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

Cursor keys
by Thomas Daly 27 Oct '14

27 Oct '14

Hello, I'm using the command line interface of BaseX 7.3. I notice the cursor keys don't behave in the normal way - instead of moving the cursor around they print strange characters. Is there something wrong with my terminal configuration or is this a shortcoming of the software?

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Reg : Group by with the top Records
by Chandrasekhar 25 Oct '14

25 Oct '14

Dear Team I am using the group by for getting top n number of record like below mentioned query (for $areaData in collection('mycollection') let $areaName := $areaData/Contry group by $areaName return $areaData )[position() lt 100] In this case i am getting first top 100 records and then it is grouping on those records.Can you please suggest me how can we get the top 100 records based on the Country name Please find the attachment for the sample data.Please do the need full on this/ Thanks&Regards Chandra Sekhar The information contained in this e-mail and any accompanying documents may contain information that is confidential or otherwise protected from disclosure. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message, including any attachments. Any dissemination, distribution or other use of the contents of this message by anyone other than the intended recipient is strictly prohibited.

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XML Oxygen search: 404 Not found when the file exists, or worse 500 error.
by France Baril 23 Oct '14

23 Oct '14

Hi, We've been having this persistent issue with our webDAV connection to XML Oxygen. How to reproduce: 1. Create a DB with 200/300 documents. 2. Create a webDAV connection to the DB within an XML Oxygen project. 3. Right click the DB from the project > Find/Replace in files, and type a keyword to search for for all files *.xml 4. Run the search 3 to 5 times. Until you notice the error. The error doesn't always occur, but I'd be surprised if you didn't see it after 3 to 5 try. Example 500 error: System ID: http://admin@localhost :8984/webdav/en-us/topics/widget-bookmark.xml Severity: error Description: 500 Internal Server Error for: http://localhost:8984/webdav/en-us/topics/widget-bookmark.xml In the case of a 500 error, you need to restart the server to be able to open or search files from the DB again. Can anything be done to improve the situation? Regards, France -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

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Re: [basex-talk] serializing an xquery flwor in csv
by Dirk Kirsten 23 Oct '14

23 Oct '14

Hi Emmanuelle, please don't forget to include the mailing list in your mails, so others can also benefit from the questions (and other people might answer you faster or better than I can). The CSV serialization works just on the element name as far as I can remember. You could simply rename the node, e.g. let $destinataire := $creation/persName[@type='destinataire'] update rename node . as "pers1" For help with XQuery Update, oyu might also want to take a look at the docs: http://docs.basex.org/wiki/Update Cheers, Dirk On 10/23/2014 03:12 PM, Emmanuelle Morlock wrote: > Hi again > there's something strange happening with the csv serialization of my query > > Two of my variables have the same element but are distinguished by their > attribute > > declare option output:method "csv"; > declare option output:csv "header=yes, separator=semicolon"; > for $lettre in db:open('myBD')//TEI > where $lettre//opener//addrLine[not(contains(.,'Adresse ?'))] > let $creation := $lettre//profileDesc/creation > let $titre := $lettre//teiHeader//title > let $date := $lettre//profileDesc//date > let $destinataire := $creation/persName[@type='destinataire'] > let $expediteur := $creation/persName[@type='expediteur'] > return > <csv> > <record>data({$date}) data({$expediteur} data({$titre} > data({$destinataire}) </record> > </csv> > > the result creates one field 'persName' with two values (separated by a > comma), whereas I wanted 2 fields > > date;persName;title > 01/01/2000;Pierre Martin,Jean Dupond;Title > > what shoud I do to avoid that and get as a result something like : > > date;persName1;title:persName2 > 01/01/2000;Pierre Martin;Title;Jean Dupond > > > thanks > emmanuelle > > > Le 23/10/2014 14:31, Dirk Kirsten a écrit : > > Hello Emmanuelle, > > > > You're very welcome to ask, even if its basic (or looks basic to you). > > We all started with XQuery at one point in time... > > > > In this case, it is even simpler than you expected I guess. As you > > want to serialize the output as csv, you don't even need the > > serialize() function. You can simply set in the prolog of your XQuery > > > > |declare| |option| |output:method ||"csv"||; > > > > | > > and your output will be automatically converted from XML to CSV. There > > is an example for CSV at ||http://docs.basex.org/wiki/Serialization, > > you can also define options in the prolog. > > > > Also, I noticed that you do $lettre//profileDesc/creation quite often. > > // is > > a quite costly operation, so you might want to put this into a > > separate variable which you then use - The optimizer might do that for > > you, but it is also shorter and cleaner to write. > > > > Cheers, > > Dirk > > > > On Thu, Oct 23, 2014 at 12:24 PM, Emmanuelle Morlock > > <emmanuelle.morlock(a)mom.fr <mailto:emmanuelle.morlock@mom.fr>> wrote: > > > > Hi all, > > > > I'm trying to do some xquery with the GUI in a standalone install. > > As I'm beginning with xquery, I rely a lot on the examples given > > in the doc. > > But I don't manage to be successful with > > http://docs.basex.org/wiki/CSV_Module for what I need. > > > > I'd like to get a result formatted in csv (separator : ';' or > > whatever) so tha I can directly import in a spreadsheet the > > results exported file. > > > > Here's the begining of my query : > > > > for $lettre in db:open('myDB')//TEI > > where $lettre//opener//addrLine[not(contains(.,'Adresse ?'))] > > let $title := $lettre//teiHeader//title > > let $destinataire := > > $lettre//profileDesc/creation/persName[@type='destinataire'] > > let $expediteur := > > $lettre//profileDesc/creation/persName[@type='expediteur'] > > let $date := $lettre//profileDesc//date > > let $locName := > > $lettre//profileDesc/creation/location/placeName[@type='PlaceExp'] > > let $locGeo := $lettre//profileDesc/creation/location/geo > > > > then I guess I should have something like : > > - a variable for the option... is let $options := > > {'separator':';'} correct ? > > something to put all the variable as a result let $fields := ... ? > > then > > return csv:serialize ($fields, $options) > > > > ??? > > thanks for helping even if this sounds too basic ! > > > > best > > > > emmanuelle > > > > -- Emmanuelle Morlock > > IGE CNRS - soutien aux projets d'édition TEI - humanités numériques > > UMR 5189 HISoMA > > http://www.hisoma.mom.fr/ > > 04 72 71 58 40 > > 06 85 84 69 16 > > @emma_morlock > > > > > > > > > > -- > > Dirk Kirsten, BaseX GmbH, http://basex.org <http://basex.org/> > > |-- Firmensitz: Blarerstrasse 56, 78462 Konstanz > > |-- Registergericht Freiburg, HRB: 708285, Geschäftsführer: > > | Dr. Christian Grün, Dr. Alexander Holupirek, Michael Seiferle > > `-- Phone: 0049 7531 28 28 676, Fax: 0049 7531 20 05 22 > > -- Dirk Kirsten, BaseX GmbH, http://basex.org |-- Firmensitz: Blarerstrasse 56, 78462 Konstanz |-- Registergericht Freiburg, HRB: 708285, Geschäftsführer: | Dr. Christian Grün, Dr. Alexander Holupirek, Michael Seiferle `-- Phone: 0049 7531 28 28 676, Fax: 0049 7531 20 05 22

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serializing an xquery flwor in csv
by Emmanuelle Morlock 23 Oct '14

23 Oct '14

Hi all, I'm trying to do some xquery with the GUI in a standalone install. As I'm beginning with xquery, I rely a lot on the examples given in the doc. But I don't manage to be successful with http://docs.basex.org/wiki/CSV_Module for what I need. I'd like to get a result formatted in csv (separator : ';' or whatever) so tha I can directly import in a spreadsheet the results exported file. Here's the begining of my query : for $lettre in db:open('myDB')//TEI where $lettre//opener//addrLine[not(contains(.,'Adresse ?'))] let $title := $lettre//teiHeader//title let $destinataire := $lettre//profileDesc/creation/persName[@type='destinataire'] let $expediteur := $lettre//profileDesc/creation/persName[@type='expediteur'] let $date := $lettre//profileDesc//date let $locName := $lettre//profileDesc/creation/location/placeName[@type='PlaceExp'] let $locGeo := $lettre//profileDesc/creation/location/geo then I guess I should have something like : - a variable for the option... is let $options := {'separator':';'} correct ? something to put all the variable as a result let $fields := ... ? then return csv:serialize ($fields, $options) ??? thanks for helping even if this sounds too basic ! best emmanuelle -- Emmanuelle Morlock IGE CNRS - soutien aux projets d'édition TEI - humanités numériques UMR 5189 HISoMA http://www.hisoma.mom.fr/ 04 72 71 58 40 06 85 84 69 16 @emma_morlock

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Re: [basex-talk] Architecture Question
by Christian Grün 23 Oct '14

23 Oct '14

Hi Mansi, Good to know! Keep us updated. Christian On Wed, Oct 22, 2014 at 8:13 PM, Mansi Sheth <mansi.sheth(a)gmail.com> wrote: > Christian, > > Actually, I am all set. I will just query using python or Angular or > whatever and do any data manipulation there and use XQUERY just to query and > no further processing. > > Btw, some initial very informal statistics: > > Took, 22 min to import ~2.1k documents with indexing as well. > ~2 min for query to return back. > > Impressive !!! > > Machine specs: 16 GB RAM, 2.7 GHz, i7 processor MacBook Pro. > > I am waiting on my colleague to get me some more production data, which > gives me access to some 10k XML files. Will keep you posted. > > - Mansi > > On Wed, Oct 22, 2014 at 12:04 PM, Mansi Sheth <mansi.sheth(a)gmail.com> wrote: >> >> Christian, >> >> Thanks for all your responses. It truly helps a lot. >> >> re: Importing data into databases: I realized, for the extent of this POC, >> I will just count no of docs in each database (currently programmed to be >> 50) and keep creating new databases. Structure of data is same, but its >> nested in nature. Like a folder can have folder, which can have file etc. >> Usually, it won't be more than 4 levels deep. Thats a good tip, to guess no >> of nodes based on byte size. I guess, for time being I will move on, with >> just storing 50 docs per DB. >> >> re: terabytes of data. Well, I am planning on using ~6 months worth of >> data for any analysis and discarding data prior to that (leaving it around >> in backups). Obviously, would be going some cloud route for such resources, >> will see how much budget I can manage to get :) Am very positive about this. >> So, no its not only a theoretical assumption as far as I can see. >> >> re: Currently, I am looking into querying these databases. I am exploring >> REST for it. From documentation, it seems our only option is supporting >> these queries (on server side) using XQUERY or RestXQ, no Java/Python ? I am >> well versed with XPATH and XSLT, gearing up towards XQUERY now. But, would >> be a little easier (just my personal preference :)) to manipulate data in >> Java/Python before serving it back to client. Is there any such facility ? >> Something like: >> >> "http://localhost:8984/rest?run=getData.java" >> >> similarly for python ? >> >> - Mansi >> >> Some preliminary statistics: Imported 2050 XML documents in 22 min >> (including indexing on attributes). >> >> On Sun, Oct 19, 2014 at 6:14 PM, Christian Grün >> <christian.gruen(a)gmail.com> wrote: >>> >>> Hi Mansi, >>> >>> > Is there some book/resource you can point me to, which helps better >>> > visualize NXD ? >>> >>> sorry for letting you wait. If you want to know more about native XML >>> databases, I recommend you to have a closer look at various articles >>> in our Wiki (e. g. [1,2]). It will also be helpful if you get into the >>> basics of XQuery [3]. >>> >>> Have you tried to realize some of the hints I gave in my previous mails? >>> >>> > I am trying to distribute data across multiple databases. I can't >>> > distribute >>> > based on day, as there could very well be situation, where single day's >>> > data >>> > could more than capacity of BaseX DB. >>> >>> If 2 billion XML nodes per day are not enough, you will probably need >>> to create more than one database per day. Via the "info db" command, >>> you see how many nodes are currently stored in a database, but there >>> is no cheap solution to find out the number of nodes of an incoming >>> document, because XML documents can be very heterogeneous. Some >>> questions back: >>> >>> * Do you have some more information on the data you want to store? >>> * Are all documents similar or do they vary greatly? If the documents >>> are somewhat similar, you can usually estimate the number of nodes by >>> looking at the byte size. >>> * Do you know that you will really need to store lots of terabytes of >>> XML data, or it is more like a theoretical assumption? >>> >>> Christian >>> >>> [1] http://docs.basex.org/wiki/Database >>> [2] http://docs.basex.org/wiki/Table_of_Contents >>> [3] http://docs.basex.org/wiki/Xquery >> >> >> >> >> -- >> - Mansi > > > > > -- > - Mansi

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locking problem
by Lizzi, Vincent 22 Oct '14

22 Oct '14

This is an update, and further problem, on a problem I posted here a few months ago. I've written a program to import XML documents into BaseX in one database, and populate a second database with a small amount of metadata about each document. This works but crashes every so often, and I have to restore the databases from backup and restart the import. To get through a large set of documents I now have the program create a backup (using the CREATE BACKUP command) after every 1000 documents imported. Since my earlier post, I found that the connection between the client and server was occasionally being dropped. I've switched to opening and closing a connection for each document instead of using one long-running connection. The client and server are running on the same machine. I'm using the latest version of BaseX (BaseX80-20141013.213520.zip). Here is the error message reported by my program when it crashes. The error occurs on the Query.execute() method of org.basex.examples.api.BaseXClient.java. Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.0 beta a91f5c2 Java: Oracle Corporation, 1.7.0_67 OS: Windows 7, amd64 Stack Trace: java.nio.channels.OverlappingFileLockException at sun.nio.ch.SharedFileLockTable.checkList(Unknown Source) at sun.nio.ch.SharedFileLockTable.add(Unknown Source) at sun.nio.ch.FileChannelImpl.tryLock(Unknown Source) at org.basex.io.random.TableDiskAccess.lock(TableDiskAccess.java:139) at org.basex.io.random.TableDiskAccess.<init>(TableDiskAccess.java:87) at org.basex.data.DiskData.init(DiskData.java:119) at org.basex.data.DiskData.<init>(DiskData.java:80) at org.basex.core.cmd.Open.open(Open.java:70) at org.basex.core.cmd.Open.run(Open.java:36) at org.basex.core.Command.run(Command.java:360) at org.basex.core.Command.execute(Command.java:94) at org.basex.server.ClientListener.run(ClientListener.java:145) The server instance reports the error with this stack trace: C:\Programs\basex\basex\bin>basexhttp BaseX 8.0 beta a91f5c2 [Server] Server was started (port: 1984) HTTP Server was started (port: 8984) java.io.FileNotFoundException: C:\Programs\basex\basex\data\article_xml_meta\doc.basex (The requested operation cannot be performed on a file with a user-mapped section open ) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(Unknown Source) at java.io.FileOutputStream.<init>(Unknown Source) at org.basex.io.out.DataOutput.<init>(DataOutput.java:47) at org.basex.io.out.DataOutput.<init>(DataOutput.java:36) at org.basex.index.resource.Docs.write(Docs.java:73) at org.basex.index.resource.Resources.write(Resources.java:51) at org.basex.data.DiskData.write(DiskData.java:141) at org.basex.data.DiskData.flush(DiskData.java:249) at org.basex.data.DiskData.finishUpdate(DiskData.java:239) at org.basex.query.up.ContextModifier.apply(ContextModifier.java:124) at org.basex.query.up.Updates.apply(Updates.java:129) at org.basex.query.QueryContext.iter(QueryContext.java:351) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:80) at org.basex.server.ServerQuery.execute(ServerQuery.java:128) at org.basex.server.ClientListener.query(ClientListener.java:492) at org.basex.server.ClientListener.run(ClientListener.java:109) Here is the update statement where the error occurs, along with a bit of the surrounding Java. BaseXClient.Query queryIndex = client.query("declare variable $indexDb external; declare variable $hash external; declare variable $database external; declare variable $path external; let $p := <properties><database>{$database}</database><path>{$path}</path><sha1>{$hash}</sha1><loadedDate>{current-dateTime()}</loadedDate></properties> return db:replace('" + indexDatabaseName + "', $path, $p)"); try { queryIndex.bind("$indexDb", indexDatabaseName); queryIndex.bind("$database", managedDatabaseName); queryIndex.bind("$path", path); queryIndex.bind("$hash", hash); queryIndex.execute(); } finally { queryIndex.close(); } Previously this code used a variable for the first parameter of db:replace() but I changed it to "hard code" the database name into the query after reading about transactions and locking in the wiki. This change doesn't appear to have helped. To put this in context, the above update is run after the XML document is imported using BaseXClient.replace(). The next thing that happens in the program is an XQuery db:replace to add more properties for the document to the metadata database. I've added a Thread.sleep(300), to create a small delay between loading each document and this has helped the program to import more documents before crashing. Adjusting the delay doesn't seem to completely stop the crashes though. I'm not sure if this is a bug or improper use. Any help would be appreciated. Thanks, Vincent

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Architecture Question
by Mansi Sheth 22 Oct '14

22 Oct '14

Hello, I have been going thru and comparing different Native XML Databases and so far I am liking BaseX. However, there are still a few questions unanswered, before I make a final choice: 1. I have 1000s of XML files (each between 50MB-400MB) and this is going to grow exponentially (~200 / per day). So, my question is how scalable is BaseX ? Can I configure it to use data from my external HDD, in my initial prototype ? 2. I plan to heavily use XPATH, for data retrieval. Does BaseX, use any multi-processing, multi-threading to speed up search ? Any concurrent processing ? 3. Can I do some post-processing on searched and retrieved data ? Like sorting, unique elements etc ? - Mansi

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Using TcpCatcher as a proxy with Basex Client
by Arto Viitanen 20 Oct '14

20 Oct '14

I am debugging a Basex client built in C#. The client is based on the Git Hub example https://github.com/BaseXdb/basex/tree/master/basex-api/src/main/c%23. The problem is, every now and then the client drops the session. It might be, that the client drops the connection if the server takes too much time to answer (or something). So I need some way to emulate slow connection or connection dropping packages. I downloaded TcpCatcher (http://www.tcpcatcher.org/) and set it as a proxy (client talks to 21984; TcpCatcher catches packages and send them to BaseX listening to 11984). But It seems that BaseX does not respond. I took BasexClient.cs and Example.cs from the github and tried with them. I get three packages; one coming from the server and two going to client; but after that nothing. The Example prints "Access Denied". I guess this comes from: socket = new TcpClient(host, port); stream = socket.GetStream(); ehost = host; string ts = Receive(); Send(username); Send(MD5(MD5(pw) + ts)); if (stream.ReadByte() != 0) { throw new IOException("Access denied."); } that is: client gets ts (timestamp?), sends username and password with timestamp; but receives nothing. So how can I use TcpCatcher (or other proxy program) with Basex client? (Basex 7.7; windows 7) Arto Viitanen Microteam Oy

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Templating
by Emmanuel Chateau 18 Oct '14

18 Oct '14

Hi, I’ve been trying to use the templating proposed by Andy Bunce here http://cubeb.blogspot.fr/2012/11/xquery-templating-engines-and-txq.html https://mailman.uni-konstanz.de/pipermail/basex-talk/2012-November/004209.h… I’ve tried with txq module in different ways. But, I can’t figure out why I couldn’t reproduce it. Here is the simpler exemple I’ve tried : In the webapp folder an xml file, named `view1.xml` wich contains : ```xml <div>{map:get($map, 'greeting')}</div> ``` In webapp a restxq file with : ```xquery module namespace test = 'test.test'; import module namespace xquery = "http://basex.org/modules/xquery"; declare function test:render($template as xs:string, $map as map(*)){ xquery:invoke($template,$map) }; declare %restxq:path('/test') %restxq:GET function test:test(){ let $map := map{ "greeting" : "hello", "who": "world"} return test:render('view1.xml', $map ) }; ``` Arrêté à /Users/emmanuelchateau/Documents/basex/webapp/view1.xq, 1/15: [XPST0008] Undefined variable $map. I’m running BaseX version 7.9 Is there still anybody with this kind of templating running ? Thanks a lot for your help. Emmanuel

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Web hosting
by spaelti 16 Oct '14

16 Oct '14

I have now tried BaseX web server on my own machine, and it works great. But what I would really like to do is to use it on my website. This website is on a commercial web provider. Is it possible to use BaseX in such a situation? How does one go about this? Would I need to ask the commercial provider to install BaseX? Or is there some other web site hosting method, that one can use? Thanks in advance for any help or suggestions. Philip Spaelti spaelti(a)mac.com

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Fw: Suggestion for a requirement
by Sateesh 16 Oct '14

16 Oct '14

? Hi Basex Team, We are starting a new project in that we have selected to use basex,i would tell you my requirement,request you to please suggest the best way to use basex. We have started a web application in that we have a requirement to create xml db's per user based means each user who logs in we need to create DB's on his xml files in the backend,for this we dont want to use the client-server architecture of the basex as we dont want that extra time to hit a http server request to basex server and get the response,what we would want is to create the DB's execute queries and drop the DB's with in the same web application and also please note that we dont have a requirement to edit the DB's data we would only read the data from those DB's by executing the queries and also note that volumes of the xml files are very huge they might go up to gb's also and query output will also be in huge volume and also we must make sure that this huge volumes of query output will not eatup all the heap memory as the number of parallel users using this site are very high and we cannot afford to go out of memory.Also we would need to configure the DB paths as this are huge volumes we cannot store them in the default locations to. Considering all the above points request you to please suggest the best way to use basex. Our web application is developed in java.Though we have used basex in our earlier projects some where i feel that we did not used it properly and gone through problems and the kind of support we got from your team in solving them earlier was immense and this time we want to go in a more systematic way so request you to please help us by suggesting the best way. Thanks & Regards SAteesh.A The information contained in this e-mail and any accompanying documents may contain information that is confidential or otherwise protected from disclosure. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message, including any attachments. Any dissemination, distribution or other use of the contents of this message by anyone other than the intended recipient is strictly prohibited.

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Crashed BaseX import
by Arjan Loeffen 16 Oct '14

16 Oct '14

This is the report, bold is my logging steps in the process: *DELETE core-cbnl-20140901.xml* Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_15 OS: Windows Server 2012, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 372 at org.basex.io.random.TableDiskAccess.flush(TableDiskAccess.java:124) at org.basex.data.DiskData.finishUpdate(DiskData.java:212) at org.basex.core.cmd.Add.run(Add.java:109) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.LocalSession.execute(LocalSession.java:122) at org.basex.server.LocalSession.execute(LocalSession.java:114) at org.basex.server.Session.execute(Session.java:50) at org.basex.http.rest.RESTCommand.run(RESTCommand.java:40) at org.basex.http.rest.RESTPost.run(RESTPost.java:108) at org.basex.http.rest.RESTServlet.run(RESTServlet.java:14) at org.basex.http.BaseXServlet.service(BaseXServlet.java:58) at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2430) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2419) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) * ADD "C:\Servers\xslweb\home\webapps\CBNL-browser-v2\work\contexts\core-cbnl-20140901.xml" CREATE INDEX ATTRIBUTE (2d) Database 'CBNL' is currently opened by another process. CREATE INDEX TEXT (2e) Database 'CBNL' is currently opened by another process. CREATE INDEX FULLTEXT (2f) * Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_15 OS: Windows Server 2012, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 0 - #used blocks: 0 - #total locks: 0 - access: -1 (0 > -1] at org.basex.util.Util.notexpected(Util.java:53) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:488) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:189) at org.basex.data.Data.kind(Data.java:282) at org.basex.query.value.node.DBNode.<init>(DBNode.java:53) at org.basex.core.cmd.OptimizeAll$DBParser.parse(OptimizeAll.java:201) at org.basex.build.Builder.parse(Builder.java:73) at org.basex.build.DiskBuilder.build(DiskBuilder.java:90) at org.basex.core.cmd.OptimizeAll.optimizeAll(OptimizeAll.java:126) at org.basex.core.cmd.OptimizeAll.run(OptimizeAll.java:44) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.LocalSession.execute(LocalSession.java:122) at org.basex.server.LocalSession.execute(LocalSession.java:114) at org.basex.server.Session.execute(Session.java:50) at org.basex.http.rest.RESTCommand.run(RESTCommand.java:40) at org.basex.http.rest.RESTPost.run(RESTPost.java:108) at org.basex.http.rest.RESTServlet.run(RESTServlet.java:14) at org.basex.http.BaseXServlet.service(BaseXServlet.java:58) at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2430) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2419) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) *OPTIMIZE ALL * Any idea what's going on here? Hope this is enough info. -- Arjan Loeffen, Armatiek BV 06-12918997

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Xpath gives multiple results, finding the one originating from the latest imported document?
by Sam Eklund 15 Oct '14

15 Oct '14

A quick question, I have this simple xquery to retrieve a node that sometimes has multiple hits, and for this reason I am using the function: head. This gives me the first node that matches the xpath, but is there a way to retrieve the node that originates from the latest imported document? My current query: xquery head (//event[eventID="12345ABC"]) // Sam

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Question re starting basexhttp
by spaelti 12 Oct '14

12 Oct '14

I have been trying to run BaseX as a web application on my mac. After some difficulties I have gotten it to work. However there is one thing that I am still unsure about. Whenever I start the web server using ‘basexhttp’ I get the following message: /usr/local/bin/basexhttp: line 11: cd: /usr/local/Cellar/basex/7.9/libexec/../basex: No such file or directory However everything thereafter seems to work fine. So why do I get this message, or what does it mean? In my installation (which I got through the brew script) there is no ‘basex’ file/folder at the specified location (which would be in the ‘7.9’ folder). Should there be? Any help or advice would be much appreciated. best Philip This is what /usr/local/Cellar/basex looks like: ---- basex 7.9 bin changelog.txt INSTALL_RECEIPT.json libexec BaseX.jar bin lib webapp license.txt readme.txt ---- --------------------------------------------------- Philip Spaelti Kobe Shoin Women's University, Graduate school ---------------------------------------------------

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zsh plugin
by Dirk Kirsten 12 Oct '14

12 Oct '14

Hello, if any of you uses the excellent zshell, you might be interested in this small plugin for BaseX for the zsh: https://github.com/dirkk/zsh-basex. Aliases might also be useful for every other shell user, because they basically shorten all basex commands (e.g. bx is defined as an alias for basex). Cheers, Dirk -- Dirk Kirsten, BaseX GmbH, http://basex.org |-- Firmensitz: Blarerstrasse 56, 78462 Konstanz |-- Registergericht Freiburg, HRB: 708285, Geschäftsführer: | Dr. Christian Grün, Dr. Alexander Holupirek, Michael Seiferle `-- Phone: 0049 7531 28 28 676, Fax: 0049 7531 20 05 22

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BaseX Cluster Solution based on Galera Cluster
by Jaco van der Merwe 09 Oct '14

09 Oct '14

Hi All, We have recently started using the Galera Cluster for MySQL which works really well as either a single or a multi-master cluster with semi-synchronous replication. See http://galeracluster.com/ for more information. The nice thing about the Galera Cluster is that the cluster and replication management functionality has been abstracted and extracted into a component (actually an .so file) called the WSREP provider. The latter provides hooks that can be integrated into your DB. I was thinking that this could be a very nice solution for providing a cluster solution for BaseX. So my question is whether anybody out there has done this already for BaseX, or may have plans for doing this. Thanks Jaco

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confused
by Rob Stapper 08 Oct '14

08 Oct '14

Hi, I'm confused. The code below results in false() for $e1 and true() for $e2. Shouldn't both be false? I must be overlooking something. Can somebody enlighten me, please? let $node := <node ID="X"><node ID="Y"/></node> let $e1 := exists( trace( $node/node[ ./@ID = "Z"], 'node: ')) let $e2 := exists( $node/node[ ./@ID = "Z"] ) return ( $e1, $e2) Thnx in advance, Rob Stapper --- Dit e-mailbericht bevat geen virussen en malware omdat avast! Antivirus-bescherming actief is. http://www.avast.com

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regex for xquery
by Rob Stapper 08 Oct '14

08 Oct '14

Hi, Basically I want to break down the path-expression of a node in my XML into its elementary steps. QName: "Q{http://www.w3.org/2005/xpath-functions}root()/Q{}A[1]/Q{}B[1]/Q{}C[1]/Q{} D[1]" must become QName-sequence: ("Q{http://www.w3.org/2005/xpath-functions}root()", "Q{}A[1] ", "Q{}B[1] ", "Q{}C[1] ", "Q{}D[1]") So I need to break the path-expression down on the "/"-characters which aren't part of the namespace-uries. I'm using the "fn:tokenize"-function for this. The function uses a "regular expression" for it's separator. Unfortunately my regex-experience is zero (well, two days by now). I came up with the next brilliant ;-) solution: fn:tokenize( path( $node), "/(?=Q)"). Again, unfortunately, this doesn't work because the xquery-flavor of regex doesn't support looking around. Sure, I can use "/Q" as pattern and subsequently stick a "Q" in front of every substring (except the first one) but I'm looking for a solid solution. I there anyone out there with enough "regex-for-xquery"- experience to help me with this? Big thanx for that in advance. @Christian: On the other hand I can imagine that within Basex the path-expression is built from these elementary steps. If so, is it in any way possibly to retrieve this elementary steps sequence instead of this path-expression? Thanx, Rob Stapper --- Dit e-mailbericht bevat geen virussen en malware omdat avast! Antivirus-bescherming actief is. http://www.avast.com

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IllegalMonitorStateException
by Gerald de Jong 07 Oct '14

07 Oct '14

Dear BaseX experts, I'm wondering if anybody can see something that I'm doing wrong. I would expect it to be possible to add documents from multiple threads. Am I wrong about that?? When I set two of my datasets saving documents to BaseX 7.9 at the same time, I get this exception: $ basexserver BaseX 7.9 [Server] Server was started (port: 1984) Exception in thread "Thread-2295" java.lang.IllegalMonitorStateException at java.util.concurrent.locks.ReentrantReadWriteLock$Sync.tryRelease(ReentrantReadWriteLock.java:374) at java.util.concurrent.locks.AbstractQueuedSynchronizer.release(AbstractQueuedSynchronizer.java:1260) at java.util.concurrent.locks.ReentrantReadWriteLock$WriteLock.unlock(ReentrantReadWriteLock.java:1131) at org.basex.core.DBLocking.release(DBLocking.java:219) at org.basex.core.Context.unregister(Context.java:249) at org.basex.core.Command.execute(Command.java:104) at org.basex.core.Command.execute(Command.java:117) at org.basex.server.ClientListener.execute(ClientListener.java:384) at org.basex.server.ClientListener.add(ClientListener.java:355) at org.basex.server.ClientListener.run(ClientListener.java:100) All I am doing is making concurrent calls in two parallel sessions: session = new ClientSession(...) session.execute(new Open(database)) session.execute(new Set("autoflush", "false")) session.add([path string], [document-bytes]) // a zillion times session.execute(new Flush()) During the execution of the parallel add commands, it crashes. The relevant code: def withSession[T](block: ClientSession => T): T = { val session = new ClientSession(host, port, user, pass) try { block(session) } finally { session.close() } } def withDbSession[T](database: String)(block: ClientSession => T): T = { withSession { session => session.execute(new Open(database)) session.execute(new Set("autoflush", "false")) val result = block(session) session.execute(new Flush()) result } } then: withDbSession { session => // many calls to session.add(...) } -- Delving BV, Vasteland 8, Rotterdam http://www.delving.eu http://twitter.com/fluxe skype: beautifulcode +31629339805

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Re: [basex-talk] $ = AltGr + É
by Dániel Kiss-Kálmán 06 Oct '14

06 Oct '14

I think I found somehing but need help to correct it. CTRL Home is the jump to top shortkey. I went to http://www.w3.org/2002/09/tests/keys.html to check CTRL Home = keycode 36, but no charcode AltGR É = keycode 0, charcode 36 (and CTRL and ALT is pressed because of AltGR. so AltGr is nothong more than CTRL + ALT). basex / basex-core / src / main / java / org / basex / gui / layout / BaseXKeys.java line 31: /** Beginning of text. */ TEXTSTART(META, MAC ? VK_UP : VK_HOME), Can oneone please tell me how to correct it if I'm on the right way? maybe check the ALT or any other way? Daniel

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XQException with Basex 7.9
by Erol Akarsu 06 Oct '14

06 Oct '14

I am having syntax error at map(*) where 74'th chracter is first '(' do you know why? I run same script basex gui with base 7.9 w/o issue. declare variable $rawProductsFile as xs:string external; declare variable $schemaFileName as xs:string external; declare variable $tableName as xs:string external; declare variable $outputFileName as xs:string external; (:(line 7 is this line:) declare function local:getFieldMap ($schemaFileName as xs:string) as map(*) javax.xml.xquery.XQException: XQJQS001 - Invalid XQuery syntax, syntax does not pass static validation. Root Cause: net.xqj.basex.bin.bx: Encountered " "(" "( "" at line 7, column 74. Was expecting one of: "*" ... "?" ... "external" ... "{" ... "+" ... at com.ferguson.xquery.RunQueries.queryForFilterData2(RunQueries.java:147) at com.ferguson.endeca.EndecaEngine.processExtractDARFilesExt(EndecaEngine.java:377) at com.ferguson.endeca.EndecaEngine.main(EndecaEngine.java:142) at com.ferguson.xquery.RunQueries.queryForFilterData2(RunQueries.java:147) at com.ferguson.endeca.EndecaEngine.processExtractDARFilesExt(EndecaEngine.java:377) at com.ferguson.endeca.EndecaEngine.main(EndecaEngine.java:142) On Mon, Oct 6, 2014 at 11:20 AM, Dániel Kiss-Kálmán < kisskalmandaniel(a)gmail.com> wrote: > Hello Basex-Talkers, > > when I try to enter a variable I need the $ char. I use hungarian > keyboard, and $ is AltGr + É keyboard combination. The only annoying thing > is when I press AltGr + É, $ appears, but just before that cursor jumps to > the first row first char position. So $ is smiling as the first char in > the first row. No other keboard combination does that, only AltGr + É. So > every time I need a variable I use clipboard instead of pressing $ char. > > Can onyone make my life a little easier to correct it if it is possible at > all? > Or help me how to try to remove that cursor jump? > > Thanks in advance, Daniel >

2 1

Eclipse vs BaseX Gui differences ?
by jean-marc Mercier 06 Oct '14

06 Oct '14

Hi all, Happy to write again in this mailing-list, hope you are all doing well guys ! I am encountering a small problem running my old xquery modules. I guess that it is a classical issue, but I can't remember how to look into BaseX archive :( Here is the description of the problem : I am running a query, calling module_of_mine.xqm, on two different environments. The first one is eclipse, linked to the latest interpreter from BaseX80-20140923.183154 (but I tested also against older interpreter). In this way, this query saturated my 12 G Java machine after some minutes. Then I installed module_of_mine.xqm into BaseX repo, and ran the same query using basex gui with 4G heap size. The query ran perfectly in some 30 sec. My first penny guess is that the built-in BaseX xquery profiler is doing some nice work there ? If so, is there a way to activate / desactivate this profiler from eclipse or from some configuration files ? Cheers, Jean-Marc

3 8

$ = AltGr + É
by Dániel Kiss-Kálmán 06 Oct '14

06 Oct '14

Hello Basex-Talkers, when I try to enter a variable I need the $ char. I use hungarian keyboard, and $ is AltGr + É keyboard combination. The only annoying thing is when I press AltGr + É, $ appears, but just before that cursor jumps to the first row first char position. So $ is smiling as the first char in the first row. No other keboard combination does that, only AltGr + É. So every time I need a variable I use clipboard instead of pressing $ char. Can onyone make my life a little easier to correct it if it is possible at all? Or help me how to try to remove that cursor jump? Thanks in advance, Daniel

1 0

deduplication problem in BaseX 7.9?
by C. M. Sperberg-McQueen 06 Oct '14

06 Oct '14

Consider the following XML document: <article> <front> <article-meta> <aff id="aff1">Tropical and Infectious Disease Hospital, Kathmandu, Nepal</aff> <aff id="aff2">Nagasaki University, Nagasaki, Japan</aff> <aff id="aff3">Department of Radiology, Kyorin University Faculty of Medicine, Tokyo, Japan</aff> <aff id="aff5">Pentax Company Limited, Tokyo, Japan</aff> <aff id="aff6">National Research Laboratory of Molecular Complex Control, Yonsei University, Seoul, Korea</aff>  <article-id pub-id-type="pmc">2570825</article-id> <article-id pub-id-type="pmid">18325280</article-id> <article-id pub-id-type="publisher-id">07-0473</article-id> <article-id pub-id-type="doi">10.3201/eid1403.070473</article-id> </article-meta> </front>  </article For convenience in trying to understand this problem, a copy of this document has been placed at [1]. When I issue the following search against this document, I get unexpected results. let $doc := doc('http://blackmesatech.com/2014/LIS590DML/data/testdata.xml') let $path1 := $doc/child::article/child::front /child::article-meta /child::aff[contains(.,"Japan")] /parent::article-meta/child::article-id, $path2 := $doc/descendant::aff[contains(.,"Japan")] /parent::article-meta/child::article-id, $path3 := $doc/article/front/article-meta/aff[contains(.,'Japan')] /../article-id, $path4 := $doc//aff[contains(.,'Japan')]/../article-id, $path5 := $doc//aff/../article-id return (count($path1), count($path2), count($path3), count($path4), count($path5)) What I expect is that path1, path2, path3, path4, and path5 should all return the same results, namely the set of four article-id elements in the document. So the sequence of counts returned should be 4 4 4 4 4. What I am finding is that path1 and path3 are returning 12 results, with each article-id present three times in the result (once, apparently, for every aff element containing the string 'Japan'). Paths 2, 4, and 5 are all returning 4 results each, as I had expected them to. So the sequence of counts actually returned is 12 4 12 4 4. In BaseX 7.6, for what it's worth, this query returns the sequence 12 12 12 12 20, which seems suggestive. Interestingly, if I initialize the variable $doc with a direct element constructor, along the lines of let $doc := document { <article>...</article> } then all counts come out as expected in 7.6, but in 7.9 the result continues to be 12 4 12 4 4. Is this an error in the handling of the / operator, or am I missing some subtle point? Many thanks. [1] http://blackmesatech.com/2014/LIS590DML/data/testdata.xml -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

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