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My task involves comparing the data mapped from one format to another. Formats I use are xml to edi, edi to edi, edi to lawson, xml to pdf etc. now I perform it manually by comparing each input with its corresponding output and then check for the specific entries in both the docs and yes,it is a time consuming process. Are there any tools for any of theses formats which could be used to automate the comparison???

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It would help if you told us which specific formats you need to compare - there are compare tools which work well for text-readable files (XML, RTF, TXT, CSV and so forth) but need plugins to compare formats like PDF, DOC, XML etc. As is, there isn't enough information to give a good answer. – Kate Paulk Jun 27 '14 at 10:19
Formats include which i have specified in the question. To be specific: XML to PDF, EDI to PDF, XML to LAWSON, EDI to PDF. – user7976 Jun 27 '14 at 10:52
Are these the only format conversions? – Kate Paulk Jun 27 '14 at 13:30
I get these formats mostly. there are other formats too but i don't get them very often – user7976 Jun 30 '14 at 5:25

No. The issue here is that these mappings are not 1-1; in other words, there is no single, definitive mapping between these formats. Each mapping requires additional heuristics that (I assume) are built into the conversion software you are interested in testing.

Still, I think there is hope. You can probably find APIs for extracting data from each of these formats. You can use those APIs, along with knowledge of how your conversion software is supposed to behave, to test your conversion software.

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Adding to user246 answer- languages like Perl or Python have libraries to read textual and non-textual formats like PDF, DOC or XML. Once you read the file into a data structure comparison is relatively easy, but keep in mind that reading itself converts the file to something new, and like user246 wrote there are no simple rules for conversion.

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