forked from MIRRI/mirri_utils
Mirri 5.1.2
This commit is contained in:
@@ -0,0 +1,3 @@
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RECORD_ID = 'RecordId'
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RECORD_NAME = 'RecordName'
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RECORD_DETAILS = 'RecordDetails'
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@@ -0,0 +1,82 @@
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from typing import List
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from mirri import rgetattr
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from mirri.entities.publication import Publication
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from mirri.biolomics.settings import PUB_MIRRI_FIELDS
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RECORD_ID = 'RecordId'
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RECORD_NAME = 'RecordName'
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PUB_MAPPING = {
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# 'record_id': 'RecordId',
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# 'record_name': 'RecordName',
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'strains': "Associated strains",
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'taxa': "Associated taxa",
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'authors': "Authors",
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# 'sequneces': "Associated sequences",
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# 'abstract': "Abstract",
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# 'collection': "Collection",
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'doi': "DOI number",
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'editor': "Editor(s)",
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# 'full_reference': "Full reference",
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# 'link': "Hyperlink",
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'isbn': "ISBN",
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'issn': "ISSN",
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'issue': "Issue",
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'journal': "Journal",
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'journal_book': "Journal-Book",
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# 'keywords': "Keywords",
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'first_page': "Page from",
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'last_page': "Page to",
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'publisher': "Publisher",
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'pubmed_id': "PubMed ID",
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'volume': "Volume",
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'year': "Year",
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}
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REV_PUB_MAPPING = {v: k for k, v in PUB_MAPPING.items()}
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def serializer_from_biolomics(ws_data, client=None) -> Publication:
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pub = Publication()
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pub.record_id = ws_data[RECORD_ID]
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pub.record_name = ws_data[RECORD_NAME]
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pub.title = ws_data[RECORD_NAME]
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for field, value in ws_data['RecordDetails'].items():
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value = value['Value']
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if not value:
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continue
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attr = REV_PUB_MAPPING.get(field, None)
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if not attr:
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continue
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if attr in ('year', 'first_page', 'last_page'):
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value = int(value)
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setattr(pub, attr, value)
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return pub
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def get_publication_record_name(publication):
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if publication.record_name:
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return publication.record_name
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if publication.title:
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return publication.title
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if publication.pubmed_id:
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return f'PUBMED:{publication.pubmed_id}'
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if publication.doi:
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return f'DOI:{publication.doi}'
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def serializer_to_biolomics(publication: Publication, client=None, update=False):
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ws_data = {}
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if publication.record_id:
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ws_data[RECORD_ID] = publication.record_id
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ws_data[RECORD_NAME] = get_publication_record_name(publication)
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details = {}
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for attr, field in PUB_MAPPING.items():
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value = getattr(publication, attr, None)
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if value is None:
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continue
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field_type = 'D' if attr == 'year' else "E"
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details[field] = {'Value': value, 'FieldType': field_type}
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ws_data['RecordDetails'] = details
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return ws_data
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@@ -0,0 +1,66 @@
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from mirri.biolomics.serializers import RECORD_ID, RECORD_NAME, RECORD_DETAILS
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from mirri.entities.growth_medium import GrowthMedium
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def serialize_from_biolomics(ws_data, client=None) -> GrowthMedium:
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medium = GrowthMedium()
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medium.record_name = ws_data.get('RecordName', None)
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medium.description = get_growth_medium_record_name(medium)
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medium.record_id = ws_data.get('RecordId', None)
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for key, value in ws_data['RecordDetails'].items():
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value = value['Value']
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if not value:
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continue
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if key == "Full description":
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medium.full_description = value
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if key == "Ingredients":
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medium.ingredients = value
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if key == 'Medium description':
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medium.description = value
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if key == 'Other name':
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medium.other_name= value
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if key == 'pH':
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medium.ph = value
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if key == 'Sterilization conditions':
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medium.sterilization_conditions = value
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return medium
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def get_growth_medium_record_name(growth_medium):
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if growth_medium.record_name:
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return growth_medium.record_name
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if growth_medium.description:
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return growth_medium.description
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if growth_medium.acronym:
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return growth_medium.acronym
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GROWTH_MEDIUM_MAPPING = {
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'acronym': 'Acronym',
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'full_description': "Full description",
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'ingredients': "Ingredients",
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'description': 'Medium description',
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'other_name': 'Other name',
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'ph': 'pH',
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'sterilization_conditions': 'Sterilization conditions'
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}
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def serialize_to_biolomics(growth_medium: GrowthMedium, client=None, update=False):
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ws_data = {}
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if growth_medium.record_id:
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ws_data[RECORD_ID] = growth_medium.record_id
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record_name = get_growth_medium_record_name(growth_medium)
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ws_data[RECORD_NAME] = record_name
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details = {}
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for field in growth_medium.fields:
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if field in ('acronym', 'record_id', 'record_name'):
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continue
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value = getattr(growth_medium, field, None)
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if value is not None:
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details[GROWTH_MEDIUM_MAPPING[field]] = {'Value': value, 'FieldType': 'E'}
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ws_data[RECORD_DETAILS] = details
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return ws_data
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@@ -0,0 +1,26 @@
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from mirri.entities.location import Location
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def serialize_from_biolomics(ws_data, client=None):
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return ws_data
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# this is a proof of concept
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def serialize_location(location: Location):
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fields = {}
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if location.country:
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fields['Country'] = {'Value': location.country, 'FieldType': 'E'}
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if location.latitude and location.longitude:
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value = {'Latitude': location.latitude,
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'Longitude': location.longitude}
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if location.coord_uncertainty:
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value['Precision'] = location.coord_uncertainty
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fields['GIS position'] = {'FieldType': 'L', 'Value': value}
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fields['Strains'] = {"FieldType": "RLink", 'Value': [{
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'Name': {'Value': None, 'FieldType': "E"},
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'RecordId': None
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}]}
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return {"RecordDetails": fields,
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"RecordName": location.country}
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@@ -0,0 +1,2 @@
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def serialize_from_biolomics(ws_data, client=None):
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return ws_data
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@@ -0,0 +1,81 @@
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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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@@ -0,0 +1,462 @@
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import re
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import sys
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import pycountry
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from mirri import rgetattr, rsetattr
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from mirri.entities.date_range import DateRange
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from mirri.entities.strain import ORG_TYPES, OrganismType, StrainId, StrainMirri, add_taxon_to_strain
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from mirri.biolomics.remote.endoint_names import (GROWTH_MEDIUM_WS, TAXONOMY_WS,
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ONTOBIOTOPE_WS, BIBLIOGRAPHY_WS, SEQUENCE_WS, COUNTRY_WS)
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from mirri.settings import (
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ALLOWED_FORMS_OF_SUPPLY,
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NAGOYA_PROBABLY_SCOPE,
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NAGOYA_NO_RESTRICTIONS,
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NAGOYA_DOCS_AVAILABLE,
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NO_RESTRICTION,
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ONLY_RESEARCH,
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COMMERCIAL_USE_WITH_AGREEMENT,
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)
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from mirri.biolomics.settings import MIRRI_FIELDS
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from mirri.utils import get_pycountry
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NAGOYA_TRANSLATOR = {
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NAGOYA_NO_RESTRICTIONS: "no known restrictions under the Nagoya protocol",
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NAGOYA_DOCS_AVAILABLE: "documents providing proof of legal access and terms of use available at the collection",
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NAGOYA_PROBABLY_SCOPE: "strain probably in scope, please contact the culture collection",
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}
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REV_NAGOYA_TRANSLATOR = {v: k for k, v in NAGOYA_TRANSLATOR.items()}
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RESTRICTION_USE_TRANSLATOR = {
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NO_RESTRICTION: "no restriction apply",
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ONLY_RESEARCH: "for research use only",
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COMMERCIAL_USE_WITH_AGREEMENT: "for commercial development a special agreement is requested",
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}
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REV_RESTRICTION_USE_TRANSLATOR = {v: k for k,
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v in RESTRICTION_USE_TRANSLATOR.items()}
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DATE_TYPE_FIELDS = ("Date of collection", "Date of isolation",
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"Date of deposit", "Date of inclusion in the catalogue")
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BOOLEAN_TYPE_FIELDS = ("Strain from a registered collection", "Dual use",
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"Quarantine in Europe", "Interspecific hybrid") # , 'GMO')
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FILE_TYPE_FIELDS = ("MTA file", "ABS related files")
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MAX_MIN_TYPE_FIELDS = ("Tested temperature growth range",
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"Recommended growth temperature")
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LIST_TYPES_TO_JOIN = ('Other denomination', 'Plasmids collections fields', 'Plasmids')
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MARKER_TYPE_MAPPING = {
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'16S rRNA': 'Sequences 16s', # or Sequences c16S rRNA
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'ACT': 'Sequences ACT',
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'CaM': 'Sequences CaM',
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'EF-1α': 'Sequences TEF1a',
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'ITS': 'Sequences ITS',
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'LSU': 'Sequences LSU',
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'RPB1': 'Sequences RPB1',
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'RPB2': 'Sequences RPB2',
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'TUBB': 'Sequences TUB' # or Sequences Beta tubulin
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}
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def serialize_to_biolomics(strain: StrainMirri, client=None, update=False,
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log_fhand=None): # sourcery no-metrics
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if log_fhand is None:
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log_fhand = sys.stdout
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strain_record_details = {}
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for field in MIRRI_FIELDS:
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try:
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biolomics_field = field["biolomics"]["field"]
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biolomics_type = field["biolomics"]["type"]
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except KeyError:
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# print(f'biolomics not configured: {field["label"]}')
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continue
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label = field["label"]
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attribute = field["attribute"]
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value = rgetattr(strain, attribute, None)
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if value is None:
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continue
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if label == "Accession number":
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value = f"{strain.id.collection} {strain.id.number}"
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if label == "Restrictions on use":
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value = RESTRICTION_USE_TRANSLATOR[value]
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elif label == "Nagoya protocol restrictions and compliance conditions":
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value = NAGOYA_TRANSLATOR[value]
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elif label in FILE_TYPE_FIELDS:
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value = [{"Name": "link", "Value": fname} for fname in value]
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elif label == "Other culture collection numbers":
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value = "; ".join(on.strain_id for on in value) if value else None
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elif label in BOOLEAN_TYPE_FIELDS:
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value = 'yes' if value else 'no'
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elif label in 'GMO':
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value = 'Yes' if value else 'No'
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elif label == "Organism type":
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org_types = [ot.name for ot in value]
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value = []
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for ot in ORG_TYPES.keys():
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is_organism = "yes" if ot in org_types else "no"
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value.append({"Name": ot, "Value": is_organism})
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elif label == 'Taxon name':
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if client:
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taxa = strain.taxonomy.long_name.split(';')
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value = []
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for taxon_name in taxa:
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taxon = get_remote_rlink(client, TAXONOMY_WS,
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taxon_name)
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if taxon:
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value.append(taxon)
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if not value:
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msg = f'WARNING: {strain.taxonomy.long_name} not found in database'
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log_fhand.write(msg + '\n')
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# TODO: decide to raise or not if taxon not in MIRRI DB
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#raise ValueError(msg)
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elif label in DATE_TYPE_FIELDS:
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year = value._year
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month = value._month or 1
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day = value._day or 1
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if year is None:
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continue
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value = f"{year}-{month:02}-{day:02}"
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elif label == 'History of deposit':
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value = " < ".join(value)
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elif label in MAX_MIN_TYPE_FIELDS:
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if isinstance(value, (int, float, str)):
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_max, _min = float(value), float(value)
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else:
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_max, _min = float(value['max']), float(value['min'])
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content = {"MaxValue": _max, "MinValue": _min,
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"FieldType": biolomics_type}
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strain_record_details[biolomics_field] = content
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continue
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elif label in LIST_TYPES_TO_JOIN:
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value = '; '.join(value)
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# TODO: Check how to deal with crossrefs
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elif label == "Recommended medium for growth":
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if client is not None:
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ref_value = []
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for medium in value:
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ws_gm = client.retrieve_by_name(GROWTH_MEDIUM_WS, medium)
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if ws_gm is None:
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raise ValueError(
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f'Can not find the growth medium: {medium}')
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gm = {"Name": {"Value": medium, "FieldType": "E"},
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"RecordId": ws_gm.record_id}
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ref_value.append(gm)
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value = ref_value
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else:
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continue
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elif label == "Form of supply":
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_value = []
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for form in ALLOWED_FORMS_OF_SUPPLY:
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is_form = "yes" if form in value else "no"
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_value.append({"Name": form, "Value": is_form})
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value = _value
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# print(label, value), biolomics_field
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elif label == "Coordinates of geographic origin":
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value = {'Latitude': strain.collect.location.latitude,
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'Longitude': strain.collect.location.longitude}
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precision = strain.collect.location.coord_uncertainty
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if precision is not None:
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value['Precision'] = precision
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elif label == "Geographic origin":
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if client is not None and value.country is not None:
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country = get_pycountry(value.country)
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if country is None:
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log_fhand.write(f'WARNING: {value.country} Not a valida country code/name\n')
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else:
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_value = get_country_record(country, client)
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if _value is None: # TODO: Remove this once the countries are added to the DB
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msg = f'WARNING: {value.country} not in MIRRI DB'
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log_fhand.write(msg + '\n')
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#raise ValueError(msg)
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else:
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content = {"Value": [_value], "FieldType": "RLink"}
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strain_record_details['Country'] = content
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_value = []
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for sector in ('state', 'municipality', 'site'):
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sector_val = getattr(value, sector, None)
|
||||
if sector_val:
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||||
_value.append(sector_val)
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||||
value = "; ".join(_value) if _value else None
|
||||
if value is None:
|
||||
continue
|
||||
|
||||
elif label == "Ontobiotope":
|
||||
if client and value:
|
||||
onto = get_remote_rlink(client, ONTOBIOTOPE_WS, value)
|
||||
value = [onto] if onto is not None else None
|
||||
elif label == 'Literature':
|
||||
if client and value:
|
||||
pub_rlinks = []
|
||||
for pub in value:
|
||||
rlink = get_remote_rlink(client, BIBLIOGRAPHY_WS, pub.title)
|
||||
if rlink:
|
||||
pub_rlinks.append(rlink)
|
||||
if pub_rlinks:
|
||||
value = pub_rlinks
|
||||
else:
|
||||
continue
|
||||
|
||||
elif label == '':
|
||||
pass
|
||||
|
||||
elif label == 'Ploidy':
|
||||
value = _translate_polidy(value)
|
||||
if value is not None:
|
||||
content = {"Value": value, "FieldType": biolomics_type}
|
||||
strain_record_details[biolomics_field] = content
|
||||
|
||||
# if False:
|
||||
# record_details["Data provided by"] = {
|
||||
# "Value": strain.id.collection, "FieldType": "V"}
|
||||
|
||||
#Markers
|
||||
if client:
|
||||
add_markers_to_strain_details(client, strain, strain_record_details)
|
||||
|
||||
strain_structure = {"RecordDetails": strain_record_details}
|
||||
if update:
|
||||
strain_structure['RecordId'] = strain.record_id
|
||||
strain_structure['RecordName'] = strain.record_name
|
||||
else:
|
||||
strain_structure["Acronym"] = "MIRRI"
|
||||
|
||||
return strain_structure
|
||||
|
||||
|
||||
def add_markers_to_strain_details(client, strain: StrainMirri, details):
|
||||
for marker in strain.genetics.markers:
|
||||
marker_name = marker.marker_id
|
||||
marker_in_ws = client.retrieve_by_name(SEQUENCE_WS, marker_name)
|
||||
if marker_in_ws is None:
|
||||
print('Marker not in web service')
|
||||
continue
|
||||
marker_type = marker.marker_type
|
||||
ws_marker = {
|
||||
"Value": [{
|
||||
"Name": {"Value": marker_in_ws.record_name,
|
||||
"FieldType": "E"},
|
||||
"RecordId": marker_in_ws.record_id
|
||||
}],
|
||||
"FieldType": "NLink"
|
||||
}
|
||||
if marker_in_ws.marker_seq:
|
||||
ws_marker['Value'][0]["TargetFieldValue"] = {
|
||||
"Value": {"Sequence": marker_in_ws.marker_seq},
|
||||
"FieldType": "N"
|
||||
}
|
||||
|
||||
details[MARKER_TYPE_MAPPING[marker_type]] = ws_marker
|
||||
|
||||
|
||||
def get_remote_rlink(client, endpoint, record_name):
|
||||
entity = client.retrieve_by_name(endpoint, record_name)
|
||||
if entity:
|
||||
# some Endpoints does not serialize the json into a python object yet
|
||||
try:
|
||||
record_name = entity.record_name
|
||||
record_id = entity.record_id
|
||||
except AttributeError:
|
||||
record_name = entity["RecordName"]
|
||||
record_id = entity["RecordId"]
|
||||
return {"Name": {"Value": record_name, "FieldType": "E"},
|
||||
"RecordId": record_id}
|
||||
|
||||
|
||||
def add_strain_rlink_to_entity(record, strain_id, strain_name):
|
||||
field_strain = {
|
||||
"FieldType": "RLink",
|
||||
'Value': [{
|
||||
'Name': {'Value': strain_name, 'FieldType': "E"},
|
||||
'RecordId': strain_id
|
||||
}]
|
||||
}
|
||||
record['RecordDetails']['Strains'] = field_strain
|
||||
return record
|
||||
|
||||
|
||||
PLOIDY_TRANSLATOR = {
|
||||
0: 'Aneuploid',
|
||||
1: 'Haploid',
|
||||
2: 'Diploid',
|
||||
3: 'Triploid',
|
||||
4: 'Tetraploid',
|
||||
9: 'Polyploid'
|
||||
}
|
||||
|
||||
REV_PLOIDY_TRANSLATOR = {v: k for k, v in PLOIDY_TRANSLATOR.items()}
|
||||
|
||||
|
||||
def _translate_polidy(ploidy):
|
||||
# print('ploidy in serializer', ploidy)
|
||||
try:
|
||||
ploidy = int(ploidy)
|
||||
except TypeError:
|
||||
return '?'
|
||||
try:
|
||||
ploidy = PLOIDY_TRANSLATOR[ploidy]
|
||||
except KeyError:
|
||||
ploidy = 'Polyploid'
|
||||
return ploidy
|
||||
|
||||
|
||||
def serialize_from_biolomics(biolomics_strain, client=None): # sourcery no-metrics
|
||||
strain = StrainMirri()
|
||||
strain.record_id = biolomics_strain.get('RecordId', None)
|
||||
strain.record_name = biolomics_strain.get('RecordName', None)
|
||||
for field in MIRRI_FIELDS:
|
||||
try:
|
||||
biolomics_field = field["biolomics"]["field"]
|
||||
except KeyError:
|
||||
# print(f'biolomics not configured: {field["label"]}')
|
||||
continue
|
||||
|
||||
label = field["label"]
|
||||
attribute = field["attribute"]
|
||||
field_data = biolomics_strain['RecordDetails'].get(biolomics_field, None)
|
||||
if field_data is None:
|
||||
continue
|
||||
is_empty = field_data.get('IsEmpty')
|
||||
if is_empty:
|
||||
continue
|
||||
if biolomics_field in ('Tested temperature growth range', 'Recommended growth temperature'):
|
||||
value = {'max': field_data.get('MaxValue', None),
|
||||
'min': field_data.get('MinValue', None)}
|
||||
else:
|
||||
value = field_data['Value']
|
||||
# if value in (None, '', [], {}, '?', 'Unknown', 'nan', 'NaN'):
|
||||
# continue
|
||||
|
||||
# print(label, attribute, biolomics_field, value)
|
||||
|
||||
if label == 'Accession number':
|
||||
number = strain.record_name
|
||||
mirri_id = StrainId(number=number)
|
||||
strain.synonyms = [mirri_id]
|
||||
coll, num = value.split(' ', 1)
|
||||
accession_number_id = StrainId(collection=coll, number=num)
|
||||
strain.id = accession_number_id
|
||||
continue
|
||||
elif label == "Restrictions on use":
|
||||
value = REV_RESTRICTION_USE_TRANSLATOR[value]
|
||||
elif label == 'Nagoya protocol restrictions and compliance conditions':
|
||||
value = REV_NAGOYA_TRANSLATOR[value]
|
||||
elif label in FILE_TYPE_FIELDS:
|
||||
value = [f['Value'] for f in value]
|
||||
elif label == "Other culture collection numbers":
|
||||
other_numbers = []
|
||||
for on in value.split(";"):
|
||||
on = on.strip()
|
||||
try:
|
||||
collection, number = on.split(" ", 1)
|
||||
except ValueError:
|
||||
collection = None
|
||||
number = on
|
||||
_id = StrainId(collection=collection, number=number)
|
||||
other_numbers.append(_id)
|
||||
value = other_numbers
|
||||
elif label in BOOLEAN_TYPE_FIELDS:
|
||||
value = value == 'yes'
|
||||
elif label == 'GMO':
|
||||
value = value == 'Yes'
|
||||
elif label == "Organism type":
|
||||
organism_types = [OrganismType(item['Name']) for item in value if item['Value'] == 'yes']
|
||||
if organism_types:
|
||||
value = organism_types
|
||||
elif label in 'Taxon name':
|
||||
value = ";".join([v['Name']['Value'] for v in value])
|
||||
add_taxon_to_strain(strain, value)
|
||||
continue
|
||||
|
||||
elif label in DATE_TYPE_FIELDS:
|
||||
# date_range = DateRange()
|
||||
value = DateRange().strpdate(value)
|
||||
|
||||
elif label in ("Recommended growth temperature",
|
||||
"Tested temperature growth range"):
|
||||
if (value['max'] is None or value['max'] == 0 or
|
||||
value['min'] is None and value['min'] == 0):
|
||||
continue
|
||||
elif label == "Recommended medium for growth":
|
||||
value = [v['Name']['Value'] for v in value]
|
||||
elif label == "Form of supply":
|
||||
value = [item['Name'] for item in value if item['Value'] == 'yes']
|
||||
elif label in LIST_TYPES_TO_JOIN:
|
||||
value = [v.strip() for v in value.split(";")]
|
||||
elif label == "Coordinates of geographic origin":
|
||||
if ('Longitude' in value and 'Latitude' in value and
|
||||
isinstance(value['Longitude'], float) and
|
||||
isinstance(value['Latitude'], float)):
|
||||
strain.collect.location.longitude = value['Longitude']
|
||||
strain.collect.location.latitude = value['Latitude']
|
||||
if value['Precision'] != 0:
|
||||
strain.collect.location.coord_uncertainty = value['Precision']
|
||||
continue
|
||||
elif label == "Altitude of geographic origin":
|
||||
value = float(value)
|
||||
elif label == "Geographic origin":
|
||||
strain.collect.location.site = value
|
||||
continue
|
||||
elif label == 'Ontobiotope':
|
||||
try:
|
||||
value = re.search("(OBT:[0-9]{5,7})", value[0]['Name']['Value']).group()
|
||||
except (KeyError, IndexError, AttributeError):
|
||||
continue
|
||||
|
||||
elif label == 'Ploidy':
|
||||
value = REV_PLOIDY_TRANSLATOR[value]
|
||||
elif label == 'Literature':
|
||||
if client is not None:
|
||||
pubs = []
|
||||
for pub in value:
|
||||
pub = client.retrieve_by_id(BIBLIOGRAPHY_WS, pub['RecordId'])
|
||||
pubs.append(pub)
|
||||
value = pubs
|
||||
|
||||
|
||||
rsetattr(strain, attribute, value)
|
||||
# fields that are not in MIRRI FIELD list
|
||||
# country
|
||||
if 'Country' in biolomics_strain['RecordDetails'] and biolomics_strain['RecordDetails']['Country']:
|
||||
try:
|
||||
country_name = biolomics_strain['RecordDetails']['Country']['Value'][0]['Name']['Value']
|
||||
country = get_pycountry(country_name)
|
||||
country_3 = country.alpha_3 if country else None
|
||||
except (IndexError, KeyError):
|
||||
country_3 = None
|
||||
if country_3:
|
||||
strain.collect.location.country = country_3
|
||||
# Markers:
|
||||
if client:
|
||||
markers = []
|
||||
for marker_type, biolomics_marker in MARKER_TYPE_MAPPING.items():
|
||||
try:
|
||||
marker_value = biolomics_strain['RecordDetails'][biolomics_marker]['Value']
|
||||
except KeyError:
|
||||
continue
|
||||
if not marker_value:
|
||||
continue
|
||||
|
||||
for marker in marker_value:
|
||||
record_id = marker['RecordId']
|
||||
marker = client.retrieve_by_id(SEQUENCE_WS, record_id)
|
||||
if marker is not None:
|
||||
markers.append(marker)
|
||||
if markers:
|
||||
strain.genetics.markers = markers
|
||||
|
||||
return strain
|
||||
|
||||
|
||||
def get_country_record(country, client):
|
||||
for attr in ('common_name', 'name', 'official_name'):
|
||||
val = getattr(country, attr, None)
|
||||
if val is not None:
|
||||
_value = get_remote_rlink(client, COUNTRY_WS, val)
|
||||
if _value is not None:
|
||||
return _value
|
||||
return None
|
||||
@@ -0,0 +1,64 @@
|
||||
|
||||
from mirri.entities.strain import Taxonomy
|
||||
|
||||
#TODO this is all wrong, needs deep revision
|
||||
|
||||
class TaxonomyMirri(Taxonomy):
|
||||
def __init__(self, **kwargs):
|
||||
super().__init__(freeze=False, **kwargs)
|
||||
|
||||
fields = ['record_id', 'record_name', 'acronym', 'full_description',
|
||||
'ingredients', 'description', 'other_name', 'ph',
|
||||
'sterilization_conditions']
|
||||
|
||||
def __init__(self, **kwargs):
|
||||
self._data = {}
|
||||
for field in self.fields:
|
||||
if field in kwargs and kwargs['field'] is not None:
|
||||
value = kwargs['field']
|
||||
setattr(self, field, value)
|
||||
|
||||
def __setattr__(self, attr, value):
|
||||
if attr == '_data':
|
||||
super().__setattr__(attr, value)
|
||||
return
|
||||
if attr not in self.fields:
|
||||
raise TypeError(f'{attr} not an allowed attribute')
|
||||
self._data[attr] = value
|
||||
|
||||
def __getattr__(self, attr):
|
||||
if attr == '_data':
|
||||
return super
|
||||
if attr not in self.fields and attr != '_data':
|
||||
raise TypeError(f'{attr} not an allowed attribute')
|
||||
return self._data.get(attr, None)
|
||||
|
||||
def dict(self):
|
||||
return self._data
|
||||
|
||||
|
||||
def serialize_from_biolomics(ws_data, client=None) -> TaxonomyMirri:
|
||||
|
||||
return ws_data
|
||||
medium = GrowthMedium()
|
||||
medium.record_name = ws_data.get('RecordName', None)
|
||||
medium.record_id = ws_data.get('RecordId', None)
|
||||
for key, value in ws_data['RecordDetails'].items():
|
||||
value = value['Value']
|
||||
if not value:
|
||||
continue
|
||||
|
||||
if key == "Full description":
|
||||
medium.full_description = value
|
||||
if key == "Ingredients":
|
||||
medium.ingredients = value
|
||||
if key == 'Medium description':
|
||||
medium.description = value
|
||||
if key == 'Other name':
|
||||
medium.other_name= value
|
||||
if key == 'pH':
|
||||
medium.ph = value
|
||||
if key == 'Sterilization conditions':
|
||||
medium.sterilization_conditions = value
|
||||
|
||||
return medium
|
||||
Reference in New Issue
Block a user