XML files dont copy to standby unit
Hi,
I have failover active/standby topology with two ASA (version 8.0.4), and Clientless SSL VPN configured.
I have created differents profiles, bookmarks and portal in this solution.
But when I try to see this files in the standby unit, I can't to see it. Why? I try it whit "write standby" but nothing... Any idea?
Best regards
The write standby command replicates the configuation to the running configuration of the peer unit; it does not save the configuration to the startup configuration. To save the configuration changes to the startup configuration, use the copy running-config startup-config command on the same unit on which you entered the write standby command. The command will be replicated to the peer unit and the configuration saved to the startup configuration.
http://www.cisco.com/en/US/docs/security/asa/asa81/command/ref/uz.html#wp1567205
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<xsd:sequence>
<xsd:element ref="CentralLab"/>
<xsd:element ref="BaseSpecimen" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="ID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="LastActiveDateTime" type="xsd:dateTime"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="BaseSpecimen">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="SpecimenCollection"/>
<xsd:element ref="SpecimenTransport" minOccurs="0"/>
<xsd:element ref="SpecimenComment" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="SpecimenMaterial" minOccurs="0"/>
<xsd:element ref="SubjectAtCollection" minOccurs="0"/>
<xsd:element ref="BaseBattery" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="ID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="10"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="BaseBattery">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="BaseTest" maxOccurs="unbounded"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="BaseTest">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="PerformingLab"/>
<xsd:element ref="LabTest"/>
<xsd:element ref="ReceiverTest" minOccurs="0"/>
<xsd:element ref="LOINCTestCode" minOccurs="0"/>
<xsd:element ref="TestLevelComment" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="BaseResult" minOccurs="0"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="Status" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="13"/>
<xsd:enumeration value="D"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="X"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="TestingDateTime" type="xsd:dateTime"/>
<xsd:attribute name="TestType">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="22"/>
<xsd:enumeration value="S"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="U"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="BaseResult">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="ToxicityGrade" minOccurs="0"/>
<xsd:element ref="SingleResult" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="ReportedResultStatus">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="11"/>
<xsd:enumeration value="P"/>
<xsd:enumeration value="F"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="AlertFlag">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="14"/>
<xsd:enumeration value="LP"/>
<xsd:enumeration value="LT"/>
<xsd:enumeration value="LN"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="HN"/>
<xsd:enumeration value="HT"/>
<xsd:enumeration value="HP"/>
<xsd:enumeration value="AB"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="DeltaFlag">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="2"/>
<xsd:enumeration value="D+"/>
<xsd:enumeration value="D-"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ExclusionFlag">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="12"/>
<xsd:enumeration value="LX"/>
<xsd:enumeration value="HX"/>
<xsd:enumeration value="EX"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="BlindingFlag">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="24"/>
<xsd:enumeration value="S"/>
<xsd:enumeration value="I"/>
<xsd:enumeration value="B"/>
<xsd:enumeration value="C"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ReportedDateTime" type="xsd:dateTime"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="TransmissionSource">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="Sex">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="1"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="Race">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="CentralLab">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="SpecimenCollection">
<xsd:complexType>
<xsd:attribute name="ActualCollectionDateTime" type="xsd:dateTime" use="required"/>
<xsd:attribute name="PlannedCollectionTimeElapsed">
<xsd:annotation>
<xsd:documentation>Expected format is DDD-HH-MM, where DDD represents days [000-999], HH represents hours [00-23] and MM represents minutes [00-69].</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:length value="9"/>
<xsd:pattern value="\d\d\d-([01]\d|2[0123])-[012345]\d"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="PlannedCollectionTimeElapsedDescription">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CollectionEndDateTime" type="xsd:dateTime"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="SpecimenTransport">
<xsd:complexType>
<xsd:attribute name="ReceivedDateTime" type="xsd:dateTime"/>
<xsd:attribute name="SpecimenCondition">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="2048"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="SpecimenComment">
<xsd:complexType>
<xsd:attribute name="Source">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="12"/>
<xsd:enumeration value="I"/>
<xsd:enumeration value="L"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Text" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="2048"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="SpecimenMaterial">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="SubjectAtCollection">
<xsd:complexType>
<xsd:attribute name="AgeAtCollection">
<xsd:simpleType>
<xsd:restriction base="xsd:double">
<xsd:minInclusive value="0"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="AgeUnits" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="6"/>
<xsd:enumeration value="Y"/>
<xsd:enumeration value="M"/>
<xsd:enumeration value="D"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="FastingStatus">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="7"/>
<xsd:enumeration value="Y"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="U"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="PerformingLab">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="LabTest">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="100"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="AdditionalDescription">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="100"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="ReceiverTest">
<xsd:complexType>
<xsd:attribute name="ID" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Name">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="100"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="LOINCTestCode">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="10"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="TestLevelComment">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="2048"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element name="SingleResult">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="TextResult" minOccurs="0"/>
<xsd:element ref="NumericResult" minOccurs="0"/>
<xsd:element ref="ResultReferenceRange" minOccurs="0"/>
<xsd:element ref="ResultUnits" minOccurs="0"/>
<xsd:element ref="TransactionType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="ResultClass" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="12"/>
<xsd:enumeration value="R"/>
<xsd:enumeration value="C"/>
<xsd:enumeration value="S"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ResultType" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="12"/>
<xsd:enumeration value="C"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="T"/>
<xsd:enumeration value="G"/>
<xsd:enumeration value="L"/>
<xsd:enumeration value="R"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="TextResult">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="2048"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="NumericResult">
<xsd:complexType>
<xsd:attribute name="Value" type="xsd:double" use="required"/>
<xsd:attribute name="Precision" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="5"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="ResultReferenceRange">
<xsd:complexType>
<xsd:attribute name="ReferenceRangeLow">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ReferenceRangeHigh">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="ResultUnits">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="ToxicityGrade">
<xsd:complexType>
<xsd:attribute name="Value" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="1"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="CodeListID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="40"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="SubjectID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element name="ScreenID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element name="SpareSubjectID">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="20"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element name="Confidential">
<xsd:complexType>
<xsd:attribute name="Initials">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="4"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Birthdate" type="xsd:date"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="TransactionType">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:maxLength value="10"/>
<xsd:enumeration value="M"/>
<xsd:enumeration value="I"/>
<xsd:enumeration value="R"/>
<xsd:enumeration value="U"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
</xsd:schema>
** LAB - Base http://tsglab1:8080/home/DEV/xsd
BEGIN
dbms_xmlschema.registerschema(
'http://tsglab1:8080/home/DEV/xsd/LabReviewBaseSchema.xsd',
sys.urifactory.geturi('/home/DEV/xsd/LabReviewBaseSchema.xsd'));
END;
However, I am unable to ftp or copy the following well formed and valid xml file to the repository.
<?xml version="1.0" encoding="UTF-8"?>
<GTP xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://tsglab1:8080/home/DEV/xsd/LabReviewBaseSchema.xsd" ModelVersion="01-0-01" CreationDateTime="2004-03-27T14:09:44-05:00">
<TransmissionSource ID=""/>
<Study ID="101" TransmissionType="C"/>
</GTP>
When I put a larger file in the repository.. it saved but did not shred?
I ran each file through xmlspy all seem to be well formed and valid.
Not sure what's incorrect about the file or process?
Thx.Mark,
I've tried this in 10.1.0.2.0 as suggested and it didn't work for me.
My dateTime field is annotated in the schema with the xdb:SQLType="TIMESTAMP WITH TIME ZONE" attribute as suggested.
My xml element looks like this:
<ForecastDate>2004-03-05T06:00:19.876+00:00</ForecastDate>
But I still get this error:
Unable to load doc into database: ORA-01830: date format picture ends before converting entire input string
Any idea where I'm going wrong?
Thanks,
Brad. -
Using an online XML file v. a local copy
I'm working on a web project that reads in XML data and processes it accordingly. The system seems to work as it should except that it will only read the XML file if it is stored on a local drive and not through a URL. When trying to access it through a web address I get file not found alerts. Is there a different way I need to reference online files vs. ones stored locally? Thanks for any advice.
I would use a URL to reference both local and remote resources. (Don't call them "files" or you may be tempted to use a File object for both, and of course that doesn't work.)
But you do have to have valid URLs that point to actual resources, and you do have to have a network configuration that allows you to get to those resources, and so on.
Sorry if that seems vague, but it matches the question. -
Update Database Through XML file using SAP B1 business objects
Hello everyone,
I am facing a problem ie I am not able to update the Database(SQL 2000) through an XML file.
Though i am able to insert the data in the databse using xml file but unable to update that data.
The tables i want to update are OITM,ITM1,OITW. While i was trying to update the Databse i was getting an error ie " -1107 Object's key is not set".
I dont want to use DTW for importing or anything.
Kindly help me out why i am facing this problem asap...Hi Pranay,
My case was that I wanted to replicate an item from one company to another (I guess that's your case also). What I finally did is copy field by field the objects I needed. Later I've find out the solution given here,
Copy items between databases
but I haven't try it out. I expect your comments about it :).
Regards,
Ian -
XML file too large or XML element too large
I am attempting to import an xml file into the repository and have it shred into the object-relational tables. I registered a schema and it created object-relational xml_tables, triggers, and types. The full xml file is > 80MB. XDB created all the fields as VARCHAR2(4000).
error code when importing the full XML file. This is what I need to ultimately fix.
DECLARE
res BOOLEAN;
BEGIN
res := DBMS_XDB.createResource('/home/pharma/drugbank.xml',
bfilename('XMLPHARMA', 'drugbank.xml'),
nls_charset_id('AL32UTF8'));
END;
COMMIT;
XML file encounters errors on the import.
An error was encountered performing the requested operation
ORA-30951: Element or attribute at Xpath references exceeds maximum length
ORA-06512 at "XDB.DBMS_XDB", line 315
ORA-06512 at line 4
30951.00000 - "Element or attribute at Xpath %x exceeds maximum length"
*Cause: An attempt was made to insert a node of length exceeding the maximum length (specified by the maxLength facet) into an XML document.
*Action: Do not attempt to add a node exceeding the maximum length to XML documents.
Vendor code 30951Error at Line:18I would guess that some of the fields have max lengths > 4000. I plan to annotate the schema with SQLType="CLOB", but need to know which fields to change. I was able to copy the xml file and reduce that xml file to one record, which imported into the tables. My plan was to write a view over the bfile to get the lengths of certain fields, annotate the .xsd with CLOBS where needed, and then import again. In order to do that, I have a 1 record file imported into a table and as a bfile.
Here is my code selecting length from a generated object-relational table of only one record.
CREATE OR REPLACE VIEW pharma.drugs_vw AS
SELECT d.*
FROM drugs, XMLTABLE
('/drugs' PASSING OBJECT_VALUE COLUMNS
drugbank_id VARCHAR2(20) PATH 'drug/drugbank-id',
name VARCHAR2(50) PATH 'drug/name',
description VARCHAR2(4000) PATH 'drug/description'
) d
select max(length(drugbank_id)) as dbidlen,
max(length(name)) as nmlen,
max(length(description)) as desclen
from drugs_vw;
DBIDLEN NMLEN DESCLEN
7 9 229
1 row selected.Here is the code for the bfile. Same results, but using deprecated functions. I read the whitepaper, Oracle XML DB: Best practices to get optimal performance out of XML Queries. It says that extract(), extractvalue(), Table(XMLSequence()), and XMLType() are deprecated in 11gr2.
-- Note extractvalue is deprecated in 11gr2 replaced by W3C standard
-- XMLCast(XMLQuery())
-- TABLE(XMLSequence) is replaced by XMLTable
-- XMLType() is replaced by XMLParse()
SELECT max(length(extractvalue(column_value, '/drug/drugbank-id'))) dbidlen,
max(length(extractvalue(column_value, '/drug/name'))) nmlen,
max(length(extractvalue(column_value, '/drug/description'))) desclen
FROM TABLE(XMLSequence(XMLTYPE(bfilename('XMLPHARMA',
'db00001.xml'),nls_charset_id('AL32UTF8')).extract('/drugs/drug'))) d
WHERE ROWNUM <= 5;
DBIDLEN NMLEN DESCLEN
7 9 229Is this better code for getting the maximum length of xml fields from a bfile? Here is what I have so far. This works on a single drugbank-id.
SELECT max(length(drugbank_id)) AS dbidlen,
max(length(name)) AS nmlen,
max(length(description)) AS desclen
FROM (XMLTABLE('*'
PASSING (XMLType(bfilename('XMLPHARMA', 'db00001.xml'),nls_charset_id('AL32UTF8')))
COLUMNS
drugbank_id VARCHAR2(20) PATH 'drug/drugbank-id',
name VARCHAR2(50) PATH 'drug/name',
description VARCHAR2(4000) PATH 'drug/description'
);I try to run it on the full file and get this error
Error report:
SQL Error: ORA-31011: XML parsing failed
ORA-19202: Error occurred in XML processing
LPX-00007: unexpected end-of-file encountered
31011. 00000 - "XML parsing failed"
*Cause: XML parser returned an error while trying to parse the document.
*Action: Check if the document to be parsed is valid.The code to create schema and object-relational tables. This worked fine.
set serveroutput on
-- Create resource file for schema
DECLARE
res BOOLEAN;
BEGIN
res := DBMS_XDB.createResource('/home/pharma/drugbank.xsd',
bfilename('XMLPHARMA', 'drugbank.xsd'),
nls_charset_id('AL32UTF8'));
COMMIT;
END;
-- optional debugging of create types and tables if you want a trace
ALTER SESSION SET EVENTS = '31098 TRACE NAME CONTEXT FOREVER';
BEGIN
DBMS_XMLSCHEMA.registerSchema(
SCHEMAURL => 'http://localhost:8080/home/pharma/drugbank.xsd',
SCHEMADOC => bfilename('XMLPHARMA', 'drugbank.xsd'),
CSID => nls_charset_id('AL32UTF8'),
LOCAL => TRUE,
GENTYPES => TRUE,
GENTABLES => TRUE,
OWNER => 'PHARMA');
COMMIT;
END;
SQL> select * from v$version;
BANNER
Oracle Database 11g Release 11.2.0.2.0 - Production
PL/SQL Release 11.2.0.2.0 - Production
CORE 11.2.0.2.0 Production
TNS for 32-bit Windows: Version 11.2.0.2.0 - Production
NLSRTL Version 11.2.0.2.0 - ProductionThe xml schema follows. Sorry about the length, but I think I might break something if I snipped it.
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:xdb="http://xmlns.oracle.com/xdb"
>
<!-- General type definitions -->
<xs:simpleType name="DecimalOrEmptyType">
<xs:union memberTypes="xs:decimal EmptyStringType"/>
</xs:simpleType>
<xs:simpleType name="EmptyStringType">
<xs:restriction base="xs:string">
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
<!-- Element Definitions -->
<!-- Drug secondary accession number definition begins -->
<xs:element name="secondary-accession-numbers" xdb:defaultTable="SECONDARY_ACCESSION_NUMBERS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="secondary-accession-number" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug secondary accession number definition ends -->
<!-- Drug groups definition begins -->
<xs:element name="groups" xdb:defaultTable="GROUPS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="group">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="approved"/>
<xs:enumeration value="illicit"/>
<xs:enumeration value="experimental"/>
<xs:enumeration value="withdrawn"/>
<xs:enumeration value="nutraceutical"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug groups definition ends -->
<!-- Drug taxonomy definition begins -->
<xs:element name="substructure">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="class" type="xs:string" use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element name="substructures" xdb:defaultTable="SUBSTRUCTURES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="substructure"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="taxonomy" xdb:defaultTable="TAXONOMY">
<xs:complexType>
<xs:sequence>
<xs:element name="kingdom" type="xs:string"/>
<xs:element ref="substructures"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug taxonomy definition ends -->
<!-- Drug brands definition begins -->
<xs:element name="brands" xdb:defaultTable="BRANDS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="brand" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug brands definition ends -->
<!-- Drug mixtures definition begins -->
<xs:element name="mixture">
<xs:complexType>
<xs:sequence>
<xs:element name="name" type="xs:string"/>
<xs:element name="ingredients" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="mixtures" xdb:defaultTable="MIXTURES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="mixture"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug mixtures definition ends -->
<!-- Drug packagers definition begins -->
<xs:element name="packager">
<xs:complexType>
<xs:sequence>
<xs:element name="name" type="xs:string"/>
<xs:element name="url" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="packagers" xdb:defaultTable="PACKAGERS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="packager"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug packagers definition ends -->
<!-- Drug manufacturers definition begins -->
<xs:element name="manufacturer">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="generic" type="xs:string" use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element name="manufacturers" xdb:defaultTable="MANUFACTURERS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="manufacturer"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug manufactures definition ends -->
<!-- Drug pricing definition begins -->
<xs:element name="cost">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="currency" type="xs:string" use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element name="price">
<xs:complexType>
<xs:sequence>
<xs:element name="description" type="xs:string"/>
<xs:element ref="cost"/>
<xs:element name="unit" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="prices" xdb:defaultTable="PRICES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="price"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug pricing definition ends -->
<!-- Drug categories definition begins -->
<xs:element name="categories" xdb:defaultTable="CATEGORIES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="category" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug categories definition ends -->
<!-- Drug affected orgainsms definition begins -->
<xs:element name="affected-organisms" xdb:defaultTable="AFFECTED_ORGANISMS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="affected-organism" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug affected organisms definition ends -->
<!-- Drug dosage definition begins -->
<xs:element name="dosage">
<xs:complexType>
<xs:sequence>
<xs:element name="form" type="xs:string"/>
<xs:element name="route" type="xs:string"/>
<xs:element name="strength" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="dosages" xdb:defaultTable="DOSAGES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="dosage"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug dosages definition ends -->
<!-- Drug ATC codes definition begins -->
<xs:element name="atc-codes" xdb:defaultTable="ATC_CODES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="atc-code" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug ATC codes definition ends -->
<!-- Drug AHFS codes definition begins -->
<xs:element name="ahfs-codes" xdb:defaultTable="AHFS_CODES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="ahfs-code" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug AHFS codes definition ends -->
<!-- Drug Patent definition begins -->
<xs:element name="patent">
<xs:complexType>
<xs:sequence>
<xs:element name="number" type="xs:string"/>
<xs:element name="country" type="xs:string"/>
<xs:element name="approved" type="xs:string"/>
<xs:element name="expires" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="patents" xdb:defaultTable="PATENTS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="patent"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug patent definition ends -->
<!-- Drug food interactions definition begins -->
<xs:element name="food-interactions" xdb:defaultTable="FOOD_INTERACTIONS">
<xs:complexType>
<xs:sequence>
<xs:element name="food-interaction" type="xs:string" maxOccurs="unbounded" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug food interactions definition ends -->
<!-- Drug drug interactions definition begins -->
<xs:element name="drug-interaction">
<xs:complexType>
<xs:sequence>
<xs:element name="drug" type="xs:integer"/>
<xs:element name="description" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="drug-interactions" xdb:defaultTable="DRUG_INTERACTIONS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="drug-interaction"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug drug interactions definition ends -->
<!-- Drug protein sequences (biotech) definition begins -->
<xs:element name="protein-sequences" xdb:defaultTable="PROTEIN_SEQUENCES">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="protein-sequence" type="SequenceType"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug protein sequences (biotech) definition ends-->
<!-- Drug external links definition begins -->
<xs:element name="external-link">
<xs:complexType>
<xs:sequence>
<xs:element name="resource" type="xs:string"/>
<xs:element name="url" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="external-links" xdb:defaultTable="EXTERNAL_LINKS">
<xs:complexType>
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element ref="external-link"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug external links definition ends -->
<!-- Drug targets definition begins -->
<xs:element name="targets" xdb:defaultTable="TARGETS">
<xs:complexType>
<xs:sequence>
<xs:element name="target" type="TargetBondType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug targets definition ends -->
<!-- Drug enzymes definition begins -->
<xs:element name="enzymes" xdb:defaultTable="ENZYMES">
<xs:complexType>
<xs:sequence>
<xs:element name="enzyme" type="BondType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug enzmes definition ends -->
<!-- Drug transporters definition begins -->
<xs:element name="transporters" xdb:defaultTable="TRANSPORTERS">
<xs:complexType>
<xs:sequence>
<xs:element name="transporter" type="BondType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug transporters definition ends -->
<!-- Drug carriers definition begins -->
<xs:element name="carriers" xdb:defaultTable="CARRIERS">
<xs:complexType>
<xs:sequence>
<xs:element name="carrier" type="BondType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Drug carriers definition ends -->
<!-- Partner Pfams definition begins -->
<xs:element name="pfam">
<xs:complexType>
<xs:sequence>
<xs:element name="identifier" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="pfams" xdb:defaultTable="PFAMS">
<xs:complexType>
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:element ref="pfam"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Partner Pfams definition end -->
<!-- Partner GO Classification definition begins -->
<xs:element name="go-classifier">
<xs:complexType>
<xs:sequence>
<xs:element name="category" type="xs:string"/>
<xs:element name="description" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="go-classifiers" xdb:defaultTable="GO_CLASSIFIERS">
<xs:complexType>
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:element ref="go-classifier"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<!-- Partner GO Classification definition ends -->
<!-- Partner Essentiality definition begins -->
<xs:element name="essentiality">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Essential"/>
<xs:enumeration value="Non-Essential"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<!-- Partner Essentiality definition ends -->
<!-- Complex Type Definitions -->
<xs:complexType name="SequenceType">
<xs:sequence>
<xs:element name="header" type="xs:string"/>
<xs:element name="chain" type="xs:string"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="PropertyType">
<xs:sequence>
<xs:element name="kind">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="logP"/>
<xs:enumeration value="logS"/>
<xs:enumeration value="logP/hydrophobicity"/>
<xs:enumeration value="Water Solubility"/>
<xs:enumeration value="caco2 Permeability"/>
<xs:enumeration value="pKa"/>
<xs:enumeration value="IUPAC Name"/>
<xs:enumeration value="Molecular Weight"/>
<xs:enumeration value="Monoisotopic Weight"/>
<xs:enumeration value="SMILES"/>
<xs:enumeration value="Molecular Formula"/>
<xs:enumeration value="InChI"/>
<xs:enumeration value="InChIKey"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="value" type="xs:string"/>
<xs:element name="source">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="JChem"/>
<xs:enumeration value="ALOGPS"/>
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:complexType name="PropertiesType">
<xs:sequence>
<xs:element name="property" type="PropertyType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="SynonymsType">
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="synonym" type="xs:string"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="IdentifiersType">
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="external-identifier">
<xs:complexType>
<xs:sequence>
<xs:element name="resource" type="xs:string"/>
<xs:element name="identifier" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:complexType name="BondActionsType">
<xs:sequence maxOccurs="unbounded" minOccurs="0">
<xs:element name="action" type="xs:string"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="BondType">
<xs:sequence>
<xs:element name="actions" type="BondActionsType"/>
<xs:element name="references" type="xs:string"/>
</xs:sequence>
<xs:attribute name="position" type="xs:integer" use="optional"/>
<xs:attribute name="partner" type="xs:integer"/>
</xs:complexType>
<xs:complexType name="TargetBondType">
<xs:complexContent>
<xs:extension base="BondType">
<xs:sequence>
<xs:element name="known-action">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="yes"/>
<xs:enumeration value="no"/>
<xs:enumeration value="unknown"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="PartnerType">
<xs:sequence>
<xs:element name="name" type="xs:string"/>
<xs:element name="general-function" type="xs:string"/>
<xs:element name="specific-function" type="xs:string"/>
<xs:element name="gene-name" type="xs:string"/>
<xs:element name="locus" type="xs:string"/>
<xs:element name="reaction" type="xs:string"/>
<xs:element name="signals" type="xs:string"/>
<xs:element name="cellular-location" type="xs:string"/>
<xs:element name="transmembrane-regions" type="xs:string"/>
<xs:element name="theoretical-pi" type="DecimalOrEmptyType"/>
<xs:element name="molecular-weight" type="DecimalOrEmptyType"/>
<xs:element name="chromosome" type="xs:string"/>
<xs:element ref="essentiality"/>
<xs:element name="references" type="xs:string"/>
<xs:element name="external-identifiers" type="IdentifiersType"/>
<xs:element name="synonyms" type="SynonymsType"/>
<xs:element name="protein-sequence" type="SequenceType" minOccurs="0"/>
<xs:element name="gene-sequence" type="SequenceType" minOccurs="0"/>
<xs:element ref="pfams"/>
<xs:element ref="go-classifiers"/>
</xs:sequence>
<xs:attribute name="id" type="xs:integer" use="required"/>
</xs:complexType>
<xs:complexType name="DrugType">
<xs:sequence>
<xs:element name="drugbank-id" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
<xs:element name="description" type="xs:string"/>
<xs:element name="cas-number" type="xs:string"/>
<xs:element name="general-references" type="xs:string"/>
<xs:element name="synthesis-reference" type="xs:string"/>
<xs:element name="indication" type="xs:string"/>
<xs:element name="pharmacology" type="xs:string"/>
<xs:element name="mechanism-of-action" type="xs:string"/>
<xs:element name="toxicity" type="xs:string"/>
<xs:element name="biotransformation" type="xs:string"/>
<xs:element name="absorption" type="xs:string"/>
<xs:element name="half-life" type="xs:string"/>
<xs:element name="protein-binding" type="xs:string"/>
<xs:element name="route-of-elimination" type="xs:string"/>
<xs:element name="volume-of-distribution" type="xs:string"/>
<xs:element name="clearance" type="xs:string"/>
<xs:element ref="secondary-accession-numbers"/>
<xs:element ref="groups"/>
<xs:element ref="taxonomy"/>
<xs:element name="synonyms" type="SynonymsType"/>
<xs:element ref="brands"/>
<xs:element ref="mixtures"/>
<xs:element ref="packagers"/>
<xs:element ref="manufacturers"/>
<xs:element ref="prices"/>
<xs:element ref="categories"/>
<xs:element ref="affected-organisms"/>
<xs:element ref="dosages"/>
<xs:element ref="atc-codes"/>
<xs:element ref="ahfs-codes"/>
<xs:element ref="patents"/>
<xs:element ref="food-interactions"/>
<xs:element ref="drug-interactions"/>
<xs:element ref="protein-sequences" minOccurs="0"/><!-- Only present for biotech drugs -->
<xs:element name="calculated-properties" type="PropertiesType" minOccurs="0"/><!-- Only present for small molecule drugs -->
<xs:element name="experimental-properties" type="PropertiesType"/>
<xs:element name="external-identifiers" type="IdentifiersType"/>
<xs:element ref="external-links"/>
<xs:element ref="targets"/>
<xs:element ref="enzymes"/>
<xs:element ref="transporters"/>
<xs:element ref="carriers"/>
</xs:sequence>
<xs:attribute name="type" use="required">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="small molecule"/>
<xs:enumeration value="biotech"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="updated" type="xs:string" use="required"/>
<xs:attribute name="created" type="xs:string" use="required"/>
<xs:attribute name="version" type="xs:decimal" use="required"/>
</xs:complexType>
<xs:element name="drugs" xdb:defaultTable="DRUGS">
<xs:complexType>
<xs:sequence>
<xs:element name="drug" type="DrugType" minOccurs="0" maxOccurs="unbounded" />
<xs:element name="partners">
<xs:complexType>
<xs:sequence>
<xs:element name="partner" type="PartnerType" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:keyref name="targetPartnerIdKeyRef" refer="partnerIdKey">
<xs:selector xpath="drug/targets/*"/>
<xs:field xpath="@partner"/>
</xs:keyref>
<xs:keyref name="enzymePartnerIdKeyRef" refer="partnerIdKey">
<xs:selector xpath="drug/enzymes/*"/>
<xs:field xpath="@partner"/>
</xs:keyref>
<xs:keyref name="transporterPartnerIdKeyRef" refer="partnerIdKey">
<xs:selector xpath="drug/transporters/*"/>
<xs:field xpath="@partner"/>
</xs:keyref>
<xs:keyref name="carrierPartnerIdKeyRef" refer="partnerIdKey">
<xs:selector xpath="drug/carriers/*"/>
<xs:field xpath="@partner"/>
</xs:keyref>
<xs:key name="partnerIdKey">
<xs:selector xpath=".//partner"/>
<xs:field xpath="@id"/>
</xs:key>
</xs:element>
</xs:schema>Query optimizing whitepaper
http://www.oracle.com/technetwork/database/features/xmldb/xmlqueryoptimize11gr2-168036.pdfI attempted to insert the xml file into an xml table and into a relational table with an xml column both based on the schema. I get the same errors.
-This creates an XML table based on the schema successfully
CREATE TABLE pharma.drugs_xmltype OF XMLTYPE
XMLSCHEMA "http://localhost:8080/home/pharma/drugbank.xsd"
ELEMENT "drugs";
Table created.
Elapsed: 00:00:02.67
SQL>desc pharma.drugs_xmltype
Name Null? Type
TABLE of SYS.XMLTYPE(XMLSchema "http://localhost:8080/home/pharma/drugbank.xsd" Element "drugs") STORAGE Object-relational TYPE "drugs1200_T"-- it refers to these types
create or replace TYPE "drugs1200_T" AS OBJECT ("SYS_XDBPD$" "XDB"."XDB$RAW_LIST_T","drug" "drug1201_COLL","partners" "partners1202_T")FINAL INSTANTIABLE
create or replace TYPE "drug1201_COLL" AS VARRAY(2147483647) OF "DrugType1121_T"
create or replace TYPE "partners1202_T" AS OBJECT ("SYS_XDBPD$" "XDB"."XDB$RAW_LIST_T","partner" "partner1203_COLL")FINAL INSTANTIABLE
create or replace TYPE "partner1203_COLL" AS VARRAY(2147483647) OF "PartnerType1190_T"
create or replace TYPE "DrugType1121_T" AS OBJECT ("SYS_XDBPD$" "XDB"."XDB$RAW_LIST_T","type" "XDB"."XDB$ENUM_T","updated" VARCHAR2(4000 CHAR),"created" VARCHAR2(4000 CHAR),"version" NUMBER,"drugbank-id" VARCHAR2(4000 CHAR),"name" VARCHAR2(4000 CHAR),"description" VARCHAR2(4000 CHAR),"cas-number" VARCHAR2(4000 CHAR),"general-references" VARCHAR2(4000 CHAR),"synthesis-reference" VARCHAR2(4000 CHAR),"indication" VARCHAR2(4000 CHAR),"pharmacology" VARCHAR2(4000 CHAR),"mechanism-of-action" VARCHAR2(4000 CHAR),"toxicity" VARCHAR2(4000 CHAR),"biotransformation" VARCHAR2(4000 CHAR),"absorption" VARCHAR2(4000 CHAR),"half-life" VARCHAR2(4000 CHAR),"protein-binding" VARCHAR2(4000 CHAR),"route-of-elimination" VARCHAR2(4000 CHAR),"volume-of-distribution" VARCHAR2(4000 CHAR),"clearance" VARCHAR2(4000 CHAR),"secondary-accession-numbers" "secondary-accession1122_T","groups" "groups1124_T","taxonomy" "taxonomy1126_T","synonyms" "SynonymsType1131_T","brands" "brands1132_T","mixtures" "mixtures1133_T","packagers" "packagers1137_T","manufacturers" "manufacturers1141_T","prices" "prices1145_T","categories" "categories1151_T","affected-organisms" "affected-organisms1152_T","dosages" "dosages1153_T","atc-codes" "atc-codes1157_T","ahfs-codes" "ahfs-codes1158_T","patents" "patents1159_T","food-interactions" "food-interactions1163_T","drug-interactions" "drug-interactions1164_T","protein-sequences" "protein-sequences1168_T","calculated-properties" "PropertiesType1171_T","experimental-properties" "PropertiesType1171_T","external-identifiers" "IdentifiersType1174_T","external-links" "external-links1177_T","targets" "targets1181_T","enzymes" "enzymes1186_T","transporters" "transporters1188_T","carriers" "carriers1189_T")NOT FINAL INSTANTIABLE -- drugs type
PHARMA@scidev> desc "drugs1200_T"
Name Null? Type
SYS_XDBPD$ XDB.XDB$RAW_LIST_T
drug drug1201_COLL
partners partners1202_T-- I planned to insert using a subselect and got the same error on the select.
Error starting at line 1 in command:
SELECT max(length(drugbank_id)) AS dbidlen
FROM (XMLTABLE('*'
PASSING (XMLType(bfilename('XMLPHARMA', 'drugbank.xml'),nls_charset_id('AL32UTF8')))
COLUMNS
drugbank_id VARCHAR2(20) PATH 'drug/drugbank-id'
Error report:
SQL Error: ORA-31011: XML parsing failed
ORA-19202: Error occurred in XML processing
LPX-00007: unexpected end-of-file encountered
31011. 00000 - "XML parsing failed"
*Cause: XML parser returned an error while trying to parse the document.
*Action: Check if the document to be parsed is valid.--This creates a row in the xmltype table from a single drug file.
INSERT INTO drugs_xmltype
VALUES(XMLType(bfilename('XMLPHARMA', 'db00001.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
'http://localhost:8080/home/pharma/drugbank.xsd'))
;-- The create using the full xml file fails.
INSERT INTO drugs_xmltype
VALUES(XMLType(bfilename('XMLPHARMA', 'drugbank.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
'http://localhost:8080/home/pharma/drugbank.xsd'))
VALUES(XMLType(bfilename('XMLPHARMA', 'drugbank.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
ERROR at line 2:
ORA-30951: Element or attribute at Xpath references exceeds maximum length
Elapsed: 00:01:17.90-- Then I tried the same using a relational table with an xml column
-- Then I created a relational table with an xml column
CREATE TABLE pharma.drugs_xmlcolumn_type (drug_xml XMLTYPE)
XMLTYPE COLUMN drug_xml STORE AS OBJECT RELATIONAL
XMLSCHEMA "http://localhost:8080/home/pharma/drugbank.xsd"
ELEMENT "drugs";
CREATE TABLE succeeded.--This command refers to the following types
SYS.XMLTYPE(XMLSchema "http://localhost:8080/home/pharma/drugbank.xsd" Element "drugs" ) STORAGE Object-relational TYPE "drugs1200_T"-- This creates a row in the xmlcolumn table from a single drug file.
INSERT INTO drugs_xmlcolumn_type
VALUES(XMLType(bfilename('XMLPHARMA', 'db00001.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
'http://localhost:8080/home/pharma/drugbank.xsd'))
;--The create using the full xml file into a relational table with an xml column fails
INSERT INTO drugs_xmlcolumn_type
VALUES(XMLType(bfilename('XMLPHARMA', 'drugbank.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
'http://localhost:8080/home/pharma/drugbank.xsd'))
VALUES(XMLType(bfilename('XMLPHARMA', 'drugbank.xml'),nls_charset_id('AL32UTF8')).CreateSchemaBasedXML(
ERROR at line 2:
ORA-30951: Element or attribute at Xpath references exceeds maximum length
Elapsed: 00:01:06.74
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