Develop Reference

Reading UTF-16 XML files with JCabi Java

I have found this JCabi snippet code that works well with UTF-8 xml encoded files, it basically reads the xml file and then prints it as a string.
XML xml;
try {
xml = new XMLDocument(new File("test8.xml"));
String xmlString = xml.toString();
System.out.println(xmlString);
} catch (FileNotFoundException e1) {
e1.printStackTrace();
}
However I need this to run this same code on a UTF-16 encoded xml it gives me the following error:
[Fatal Error] :1:1: Content is not allowed in prolog.
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Can't parse, most probably the XML is invalid
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
I have read about this error and this means that the parser it is not recognizing the prolog because it's seeing characters that are not supposed to be there because of the encoding.
I have tried other libraries that offer a way to "tell" the class which encoding the source file is encoded in, but the only library I was able to get it to work to some degree was JCabi, but I was not able to find a way to tell it that my source file is encoded in UTF-16.
Thanks, any help is appreciated.

The jcabi XMLDocument has various constructors including one which takes a string. So one approach is to use:
Path path = Paths.get("test16_LE_with_bom.xml");
XML xml = new XMLDocument(Files.readString(path, StandardCharsets.UTF_16LE));
String xmlString = xml.toString();
System.out.println(xmlString);
This makes use of java.nio.charset.StandardCharsets and java.nio.file.Files.
In my first test, my XML file was encoded as UTF-16-LE (and with a BOM at the start: FF FE for little-endian). The above approach handled the BOM OK.
My test file's prolog is as follows (with no explicit encoding - maybe that's a bad thing, here?):
<?xml version="1.0"?>
In my second test I removed the BOM and re-ran with the updated file - which also worked.
I used Notepad++ and a hex editor to verify/select encodings & to edit the test files.
Your file may be different from my test files (BE vs. LE).

CharConversionException while transforming xml file

I have a Java program which process xml files. When transforming xml into another xml file base on certain schema( xsd/xsl) it throws following error.
This error only throws for one xml file which has a xml tag like this.
<abc>xxx yyyy “ggggg vvvv” uuuu</abc>
But after removing or re-type two quotes, it doesn’t throw the error.
Anybody, please assist me to resolve this issue.
java.io.CharConversionException: Character larger than 4 bytes are not supported: byte 0x93 implies a length of more than 4 bytes
at .org.apache.xmlbeans..impl.piccolo.xml.UTF8XMLDecoder.decode(UTF8XMLDecoder.java:162)
<?xml version= “1.0’ encoding =“UTF-8” standalone =“yes “?><xyz xml s=“http://pqr.yy”><Header><abc> aaa “cccc” aaaaa vvv</abc></Header></xyz>.

As others have reported in comments, it has failed because the typographical quotation marks are encoded in Windows-1292 encoding, not in UTF-8, so the parser hasn't managed to decode them.
The encoding declared in the XML declaration must match the actual encoding used for the characters.
To find out how this error arose, and to prevent it happening again, we would need to know where this (wannabe) XML file came from, and how it was created.
My guess would be that someone used a "smart" editor; Microsoft editors in particular are notorious for changing what you type to what Microsoft think you wanted to type. If you're editing XML by hand it's best to use an XML-aware editor.

Is there any way to process my rest of xml file despite of any fatal error like SAXParserException encountered [duplicate]

Currently, I'm working on a feature that involves parsing XML that we receive from another product. I decided to run some tests against some actual customer data, and it looks like the other product is allowing input from users that should be considered invalid. Anyways, I still have to try and figure out a way to parse it. We're using javax.xml.parsers.DocumentBuilder and I'm getting an error on input that looks like the following.
<xml>
...
<description>Example:Description:<THIS-IS-PART-OF-DESCRIPTION></description>
...
</xml>
As you can tell, the description has what appears to be an invalid tag inside of it (<THIS-IS-PART-OF-DESCRIPTION>). Now, this description tag is known to be a leaf tag and shouldn't have any nested tags inside of it. Regardless, this is still an issue and yields an exception on DocumentBuilder.parse(...)
I know this is invalid XML, but it's predictably invalid. Any ideas on a way to parse such input?

That "XML" is worse than invalid – it's not well-formed; see Well Formed vs Valid XML.
An informal assessment of the predictability of the transgressions does not help. That textual data is not XML. No conformant XML tools or libraries can help you process it.
Options, most desirable first:
Have the provider fix the problem on their end. Demand well-formed XML. (Technically the phrase well-formed XML is redundant but may be useful for emphasis.)
Use a tolerant markup parser to cleanup the problem ahead of parsing as XML:
Standalone: xmlstarlet has robust recovering and repair capabilities credit: RomanPerekhrest
xmlstarlet fo -o -R -H -D bad.xml 2>/dev/null
Standalone and C/C++: HTML Tidy works with XML too. Taggle is a port of TagSoup to C++.
Python: Beautiful Soup is Python-based. See notes in the Differences between parsers section. See also answers to this question for more
suggestions for dealing with not-well-formed markup in Python,
including especially lxml's recover=True option.
See also this answer for how to use codecs.EncodedFile() to cleanup illegal characters.
Java: TagSoup and JSoup focus on HTML. FilterInputStream can be used for preprocessing cleanup.
.NET:
XmlReaderSettings.CheckCharacters can
be disabled to get past illegal XML character problems.
#jdweng notes that XmlReaderSettings.ConformanceLevel can be set to
ConformanceLevel.Fragment so that XmlReader can read XML Well-Formed Parsed Entities lacking a root element.
#jdweng also reports that XmlReader.ReadToFollowing() can sometimes
be used to work-around XML syntactical issues, but note
rule-breaking warning in #3 below.
Microsoft.Language.Xml.XMLParser is said to be “error-tolerant”.
Go: Set Decoder.Strict to false as shown in this example by #chuckx.
PHP: See DOMDocument::$recover and libxml_use_internal_errors(true). See nice example here.
Ruby: Nokogiri supports “Gentle Well-Formedness”.
R: See htmlTreeParse() for fault-tolerant markup parsing in R.
Perl: See XML::Liberal, a "super liberal XML parser that parses broken XML."
Process the data as text manually using a text editor or
programmatically using character/string functions. Doing this
programmatically can range from tricky to impossible as
what appears to be
predictable often is not -- rule breaking is rarely bound by rules.
For invalid character errors, use regex to remove/replace invalid characters:
PHP: preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $s);
Ruby: string.tr("^\u{0009}\u{000a}\u{000d}\u{0020}-\u{D7FF}\u{E000‌​}-\u{FFFD}", ' ')
JavaScript: inputStr.replace(/[^\x09\x0A\x0D\x20-\xFF\x85\xA0-\uD7FF\uE000-\uFDCF\uFDE0-\uFFFD]/gm, '')
For ampersands, use regex to replace matches with &: credit: blhsin, demo
&(?!(?:#\d+|#x[0-9a-f]+|\w+);)
Note that the above regular expressions won't take comments or CDATA
sections into account.

A standard XML parser will NEVER accept invalid XML, by design.
Your only option is to pre-process the input to remove the "predictably invalid" content, or wrap it in CDATA, prior to parsing it.

The accepted answer is good advice, and contains very useful links.
I'd like to add that this, and many other cases of not-wellformed and/or DTD-invalid XML can be repaired using SGML, the ISO-standardized superset of HTML and XML. In your case, what works is to declare the bogus THIS-IS-PART-OF-DESCRIPTION element as SGML empty element and then use eg. the osx program (part of the OpenSP/OpenJade SGML package) to convert it to XML. For example, if you supply the following to osx
<!DOCTYPE xml [
<!ELEMENT xml - - ANY>
<!ELEMENT description - - ANY>
<!ELEMENT THIS-IS-PART-OF-DESCRIPTION - - EMPTY>
]>
<xml>
<description>blah blah
<THIS-IS-PART-OF-DESCRIPTION>
</description>
</xml>
it will output well-formed XML for further processing with the XML tools of your choice.
Note, however, that your example snippet has another problem in that element names starting with the letters xml or XML or Xml etc. are reserved in XML, and won't be accepted by conforming XML parsers.

IMO these cases should be solved by using JSoup.
Below is a not-really answer for this specific case, but found this on the web (thanks to inuyasha82 on Coderwall). This code bit did inspire me for another similar problem while dealing with malformed XMLs, so I share it here.
Please do not edit what is below, as it is as it on the original website.
The XML format, requires to be valid a unique root element declared in the document.
So for example a valid xml is:
<root>
<element>...</element>
<element>...</element>
</root>
But if you have a document like:
<element>...</element>
<element>...</element>
<element>...</element>
<element>...</element>
This will be considered a malformed XML, so many xml parsers just throw an Exception complaining about no root element. Etc.
In this example there is a solution on how to solve that problem and succesfully parse the malformed xml above.
Basically what we will do is to add programmatically a root element.
So first of all you have to open the resource that contains your "malformed" xml (i. e. a file):
File file = new File(pathtofile);
Then open a FileInputStream:
FileInputStream fis = new FileInputStream(file);
If we try to parse this stream with any XML library at that point we will raise the malformed document Exception.
Now we create a list of InputStream objects with three lements:
A ByteIputStream element that contains the string: <root>
Our FileInputStream
A ByteInputStream with the string: </root>
So the code is:
List<InputStream> streams =
Arrays.asList(
new ByteArrayInputStream("<root>".getBytes()),
fis,
new ByteArrayInputStream("</root>".getBytes()));
Now using a SequenceInputStream, we create a container for the List created above:
InputStream cntr =
new SequenceInputStream(Collections.enumeration(str));
Now we can use any XML Parser library, on the cntr, and it will be parsed without any problem. (Checked with Stax library);

HL7 version 2.7 parser using java except Hapi

Is there any good parser which can parser HL7 V2.7 message using Java except HAPI. My goal is to convert the message into a XML file.

There is my own open source alternative called HL7X, which does work with any HL7v2 version. It converts your HL7 String into a XML String.
Example:
MSH|^~\&|||||20121116122025||ADT^A01|5730224|P|2.5||||||UNICODE UTF-8
EVN|A01|20130120151827
PID||0|123||Name^Firstname^^^^||193106170000|w
PV1||E|
Gets transformed to
<?xml version="1.0" encoding="UTF-8"?>
<HL7X>
<HL7X>
<MSH>
<MSH.1>^~\&</MSH.1>
<MSH.6>20121116122025</MSH.6>
<MSH.8>
<MSH.8.1>ADT</MSH.8.1>
<MSH.8.2>A01</MSH.8.2>
</MSH.8>
<MSH.9>5730224</MSH.9>
<MSH.10>P</MSH.10>
<MSH.11>2.5</MSH.11>
<MSH.17>UNICODE UTF-8</MSH.17>
</MSH>
<EVN>
<EVN.1>A01</EVN.1>
<EVN.2>20130120151827</EVN.2>
</EVN>
<PID>
<PID.2>0</PID.2>
<PID.3>123</PID.3>
<PID.5>
<PID.5.1>Name</PID.5.1>
<PID.5.2>Firstname</PID.5.2>
</PID.5>
<PID.7>193106170000</PID.7>
<PID.8>F</PID.8>
</PID>
<PV1>
<PV1.2>E</PV1.2>
</PV1>
</HL7X>

this http://www.dcm4che.org/confluence/display/ee2/Home open source Java software can receive various HL7 messages through the MLLP protocol, convert them to XML, run through XSLT transformer and then load them into database and serve to DICOM clients as needed. In order to do this in the code base there is the HL7->XML code. Just find it, copy/paste it and use it.
Once I knew where exactly this code is as I was troubleshooting message character set problem. At that time I have found that the HL7 parser is rather simple-minded and can understand only 1 character set provided in the configuration. It does not read/use character set (MSH-18, Table 0211, Grahame Grieve's encoding tips) provided in the messages neither does it support switching character sets during the message decoding (see chapter "Escape sequences supporting multiple character sets" in HL7 specification).
So I know the parser code is there. It is in Java. It produces XML inputs for the customer-specific XSLT transformation script. It should be quite easy to reuse.
You should be able to find it by yourself. Otherwise your question would turn out as plain finding a tool §4 is an off-topic :)

How to determine whether a given string is an .xml file

I have an issue that I get some some response as a String.
This String could be a normal string,number etc.. or an .xml file.
Now ,when I get an xml file, I want to treat it differently.
I am not able to distinguish between a string or an .xml file.
Also, this xml file could have some syntatic error.
Please suggest , how do I go ahead
Code is like this:
Document document = reader.read(new StringReader(xml));
where xml can be a string or an xml file itself.
If xml is a string , it is fine but if it is an xml file and with some syntax error then it should throw exception

If it is a proper XML document it should begin with a XML declaration. If that's there, it's intended to be a conforming XML document. If that's not there it cannot be a conforming XML document.

If you are using a coding language like C#, then you can use - XmlDocument.loadxml -
http://msdn.microsoft.com/en-us/library/system.xml.xmldocument.loadxml.aspx
This will throw error if the string is not in correct xml format.