BaseX-Talk

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5256 discussions

basex OOM on 30GB database upon running /dba/db-optimize/
by first name last name 06 Oct '19

06 Oct '19

Hi, Let's say there's a 30GB dataset [3] containing most threads/posts from [1]. After importing all of it, when I try to run /dba/db-optimize/ on it (which must have some corresponding command) I get the OOM error in the stacktrace attached. I am using -Xmx2g so BaseX is limited to 2GB of memory (the machine I'm running this on doesn't have a lot of memory). I was looking at [2] for some estimates of peak memory usage for this "db-optimize" operation, but couldn't find any. Actually it would be nice to know peak memory usage because.. of course, for any database (including BaseX) a common operation is to do server sizing, to know what kind of server would be needed. In this case, it seems like 2GB memory is enough to import 340k documents, weighing in at 30GB total, but it's not enough to run "dba-optimize". Is there any info about peak memory usage on [2] ? And are there guidelines for large-scale collection imports like I'm trying to do? Thanks, Stefan [1] https://www.linuxquestions.org/ [2] http://docs.basex.org/wiki/Statistics [3] https://drive.google.com/open?id=1lTEGA4JqlhVf1JsMQbloNGC-tfNkeQt2

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Does BaseX used as a command line XQuery processor build a full tree of an input document passed with -i option?
by Martin Honnen 03 Oct '19

03 Oct '19

If I use BaseX (9.2.4) simply as an XQuery 3.1 processor from the command line with e.g. basex.bat -i input.xml query.xq does BaseX then first always parse the input.xml into an XDM tree, meaning if I use huge input documents that way I can run easily run out of memory? Or does that depend on the type of query or some other settings? I was wondering whether a "tumbling window" based split algorithm like declare namespace output = "http://www.w3.org/2010/xslt-xquery-serialization"; declare option output:method 'xml'; declare option output:indent 'yes'; declare variable $chunk-size as xs:integer external := 500; for tumbling window $chunk in /*/* start at $sp when $sp mod $chunk-size = 1 count $p return put(document { element { node-name(head($chunk)/..) } { $chunk } }, 'xquery-split-result-' || $p || '.xml') would run/work without memory problems for huge inputs.

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Re: [basex-talk] HTTPServer + gzip compression
by Stefan Koch 03 Oct '19

03 Oct '19

2 1

Re: [basex-talk] Connection timeout
by Marie Starck 01 Oct '19

01 Oct '19

I am using an ssl certificate and have a keystore on my production Basex instance. Are there extra steps needed to make an HTTPS request from a server to a basex server when those are in place? On Thu, Sep 26, 2019 at 6:14 PM Marie Starck <marie.compsci14(a)gmail.com> wrote: > Hey Christian, > > This error message is from doing it with the nodejs basex client. I get > the same connection time out when doing an http or https request on 8984 > and 8986 (non-ssl and ssl respectively). > > Thank you, > > Marie > > On Thu, Sep 26, 2019 at 5:54 PM Christian Grün <christian.gruen(a)gmail.com> > wrote: > >> Hi Marie, >> >> SOCKET ERROR: { Error: connect ETIMEDOUT 159.89.126.125:1984 >>> >> >> By default, the REST endpoints are available on port 8984. >> >> Maybe this helps, >> Christian >> >> >>

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HTTPServer + gzip compression
by Stefan Koch 01 Oct '19

01 Oct '19

Hi, I'm struggling to get gzip compression working. I'm using the REST module. http://docs.basex.org/wiki/REST Version: BaseX 9.2.2 Tried to add the handler in jetty.xml as descriped here: https://www.eclipse.org/jetty/documentation/current/gzip-filter.html But it didn't work. Tried gzip filter via web.xml - but it is deprecated since jetty 9.3. Gzip handler is the correct way to do it. Searched the mailling list, similar problem was reported here: https://mailman.uni-konstanz.de/pipermail/basex-talk/2019-February/014160.h… Unfortunately no solution :( Not much experience with embedded jetty - but adding gzip compression is straight forward in tomcat or apache - no clue why it doesn't work.Shouldn't be that hard - and it's kinda a default feature. Did anybody get it to work? Any tipps? Thanks Stefan Koch B&IT Solutions Dipl.-Kfm. Rudolf Markus Petri Lietzenburger Str. 77 10719 Berlin Tel: 0049 30 8867 6099 Fax: 0049 30 8867 6159 Mail: koch(a)buit-solutions.com Web: www.buit-solutions.com

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Database corrupted on updating with RestXQ
by Marco Lettere 26 Sep '19

26 Sep '19

Hi all, starting with 9.2.1 we experience a strange error with a RESTXQ API of ours that we have been using for years. The typical pattern is lookup a document update it and store it back. We have done this milions of time and also all the tests work neatly. But when using it from inside the web application, at around the tenth operation we get the DB corrupted with the stack trace [1]. This seems to happen only when the database is nearly empty and, for sure, it doesn't appear on 8.x series. It feels like some concurrency flaw is introduced somewhere but it's hard to say because the API is eight years in age and it never changed significantly. I know it's hard without an SSCE... but while working to insulate this byzantine behaviour (I've been trying for days now) maybe someone in the list has a clue or is able to interpret the stack trace? Thanks and have a nice weekend, Marco. [1] Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 9.3 beta Java: Ubuntu, 13 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1 at org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:507) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:468) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:156) at org.basex.data.Data.kind(Data.java:304) at org.basex.query.value.node.DBNode.<init>(DBNode.java:50) at org.basex.query.value.seq.DBNodeSeq.get(DBNodeSeq.java:139) at org.basex.query.value.seq.DBNodeSeq.get(DBNodeSeq.java:164) at org.basex.query.func.db.DbOpen.value(DbOpen.java:19) at org.basex.query.func.StandardFunc.optimize(StandardFunc.java:82) at org.basex.query.expr.Arr.inline(Arr.java:69) at org.basex.query.expr.path.Path.inline(Path.java:962) at org.basex.query.expr.gflwor.ForLet.inline(ForLet.java:66) at org.basex.query.expr.gflwor.GFLWOR.inline(GFLWOR.java:804) at org.basex.query.expr.gflwor.GFLWOR.inlineLets(GFLWOR.java:339) at org.basex.query.expr.gflwor.GFLWOR.optimize(GFLWOR.java:106) at org.basex.query.expr.gflwor.GFLWOR.inline(GFLWOR.java:785) at org.basex.query.expr.Try.inline(Try.java:106) at org.basex.query.expr.gflwor.GFLWOR.inline(GFLWOR.java:816) at org.basex.query.expr.gflwor.GFLWOR.inlineLets(GFLWOR.java:339) at org.basex.query.expr.gflwor.GFLWOR.optimize(GFLWOR.java:106) at org.basex.query.func.StaticFunc.inline(StaticFunc.java:294) at org.basex.query.func.StaticFuncCall.compile(StaticFuncCall.java:67) at org.basex.query.scope.MainModule.comp(MainModule.java:81) at org.basex.query.QueryCompiler.compile(QueryCompiler.java:114) at org.basex.query.QueryCompiler.compile(QueryCompiler.java:105) at org.basex.query.QueryContext.compile(QueryContext.java:312) at org.basex.query.QueryContext.iter(QueryContext.java:331) at org.basex.http.restxq.RestXqResponse.serialize(RestXqResponse.java:73) at org.basex.http.web.WebResponse.create(WebResponse.java:63) at org.basex.http.restxq.RestXqServlet.run(RestXqServlet.java:53) at org.basex.http.BaseXServlet.service(BaseXServlet.java:65) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:865) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:542) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1700) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1345) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:480) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1667) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1247) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:505) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:370) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:267) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:698) at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:804) at java.base/java.lang.Thread.run(Thread.java:835)

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Connection timeout
by Marie Starck 26 Sep '19

26 Sep '19

Been debugging this for the past couple of days and I am a bit stumped. I am doing a simple get REST request to my BaseX server from a node server and I keep getting a connection timeout error. I also tried the basex node client and I get the same error message. All of this works fine on localhost and what's even weirder is that I can access the BaseX rest endpoint through my browser just fine. Any ideas? I have SSL installed on my BaseX server. Could that be the issue? SOCKET ERROR: { Error: connect ETIMEDOUT 159.89.126.125:1984 at TCPConnectWrap.afterConnect [as oncomplete] (net.js:1173:14) errno: 'ETIMEDOUT', code: 'ETIMEDOUT', syscall: 'connect', address: '159.89.126.125', port: 1984 } Thank you for any help you can give me, Marie

2 1

readable encryption result
by Andre Bovy 23 Sep '19

23 Sep '19

Dear all, I try to make the result of the encryption readable by converting the result either in Base64 or in Hex. Yet I am not able to convert it back to be able to decrypt. Could you help me ? André Bovy let $encrypted := crypto:encrypt('message', 'symmetric','keykeyke','DES’) let $base64 := string(convert:string-to-base64($encrypted)) let $encrypted := convert:binary-to-string(xs:base64Binary($base64)) (: generates invalid characters :) return crypto:decrypt($encrypted, 'symmetric','keykeyke','DES')

2 2

Full-text index on mixed content
by Schopper, Daniel 23 Sep '19

23 Sep '19

Dear all, chatting after a session of the ongoing TEI conference ( https://graz-2019.tei-c.org) I was asked about plans to support fulltext indexes on mixed content nodes in BaseX – I did not know of any, so I wanted to pass the question on to this list: Is there a plan to implement this feature in the near (or not-so-near) future? If not, did somebody of the core devs estimate the effort to get this done? (needless to say that it would an awsome feature to have in BaseX ;-) Thanks in advance & best Daniel (just being curious) -- Mag. Daniel Schopper Austrian Centre for Digital Humanities Working Group Data, Resources and Standards Austrian Academy of Sciences Sonnenfelsgasse 19 1010 Vienna T: +43 1 51581-2216 E: daniel.schopper(a)oeaw.ac.at

2 1

Suggestion for concurrency of RestXQ
by Marco Lettere 23 Sep '19

23 Sep '19

Dear all, on one of our applications based on RestXQ services running on 9.0.2 we experience a strange behaviour related to concurrency. It is a stateless service running on a server with http-local set to true. So no database access. We removed all accesses to sessions and the code doesn't even write to files or other external resources. It's really only computation. When I run multiple requests, I can clearly see that they are accepted simultaneously (up to 8 which matches PARALLEL). They even complete out of order according to the session id reported in the log. [1] The strange thing is: performance seems to be as if calls were executed serially. If T is the time to complete one call then the pattern is T + T + T + T + T. I have to add that the algorithm is rather complex. Lots of functions (possibly inlined, private and the main one even recursive) which filter and transform a large XML request into a possibly large XML output. If I simplify the called RestXQ to something like [2] then I get a log like [3] which shows a pattern like the one I'm expecting T+d+d+d+d where d is just a slight overhead (orders of magnitude smaller). My question is what do I have to check in order to understand where the hard synchronization of the calls occurs? Might this be related to non-deterministic functions? What else? I've tried to isolate parts of the code but I'm unable to get predictable results. Thank you very much for all the hints you will be able to provide! Regards, Marco. [1] 17:10:19.204 127.0.0.1:58038 admin REQUEST [POST] http://localhost:8081/rate-selector/select-matching-rates 17:10:19.204 127.0.0.1:58040 admin REQUEST [POST] http://localhost:8081/rate-selector/select-matching-rates 17:10:19.205 127.0.0.1:58042 admin REQUEST [POST] http://localhost:8081/rate-selector/select-matching-rates 17:10:19.205 127.0.0.1:58044 admin REQUEST [POST] http://localhost:8081/rate-selector/select-matching-rates 17:10:19.208 127.0.0.1:58046 admin REQUEST [POST] http://localhost:8081/rate-selector/select-matching-rates 17:10:21.325 127.0.0.1:58040 admin 200 2121.01 ms 17:10:23.174 127.0.0.1:58046 admin 200 3965.74 ms 17:10:25.035 127.0.0.1:58038 admin 200 5830.63 ms 17:10:26.889 127.0.0.1:58044 admin 200 7683.76 ms 17:10:28.739 127.0.0.1:58042 admin 200 9534.46 ms [2] (:~ : Test concurrency :) declare %rest:path("/test") %rest:POST("{$body}") function rs:test($body as node()) { <a>{$body}{fold-left(1 to 10000000, 0, function($acc, $next){ $acc + math:sqrt($next)})}</a> }; [3] 17:48:02.782 127.0.0.1:48262 admin REQUEST [POST] http://localhost:8081/rate-selector/test 17:48:02.783 127.0.0.1:48252 admin REQUEST [POST] http://localhost:8081/rate-selector/test 17:48:02.783 127.0.0.1:48258 admin REQUEST [POST] http://localhost:8081/rate-selector/test 17:48:02.784 127.0.0.1:48260 admin REQUEST [POST] http://localhost:8081/rate-selector/test 17:48:02.784 127.0.0.1:48254 admin REQUEST [POST] http://localhost:8081/rate-selector/test 17:48:04.428 127.0.0.1:48262 admin 200 1646.03 ms 17:48:04.509 127.0.0.1:48260 admin 200 1725.45 ms 17:48:04.710 127.0.0.1:48254 admin 200 1926.27 ms 17:48:04.772 127.0.0.1:48258 admin 200 1988.41 ms 17:48:04.904 127.0.0.1:48252 admin 200 2120.33 ms

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