I’m trying to parse text from a file that comes in a pseudo XML format. I can get a DOM document out of it when it comes in the following structure:
<product>
<product_id>234567</product_id>
<description>abc</description>
</product>
The problem I’m running into happens when the structure is similar to the following:
<product>
<product_id>234567</product_id>
<description>abc</description>
<quantity 1:2>
<version>1.1</version>
</quantity 1:2>
<version>1.2</version>
<quantity 2:2>
</quantity 2:2>
</product>
It generates the following exception due to the space in <quantity 1:2>:
org.xml.sax.SAXParseException:[Fatal Error] :1:167: Element type " quantity " must be followed by either attribute specifications, ">" or "/>"
I can get around this by replacing the space with an underscore. The problem is the structure can be vary in size and include several child nodes with the same format (<node 1:x>) and the file can contain hundreds of structures to parse. Is there a class available that will parse text like this a return a tree-like object?
Your file is not an XML at all, and SAX is for XML (Simple API for XML). You should re-think your structure so you can do something like:
<quantity myAttr="1.2">
<version>1.2</version>
</quantity>
<quantity myAttr="1.x">
<version>1.1</version>
</quantity>
<version>1.0</version>
Or something like that.
Preprocess the file and change elements with that x:y form to <element value="x:y"/> then your DOM/SAX parsers will not choke.
I would suggest using a regular expression to help but that way leads to madness.
It generates the following exception due to the space in <quantity 1:2>
This is not the root cause of the error, the root cause is, as people have already mentioned, your file format is not valid XML. A valid XML tag would look like <quantity attr1="val1" attr2="val2>.
It sounds like you have no control over the file format. In this case I think the easiest way is to preprocess your file into valid XML then have DOM/SAX parser to parse it:
FileInputStream file = new FileInputStream("pseudo.pxml");
ByteArrayOutputStream temp = new ByteArrayOutputStream();
int c = -1;
while ((c=file.read()) >= 0){
temp.write(c);
}
String xml = new String(temp.toByteArray());
xml = xml.replaceAll("([^:\s]+:[^:\s]+)", "value=\"\\1\"");
ByteArrayInputStream xmlIn = new ByteArrayInputStream(xml.getBytes());
/* use xmlIn for your XML parsers */
Note that I did not test this code nor is it optimized; just wanted to give you an idea.
Related
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);
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);
I am using xstream to marshal / unmarshal between java object to / from xml, one question is, is there a right solution to solve my problem (using xstream or other advanced method, instead of pure java API).
The existing XML file can grow quite big (more than 200 mb, for example), and I like to append the new xml to this existing XML file, but without unmarshal the existing XML file first, simply append it to the end (before the root element).
Please advice, thanks.
You could load the first XML as org.w3c.dom.Document and import the second one as org.w3c.dom.Element:
Element nodeToImport = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse( secondXmlFile ).getDocumentElement();
dom.importNode( nodeToImport, true );
...
There is a similar example here, but with a new node around the root one: Add an element around root element of given XML file that is stored in org.w3c.dom.Document
I have a number of pre-generated, static xml files containing soap requests. I can read them, send the request, and get back and answer from the server. I would like to get some advice on how to create a dynamic process:
<?xml version="1.0" encoding="utf-8"?>
<soap:Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/">
<soap:Body>
<getProject xmlns="http://myserver/">
<atr1>string</atr1>
<atr2>string</atr2>
</getProject>
</soap:Body>
</soap:Envelope>
So, I want to be able to read these xml files, change the values of the nodes , etc. to real values gathered from user input at run-time. What would be the best way to go: read the xml file line by line and use a regex to replace value, or maybe make a temp copy of the xml file, use sax to replace the node value, then send the new xml, or completely discard the pre-generated xml files and instead create them on-the-fly, or how? Any suggestions would be appreciated.
Using regexes would be fragile, because the formatting of the XML could change in ways you're not expecting, and still be well-formed and valid XML, but not fit your regexes. In general it's not recommended to use regexes to parse XML.
Using SAX to read in the XML file (why make a temp copy?), copy all nodes to the output, modifying certain ones to put in the user-supplied values. That sounds like a good, workable solution.
Create the XML from scratch: that does sound simpler, if you know their structure in advance, and it's not too big. One way to do this would be to use an XSLT stylesheet, and pass in the user-supplied values as parameters.
You could use castor and create objects from the xml, and xml from the objects.
private void changeTagData(List<String> tagNameList, SOAPBody body) {
for(String tagName : tagNameList){
NodeList nodeList = body.getElementsByTagName(tagName);
int length = nodeList.getLength();
Node node;
for (int i = 0; i < length; i++) {
node = (Node) nodeList.item(i);
node.setTextContent("change tag data");
}
}
}
XStream can also be used in this process i am also doing some what same thing. If you like you can try XStream also.
I inherited an "XML" license file containing no root element, but rather two XML fragments (<XmlCreated> and <Product>) so when I try to parse the file, I (expectantly) get an error about a document that is not-well-formed.
I need to get both the XmlCreated and Product tags.
Sample XML file:
<?xml version="1.0"?>
<XmlCreated>May 11 2009</XmlCreated>
<!-- License Key file Attributes -->
<Product image ="LicenseKeyFile">
<!-- MyCompany -->
<Manufacturer ID="7f">
<SerialNumber>21072832521007</SerialNumber>
<ChassisId>72060034465DE1C3</ChassisId>
<RtspMaxUsers>500</RtspMaxUsers>
<MaxChannels>8</MaxChannels>
</Manufacturer>
</Product>
Here is the current code that I use to attempt to load the XML. It does not work, but I've used it before as a starting point for well-formed XML.
public static void main(String[] args) {
try {
File file = new File("C:\\path\\LicenseFile.xml");
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(file);
} catch (Exception e) {
e.printStackTrace();
}
}
At the db.parse(file) line, I get the following Exception:
[Fatal Error] LicenseFile.xml:6:2: The markup in the document following the root element must be well-formed.
org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at com.mycompany.licensesigning.LicenseSigner.main(LicenseSigner.java:20)
How would I go about parsing this frustrating file?
If you know this document is always going to be non-well formed... make it so. Add a new dummy <root> tag after the <?xml...>and </root> after the last of the data.
You're going to need to create two separate Document objects by breaking the file up into smaller pieces and parsing those pieces individually (or alternatively reconstructing them into a larger document by adding a tag which encloses both of them).
If you can rely on the structure of the file it should be easy to read the file into a string and then search for substrings like <Product and </Product> and then use those markers to create a string you can pass into a document builder.
How about implementing a simple wrapper around InputStream that wraps the input from the file with a root-level tag, and using that as the input to DocumentBuilder.parse()?
If the expected input is small enough to load into memory, read into a string, wrap it with a dummy start/end tag and then use:
DocumentBuilder.parse(new InputSource(new StringReader(string)))
I'd probably create a SequenceInputStream where you sandwich the real stream with two ByteArrayInputStreams that return some dummy root start tag, and end tag.
Then i'd use use the parse method that takes a stream rather than a file name.
I agree with Jim Garrison to some extent, use an InputStream or StreamReader and wrap the input in the required tags, its a simple and easy method. Main problem i can forsee is you'll have to have some checks for valid and invalid formatting (if you want to be able to use the method for both valid and invalid data), if the formatting is invalid (because of root level tags missing) wrap the input with the tags, if its valid then don't wrap the input. If the input is invalid for some other reason, you can also alter the input to correct the formatting issues.
Also, its probably better to store the ipnut in a collection of strings (of some sort) rather than a string itself, this will mean that you wont have as much of a limit to your input size. Make each string one line from the file. You should end up with a logical and easy to follow structure which mwill make it easier to allow for corrections of other formatting issues in the future.
Hardest part about that is figuring out what has caused the invalid formatting. In your case just check for root level tags, if the tags exist and are formatted correctly, dont wrap, If not, wrap.