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Memory management
by meumapple 24 Jan '17

24 Jan '17

I have 223 XML files and I need to perform some actions on each of them, so that the output should be the modified texts (223 new files). What I have noticed is that if I apply my script recursively to each file and then save the results in new files (file:write()), everything works fast. On the other hand, If I do not write out the results in new files (but I expect the results from all the files in the GUI), the GUI freezes and then runs out of memory. My question is: is there a way to get the script working well without using file:write()? Should I always apply this script strategy when I work with many files? Thanks, Joseph

2 5

basex, nfs, and local storage
by Baysdon, Joseph 24 Jan '17

24 Jan '17

My baseX database is accessed via an NFS mount, and I’d like to improve its performance by moving its re-creatable files (e.g. indices) to a local disk. For the sake of NFS backup & restore, I’d like to keep the db files which cannot be re-created on the NFS servers. Would someone please identify which db files I can move to a local disk, and which files cannot be re-created and therefore, must remain on NFS? Thanks, Joe

2 7

RestXQ returning JSON
by Marco Lettere 24 Jan '17

24 Jan '17

Hello all, this morning just stumbled into this issue and I'm wondering whether it could be somehow smoothed up ... I have the following RestXQ function: declare %rest:path("/f") %rest:GET %output:method("json") function a:f() { (:code ...:) }; 1) Replacing comment with the following code correctly returns an empty object: let $out := (<json type="object"></json>) return $out 2) Replacing comment with the following code correctly returns an expected exception (" [SERE0023] Only one item can be serialized with JSON." : let $out := (<json type="object"></json>, <json type="object"></json>) return $out 3) Replacing comment with the following code returns a somewhat less expected Null-pointer exception : let $out := (<json type="object"></json>, <json type="object"></json>) return array{$out} 4) In order to get the expected Json array I need to write the code like the following: let $out := (<json type="object"></json>, <json type="object"></json>) return array{ $out ! json:parse(json:serialize(.), map{ "format" : "map"}) } I'm not sure whether the array could be inferred from the sequence directly in a pattern like 2. But I would expect that 3) should work. Isn't it? Thanks for any explanation. Regards, Marco.

3 3

Progress monitoring of XML import
by Shaun Flynn 23 Jan '17

23 Jan '17

Hello there, I am writing an application using JavaFx 8. A facility I would like to have is a progress bar showing how the db:add command is running, similar to what the Basex GUI shows when creating a new database. Is it possible to send updates from BaseX to another application? Shaun

2 1

Losing some space entities
by France Baril 20 Jan '17

20 Jan '17

Hi, When I serialize content to HTML5, I lose some entities. xquery: adds '‍' in front of some content and outputs html html: should have '&zwj;', but doesn't. I've tried with 8204 and even the half space 8201. The only special space that seems to work is  , but it won't do for what I need right now. Code sample: *let* *$target-table* := *copy* *$copy* := *$base-table* *modify*( *for **$td* *in **$copy*//*tr*/*td*[*position*()= *$column-to-filter-by*] *let* *$new-value* := ('‍', *for **$node* *in **$td*/*node*() *return **$node*) *return replace* *value* *of* *node* *$td* *with **$new-value* ) *return **$copy* *return * *$target-table* Is there any way to solve this? -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

3 11

fn:unparsed-text fails in command line XQuery
by Gunther Rademacher 20 Jan '17

20 Jan '17

Hello list, I have a file some.xml containing <xml>hello world!</xml> and I can read it in BaseX code like this: java org.basex.BaseX "declare namespace fn='http://www.w3.org/2005/xpath-functions';fn:doc('some.xml')" However I cannot use fn:unparsed-text() from a command line, when a namespace declaration with a protocol is present. I have tried to do java org.basex.BaseX "declare namespace fn='http://www.w3.org/2005/xpath-functions';fn:unparsed-text('some.xml')" but I keep getting this: Stopped at ., 1/79: [FOUT1170] Static Base URI is undefined. This is strange, because the command works fine without the namespace declaration: java org.basex.BaseX "unparsed-text('some.xml')" What can I do to use both namespace declarations and fn:unparsed-text from within a single command line? Best regards Gunther

2 2

Access-Control-Allow-Origin
by lambert strether 18 Jan '17

18 Jan '17

Hi: This is probably an extremely newbie-ish question. I'm developing on localhost using MAMP/PHP at port 8888, and basex at port 8984. So I am running into "Cross-Origin Resource Sharing" issues, apparently, when I have the PHP server issue an XMLHttpRequest to the Basex server. I would have thought that this line in my REST GET function %rest:header-param("Access-Control-Allow-Origin", "http://localhost:8888") in my *.xqm file would have solved the problem. Instead, I'm getting this error: 400 (Stopped at /Users/shunting/basex/webapp/restxq.xqm, 395/14: [bxerr:BASX0003] Invalid path template: "http://localhost:8888".) I'm stymied because I don't see how a URL could match a path template in the first place. Is the "Access-Control-Allow-Origin" not a supported parameter? All I want to do is get my two servers on my machine to talk to each other. If this isn't the right way, is there another one? Thank you! * * * Every communication from this account is off the record, unless explicitly put on the record.

2 1

Gravierende Performance-Einbüße bei Persistierung von mehr als 5000, 160 KB große XML Datenstrukturen.
by Bularca, Lucian 18 Jan '17

18 Jan '17

Guten Tag, im Rahmen einer Performance-Evaluierung der Persistierung von XML Datenstrukturen in einer BaseX Datenbank, haben wir stetig absinkende Persistierungs-Raten umgekehrt proportional zu der Datenbank-Größe festgestellt. Dieses Verhalten ist erklährbar und wäre auch einnehmbar, wenn nicht die Dauer der Persistierung einer ~ 160 KB großen XML Datenstruktur, von Anfang ~ 10 ms auf ~ 2500 ms kommne würde, nach ~ 50.000 Persistierungs-Vorgänge. Dabei versuchen wir 100.000 unterschiedliche, ungefähr 160 KB große XML Datenstrukturen mittels der Java API in eine BaseX Datenbank zu speichern um dabei die Gesammt-Dauer bzw. die Dauer der einzelnen Persistierungs-Vorgänge zu messen. Die BaseX Datenbank wurde im HTTP Modus (basexhttp) mit -Xmx 4048m gestartert. Die oben genannte Messwerte blieben gleich, unabhängig davon, ob alle XM Datenstrukturen in eine einzige Session gespeichert wurden, oder wenn alle 500 Persistierungs-Vorgänge der Socket (DB-Anbindung) geschlossen und erneut geöffnet wurde. Eine Indizierung der Datenbank (mittels der GUI "Optimize All", bzw. "Create Text Index") zwischendurch konnte die Persistierungs-Raten nicht beeinflussen bzw. optimieren. Ein Beispiel der Test-Klassen (nur exemplarisch, nicht kompilierbar !) die wir dazu benutzt haben, sind im Anhang BaseXClient.java.zip zu dieser E-Mail zu finden. Sind generell, Persistierungs-Raten von mehr als 160 KB / 2500 ms bei mehr als 30.000 vorhandene Einträge in der BaseX zu erwarten, oder können wir diese Persistierungs-Zeiten drastisch optimieren (und wenn ja, wie)? Mit freundlichen Grüßen, Lucian Bularca

4 11

How to optimally and reliably go about sequentially applying updates with long running transactions?
by Mustard Seed 14 Jan '17

14 Jan '17

I'm new to BaseX and XQuery, so I apologize if there's some glaring thing I've missed. What I have are three updating functions that I'm wanting to have executed sequentially, successfully, to BaseX. When I simply place them in my RestXQ function, delimited by commas, they all execute, but since at times certain ones take longer than others, and since their results can overwrite/negate the results of each other, I can't manage to get them to consistently execute in the same order. It seems to me that since it seemingly is running in parallel that whatever happens to end last determines what my final state is. I imagine there's got to be some blatantly obvious way to do this, but I'm just not finding it, I went through the BaseX manual a second time and have searched every possible combination of things I can think of to try and figure out a way around this. One function does a mass delete of all dbs with a given prefix, another repopulates from a sql query, and a third updates the repopulated dbs based on yet another sql query. That's the order I want it to execute in, I'm just about at my wits end trying to figure out how to do this. I was even getting into trying to pull off a hackish attempt at making jobs which I'd schedule based on a rough guess of the longest expected execution times for the functions. But even that wasn't working. Any help will be greatly appreciated as insuring the order of execution is rather vital for the overall project I'm trying to do, so I need to not only find a solution for the present use case, but I need to understand how to insure such for any future composite functions. Thanks, --Nicolai

2 2

format-number rounding
by George Sofianos 14 Jan '17

14 Jan '17

Hi there, I was wondering if there is a similar function to format-number, but without rounding, so I don't have to create a custom one that involves string manipulation. For example I have two values: let $x := <value>15.224134</value> let $y := <value>15.2249348734</value> The following command will create different output for the two values (result for $x will be 15.224, result for $y will be 15.225) format-number(xs:decimal($x), "0.000")) Thanks, George

2 1

Speeding up fn:id()
by Sebastian Zimmer 12 Jan '17

12 Jan '17

Hi all, I am surprised that fn:id() does take quite a long time in contrast to (almost) equivalent XPaths. An example: > XQUERY collection('zk/')//id('zkI_108-5_R') <div xmlns="http://www.tei-c.org/ns/1.0" xml:id="zkI_108-5_R"> ... </div> Query executed in 5956.43 ms. > XQUERY collection('zk/')//*[@xml:id='zkI_108-5_R'] <div xmlns="http://www.tei-c.org/ns/1.0" xml:id="zkI_108-5_R"> ... </div> Query executed in 9.43 ms. Couldn't the first XQuery be optimized into the second? If not, maybe an xml:id index would be a good feature. eXist-db does have one, particularly dedicated to speed up fn:id() [1]. Best regards, Sebastian Zimmer [1] http://exist-db.org/exist/apps/doc/indexing.xml -- <---------- Sebastian Zimmer sebastian.zimmer(a)uni-koeln.de Cologne Center for eHumanities (CCeH) - Universität zu Köln - http://www.cceh.uni-koeln.de ------------------------------------>

2 1

BaseX
by Hans-Juergen Rennau 11 Jan '17

11 Jan '17

Dear BaseX team - no bug, no question, no feature request - only the urge to thank you for your work. About a year ago I embarked on a piece of research work which has kept me busy and excited ever since. This work is important to me because so much seems to go into it, of what I have come to think and be convinced of in the course of several years. At every step, BaseX has been my tool to turn ideas into reality. It has not failed me once, in spite of heavy use of advanced features like function items and partial function invocations. And several times I was so glad to find that BaseX offered exactly the extensions I needed. I think BaseX has achieved an admirable combination of standard conformance and reliability, on the one hand, and bold and generous extension on the other hand. So, summing up - thank you very much. Hans-Jürgen Rennau

1 0

fn:doc weirdness with imported files
by Marc van Grootel 11 Jan '17

11 Jan '17

Hi all, Happy new year btw! I got bitten by something and can't explain this behaviour. So the situation is that I have an XML file on the file system in F:/tmp/foo.xml I also have this file imported into a database named "foo" (and the path "/foo.xml". Now in the GUI (and on 8.5.3) I have the following. When I have the database closed in the GUI base-uri(doc('F:/tmp/foo.xml')) => file:///F:/tmp/foo.xml And when I open the database "foo" from the GUI base-uri(doc('F:/tmp/foo.xml')) => /foo/foo.xml Is that right? Also db:* functions also get a database node from the latter and return a node-id for example. When the foo.xml is moved to another filesystem directory then this doesn't happen so it appears as if this happens only when I try to read the file from the original import location. Shouldn't these two situations have the same result? Cheers, --Marc

2 4

Async unit testing
by Andy Bunce 05 Jan '17

05 Jan '17

Hi, Around version 7.8 there was a function that allowed unit tests to be invoked from XQuery: unit:test-uris($uris as xs:string*) as element(testsuites) Later this was removed, but ability to run updating tests was added. Which was great. I wonder how easy it would be, using the jobs module, to implement a function as below? jobs:test-uris($uris as xs:string*, $options as map(xs:string, xs:string)) as xs:string Asynchronously runs all functions in the specified modules that have unit annotations.A test report is generated and optionally cached, which resembles the format returned by other xUnit testing frameworks, such as the Maven Surefire Plugin. returns a job id /Andy

2 4

XML Prague Meeting... Postponed
by Christian Grün 04 Jan '17

04 Jan '17

Dear all, This year, there will be no BaseX Preconference Meeting in XML Prague. Sorry for that! The reason is simple: We were too busy in order to prepare ourselves for the event, look for speakers, etc. At least we are happy to announce that BaseX 8.6 will finally be released this month. Stay tuned! All the best, Christian

2 1

archive:entries - no representation of empty folders
by Hans-Juergen Rennau 03 Jan '17

03 Jan '17

Dear BaseX team, a question concerning the reading of archive files (e.g. .zip) via archive:entries. If I don't overlook something, the read function archive:entries returns one <archive:entry> per file contained in the archive. Folders containing files (directly or recursively) can be inferred, but empty folders cannot be inferred, and therefore it is not possibly to extract the contents of archives in a reliably complete way: any empty folders are ignored. Is that correct? If so, are there plans to add support for the retrieval of empty folders? Personally, I think the ability to unpack archives completely is important, for example because subsequent operations may fail in the absence of the expected folder. One conceivable solution would be to return for each empty folder an entry with an additional attribute: <archive:entry isFolder="true" .../>. Cheers,Hans-Jürgen

1 0

converting xq to java classes
by Tushar Deshmukh 03 Jan '17

03 Jan '17

Namaste, I have a xq files which is working well. But now I want to convert it to java class. Is there any easy way to do so ? Please help. Regards, Tushar Deshmukh

2 1

Images
by meumapple 03 Jan '17

03 Jan '17

Hi All, Is there a way to access images in BaseX as sequences of pixels? Thanks. Joseph

3 4

Namespaces in element constructors
by Bridger Dyson-Smith 02 Jan '17

02 Jan '17

Hi all - I think that I weak grasp of the practical requirements, but I'm unable to find a reference in the spec to clarify what's happening in the following: I have a constructor: return( for $item in $file-list let $item-less := replace($item, '^\d{1,}-', '') (: returns "missing" supplemental files :) where ($item-less[(not(. = ($files-titles, $excludes)))]) or ($item-less[(. = $files-titles)]) return( <relatedItem> <title>{$item-less}</title> <mimeType> {if ($item-less = $files-titles) then ($content/files/file/name[. = $item-less]/following-sibling::mimetype/text()) else (fetch:content-type(concat(file:parent(document-uri($doc)),$item)))} </mimeType> <uri>{file:parent(document-uri($doc))}</uri> </relatedItem> ) ) and it works fine so long at the <relatedItem> is not namespaced. As soon as the <relatedItem> is namespaced; e.g. <relatedItem xmlns=" http://bridger.net">, then I need to use the following XPath in the `then` keyword: ($content/*:files/*:file/*:name[. = $item-less]/following-sibling::*:mimetype/text()) The input documents (in the SSCCE, under sample-data/*/metadata.xml) are not in a namespace. Would someone mind providing some context for the "why" here? I've been looking through Priscilla Walmsley's 2nd edition, and the specification, but haven't been able to find an answer. I'm almost certainly looking for the wrong thing(s). Any help will be greatly appreciated! Thank you in advance. Best, Bridger

2 3

Schema Validation issues
by George Sofianos 02 Jan '17

02 Jan '17

Because of issues with schema validation (can't properly use doc() in the validate function - see https://github.com/BaseXdb/basex/issues/1324), I'm not using BaseX to do schema validation in my workflow. But I needed it today to make some result comparisons with my own implementation of XML Validator, and I noticed that using the beta Xerces version which is documented in the wiki <http://docs.basex.org/wiki/Validation_Module#XML_Schema_Validation> can make it crash, so I thought I should report it here. Other than that, I noticed one some XML files that it only reports fatal errors, and hides any other non-fatal error. I think it has something to do with the process <https://github.com/BaseXdb/basex/blob/86a12cf0c75010b3058c18f81c4689bc511b7…> method but I'm not sure.

2 1

TagSoup and html5 support
by Alexander Shpack 21 Dec '16

21 Dec '16

Hi team! As you know, TagSoup 1.2.1 doesn't support correct HTML5 tag nesting. For example, this string <b><p>Test</p></b> will be parsed as <b/><p><b></b></p><b/> But html5 code <b><aside>Test</aside></b> will be parsed as is. How to implement in BaseX the html5 support? I've found this project, but not sure that it's possible to add it into basex code https://github.com/UniversityofWarwick/tagsoup-html5 Thanks!

3 9

How to save Table views as spreadsheet
by kalamegham＠gmail.com 21 Dec '16

21 Dec '16

I am new to BaseX which I find as a powerful tool to work on xml data. The BaseX GUI is great. My question is: how can I save the Tables in the visualization as spreadsheet(s). I understand there are multiple views but it should be possible to save them as separate tables or tabs in a single spreadsheet. I apologize if this has been addresses in an earlier talk. I would like to know if there is a way to quickly search the base-talk archives without having to look through them all (arranged by month). Thanks! -R. Kalamegham

4 3

Understanding the WRITEBACK option, help
by Enea Parimbelli 20 Dec '16

20 Dec '16

Dear BaseX folks, I'm having trouble understanding the subtleties of the WRITEBACK option. I found this issue report that seems to describe my case as well but it refers to a rather old baseX version. https://github.com/BaseXdb/basex/issues/848 As I understand it the WRITEBACK option will only work for files directly read from disk and not for those that have been added to a database at time of creation. I have created my database with a input path that already held all the xmls I needed to import: Resource Properties Input Path: /home/enea/tmp/AF PHR extraction ALL DATA Input Size: 74 MB Timestamp: 2016-12-19T08:45:34.841Z Encoding: UTF-8 CHOP: true Does the above still apply to baseX 8.2.3? If the issue has been addressed can you describe how the current implementation works? Is the only workaround to this explicitly calling EXPORT after all the update/insertion/deletion queries to see the modifications reflected in the original files on disk? Thanks for your help, Enea -- *Enea Parimbelli, Ph.D.* Post-doc research fellow | Biomedical informatics lab "Mario Stefanelli" Department of Electrical, Computer and Biomedical Engineering University of Pavia Via Ferrata 5, 27100, Pavia (Italy)

2 2

Waiting for BaseX 8.6?
by Christian Grün 19 Dec '16

19 Dec '16

Hi everyone, I know some of you are waiting for BaseX 8.6, and I promised to make it happen until end of this year. I am afraid we won’t make it in time, but you can definitely expect the new version in January! Until then, as usual, we are looking forward to your feedback on our latest snapshot [1]. All the best, Christian [1] http://files.basex.org/releases/latest/

1 0

BaseX Client for PL/SQL
by Zachary N. Dean 06 Dec '16

06 Dec '16

Hi all, I've seen that quite a few people use BaseX to pull data from RDBMS's. I've started a project (https://github.com/zadean/pl-sql-BaseX) that goes the other direction. Using DB sessions as BaseX client sessions. It's currently only for Oracle (maybe postgres would work with only minor changes?) (other DB's to come. maybe :) ) . Some things just aren't that nice to do in the DB, and the XQuery processors in the DB do their own thing. So, this seemed like a nice way to get the benefits of BaseX from within the DB itself. Hope it comes in handy! Happy coding, Zachary Dean

2 1

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