bash - Import XML files to PostgreSQL

Question

I do have a lot of XML files I would like to import in the table xml_data:

create table xml_data(result xml);

To do this I have a simple bash script with loop:

#!/bin/sh
FILES=/folder/with/xml/files/*.xml
for f in $FILES
do
  psql psql -d mydb -h myhost -U usr -c 'copy xml_data from $f '
done

However this will try to import each line of every file as separate row. This leads to error:

ERROR:  invalid XML content
CONTEXT:  COPY address_results, line 1, column result: "<?xml version="1.0" encoding="UTF-8"?>"

I understand why it fails, but cannot figure out how to make copy to import the whole file at once into single row.

Answer 1

Necromancing: For those that need a working example:

DO $$
   DECLARE myxml xml;
BEGIN

myxml := XMLPARSE(DOCUMENT convert_from(pg_read_binary_file('MyData.xml'), 'UTF8'));

DROP TABLE IF EXISTS mytable;
CREATE TEMP TABLE mytable AS 

SELECT 
     (xpath('//ID/text()', x))[1]::text AS id
    ,(xpath('//Name/text()', x))[1]::text AS Name 
    ,(xpath('//RFC/text()', x))[1]::text AS RFC
    ,(xpath('//Text/text()', x))[1]::text AS Text
    ,(xpath('//Desc/text()', x))[1]::text AS Desc
FROM unnest(xpath('//record', myxml)) x
;

END$$;


SELECT * FROM mytable;

Or with less noise

SELECT 
     (xpath('//ID/text()', myTempTable.myXmlColumn))[1]::text AS id
    ,(xpath('//Name/text()', myTempTable.myXmlColumn))[1]::text AS Name 
    ,(xpath('//RFC/text()', myTempTable.myXmlColumn))[1]::text AS RFC
    ,(xpath('//Text/text()', myTempTable.myXmlColumn))[1]::text AS Text
    ,(xpath('//Desc/text()', myTempTable.myXmlColumn))[1]::text AS Desc
    ,myTempTable.myXmlColumn as myXmlElement
FROM unnest(
    xpath
    (    '//record'
        ,XMLPARSE(DOCUMENT convert_from(pg_read_binary_file('MyData.xml'), 'UTF8'))
    )
) AS myTempTable(myXmlColumn)
;

With this example XML file (MyData.xml):

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<data-set>
    <record>
        <ID>1</ID>
        <Name>A</Name>
        <RFC>RFC 1035[1]</RFC>
        <Text>Address record</Text>
        <Desc>Returns a 32-bit?IPv4?address, most commonly used to map?hostnames?to an IP address of the host, but it is also used for?DNSBLs, storing?subnet masks?in?RFC 1101, etc.</Desc>
    </record>
    <record>
        <ID>2</ID>
        <Name>NS</Name>
        <RFC>RFC 1035[1]</RFC>
        <Text>Name server record</Text>
        <Desc>Delegates a?DNS zone?to use the given?authoritative name servers</Desc>
    </record>
</data-set>

Note:
MyData.xml needs to be in the PG_Data directory (the parent-directory of the pg_stat directory).
e.g. /var/lib/postgresql/9.3/main/MyData.xml
This requires PostGreSQL 9.1+

Overall, you can achive it fileless, like this:

SELECT 
     (xpath('//ID/text()', myTempTable.myXmlColumn))[1]::text AS id
    ,(xpath('//Name/text()', myTempTable.myXmlColumn))[1]::text AS Name 
    ,(xpath('//RFC/text()', myTempTable.myXmlColumn))[1]::text AS RFC
    ,(xpath('//Text/text()', myTempTable.myXmlColumn))[1]::text AS Text
    ,(xpath('//Desc/text()', myTempTable.myXmlColumn))[1]::text AS Desc
    ,myTempTable.myXmlColumn as myXmlElement 
    -- Source: https://en.wikipedia.org/wiki/List_of_DNS_record_types
FROM unnest(xpath('//record', 
 CAST('<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<data-set>
    <record>
        <ID>1</ID>
        <Name>A</Name>
        <RFC>RFC 1035[1]</RFC>
        <Text>Address record</Text>
        <Desc>Returns a 32-bit IPv4 address, most commonly used to map hostnames to an IP address of the host, but it is also used for DNSBLs, storing subnet masks in RFC 1101, etc.</Desc>
    </record>
    <record>
        <ID>2</ID>
        <Name>NS</Name>
        <RFC>RFC 1035[1]</RFC>
        <Text>Name server record</Text>
        <Desc>Delegates a DNS zone to use the given authoritative name servers</Desc>
    </record>
</data-set>
' AS xml)   
)) AS myTempTable(myXmlColumn)
;

Note that unlike in MS-SQL, xpath text() returns NULL on a NULL value, and not an empty string.
If for whatever reason you need to explicitly check for the existence of NULL, you can use [not(@xsi:nil="true")], to which you need to pass an array of namespaces, because otherwise, you get an error (however, you can omit all namespaces but xsi).

SELECT 
     (xpath('//xmlEncodeTest[1]/text()', myTempTable.myXmlColumn))[1]::text AS c1

    ,(
    xpath('//xmlEncodeTest[1][not(@xsi:nil="true")]/text()', myTempTable.myXmlColumn
    ,
    ARRAY[
        -- ARRAY['xmlns','http://www.w3.org/1999/xhtml'], -- defaultns
        ARRAY['xsi','http://www.w3.org/2001/XMLSchema-instance'],
        ARRAY['xsd','http://www.w3.org/2001/XMLSchema'],        
        ARRAY['svg','http://www.w3.org/2000/svg'],
        ARRAY['xsl','http://www.w3.org/1999/XSL/Transform']
    ]
    )
    )[1]::text AS c22


    ,(xpath('//nixda[1]/text()', myTempTable.myXmlColumn))[1]::text AS c2 
    --,myTempTable.myXmlColumn as myXmlElement
    ,xmlexists('//xmlEncodeTest[1]' PASSING BY REF myTempTable.myXmlColumn) AS c1e
    ,xmlexists('//nixda[1]' PASSING BY REF myTempTable.myXmlColumn) AS c2e
    ,xmlexists('//xmlEncodeTestAbc[1]' PASSING BY REF myTempTable.myXmlColumn) AS c1ea
FROM unnest(xpath('//row', 
     CAST('<?xml version="1.0" encoding="utf-8"?>
    <table xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
      <row>
        <xmlEncodeTest xsi:nil="true" />
        <nixda>noob</nixda>
      </row>
    </table>
    ' AS xml)   
    )
) AS myTempTable(myXmlColumn)
;

You can also check if a field is contained in an XML-text, by doing

 ,xmlexists('//xmlEncodeTest[1]' PASSING BY REF myTempTable.myXmlColumn) AS c1e

for example when you pass an XML-value to a stored-procedure/function for CRUD. (see above)

Also, note that the correct way to pass a null-value in XML is <elementName xsi:nil="true" /> and not <elementName /> or nothing. There is no correct way to pass NULL in attributes (you can only omit the attribute, but then it gets difficult/slow to infer the number of columns and their names in a large dataset).

e.g.

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<table>
    <row column1="a" column2="3" />
    <row column1="b" column2="4" column3="true" />
</table>

(is more compact, but very bad if you need to import it, especially if from XML-files with multiple GB of data - see a wonderful example of that in the stackoverflow data dump)

SELECT 
     myTempTable.myXmlColumn
    ,(xpath('//@column1', myTempTable.myXmlColumn))[1]::text AS c1
    ,(xpath('//@column2', myTempTable.myXmlColumn))[1]::text AS c2
    ,(xpath('//@column3', myTempTable.myXmlColumn))[1]::text AS c3
    ,xmlexists('//@column3' PASSING BY REF myTempTable.myXmlColumn) AS c3e
    ,case when (xpath('//@column3', myTempTable.myXmlColumn))[1]::text is null then 1 else 0 end AS is_null 
FROM unnest(xpath('//row', '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<table>
    <row column1="a" column2="3" />
    <row column1="b" column2="4" column3="true" />
</table>'
))  AS myTempTable(myXmlColumn)