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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);

Is it possible to validate XML against schemas present in that XML file using Java?

So I have an XML that already has all the schemas specified in the root tag like this
<Waybill xmlns="urn:some:uri1"
xmlns:cac="urn:some:uri2"
xmlns:cbc="urn:some:uri3"
xmlns:ext="urn:some:uri4" xmlns:xxx="http://some.url.com">
Is it possible to validate my XML against these in the Java code in such a way that I don't have to repeat them in the Java code again?
All the examples I found so far require you to specify the url explicitly in the code

Try this: Validating XML against XSD
The magic seems to be in this: XMLConstants.W3C_XML_SCHEMA_NS_URI.

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 :)

Validating XSD itself

Could anyone please tell me how to validate an XSD file itself (not XML against XSD)? I have checked many forums and sites (including SO) and most of them refers some or the other online validator. But this is not a one-time check for us. Our application involves an XSL transformation using an XSD, so we need to determine whether the XSD to be used is itself in a valid format or not, as in, all the tags match, with a starting and a closing one. Certain tags aren't allowed as a child tag, etc. That's why we need a proper java code to achieve the same.
Any help would be highly appreciated.

You can validate an XSD file against the w3 XSD schema that can be found here.
Use the same validation techniques you validate any other XML file with an XSD file, only the source document would be your XSD file.

you can use xmllint for that:
xmllint --noout --dtdvalid http://www.w3.org/2001/XMLSchema.dtd my-schema.xsd

You can try javax.xml.validation package
SchemaFactory f = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Schema s = f.newSchema(new File("1.xsd"));
Schema.newSchema() API
Parses the specified File as a schema and returns it as a Schema

You can validate your XSD online here.
Just copy and paste your XSD here and click on validate Schema , it will give you the result.

Force resolution of xsl:include, xsl:import in Java

I'm using Saxon 9.3 HE and Java 1.6. I can resolve xsl:include and xsl:import statements in the xsl by supplying a resolver to setURIResolver on the TransformerFactory instance.
However the Source resolve(String includee, String includer) method doesn't get called if the file was resolved previously. This is a problem for me because I want to resolve differently based on the includer file. For example <xsl:include href="foo.xsl"/> in file1.xsl would be a different file from <xsl:include href="foo.xsl"/> in file2.xsl, and file1.xsl and file2.xsl would be included by file3.xsl. I have some "base" code and "customer-specific" code that can override the template file and I need to resolve them differently for a framework I'm building.

The XSLT specification is clear that resolving a relative URI in the href attribute against the base URI of the containing element must be done according to the standard rules for handling relative URIs, while dereferencing the resulting absolute URI can be done any way the implementation likes. I'd suggest rethinking your design to take account of this.

I would have expected that because the two XSLs that have that includes in them have different base URIs that the URIResolver would need to be called for each one (what if they are in different directories?).
When creating sources for file1.xsl and file2.xsl, what are their system IDs? If they are null, exist in the same directory or don't have any path information (i.e. systemId is just file1.xsl and file2.xsl) maybe Saxon is trying to do an optimization by assuming they are in the same directory and therefore assuming foo.xsl referred to by each one is the same file.
Maybe try explicitly setting the systemId of the source of the base files and make them have different directories?