How to optimize xquery expression ?

Question

hi,
i got berkeley db xml database with containers: dicom.dbxml and instancemetadata.dbxml.
dicom.dbxml contains documents as follow:
<?xml version="1.0" encoding="UTF-8"?>
<instance docid="dicom_1009">
     <dicom_item>
          <dicom_header>
               <dicom_tag group="0002" element="0000" vr="UL">194</dicom_tag>
               <dicom_tag group="0002" element="0001" vr="OB"/>
               <dicom_tag group="0002" element="0002" vr="UI">1.2.840.10008.5.1.4.1.1.2</dicom_tag>
               <dicom_tag group="0002" element="0003" vr="UI">2.16.840.1.113662.2.1.4519.41582.4105152.419990505.410523251</dicom_tag>
               <dicom_tag group="0002" element="0010" vr="UI">1.2.840.10008.1.2.1</dicom_tag>
               <dicom_tag group="0002" element="0012" vr="UI">2.16.840.1.113662.2.1.1</dicom_tag>
               <dicom_tag group="0002" element="0016" vr="AE">PHOENIXSCP</dicom_tag>
          </dicom_header>
          <dicom_body>
               <dicom_tag group="0008" element="0000" vr="UL">596</dicom_tag>
               <dicom_tag group="0008" element="0005" vr="CS">ISO_IR 100</dicom_tag>
               <dicom_tag group="0008" element="0008" vr="CS">ORIGINAL\PRIMARY\AXIAL</dicom_tag>
               <dicom_tag group="0008" element="0012" vr="DA">1999.05.05</dicom_tag>
               <dicom_tag group="0008" element="0013" vr="TM">10:52:34.530000</dicom_tag>
               <dicom_tag group="0008" element="0016" vr="UI">1.2.840.10008.5.1.4.1.1.2</dicom_tag>
               <dicom_tag group="0008" element="0018" vr="UI">2.16.840.1.113662.2.1.4519.41582.4105152.419990505.410523251</dicom_tag>
               <dicom_tag group="0008" element="0020" vr="DA">1999.05.05</dicom_tag>
               <dicom_tag group="0008" element="0021" vr="DA">1999.05.05</dicom_tag>
               <dicom_tag group="0008" element="0022" vr="DA">1999.05.05</dicom_tag>
               <dicom_tag group="0008" element="0023" vr="DA">1999.05.05</dicom_tag>
               <dicom_tag group="0008" element="0030" vr="TM">10:52:34.530000</dicom_tag>
               <dicom_tag group="0008" element="0031" vr="TM">10:52:34.530000</dicom_tag>
               <dicom_tag group="0008" element="0032" vr="TM">10:52:34.530000</dicom_tag>
               <dicom_tag group="0008" element="0033" vr="TM">10:52:32.510000</dicom_tag>
               <dicom_tag group="0008" element="0060" vr="CS">CTTR</dicom_tag>
          </dicom_body>
     </dicom_item>
</instance>
instancemetadata.dbxml contains documents as follow:
<?xml version="1.0" encoding="UTF-8"?>
<instancemetadata xmlns="imuba.med" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="imuba.med Instancemetadata.xsd">
          <name/>
          <notes/>
          <id>instancemetadata_1</id>
          <instanceid>dicom_1</instanceid>
          <createusername>dd</createusername>
          <createdate>Tue May 02 21:08:06 CEST 2006</createdate>
          <lastmodusername>dd</lastmodusername>
          <lastmoddate>Tue May 02 21:08:06 CEST 2006</lastmoddate>
     </instancemetadata>
and i got XQuery expression:
declare namespace n = "imuba.med";
declare variable $insCont external;
for $ins in collection(concat(concat("dbxml:containers/", string($insCont)),".dbxml"))/instance,
     $met in collection("dbxml:containers/instancemetadata.dbxml")/n:instancemetadata
where
$ins/dicom_item/dicom_body/dicom_tag[@group='0008' and @element='0060'] = "CTTR" and
$ins/@docid = $met/n:instanceid
return
<row>
{ $ins/@docid }
{ $met/n:name }
{ $met/n:notes }
{ $met/n:id }
{ $met/n:instanceid }
     { $met/n:createusername }
{ $met/n:createdate }
{ $met/n:lastmodusername }
{ $met/n:lastmoddate }
</row>
while i got 5000 documents in dicom container, the xquery execution time is close to 10 secs. i've tried to create indices using commands:
                    XmlIndexSpecification is = xcDicom.getIndexSpecification();
                    is.addIndex("", "docid", "unique-node-attribute-equality-string");
and
                    XmlIndexSpecification iss = xcIns.getIndexSpecification();
                    iss.addIndex("imuba.med", "instanceid", "unique-node-element-equality-string");
And then the execution time is nearly about 7-8 sec, but it's still big (the database contains only 5000 documents).
Have you any idea how to optimize it ? I suppose the index on element i'm using in the WHERE clause would be helpful (dicom_item/dicom_body/dicom_tag[@group='0008' and @element='0060']). Well, i haven't found concept how to add index on element which can be shown using xpath expression.
thanks for any help
Darek

Answer 1

Hi Darek,
First off, why not try adding these indexes to see what happens:
is.addIndex("", "dicom_tag", "node-element-equality-string");
is.addIndex("", "group", "node-attribute-equality-string");
is.addIndex("", "element", "node-attribute-equality-string");
Secondly, what storage model are you using? I would expect you to get better query times using a NodeContainer, with the DBXML_INDEX_NODES flag enabled.
Thirdly, your "instance" document is not very "XML" like, so you will struggle to get very good query times using that format. If you have control over the format of the document, I would suggest incorporating one or more of the "group", "element", and "vr" attributes into the name of the element - so that you will get multiple elements with different names, instead of one element name with multiple permutations of attributes. Selecting an element by name will always be faster than selecting it by some kind of value.
Let me know how you get on with these suggestions,
John