November 2012 - BaseX-Talk - mailman.uni-konstanz.de

Options in Basex 7.5
by Andy Bunce 15 Nov '12

15 Nov '12

There are many ways to set options [1] but it is not clear to me which one wins in the case where different values are specified for the same option by the different ways. I guess it is the 1st one to be set. So SystemProperty, then command line, then .basex? I am often getting caught out by the fact that in recent 7.5 builds the http properties are ignored unless they are set by editing jetty.xml. I wonder if the supplied jetty.xml could use <SystemProperty>. Something like: <New class="org.eclipse.jetty.server.nio.SelectChannelConnector">  <Set name="host"><SystemProperty name="org.basex.serverhost" default=""/></Set> <Set name="port"><SystemProperty name="org.basex.serverport" default="8984"/></Set> <Set name="confidentialPort"><SystemProperty name="org.basex.??" default="??"/></Set> <Set name="maxIdleTime">60000</Set> <Set name="reuseAddress">false</Set> <Set name="Acceptors">2</Set> </New> /Andy [1] http://docs.basex.org/wiki/Options

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for ... group by - minor bug
by Hans-Juergen Rennau 15 Nov '12

15 Nov '12

Hello, the support for XQuery 3.0 is really wonderful! Thank you. Just a trifle: I think there is a little bug concerning the "group by" clause and the case that a non-grouping variable is reused as grouping variable, but the shorthand notation for this is not used. According to the spec, these expressions should be equivalent: group by $x group by $x := $x I observed that in the shorthand notation $x references the grouping variable, that is, one value per group, as it should. But in the longhand notation, $x references the variable in the pre-grouping variable, and I suppose this should not be so. For a full example, see below. Kind regards, Hans-Juergen PS: Full example: Code: for $x in (1, 1, 2) group by $x := $x return <r x="{$x}"/> Output: <r x="1 1"/> <r x="2"/>

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sql query result - formated xml from mysql database
by Jarosław Kowalewski 15 Nov '12

15 Nov '12

Hi, I've in my mysql database field with xml (formated xml). By using sql module i get something like that: <sql:column xmlns:sql="http://basex.org/modules/sql" name="xml"> <?xml version="1.0" encoding="UTF-8"?> <Document xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="wniosek.xsd"> </Document> and I can't query it like regular xml by xquery. It's possible to get only content of xml column? Or it's other way to query this content? Jarek

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Re: [basex-talk] xquery sql module init driver
by Jarosław Kowalewski 15 Nov '12

15 Nov '12

Thanks a lot. That works!:) Mayby it's a good idea to write about that in manual or FAQ? Jarek 2012/11/15 <basex-talk-request(a)mailman.uni-konstanz.de>: > Message: 4 > Date: Wed, 14 Nov 2012 15:55:34 +0100 (CET) > From: Antoni Mylka <amy(a)basis06.ch> > To: basex-talk <basex-talk(a)mailman.uni-konstanz.de> > Subject: Re: [basex-talk] xquery sql module init driver > Message-ID: <701444465.74583.1352904934339.JavaMail.root(a)basis06.ch> > Content-Type: text/plain; charset=utf-8 > > Hi Jarek, > > And what about > > java -cp pathto/mysql-connector-java-5.1.21-bin.jar:BaseX73.jar org.basex.BaseXGUI > > ? > > quoting from: > > http://stackoverflow.com/questions/945962/java-problem-running-a-jar-file-i… > > "If you're running a jar file with java -jar, the -classpath argument is ignored." > > -- > Antoni My?ka > Software Engineer > > basis06 AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 311 32 22 > http://www.basis06.ch - source of smart business > > ----- Urspr?ngliche Mail ----- > Von: "Jaros?aw Kowalewski" <jaroslaw.kowalewski(a)students.waw.pl> > An: basex-talk(a)mailman.uni-konstanz.de > Gesendet: Mittwoch, 14. November 2012 13:16:37 > Betreff: [basex-talk] xquery sql module init driver > > Hi, > I try to connect with my database directly by sql module. > > sql:init("com.mysql.jdbc.Driver"), > > let $conn := sql:connect("jdbc:mysql://dbhost:port/dbname") > return sql:execute($conn, "SELECT * FROM coffees WHERE price < 10") > > but I've problem with and I get error "[BXSQ0007] Could not initialize > specified driver: 'com.mysql.jdbc.Driver'" > > java -cp pathto/mysql-connector-java-5.1.21-bin.jar -jar BaseX73.jar > > Thanks for a help > > Jarek >

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Re: [basex-talk] Database corruption
by Antoni Mylka 15 Nov '12

15 Nov '12

Hi, Two further questions: 1. What's the cleanest way to get a log containing the actual query strings? AFAIU BaseX doesn't use any logging framework and the BaseXServlet.service has a finally block that prints the request headers (if Prop.debug is enabled) but not the request body. I thought about writing my own Filter for that purpose. 2. I've been trying to update BaseX to the latest snapshot, but the queries generated by my application, that used to work with 7.2.1 and 7.3 don't seem to work now. The body of a POST looks like this (\n means a newline character): <?xml version="1.0" encoding="UTF-8"?>\n <command xmlns="http://basex.org/rest"><text><![CDATA[\n ADD TO 5d03ebad-dc6a-492c-9527-bd2ce3830080\n <tx id="5d03ebad-dc6a-492c-9527-bd2ce3830080"\n dbId=""\n xmlns="http://our.namespace.com/xmlns/"\n xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n xmlns:xs="http://www.w3.org/2001/XMLSchema"\n <commit />\n <skip />\n </tx>\n \n ]]></text></command> Now the question is what's wrong with this query. I get a 400 Bad Request response with the following error message. Stopped at line 1, column 43:\n Syntax: ADD (TO [path]) [input]\n Add resource to database.\n \n Adds [input] as [path] to the database.\n As I said this used to work with 7.3. I tried to diff the StringParser class between 7.3 and the current trunk. It seems to use the InputParser on a single line and not on the entire query. I can't spot anything that would explain this behaviour though. All kinds of comments welcome. -- Antoni Myłka Software Engineer basis06 AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 311 32 22 http://www.basis06.ch - source of smart business -- Antoni Myłka Software Engineer basis06 AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 311 32 22 http://www.basis06.ch - source of smart business ----- Ursprüngliche Mail ----- Von: "Antoni Mylka" <amy(a)basis06.ch> An: "Christian Grün" <christian.gruen(a)gmail.com> Gesendet: Montag, 12. November 2012 15:42:42 Betreff: Re: [basex-talk] Database corruption Dear Christian, Thanks for the tip. Will fix the logging settings and retest with the latest snapshot. Best regards, -- Antoni Myłka Software Engineer basis06 AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 311 32 22 http://www.basis06.ch - source of smart business ----- Ursprüngliche Mail ----- Von: "Christian Grün" <christian.gruen(a)gmail.com> An: "Antoni Mylka" <amy(a)basis06.ch> CC: "basex-talk" <basex-talk(a)mailman.uni-konstanz.de> Gesendet: Montag, 12. November 2012 15:34:23 Betreff: Re: [basex-talk] Database corruption Dear Antoni, without having read all the elaborate details in your mail (thanks), I would strongly advise to try the latest stable 7.5 snapshot [1], which contains some important improvements reg. concurrent updates. I'm well aware that it feels inconvenient to use beta releases in productive environments, but the current version of 7.5 is very stable, and will be released soon without any major enhancements or legacy issues. Hope this helps, Christian [1] http://files.basex.org/releases/latest/ ___________________________ On Mon, Nov 12, 2012 at 3:30 PM, Antoni Mylka <amy(a)basis06.ch> wrote: > Hi, > > We're developing an application that uses BaseX. In our tests, the application works properly for a couple of hours, makes queries to BaseX adds and removes data. Then suddenly some BaseX request will return the HTTP 500 response. From that point on all queries that make modifications in the database end in an error and the entire system grinds to a screeching halt. One of the experiments ran for four days, then we examined the access log to see that only the first 6 hours were OK, after that all BaseX queries would end in error. > > I'm going to investigate and will try to come up with as detailed a description of the issue as possible. For now the things I know are: > > 1. In our experiment, the application would make about 80000 successful queries over a period of 6 hours. Then it would get the first 500 error. > 2. Afterwards it "seems" that the queries which don't modify anything end with 200, while all the modification queries end with a 500 error. That's to be confirmed. > 3. BaseX 7.2.1 runs in a war deployed on Tomcat 7.0.32 on a linux system. > 4. The access logs don't show anything interesting. > 5. The catalina.out that shows the Tomcat standard output contains hundreds of exceptions of the following kind: > > Exception in thread "Thread-78197" java.lang.RuntimeException: Data Access out of bounds [pre:1422612, indexSize:5540, access:5540 > 5539] > at org.basex.util.Util.notexpected(Util.java:55) > at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:478) > at org.basex.io.random.TableDiskAccess.read5(TableDiskAccess.java:211) > at org.basex.data.Data.textOff(Data.java:432) > at org.basex.data.DiskData.text(DiskData.java:228) > at org.basex.index.value.DiskValues.get(DiskValues.java:295) > at org.basex.index.value.UpdatableDiskValues.index(UpdatableDiskValues.java:133) > at org.basex.data.DiskData$1.run(DiskData.java:461) > > The thread name is different every time and the numbers in square brackets are also different. I don't see any patterns (yet). > 6. BaseX is accessed from a single thread in a single application. AFAIK there are no concurrent requests, though that is to be confirmed. > 7. The GC log shows that basex stays below 100M of used heap, which is well below the allotted Xmx setting of 2G. > 8. We did three experiments and the same effect has been observed in all three, albeit after different periods of time: (59K queries and 4:25 hours, 37K queries and 2:56 hours, 76.8K queries and 6 hours). > > Things I intend to do: > 1. Set up proper logging for BaseX, so that these errors don't end up in catalina.out, but in the proper log file. > 2. Catch the first offending query, see if there is anything unusual about it. It certainly doesn't differ much from the successful queries. It simply updates the BaseX state to keep it in sync with an external data source. All the update queries are generated by the same template and there have been hundreds of successful ones before the first error occurs. > 3. Manipulate the log settings, to see if it's possible to get something more meaningful out of them. > 4. Try newer versions: 7.3 and the current trunk. > > I've seen emails similar about "Data Access out of bounds" but they don't seem relevant. > > As I said, I'll try to come up with more information, but if the error or the stack trace looks familiar - I'd be grateful for pointers. > > Thanks in advance, > > -- > Antoni Myłka > Software Engineer > > basis06 AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 311 32 22 > http://www.basis06.ch - source of smart business > > _______________________________________________ > BaseX-Talk mailing list > BaseX-Talk(a)mailman.uni-konstanz.de > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk

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xquery sql module init driver
by Jarosław Kowalewski 14 Nov '12

14 Nov '12

Hi, I try to connect with my database directly by sql module. sql:init("com.mysql.jdbc.Driver"), let $conn := sql:connect("jdbc:mysql://dbhost:port/dbname") return sql:execute($conn, "SELECT * FROM coffees WHERE price < 10") but I've problem with and I get error "[BXSQ0007] Could not initialize specified driver: 'com.mysql.jdbc.Driver'" java -cp pathto/mysql-connector-java-5.1.21-bin.jar -jar BaseX73.jar Thanks for a help Jarek

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Re: [basex-talk] (no subject)
by Christian Grün 14 Nov '12

14 Nov '12

Hi John, there is no complete 7.5 available yet, but you may want to check out our documentation (search for 7.5) and the GitHub issue list (limit to Milestone 7.5) in order to get a first impression. Best, Christian Am 14.11.2012 05:18 schrieb "John Best" <johnbest5673(a)gmail.com>:

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(no subject)
by John Best 14 Nov '12

14 Nov '12

Dear BaseX Team What are the NEW features in the coming version and where can I find the list of the same..?? -- Regards -- Have a nice day JBest

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what is the best way to add/replace a lot of documents ?
by Fabrice ETANCHAUD 12 Nov '12

12 Nov '12

Dear all at basex, I am wondering what could be the most efficient way to add/replace a lot of documents (several thousands) at the same time. I tried db:add/db:replace but this gives heap memory overflow because of the pending list... Will I have better results with a .bxs with add/replace commands (and autoflush deactivated) ? Did any other user find his way in this use case ? Best regards, Fabrice

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Function will return node(), but db:output(node()) returns 'Attribute xmlns redefined'
by France Baril 12 Nov '12

12 Nov '12

Hi, My search function used to return $html correctly *let* *$html* := <html *xmlns*=*"http://www.w3.org/1999/xhtml"*> <head><link *href*=*"*{*$cssfile*}*"* *rel*=*"stylesheet"* *type*=* "text/css"*/><title>Search help</title> <script *type*=*"text/javascript"* *xmlns*=*" http://www.w3.org/1999/xhtml"*>{*app:get-google-analytics-script*()/*text* ()}</script> </head> <body> <div> (…) <div>{*$result-list*}</div> </div></body></html> *return $html* I am now trying to keep records of users most popular queries in my DB, so I made the function an updating function and adapted the return value: *let* *$html* := <html *xmlns*=*"http://www.w3.org/1999/xhtml"*> <head><link *href*=*"*{*$cssfile*}*"* *rel*=*"stylesheet"* *type*=* "text/css"*/><title>Search help</title> <script *type*=*"text/javascript"* *xmlns*=*" http://www.w3.org/1999/xhtml"*>{*app:get-google-analytics-script*()/*text* ()}</script> </head> <body> <div> (…) <div>{*$result-list*}</div> </div></body></html> *return *(*feedback:analyze-user-search-and-result*(*$keywords*, * $result-ids*, *$this-menu*, *$application*, *$carrier*, *$country*, *$lang*, *$model*, *$os*), *db:output*(*$html*)) I got this error: error on line 30 at column 25: Attribute xmlns redefined After lots of research, I figured that when using db:output, the top element of $result-list is interpreted as coming from a different namespace. Adding xmlns="http://www.w3.org/1999/xhtml" to that top element resolved my issue, but I still don't get why this is happening, can you explain? More specifically, here are definitions of $result-lists and what they produce: let $result-list := <div/> would work when used in the 1st code sample, but not the second (updating function). let $result-list := <div xmlns:="http://www.w3.org/1999/xhtml"/> resolves the issue for the second (updating function). Thanks, France -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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