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

Re: [basex-talk] java binding standardfunc and querymodule
by Kendall Shaw 26 Sep '16

26 Sep '16

To answer my own question, maybe, see: ModuleDemo.java in the examples. With that I can operate on an ANode or a Value, at least. For now, that is all that I need. I will have to look into what method signatures are recognized. Kendall From: <basex-talk-bounces(a)mailman.uni-konstanz.de> on behalf of Kendall Shaw <kendall.shaw(a)workday.com> Date: Monday, September 26, 2016 at 1:21 PM To: "basex-talk(a)mailman.uni-konstanz.de" <basex-talk(a)mailman.uni-konstanz.de> Subject: [basex-talk] java binding standardfunc and querymodule The documentation describes extending QueryModule for writing a module in java. I want to write functions that are passed items. If I look at the concat function it uses Expr.atomItem passing QueryContext and InputInfo. Is there a way to get at InputInfo from a class that extends QueryModule? Or, another way to write functions that transform items? Kendall

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java binding standardfunc and querymodule
by Kendall Shaw 26 Sep '16

26 Sep '16

The documentation describes extending QueryModule for writing a module in java. I want to write functions that are passed items. If I look at the concat function it uses Expr.atomItem passing QueryContext and InputInfo. Is there a way to get at InputInfo from a class that extends QueryModule? Or, another way to write functions that transform items? Kendall

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Docker images user permissions
by George Sofianos 24 Sep '16

24 Sep '16

Hi, I just wanted to let you know that pulling previous docker images (for example 8.4.4) after the latest changes, made them unable to run. The error is: > touch: cannot touch ‘/root/.m2/copy_reference_file.log’: Permission denied > Can not write to /root/.m2/copy_reference_file.log. Wrong volume permissions? I suspect this is connected to the changes made here: https://github.com/BaseXdb/basex/pull/1347/files Are we forced to upgrade, or there is a workaround for this? Thanks

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(no subject)
by Tushar Deshmukh 23 Sep '16

23 Sep '16

Namaste All, I want to use basex locally in Java swing project. I wanted to create database in the executable jar file's directory. Suppose my directory is on c:\tdd My code is as below public static void createdatabase() throw s Exception { Context cts = new Context(); new Set(StaticOptions.DBPATH,"c:\\tdd ). execute(cts); new CreateDB("collection"). execute(cts); cts.close(); } I am getting an error Global option ' DBPATH' cannot be set. Please guide As user input from GUI is getting saved in local database. Thanks Tushar Deshmukh.

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get multipart entry of file upload (RESTXQ)
by Maximilian Gärber 23 Sep '16

23 Sep '16

Hi, I can't find where I would access the other entries returned by a file upload. What gets sent is -----------------------------175432198730168 Content-Disposition: form-data; name="file"; filename="base.png" Content-Type: image/png ‰PNG as base64... ---------------------------- The file is in the $file map but how can I get the Content-Type for example? %rest:POST("{$post}") %rest:form-param("file", "{$file}") Regards, Max

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Re: [basex-talk] using basex locally
by Tushar Deshmukh 23 Sep '16

23 Sep '16

On 23-Sep-2016 11:23 am, "Tushar Deshmukh" <tdlwala(a)gmail.com> wrote: Namaste All, I want to use basex locally in Java swing project. I wanted to create database in the executable jar file's directory. Suppose my directory is on c:\tdd My code is as below public static void createdatabase() throw s Exception { Context cts = new Context(); new Set(StaticOptions.DBPATH,"c:\\tdd ). execute(cts); new CreateDB("collection"). execute(cts); cts.close(); } I am getting an error Global option ' DBPATH' cannot be set. Please guide As user input from GUI is getting saved in local database. Thanks Tushar Deshmukh.

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using rest api to move a file
by Adil Hasan 22 Sep '16

22 Sep '16

Hello, I hope you can help me I'm going a bit mad with this (I had it working before, but don't have the notes of what I did). I have in a database an xml file: http://localhost:8484/rest/test/test1.xml I would like to move the xml file to a different database: http://localhost:8984/rest/test-moved I tried the following: curl -utest:test -X POST -H "Content-Type: application/xml;charset=UTF-8" -d '@/home/hasan/move.xml' -i "http://localhost:8984/rest/test" where my move.xml has: <command xmlns="http://basex.org/rest"> <text> rename test1.xml test-moved/test1.xml </text> </command> The command returns a 200, but nothing has moved. I am clearly doing something wrong. If I change the URL in the cURL request to "http://localhost:8984/rest" I get a java null pointer exception. Do you know they syntax I should use for the REST API to move a file? many thanks, adil

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Re: [basex-talk] Accessing file within repository or package
by Kendall Shaw 22 Sep '16

22 Sep '16

Whoops. Never mind. It works to use a path relative to the xquery file: doc(‘hella.xsl’). That was not working earlier, presumably because of some unrelated problem. Kendall From: <basex-talk-bounces(a)mailman.uni-konstanz.de> on behalf of Kendall Shaw <kendall.shaw(a)workday.com> Date: Thursday, September 22, 2016 at 1:28 PM To: BaseX <basex-talk(a)mailman.uni-konstanz.de> Subject: [basex-talk] Accessing file within repository or package I have a module packaged as a XAR and installed in the repo. In xquery I want to load xslt. This did not work: <package name="http://example.com/hellaworld" abbrev="hella" version="1.0.0" spec="1.0" xmlns="http://expath.org/ns/pkg"> <title>Hella world functions</title> <dependency processor="basex"/> <xslt> <import-uri>http://example.com/hellaworld/hella.xsl</import-uri> <file>hella.xsl</file> </xslt> <xquery> <import-uri>http://example.com/hellaworld</import-uri> <file>hella.xq</file> </xquery> </package> Then using the import-uri with doc, e.g.: (: within hella.xq in the package :) xslt:transform($some, doc(‘http://example.com/hellaworld/hella.xsl’)) It does work, to use a path relative to the root of tomcat which I’m running basex in: doc(‘webapps/basex/repo/http-example.com-hellaworld-1.0.0/hella/hella.xsl’) but, I hope there is another way. How can I reference another file that is within the XAR package? Kendall

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Accessing file within repository or package
by Kendall Shaw 22 Sep '16

22 Sep '16

I have a module packaged as a XAR and installed in the repo. In xquery I want to load xslt. This did not work: <package name="http://example.com/hellaworld" abbrev="hella" version="1.0.0" spec="1.0" xmlns="http://expath.org/ns/pkg"> <title>Hella world functions</title> <dependency processor="basex"/> <xslt> <import-uri>http://example.com/hellaworld/hella.xsl</import-uri> <file>hella.xsl</file> </xslt> <xquery> <import-uri>http://example.com/hellaworld</import-uri> <file>hella.xq</file> </xquery> </package> Then using the import-uri with doc, e.g.: (: within hella.xq in the package :) xslt:transform($some, doc(‘http://example.com/hellaworld/hella.xsl’)) It does work, to use a path relative to the root of tomcat which I’m running basex in: doc(‘webapps/basex/repo/http-example.com-hellaworld-1.0.0/hella/hella.xsl’) but, I hope there is another way. How can I reference another file that is within the XAR package? Kendall

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'Path "/{$id}" assigned to several functions:' error with content negotiation in a browser
by Steve Baskauf 22 Sep '16

22 Sep '16

I am attempting to set up content negotiation for HTTP requests for various serializations of RDF. I have set up a restxq module file to control the API, started the server, and performed GET requests the the localhost with Accept: headers for the various Content-Types that the restxq file is designed to handle. You can see a simplified version of the file at https://gist.github.com/baskaufs/00f471b905ae9b862677fedf9f047bcb . Everything works according to expectations when I request a single content type using cURL, Chrome Advanced REST Client, etc. However, when I use a browser, I get the error 400 Stopped at C:/Program Files (x86)/BaseX/webapp/restxq.xqm, 6/12: [bxerr:BASX0003] Path "/{$id}" assigned to several functions: C:/Program Files (x86)/BaseX/webapp/restxq.xqm, 6/12 C:/Program Files (x86)/BaseX/webapp/restxq.xqm, 20/12 C:/Program Files (x86)/BaseX/webapp/restxq.xqm, 34/12 C:/Program Files (x86)/BaseX/webapp/restxq.xqm, 48/12 I checked the Accept: request header sent by Chrome and it is 1. Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8 So I tried sending a GET using Advanced Rest Client and the same Accept: header. That produced the same error. I experimented with changing the Accept header and the problem seems to be caused by the "*/*" wildcard in the Accept: header. Any combination I use without */* works, but any combination including it fails. According to what I've read at http://docs.basex.org/wiki/RESTXQ#Content_Negotiation and http://exquery.github.io/exquery/exquery-restxq-specification/restxq-1.0-sp… (section 5.2.3), the more specific media type should be used to process the request, so it doesn't seem like there should be a problem with the client specifying multiple content types, including */*. Any advice you can offer would be appreciated. I'm running BaseX 8.5.3 on a 64 bit Windows 10 system. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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XML files are not indented anymore with DTD = true and CATFILE
by Maximilian Gärber 22 Sep '16

22 Sep '16

Hi, I just noticed that when using a config with following settings: # Local Options DTD = true CATFILE = C:\Program Files\Oxygen XML Editor 18\frameworks\dita\DITA-OT\catalog-dita.xml CHOP = false Then all output (e.g. in the DBA) will not be indented anymore. Bug? Or am I missing another Option? Best, Max

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new Add(
by Jens Huelscher 21 Sep '16

21 Sep '16

Hello, can someone please give an example in java of context = new Context(); new Open("DBexample").execute(context); new Add(Target,Path)????? I want to add a dir to "DBexample". new Add("C:\\Users\\jens\\BaseXData\\DBexample", "input\foo"); does not work v7.3.1 Thank you!

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replace expression
by Joseph 16 Sep '16

16 Sep '16

I am trying to substitute the content of an element with its content in a document, using copy $e := doc("document") modify ( for $x in $e//C return replace node $x with $x/text() ) return $e Although this seems to be a plain query, it never ends when launched, so that I am forced to quit BaseX. Any suggestions? Thanks! PS: my document contains a lot of the elements I want to change. I do not know whether there si an "easy" alternative to "copy"/"replace" Best, Joseph

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Try/catch
by meumapple 15 Sep '16

15 Sep '16

Hi, I have been working with a collection of XML files, trying to make changes using the copy clause. It may happen that sometimes I get an error message because of one of the files I am trying to change. My question is whether there is a way to know which file and at which line/column the error occurs. I have tried try/catch but it seems not to be designed for this (or am I missing something here?). Thanks! Best, Joseph

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Re: [basex-talk] FYI: Balisage talk involving BaseX
by Christian Grün 13 Sep '16

13 Sep '16

Hi all, I’d like to point you to an interesting talk from Amanda Galtman on RESTXQ and JavaScript… http://balisage.net/Proceedings/vol17/html/Galtman01/BalisageVol17-Galtman0… http://balisage.net/Proceedings/vol17/author-pkg/Galtman01/BalisageVol17-Ga… Have fun, Christian

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csv:parse in the age of XQuery 3.1
by Joe Wicentowski 12 Sep '16

12 Sep '16

Dear BaseX developers, I noticed in example 3 under http://docs.basex.org/wiki/CSV_Module#Examples that csv:parse() with option { 'format': 'map' } returns a map of maps, with hardcoded row numbers: map { 1: map { "City": "Newton", "Name": "John" }, 2: map { "City": "Oldtown", "Name": "Jack" } } Using maps, which are unordered, to represent something ordered like rows in a CSV, hardcoded row numbers are necessary for reassembling the map in document order. I assume this was a necessary approach when the module was developed in the map-only world of XQuery 3.0. Now that 3.1 supports arrays, might an array of maps be a closer fit for CSV parsing? array { map { "City": "Newton", "Name": "John" }, map { "City": "Oldtown", "Name": "Jack" } } I'm also curious, do you know of any efforts to create an EXPath spec for CSV? Putting spec and CSV in the same sentence is dangerous, since CSV is a notoriously under-specified format: "The CSV file format is not standardized" (see https://en.wikipedia.org/wiki/Comma-separated_values). But perhaps there is a common enough need for CSV parsing that such a spec would benefit the community? I thought I'd start by asking here, since BaseX's seems to be the most developed (or only?) CSV module in XQuery. Then there's the question of how to approach implementations of such a spec. While XQuery is probably capable of parsing and serializing small enough CSV, CSVs do get large and naive processing with XQuery would tend to run into memory issues (as I found with xqjson). This means implementations would tend to write in a lower-level language. eXist, for example, uses Jackson for fn:parse-json(). I see Jackson has a CSV extension too: https://github.com/FasterXML/jackson-dataformat-csv. Any thoughts on the suitability of XQuery for the task? Joe

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8.5.3 and xquery:invoke ...
by Marco Lettere 11 Sep '16

11 Sep '16

Hello again, at the end I managed to reproduce the issue we are currently facing with xquery:invoke in 8.5.3 (and also in latest snapshot). Please consider the three queries [1,2,3]. The store [2] into a subdirectory src of the directory containing [1] and store [3] into a directory src2 of src. You should get the error message [4]. If instead you change the parameter of xquery:invoke to "src/src2/q2.xqm" it works. Seems like the reference for static-base-uri in [2] remains the one of [1] even if it is reported by static-base-uri() to be correctly "/home/user/src/q1.xqm"(I've double-checked this). Sorry it's not clear to me whether this is meant to be the correct behaviour ... Thanks for any help, Marco. [1] q.xqm import module namespace q1="urn:q1" at "src/q1.xqm"; q1:f() [2] q1.xqm module namespace q1 = "urn:q1"; declare function q1:f(){ xquery:invoke("src2/q2.xqm") }; [3] q2.xqm 1 = 1 [4] Stopped at /home/user/src/q1.xqm, 4/16: [FODC0002] Resource 'src2/q2.xqm' does not exist.

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question on starting multiple instance of basex
by Wang, Genneva 11 Sep '16

11 Sep '16

Hi I’m trying to set up to having multiple instance of basex in my local dev environment, presumably to simulate production environment where our application is pointing to two different basex that running a different server. I’ve running basex as client server application in dev environment. Is there a way to do that? I’ve tried to start basex server with 2 different ports A and B, and also starting client with port A and B, but both seemed to be pointing to the same list of the databases that was created. Any tips would be greatly appreciated. Thanks! Regards, -Genneva

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fork-join and recursive function
by Carl Leitner 11 Sep '16

11 Sep '16

Hi All, I have hierarchical information encoded an XML document that looks something like: <organization entityID=“1”> <organization entityID=“2"> <parent entityID=“1”> </organization> <organization entityID=“3"> <parent entityID=“2”> </organization> <organization entityID=“4"> <parent entityID=“1”> </organization> There are around 80,000 entries like this and I need to regular do extractions of sub-hiearchies (see the commented out version of the below function). The commented-out version runs in about a minute using a modest amount of memory. Hoping to take advantage of this <https://github.com/BaseXdb/basex/commit/ac86bbbc3cd1f71461ce94d803cab46f21e…>, I modified the function (the uncommented version) which tries to use xquery:fork-join in 8.5.2beta (the July 12th snapshot). The parallelized one chews up the 3g of available memory, unceremoniously throws exceptions (Exception in thread "qtp198198276-19” ), with the occasional: java.lang.OutOfMemoryError: GC overhead limit exceeded at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.addConditionWaiter(AbstractQueuedSynchronizer.java:1857) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2073) Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "qtp198198276-19" java.lang.OutOfMemoryError: GC overhead limit exceeded Exception in thread "qtp198198276-14" java.lang.OutOfMemoryError: GC overhead limit exceeded and runs for tens of minutes (perhaps more - I always kill the process). Any ideas on what I can do to improve the situation? Thanks in advance. Cheers, -carl declare function csd_bl:get_child_orgs($orgs,$org) { let $org_id := $org/@entityID return if (functx:all-whitespace($org_id)) then () else let $c_orgs := $orgs[./parent[@entityID = $org_id]] let $t0 := trace($org_id, "creating func for ") let $t1 := trace(count($c_orgs), " func checks children: ") let $c_org_funcs:= for $c_org in $c_orgs return function() { ( trace($org_id, "executing child func for ") , $c_org, csd_bl:get_child_orgs($orgs,$c_org))} return xquery:fork-join($c_org_funcs) (: let $c_orgs := if (functx:all-whitespace($org_id)) then () else $orgs[./parent[@entityID = $org_id]] return for $c_org in $c_orgs let $t0 := trace($org_id, "processing children for ") return ($c_org,csd_bl:get_child_orgs($orgs,$c_org)) :) };

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Serialize a string to unencode XML entities?
by Hondros, Constantine (ELS-AMS) 11 Sep '16

11 Sep '16

Ok, this must be possible. Can someone point me towards the correct serialization $params such that let $doi := <doi>10.1002/1521-4141(200207)32:7<2021::AID-IMMU2021>3.0.CO;2-J</doi> return serialize($doi, $params) will return (to a calling Java application) the UTF-8 string 10.1002/1521-4141(200207)32:7<2021::AID-IMMU2021>3.0.CO;2-J where the entities < and > have been replaced with the UTF-8 byte representation for U+003C and U+003E respectively? Thanks in advance, C. ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

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Using the same database in many BaseX instances
by cmarchand＠oxiane.com 11 Sep '16

11 Sep '16

Hello, as discussed here few monthes ago, I do this : Install many instances (8) of BaseX on the same computer Start one instance, here called "main-instance" Create a database "library" , and load a filesystem directory into "library" Stop main-instance For each "other-instance", create a sym-link to main-instance/data/library Start "other-instances" On each instance, create 2 new databases "input" and "output", load a file in "input", process it and store result in "output". The process queries a lot "library", but never modifies "library". Then export "output" and drop databases "input" and "output". I have about 100 files to process; and I distribute them on the various instances I had a first test environment, with only 4 isntances, and everything was working perfectly. Now, I'm working on target environment, a bigger computer with 8 instances. Process fails, at least one time per instance, so between 8 and 12 times on 100 process. The exception is java.lang.NullPointerException at org.basex.data.DiskData.write(DiskData.java:136) at org.basex.data.DiskData.close(DiskData.java:151) at org.basex.core.Datas.unpin(Datas.java:54) at org.basex.core.cmd.Close.close(Close.java:45) at org.basex.query.QueryResources.close(QueryResources.java:110) at org.basex.query.QueryContext.close(QueryContext.java:596) at org.basex.query.QueryProcessor.close(QueryProcessor.java:251) at org.basex.core.cmd.AQuery.query(AQuery.java:124) 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) If I change the sym-links by a true copy (cp -r main/data/library other/data/), it now works correctly, but the copy takes a long time (database is about 30gb), and it consumes disk space. The computer I use has many available cores, and many RAM to use, so I'd love to add other instance, many 16 more to reach 24 isntances, but if database grow, I'm going to have disk-space troubles... 1 - is it legal to share a database (and files) between many instances as far as database is access read-only ? 2 - is there a way to configure a database to be read-only ? 3 - why symbolic links were perfectly usable with 4 instances, and do not with 8 instances ? (Hum I have to try symlinks with only 4 instances on the new computer...) 4 - are there other specific things to check to do what I need ? Best regards, Christophe

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bug (?) in fn:serialize
by Hans-Juergen Rennau 09 Sep '16

09 Sep '16

Dear BaseX team, is this a bug? serialize(<e> </e>) returns <e/> I need my blanks! Hans-Jürgen

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read grant to anonymous user
by raffaele messuti 08 Sep '16

08 Sep '16

hi, i'm quite a newbie to basex (and generally xquery) a simple question (i'm not finding answers in the wiki): how i can grant a read permission to an anonymous (no password) user? the common use case is to access raw xml files via rest /rest/{db}/{file.xml}. this don't work: > grant read on [db] to * Admin user cannot be modified. as a solution i was thinking to proxy basex through nginx and use "proxy_set_header Authorization" thanks PS/ my first attempt to learn xquery is here, into a jupyter notebook maybe is interesting for someone: https://github.com/atomotic/bni-xquery/blob/master/bni-xquery.ipynb -- raffaele

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Upgrade from 7.9 to 8.3
by Bram Vanroy 07 Sep '16

07 Sep '16

Hi everyone We're in a bit of a pickle. We upgraded to BaseX 8.3 after some hard drives failed, but now the PHP Basex client can't connect to the server any more. Here is the general idea: - basexserver is launched from server A, but the .basex configuration file it uses is stored on server B. This is the unchanged file we used in BaseX 7.9; - the data that the .basex file refers to is on server C, this has not changed either since the hard drive crash; - the PHP basex client is on server D, this file has not been changed either. So I am guessing that either we need to update one of our files, OR we'd need to re-import our data into the new BaseX server. Do you have any idea how to handle this? Kind regards Bram

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Re: [basex-talk] REST API performance, massive disk IO
by Jens Erat 06 Sep '16

06 Sep '16

Hi Benedikt, sorry for not answering for a week. > our storage driver is the default aufs: > > Storage Driver: aufs > Root Dir: /var/lib/docker/aufs > Backing Filesystem: extfs > Dirs: 189 > Dirperm1 Supported: false > > ... based on ext4, also with default option (journaling only on metadata). That should be fine. Copy on write file systems in general require some attention when using databases (and other applications with massive small writes), but you don't use one (so you shouldn't have an issue with the file system here). > However, we have a persistent volume for the BaseX database files pointed to a regular folder on the host (ext4). To my understanding the storage driver isn't used in this case. You're right. > Is there a recommendation for a basex filesystem? The file system is not too important, as long as no copy on write is applied (chattr +t for BTRFS, but read up on that before using it). Ext4, XFS, ... should not require any special attention. I'm not aware anybody every considered different file systems and BaseX performance in a reasonable benchmark yet, but BaseX' access patterns do not differ substantially from other database systems. Regards, Jens -- Jens Erat Universität Konstanz Kommunikations-, Infomations-, Medienzentrum (KIM) Abteilung Basisdienste D-78457 Konstanz Mail: jens.erat(a)uni-konstanz.de

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