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common_subject.py

Subject

Bases: SpyglassIngestion, Manual

Source code in src/spyglass/common/common_subject.py 
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@schema
class Subject(SpyglassIngestion, dj.Manual):
    definition = """
    subject_id: varchar(80)
    ---
    age = NULL: varchar(200)
    description = NULL: varchar(2000)
    genotype = NULL: varchar(2000)
    sex = "U": enum("M", "F", "U")
    species = NULL: varchar(200)
    """
    _expected_duplicates = True

    @property
    def table_key_to_obj_attr(self):
        return {
            "self": {
                "subject_id": "subject_id",
                "age": "age",
                "description": "description",
                "genotype": "genotype",
                "sex": self.standardized_sex_string,
                "species": "species",
            }
        }

    @property
    def _source_nwb_object_type(self):
        return pynwb.file.Subject

    @staticmethod
    def standardized_sex_string(subject, warn=True):
        """Takes subject.sex and returns 'M', 'F', or 'U'."""
        if isinstance(subject, dict):
            sex_field = subject.get("sex", "U") or "U"
        else:
            sex_field = getattr(subject, "sex", "U") or "U"
        if (sex := sex_field[0].upper()) in ("M", "F", "U"):
            return sex
        elif warn:
            logger.info(
                f"Unrecognized sex identifier {sex_field}, setting to 'U'"
            )
        return "U"

    def _adjust_keys_for_entry(self, keys):
        """Fill in any NULL values in the key with defaults."""
        # Avoids triggering 'accept_divergence' on reinsert
        adjusted = []
        for key in keys.copy():
            key["sex"] = self.standardized_sex_string(key, warn=False)
            adjusted.append(key)
        return super()._adjust_keys_for_entry(adjusted)

standardized_sex_string(subject, warn=True) staticmethod

Takes subject.sex and returns 'M', 'F', or 'U'.

Source code in src/spyglass/common/common_subject.py 
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@staticmethod
def standardized_sex_string(subject, warn=True):
    """Takes subject.sex and returns 'M', 'F', or 'U'."""
    if isinstance(subject, dict):
        sex_field = subject.get("sex", "U") or "U"
    else:
        sex_field = getattr(subject, "sex", "U") or "U"
    if (sex := sex_field[0].upper()) in ("M", "F", "U"):
        return sex
    elif warn:
        logger.info(
            f"Unrecognized sex identifier {sex_field}, setting to 'U'"
        )
    return "U"