82 lines
2.4 KiB
Python
82 lines
2.4 KiB
Python
from mirri.entities.sequence import GenomicSequence
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from mirri.biolomics.serializers import RECORD_ID, RECORD_NAME, RECORD_DETAILS
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class GenomicSequenceBiolomics(GenomicSequence):
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def __init__(self, **kwargs):
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super().__init__(freeze=False, **kwargs)
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@property
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def record_id(self) -> int:
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return self._data.get(RECORD_ID, None)
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@record_id.setter
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def record_id(self, value: int):
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self._data[RECORD_ID] = value
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@property
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def record_name(self) -> str:
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return self._data.get(RECORD_NAME, None)
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@record_name.setter
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def record_name(self, value: str):
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self._data[RECORD_NAME] = value
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def dict(self):
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_data = super(GenomicSequenceBiolomics, self).dict()
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if self.record_id:
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_data[RECORD_ID] = self.record_id
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if self.record_name:
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_data[RECORD_NAME] = self.record_name
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return _data
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def serialize_to_biolomics(marker: GenomicSequenceBiolomics, client=None, update=False):
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ws_sequence = {}
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print()
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if marker.record_id:
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ws_sequence[RECORD_ID] = marker.record_id
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if marker.record_name:
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ws_sequence[RECORD_NAME] = marker.record_name
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else:
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ws_sequence[RECORD_NAME] = marker.marker_id
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details = {}
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if marker.marker_id:
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details["INSDC number"] = {"Value": marker.marker_id,
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"FieldType": "E"}
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if marker.marker_seq:
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details["DNA sequence"] = {
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"Value": {"Sequence": marker.marker_seq},
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"FieldType": "N"}
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if marker.marker_type:
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details['Marker name'] = {"Value": marker.marker_type, "FieldType": "E"}
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ws_sequence[RECORD_DETAILS] = details
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return ws_sequence
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MAPPING_WS_SPEC_TYPES = {
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'Beta tubulin': 'TUBB'
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}
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def serialize_from_biolomics(ws_data, client=None) -> GenomicSequenceBiolomics:
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marker = GenomicSequenceBiolomics()
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marker.record_id = ws_data[RECORD_ID]
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marker.record_name = ws_data[RECORD_NAME]
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for key, value in ws_data['RecordDetails'].items():
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value = value['Value']
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if key == 'INSDC number' and value:
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marker.marker_id = value
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elif key == 'Marker name' and value:
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kind = MAPPING_WS_SPEC_TYPES.get(value, None)
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value = kind if kind else value
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marker.marker_type = value
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elif key == 'DNA sequence' and 'Sequence' in value and value['Sequence']:
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marker.marker_seq = value['Sequence']
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return marker
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