.getSequenceAsStream()); StreamResult resultSR = new StreamResult(System.out); TransformerFactory factory = TransformerFactory.newInstance(); Transformer tr = factory.newTransformer(); tr.setOutputProperty(OutputKeys.INDENT, "yes"); tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no"); tr.setOutputProperty("{http://xml.apache.org/xslt}indent-amount","2"); tr.transform(resultXML, resultSR); where static String getEventString(final XMLStreamReader reader) { switch(reader.getEventType()) { case XMLStreamConstants.START_ELEMENT: return "START_ELEMENT:\t\"" + reader.getLocalName() + "\""; case XMLStreamConstants.END_ELEMENT: return "END_ELEMENT:\t\"" + reader.getLocalName() + "\""; case XMLStreamConstants.START_DOCUMENT: return "START_DOCUMENT"; case XMLStreamConstants.END_DOCUMENT: return "END_DOCUMENT"; case XMLStreamConstants.CHARACTERS: return "CHARACTERS:\t\"" + reader.getText() + "\""; } return ""; } I get: Iteration on XMLStreamReader... START_ELEMENT: "title" CHARACTERS: "Book01" END_ELEMENT: "title" END_DOCUMENT START_ELEMENT: "title" CHARACTERS: "Book02" END_ELEMENT: "title" END_DOCUMENT Using a Transformer... <?xml version="1.0" encoding="UTF-8"?> <title>Book01</title> It's not good! When I use a Transformer I should get something similar to: <?xml version="1.0" encoding="UTF-8"?> <result> <title>Book01</title> <title>Book02</title> <result> That is, if result sequence length is greater than 1, getSequenceAsStream should wrap the sequence in a containing result element, so to not break JAXP Transformers and XMLStreamReader events. Is there any solution in BaseX ? Thanks a lot! Isidre Guixà

3 2

Concurrency problems with REST API
by Tobias Hofer 01 Apr '12

01 Apr '12

Hi, I'm using the REST API of BaseX 7.2 and run into concurrency problems. If I add new documents in parallel then the server will stop working after adding a few documents. My command template looks like: <?xml version="1.0" encoding="UTF-8"?> <command xmlns="http://basex.org/rest"><text><![CDATA[ ADD TO $KEY$ <node id="$KEY$" /> ]]></text></command> I call the REST API using curl: for ((i=0; i<10; i++)); do (cp tx-template tx$i; replace '$KEY$' $i -- tx$i; curl -i -X POST -H "Content-Type: application/xml" -T tx$i "admin:admin@localhost:8984/rest/QDEV") & done After four or less insert the following error occurs: HTTP/1.1 400 Bad Request Content-Type: text/plain; charset=utf-8 Content-Length: 2247 Server: Jetty(6.1.26) java.lang.NullPointerExceptionjava.lang.NullPointerExceptionjava.lang.NullPointerExceptionorg.xml.sax.SAXParseException: cvc-type.3.1.2: Element 'command' is a simple type, so it must have no element information item [children].org.xml.sax.SAXParseException: cvc-type.3.1.2: Element 'command' is a simple type, so it must have no element information item [children].Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.2 Java: Sun Microsystems Inc., 1.6.0_26 OS: Linux, amd64 Stack Trace: java.lang.NullPointerException org.basex.core.cmd.Add.run(Add.java:92) org.basex.core.Command.run(Command.java:345) org.basex.core.Command.exec(Command.java:324) org.basex.core.Command.execute(Command.java:76) org.basex.server.LocalSession.execute(LocalSession.java:134) org.basex.server.LocalSession.execute(LocalSession.java:126) org.basex.server.Session.execute(Session.java:51) org.basex.http.rest.RESTCommand.run(RESTCommand.java:40) org.basex.http.rest.RESTPost.run(RESTPost.java:129) org.basex.http.rest.RESTServlet.run(RESTServlet.java:14) org.basex.http.BaseXServlet.service(BaseXServlet.java:38) javax.servlet.http.HttpServlet.service(HttpServlet.java:820) org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:401) org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766) org.mortbay.jetty.handler.HandlerList.handle(HandlerList.java:49) org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) org.mortbay.jetty.Server.handle(Server.java:326) org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:945) org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:756) org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212) org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) Now, the server cannot be accessed any more. Any further call will return "Database 'MYDB' is currently opened by another client. A restart helps. The error does not happen if the commands are executed in sequence. Please help. Regards, Tobias Hofer

2 1

possible bug? or opportunity for documentation enhancement? [2d sending]
by C. M. Sperberg-McQueen 01 Apr '12

01 Apr '12

[2d posting - this time with the promised attachment] I got some error messages today which seem to indicate a problem, either in BaseX or in (my understanding of) the documentation. Since the error messages (in the attached log) suggest contacting you about it, I am doing so. The document at http://www.w3.org/TR/xsd-unicode-blocknames/ includes a table of Unicode block names created by querying a database consisting of XML representations of the various versions of the Unicode Database. Today I noticed that a new version of the Unicode Database was issued in January, and so I downloaded the XML data and added the document to my existing BaseX database of Unicode information. The command seemed to run successfully, but when I ran my old query, I got an error message saying "Data access out of bounds". I installed version 7.2 then, which gave the same error message. Rebuilding the database from scratch allowed me to run the query without any problems, so I don't actually have a problem at the moment. But I'm sending this problem report in the hopes that it may help you diagnose either a problem with dynamic adds to a database or perhaps a problem with the server command language documentation (it's entirely possible that I did something wrong when adding the new document to the database). If there is any information I can provide that would be helpful, please let me know. best, Michael Sperberg-McQueen -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

2 1

possible bug? or opportunity for documentation enhancement?
by C. M. Sperberg-McQueen 30 Mar '12

30 Mar '12

I got some error messages today which seem to indicate a problem, either in BaseX or in (my understanding of) the documentation. Since the error messages (in the attached log) suggest contacting you about it, I am doing so. The document at http://www.w3.org/TR/xsd-unicode-blocknames/ includes a table of Unicode block names created by querying a database consisting of XML representations of the various versions of the Unicode Database. Today I noticed that a new version of the Unicode Database was issued in January, and so I downloaded the XML data and added the document to my existing BaseX database of Unicode information. The command seemed to run successfully, but when I ran my old query, I got an error message saying "Data access out of bounds". I installed version 7.2 then, which gave the same error message. Rebuilding the database from scratch allowed me to run the query without any problems, so I don't actually have a problem at the moment. But I'm sending this problem report in the hopes that it may help you diagnose either a problem with dynamic adds to a database or perhaps a problem with the server command language documentation (it's entirely possible that I did something wrong when adding the new document to the database). If there is any information I can provide that would be helpful, please let me know. best, Michael Sperberg-McQueen -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

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