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

Error: Processing instruction has illegal name: xml
by Thomas Zehrer 16 Jan '18

16 Jan '18

Hi there, if i want start a new xml document or open a exist one (factbook.xml e.g.), every time i get this error: Error: Processing instruction has illegal name: 'xml' i have already searched your website first steps and crawled the internet. there was just one entry on stackoverflow, the solution there wont work. how can i go on with it? thanks a lot. Thomas

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DFDL module
by Kristian Kankainen 15 Jan '18

15 Jan '18

Hello, I started writing a small wrapper module for using DFDL with XQuery in BaseX. For this I simply use system calls. This is not an elegant way of doing it, so I wonder, has anyone else had any experience with using DFDL or even integrated it in a more sustainable way? My project will evolve here: https://github.com/keeleleek/basex-daffodil I would like to add a sentence on how cool DFDL is, but I wont. Best regards, Kristian K

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Encoding problem with proc:system
by Kristian Kankainen 15 Jan '18

15 Jan '18

Hello all, I am running a system command with proc:system. The command should return xml, but because of non-ascii letters, the returned string gets scrambled. (I am aware that proc:system receives a string, proc:execute returns an element.) Running the system command in a shell works fine, I get this (snippet) <element>aapõ</element> When running the command through proc:system, I get this instead <element>aap....lement> Where the õ (= C3 B5 in hex representation) has been replaced with F5 BC AF B0. I get the same result specifying the encoding option of proc:system with "utf-8" or just leaving blank. My shell uses utf-8. How could I find out what encoding I need to use in the proc:system function? Best regards, Kristian K

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java.lang.NegativeArraySizeException
by Stefanie Nageldiek 15 Jan '18

15 Jan '18

Hi! I'm trying to move a XSLT Transformation into XQuery. First step is Creating a db and trying to run the XSLT with XQuery. I have a small input file (50 MB) and a large input file (2GB) for testing. So I set up the db with the small input file, ran a parametrizised query calling the XSLT Transformation and everything went well. To be sure everything will work on the bigger db too, I tried to do the same, which fails - I had to allow for more memory which I did. (To be sure the stylesheet works with the big input file for the db I checked it (it takes 20 Minutes to produce a ~1 GB File). This is the error I get: Error: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.6.7 Java: Oracle Corporation, 1.8.0_151 OS: Windows 10, amd64 Stack Trace: java.lang.NegativeArraySizeException at java.util.Arrays.copyOf(Unknown Source) at org.basex.io.out.ArrayOutput.write(ArrayOutput.java:25) at org.basex.io.out.PrintOutput.print(PrintOutput.java:76) at org.basex.io.out.NewlineOutput.print(NewlineOutput.java:33) at org.basex.io.serial.MarkupSerializer.printChar(MarkupSerializer.java:254) at org.basex.io.serial.MarkupSerializer.attribute(MarkupSerializer.java:131) at org.basex.io.serial.Serializer.node(Serializer.java:416) at org.basex.io.serial.Serializer.node(Serializer.java:158) at org.basex.io.serial.StandardSerializer.node(StandardSerializer.java:105) at org.basex.io.serial.AdaptiveSerializer.node(AdaptiveSerializer.java:75) at org.basex.io.serial.Serializer.serialize(Serializer.java:109) at org.basex.io.serial.AdaptiveSerializer.serialize(AdaptiveSerializer.java:66) at org.basex.query.value.Value.serialize(Value.java:222) at org.basex.query.value.Value.serialize(Value.java:205) at org.basex.query.func.xslt.XsltTransform.read(XsltTransform.java:75) at org.basex.query.func.xslt.XsltTransform.transform(XsltTransform.java:47) at org.basex.query.func.xslt.XsltTransform.item(XsltTransform.java:33) at org.basex.query.expr.ParseExpr.value(ParseExpr.java:65) at org.basex.query.QueryContext.value(QueryContext.java:406) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:185) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:93) at org.basex.query.scope.MainModule$1.next(MainModule.java:125) at org.basex.query.QueryContext.cache(QueryContext.java:618) at org.basex.query.QueryProcessor.cache(QueryProcessor.java:112) at org.basex.core.cmd.AQuery.query(AQuery.java:86) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.gui.GUI.exec(GUI.java:474) at org.basex.gui.GUI.access$4(GUI.java:428) at org.basex.gui.GUI$6.run(GUI.java:416) Compiling: - pre-evaluate root() to document-node() - pre-evaluate map { "param1":"default", "param2":"products" } to map - pre-evaluate map { "method":"xml", "indent":"no", "omit-xml-declaration":"no" } to map - inline $path_2 - pre-evaluate concat("c:/work/xslt_to_xquery/", "xslt_post_processing_bmwp-2526.xsl") to xs:string - inline $style_3 Optimized Query: let $document_4 := xslt:transform(db:open-pre("big-xml",0)/*, "c:/work/xslt_to_xquery/i-know-which.xsl", map { "param1": "default", "param2": "products", ... }) return file:write(concat("c:/work/xslt_to_xquery/", db:name(.), "_out_", "default", "products", ".xml"), $document_4, map { "omit-xml-declaration": "no", "method": "xml", ... }) Query: declare variable $param1 external := "default"; declare variable $param2 external := "products"; let $path := 'c:/work/xslt_to_xquery/' let $style := concat($path, 'i-know-which.xsl') let $document := xslt:transform(/*, $style, map { "param1": $param1, "param2": $param2 }) return file:write(concat($path, db:name(.), '_out_', $param1, $param2, '.xml'), $document, map { "method": "xml", "indent": "no", "omit-xml-declaration":"no" }) Query plan: <QueryPlan compiled="true"> <GFLWOR> <Let> <Var name="$document" id="4"/> <XsltTransform name="transform(input,stylesheet[,params[,options]])"> <IterPath> <DBNode name="big-xml" pre="0"/> <IterStep axis="child" test="*"/> </IterPath> <Str value="c:/work/xslt_to_xquery/i-know-which.xsl" type="xs:string"/> <Map size="2"> <Str value="param1" type="xs:string"/> <Str value="default" type="xs:string"/> <Str value="param2" type="xs:string"/> <Str value="products" type="xs:string"/> </Map> </XsltTransform> </Let> <FileWrite name="write(path,data[,params])"> <FnConcat name="concat(atom1,atom2[,...])"> <Str value="c:/work/xslt_to_xquery/" type="xs:string"/> <DbName name="name(node)"> <ContextValue/> </DbName> <Str value="_out_" type="xs:string"/> <Str value="default" type="xs:string"/> <Str value="products" type="xs:string"/> <Str value=".xml" type="xs:string"/> </FnConcat> <VarRef> <Var name="$document" id="4"/> </VarRef> <Map size="3"> <Str value="omit-xml-declaration" type="xs:string"/> <Str value="no" type="xs:string"/> <Str value="method" type="xs:string"/> <Str value="xml" type="xs:string"/> <Str value="indent" type="xs:string"/> <Str value="no" type="xs:string"/> </Map> </FileWrite> </GFLWOR> </QueryPlan> Please let me know which information you need. Many thanks Steffie

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update Java
by Giuseppe Celano 15 Jan '18

15 Jan '18

Hi, I write to ask whether it is now advisable to update to Java 9 (while using the BaseX 8.6.x). Thanks. Best, Giuseppe

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Isilex on GIT
by xavierlaurent.salvador 08 Jan '18

08 Jan '18

I was told to post again this little news because of holydays, so sorry ;) if you wish to collaborate... it would be cool Hi List, just a small message to draw your attention on our new Git Repo dedicated to Isilex. We put all our stuff into : https://github.com/Isilex/download and all the web documentation at: https://isilex.github.io/easy-xml/ and https://isilex.github.io/easy-xml-fr/ Cheers, Envoyé depuis mon smartphone Samsung Galaxy.

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How to set DBPath in BaseX version 8.6.7 as in version 7.3.1?
by Bang Pham Huu 05 Jan '18

05 Jan '18

Hello, I'm using BaseX version 7.3.1 and I can set dbpath where the collections are created with this code: new Set("dbpath", "/home/xxxx/basex-database").execute(context); However, when changing to BaseX version 8.6.7, this statement will throw exception "org.basex.core.BaseXException: Global option 'DBPATH' cannot be set." and instead it tries to create new collections to a default folder: /home/xxxx/BaseXData How can I set BaseX to work on existing dbpath folder (/home/xxxx/basex-database) as in version 7.3.1? Because I have existing data here and not the newly created one. Thanks,

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BaseX Sharding with ActiveMQ & Docker
by James Sears 05 Jan '18

05 Jan '18

In the past I hit a scalability limit with BaseX - a billion+ nodes kind of a made querying it a bit slower than I liked. I thought I'd try and address this, so I’ve written some code and placed it in GitHub: https://github.com/jameshnsears/xqa-documentation What I've done is proof of concept, that's all - no way "finished". I'm emailing the list in the hope that what I've done so far might generate some constructive criticism. Maybe my approach has potential, maybe it doesn't? There are only four components so far, the first three are Docker containers: * an ActiveMQ instance * a load balancer * a shard * a command line client exists to load the XML, from file, into an ActiveMQ queue. The software requires close to zero configuration. For example, each shard you start will automatically receive XML from the load balancer. And the load balancer distributes XML so that each shard holds the same # of documents. There's a Travis project associated with the above link - it shows how easy it is to run the software end to end. So far my effort is all about ingesting the XML, before I move further I thought I'd canvass some feedback - so if anyone has any then please give it :-) Thanks.

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Hundreds of thousands of java.io.IOException: Stream Closed in BaseX 7.3.1 from only catalina.out of Tomcat's log?
by Bang Pham Huu 05 Jan '18

05 Jan '18

Hello, I've been using BaseX (version 7.3.1 with Tomcat 8) to store an XML database from XML files and using XQuery to query the database. It works great before with simple Java servlet as I recall. After that, I updated to use Spring Boot (version 1.5.2) for this web application (only update from Java servlet to Spring Controller, the core to query BaseX doesn't change), and it seems this weird exception java.io.IOException: Stream Closed appears randomly by 100000 times in Tomcat's log (catalina.out). I tried to catch this exception in my web application but it is not able to catch. My web application's log (secore.log) also couldn't catch this error, only Tomcat's log (catalina.out) logs this error but with 100000 times (the log file is huge). Any idea to solve this problem will help me a lot? Here is the stack trace in catalina.out for 1 exception: https://pastebin.com/XGu7Vr2f And here is the configuration for log4j to log to both console and file (secore.log) and only console (catalina.out) contains this exception: https://pastebin.com/09ma3eyw Thanks,

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Isilex on GitHub
by Xavier-Laurent SALVADOR 02 Jan '18

02 Jan '18

Hi List, just a small message to draw your attention on our new Git Repo dedicated to Isilex. We put all our stuff into : https://github.com/Isilex/download and all the web documentation at: https://isilex.github.io/easy-xml/ <https://isilex.github.io/easy-xml/> and https://isilex.github.io/easy-xml-fr/ Cheers, -- Ce message peut contenir des informations réservées exclusivement à son destinataire. Toute diffusion sans autorisation est interdite. Si vous n'en êtes pas le destinataire, merci de prendre contact avec l'expéditeur et de détruire ce message. *This email may contain material for the sole use of the intended recipient. Any forwarding without express permission is prohibited. If you are not the intended recipient, please contact the sender and delete all copies*.

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Basex API: repeated execution of same query over different input
by Hondros, Constantine (ELS-AMS) 27 Dec '17

27 Dec '17

I want to be able to execute the same XQuery hundreds of thousands (even millions) of times over different XML input. Is there a way to avoid re-compiling the query itself every time? It looks to me like using either XQuery.execute(ctx) or the QueryProcessor class will end up re-parsing the query itself. I know that Basex is fast in this, but I will end up with a performance hit over time. Just wondering whether things have evolved since this thread: https://www.mail-archive.com/basex-talk@mailman.uni-konstanz.de/msg03064.ht… Thanks, Constantine Hondros Senior Manager Content Analytics & Content Engineering Digital Transformation Elsevier BV Radarweg 29 | 1043 NX Amsterdam | the Netherlands Tel: +31 20 4852772 | Mob: +31610735630 E-mail: c.hondros(a)elsevier.com<mailto:m.nauta@elsevier.com> [cid:image001.jpg@01CBEEC6.C17A8AC0] Amsterdam | Chennai | Exeter | Oxford | Shannon | St. Louis ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

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Properly sending/receiving JSON?
by Robert Crews 24 Dec '17

24 Dec '17

First off, thank you for the fast answer to my previous question. Now, I'm having trouble understanding how to send JSON to BaseX. Ultimately, I want to send JSON and store it (allowing BaseX to convert it to XML first, of course). For now, however, I am having trouble just receiving the JSON data. Here's my test XQM file: module namespace hwxdocs = "urn:com:hortonworks:docs"; declare %rest:POST("{$body}") %rest:path("hello/json") %rest:consumes("application/json") %output:media-type("application/json") function hwxdocs:hello2( $body ) { "Request body: " || $body }; I send data with this command: curl -iL -X POST \ --header 'Content-Type: application/json' \ --header 'Accept: application/json' \ --data-binary '{"foo":{"bar":"baz"}}' \ http://localhost:8984/hello/json I expect to get Request body: {"foo":{"bar":"baz"}} (I’m assuming I can pass '{"foo":{"bar":"baz”}}’ to json:parse to convert to a BaseX XML that can be stored in the database.) However, instead, I get Request body: baz Can someone tell me what my error is? Thank you, Robert

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Real time DB population using Nifi
by Juan Pablo Gardella 22 Dec '17

22 Dec '17

Hello team, First of all, congratulations for the awesome tool! BaseX is amazing. We are starting using it for querying some XML data that we are receiving from a queue. I've developed a Nifi processor based on https://github.com/BaseXdb/basex/blob/master/basex-examples/src/main/java/o… class. The problem that I'm facing is that write throughput is very slow. Do you know any way to increase the write throughput? All the XML files are stored in the same DB. So basically I'm doing: 1) open db 2) replace (xml id path, inputstream) Thanks, Juan

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Handling exceptions in the Python Client API
by Jonathan Robie 21 Dec '17

21 Dec '17

I am now happily using BaseX from Jupyter Notebooks for Greek data - see these links: http://jonathanrobie.biblicalhumanities.org/blog/2017/12/08/jupyter-tutoria… http://jonathanrobie.biblicalhumanities.org/assets/greeksyntax-tutorial-pro… But I need to know how to handle exceptions, e.g. if the notebook user writes a query with an error in it. And I would also like to return some result if the query returns an empty sequence. Here is the current code: https://github.com/biblicalhumanities/greek-new-testament/blob/master/labno… How can I improve what I am doing? Jonathan

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Setting a default collation for a database
by Jonathan Robie 19 Dec '17

19 Dec '17

I would like to set a default collation for a database, a collation that will be used for all queries unless the user asks for a different collation. My use case: a database in Greek will never be sensibly sorted using an English collation, and I don't want users to need to specify collations over and over. Is this possible? Jonathan

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Bulk adding with "add" in client
by Robert Crews 19 Dec '17

19 Dec '17

With a database created and opened, I can recursively bulk add the all the *.xml files in a directory called /opt/sources With this command > add /opt/sources http://docs.basex.org/wiki/Commands#ADD In the GUI, I can change the pattern to, for example, "*.dita*", to load all the *.dita and *.ditamap files instead of the *.xml files. Is there a way I can define a glob pattern for bulk loads using the add command or some other command from the client? Thanks, Robert

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TLS 1.2
by Marco Lettere 18 Dec '17

18 Dec '17

Hi list, I need to perform an integration with a service that talks HTTP over TLS 1.2. I have the mutual certificates and all the rest. My idea was to do as less as possible (mostly handshaking) in Java and then use the Java call the code from inside XQuery where all the rest happens. Just wanted to be sure that there isn't a way to do everything in XQuery. Is it? Thanks, Marco.

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queries and setting on temp directory
by Stefania Axo 18 Dec '17

18 Dec '17

Hi all, i noticed that queries (http://localhost:8984/dba/queries) and the dba setting are saved in the temp directory and not on the \basex\data dir. For example: - C:\Users\IBM_ADMIN\AppData\Local\Temp\dba\ if BaseX is installed from the zip file in Wndows Os - C:\Program Files\IBM\WebSphere\Liberty\usr\servers\myApp\temp\dba if BaseX is installed as BaseX.war on WebSphere Liberty in Windows OS All the other data seems to be under the home basex\data directory: logs, databases, users. Is that a reason for that? thanks Stefania

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XML + HTML to JSON
by Maximilian Gärber 14 Dec '17

14 Dec '17

Hi, we've content similar to: <info> <name>Foo</name> <xhtml> <p>Some para </p> </xhtml> </info> How can I tell the JSON serializer to treat the content of <xhtml> as html? Br, Max

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Item to string in java
by Tushar Deshmukh 13 Dec '17

13 Dec '17

Namaste, Sorry it might be documented but I m unable to find it. Please please point in correct direction. How can we convert item from restxq to string in java. My restxq is as below import tallyfunction:"tdd.Tfunctions" %rest:post("{$data}") Function checkInJava($data as item()) { tallyfunction:checktosave() }; My java class package tdd public class Tfunctions{ public String checktosave(Item xml) { return xml.toString(); } } I m getting 64bit string Not original string sent by clients. Thanks in advance. Mangal bhavna sahit, Tushar

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Re: [basex-talk] TLS 1.2
by Kristian Kankainen 13 Dec '17

13 Dec '17

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XQuery 3.1/Build array of maps dynamically
by Hondros, Constantine (ELS-AMS) 12 Dec '17

12 Dec '17

Hello all, I want to dynamically build a map where the value is an array of maps. I am having a problem with the syntax. (My use-case is to deliver this as JSON for simple ingestion to Spark, by the way). Here's my test code, which translates cleanly into JSON: declare option output:method 'json'; map { "authors": [ map{"fn":"John", "ln":"Smith"}, map{"fn":"Jane", "ln":"Doe"} ] } However, when I try to build the same map dynamically, I get the error "Value has more than one item". I guess this is because my for loop is returning a sequence, but I can't figure out the syntax to get it working. Any ideas? declare option output:method 'json'; map { "authors": [ (for $b in $authors return (: just assume $authors is populated ...:) map{"fn":$b/*:given-name/text(), "ln":$b/*:surname/text()}) ] } TIA! ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

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bat problem with latest builds v9
by Andy Bunce 12 Dec '17

12 Dec '17

Hi, Bat files for reecent builds are not running for me and contain a line like: set CP=%MAIN%\target\classes;%MAIN%\lib\*;%MAIN%\lib\custom\* Looks like a substition is not happening somewhere. I think should be: set CP=%MAIN%\BaseX.jar;%MAIN%\lib\*;%MAIN%\lib\custom\* /Andy

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Problem with basexgui and MacOS
by Florian Eckey 06 Dec '17

06 Dec '17

Hi there, i have a problem with using BaseX GUI and MacOS 10.13.1 (or further 10.12.6). When i start the basexgui.sh i get the following error: „Failed to initialize native Mac OS X interface“ I tried it with the versions 8.6.6 and 8.6.7 unsuccessful. Stack-Trace: WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.basex.gui.GUIMacOSX (file:/Users/florianeckey/Daten/Privat/basex/BaseX.jar) to method com.apple.eawt.Application.getApplication() WARNING: Please consider reporting this to the maintainers of org.basex.gui.GUIMacOSX WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Failed to initialize native Mac OS X interface Unfortunally it is a very global exception from BaseX. Does anyone else have this problem and solved it? Best Florian

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Scripting and modules
by Kristian Kankainen 02 Dec '17

02 Dec '17

Hello, I need to run several updating queries in sequel on a database and a good candidate for this should be a simple .bxs script. But is there a convenient way to reference functions defined in an external module? I have all functions defined in an external XQuery module and I would like to be able to write the script in such a way, that I use just the names of the allready defined functions. E.g something like this: # script.bxs # open the database OPEN testdb; # make backup of the initial state CREATE BACKUP init; # run all updating queries XQUERY updateFunctionA(); XQUERY updateFunctionB(); # etc ... # make a backup of the final state CREATE BACKUP final; I guess I can recap my question with just the following: what would be the most convenient way for me to organize this kind of automation of running allready defined module functions? Thank you, Kristian K

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