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Fwd: Re: BaseX, Zorba, e-mail module
by Christian Grün 05 Feb '16

05 Feb '16

Hi Vincent, Sorry, I overlooked that my mail with the sources did not reach the list. Here it is. Christian ---------- Weitergeleitete Nachricht ---------- Von: "Christian Grün" <christian.gruen(a)gmail.com> Datum: 23.09.2015 3:51 nachm. Betreff: Re: [basex-talk] BaseX, Zorba, e-mail module An: "Tim Thompson" <timathom(a)gmail.com> Cc: > Is there an XSD for the e-mail document format being used? (And this module > is compatible with the BaseX open source license, correct?) No, sorry, there is no XSD available. However, you are invited to create one; I have attached the Java sources to this mail, which should contain all information you need. The Java code is based on the standard Java JavaMail API [1,2]. Hope this helps, Christian [1] http://www.oracle.com/technetwork/java/javamail/index.html [2] https://java.net/projects/javamail/pages/License > Tim A. Thompson > Metadata Librarian (Spanish/Portuguese Specialty) > Princeton University Library > > > On Wed, Sep 23, 2015 at 3:24 AM, Christian Grün <christian.gruen(a)gmail.com > > wrote: >> >> Hi Tim, >> >> We have implemented an XQuery/Java e-mail module quite some time ago, >> which we are using in various commercial projects. The main reason why >> we didn't make it public yet is that we didn't have time to document >> it properly. I have just uploaded this module, and you can install it >> via: >> >> repo install >> http://files.basex.org/modules/org/basex/modules/email/EMail.jar >> >> The jar file contains two simple example for sending mails (in the >> xquery sub-directory). >> >> Looking forward to your feedback. >> Christian >> ___________________________________ >> >> On Wed, Sep 23, 2015 at 7:04 AM, Tim Thompson <timathom(a)gmail.com> wrote: >> > 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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BaseX, Zorba, e-mail module
by Tim Thompson 05 Feb '16

05 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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Multithread lock
by Bondeson, Carl 04 Feb '16

04 Feb '16

I have a highly multithreaded application that uses BaseX as a translation/transformation engine. It has been functioning in production for almost a year. From time to time I see the following in the nightly report the application generates which is sent from the server hosting the application. It requires a restart of JBoss, used as the application server. Any ideas? Name: Embedded EIP BaseX Server Thread : blocked Blocked on: java.net.SocksSocketImpl@5915a689 Blocked by: 1428 (Thread-1368) Blocked Count: 1 Lock Info: java.net.SocksSocketImpl@5915a689 Stack Trace: java.net.PlainSocketImpl.accept(PlainSocketImpl.java:194) java.net.ServerSocket.implAccept(ServerSocket.java:545) java.net.ServerSocket.accept(ServerSocket.java:513) org.basex.BaseXServer.run(BaseXServer.java:142) com.pilotfish.eip.basex.BaseXServerRunner$1.run(BaseXServerRunner.java:93) java.lang.Thread.run(Thread.java:745) Name: C3P0PooledConnectionPoolManager[identityToken->2szqjh9e17wbsc31kua7k9|58166f21]-HelperThread-#2 : timed_waiting Thank you Carl R Bondeson Systems Developer Department of Public Health Data Processing 410 Capitol Ave Hartford, CT 06134 Phone: 860-509-7434 carl.bondeson(a)ct.gov<mailto:carl.bondeson@ct.gov> [logosmall]

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Rép: Re: Rép: Re: Slow XQueries on a quite small database but great number of docs
by ansel.jm 02 Feb '16

02 Feb '16

Hi I don't know why but the problem is present even with the basex simple client (not client/server ). It seems java (tried many versions) doesn't execute normally : display or computation is halting, jolting.... The result of the query is quite fast but the display of the result very very halting. I'm on a readynas server running on an ARM processor. I think the io library of java (buffered io or something like that) has a problem. I'm very disappointed because that database seems very well adapted for my project... Jm Christian Grün <christian.gruen(a)gmail.com> a écrit : >> I can't run the GUI, I don't know why, I'm over a VPN and when I try the administrator login on the 1984 port, the GUI answers : access denied... >> >> I have tried basexclient -o output.xml : Same result, the query you know takes 11s... > >So I’m pretty sure it must be your connection, and not the query >processor of BaseX, that slows down the query. > >What about running the GUI locally? It’s not based on the >client/server architecture [1]. > >Christian > >[1] http://docs.basex.org/wiki/GUI > > > >> >> ----- Mail original ----- >> De: "Christian Grün" <christian.gruen(a)gmail.com> >> À: "Jean Marc Ansel" <ansel.jm(a)free.fr>, "BaseX" <basex-talk(a)mailman.uni-konstanz.de> >> Envoyé: Dimanche 31 Janvier 2016 17:49:00 >> Objet: Re: Rép: Re: [basex-talk] Slow XQueries on a quite small database but great number of docs >> >> Hi Jean Marc (cc to the list), >> >> What happens if you run the query in the GUI (how long does it take)? >> How much time is spent if you write the client output to a file >> (basexclient -o output.xml)? Which client do you use? >> >> >> >> >> On Sun, Jan 31, 2016 at 5:41 PM, <ansel.jm(a)free.fr> wrote: >>> Many many thanks for your quickness ! >>> Yes I optimized the database (OPTIMIZE ALL). I don't undestand where the pb is. >>> The query I ran is the one I have transmitted to you in the last mail. So there is a pb with the server I'm afraid. May be with java ? >> >>> When I try to execute the query from basexclient, I'have a immediate answer but a very very very slow display : lines are displayed in blocks of one or two screen terminals... There is a problem with the data exchange between the daemon and the client I think...

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file:write and include-content-type
by James Ball 31 Jan '16

31 Jan '16

Hello, I’m getting an unexpected behaviour with the serialization option include-content-type and file:write with HTML. If I write a document without a <head> element then one doesn’t get added and nothing happens. file:write("test.htm",<html><body/></html>,map {"method":"html", "html-version":"4.0","include-content-type":"yes”}) returns: <html> <body></body> </html> Is this correct? If there is a head then the <meta> gets added with no problems - unless there is already a meta element, in which case it gets replaced. file:write("/Users/jb8748/test.htm",<html><head><meta http-equiv="refresh" content="60" /></head><body/></html>,map {"method":"html", "html-version":"4.0","include-content-type":"yes”}) returns: <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> <body></body> </html> Is this correct? All running Running Beta 8.4 f5341cc Many thanks, James

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basexhttp jetty 413 (Request Entity Too Large: head) / consecutive queries
by Günter Dunz-Wolff 31 Jan '16

31 Jan '16

Hi everyone, searching the basex rest-interface with a VERY long query ends in the following error-message: In Terminal basexhttp: [qtp1513712028-21] WARN org.eclipse.jetty.http.HttpParser - HttpParser Full for SCEP@5be8c98d{l(/0:0:0:0:0:0:0:1:49641)<->r(/0:0:0:0:0:0:0:1:8984),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=0r}-{AsyncHttpConnection@5d928144,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-10,l=0,c=-3},r=0} In the Browser: 413 (Request Entity Too Large: head) Is there any way, to enhance the memory for the HttpParser or is the only way to limit the http-request params? Here is the request, I know, it's a little bit crazy, but it's searching for synonyms and their wordforms for the german word "zahlen": http://localhost/rest?run=xqs/search_new.xq&$suche=zahlen&collect=all_kleis… Alternativ perhaps I could use consecutive queries in xquery, but I can't figure out the right approach. Where and how to store the temporary sub-sequences? Thanks for any help! Best regards, Günter

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Re: [basex-talk] Rép: Re: Slow XQueries on a quite small database but great number of docs
by Christian Grün 31 Jan '16

31 Jan '16

Hi Jean Marc (cc to the list), What happens if you run the query in the GUI (how long does it take)? How much time is spent if you write the client output to a file (basexclient -o output.xml)? Which client do you use? On Sun, Jan 31, 2016 at 5:41 PM, <ansel.jm(a)free.fr> wrote: > Many many thanks for your quickness ! > Yes I optimized the database (OPTIMIZE ALL). I don't undestand where the pb is. > The query I ran is the one I have transmitted to you in the last mail. So there is a pb with the server I'm afraid. May be with java ? > When I try to execute the query from basexclient, I'have a immediate answer but a very very very slow display : lines are displayed in blocks of one or two screen terminals... There is a problem with the data exchange between the daemon and the client I think...

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BaseX fn:collection() questions
by Bridger Dyson-Smith 31 Jan '16

31 Jan '16

Hi all, I'm using BaseX 8.3.1 and am trying to access a directory structure like so: declare namespace t = "http://www.tei-c.org/ns/1.0"; for $ready in fn:collection("/usr/home/bridger/Documents/foo/bar/?select=*.xml;recurse=yes")/t:TEI let $title := fn:data($ready/t:teiHeader/t:fileDesc/t:titleStmt/t:title) return $title The structure under bar/ looks something like bar/ 001/ 001.xml 002/ 002.xml 003/ 003.xml ... ... 009/ 009.xml Does BaseX's fn:collection() allow for recursion into a directory structure like this with the /?select syntax options or should I use a combination of functions from the File Module to move through these directories? Note: I'm not pulling these files into a database, rather I'm just using BaseX as a query processor. Thanks for your time. Best, Bridger

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tumbling window and db:add in same expression
by Hondros, Constantine (ELS-AMS) 30 Jan '16

30 Jan '16

Hello all, BaseX doesn't seem to like the query below. Any particular reason - it makes sense to me. I'm trying to add items to a DB incrementally to (attempt to) avoid running into out of memory exceptions when cutting a slice of a large DB into a smaller one. for tumbling window $w in db:open(myDB')//ani:ref-authors/ani:author start at $s when $s mod 50000 = 1 return db:add( 'sliceDB', <index>{$w}</index>, 'somepath.xml' ) Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.3 Java: Oracle Corporation, 1.8.0_40 OS: Windows 7, amd64 Stack Trace: java.lang.NullPointerException at org.basex.query.expr.ParseExpr.checkAllUp(ParseExpr.java:219) at org.basex.query.expr.ParseExpr.checkNoneUp(ParseExpr.java:203) at org.basex.query.expr.gflwor.Window.checkUp(Window.java:341) at org.basex.query.expr.gflwor.GFLWOR.checkUp(GFLWOR.java:791) at org.basex.query.QueryContext.check(QueryContext.java:265) at org.basex.query.QueryParser.finish(QueryParser.java:279) at org.basex.query.QueryParser.parseMain(QueryParser.java:176) at org.basex.query.QueryContext.parseMain(QueryContext.java:221) at org.basex.query.QueryProcessor.parse(QueryProcessor.java:56) at org.basex.core.cmd.AQuery.parse(AQuery.java:144) at org.basex.core.cmd.AQuery.updating(AQuery.java:158) at org.basex.core.cmd.AQuery.updating(AQuery.java:288) at org.basex.gui.GUI.exec(GUI.java:458) at org.basex.gui.GUI.access$400(GUI.java:43) at org.basex.gui.GUI$7.run(GUI.java:412) ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

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Unrecognized Options Running Basex in Docker Container
by Eliot Kimber 29 Jan '16

29 Jan '16

I'm seeing a difference in how the .basex file is processed between running a server under OS X directly and running it in a Docker container. In particular, my local settings are being rejected as unrecognized. Here's the startup messages from within the basex container: basex@611404b26b04:~$ basexhttp /home/basex/.basex: Unknown option 'CATFILE'. /home/basex/.basex: Unknown option 'DTD'. /home/basex/.basex: Unknown option 'SKIPCORRUPT'. /home/basex/.basex: Unknown option 'CHOP'. /home/basex/.basex: writing new configuration file. [main] INFO org.eclipse.jetty.server.Server - jetty-8.1.17.v20150415 [main] INFO org.eclipse.jetty.webapp.StandardDescriptorProcessor - NO JSP Support for /, did not find org.apache.jasper.servlet.JspServlet BaseX 8.3 [Server] Server was started (port: 1984). [main] INFO org.eclipse.jetty.server.AbstractConnector - Started SelectChannelConnector@0.0.0.0:8984 HTTP Server was started (port: 8984). I verified that with the same .basex file running 8.3 under OS X the options are recognized and set as expected. What would cause this difference in behavior? Here is the .basex file in the /home/basex directory when the server starts: USER = admin PASSWORD = admin DEBUG = false DBPATH = /home/basex/basex/data REPOPATH = /home/basex/basex/repo LANG = English LANGKEYS = false GLOBALLOCK = false # Client/Server Architecture HOST = localhost PORT = 1984 SERVERPORT = 1984 SERVERHOST = PROXYHOST = PROXYPORT = 0 NONPROXYHOSTS = IGNORECERT = false TIMEOUT = 30 KEEPALIVE = 600 PARALLEL = 8 LOG = true LOGMSGMAXLEN = 1000 # HTTP Services WEBPATH = /home/basex/basex/webapp RESTPATH = RESTXQPATH = CACHERESTXQ = false HTTPLOCAL = false STOPPORT = 8985 AUTHMETHOD = Basic # Local options CATFILE = /opt/dita-ot/DITA-OT/catalog-dita.xml DTD = true SKIPCORRUPT = true CHOP = false -- (this is the end of the file) -- After the server starts the offending options are omitted from the rewritten .basex file. The only difference I can think of is the Java version. The container uses the OpenJDK while I have Oracle Java running in OS X: basex@611404b26b04:~$ java -version openjdk version "1.8.0_66-internal" OpenJDK Runtime Environment (build 1.8.0_66-internal-b17) OpenJDK 64-Bit Server VM (build 25.66-b17, mixed mode) basex@611404b26b04:~$ But otherwise it's exactly the same code running in both environments and the same config file. Thanks, Eliot ---- Eliot Kimber, Owner Contrext, LLC http://contrext.com

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