Thanks Martin. Below is the modified query with the namespace specification and usage. It works but is cumbersome.

Is there a way simpler way around this - other than modifying the input header to remove the namespace declaration?

declare namespace xs="http://www.drugbank.ca";

for $drug in db:open('DrugBankFail')/xs:drugbank/xs:drug

where not(empty($drug/xs:atc-codes/xs:atc-code))

return <drug> {

<ATC5> { string-join(distinct-values($drug/xs:name), ' | ') } </ATC5>,

<ATC4> { string-join(distinct-values(for $level in $drug/xs:atc-codes/xs:atc-code/xs:level return if (fn:string-length($level/@code) = 5) then $level/text() else ()), ' | ') } </ATC4>,

<ATC3> { string-join(distinct-values(for $level in $drug/xs:atc-codes/xs:atc-code/xs:level return if (fn:string-length($level/@code) = 4) then $level/text() else ()), ' | ') } </ATC3>,

<ATC2> { string-join(distinct-values(for $level in $drug/xs:atc-codes/xs:atc-code/xs:level return if (fn:string-length($level/@code) = 3) then $level/text() else ()), ' | ') } </ATC2>,

<ATC1> { string-join(distinct-values(for $level in $drug/xs:atc-codes/xs:atc-code/xs:level return if (fn:string-length($level/@code) = 1) then $level/text() else ()), ' | ') } </ATC1>

} </drug>

On 01.09.2017 18:03, Ron Katriel wrote:

> The attached 4 files that should let you reproduce the issue. The XML
> files are the minimal imports (fail, work) and the XQ files are the
> queries (fail, work). Below is the output from the query that works. The
> one that fails returns nothing.

It appears to be the usual problem of dealing with a default namespace
in the input XML, your path drugbank/drug would select elements in no
namespace unless you set up a default element namespace (which however
with XQuery would also change the namespace of the result elements) or
declare a prefix in your query for the input XML namespace and use that
or as a third option use a wildcard *:drugbank/*:drug.