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Welcome => Bug reports => Topic started by: Bernhard10 on November 29, 2018, 04:39:59 am

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Title: JSON output should escape backslashes
Post by: Bernhard10 on November 29, 2018, 04:39:59 am

When I give DSSR a filename which contains a backslash (e.g. as a path seperator on Windows), this backslash gets included in the created JSON in the fields "command", "input_file" and possibly "str_id".
This makes the JSON invalid and impossible to parse, because backslashes are escape characters in JSON and have to be escaped as "\\" to produce valid JSON.

Example:
rename 1rnk.pdb into '1rnk\something.pdb'
./x3dna-dssr -i='1rnk\something.pdb' --json

Gives a JSON including
{"command":"x3dna-dssr -i=1rnk\something.pdb --json","input_file":"1rnk\something.pdb","str_id":"1rnk\something"

instead of
{"command":"x3dna-dssr -i=1rnk\\something.pdb --json","input_file":"1rnk\\something.pdb","str_id":"1rnk\\something"

Title: Re: JSON output should escape backslashes
Post by: xiangjun on November 29, 2018, 10:24:14 am

Thanks for reporting the JSON string escape bug in DSSR. Your bug report is exemplary in its clarity. I'll fix this bug and release an updated DSSR version, hopefully shortly.

Best regards,

Xiang-Jun

Title: Re: JSON output should escape backslashes
Post by: xiangjun on November 29, 2018, 11:14:45 am

I've updated DSSR to v1.8.5-2018nov29. The bug of not escaping backslash (or double quote) in DSSR JSON output has been fixed.

Please have a try and report back how it goes.

Best regards,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University