forked from MIRRI/mirri_utils
297 lines
10 KiB
Python
297 lines
10 KiB
Python
from pathlib import Path
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DATA_DIR = Path(__file__).parent / "data"
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ACCESSION_NUMBER = "accession_number"
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RESTRICTION_ON_USE = "restriction_on_use"
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NAGOYA_PROTOCOL = "nagoya_protocol"
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ABS_RELATED_FILES = "abs_related_files"
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MTA_FILES = "mta_file"
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OTHER_CULTURE_NUMBERS = "other_culture_collection_numbers"
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STRAIN_FROM_REGISTERED_COLLECTION = "strain_from_a_registered_collection"
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RISK_GROUP = "risk_group"
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DUAL_USE = "dual_use"
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QUARANTINE = "quarantine"
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ORGANISM_TYPE = "organism_type"
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TAXON_NAME = "taxon_name"
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INFRASUBSPECIFIC_NAME = "infrasubspecific_names"
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COMMENTS_ON_TAXONOMY = "comments_on_taxonomy"
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STATUS = "status"
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HISTORY_OF_DEPOSIT = "history_of_deposit"
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DEPOSITOR = "depositor"
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DATE_OF_DEPOSIT = "date_of_deposit"
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COLLECTED_BY = "collected_by"
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DATE_OF_COLLECTION = "date_of_collection"
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ISOLATED_BY = "isolated_by"
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DATE_OF_ISOLATION = "date_of_isolation"
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DATE_OF_INCLUSION = "date_of_inclusion_on_catalog"
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TESTED_TEMPERATURE_GROWTH_RANGE = "tested_temperature_growth_range"
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RECOMMENDED_GROWTH_TEMP = "recommended_growth_temperature"
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RECOMMENDED_GROWTH_MEDIUM = "recommended_media_for_growth"
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FORM_OF_SUPPLY = "form_of_supply"
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GEO_COORDS = "coordinates_of_geographic_origin"
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ACCESSION_NAME = "other_denomination"
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ALTITUDE = "altitude_of_geographic_origin"
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GEOGRAPHIC_ORIGIN = "geographic_origin"
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GMO = "gmo"
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GMO_CONSTRUCTION_INFO = "gmo_construction_information"
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MUTANT_INFORMATION = "mutant_information"
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GENOTYPE = "genotype"
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LITERATURE = "literature"
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SEXUAL_STATE = "sexual_state"
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PLOIDY = "ploidy"
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INTERSPECIFIC_HYBRID = "interspecific_hybrid"
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HYBRIDS = 'hybrids'
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PLANT_PATHOGENICITY_CODE = "plant_pathogenicity_code"
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PATHOGENICITY = "pathogenicity"
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ENZYME_PRODUCTION = "enzyme_production"
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PRODUCTION_OF_METABOLITES = "production_of_metabolites"
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APPLICATIONS = "applications"
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REMARKS = "remarks"
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PLASMIDS = "plasmids"
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PLASMIDS_COLLECTION_FIELDS = "plasmids_collections_fields"
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SUBSTRATE_HOST_OF_ISOLATION = "substrate_host_of_isolation"
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ISOLATION_HABITAT = "isolation_habitat"
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ONTOBIOTOPE_ISOLATION_HABITAT = "ontobiotope_term_for_the_isolation_habitat"
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LITERATURE_LINKED_TO_SEQ_GENOME = "literature_linked_to_the_sequence_genome"
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# StrainId
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STRAIN_ID = "id"
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COLLECTION_CODE = "collection_code"
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STRAIN_PUI = "strain_pui"
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STRAIN_URL = "strain_url"
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ID_SYNONYMS = 'id_synonyms'
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# Taxonomy
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GENUS = "genus"
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SPECIES = "species"
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# Location
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COUNTRY = "countryOfOriginCode"
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SITE = "site"
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STATE = "state"
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PROVINCE = "province"
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MUNICIPALITY = "municipality"
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ISLAND = "island"
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OTHER = "other"
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LATITUDE = "latitude"
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LONGITUDE = "longitude"
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ALTITUDE = "altitude"
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GEOREF_METHOD = "georeferencingMethod"
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COORDUNCERTAINTY = "coordUncertainty"
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COORD_SPATIAL_REFERENCE = "coordenatesSpatialReference"
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LOCATION = "location"
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ALLOWED_COLLECTING_SITE_KEYS = [
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COUNTRY,
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STATE,
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PROVINCE,
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ISLAND,
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MUNICIPALITY,
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OTHER,
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SITE,
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LATITUDE,
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LONGITUDE,
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ALTITUDE,
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GEOREF_METHOD,
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COORDUNCERTAINTY,
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COORD_SPATIAL_REFERENCE,
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]
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MIRRI_FIELDS = [
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{"attribute": "id", "label": "Accession number"},
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{"attribute": "restriction_on_use", "label": "Restrictions on use"},
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{"attribute": "nagoya_protocol",
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"label": "Nagoya protocol restrictions and compliance conditions"},
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{"attribute": ABS_RELATED_FILES, "label": "ABS related files"},
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{"attribute": "mta_files", "label": "MTA file"},
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{"attribute": "other_numbers", "label": "Other culture collection numbers"},
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{"attribute": "is_from_registered_collection",
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"label": "Strain from a registered collection"},
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{"attribute": "risk_group", "label": "Risk Group"},
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{"attribute": "is_potentially_harmful", "label": "Dual use"},
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{"attribute": "is_subject_to_quarantine", "label": "Quarantine in Europe"},
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{"attribute": "taxonomy.organism_type", "label": "Organism type"},
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{"attribute": "taxonomy.taxon_name", "label": "Taxon name"},
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{"attribute": "taxonomy.infrasubspecific_name",
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"label": "Infrasubspecific names"},
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{"attribute": "taxonomy.comments", "label": "Comment on taxonomy"},
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{"attribute": "taxonomy.interspecific_hybrid",
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"label": "Interspecific hybrid"},
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{"attribute": "status", "label": "Status"},
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{"attribute": "history", "label": "History of deposit", },
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{"attribute": "deposit.who", "label": "Depositor"},
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{"attribute": "deposit.date", "label": "Date of deposit"},
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{"attribute": "catalog_inclusion_date",
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"label": "Date of inclusion in the catalogue"},
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{"attribute": "collect.who", "label": "Collected by"},
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{"attribute": "collect.date", "label": "Date of collection"},
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{"attribute": "isolation.who", "label": "Isolated by"},
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{"attribute": "isolation.date", "label": "Date of isolation"},
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{"attribute": "isolation.substrate_host_of_isolation",
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"label": "Substrate/host of isolation"},
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{"attribute": "growth.tested_temp_range",
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"label": "Tested temperature growth range"},
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{"attribute": "growth.recommended_temp",
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"label": "Recommended growth temperature"},
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{"attribute": "growth.recommended_media",
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"label": "Recommended medium for growth"},
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{"attribute": "form_of_supply", "label": "Form of supply"},
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{"attribute": "other_denominations", "label": "Other denomination"},
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{"attribute": "collect.location.coords",
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"label": "Coordinates of geographic origin"},
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{"attribute": "collect.location.altitude",
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"label": "Altitude of geographic origin"},
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{"attribute": "collect.location", "label": "Geographic origin"},
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{"attribute": "collect.habitat", "label": "Isolation habitat"},
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{"attribute": "collect.habitat_ontobiotope",
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"label": "Ontobiotope term for the isolation habitat"},
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{"attribute": "genetics.gmo", "label": "GMO"},
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{"attribute": "genetics.gmo_construction",
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"label": "GMO construction information"},
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{"attribute": "genetics.mutant_info", "label": "Mutant information"},
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{"attribute": "genetics.genotype", "label": "Genotype"},
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{"attribute": "genetics.sexual_state", "label": "Sexual state"},
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{"attribute": "genetics.ploidy", "label": "Ploidy"},
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{"attribute": "genetics.plasmids", "label": "Plasmids"},
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{"attribute": "genetics.plasmids_in_collections",
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"label": "Plasmids collections fields"},
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{"attribute": "publications", "label": "Literature"},
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{"attribute": PLANT_PATHOGENICITY_CODE, "label": "Plant pathogenicity code"},
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{"attribute": "pathogenicity", "label": "Pathogenicity"},
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{"attribute": "enzyme_production", "label": "Enzyme production"},
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{"attribute": "production_of_metabolites",
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"label": "Production of metabolites"},
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{"attribute": "applications", "label": "Applications", },
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{"attribute": "remarks", "label": "Remarks"},
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{"attribute": LITERATURE_LINKED_TO_SEQ_GENOME,
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"label": "Literature linked to the sequence/genome"},
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]
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ALLOWED_SUBTAXA = ["subspecies", "variety", "convarietas", "group", "forma",
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'forma.specialis']
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ALLOWED_TAXONOMIC_RANKS = ["family", "genus", "species"] + ALLOWED_SUBTAXA
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# nagoya
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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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ALLOWED_NAGOYA_OPTIONS = [NAGOYA_NO_RESTRICTIONS,
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NAGOYA_DOCS_AVAILABLE, NAGOYA_PROBABLY_SCOPE]
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# Use restriction
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NO_RESTRICTION = "no_restriction"
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ONLY_RESEARCH = "only_research"
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COMMERCIAL_USE_WITH_AGREEMENT = "commercial_use_with_agreement"
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ALLOWED_RESTRICTION_USE_OPTIONS = [
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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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ALLOWED_RISK_GROUPS = ["1", "2", "3", "4"]
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AGAR = "Agar"
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CRYO = "Cryo"
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DRY_ICE = "Dry Ice"
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LIQUID_CULTURE_MEDIUM = "Liquid Culture Medium"
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LYO = "Lyo"
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OIL = "Oil"
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WATER = "Water"
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ALLOWED_FORMS_OF_SUPPLY = [AGAR, CRYO, DRY_ICE,
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LIQUID_CULTURE_MEDIUM, LYO, OIL, WATER]
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DEPOSIT = "deposit"
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ISOLATION = "isolation"
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COLLECT = "collect"
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GROWTH = "growth"
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GENETICS = "genetics"
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TAXONOMY = "taxonomy"
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# Markers
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MARKERS = "markers"
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MARKER_TYPE = "marker_type"
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MARKER_INSDC = "INSDC"
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MARKER_SEQ = "marker_seq"
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ALLOWED_MARKER_TYPES = [
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{"acronym": "16S rRNA", "marker": "16S rRNA"},
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{"acronym": "ACT", "marker": "Actin"},
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{"acronym": "CaM", "marker": "Calmodulin"},
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{"acronym": "EF-1α", "marker": "elongation factor 1-alpha (EF-1α)"},
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{"acronym": "ITS",
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"marker": "nuclear ribosomal Internal Transcribed Spacer (ITS)"},
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{"acronym": "LSU", "marker": "nuclear ribosomal Large SubUnit (LSU)"},
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{"acronym": "RPB1", "marker": "Ribosomal RNA-coding genes RPB1"},
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{"acronym": "RPB2", "marker": "Ribosomal RNA-coding genes RPB2"},
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{"acronym": "TUBB", "marker": "β-Tubulin"},
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]
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PUBLICATIONS = "publications"
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PUB_ID = "id"
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PUB_DOI = "pub_doi"
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PUB_PUBMED_ID = ''
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PUB_FULL_REFERENCE = "full_reference"
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PUB_TITLE = "title"
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PUB_AUTHORS = "authors"
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PUB_JOURNAL = "journal"
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PUB_YEAR = "year"
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PUB_VOLUME = "volume"
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PUB_ISSUE = "issue"
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PUB_FIRST_PAGE = "first_page"
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PUB_LAST_PAGE = "last_page"
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BOOK_TITLE = "book_title"
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BOOK_EDITOR = "book_editor"
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BOOK_PUBLISHER = "book_publisher"
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PUBLICATION_FIELDS = [
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{"label": "ID", "attribute": PUB_ID},
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{"label": "Full reference", "attribute": PUB_FULL_REFERENCE},
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{"label": "Authors", "attribute": PUB_AUTHORS},
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{"label": "Title", "attribute": PUB_TITLE},
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{"label": "Journal", "attribute": PUB_JOURNAL},
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{"label": "Year", "attribute": PUB_YEAR},
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{"label": "Volume", "attribute": PUB_VOLUME},
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{"label": "Issue", "attribute": PUB_ISSUE},
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{"label": "First page", "attribute": PUB_FIRST_PAGE},
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{"label": "Last page", "attribute": PUB_FIRST_PAGE},
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{"label": "Book title", "attribute": BOOK_TITLE},
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{"label": "Editors", "attribute": BOOK_EDITOR},
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{"label": "Publisher", "attribute": BOOK_PUBLISHER},
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]
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# ploidy
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ANEUPLOID = 0
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HAPLOID = 1
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DIPLOID = 2
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TRIPLOID = 3
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TETRAPLOID = 4
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POLYPLOID = 9
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ALLOWED_PLOIDIES = [ANEUPLOID, HAPLOID, DIPLOID, TRIPLOID, TETRAPLOID,
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POLYPLOID]
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SUBTAXAS = {
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"subsp.": "subspecies",
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"var.": "variety",
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"convar.": "convarietas",
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"group.": "group",
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"f.": "forma",
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"f.sp.": "forma.specialis"
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}
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# Excel sheet name
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LOCATIONS = "Geographic origin" # 'Locations'
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GROWTH_MEDIA = "Growth media"
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GENOMIC_INFO = "Genomic information"
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STRAINS = "Strains"
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LITERATURE_SHEET = "Literature"
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SEXUAL_STATE_SHEET = "Sexual states"
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RESOURCE_TYPES_VALUES = "Resource types values"
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FORM_OF_SUPPLY_SHEET = "Forms of supply"
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PLOIDY_SHEET = "Ploidy"
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ONTOBIOTOPE = "Ontobiotope"
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MARKERS = "Markers"
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