PEDIA-Charite / PEDIA-workflow

PEDIA-workflow prioritizes the disease-causing gene by integrating facial analysis and exome sequencing data.
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Log filtered empty cases #52

Closed la60312 closed 6 years ago

la60312 commented 6 years ago

Some empty cases are filtered out in the first filtering process in QC. F2G sometimes will transfer empty JSON files to us even if the cases were annotated features and photos. Therefore, we need to log these case in our report then we can report to them these is something wrong with the data transfer.

I guess it is in this function in json_parser.py.

    def check(self) -> bool:
        '''Check whether Json fulfills all provided criteria.
        The criteria are:
            picture has been provided - gestalt_score in detected_syndromes
            should be greater than 0
            clinical diagnosis - selected_syndromes should not be empty
            single monogenetic disease - not multiple syndromes selected and
            not multiple pathogenic mutations in different genes
            SNP mutations - no microdel/dup or other large scale aberrations
xiamaz commented 6 years ago

I am going to add some logging for these cases.