Crash when a tag that usually contains a list is not in the JSON sidecar but present in the criteria of the config file

po09i commented 2 weeks ago

Summary

Dcm2bids crashes when the configuration file is set up with a list as a criteria but the tag is not defined in the JSON sidecar. I'm assuming that this is unintended behaviour and it should not match the criteria rather than crash the program.

Terminal output

``` lib/python3.10/site-packages/dcm2bids/dcm2bids_gen.py:116: in run parser.build_graph() lib/python3.10/site-packages/dcm2bids/sidecar.py:274: in build_graph if criteria and self.isLink(sidecar.data, criteria): lib/python3.10/site-packages/dcm2bids/sidecar.py:400: in isLink result.append(compare(name, pattern)) lib/python3.10/site-packages/dcm2bids/sidecar.py:294: in compare return bool(re.match(pattern, name)) lib/python3.10/re.py:190: in match return _compile(pattern, flags).match(string) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pattern = ['.*', '.*', 'M', '.*'], flags = 0 def _compile(pattern, flags): # internal: compile pattern if isinstance(flags, RegexFlag): flags = flags.value try: > return _cache[type(pattern), pattern, flags] E TypeError: unhashable type: 'list' lib/python3.10/re.py:293: TypeError ```

To reproduce:

Example config file:

{
    "search_method": "re",
    "case_sensitive": false,
    "descriptions": [
        {
            "datatype": "anat",
            "suffix": "magnitude1",
            "criteria": {
                "ImageType": [".*", ".*", "M", ".*"]
            }
        }
    ]
}

Example JSON sidecar (CRASH)

{
    "Modality": "MR"
}

Example JSON sidecar (NO CRASH)

{
    "Modality": "MR"
         "ImageType": []
}

Suggestion

I believe the problem comes from here where the default value is set to a string if the tag does not exist but is later compared to a list which creates the crash. The default value should probably be an empty list for these tags.

Linked files

I uploaded my test files for easier replication crash.json pass.json dcm2bids_test.json

UNFmontreal / Dcm2Bids