100 lines
3.7 KiB
Python
100 lines
3.7 KiB
Python
from mirri.biolomics.serializers.strain import StrainMirri
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from mirri.entities.strain import StrainId, OrganismType
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from mirri.entities.sequence import GenomicSequence
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from mirri.entities.date_range import DateRange
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from mirri.entities.publication import Publication
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from mirri.settings import NAGOYA_NO_RESTRICTIONS
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VERSION = 'v2'
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SERVER_URL = 'https://webservices.bio-aware.com/mirri_test'
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def create_full_data_strain():
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strain = StrainMirri()
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strain.id.number = "1"
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strain.id.collection = "TESTCC"
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strain.id.url = "https://cect/2342"
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strain.restriction_on_use = "no_restriction"
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strain.nagoya_protocol = NAGOYA_NO_RESTRICTIONS
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strain.abs_related_files = ['https://example.com']
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strain.mta_files = ['https://example.com']
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strain.other_numbers.append(StrainId(collection="aaa", number="a"))
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strain.other_numbers.append(StrainId(collection="aaa3", number="a3"))
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strain.is_from_registered_collection = False
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strain.risk_group = '1'
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strain.is_potentially_harmful = True
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strain.is_subject_to_quarantine = False
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strain.taxonomy.organism_type = [OrganismType(2)]
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strain.taxonomy.genus = 'Escherichia'
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strain.taxonomy.species = 'coli'
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strain.taxonomy.interspecific_hybrid = False
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strain.taxonomy.infrasubspecific_name = 'serovar tete'
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strain.taxonomy.comments = 'lalalalla'
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strain.status = "type of Bacillus alcalophilus"
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strain.history = 'firstplave < seconn place < third place'
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strain.deposit.who = "NCTC, National Collection of Type Cultures - NCTC, London, United Kingdom of Great Britain and Northern Ireland."
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strain.deposit.date = DateRange(year=1985, month=5, day=2)
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strain.catalog_inclusion_date = DateRange(year=1985, month=5, day=2)
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strain.collect.location.country = "ESP"
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strain.collect.location.state = "una state"
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strain.collect.location.municipality = "one municipality"
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strain.collect.location.longitude = 23.3
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strain.collect.location.latitude = 23.3
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strain.collect.location.altitude = 121
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strain.collect.location.site = "somewhere in the world"
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strain.collect.habitat_ontobiotope = "OBT:000190"
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strain.collect.habitat = 'some habitat'
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strain.collect.who = "the collector"
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strain.collect.date = DateRange(year=1991)
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strain.isolation.date = DateRange(year=1900)
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strain.isolation.who = 'the isolator'
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strain.isolation.substrate_host_of_isolation = 'some substrate'
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# already existing media in test_mirri
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strain.growth.recommended_temp = {'min': 30, 'max': 30}
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strain.growth.recommended_media = ["AAA"]
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strain.growth.tested_temp_range = {'min': 29, 'max': 32}
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strain.form_of_supply = ["Agar", "Lyo"]
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#strain.other_denominations = ["lajdflasjdldj"]
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gen_seq = GenomicSequence()
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gen_seq.marker_id = "pepe"
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gen_seq.marker_type = "16S rRNA"
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strain.genetics.markers.append(gen_seq)
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strain.genetics.ploidy = 9
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strain.genetics.genotype = 'some genotupe'
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strain.genetics.gmo = True
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strain.genetics.gmo_construction = 'instructrion to build'
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strain.genetics.mutant_info = 'x-men'
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strain.genetics.sexual_state = 'MT+A'
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strain.genetics.plasmids = ['asda']
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strain.genetics.plasmids_in_collections = ['asdasda']
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pub = Publication()
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pub.title = "The genus Amylomyces"
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strain.publications = [pub]
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strain.plant_pathogenicity_code = 'PATH:001'
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strain.pathogenicity = 'illness'
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strain.enzyme_production = 'some enzimes'
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strain.production_of_metabolites = 'big factory of cheese'
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strain.applications = 'health'
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strain.remarks = 'no remarks for me'
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return strain
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if __name__ == '__main__':
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strain = create_full_data_strain()
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print(strain.collect.habitat_ontobiotope)
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