BaseX-Talk November 2017

basex-talk@mailman.uni-konstanz.de

27 participants
44 discussions

Can't update or delete JSON objects
by E. Wray Johnson 13 Nov '17

13 Nov '17

I have tried XQUERY updates that should work but they don't work. My technique of storing JSON documents is perhaps not traditional. I have reduced my example to this simple example. FRIST CREATE DATABASE WITH ONE DOCUMENT: db:create('geography', json:parse('{ "code": "USA", "name": "United States of America", "birth": 1776 }'), '/country') THEN ADD ANOTHER DOCUMENT: db:add('geography', json:parse('{ "code": "CAN", "name": "Canada", "birth": 1867 }'), '/country') 1. How can I update either of these documents using 'code' as the unique identifier? 1. How can I change the 'name' or 'birth'? 2. How can I add a 'population' number? 2. How can I delete either of these documents using 'code' as the unique identifier?

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GEO module not found with BaseX GUI
by E. Wray Johnson 12 Nov '17

12 Nov '17

Error: Stopped at D:/projects/xquery/geo test.xq, 1/57: [XQST0059] Module not found: http://expath.org/ns/geo. Query: import module namespace geo = "http://expath.org/ns/geo"; declare namespace gml='http://www.opengis.net/gml'; for $x in db:open('geonames2','country') where index-of(['US'], $x/json/countryCode)>0 return geo:envelope( <gml:LinearRing> <gml:coordinates>($x/west, $x/south), ($x/east, $x/south), ($x/east, $x/north), ($x/west, $x/north), ($x/west, $x/south)</gml:coordinates> </gml:LinearRing> ) OS: Windows 7 Installation Method: Windows installer Launch: basexgui.bat I had this problem long ago. https://www.mail-archive.com/search?l=basex-talk@mailman.uni-konstanz.de&q=…

3 12

repo install
by Kendall Shaw 10 Nov '17

10 Nov '17

I have been updating packages by modifying the files in REPOPATH instead of creating a xar file and using repo install. Is it safe to expect that to continue to work for the foreseeable future? Kendall

2 1

HTTPS:PATCH - Request using http:send-request()
by Wissemann, Bodo 07 Nov '17

07 Nov '17

1 0

Issue with Full Text Retrieval
by Ron Katriel 06 Nov '17

06 Nov '17

Hi, I am seeing strange behavior with Full Text retrieval. The following query fails for a number of words that are in the XML document (see attached): for $trial in db:open('CTGovDebug') (: [clinical_study/id_info/nct_id='NCT00473512'] :) return $trial contains text { 'neoplasms' } It fails on a good number of words including neoplasms, cougar, industry, yes, completed, november, 2005, interventional, single, male, female, assignment, none, research, principal, primary, secondary, age, years, gender, etc. But it matches most of the words in the file. Observation: The words that fail are located at the beginning and/or end of the text *and* do not occur anywhere else in the middle of any text. The document is the only one in the database. It does not make a difference whether full text indexing is on or off. My BaseX version is 8.6.4. Thanks, Ron Ron Katriel, Ph.D. | Principal Data Scientist | Medidata Solutions <http://www.mdsol.com/> 350 Hudson Street, 7th Floor, New York, NY 10014 rkatriel(a)mdsol.com <tbrophy(a)mdsol.com> | direct: +1 201 337 3622 <//201 337 3622> | mobile: +1 201 675 5598 <//+1 201 675 5598> | main: +1 212 918 1800 <//+1 212 918 1800>

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Re: [basex-talk] Memory requirements, release memory, heap shrink
by Dinu Marina 04 Nov '17

04 Nov '17

Indeed, I use the create function from the GUI, I just assumed it's the same 2 separate operations. Indeed, with CREATE DB it doesn't get out of memory at 1G. And it also gets GC'ed and returned to system afterwards with no additional intervention, after CREATE DB memory shrinks immediately back to ~30M. So confirmed, huge memory usage and memory "leak" (or whatever it is) is linked to ADD only. Thanks, Dinu On 04.11.2017 18:46, Christian Grün wrote: > Hi Dinu, > > yes, I have downloaded the file. > > Just one more question: > >> 2) using basexclient: >> >> CHECK somedb >> ADD /path/to/1_feed.zip > If you use the GUI, do you really add your zip file to an existing > database, or do you specify it as initial input when creating a new > database? The latter option is definitely more efficient, and the > command-line equivalent would be > > CREATE DB somedb /path/to/1_feed.zip > > For adding resources to existing databases, enabling ADDCACHE can help [1]. > > Cheers, > Christian > > [1] http://docs.basex.org/wiki/Options#ADDCACHE > > > >> Result: >> Out of Main Memory. >> >> To reproduce 2), start server with -Xmx2048m, repeat operations, then drop >> db, close client, check server memory usage. >> >> Thanks, >> Dinu >> >> >> >> On 04.11.2017 18:18, Christian Grün wrote: >>>> The fact is, the GUI runs with no problem with -Xmx512M to do the same >>>> thing, while basexclient fails without -Xmx2048M. >>> That’s surprising indeed – mostly because I would have expected the >>> BaseX client to always consume a small and constant amount of memory >>> (the BaseX server instance should be the process to consume all the >>> memory). I did some quick tests with large zipped input, but I failed >>> to reproduce the behavior you described. Feel free to provide me with >>> a step-by-step guide. >>> >>>> I will try that, thanks, but shouldn't this be the case automatically? >>>> Since >>>> I assume BaseX does free references to data structures, at least to a >>>> dropped DB? >>> Absolutely. Anything that’s reproducible is welcome. >>> >>> >>> >>>> On 04.11.2017 18:00, Christian Grün wrote: >>>>> Hi Dinu, >>>>> >>>>>> Question 1: >>>>> Memory consumption of the BaseX GUI is similar as on command-line, but >>>>> it may be due to garbage collection that some memory will be freed. >>>>> How do you add documents outside the GUI? >>>>> >>>>>> Question 2: >>>>> If a certain amount of memory is reserved by Java’s virtual machine, >>>>> it may still be used by other applications on your system (provided >>>>> that the memory can be freed by garbage collection). You can enforce >>>>> some GC calls by running the following XQuery expression (this should >>>>> only be done for testing purposes): >>>>> >>>>> (1 to 5) ! Q{java:java.lang.System}gc() >>>>> >>>>> Best, >>>>> Christian >>>>> >>>>> >>>>>> After the data is extracted, it's no longer needed and I DROP the DB; >>>>>> also >>>>>> connection is closed. But memory (the huge 2G mentioned above) is never >>>>>> returned to the system. >>>>>> >>>>>> The script I use to run BaseX is: >>>>>> >>>>>> export BASEX_JVM="-Xmx2048m -XX:MinHeapFreeRatio=10 >>>>>> -XX:MaxHeapFreeRatio=20 >>>>>> -XX:+UseSerialGC -Dorg.basex.LOG=false >>>>>> -Dorg.basex.DBPATH=/var/basex/data >>>>>> -Dorg.basex.REPOPATH=/var/basex/repo" >>>>>> BaseX/bin/basexserver -S >>>>>> >>>>>> So basically I tried specifying MaxHeapFreeRatio and SerialGC for java, >>>>>> but >>>>>> it's no improvement and it doesn't help so I assume the memory isn't >>>>>> hogged >>>>>> in java... is there a way to free up the memory once operations >>>>>> complete >>>>>> (like mentioned above, "complete" means created DB is dropped, >>>>>> connection >>>>>> closed, waiting for another batch to start over). >>>>>> >>>>>> Thanks, >>>>>> Dinu >>>>>>

2 11

Memory requirements, release memory, heap shrink
by Dinu Marina 04 Nov '17

04 Nov '17

Hi guys, I'm running BaseX as server; it has some processing to do every now and then, huge pieces of data. But most of the times it's idle. The "pieces of data" are huge XML files that are ADD'ed to a new DB, then read. Basically I'm using BaseX as an intermediate random-access parser/indexer for some huge XML files. Question 1: XML files are such that I need to specify -Xmx2048M, otherwise I get an out of memory error when ADDing the files. However, I notice that in the BaseX GUI adding the same XML files reports a memory usage of <300M. Is there some special option that the GUI is using that I could use too on the server so that memory usage is not so severe? Question 2: After the data is extracted, it's no longer needed and I DROP the DB; also connection is closed. But memory (the huge 2G mentioned above) is never returned to the system. The script I use to run BaseX is: export BASEX_JVM="-Xmx2048m -XX:MinHeapFreeRatio=10 -XX:MaxHeapFreeRatio=20 -XX:+UseSerialGC -Dorg.basex.LOG=false -Dorg.basex.DBPATH=/var/basex/data -Dorg.basex.REPOPATH=/var/basex/repo" BaseX/bin/basexserver -S So basically I tried specifying MaxHeapFreeRatio and SerialGC for java, but it's no improvement and it doesn't help so I assume the memory isn't hogged in java... is there a way to free up the memory once operations complete (like mentioned above, "complete" means created DB is dropped, connection closed, waiting for another batch to start over). Thanks, Dinu

2 3

Thanks for Enforce Index Rewriting!
by Omar Siam 03 Nov '17

03 Nov '17

This sounds like a great improvement for our code: http://docs.basex.org/wiki/Indexes#Enforce_Rewritings. Many thanks!

1 0

losses von tags?
by michael4you＠arcor.de 02 Nov '17

02 Nov '17

Hello, There is a problem in transforming data vom XML in HTML. In XML there are HTML-tags included. XML original: <dat>text is <b>important</b>.</dat> HTML goal: <div>text is <b>important</b>.</div> (1) result: <div>text is important.</div> let $data := <dat>text is <b>important</b>.</dat> return <div>{$data/data()}</div> (2) result: <div>text is important.</div> let $data := <dat>text is <b>important</b>.</dat> return <div>{$data/text()}</div> (3) result: <div><dat>text is <b>important</b>.</dat></div> let $data := <dat>text is <b>important</b>.</dat> return <div>{$data}</div> Is there another possibility to get the result desired? Thanking you, Michael

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Re: [basex-talk] Rounding/parsing decimal vs float
by Marco Lettere 01 Nov '17

01 Nov '17

Thanks Kristian, unfortunately this introduces rounding errors which I'm trying to avoid because managing units, measures and monetary amounts. M. Il 01 nov 2017 12:57 PM, "Kristian Kankainen" <kristian(a)keeleleek.ee> ha scritto: You need to use xs:float or xs:double instead of xs:decimal to be able to use the 'e' or 'E' as the exponent separator. Br, Kristian K1. nov 2017 13:18 kirjutas kuupäeval Marco Lettere < m.lettere(a)gmail.com>: > > Hi all, > > I thought of asking this in parallel of hacking my own parsing procedure > ... > > Is there a native way to parse scientific notation string into > xs:decimal since a direct casting (xs:decimal("1e1")) is not allowed? > > Thanks, > > Marco. >

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BaseX-Talk November 2017