Question

我想在表xml_data中导入很多XML文件：

create table xml_data(result xml);

要做到这一点，我有一个带循环的简单bash脚本：

#!/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

但是，这会尝试将每个文件的每一行导入为单独的行。这会导致错误：

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

我理解它失败的原因，但无法弄清楚如何让\copy一次将整个文件导入单行。

Answer 1

Necromancing：对于那些需要一个工作实例的人：

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;

或者噪音较小

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)
;

使用此示例XML文件（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>

注意：
MyData.xml需要位于PG_Data目录（pg_stat目录的父目录）中。
例如/var/lib/postgresql/9.3/main/MyData.xml
这需要PostGreSQL 9.1 +

总的来说，你可以实现无文件化，如下所示：

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)
;

请注意，与MS-SQL不同，xpath text（）在NULL值上返回NULL，而不是空字符串。
如果由于某种原因你需要显式检查是否存在NULL，你可以使用[not(@xsi:nil="true")]，你需要传递一个命名空间数组，否则你会得到一个错误（但是，你可以省略所有名称空间但是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)
;

您还可以通过执行

检查XML文本中是否包含字段

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

例如，当您将XML值传递给CRUD的存储过程/函数时。（见上文）

另请注意，在XML中传递空值的正确方法是<elementName xsi:nil="true" />而不是<elementName />或者没有。没有正确的方法在属性中传递NULL（您只能省略该属性，但是在大型数据集中推断列数及其名称变得困难/缓慢）。

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>

（更紧凑，但是如果你需要导入它会非常糟糕，特别是如果来自具有多GB数据的XML文件 - 请参阅stackoverflow数据转储中的一个很好的例子）

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)

Answer 2

我会尝试不同的方法：将XML文件直接读入plpgsql函数内的变量并从那里继续。应该快得多并且更强大。

CREATE OR REPLACE FUNCTION f_sync_from_xml()
  RETURNS boolean AS
$BODY$
DECLARE
    myxml    xml;
    datafile text := 'path/to/my_file.xml';
BEGIN
   myxml := pg_read_file(datafile, 0, 100000000);  -- arbitrary 100 MB max.

   CREATE TEMP TABLE tmp AS
   SELECT (xpath('//some_id/text()', x))[1]::text AS id
   FROM   unnest(xpath('/xml/path/to/datum', myxml)) x;
   ...

您需要超级用户权限，并且文件必须是本地数据库服务器，位于可访问目录中。
完整的代码示例以及更多解释和链接：

XML data to PostgreSQL database

Answer 3

扩展@ stefan-steiger的优秀答案，这是一个从包含多个兄弟节点（例如，多个<synonym>元素的子节点中提取XML元素的示例，用于特定的<synomyms>父节点节点）。

我的数据遇到了这个问题，搜索了很多解决方案;对我来说，他的回答是最有帮助的。

示例数据文件hmdb_metabolites_test.xml：

<?xml version="1.0" encoding="UTF-8"?>
<hmdb>
<metabolite>
  <accession>HMDB0000001</accession>
  <name>1-Methylhistidine</name>
  <synonyms>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid</synonym>
    <synonym>1-Methylhistidine</synonym>
    <synonym>Pi-methylhistidine</synonym>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate</synonym>
  </synonyms>
</metabolite>
<metabolite>
  <accession>HMDB0000002</accession>
  <name>1,3-Diaminopropane</name>
  <synonyms>
    <synonym>1,3-Propanediamine</synonym>
    <synonym>1,3-Propylenediamine</synonym>
    <synonym>Propane-1,3-diamine</synonym>
    <synonym>1,3-diamino-N-Propane</synonym>
  </synonyms>
</metabolite>
<metabolite>
  <accession>HMDB0000005</accession>
  <name>2-Ketobutyric acid</name>
  <synonyms>
    <synonym>2-Ketobutanoic acid</synonym>
    <synonym>2-Oxobutyric acid</synonym>
    <synonym>3-Methyl pyruvic acid</synonym>
    <synonym>alpha-Ketobutyrate</synonym>
  </synonyms>
</metabolite>
</hmdb>

除此之外：原始XML文件在文档元素中有一个URL

<hmdb xmlns="http://www.hmdb.ca">

阻止xpath解析数据。它将运行（没有错误消息），但关系/表是空的：

[hmdb_test]# \i /mnt/Vancouver/Programming/data/hmdb/sql/hmdb_test.sql
DO
 accession | name | synonym 
-----------+------+---------

由于源文件是3.4GB，我决定使用sed编辑该行：

sed -i '2s/.*hmdb xmlns.*/<hmdb>/' hmdb_metabolites.xml

[添加2（指示sed编辑＆＃34;第2行＆＃34;） - 巧合的是，在这种情况下 - 加倍sed命令执行速度。]

我的postgres数据文件夹（PSQL：SHOW data_directory;）是

/mnt/Vancouver/Programming/RDB/postgres/postgres/data

所以，作为sudo，我需要将我的XML数据文件复制到那里并chown将其用于PostgreSQL：

sudo chown postgres:postgres /mnt/Vancouver/Programming/RDB/postgres/postgres/data/hmdb_metabolites_test.xml

脚本（hmdb_test.sql）：

DO $$DECLARE myxml xml;

BEGIN

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

DROP TABLE IF EXISTS mytable;

-- CREATE TEMP TABLE mytable AS 
CREATE TABLE mytable AS 
SELECT 
    (xpath('//accession/text()', x))[1]::text AS accession
    ,(xpath('//name/text()', x))[1]::text AS name 
    -- The "synonym" child/subnode has many sibling elements, so we need to
    -- "unnest" them,otherwise we only retrieve the first synonym per record:
    ,unnest(xpath('//synonym/text()', x))::text AS synonym
FROM unnest(xpath('//metabolite', myxml)) x
;

END$$;

-- select * from mytable limit 5;
SELECT * FROM mytable;

执行，输出（在PSQL中）：

[hmdb_test]# \i /mnt/Vancouver/Programming/data/hmdb/hmdb_test.sql

accession  |        name        |                         synonym                          
-------------+--------------------+----------------------------------------------------------
HMDB0000001 | 1-Methylhistidine  | (2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid
HMDB0000001 | 1-Methylhistidine  | 1-Methylhistidine
HMDB0000001 | 1-Methylhistidine  | Pi-methylhistidine
HMDB0000001 | 1-Methylhistidine  | (2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate
HMDB0000002 | 1,3-Diaminopropane | 1,3-Propanediamine
HMDB0000002 | 1,3-Diaminopropane | 1,3-Propylenediamine
HMDB0000002 | 1,3-Diaminopropane | Propane-1,3-diamine
HMDB0000002 | 1,3-Diaminopropane | 1,3-diamino-N-Propane
HMDB0000005 | 2-Ketobutyric acid | 2-Ketobutanoic acid
HMDB0000005 | 2-Ketobutyric acid | 2-Oxobutyric acid
HMDB0000005 | 2-Ketobutyric acid | 3-Methyl pyruvic acid
HMDB0000005 | 2-Ketobutyric acid | alpha-Ketobutyrate

[hmdb_test]#

Answer 4

我使用tr用空格替换所有换行符。这将创建仅包含一行的XML文件。这样的文件我可以使用\copy轻松导入一行。

显然，如果你在XML中有多行值，这不是一个好主意。幸运的是，这不是我的情况。

要导入文件夹中的所有XML文件，您可以使用此bash脚本：

#!/bin/sh
FILES=/folder/with/xml/files/*.xml
for f in $FILES
do
  tr '\n' ' ' < $f > temp.xml
  psql -d database -h localhost -U usr -c '\copy xml_data from temp.xml'
done

将XML文件导入PostgreSQL

4 个答案: