August 2016 - BaseX-Talk - mailman.uni-konstanz.de

Docker run basexhttp and permission issues
by Michael Seiferle 28 Aug '16

28 Aug '16

Hi BaseX-Talk, in case any of you is using our docker images, in recent builds there seems to be a bug related to the ENTRYPOINT and the PARENT mvn Image we are using. If you encounter the following error message (in fact you should if you docker pulled recently ;-)): > ⇒ docker run basex/basexhttp > touch: cannot touch ‘/root/.m2/copy_reference_file.log’: Permission denied > Can not write to /root/.m2/copy_reference_file.log. Wrong volume permissions? You might want to override the ENTRYPOINT yourself: > docker run --entrypoint=basexhttp basex/basexhttp I already proposed a fix but I’d like someone with docker-expertise have a look, maybe s/o might want to add her or his 5cts ;-) https://github.com/BaseXdb/basex/pull/1346 <https://github.com/BaseXdb/basex/pull/1346> Best Michael -- Michael Seiferle, BaseX GmbH, http://www.basexgmbh.de |-- Firmensitz: Blarerstrasse 56, 78462 Konstanz |-- Registergericht Freiburg, HRB: 708285, Geschäftsführer: | Dr. Christian Grün, Dr. Alexander Holupirek, Michael Seiferle `-- Fon: +49 7531 916 82 77

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ignoring macos turds via webdav
by Kendall Shaw 19 Aug '16

19 Aug '16

Finder and /bin/cp leave turds wherever they go in some situations. If I use finder or cp in macos to write a file to a basex db mounted via webdav, the log shows something like: [propfind ] …/a.xml [put] …/a.xml [propfind] …/._a.xml [lock] .../a.xml [propfind] .../a.xml [propfind] …/._. [propfind] …/ Then finder complains “some data could not be read or written”, or cp complains “interrupted system call”. I imagine some sort of intermediate between Milton and basex could respond in a way that ignores the turds and responds as expected to macos. Assuming that it is the turds that are causing the problem, do you know of an existing server-side solution? Kendall

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Strange Exception
by Christophe Marchand 19 Aug '16

19 Aug '16

Hello, I have a strange exception : Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.2.3 Java: Oracle Corporation, 1.8.0_91 OS: Linux, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 120241192 - #used blocks: 469694 - #total locks: 469770 - access: 469693 (469694 > 469693] at org.basex.util.Util.notExpected(Util.java:60) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:458) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:148) at org.basex.data.Data.kind(Data.java:306) at org.basex.query.value.node.DBNode.<init>(DBNode.java:51) at org.basex.query.value.seq.DBNodeSeq.itemAt(DBNodeSeq.java:68) at org.basex.query.value.seq.DBNodeSeq.itemAt(DBNodeSeq.java:22) at org.basex.query.value.seq.Seq$1.next(Seq.java:77) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:58) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:36) at org.basex.query.expr.gflwor.For$1.next(For.java:79) at org.basex.query.expr.gflwor.GroupBy$1.init(GroupBy.java:131) at org.basex.query.expr.gflwor.GroupBy$1.next(GroupBy.java:98) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:174) at org.basex.query.expr.gflwor.For$1.next(For.java:99) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:95) at org.basex.query.expr.List$1.next(List.java:135) at org.basex.query.MainModule.cache(MainModule.java:91) at org.basex.query.QueryContext.iter(QueryContext.java:352) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:80) at org.basex.core.cmd.AQuery.query(AQuery.java:89) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:398) at org.basex.core.Command.execute(Command.java:100) at org.basex.server.ClientListener.run(ClientListener.java:136) The XQuery is : for $fs in collection('FichiersBase')/forms group by $s := $fs/@supp return let $mv := max($fs/@omversion) for $f in $fs return if (empty($mv) or $f/@omversion >= $mv) then () else db:delete('FichiersBase', db:path($f)) ), db:optimize('FichiersBase') After this, trying a OPTIMIZE ALL on DATABASE FichiersBase, I have this exception : > OPEN FichiersBase Database 'FichiersBase' was opened in 744.68 ms. > OPTIMIZE ALL Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.2.3 Java: Oracle Corporation, 1.8.0_91 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 1 at org.basex.data.Namespaces.values(Namespaces.java:201) at org.basex.data.Data.namespaces(Data.java:450) at org.basex.io.serial.Serializer.node(Serializer.java:449) at org.basex.io.serial.Serializer.node(Serializer.java:176) at org.basex.io.serial.Serializer.serialize(Serializer.java:126) at org.basex.core.cmd.OptimizeAll$DBParser.parse(OptimizeAll.java:202) at org.basex.build.Builder.parse(Builder.java:73) at org.basex.build.DiskBuilder.build(DiskBuilder.java:85) at org.basex.core.cmd.OptimizeAll.optimizeAll(OptimizeAll.java:131) at org.basex.core.cmd.OptimizeAll.run(OptimizeAll.java:47) at org.basex.core.Command.run(Command.java:398) at org.basex.core.Command.execute(Command.java:100) at org.basex.server.ClientListener.run(ClientListener.java:136) Any idea ? Does this mean my database is corrupted ? Best, Christophe

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Python API error
by Sayth Renshaw 19 Aug '16

19 Aug '16

I created an issue on github #1342 it has been closed until mailing list confirms its a bug On Windows and Fedora with Python 2.7 and 3.5 I cannot import Session from the BaseXClient >> import BaseXClient >>> from BaseXClient import Session Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: cannot import name Session Not sure if there is an obvious thing I am missing I was following the example on github https://github.com/BaseXdb/basex/blob/master/basex-api/src/main/python/Quer… Is there something super simple missing? Sayth

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Example concatenates iterable to database name
by Sayth Renshaw 19 Aug '16

19 Aug '16

Hi Running 8.5.3 on windows. Currently open database is RaceXML1. I am running the example from here http://docs.basex.org/wiki/Databases for $i in 1 to 100 return db:open('books' || $i)//book/title as for $i in 1 to 100 return db:open('RaceXML1' || $i)//meeting/race What occurs though is that the iterable is concatenated to the database name and subsequently not found. Error: Stopped at C:/Users/Sayth/Documents/firstquery.xq, 2/15: [bxerr:BXDB0002] Database 'RaceXML11' was not found. To new to xquery to know why this is wrong. Full error is Error: Stopped at C:/Users/Sayth/Documents/firstquery.xq, 2/15: [bxerr:BXDB0002] Database 'RaceXML11' was not found. Compiling: - pre-evaluating (1 to 100) - rewriting descendant-or-self step(s) Optimized Query: for $i_0 in (1 to 100) return db:open(concat("RaceXML1", $i_0))/descendant::meeting/race Query: for $i in 1 to 100 return db:open("RaceXML1" || $i)//meeting/race Query plan: <QueryPlan compiled="true"> <GFLWOR> <For> <Var name="$i" id="0"/> <RangeSeq from="1" to="100"/> </For> <CachedPath> <DbOpen name="open(database[,path])"> <FnConcat name="concat(atom1,atom2[,...])"> <Str value="RaceXML1" type="xs:string"/> <VarRef> <Var name="$i" id="0"/> </VarRef> </FnConcat> </DbOpen> <IterStep axis="descendant" test="meeting"/> <IterStep axis="child" test="race"/> </CachedPath> </GFLWOR> </QueryPlan> Can you help? Sayth

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XPath query with special char & fails
by Martin Manthey 19 Aug '16

19 Aug '16

Dear all, we use BaseX version 7.9 BaseX nodes and the XPath query of the getNodes()-method contains the char "&" and an exception is thrown. Example: //File[@originalLocation='E:\data\bugs\prom-9366\file & codemodel']/CopiedLocations/CopiedLocation If we use JDOM Nodes the query does not fail in this case. Why JDom can execute this query and BaseX cannot? Is there a general possibility to avoid this special char in a BaseX query, except masked it, or could it be solved in a higher version of BaseX? best regards

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Using BaseXServer and BaseXHTTP at the same time?
by Kendall Shaw 18 Aug '16

18 Aug '16

Hi, Does the fact that basexhttp starts servers on 1984 and 8984 mean that I can have one program using client/server and another using rest using the same databases at the same time? Kendall

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question on XML with prolog
by Wang, Genneva 18 Aug '16

18 Aug '16

Hi Christian, As I was testing some xml files, I realized that xml file with prolog, the prolog will always get removed when persisted in basex. Is that the expected behavior? Is there some option that the prologs can be saved along with the xml file ? Any tips would be greatly appreciated. Thanks! Regards, -Genneva

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Uploading a binary file through RestXQ
by Marco Lettere 16 Aug '16

16 Aug '16

Hello all, I'm currently trying to implement a service for uploading Images to a Basex db. There is a frontend service that serves an HTML + Javascript page which receives the upload as an AJAX call from the browser then POSTs the request to the backend service for storing into the db. There is no big issue when doing it directly by a command or a query. I've been even able to do it by using the following code inside the RestXQ of the frontend service: client:connect("localhost", 1984, "user", "pass") ! client:query(., "db:store('files', '" || $name || "', .)", map{ "" : $file}) But when I POST the data to the backend RestXQ I always get the data stored into the DB as *base64* encoded text which messes up the successive retrieves. This is the code I use on the backend: declare %rest:path("/service/files/{$name}") %rest:POST("{$body}") %rest:consumes("image/png", "image/jpg", "image/jpeg", "image/gif", "image/svg+xml") %output:method("text") function m:upload-maps($userid as xs:string, $name as xs:string, $body as item()){ let $stored := db:store("files", $name, $body) return <rest:response> <http:response status="201"/> </rest:response> }; I call this service from the frontend service with the following request where the media-type is according to the uploaded file extension: <http:request href="{$url}" method="POST"> <http:body media-type="image/png"> {$data} </http:body> </http:request> How do I ensure that the data gets into the DB with its correct raw binary format? Thanks, Marco.

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Re: [basex-talk] Autocommit option using sql:connect to Oracle 11.2.0.3 with ojdbc6.jar
by Christian Grün 15 Aug '16

15 Aug '16

Hi Chris (cc to the list), > I've also attached the basexdebug.txt but it just shows the requests so > probably not useful. Sounds ok so far. I have slightly revised our SQL code (although it shouldn’t make a big difference), and I have uploaded a new snapshot [1]. Could you give it a try? In general, our SQL wrapper is pretty simple [1,2]. Maybe you could check if you get autocommit=false running with a plain Java JDBC code snippet? Hope this helps, Christian [1] http://files.basex.org/releases/latest/ [1] https://github.com/BaseXdb/basex/blob/9a700bf1f663b18eb578acb1a8aa8bbb4d4dd… [2] https://github.com/BaseXdb/basex/blob/9a700bf1f663b18eb578acb1a8aa8bbb4d4dd… > > Thanks, > > chris > > On 12 August 2016 at 14:46, Christian Grün <christian.gruen(a)gmail.com> > wrote: >> >> Could you try the -d command-line flag (or the command SET DEBUG true >> in the GUI) and check if you get some helpful feedback on stderr? >> >> >> On Fri, Aug 12, 2016 at 3:44 PM, chrisis <chrisisanon(a)gmail.com> wrote: >> > The connection is opened successfully.Not getting any feedback. >> > I'm doing a lot of inserts in a loop and it's committing after every >> > insert. >> > My issue is with the overhead of all the extra commits >> > >> > >> > >> > >> > >> > >> > Thanks, >> > >> > chris >> > >> > >> > On 12 August 2016 at 14:19, Christian Grün <christian.gruen(a)gmail.com> >> > wrote: >> >> >> >> > I'm trying to set the autocommit option off and I can't seem to get >> >> > it >> >> > to >> >> > work. >> >> > I'm passing the option to sql:connect as a map >> >> > map { 'autocommit': false() } >> >> > I also tried map { 'autoCommit': false() } as the Oracle JDBC docs >> >> > seem >> >> > to >> >> > suggest. >> >> >> >> What’s happening? Do you get any feedback? >> >> >> >> Thanks >> >> Christian >> > >> > > >

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