- BaseX-Talk - mailman.uni-konstanz.de

java.io.IOException: Stream Closed
by Ketill Fenne 10 Jun '15

10 Jun '15

Hi! >From time to time I see the following error: java.io.IOException: Stream Closed at java.io.RandomAccessFile.seek0(Native Method) at java.io.RandomAccessFile.seek(RandomAccessFile.java:557) at org.basex.io.random.TableDiskAccess.readBlock(TableDiskAccess.java:520) at org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:485) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:464) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:148) at org.basex.data.Data.kind(Data.java:307) at org.basex.query.value.node.DBNode$4.next(DBNode.java:349) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:32) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:58) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:36) at org.basex.query.expr.gflwor.For$1.next(For.java:79) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:95) at org.basex.query.MainModule$1.next(MainModule.java:114) at org.basex.server.ServerQuery.execute(ServerQuery.java:130) at org.basex.api.client.LocalQuery.cache(LocalQuery.java:48) at org.basex.api.client.Query.more(Query.java:76) An example of how I query and iterate: DBResult dbResult = null; LocalQuery results = null; try { xPath = xPath.indexOf("/") == -1 ? "/" + xPath : xPath; String myQuery = "for $doc in (" + getContentCollectionQuery(PPSCONTENT_DATABASE_NAME) + " ) " + xPath + createNameCondition(name, PPSCONTENT_DATABASE_NAME) + createDateCondition(version) + " " + " return (data($doc/topic/@id))"; dbResult = runQuery(myQuery); results = dbResult.getXmlResults(); String topic = null; if (results.more()) { topic = results.next(); } return topic; } catch (QueryException e) { PPLogger.getInstance().error("Error in getTopicForDocWithName: " + e.getMessage()); return null; } catch (IOException e) { PPLogger.getInstance().error("Error in getTopicForDocWithName: " + e.getMessage()); return null; } finally { if (results != null) results.close(); if (dbResult != null) dbResult.close(); } The error occurs randomly, but is always "triggered" by "results.more()" and I am not able to reproduce it at will. Is there something wrong or missing in how I iterate the results? I am using BaseX8.2.1 on windows 7. Kind regards Ketill Fenne

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DBA and long-running queries
by Kristian Kankainen 10 Jun '15

10 Jun '15

I want to add a big (150mb) xml file as a resource to my database. The machine is behind a reverse proxy, so the easiest way would be through the DBA. I have the file locally on the same machine I run Tomcat on, but when I run the db:add() query, I get a timeout (504 Gateway Time-out 504 Gateway Time-out nginx/1.2.1). Is there a way of circumventing this? Perhaps instead of running the db:add() straight from the DBA, I should have it as a function in my XQrepo and trigger it somehow? Kristian

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Doc mistake for map:get() for NaN key
by Amanda Galtman 09 Jun '15

09 Jun '15

Hi, I think the following is a mistake in the doc, but before changing the wiki, I wanted to double-check. The documentation for map:get says, "If the supplied key is the xs:float or xs:double value NaN, the function returns an empty sequence." BaseX 8.1 returns the value that corresponds to the NaN key (if present). The software behavior seems correct to me. For example: INPUT let $mymap := map:entry(xs:double('NaN'),'abc') return map:get($mymap,xs:double('NaN')) OUTPUT abc Thanks, Amanda

2 1

BaseX 8.2.1
by Christian Grün 09 Jun '15

09 Jun '15

Dear all, BaseX 8.2.1 has been released today. It contains bug fixes and, additionally, some new DBA features: - Code highlighting (thanks, James Ball!) - New panel for up- and downloading files - Queries and files are now stored in a temporary directory You can also test some of the features that will officially be available with 8.3, such as RelaxNG validation (see http://docs.basex.org/index.php?search=8.3 for more information). Have fun, Christian

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Function to throw an exception
by cmarchand＠oxiane.com 09 Jun '15

09 Jun '15

Hello, Before doing some updates, I want to check many things. If those checks fail, I want to throw an error, to allow the calling program be notified of the error. I do not want to avoid the updates, but really want to throw an error. Is there such a function ? Christophe

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Re: [basex-talk] Using python to query BaseX server on localhost
by Christian Grün 08 Jun '15

08 Jun '15

Hi Werner, > I now want to query the database with BaseXClient.py using a list from > stdout from another script. How do I do that in python? Have you already tried the (few) examples we are providing (e.g. [1, 2])? > What I want to accomplish is use the variables in the list from the other > script to search through the XML files in BaseX and if the variables are > found in an XML file, text must be returned from within > "<name>example</name>" in the same file. I think we need more information on what you mean with "search through the XML files". Could you provide us the Python and XPath/XQuery snippets you have written so far? Best, Christian [1] https://github.com/BaseXdb/basex/blob/master/basex-api/src/main/python3/Que… [2] https://github.com/BaseXdb/basex/blob/master/basex-api/src/main/python3/Que…

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Issue with UPDINDEX and db:replace (8.2.1 beta)
by James Ball 05 Jun '15

05 Jun '15

Hello, I’m running into some problems again with replacing documents when a database has updating indexes turned on. Basically I can add a certain number of documents and then replacing a document will cause an error. Unexpected error: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.2.1 beta 0e44488 Java: Oracle Corporation, 1.8.0_31 OS: Mac OS X, x86_64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException And then I can’t add anything. Things I’ve tried: - turn off UPDINDEX: everything works correctly - use db:add instead of db:replace: everything works correctly From this I don’t think there’s anything wrong with my code, or the documents themselves but instead something is amiss in the logic for updating an index. But I’m not sure exactly where to look - the trace isn’t very detailed. I can’t narrow it down perfectly but I have managed to create a set of 5 messages (about 40kB) that will cause the error every time on my system. I can’t share these publicly but I can send them over privately for the purposes of testing if required. I’m happy to try to look a bit closer but I’m not sure what to look at and I think you have made some changes to the updating indexes in recent versions. Many thanks for your help, James To recreate the error I’m using RESTXQ with the following function: module namespace _ = 'push'; import module namespace Request = 'http://exquery.org/ns/request'; import module namespace functx = "http://www.functx.com”; declare %rest:POST("{$data}") %rest:path("/push") %updating function _:test($data) { let $odf := $data/OdfBody let $discipline := substring($odf/@DocumentCode,1,2) let $path := functx:pad-string-to-length($odf/@DocumentCode,"_",9) || functx:pad-string-to-length($odf/@DocumentSubcode,"_",10) || functx:pad-string-to-length($odf/@DocumentType,"_",30) || functx:pad-string-to-length($odf/@DocumentSubtype,"_",20) || functx:pad-string-to-length($odf/@FeedFlag,"_",1) || functx:pad-string-to-length($odf/@Language,"_",3) || ".xml" return ( if (db:exists("ODF-MIN-" || $discipline)) then ( db:replace("ODF-MIN-"||$discipline,$path,$data) (: db:add("ODF-MIN-"||$discipline,$data,$path) :) ) else ( db:create("ODF-MIN-"||$discipline,$data,$path,map { 'textindex': true(), 'attrindex':true(), 'updindex':true() }) (: db:create("ODF-MIN-"||$discipline,$data,$path) :) ) ) }; Delete the database if it exists then load the five files one at a time. I use this bash script to upload each file from a folder: #!/bin/bash # Usage: push all .xml files in the supplied directory (or single xml file) to server shopt -s nullglob echo $1 PASSED=$1 if [[ -d "$PASSED" ]]; then echo "Directory" FILES="$PASSED/*.xml" elif [[ -f "$PASSED" ]]; then if [[ ( $PASSED == *.xml ) || ( $PASSED == *.XML ) ]]; then FILES=$PASSED else echo "Not an XML file" exit 0 fi else echo "Not valid file or directory" exit 0 fi for f in $FILES do echo "Pushing file - $f" curl -X POST -H 'Content-Type:text/xml' --data @$f http://localhost:8984/push done

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validate:xsd
by France Baril 01 Jun '15

01 Jun '15

Hi, The function returns incomplete error messages on 8.2. It makes it difficult to figure out what the problem is. *validate:xsd*(*$node*, *$staged-xsd*) returns: Stopped at /Users/archie/BX-Acc/webapp/Accounting_ValidationSchemas.xqm, 13/41: [bxerr:BXVA0001] Validation failed. "Fatal:The version is required i... I'd really like to see what ... stands for. Is it possible to get more complete messages? Regards, France -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

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Catch a user event/work with triggers
by France Baril 01 Jun '15

01 Jun '15

Hi, I couldn't find documentation about catching events that occur on a db from an xquery module. What I am trying to achieve: Context: Writers create content in XML Oxygen and are connected through the data source which uses WebDAV. 1. A writer modifies an .xml file and saves the changes. An event that can be caught by an xquery function is triggered. 2. My xquery function adds an @id to all elements that don't have one and saves the document again. There is a way to differenciate users 'replace' from query 'replace' so that if an event is triggered again here, we will not loop indefinitely. I know you are working on triggers, but I'm not sure it applies to this use case. Can this currently be done? Thanks! -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

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Strange path problem (revisited)
by Kristian Kankainen 01 Jun '15

01 Jun '15

Hello! I noticed that I get different results if I visit the following two urls: http://myhost.domain/webappname/ http://myhost.domain/webappname The only difference is the trailing slash. My RESTXQ has a path for '/' but not for ''. My setup is with Tomcat. The difference seems to be the basepath for the webapp. Static files etc are not found. This also applies for the BaseX DBA: http://myhost.domain/webappname/dba/login resolves correctly http://myhost.domain/webappname/dba/login/ doesn't find it's static files etc. For my own webapp, it's the other way around --- with the trailing slash everything works fine, without it the static files etc aren't found. Is it yet another Tomcat problem or can it be reproduced on your setups? Cheers! Kristian

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Re: [basex-talk] Multiple BaseX Tomcat webapps
by Kristian Kankainen 01 Jun '15

01 Jun '15

Since this conversation accidentally went off-list somewhere on it's way... I am happy to announce that Christian now has solved the Tomcat problem. Cheers! Kristian 29.05.2015 20:48, Christian Grün kirjutas: > Hi Kristian, > > I'm quite positive I could fix some potential Tomcat-related issues > today! It shouldn't happen anymore that the database paths of multiple > instances are mixed up. Your feedback on the latest snapshot [1] is > welcome. > > Have a nice evening or even weekend, > Christian > > [1] http://files.basex.org/releases/latest/ > > > > On Fri, May 29, 2015 at 11:55 AM, Kristian Kankainen > <kristian(a)keeleleek.ee> wrote: >> Hi, I try to describe a possible solution scenario even though I am not at >> all familiar with Java. Please bare with me and help me to debug my scenario >> :-) >> >> I found Tomcat documentation for class loaders[1]. Since I don't know any >> Java, I can't really understand any of it. But it does state, that Tomcats >> way of loading classes is fundamentally different from standard Java class >> loading. Maybe this can be part of the problem? >> >> Also the comment at the end of the documentation asks about an attribute >> "delegate=true" that can impose (I guess) the standard Java way of loading >> classes... >> >> As I understand it, there is a way of achieving class loading in a way that >> allready loaded classes are re-used -- this I understand as the situation of >> our problem. >> >> Maybe the way of loading classes has to be explicitly spelled out in a >> context.xml file which BaseX doesn't have? >> >> Cheers >> Kristian >> >> [1] http://tomcat.apache.org/tomcat-7.0-doc/class-loader-howto.html >> >> >> >> 28.05.2015 12:45, Christian Grün kirjutas: >>> Hi Kristian, >>> >>> Thanks, keep on going, every feedback is valuable. >>> >>> Christian >>> >>> >>> On Thu, May 28, 2015 at 9:22 AM, Kristian Kankainen >>> <kristian(a)keeleleek.ee> wrote: >>>> I haven't found any solutions, but I wrote down what I noticed: >>>> >>>> None of my webapps have a corresponding context.xml file in: >>>> $CATALINA_BASE/conf/[enginename]/[hostname]/ >>>> >>>> Neither is there any default context file in: >>>> $CATALINA_BASE/conf/[enginename]/[hostname]/context.xml.default >>>> >>>> So the only default values are read from: >>>> $CATALINA_BASE/conf/context.xml >>>> >>>> When looking at the WEB-INF/web.xml that is shipped with BaseX I notice >>>> it >>>> doesn't give the context parameter for: >>>> * restpath >>>> * webpath >>>> >>>> Comparing both of my webapps >>>> http://[...]/rest?command=info >>>> I noticed that one has EVENTPORT: 1985 set while the other lacks it >>>> completely, >>>> one has CACHEQUERY: false while the other lacks it completely, >>>> one has MAXHITS: -1 while the other lacks it completely. >>>> >>>> Please tell me to stop if you feel I clutter the list. I thought maybe it >>>> helps to share my observations. >>>> >>>> Best wishes >>>> Kristian >>>> >>>> >>>> >>>> 28.05.2015 09:03, Kristian Kankainen kirjutas: >>>>> I think it has to do with Tomcat webapps' context settings [1]. It >>>>> states >>>>> that there is some kind of default context that will be used if no other >>>>> contexts are matched. I'm reading it now and will try some >>>>> experimenting. >>>>> >>>>> I also note that my Tomcat setup is not configured for multiple >>>>> instances, >>>>> thus my CATALINA_BASE is the same as CATALINA_HOME. >>>>> >>>>> Cheers >>>>> Kristian >>>>> >>>>> [1]: http://tomcat.eki.ee/docs/config/context.html >>>>> >>>>> 27.05.2015 13:53, Christian Grün kirjutas: >>>>>> Hi Kristian, >>>>>> >>>>>>> I previously had BaseX 8.1.1 working as a Tomcat webapp and it all >>>>>>> worked >>>>>>> fine. I know tried to simply put BaseX82.war as another webapp, but >>>>>>> the >>>>>>> second webapp seems to connect to the BaseX instance in the first >>>>>>> webapp. >>>>>> True, same on my machine. It doesn't seem to be due to 8.2. Instead, >>>>>> Tomcat seems to adopts some options from a running BaseX instance (and >>>>>> the primary instance might differ after a restart of Tomcat): >>>>>> >>>>>> http://localhost:8080/BaseX811/rest?query=db:system() >>>>>> >>>>>> <system> >>>>>> <generalinformation> >>>>>> <version>8.1.1</version> >>>>>> </generalinformation> >>>>>> <globaloptions> >>>>>> <dbpath>C:\Program Files\Apache Software Foundation\Tomcat >>>>>> 8.0\webapps\BaseX811\data</dbpath> >>>>>> ... >>>>>> >>>>>> http://localhost:8080/BaseX82/rest?query=db:system() >>>>>> >>>>>> <system> >>>>>> <generalinformation> >>>>>> <version>8.2</version> >>>>>> <usedmemory>37 MB</usedmemory> >>>>>> </generalinformation> >>>>>> <globaloptions> >>>>>> <authmethod>Basic</authmethod> >>>>>> <dbpath>C:\Program Files\Apache Software Foundation\Tomcat >>>>>> 8.0\webapps\BaseX811\data</dbpath> >>>>>> ... >>>>>> >>>>>> I currently have no idea if this can be fixed in Tomcat or BaseX (I >>>>>> don't know such a behavior from Jetty), but... I'll try to find out >>>>>> more. >>>>>> >>>>>> Christian >>>>>

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rest:resource vs db:list-details resource
by James Ball 01 Jun '15

01 Jun '15

Hello, If I use the REST interface to get details of the resources in a database (http://localhost:8984/rest/TEST-DATABASE for example) the result is rest:resource elements that include size. <rest:resource type="xml" content-type="application/xml" size="46”> I assumed that db:list-details was the XQuery equivalent but the resource elements it returns do not include size. <resource raw="false" content-type="application/xml" modified-date="2015-05-31T17:12:32.907Z”> I’m sure it is staring me in the face but I can’t work out how to get the size value from within XQuery. Can someone point me in the right direction? I’m trying to do some database pruning based on the size of the documents which would be very easy if I had rest:resource elements. Many thanks, James

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[DELIVER]<output:indent value='no'/> fn:serialize
by Adam Law 30 May '15

30 May '15

I may be doing something wrong but <output:indent value='no'/> does not appear to work with fn:serialize Adam let $ve_collectlocations := <collections><collection>{$page:collection_main_private}</collection></col lections> let $parameters := <output:serialization-parameters> <output:method value='xml'/> <output:indent value='no'/> <output:omit-xml-declaration value='yes'/> <output:encoding value='utf-8'/> </output:serialization-parameters> let $vs_result:= <Items>{for $collectlocation in $ve_collectlocations//collection/text() for $collect in collection($collectlocation)/* for $deadline in $collect//Deadline/Open let $irn := ($collect//FIN)[1] let $xs_string:= string(fn:serialize($collect,$parameters)) let $md5 := <md5>{xs:hexBinary(hash:md5($xs_string))}</md5> let $vs_result := <Hit>{md5}</Hit> return $vs_result }</Items> return $vs_result };

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Issues with new json xml function and copy clause
by James Wright 29 May '15

29 May '15

I am having issues with the new json-to-xm functions with a copy clause. I would expect the following query to work: *let $json := '{"age":23,"name":"Bob"}'return copy $out := json-to-xml($json) modify delete node $out//*[@key='age'] return xml-to-json($out)* Instead I get an error when calling xml-to-json: [FOJS0006] Element 'map' has invalid namespace: ''. It appears the copy clause is dropping the namespace on the map object. Is this something I must manually prevent or a bug? Thanks for all your time. - James

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Multiple BaseX Tomcat webapps
by Kristian Kankainen 28 May '15

28 May '15

Hello! I previously had BaseX 8.1.1 working as a Tomcat webapp and it all worked fine. I know tried to simply put BaseX82.war as another webapp, but the second webapp seems to connect to the BaseX instance in the first webapp. For example: the address http://tomcat.myhost.ee/BaseX82/rest/ lists all the databases that are in http://tomcat.myhost.ee/BaseX811/ even though the new BaseX82 instance should be empty. I have problems understanding if this concerns BaseX configuration or Tomcat configuration... Which files should I check? Looking at the both's webapps' WEB-INF/web.xml they seem logically fine to me. Best regards Kristian K

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Creating a batch BaseX program
by Noam Green 28 May '15

28 May '15

Hi, I'm new to BaseX, so apologize if this is a repetitive question. I have created an XQuery which currently runs on a specific XML file. What I'd like to do is to be able to create a batch command, which would receive as input a different XML source file, run the XQuery command, and save the results in a CSV file. Is there a way to do such a process? Thanks, Noam

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SQL Module
by James Wright 27 May '15

27 May '15

Hey Everyone, I am having issues with using the Oracle 1.7 JDBC driver. I copied the ojdbc7.jar file into the lib directory Ran the basexgui.bat to add to class path Tried to run this script: let $conn := sql:init('jdbc:oracle:thin:pnm/pnm@orc1n.giants') return (sql:execute($conn, 'SELECT owner, table_name FROM dba_tables '), sql:close($conn)) It states that it cannot initialize the jdbc:oracle:thin driver. Any ideas why that would be? Am I missing something? - James

2 1

Limitation of No of Database In Main Memory Mode.
by ankit kumar 27 May '15

27 May '15

Hi, I just wanted to know that, is there any limitation of no of database created in main memory mode using Java Application. Also if it is possible to create no of databases, Am i able to open multiple database in main memory mode at a time ?. Thanks, Ankit

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BaseX on Android
by Tojo Rakotoarison 26 May '15

26 May '15

Hi all ! Has someone already tried to embed BaseX in an Android app for a mobile device ? Would you recommend it for this case or not ? Thanks in advance ! Tojo Rakotoarison

2 1

Inspect custom annotations
by Marco Lettere 26 May '15

26 May '15

Hi all, isn't there any chance of showing up custom annotations in the inspect:function result? declare %local:ann function local:f3() as xs:string{ () }; (inspect:functions() ! inspect:function(.)) yields: <function name="local:f3" uri="http://www.w3.org/2005/xquery-local-functions"> <return type="xs:string"/> </function> I thought of: <function name="local:f3" uri="http://www.w3.org/2005/xquery-local-functions"> <annotation name="local:ann"/> <return type="xs:string"/> </function> Thanks, Marco.

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Re: [basex-talk] Multiple server instances on a single computer?
by Christian Grün 26 May '15

26 May '15

Hi Johan, > I have noticed that when using two different versions of BaseX in embedded > mode, in two different applications on the same application server. Errors > are logged about rewriting the .basex file. No exceptions are throw, just > the message in the log appears. Is there a way to create a QueryProcessor > without the need for these files to be created? Currently no. We could add another startup flag to prevent reading and writing the configuration files. However, I am curious: What do you think would be the major advantage if the file would be ignored? Christian

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8.2 on Windows. RESTXQ demo doesn't work.
by Alexander Shpack 26 May '15

26 May '15

Hi BaseX team! It doesn't work, because WEBPATH contains (by default) a path to a local user's BaseXWeb folder, not to a webapp folder inside BaseX installation folder I was confused a bit, why clean installation of 8.2 doesn't work, when 8.1 works fine Thanks -- s0rr0w

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Losing part of document name when renaming directory
by Ketill Fenne 26 May '15

26 May '15

Hi! I am running BaseX 8.1. This is my test case: create database test add to /doc/title/version=1 c:/temp/xml.xml Running query: *for $doc in (collection('test')) return (base-uri($doc))* Result: *test/doc/title/version=1* Executing this command: *rename /doc/title/ /doc/title2/* Running query once again: for $doc in (collection('test')) return (base-uri($doc)) Result: *test/doc/title2/ersion=1* So, I am losing the "v" in version, that is the first letter after the directory that is renamed, seems to disappear with each rename. A bug, or improper usage? Kind regards Ketill Fenne

2 2

db:event
by Marco Lettere 26 May '15

26 May '15

Hi Christian, I read that starting with 8.2 the db:event API has been removed and will be replaced by triggers. Since we wanted to start using db:event in order to chain activities in our workflows in a loosely coupled way, I'd like to know when the new feature based on triggers will be available. Are there any hints on how the API will possibly look? Will it be possible to fire explicit applicative events not only based on db activities? Thanks. BR, Marco.

3 2

JTattoo's themes not recognized.
by Alex R. Loayza 26 May '15

26 May '15

Hello, To use the dark themes for the GUI mentioned in http://docs.basex.org/wiki/Graphical_User_Interface#Look_and_Feels, I downloaded JTattoo-1.6.11.jar and placed it in BaseX/lib. Upon restarting the GUI, I go to Options/Preferences/Visualization/Look & Feel, where I expect to see the additional themes provided by JTattoo. However, none of them show up in the drop-down menu. Is there something else I need to do? Thank you very much! Alex

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