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Xquery returns 'Out of Main Memory'
by DAIANE ROBERTA CANDIDA 03 Feb '14

03 Feb '14

Hello, The query below returns 'Out of Main Memory': XQUERY collection("/home/arwen/daiane_oracle/loading_inex2009/xml_pages/")//article[.//text() contains text "Nobel" ftand "prize"] I am using basexclient. I have a collection of xml files that have 14GB size. -------------------------------------------------------------------- > LIST name Resources Size Input Path ---------------------------------------------------------------------- bd_inex2009 730283 16263937902 --------------------------------------------------------------------- I dumped those files by the commands below: ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles1/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles2/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles3/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles4/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles5/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles6/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles7/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles8/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles9/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles10/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles11/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles12/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles13/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles14/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles15/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles16/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles17/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles18/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles19/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles20/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles21/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles22/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles23/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles24/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles25/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles26/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles27/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles28/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles29/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles30/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles31/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles32/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles33/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles34/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles35/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles36/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles37/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles38/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles39/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles40/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles41/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles42/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles43/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles44/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles45/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles46/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles47/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles48/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles49/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles50/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles51/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles52/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles53/; ADD /home/arwen/daiane_oracle/loading_inex2009/xml_pages/xmlfiles54/; ---------------------------------------------------------------------------------------- The command INFO returns: INFO General Information Version: 7.7.2 Used Memory: 79 MB Main Options DBPATH: /home/arwen/BaseXData DEBUG: false EVENTPORT: 1985 GLOBALLOCK: false HOST: localhost HTTPLOCAL: false KEEPALIVE: 0 LANG: English LANGKEYS: false LOG: true LOGMSGMAXLEN: 1000 NONPROXYHOSTS: PARALLEL: 8 PASSWORD: PORT: 1984 PROXYHOST: PROXYPORT: 80 REPOPATH: /home/arwen/BaseXRepo RESTXQPATH: SERVERHOST: SERVERPORT: 1984 STOPPORT: 8985 TIMEOUT: 0 USER: WEBPATH: /home/arwen/BaseXWeb Options ADDARCHIVES: true ADDCACHE: false ADDRAW: false ATTRINDEX: true AUTOFLUSH: true BINDINGS: CACHEQUERY: false CASESENS: false CATFILE: CHECKSTRINGS: true CHOP: true COMPPLAN: true CREATEFILTER: *.xml CREATEONLY: false DIACRITICS: false DOTCOMPACT: false DOTDISPLAY: true DOTPLAN: false DOTTY: dotty DTD: false EXPORTER: FORCECREATE: false FTINDEX: false FTINDEXSPLITSIZE: 0 HTMLOPT: html=false,omit-xml-declaration=false,method=xml,nons=false,nobogons=false,nodefaults=false,nocolons=false,norestart=false,ignorable=false,emptybogons=false,any=false,norootbogons=false,nocdata=false,lexical=false,encoding=utf-8 INDEXSPLITSIZE: 0 INLINELIMIT: 0 INTPARSE: true LANGUAGE: en LSERROR: 0 MAINMEM: false MAXCATS: 100 MAXHITS: -1 MAXLEN: 96 MAXSTAT: 30 PARSER: xml PARSEROPT: encoding=UTF-8,flat=false,header=false,jsonml=false,lines=true,separator=comma QUERYINFO: false QUERYPATH: RUNS: 1 SERIALIZE: true SERIALIZER: SKIPCORRUPT: false STEMMING: false STOPWORDS: STRIPNS: false TAILCALLS: 256 TEXTINDEX: true UPDINDEX: false WRITEBACK: false XMLPLAN: false XQUERY3: true ----------------------------------------------------------- How can I run XQuery in that collection? Regards, Daiane

2 1

XML DOCTYPE Problem
by Martin Reckziegel 03 Feb '14

03 Feb '14

Hello everybody, i'm using basex 7.7.2 in a university based project. I'm trying to store TEI XML files in the database but there is an error storing certain valid files. Using a rest PUT request to store a file starting like this: <?xml version="1.0"?> <!DOCTYPE TEI.2 PUBLIC "-//TEI P4//DTD Main DTD Driver File//EN" "http://www.tei-c.org/Guidelines/DTD/tei2.dtd" [ <!ENTITY % TEI.XML "INCLUDE"> <!ENTITY % PersProse PUBLIC "-//Perseus P4//DTD Perseus Prose//EN" "http://www.perseus.tufts.edu/DTD/1.0/PersProse.dtd" > %PersProse; ]> <TEI.2> <teiHeader type="text" status="new"> .... results in this error: > "tlg0003.xml.xml" (Line 5): ']' expected, '<' found. (Line 5 is %PersProse;) I have no clue how to interpret the error since non of the mention characters are in that line. Maybe this is resulting in some internal replacement? Anyway deleting line 5 resolves the error (but of course does not solve my problem since i don't want to alter the files) The problematic files are all valid, at least according to http://www.validome.org/xml/validate/ and http://validator.w3.org/check so i wonder why they are rejected by basex? kind regards, Martin Reckziegel

2 10

Comparision of basex with other xml databases.
by Shalin Makhija 03 Feb '14

03 Feb '14

Hello, I am a newbie to using XML- databases. I am working on "SEMANTIC SEARCH ENGINE" on java that uses a parser to parse the input and generates output in xml. I need to use a xml database for storing all those xml files and fire xpath/xqueries to retrieve my result from java clients. My dilemma is which one to use between BASE-X and EXIST-DB. Both have their own selling points. A W3C test summary reads using base-x is efficient. I will be highly obliged to you if you can give some more concrete points that insist on using base-x so that I can make a fair decision. Thanx in advance. -- *-Regards* *Shalin Makhija*

2 1

function idref() and one-to-many
by Tsvetanka Georgieva-Trifonova 02 Feb '14

02 Feb '14

Hi BaseX, My question is about function idref(). How it should be applied in case of one-to-many relationships? For example: <root> <a id = "a1" idref = "b1"> aaa1</a> <a id = "a2" idef = "b1">aaa2</a> <a id = "a3" idef= "b2"> aaa3</a> bb1 bb2 </root> The expression: idref("a3")/.. gives the following result: bb2 But the expression: idref("a1")/.. does not give any result. Thanks & regards, Tsvetanka

2 1

Introspection bug in BaseX7.8 beta 4cfa54c ?
by jean-marc Mercier 01 Feb '14

01 Feb '14

Hello, As bug https://github.com/BaseXdb/basex/issues/839 has been closed, I tried to upgrade from BaseX7.8 6aeaebf to BaseX beta_4cfa54c. Unfortunately, this bug still appears in 4cfa54c, and I rolled back again to beta 6aeaebf . Did I misunderstoog something ? Cheers

2 8

Make external variable declarations mandatory #833
by jean-marc Mercier 01 Feb '14

01 Feb '14

Hi, I am extensively using a function wrapping xquery:eval. My use case is roughly the following : declare function local:eval_helper($exp, $args){xquery:eval('$xml'||$exp,map{'$xml' := $args})}; declare variable $test := <toto><tata>1</tata></toto>; local:eval_helper3('//tata', $test) Since the following correction : [1] https://github.com/BaseXdb/basex/issues/833, the previous code raises now a [XPST0008] Undefined variable $xml. I have tried several combinations to find a workaround, none are working : - declare function local:eval_helper($exp, $args){xquery:eval(''||$exp,map{'' := $args})}; ([XPDY0050] Root of the context item must be a document node.). - declare function local:eval_helper($exp, $args){xquery:evaluate($arg||$exp)}; [XPTY0019] Steps within a path expression must yield nodes; xs:integer found. -- declare variable $xml external := "xml", : [XPST0008] Undefined variable $xml. What is the correct workaround ? Cheers Jean-Marc

3 4

Searching text using wildcards options
by John Best 31 Jan '14

31 Jan '14

Hi team, For the following query, using wildcards option, I am getting result as last 2 <a> nodes, but I am expecting the first 2 <a> nodes. !! let $a := <A> <a>Famu.</a> <a>Famu.Don</a> <a>FamuDon</a> <a>FamuDon.</a> </A> for $x in $a//a[text() contains text 'Famu..*' using wildcards] return $x Whats wrong? -- Have a nice day JBest

2 1

FW: How do I increase Java's heap size with the flag -Xmx<size>?
by DAIANE ROBERTA CANDIDA 31 Jan '14

31 Jan '14

Hello Dirk, You were right about the command used to increase Java's heap size, but my loading files don't work yet. The server has memory 988g When I put 500g in the option -Xmx it raised the error below: Error occurred during initialization of VM Unable to allocate bit map for parallel garbage collection for the requested heap size. Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. So I decreased it from 500 to 350 then the following error appears Out of Main Memory. You can try to: - increase Java's heap size with the flag -Xmx<size> - deactivate the text and attribute indexes. I already deactivated the indexes FTINDEX: OFF TEXTINDEX: OFF ATTRINDEX: OFF What should I do to import data into the basex? Regards, Daiane.

2 1

Use of attribute index
by Robert schlichtner 31 Jan '14

31 Jan '14

Hello, I found that a number of similar queries have quite different performance: xquery doc('mcev_temp_5/20140130_11_55_40.xml')//column[@name='KLV_m1_rdr']/v takes only 0.68ms, which is great. But xquery doc('mcev_temp_5/20140130_11_55_40.xml')//column[@name='KLV_m1_rdr']/v[1] takes 1479.81ms. If I change this to the equivalent (for my data) xquery (doc('mcev_temp_5/20140130_11_55_40.xml')//column[@name='KLV_m1_rdr'])/v[1] it runs fast again (0.53ms) Checking the query execution plan I found that only query 1 and 3 utilize the attribute index. I find this rather surprising, and I would like to ask if there is some general reason/rule why the second can not use the index, so I can avoid such 'bad' queries in the future. Thanks! (I am using BaseX 7.7.2 on Windows XP.) Regards, Robert

2 2

html and css
by Lars Johnsen 31 Jan '14

31 Jan '14

When running BaseX http-server, I wondered where resources like javascript and css should be located. The .xqm-file for the welcome RESTXQ module seems to fetch its svg and css from a static directory under webapp. However, when sending HTML code from within a home made query, it won't connect to any css neither within webapp nor webapp/static, nor even with an absolute path. Best Lars G Johnsen National Library of Norway

2 1