forked from MIRRI/mirri_utils
83 lines
2.4 KiB
Python
83 lines
2.4 KiB
Python
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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