try: from mirri.biolomics.secrets import CLIENT_ID, SECRET_ID, USERNAME, PASSWORD except ImportError: raise ImportError( 'You need a secrets.py in the project dir. with CLIENT_ID, SECRET_ID, USERNAME, PASSWORD') MIRRI_FIELDS = [ { "attribute": "id", "label": "Accession number", "mandatory": True, "biolomics": {"field": "Collection accession number", "type": "E"}, }, { "attribute": "restriction_on_use", "label": "Restrictions on use", "mandatory": True, "biolomics": {"field": "Restrictions on use", "type": "T"}, }, { "attribute": "nagoya_protocol", "label": "Nagoya protocol restrictions and compliance conditions", "mandatory": True, "biolomics": {"field": "Nagoya protocol restrictions and compliance conditions", "type": "T"}, }, { "attribute": "abs_related_files", "label": "ABS related files", "mandatory": False, "biolomics": {"field": "ABS related files", "type": "U"}, }, { "attribute": "mta_files", "label": "MTA file", "mandatory": False, "biolomics": {"field": "MTA files URL", "type": "U"}, }, { "attribute": "other_numbers", "label": "Other culture collection numbers", "mandatory": False, "biolomics": {"field": "Other culture collection numbers", "type": "E"}, }, { "attribute": "is_from_registered_collection", "label": "Strain from a registered collection", "mandatory": False, "biolomics": {"field": "Strain from a registered collection", "type": "T"}, }, { "attribute": "risk_group", "label": "Risk Group", "mandatory": True, "biolomics": {"field": "Risk group", "type": "T"}, }, { "attribute": "is_potentially_harmful", "label": "Dual use", "mandatory": False, "biolomics": {"field": "Dual use", "type": "T"}, }, { "attribute": "is_subject_to_quarantine", "label": "Quarantine in Europe", "mandatory": False, "biolomics": {"field": "Quarantine in Europe", "type": "T"}, }, { "attribute": "taxonomy.organism_type", "label": "Organism type", "mandatory": True, "biolomics": {"field": "Organism type", "type": "C"}, }, { "attribute": "taxonomy.long_name", "label": "Taxon name", "mandatory": True, "biolomics": {"field": "Taxon name", "type": "SynLink"}, }, { "attribute": "taxonomy.infrasubspecific_name", "label": "Infrasubspecific names", "mandatory": False, "biolomics": {"field": "Infrasubspecific names", "type": "E"}, }, { "attribute": "taxonomy.comments", "label": "Comment on taxonomy", "mandatory": False, "biolomics": {"field": "Comment on taxonomy", "type": "E"}, }, { "attribute": "taxonomy.interspecific_hybrid", "label": "Interspecific hybrid", "mandatory": False, "biolomics": {"field": "Interspecific hybrid", "type": "T"}, }, { "attribute": "status", "label": "Status", "mandatory": False, "biolomics": {"field": "Status", "type": "E"}, }, { "attribute": "history", "label": "History of deposit", "mandatory": False, "biolomics": {"field": "History", "type": "E"}, }, { "attribute": "deposit.who", "label": "Depositor", "mandatory": False, "biolomics": {"field": "Depositor", "type": "E"}, }, { "attribute": "deposit.date", "label": "Date of deposit", "mandatory": False, "biolomics": {"field": "Deposit date", "type": "H"}, }, { "attribute": "catalog_inclusion_date", "label": "Date of inclusion in the catalogue", "mandatory": False, "biolomics": {"field": "Date of inclusion in the catalogue", "type": "H"}, }, { "attribute": "collect.who", "label": "Collected by", "mandatory": False, "biolomics": {"field": "Collector", "type": "E"}, }, { "attribute": "collect.date", "label": "Date of collection", "mandatory": False, "biolomics": {"field": "Collection date", "type": "H"}, }, { "attribute": "isolation.who", "label": "Isolated by", "mandatory": False, "biolomics": {"field": "Isolator", "type": "E"}, }, { "attribute": "isolation.date", "label": "Date of isolation", "mandatory": False, "biolomics": {"field": "Isolation date", "type": "H"}, }, { "attribute": "isolation.substrate_host_of_isolation", "label": "Substrate/host of isolation", "mandatory": False, "biolomics": {"field": "Substrate of isolation", "type": "E"}, }, { "attribute": "growth.tested_temp_range", "label": "Tested temperature growth range", "mandatory": False, "biolomics": {"field": "Tested temperature growth range", "type": "S"}, }, { "attribute": "growth.recommended_temp", "label": "Recommended growth temperature", "mandatory": True, "biolomics": {"field": "Recommended growth temperature", "type": "S"}, }, { "attribute": "growth.recommended_media", "label": "Recommended medium for growth", "mandatory": True, "biolomics": {"field": "Recommended growth medium", "type": "RLink"}, }, { "attribute": "form_of_supply", "label": "Form of supply", "mandatory": True, "biolomics": {"field": "Form", "type": "C"}, }, { "attribute": "other_denominations", "label": "Other denomination", "mandatory": False, "biolomics": {"field": "Other denomination", "type": "E"}, }, { # here we use latitude to check if there is data in some of the fields "attribute": "collect.location.latitude", "label": "Coordinates of geographic origin", "mandatory": False, "biolomics": {"field": "Coordinates of geographic origin", "type": "L"}, }, { "attribute": "collect.location.altitude", "label": "Altitude of geographic origin", "mandatory": False, "biolomics": {"field": "Altitude of geographic origin", "type": "D"}, }, { "attribute": "collect.location", "label": "Geographic origin", "mandatory": True, "biolomics": {"field": "Geographic origin", "type": "E"}, }, { "attribute": "collect.habitat", "label": "Isolation habitat", "mandatory": False, "biolomics": {"field": "Isolation habitat", "type": "E"}, }, # { # "attribute": "collect.habitat_ontobiotope", # "label": "Ontobiotope term for the isolation habitat", # "mandatory": False, # "biolomics": {"field": "Ontobiotope term for the isolation habitat", "type": "E"}, # }, { "attribute": "collect.habitat_ontobiotope", "label": "Ontobiotope", "mandatory": False, "biolomics": {"field": "Ontobiotope", "type": "RLink"}, }, { "attribute": "genetics.gmo", "label": "GMO", "mandatory": False, "biolomics": {"field": "GMO", "type": "V"}, }, { "attribute": "genetics.gmo_construction", "label": "GMO construction information", "mandatory": False, "biolomics": {"field": "GMO construction information", "type": "E"}, }, { "attribute": "genetics.mutant_info", "label": "Mutant information", "mandatory": False, "biolomics": {"field": "Mutant information", "type": "E"}, }, { "attribute": "genetics.genotype", "label": "Genotype", "mandatory": False, "biolomics": {"field": "Genotype", "type": "E"}, }, { "attribute": "genetics.sexual_state", "label": "Sexual state", "mandatory": False, "biolomics": {"field": "Sexual state", "type": "E"}, }, { "attribute": "genetics.ploidy", "label": "Ploidy", "mandatory": False, "biolomics": {"field": "Ploidy", "type": "T"}, }, { "attribute": "genetics.plasmids", "label": "Plasmids", "mandatory": False, "biolomics": {"field": "Plasmids", "type": "E"}, }, { "attribute": "genetics.plasmids_in_collections", "label": "Plasmids collections fields", "mandatory": False, "biolomics": {"field": "Plasmids collections fields", "type": "E"}, }, { "attribute": "publications", "label": "Literature", "mandatory": False, "biolomics": {"field": "Literature", "type": "RLink"}, }, { "attribute": "pathogenicity", "label": "Pathogenicity", "mandatory": False, "biolomics": {"field": "Pathogenicity", "type": "E"}, }, { "attribute": "enzyme_production", "label": "Enzyme production", "mandatory": False, "biolomics": {"field": "Enzyme production", "type": "E"}, }, { "attribute": "production_of_metabolites", "label": "Production of metabolites", "mandatory": False, "biolomics": {"field": "Metabolites production", "type": "E"}, }, { "attribute": "applications", "label": "Applications", "mandatory": False, "biolomics": {"field": "Applications", "type": "E"}, }, { "attribute": "remarks", "label": "Remarks", "mandatory": False, "biolomics": {"field": "Remarks", "type": "E"}, }, { "attribute": "literature_linked_to_the_sequence_genome", "label": "Literature linked to the sequence/genome", "mandatory": False, # "biolomics": {"field": "MTA files URL", "type": "U"}, }, ] PUB_MIRRI_FIELDS = [ { "attribute": "pub_id", "mandatory": False, "biolomics": {"field": "", "type": "E"}, }, { "attribute": "pubmed_id", "mandatory": False, "biolomics": {"field": "PubMed ID", "type": "E"}, }, { "attribute": "doi", "mandatory": False, "biolomics": {"field": "DOI number", "type": "E"}, }, { "attribute": "title", "mandatory": False, "biolomics": {"field": "Title", "type": "E"}, }, { "attribute": "authors", "mandatory": False, "biolomics": {"field": "Authors", "type": "E"}, }, { "attribute": "journal", "mandatory": False, "biolomics": {"field": "Journal", "type": "E"}, }, { "attribute": "volumen", "mandatory": False, "biolomics": {"field": "Volume", "type": "E"}, }, { "attribute": "issue", "mandatory": False, "biolomics": {"field": "Issue", "type": "E"}, }, { "attribute": "first_page", "mandatory": False, "biolomics": {"field": "Page from", "type": "E"}, }, { "attribute": "last_page", "mandatory": False, "biolomics": {"field": "Page to", "type": "E"}, }, { "attribute": "last_page", "label": "", "mandatory": False, "biolomics": {"field": "", "type": "E"}, }, { "attribute": "last_page", "label": "", "mandatory": False, "biolomics": {"field": "", "type": "E"}, }, { "attribute": "book_title", "label": "", "mandatory": False, "biolomics": {"field": "Book title", "type": "E"}, }, { "attribute": "publisher", "label": "", "mandatory": False, "biolomics": {"field": "Publisher", "type": "E"}, }, { "attribute": "editor", "label": "", "mandatory": False, "biolomics": {"field": "Editor(s)", "type": "E"}, }, ]