ND2 defensive parsing #691
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--test nd2 |
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Excluding, as this caused http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-full-repository-stable/335/ to fail. Most likely, wrapping all of the metadata parsing in a single try/catch block prevents something from executing, but what exactly is not obvious from the diff. For a more manageable example to test locally, this should result in 11 test failures with this PR's branch:
The same test with dev_4_4 alone results in 0 failures. |
Several numerical parsing methods throw NumberFormatException when the input string is not actually a number. In particular: * Integer.parseInt(String) * Double.parseDouble(String) * new Integer(String) * new Double(String) The ND2 handler parses a large number of string key/value pairs, converting values into numbers in many cases. But in almost every case, no error handling was done in case the input value was not a number. This change adds a blanket try/catch for NumberFormatException around areas that parse lots of numbers, emitting a warning for any non-conforming key/value pairs. This allows parsing to continue, hopefully resulting in a less fragile ND2 reader. It also catches NumberFormatException separately within the nested TextInfoItem parse loop, so that parsing of TextInfoItem entries fail individually rather than all-or-nothing. Note that this change is nearly all whitespace indentation; the easiest way to view the "real" change is using "git show -b" on the commit.
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Thanks @melissalinkert. The problem was that the All the tests now pass on my system for |
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Builds as of today looked good, @ctrueden. @melissalinkert ? |
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Thanks @joshmoore. 😂 |
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--rebased-to #700 |
This change is an attempted fix for Fiji bug #655.
Several numerical parsing methods throw
NumberFormatExceptionwhen the input string is not actually a number. In particular:Integer.parseInt(String)Double.parseDouble(String)new Integer(String)new Double(String)The ND2 handler parses a large number of string key/value pairs, converting values into numbers in many cases. But in almost every case, no error handling was done in case the input value was not a number.
This change adds a blanket try/catch for
NumberFormatExceptionaround areas that parse lots of numbers, emitting a warning for any non-conforming key/value pairs. This allows parsing to continue, hopefully resulting in a less fragile ND2 reader.Note that this change is nearly all whitespace indentation; the easiest way to view the "real" change is using
git show -bon the commit.