I guess you'll simply have to use file:write-text instead of
file:write (which serializes texts with the default XML output method
[1]).

[1] http://www.w3.org/TR/xslt-xquery-serialization-31/

On Wed, Oct 28, 2015 at 5:42 PM, Ron Katriel <rkatriel@mdsol.com> wrote:
> Hi Christian,
>
> You can use the attached XML file to populate a database. I verified that it
> is sufficient to replicate the issue.
>
> Thanks,
> Ron
>
>
> On October 28, 2015 at 12:33:14 PM, Christian Grün
> (christian.gruen@gmail.com) wrote:
>
> Hi Ron,
>
> I don't have the CTGov database on my machine… Could you build us a
> little self-contained example?
>
> Thanks in advance,
> Christian
>
>
> On Wed, Oct 28, 2015 at 5:31 PM, Ron Katriel <rkatriel@mdsol.com> wrote:
>> Hi,
>>
>> When serializing XML to CSV, special characters (e.g., &) are not
>> converted to their textual representations (e.g., ‘&’).
>>
>> For example, the code below outputs
>>
>> conditionid nctid condition
>> 1 NCT00130377 Cardiovascular System Diseases (& [Cardiac])
>>
>> vs. the expected
>>
>> conditionid nctid condition
>> 1 NCT00130377 Cardiovascular System Diseases (& [Cardiac])
>>
>> This seems like a bug. Am I missing an option? I did not see anything
>> related in the documentation.
>>
>> Thanks,
>> Ron
>>
>>
>> let $options := map { 'lax': false(), 'quotes' : false(), 'separator' :
>> 'tab', 'header' : true() }
>>
>> return file:write('conditions.tsv',
>> csv:serialize(
>> <matches> {
>> for $article in db:open('CTGov')/clinical_study
>> where $article//nct_id = 'NCT00130377'
>> for $condition in $article/condition
>> count $c
>> return
>> <match>
>> <conditionid> { $c } </conditionid>,
>> <nctid> { normalize-space($article/id_info/nct_id/text()) }
>> </nctid>,
>> <condition> { normalize-space($condition/text()) } </condition>
>> </match> }
>> </matches>,
>> $options)
>> )
>>
>>