BaseX-Talk October 2015

basex-talk@mailman.uni-konstanz.de

24 participants
28 discussions

BaseX, Zorba, e-mail module
by Tim Thompson 04 Feb '16

04 Feb '16

Hello, I would like to be able to send e-mail from a Web app I am developing in BaseX and was wondering whether anyone else had implemented this functionality (or whether a BaseX e-mail module might be in the works?). I see that Zorba has an e-mail module with support for SMTP and IMAP (not to mention many other useful modules), which leads me to wonder whether anyone has worked on a BaseX connector for Zorba. In the meantime, I decided to try using the BaseX process module to call Zorba, like so: proc:system( 'zorba', ( '-q', convert:binary-to-string( db:retrieve( 'out', 'email.xq' ) ) ) ) I stored the XQuery code for Zorba as a raw file in the BaseX database, since storing it in the webapp directory caused an error, due to the unrecognized Zorba module declarations. This approach seems to work adequately, but does anyone have any suggestions for improvement, or a different approach? Thanks in advance, Tim -- Tim A. Thompson Metadata Librarian (Spanish/Portuguese Specialty) Princeton University Library

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GUI feature request "Add as import"
by Andy Bunce 03 Jan '16

03 Jan '16

Hi, I often find myself adding module imports in the GUI and I wonder if the following suggestion might speed up that process. Add a new menu item to the filelist right click context menu "Add as import" when the file selection is a XQuery module. The action would be to add a line to the current edit window source with import module namespace {$prefix} = '{$namespace}' at {$path}; Where $prefix and $namespace} are read from the source of the selected file, and $path is calculated from the relative path from the edit file source to the selected filelist source. The line would be inserted at a suitable place in the prologue or at the current location if that is too tricky. /Andy

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request concerning unittest in the GUI
by Rob Stapper 02 Nov '15

02 Nov '15

Hi Christian, For debugging my xquery-code I using the test-facilities from the unit-module in combination with trace and prof:dump command in the code for code-tracing. The problem is that when a unit-test fails it overwrites the trace-output in the Query-info window. So the code-tracing-info is gone just when I need it. It would make debugging a lot easier if the trace-output is appended after the unit-test-output in the Info-window of the GUI. Best, Rob --- Dit e-mailbericht is gecontroleerd op virussen met Avast antivirussoftware. https://www.avast.com/antivirus

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Best way to batch up a set of DB creates, updates and queries?
by Hondros, Constantine (ELS-AMS) 01 Nov '15

01 Nov '15

I'm looking for the best way to batch up a series of updating operations into a single pipeline that can be run at once. To give you an idea, we have to create multiple databases, perform a number of updating post-processes on each, before finally pulling certain fields out. I've got a lot of parameters that need to externalised somehow - database creation options, location of DTDs, XSDs, Catalogs, and unless I am trying this the wrong way I am finding it quite difficult. I can't write it all XQuery - I have a mixture of updating and non-updating functions. I can't get much traction out of the BXS scripting syntax - for example, I can't seem to create and use variables using this. What do other people out there use to glue these sorts of operations together? TIA, Constantine ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

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WebDav issues and auth clarification
by Régis Robineau 30 Oct '15

30 Oct '15

Hi all, I'm a beginner in BaseX and I'd need some clarification about the setup and configuration, especially about authentication process. The context is: - Debian 8 Jessie, with Basex 8.3 manually installed (i.e. not from APT). I'm using Apache in front of Tomcat to access web apps (through mod_proxy and mod_proxy_ajp): ProxyPass /BaseX83 ajp://localhost:8009/BaseX83 ProxyPassReverse /BaseX83 ajp://localhost:8009/BaseX83 - Webapp (WEBPATH): "/var/lib/tomcat7/webapps/BaseX83" - Data (DBPATH) : "/var/data/basex" (owned by tomcat7 user) - Client/server binaries (BaseX83): "/opt/basex/bin/" - conf file: "/opt/basex/.basex" Here are the main variables in my ".basex" file: DBPATH = /var/data/basex REPOPATH = /var/lib/tomcat7/webapps/BaseX83/repo HOST = localhost PORT = 1984 SERVERPORT = 1984 PROXYPORT = 80 WEBPATH = /var/lib/tomcat7/webapps/BaseX83 HTTPLOCAL = false STOPPORT = 8985 AUTHMETHOD = Basic And in my "WEB-INF/web.xml" I've set: - the value of "org.basex.dbpath" to reflect my local path (i.e. "/var/data/basex") - a new "org.basex.password" for the "org.basex.user" (admin) I have access to dba and REST service but I encounter various issues regarding authentication and WebDAV: 1/ I can't connect to WebDav service using the Finder (on Mac OS X 10.8.5) when "org.basex.authmethod" is set to "Digest". WebDav only works with the "Basic" auth method 2/ When the WebDav folder is mounted in the Finder, I can't copy files into it (permissions issues?). I've both tested as admin and as a test user with read/write permissions to the database... An empty file is created (zero byte, no content). But on the other hand, I'm able to access the REST interface with the same users (admin and test). I've created the test user like so: $ ./basexserver // in a second tab: $ ./basexclient -w > CREATE DB testdb > CREATE USER test password > GRANT READ ON testdb TO test > GRANT WRITE ON testdb TO test > SHOW USERS ON testdb 3/ The "org.basex.password" in WEB-INF/web.xml has no effect. The only way to define a password for admin is to use the console (ALTER PASSWORD admin password). Moreover the "service-specific credentials" for WebDav has no effect either. It just don't work. You can only connect to WebDav with the user credentials you defined in basex console (hence listed in users.xml). So what is the purpose of the "org.basex." settings? Does anybody ever faced the same issues with WebDav? Should I downgrade to 7.9 ? Thanks for your help. Regis

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Creating Tim, ADate, Dtn, Map programatically
by James Wright 30 Oct '15

30 Oct '15

I have some Java methods which return time elements and or Maps and I was trying to convert these into XQuery atomic values with no luck. Is there a utility for these? Array has ``fromValues`` and all other types like ``Str`` have ``get`` but Map, Tim, Dtn, ADate do not appear to be construct-able. Any help would be appreciated. - James

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BasexGui
by meumapple 28 Oct '15

28 Oct '15

Hi All, I love using the gui but I have a hard time dealing with autocomplete: is there a way to disable it in the txt editor? I think that it would also be very useful to allow view of whitespaces and tabs and have a function to prettify the code itself (do you know any for xquery?) Thank you very much for your work! Joseph

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repo install issue
by Andy Bunce 28 Oct '15

28 Oct '15

Hi, The following installs in the repository, and can be used: " https://raw.githubusercontent.com/james-jw/xq-mustache/master/src/xq-mustac… " !repo:install(.) But it does not appear the repo:list() or the UI repository list.. I suspect the issue is the form of the namespace module namespace mustache = 'http://xq-mustache'; Regards /Andy

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Change basex home in the same execution enviroment
by Antonio Mele 28 Oct '15

28 Oct '15

Hello, I am using basex version 8.3-SNAPSHOT in a java stand alone application. After i set the property org.basex.path with the path of my DB (ex. /mnt/test/db_1) I call a new Context and then CreateDB. It creates the folder /mnt/test/db_1/data/db_1 After that (in the same execution enviroment) I change the property to another DB (ex. /mnt/test/db_2). It creates the folder /mnt/test/db_1/data/db_2 I would like to create the db_2 in the path /mnt/test/db_2/data/db_2. Follow the code I wrote, where inputFolder is a folder with inside some xml files Thanks in advance. System.setProperty("org.basex.path", "/mnt/test/db_1"); Context context = new Context(false); new CreateDB("db_1", inputFolder).execute(context); context.close(); System.setProperty("org.basex.path", "/mnt/test/db_2"); context = new Context(false); new CreateDB("db_2", inputFolder).execute(context); context.close();

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Re: [basex-talk] Full-text index with lots of data
by Chuck Bearden 21 Oct '15

21 Oct '15

Sorry for not using "Reply All" earlier. Setting FTINDEXSPLITSIZE to 20000000 enabled the process to get a little further, if the meaning of each dot is the same. FTINDEXSPLITSIZE at default: ..............................|..................................................................|..........................................................................|...............................................................................|.. FTINDEXSPLITSIZE = 20000000 .......|.......|........|.......|......|........|.............|.............|.............|.............|.............|.............|.............|.............|..............|.............|.............|.............|.............|.............|.............|............ If it's a matter of making the indexing process take longer, that's not a problem. Thanks, Chuck On Tue, Oct 20, 2015 at 1:27 PM, Chuck Bearden <cfbearden(a)gmail.com> wrote: > Thanks Christian, I'll try the FTINDEXSPLITSIZE option. > > I'm also open to modifying the XML files it that would help. Because > of limitations of the service from which we harvest them RESTfully, I > have only 20 actual content elements in each file. If you think it > would make a difference, I could consolidate them to have, say, 200 or > 500 of the actual content elements per file, but I have no idea if > that would change how the indexing falls out. > > The files also have structures where some properties of each record > are each represented by a URL, and ID value, and a string. I could > XSLT the files to remove all but the string (human readable is better > for our purposes) to make them less verbose. > > BaseX is really super for doing data quality assessments of the XML, > and if we could get full-text indexing working, it would speed things > up considerably. Thanks to you & your team for all the work you've put > in to the application! > > Alles Gute > Chuck Bearden > > On Tue, Oct 20, 2015 at 12:55 PM, Christian Grün > <christian.gruen(a)gmail.com> wrote: > > I see; it seems that the index creation is failing at the very final > > step, in which partial index structures, which are temporarily written > > to disk, are merged. > > > > You could either to increase Xmx even more (to 6 or 7G?). If this > > doesn't work, you could try assign different values to the > > FTINDEXSPLITSIZE option [1] (start e.g. with 20000000). > > > > Sorry for the trouble. Feel free to keep me updated, maybe we find a > > way to fix this, > > Christian > > > > [1] http://docs.basex.org/wiki/Options#FTINDEXSPLITSIZE > > > > > > On Tue, Oct 20, 2015 at 7:48 PM, Chuck Bearden <cfbearden(a)gmail.com> > wrote: > >> Here's the stack trace: > >> > >> > =.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= > >>> create db pure_20151019 pure_20151019 > >> Creating Database... > >> > ..;..;..;..;..;..;.;..;..;..;..;..;.;..;.;.;.;.....;.....;.....;......;.....;.....;.......;.;.;;.;.;;.;.;;.;.;;.;.;;.;.;;.;.................................................;..........................................................;..........................................................;..........................................................;..........................................................;..........................................................;................................................... > >> 677584.62 ms (1435 MB) > >> Indexing Text... > >> > ........................................................................................................................................................................................................................................................... > >> 98215794 operations, 178526.99 ms (1611 MB) > >> Indexing Attribute Values... > >> > ........................................................................................................................................................................................................................................................... > >> 178304119 operations, 135613.26 ms (2005 MB) > >> Indexing Full-Text... > >> > ..............................|..................................................................|..........................................................................|...............................................................................|..java.lang.OutOfMemoryError: > >> Java heap space > >> at org.basex.index.ft.FTList.next(FTList.java:93) > >> at org.basex.index.ft.FTBuilder.merge(FTBuilder.java:236) > >> at org.basex.index.ft.FTBuilder.write(FTBuilder.java:140) > >> at org.basex.index.ft.FTBuilder.build(FTBuilder.java:85) > >> at org.basex.index.ft.FTBuilder.build(FTBuilder.java:23) > >> at org.basex.data.DiskData.createIndex(DiskData.java:187) > >> at org.basex.core.cmd.CreateIndex.create(CreateIndex.java:103) > >> at org.basex.core.cmd.CreateIndex.create(CreateIndex.java:91) > >> at org.basex.core.cmd.CreateDB.run(CreateDB.java:104) > >> at org.basex.core.Command.run(Command.java:398) > >> at org.basex.core.Command.execute(Command.java:100) > >> at org.basex.api.client.LocalSession.execute(LocalSession.java:132) > >> at org.basex.api.client.Session.execute(Session.java:36) > >> at org.basex.core.CLI.execute(CLI.java:103) > >> at org.basex.core.CLI.execute(CLI.java:87) > >> at org.basex.BaseX.console(BaseX.java:191) > >> at org.basex.BaseX.<init>(BaseX.java:166) > >> at org.basex.BaseX.main(BaseX.java:42) > >> org.basex.core.BaseXException: Out of Main Memory. > >> You can try to: > >> - increase Java's heap size with the flag -Xmx<size> > >> - deactivate the text and attribute indexes. > >> at org.basex.core.Command.execute(Command.java:101) > >> at org.basex.api.client.LocalSession.execute(LocalSession.java:132) > >> at org.basex.api.client.Session.execute(Session.java:36) > >> at org.basex.core.CLI.execute(CLI.java:103) > >> at org.basex.core.CLI.execute(CLI.java:87) > >> at org.basex.BaseX.console(BaseX.java:191) > >> at org.basex.BaseX.<init>(BaseX.java:166) > >> at org.basex.BaseX.main(BaseX.java:42) > >> Out of Main Memory. > >> You can try to: > >> - increase Java's heap size with the flag -Xmx<size> > >> - deactivate the text and attribute indexes. > >>> d > >> > =.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= > >> > >> Here's how the process looked in the output of 'ps -ef', in case > >> that's relevant: > >> > >> > =.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= > >> cfbeard+ 88769 88757 46 12:15 pts/7 00:00:24 java -cp > >> > /home/cfbearden/opt/basex-8.3.0/BaseX.jar:/home/cfbearden/opt/basex-8.3.0/lib/basex-api-8.3.jar:/home/cfbearden/opt/basex-8.3.0/lib/basex-xqj-1.5.0.jar:/home/cfbearden/opt/basex-8.3.0/lib/commons-codec-1.4.jar:/home/cfbearden/opt/basex-8.3.0/lib/commons-fileupload-1.3.1.jar:/home/cfbearden/opt/basex-8.3.0/lib/commons-io-1.4.jar:/home/cfbearden/opt/basex-8.3.0/lib/igo-0.4.3.jar:/home/cfbearden/opt/basex-8.3.0/lib/jansi-1.11.jar:/home/cfbearden/opt/basex-8.3.0/lib/javax.servlet-3.0.0.v201112011016.jar:/home/cfbearden/opt/basex-8.3.0/lib/jdom-1.1.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-continuation-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-http-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-io-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-security-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-server-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-servlet-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-util-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-webapp-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jetty-xml-8.1.17.v20150415.jar:/home/cfbearden/opt/basex-8.3.0/lib/jing-20091111.jar:/home/cfbearden/opt/basex-8.3.0/lib/jline-2.13.jar:/home/cfbearden/opt/basex-8.3.0/lib/jts-1.13.jar:/home/cfbearden/opt/basex-8.3.0/lib/lucene-stemmers-3.4.0.jar:/home/cfbearden/opt/basex-8.3.0/lib/milton-api-1.8.1.4.jar:/home/cfbearden/opt/basex-8.3.0/lib/mime-util-2.1.3.jar:/home/cfbearden/opt/basex-8.3.0/lib/slf4j-api-1.7.12.jar:/home/cfbearden/opt/basex-8.3.0/lib/slf4j-simple-1.7.12.jar:/home/cfbearden/opt/basex-8.3.0/lib/tagsoup-1.2.1.jar:/home/cfbearden/opt/basex-8.3.0/lib/xmldb-api-1.0.jar:/home/cfbearden/opt/basex-8.3.0/lib/xml-resolver-1.2.jar:/home/cfbearden/opt/basex-8.3.0/lib/xqj2-0.2.0.jar:/home/cfbearden/opt/basex-8.3.0/lib/xqj-api-1.0.jar: > >> -Xmx4g org.basex.BaseX -d > >> > >> > >> On Tue, Oct 20, 2015 at 12:38 PM, Chuck Bearden <cfbearden(a)gmail.com> > wrote: > >>> It hasn't failed yet; I've gotten the progress indicators, along with > >>> the phases that have been completed: > >>> > >>> Creating Database... > >>> Indexing Text... > >>> Indexing Attribute Values... > >>> > >>> It's still working on "Indexing Full-Text...". I'll post whatever I > >>> get when it fails. Maybe it won't this time :) > >>> > >>> Chuck > >>> > >>> On Tue, Oct 20, 2015 at 12:33 PM, Christian Grün > >>> <christian.gruen(a)gmail.com> wrote: > >>>>> Creating Database... > >>>>> ..;..;..;..;..;..;.;..;.. > >>>> > >>>> Do you get any output after this line (I would expected to see a stack > >>>> trace, or at least an error message…)? > >>>> > >>>> > >>>> > >>>>> Where 'pure_20151019' is both the name of the database and the > >>>>> subdirectory where all my XML files are. > >>>>> > >>>>> It could well be that I'm missing a crucial option; I'm still > >>>>> relatively new to BaseX. It's great stuff, though. > >>>>> > >>>>> Because of my employer's IT environment, I have to run my Linux > >>>>> workstation in a VMWare VM, though I doubt that that makes a > >>>>> difference. > >>>>> > >>>>> Thanks, > >>>>> Chuck > >>>>> > >>>>> On Tue, Oct 20, 2015 at 11:15 AM, Christian Grün > >>>>> <christian.gruen(a)gmail.com> wrote: > >>>>>> Hi Chuck, > >>>>>> > >>>>>> Usually, 4G is more than enough to create a full-text index for 16G > of > >>>>>> XML. Obviously, however, that's not the case for your input data. > You > >>>>>> could try to distribute your documents in multiple database. As as > >>>>>> alternative, we could have a look at your data and try to find out > >>>>>> what's going wrong. You can also use the -d flag and send us the > stack > >>>>>> trace. > >>>>>> > >>>>>> Best, > >>>>>> Christian > >>>>>> > >>>>>> > >>>>>> On Tue, Oct 20, 2015 at 4:19 PM, Chuck Bearden <cfbearden(a)gmail.com> > wrote: > >>>>>>> Hi all, > >>>>>>> > >>>>>>> I have about 16G of XML data in about 52000 files, and I was > hoping to > >>>>>>> build a full-text index over it. I've tried two approaches: enable > >>>>>>> full-text indexing as I create the database and then loading the > data, > >>>>>>> and creating the full-text index after loading the data. If I > enable > >>>>>>> ADDCACHE and modify the basex shell script to use 4g of RAM > instead of > >>>>>>> 512M, I have no problem loading the data. If I try to load with > >>>>>>> FTINDEX or create the index afterward, the process runs out of > memory. > >>>>>>> > >>>>>>> I could believe that I'm overlooking some option that would make > this > >>>>>>> possible, but I suspect I just have too much data. I welcome your > >>>>>>> thoughts & suggestions. > >>>>>>> > >>>>>>> All the best, > >>>>>>> Chuck Bearden >

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BaseX-Talk October 2015