BaseX-Talk

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13 participants
5244 discussions

"Out of Memory" when inserting data from one DB to another
by BIRKNER Michael 30 Oct '19

30 Oct '19

Hi to all, I get an "Out of Memory" error (using the BaseX GUI on Ubuntu Linux) when I try to insert quite a lot of data into a BaseX database. The use case: I have a database (size is about 2600 MB, 13718400 nodes) with information in <record> elements that should be added to <record> elements in another database. The <record>s have a 1 to 1 connection identified by an ID that is available in both databases. An example (simplified) of the DB with the information I want to add to the other DB: <collection> <record> <id>1</id> <data>Some data</data> <data>More data</data> <data>More data</data> ... </record> <record> <id>2</id> <data>Some data</data> <data>More data</data> <data>More data</data> ... </record> <record> <id>3</id> <data>Some data</data> <data>More data</data> <data>More data</data> ... </record> ... many many more <record>s </collection> Here an example (simplified) of the DB to which the above <data> elements should be added: <collection> <record> <id>1</id> <mainData>Main data</mainData> <mainData>More main data</mainData> <mainData>More main data</mainData> ...  </record> <record> <id>2</id> <mainData>Main data</mainData> <mainData>More main data</mainData> <mainData>More main data</mainData> ...  </record> <record> <id>3</id> <mainData>Main data</mainData> <mainData>More main data</mainData> <mainData>More main data</mainData> ...  </record> ... many many more <record>s </collection> This is the XQuery I use to insert the given <data> elements from the <record> in one database to the corresponding <record> in the other database. It results in an "Out of Memory" error: let $infoRecs := db:open('db-with-data')/collection/record let $mainRecs := db:open('db-to-insert-data')/collection/record for $infoRec in $infoRecs let $id := data($infoRec/id) let $mainRec := $mainRecs[id=$id] let $dataToInsert := $infoRec/*[not(name()='id')] return insert node ($dataToInsert) into $mainRec I assume that the error is a result of the large amount of data that is processed. My question is if a strategy exists to work with such an amount of data without getting an "Out of Memory" error? Thanks very much to everyone in advance for any hint and advice. If you need more information about DB setup or options just let me know. Best regrads, Michael Dieses Mail ist ausschließlich für die Verwendung durch die/den darin genannten AdressatInnen bestimmt und kann vertrauliche bzw rechtlich geschützte Informationen enthalten, deren Verwendung ohne Genehmigung durch den/ die AbsenderIn rechtswidrig sein kann. Falls Sie dieses Mail irrtümlich erhalten haben, informieren Sie uns bitte und löschen Sie die Nachricht. UID: ATU 16209706 I https://wien.arbeiterkammer.at/datenschutz

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http:request parsing question
by Bridger Dyson-Smith 29 Oct '19

29 Oct '19

Hi all - I was hoping that someone on the list could help with my thinking about parsing the http:response values from a request; I've tried the following, but I'm not thinking about this correctly. declare namespace oai = "http://www.openarchives.org/OAI/2.0/"; declare namespace h = "http://expath.org/ns/http-client"; http:send-request(<http:request method='get' href=' http://export.arxiv.org/oai2?verb=Identify'/>)//@status/data() returns '200', but trying http:send-request(<http:request method='get' href=' http://export.arxiv.org/oai2?verb=Identify'/>)/h:response/@status fails. I'm guessing (but am not sure) that the combination of the <http:response> with the body of the response is causing my problem, but I'm not sure how to wiggle my way around it. Note: this is not in a RESTXQ context (yet), but for my simple trials is there a way to get at the http -namespace elements? Thank you for your time and trouble. Best, Bridger

3 5

Binding a variable
by Ben Engbers 29 Oct '19

29 Oct '19

Hi, When experimenting with my RBaseX-package (I had hoped to submit it to CRAN today), I use the following pattern: 1 Define a query 2 Create a query-object 3 Bind variables (optional) 4 Execute the query When used this pattern on the following query, everything functions as expected: declare variable $name external; for $i in 1 to 3 return element { $name } { $i } The following query is also functioning: paste("declare variable $greet external;", "declare variable $friend external;", "declare variable $into external;", "let $greet := 'Greetings, my '", "let $friend := 'friend'", "for $i in 1 to 3", "let $friend_num := $greet || $friend || $i", "return insert nodes element { $friend } { $friend_num }", "into root", sep = " ") When I modify "into root" to "into $p" and bind $p to root Bind(query_obj, "$p", "root") I get the following error: [XPST0008] Undeclared variable $p The Bind-function returns with code \00, indicating that it is executed without errors. Does this mean that there is a bug in my code or am I violating XQuery-syntax? Ben Engbers

2 2

Understanding the path index
by Beck, Julia 29 Oct '19

29 Oct '19

Hi, first of all: thank you, the fix for [1] did the trick and in 9.2.4 the query is working as expected. Today, I come back to you with another challenge in performance which again seems to have something to do with indexing(?). So here's the situation: I have two databases "abc" and "def". "abc" contains 1 xml doc with about 150.000 nodes and "def" contains 1 xml doc with about 400.000 nodes. Both are similarly strutured and have their up-to-date text and attr indexes. The xml docs look both (simplified) like the following: <rdf:RDF> <ore:Aggregation rdf:about="123"> <edm:object rdf:resource="urn1"/> <...> </ore:Aggregation> <edm:WebResource rdf:about="urn1"> <...> </edm:WebResource> <ore:Aggregation rdf:about="124"> <edm:object rdf:resource="urn2"/> <...> </ore:Aggregation> <edm:WebResource rdf:about="urn2"> <...> </edm:WebResource> <ore:Aggregation rdf:about="125"> <edm:object rdf:resource="urn2"/> <edm:object rdf:resource="urn3"/> <...> </ore:Aggregation> <edm:WebResource rdf:about="urn3"> <...> </edm:WebResource> <...> </rdf:RDF> So one aggregation refers to one (or more) web resources. I boiled down my original query to the following purpose to keep it simple: for each aggregation give me the corresponding web resource. for $agg in db:open($db_name)/rdf:RDF/ore:Aggregation return for $urn in $agg/edm:object/@rdf:resource return (# db:enforceindex #) {db:open($db_name)/rdf:RDF/edm:WebResource[@rdf:about=$urn]} For both databases the query gives me the required result and the query info tells me that the attribute index for $urn is applied in both cases (this is also the case if I leave out the pragma). However, oddly enough, for the "larger" database "def" with a larger attribute index it takes roughly 1 second while the "smaller" database "abc" with a smaller attribute index takes 20 seconds. This is not very long but the original query is more complicated and I have bigger databases with the same structure where it starts to matter. The only (and I think important) difference between "abc" and "def" is that "abc" contains only 3 web resources that all 5.000 aggregations refer to. While in "def" each aggregation refers to a particular web resource (== 7.000 aggregations and 7.000 web resources). With index:facets I had a look at the facet values and learned that there is a "maximum number of distinct values to store per name". Is there a difference in performance because of that? Maybe I do not get the index structures but it feels strange that it takes longer to find the correct attribute in a range of 3 different values than in a range of 7.000. Maybe there is also another problem in my query, databases or my reasoning that I do not see? Either way, I need help in understanding this phenomenon :-) I hope you could follow, please don't hesitate to ask if you need anything to reproduce this situation (I am using BaseX 9.2.4). Julia [1] https://mailman.uni-konstanz.de/pipermail/basex-talk/2019-July/014511.html

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http:send-request - problem with response
by Bogdan Bogucki 29 Oct '19

29 Oct '19

Hello, I encounter problem with http:send-request function. I need handle multiple forward requests (3) with cookies. First request returns cookies information which are required with next requests. Output from http:send-request dosen't contains all fields which are returned by server. Response from browser is flowing: cache-control private cf-cache-status DYNAMIC cf-ray 52b3cedc5b9bcc9f-WAW content-type text/html; charset=utf-8 date Fri, 25 Oct 2019 11:21:37 GMT expect-ct max-age=604800, report-uri="ht….com/cdn-cgi/beacon/expect-ct" location http://www.pracuj.pl/praca/jav…eloper-warszawa,oferta,7171988 server cloudflare set-cookie __cfduid=daf54110b2a87d66c2a53…; domain=.pracuj.pl; HttpOnly set-cookie _yaic=13; expires=Fri, 31-Dec-9999 23:59:59 GMT; path=/ set-cookie _urnadiam=A; domain=.pracuj.pl…3:00:00 GMT; path=/; HttpOnly x-aspnet-version 4.0.30319 x-aspnetmvc-version 5.2 X-Firefox-Spdy h2 x-powered-by ASP.NET x-ua-compatible IE=edge Request: http:send-request( <http:request method='get' follow-redirect='false'> <http:header name="User-Agent" value="Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:69.0) Gecko/20100101 Firefox/69.0"/> <http:header name="Accept" value="text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8"/> <http:header name="Accept-Languag" value="pl,en-US;q=0.7,en;q=0.3"/> <http:header name="DNT" value="1"/> <http:header name="Connection" value="keep-alive"/> <http:header name="Upgrade-Insecure-Requests" value="1"/> <http:body media-type='application/x-www-form-urlencoded; charset=UTF-8'/> </http:request>, 'https://www.pracuj.pl/praca/java-developer-warszawa,oferta,7171988') Response form http:send-request is: <http:response xmlns:http="http://expath.org/ns/http-client" status="302" message="Found"> <http:header name="Transfer-Encoding" value="chunked"/> <http:header name="CF-RAY" value="52b3d0de097fb839-WAW"/> <http:header name="Server" value="cloudflare"/> <http:header name="Connection" value="keep-alive"/> <http:header name="Date" value="Fri, 25 Oct 2019 11:23:00 GMT"/> <http:header name="X-AspNetMvc-Version" value="5.2"/> <http:header name="X-UA-Compatible" value="IE=edge"/> <http:header name="CF-Cache-Status" value="DYNAMIC"/> <http:header name="Cache-Control" value="private"/> <http:header name="X-AspNet-Version" value="4.0.30319"/> <http:header name="Set-Cookie" value="_urnadiam=B; domain=.pracuj.pl; expires=Tue, 31-Dec-2019 23:00:00 GMT; path=/; HttpOnly"/> <http:header name="Expect-CT" value="max-age=604800, report-uri="https://report-uri.cloudflare.com/cdn-cgi/beacon/expect-ct…"/> <http:header name="X-Powered-By" value="ASP.NET"/> <http:header name="Content-Type" value="text/html; charset=utf-8"/> <http:body media-type="text/html"/> </http:response> Two set-cookie fields is missing. How should I invoke http:send-request to receive proper result ? Regards Bogdan

2 1

Optimization issue?
by Johannes Echterhoff 25 Oct '19

25 Oct '19

Hello, I'm experiencing some strange behavior when executing the following query in the BaseX 9.2.4 GUI (nevermind the awkward query structure - that is just to be able to inspect the results of the individual evaluation steps): let $t := <x>200.0000</x> let $num := number($t) let $gt5000 := $num gt 5000 let $ltMinus5000 := $num lt -5000 return $gt5000 or $ltMinus5000 The result is true, although it should be false. The compilation and optimization logs for this query in the GUI tell us the following: ---------- Compiling: - rewrite > comparison to range comparison: ($num_1 > 5000) -> ($num_1 >= 5000.000000000001) - rewrite 'gt' comparison to range comparison: ($num_1 gt 5000) -> ($num_1 >= 5000.000000000001) - pre-evaluate unary expression to xs:integer item: -5000 - rewrite < comparison to range comparison: ($num_1 < -5000) -> ($num_1 <= -5000.000000000001) - rewrite 'lt' comparison to range comparison: ($num_1 lt -5000) -> ($num_1 <= -5000.000000000001) - inline $gt5000_2 - inline $ltMinus5000_3 - simplify or: (true()) - pre-evaluate or to xs:boolean item: (true()) -> true() - remove unused variable $num_1 - remove unused variable $t_0 - simplify FLWOR expression: true() Optimized Query: true() ---------- When the return statement is changed to "return ($num,$gt5000,$ltMinus5000,$gt5000 or $ltMinus5000)" then the result of the boolean operation (last element of the result sequence) is false, as expected. The GUI log then is: ---------- Compiling: - rewrite > comparison to range comparison: ($num_1 > 5000) -> ($num_1 >= 5000.000000000001) - rewrite 'gt' comparison to range comparison: ($num_1 gt 5000) -> ($num_1 >= 5000.000000000001) - pre-evaluate unary expression to xs:integer item: -5000 - rewrite < comparison to range comparison: ($num_1 < -5000) -> ($num_1 <= -5000.000000000001) - rewrite 'lt' comparison to range comparison: ($num_1 lt -5000) -> ($num_1 <= -5000.000000000001) Optimized Query: let $t_0 := element x { ("200.0000") } let $num_1 := number($t_0) let $gt5000_2 := ($num_1 >= 5000.000000000001) let $ltMinus5000_3 := ($num_1 <= -5000.000000000001) return ($num_1, $gt5000_2, $ltMinus5000_3, ($gt5000_2 or $ltMinus5000_3)) ---------- Am I missing something, or could this be a bug in BaseX 9.2.4? With BaseX 9.0.2, both queries (with the different return statements) returned the expected value false for the boolean operation. Best regards, Johannes

2 3

Question about WITHDB option
by France Baril 24 Oct '19

24 Oct '19

I am looking at the documentation for WITHDB and I want to ask for further explanation 'If db:open is consistently used to access documents', does it means as opposed to having a DEFAULTDB or does it mean that we use db:open but not local queries on the document obtained (example below), or since there is a notion of lock, do you mean db:open as opposed to db:add or db:replace? In short, I lack context to interpret the explanation. let $current-doc := db:open($lang)/*[@id=x] (: Query document further without db:opened :) let $avaliable-sections := $current-doc/descendant::*[name()=''section][@status !='archived'] >From the documentation: WITHDB Introduced with Version 9.3. *Signature* WITHDB *Default* true *Summary* By default, URIs specified in the fn:doc <http://docs.basex.org/wiki/Databases#XML_Documents> and fn:collection <http://docs.basex.org/wiki/Databases#XML_Documents> functions will also be resolved against existing databases. If db:open <http://docs.basex.org/wiki/Database_Module#db:open> is consistently used to access database documents, it is recommendable to disable this option: - Access to local and external resources will be faster, as the database lookup will be skipped. - No locks will be created by the two functions (see limitations of database locking <http://docs.basex.org/wiki/Transaction_Management#Limitations> for more details). -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

2 3

catalog.xml - xsd - urn
by SW-Service 22 Oct '19

22 Oct '19

Good day, Where is the catalog.xml file stored? I want to validate xml files against XSD, but the xsd is referenced via an urn. thank you very much Guten Tag, Wo wird die catalog.xml Datei abgelegt? Ich möchte xml-Dateien gegen XSD validieren, aber die XSD wird über einen urn referenziert. Herzlichen Dank <xdomea:Aussonderung.Aussonderung.0503 xmlns:xdomea="urn:xoev-de:xdomea:schema:2.3.0">

2 2

Re: [basex-talk] Backups
by Christian Grün 21 Oct '19

21 Oct '19

Hi Christoph, > db_alter() has not changed. It alters the name of the database but the corresponding backups stay unchanged. I combine it with db:drop-backup() That’s true: db:alter() will only rename databases. This has been a deliberate design choice (in analogy with db:drop, a user might want to treat backups differently than the currently active instance); but I think we should add an additional db:alter-backup function. I have just created an issue for that [1]; Thanks for the observation. > I copied the old data, restxq etc. into the new structure. > … > In both cases I lost my users. How can I upgrade without loosing them? Users are stored in the data directory in the users.xml file. Did you copy this file as well? Maybe the BaseX server was still running while you were copying the files? For databases, this shouldn’t matter (database are dynamically accessed), but the users.xml file will only be parsed at startup time. Best, Christian [1] https://github.com/BaseXdb/basex/issues/1742 On Mon, Oct 21, 2019 at 1:47 PM Christoph Gaukel <christoph.gaukel(a)gmx.de> wrote: > > Hi Christian, > > thank you for your answer. I upgraded from 9.1.2 to 9.2.4 and indeed: > > the output of db:backups('test_balance_tmp') changed from: > <backup database="test_balance_tmp" date="2019-10-18T00:05:50" size="2230">test_balance_tmp-2019-10-18-00-05-50</backup> > to: > <backup database="test_balance_tmp" date="2019-10-17T22:05:50Z" size="2230">test_balance_tmp-2019-10-18-00-05-50</backup> > > The same with db:drop(), now it deletes the database but not the backups. > > db_alter() has not changed. It alters the name of the database but the corresponding backups stay unchanged. I combine it with db:drop-backup() > > > From doing the upgrade, I got a new question. I have done two trials: > > I copied the old data, restxq etc. into the new structure. > I copied BaseX.jar and basex/lib into the old structure > > In both cases I lost my users. How can I upgrade without loosing them? > > > Thanks, > > Christoph > > Am 18.10.19 um 10:25 schrieb Christian Grün: > > Hi Christoph, > > Welcome back to the list. > > db:drop deletes both, the database and the corresponding backups > > The function should only delete database and preserve backups. For > deleting backups, db:drop-backup can be used. Maybe there was a bug in > an older version of BaseX? > > db:info($db)/resourceproperties/inputdate is a UTC dateTime with a time zone offset > db:backups($db)/@date is a local dateTime without a time zone offset > > Same here: Both returned timezones should be a UTC dateTime with the Z > time offset. > > Maybe you need to switch to the latest version of BaseX? > Feel free to give us an update if the problems persist with BaseX 9.x. > > Hope this helps, > Christian >

1 0

HTTP request
by Giuseppe G. A. Celano 18 Oct '19

18 Oct '19

Hi, I have a curl request of the kind curl --data "something" http://something <http://something/> which I would like to perform using the HTTP module, but I cannot specify the data argument in the query. Any help? The following does not work: http:send-request(<http:request method="post"></http:request>, 'http://something' , "something" ) Best, Giuseppe

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