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

querying xml with namespaces.
by Witold E Wolski 01 Mar '17

01 Mar '17

Apologies if I am hard to understand but I am new to the XML querying. I would like to query an XML with namespaces. As I did learn, you can do it in BaseX by including an *: in your path, e.g., db:open("myrimatchSubset","20160312_17_B3_myrimatch_2_2_140.xml")/*:MzIdentML/*:SequenceCollection/*:Peptide But I would like to be more specific than *. I did search the schema for the XML and all I found related to the search term namespace is not brief name, but: targetNamespace="http://psidev.info/psi/pi/mzIdentML/1.1" I did also found the following entry on stack overflow: http://stackoverflow.com/questions/5239685/xml-namespace-breaking-my-xpath And If I interpret the answer there correctly somehow one can register his own acronym for a namespace? Is this correct? So I am wondering if I could do the same somehow in BaseX? Alternatively, I am wondering if I could tell BaseX to disable namespace checking? Thank you a lot -- Witold Eryk Wolski

2 3

A suggestion (csv:doc, ...)
by Hans-Juergen Rennau 28 Feb '17

28 Feb '17

Dear BaseX team, if you are interested in further boosting the power of BaseX as a resource monitoring tool, you might consider the tiny, yet useful extension described below. Currently we have various functions for parsing non-XML formats into node trees: json:parse($text ...) csv:parse($text ...) html:parse($text ,,, These functions expect as input the text to be parsed, not the URI from which to retrieve the text. Of course, it is trivial to combine retrieval and parsing, using fn:unparsed-text(), like so: unparsed-text('foo.json') ! json:parse(.) However, the resulting document does not have a document URI, and it would be cumbersome to associate it with one. So how about adding three functions json:doc($uri ...) csv:doc($uri ...) html:doc($uri ...) Two advantages: first the document URI is available, second - sheer elegance. As an example of this elegance, consider the task to create a list of all .csv files found in a directory tree which have inconsistent record lengths. Using csv:doc, the solution is a simple expression, rather than a program: file:list($dir, true(), "*.csv") ! concat($dir, '/', .) ! csv:doc(.) [1 eq count(//record/count(*) => distinct-values())] / document-uri(.) Cheers,Hans-Jürgen

1 0

Help with understanding collections and user management
by kalibuk＠centrum.cz 28 Feb '17

28 Feb '17

Hallo, I have few questions while trying to get used to and use BaseX database in our solution. A) Could be empty collection in a database created? This query db:add("MyDBName","","/NewCollectionName") perforemed in GUI creates collection NewCollectionName but copies there also bunch of other things used as example… I tried also to ADD a xml file to NewCollection which works , new collection was created, but when I deleted that file, collection disappered also ! B) Is it possible to grant various users different access rights to different collections under one database ? Eg. granting access rights to groups of users and/or creating roles ? Regards and thanks for your good job, Jan Matuszek

2 1

Exit a for-loop?
by Joseph 27 Feb '17

27 Feb '17

Hi, I have two sets of numbers, and I would like to write a for-loop for comparison, so that I get only the first match between the numbers. I was thinking of a double for-loop, but I do not know how to exit the comparison as soon as I get the first match. Any idea? Thanks. Joseph

3 2

A suggestion (json:doc, etc.)
by Hans-Juergen Rennau 26 Feb '17

26 Feb '17

Dear BaseX team, if you are interested in further boosting the power of BaseX as a resource monitoring tool, you might consider the tiny, yet useful extension described below. Currently we have various functions for parsing non-XML formats into node trees: json:parse($text ...) csv:parse($text ...) html:parse($text ,,, These functions expect as input the text to be parsed, not the URI from which to retrieve the text. Of course, it is trivial to combine retrieval and parsing, using fn:unparsed-text(), like so: unparsed-text('foo.json') ! json:parse(.) However, the resulting document does not have a document URI, and it would be cumbersome to associate it with one. So how about adding three functions json:doc($uri ...) csv:doc($uri ...) html:doc($uri ...) Two advantages: first the document URI is available, second - sheer elegance. As an example of this elegance, consider the task to create a list of all .csv files found in a directory tree which have inconsistent record lengths. Using csv:doc, the solution is a simple expression, rather than a program: file:list($dir, true(), "*.csv") ! concat($dir, '/', .) ! csv:doc(.) [1 eq count(//record/count(*) => distinct-values())] /document-uri(.) Alaaf!Hans-Jürgen

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Somewhat unusual question
by Marco Lettere 26 Feb '17

26 Feb '17

Hi to everyone, probably this is not the right place for such a discussion but the BaseX communitiy is the one I'm better introduced to and the one I trust the most. So I hope that this somewhat unusual excursus will anyway be of interest to some of you. As for myself I fell in love with XQuery and its power in terms of data manipulation many years ago. I wouldn't change it with anything else and BTW we're using it (thanks to the incredible BaseX runtime) much beyond data-processing being it the backbone of all our micro-service oriented architectures. Now, to the point, in the near future I probably will be called to face a somewhat skeptical customer who will argue about the technological choice of XQuery. My point will be to make a comparison with the technologies they're currently using and I would like to demonstrate that for a rather XML- (and in general data-) intensive workflow XQuery is perfectly suitable and probably better than many other alternatives. I would tend to exclude XSLT because it would face similar opposition. I would also exclude languages at a lower level of abstraction like Java, Python, Javascript, C/C++ and so on for obvious architectural reasons. But then only templating languages/engines come to my mind. Those would still be probably novel technologies to learn and wouldn't offer the structural, syntactic and semantic power of XQuery anyway. So I ask you kindly, in order to complete my preparation on these matters, is there anyone that has experience with other tools or languages that can be compared with XQuery when used for XML querying, generation, transformation, templating, composition and so on? Thanks a lot! Marco.

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Improper use? Potential bug?
by Rob Stapper 25 Feb '17

25 Feb '17

Hi Christian, I encountered this error-message. I have a strong feeling that this error is related to previous reports, see . my email dd 13-05-2013 and 03-12-2014 My program is heavily recursive so it is hard to create a running snippet but I will try. Hopefully in the mean time you can have a look at the error. TIA, Rob Stapper ===================================== Error: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.6.1 beta 855f949 Java: Oracle Corporation, 1.8.0_31 OS: Windows Vista, x86 Stack Trace: java.lang.RuntimeException: $seq_1644 as (function(*))? index: 87, slot: 9 at org.basex.util.Util.notExpected(Util.java:62) at org.basex.query.var.QueryStack.pos(QueryStack.java:101) at org.basex.query.var.QueryStack.set(QueryStack.java:123) at org.basex.query.QueryContext.set(QueryContext.java:756) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:184) at org.basex.query.expr.gflwor.GFLWOR.item(GFLWOR.java:58) at org.basex.query.expr.ParseExpr.toItem(ParseExpr.java:488) at org.basex.query.expr.ParseExpr.toArray(ParseExpr.java:663) at org.basex.query.func.fn.FnApply.value(FnApply.java:32) at org.basex.query.func.Closure.item(Closure.java:288) at org.basex.query.func.Closure.value(Closure.java:321) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:159) at org.basex.query.value.item.FItem.invokeValue(FItem.java:44) at org.basex.query.func.fn.FnApply.value(FnApply.java:38) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:159) at org.basex.query.value.item.FItem.invokeValue(FItem.java:44) at org.basex.query.func.fn.FnApply.value(FnApply.java:38) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.If.value(If.java:128) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.If.value(If.java:128) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.If.value(If.java:128) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.If.value(If.java:128) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invokeTail(FuncCall.java:123) at org.basex.query.func.FuncCall.value(FuncCall.java:60) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.func.StaticFunc.invValue(StaticFunc.java:182) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:61) at org.basex.query.expr.TypeCheck.value(TypeCheck.java:131) at org.basex.query.func.Closure.item(Closure.java:288) at org.basex.query.func.Closure.value(Closure.java:321) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:159) at org.basex.query.value.item.FItem.invokeValue(FItem.java:44) at org.basex.query.func.fn.FnApply.value(FnApply.java:38) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:159) at org.basex.query.value.item.FItem.invokeValue(FItem.java:44) at org.basex.query.func.fn.FnApply.value(FnApply.java:38) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:182) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:95) at org.basex.query.expr.ParseExpr.item(ParseExpr.java:51) at org.basex.query.expr.ParseExpr.value(ParseExpr.java:65) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.value.item.FuncItem.invValue(FuncItem.java:117) at org.basex.query.func.FuncCall.invoke(FuncCall.java:87) at org.basex.query.func.FuncCall.value(FuncCall.java:159) at org.basex.query.value.item.FItem.invokeValue(FItem.java:44) at org.basex.query.func.fn.FnFoldLeft.value(FnFoldLeft.java:22) at org.basex.query.QueryContext.value(QueryContext.java:405) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:182) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:95) at org.basex.query.scope.MainModule$1.next(MainModule.java:121) at org.basex.query.QueryContext.cache(QueryContext.java:635) at org.basex.query.QueryProcessor.cache(QueryProcessor.java:113) at org.basex.core.cmd.AQuery.query(AQuery.java:86) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:95) at org.basex.gui.GUI.exec(GUI.java:471) at org.basex.gui.GUI.access$3(GUI.java:425) at org.basex.gui.GUI$6.run(GUI.java:413)

2 7

Cross-Origin Resource Sharing ( CORS) not available in jetty version 8
by Rob Stapper 25 Feb '17

25 Feb '17

Hi Christian, I'm trying to build a web based frontend with Angular(2) with Basex as backend. Since Angular uses localhost:3000 and basex uses localhost:8984 I need CORS to be activated in the bachend's jetty-service. If I try to activate this by editing the web.xml file I get the message from the jetty that this service is not available. Obviously version 8 of jetty does not support CORS. According to the documentation Jetty 9 should support CORS. Is replacing jett 8 with version 9 somewere on the agenda? Or can I do this myself? (new area for me) I wouldn't mind testrunning it. TIA, Rob Stapper PS. I see the request the request being handled and send back by the backend (basex) but it misses the necessary header. Debugging my Angular app in the browser say that CORS-header is missing.

4 4

BaseX 8.6.1
by Christian Grün 24 Feb '17

24 Feb '17

Dear all, A new minor update of BaseX is available (version 8.6.1, see [1] for more details). If you use BaseX with many users in parallel, we recommend you to switch to this version, which provides an improved locking strategy for excessive parallelism. Have fun, and (just in case) a nice weekend, Christian PS: Thanks everyone for the interesting mailing list discussion on XQuery in commercial environments. The good thing: Once you convince your customers or CTOs that XQuery is an attractive alternative, and once your project is a success, they usually want to realize everything with XQuery, no matter if it makes sense... Keep on going, don't give up too early! [1] https://github.com/BaseXdb/basex/blob/master/CHANGELOG

2 1

Gzip/RESTXQ
by meumapple 23 Feb '17

23 Feb '17

Hi All, I am wondering whether for RESTXQ one should enable gzip encoding to improve data transmission: if the database is used for storage (where the data are in binary form), is the gzip option still useful? Best, Joseph

4 6