forked from MIRRI/mirri_utils
549 lines
15 KiB
Python
549 lines
15 KiB
Python
from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROSSREF_NAME, DATE,
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ERROR_CODE, FIELD, MANDATORY, MATCH,
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MISSING, MULTIPLE, NAGOYA, NUMBER, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE,
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UNIQUE,
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VALIDATION, VALUES, BIBLIO)
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from mirri.settings import (GEOGRAPHIC_ORIGIN, ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO,
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STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET)
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# MARKERS,
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# SEXUAL_STATE_SHEET,
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# RESOURCE_TYPES_VALUES,
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# FORM_OF_SUPPLY_SHEET,
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# PLOIDY_SHEET)
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STRAIN_FIELDS = [
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{
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FIELD: "Accession number",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: 'STD01'},
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{TYPE: UNIQUE, ERROR_CODE: 'STD03'},
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{TYPE: MISSING, ERROR_CODE: "STD02"},
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{TYPE: REGEXP, MATCH: "[^ ]* [^ ]*", ERROR_CODE: "STD04"}
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]
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},
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{
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FIELD: "Restrictions on use",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD05"},
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{TYPE: MISSING, ERROR_CODE: "STD06"},
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{TYPE: CHOICES, VALUES: ["1", "2", "3"],
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MULTIPLE: False, ERROR_CODE: "STD07"}
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]
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},
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{
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FIELD: "Nagoya protocol restrictions and compliance conditions",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD08"},
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{TYPE: MISSING, ERROR_CODE: "STD09"},
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{TYPE: CHOICES, VALUES: ["1", "2", "3"],
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MULTIPLE: False, ERROR_CODE: "STD10"}
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]
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},
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{
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FIELD: "ABS related files",
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VALIDATION: [],
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},
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{
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FIELD: "MTA file",
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VALIDATION: [],
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},
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{
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FIELD: "Other culture collection numbers",
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# VALIDATION: [
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# {TYPE: REGEXP, "match": "[^ ]* [^ ]*", ERROR_CODE: "STD07",
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# MULTIPLE: True, SEPARATOR: ";"}
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# ]
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},
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{
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FIELD: "Strain from a registered collection",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD11"}
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]
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},
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{
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FIELD: "Risk Group",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD12"},
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{TYPE: MISSING, ERROR_CODE: "STD13"},
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{TYPE: CHOICES, VALUES: ["1", "2", "3", "4"],
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MULTIPLE: False, ERROR_CODE: "STD14"}
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]
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},
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{
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FIELD: "Dual use",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD15"}
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]
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},
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{
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FIELD: "Quarantine in Europe",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD16"}
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]
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},
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{
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FIELD: "Organism type",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD17"},
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{TYPE: MISSING, ERROR_CODE: "STD18"},
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{TYPE: CHOICES, VALUES: ["Algae", "Archaea", "Bacteria",
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"Cyanobacteria", "Filamentous Fungi",
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"Phage", "Plasmid", "Virus", "Yeast",
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"1", "2", "3", "4", "5", "6", "7", "8", "9"],
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MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD19"}
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]
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},
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{
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FIELD: "Taxon name",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD20"},
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{TYPE: MISSING, ERROR_CODE: "STD21"},
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{TYPE: TAXON, ERROR_CODE: "STD22", MULTIPLE: True,
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SEPARATOR: ';'}
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]
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},
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{
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FIELD: "Infrasubspecific names",
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},
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{
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FIELD: "Comment on taxonomy",
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},
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{
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FIELD: "Interspecific hybrid",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD23"}
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]
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},
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{
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FIELD: "Status",
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},
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{
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FIELD: "History of deposit",
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VALIDATION: [
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# {TYPE: REGEXP, "match": "[^ ]* [^ ]*", ERROR_CODE: "STD24", # modify the regex
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# MULTIPLE: True, SEPARATOR: ";"}
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]
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},
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{
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FIELD: "Depositor"
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},
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{
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FIELD: "Date of deposit",
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VALIDATION: [
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{TYPE: DATE, ERROR_CODE: "STD25"},
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]
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},
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{
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FIELD: "Date of inclusion in the catalogue",
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VALIDATION: [
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{TYPE: DATE, ERROR_CODE: "STD26"},
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]
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},
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{
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FIELD: "Collected by",
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},
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{
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FIELD: "Date of collection",
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VALIDATION: [
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{TYPE: DATE, ERROR_CODE: "STD27"},
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]
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},
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{
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FIELD: "Isolated by",
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},
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{
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FIELD: "Date of isolation",
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VALIDATION: [
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{TYPE: DATE, ERROR_CODE: "STD28"},
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]
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},
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{
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FIELD: "Substrate/host of isolation",
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},
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{
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FIELD: "Tested temperature growth range",
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VALIDATION: [
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{TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
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ERROR_CODE: "STD29", MULTIPLE: True, SEPARATOR: ";"}
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]
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},
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{
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FIELD: "Recommended growth temperature",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD30"},
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{TYPE: MISSING, ERROR_CODE: "STD31"},
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{TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
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ERROR_CODE: "STD32",
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MULTIPLE: True, SEPARATOR: ";"}
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]
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},
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{
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FIELD: "Recommended medium for growth",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD33"},
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{TYPE: MISSING, ERROR_CODE: "STD34"},
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{TYPE: CROSSREF, CROSSREF_NAME: "Growth media",
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MULTIPLE: True, SEPARATOR: "/", ERROR_CODE: "STD35"}
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]
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},
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{
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FIELD: "Form of supply",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD36"},
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{TYPE: MISSING, ERROR_CODE: "STD37"},
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{TYPE: CHOICES, VALUES: ['Agar', 'Cryo', 'Dry Ice', 'Liquid Culture Medium',
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'Lyo', 'Oil', 'Water'],
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MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD38"}
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]
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},
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{
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FIELD: "Other denomination",
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},
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{
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FIELD: "Coordinates of geographic origin",
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VALIDATION: [
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{TYPE: COORDINATES, ERROR_CODE: "STD39"},
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]
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},
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{
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FIELD: "Altitude of geographic origin",
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VALIDATION: [
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{TYPE: NUMBER, 'max': 8000, 'min': -200, ERROR_CODE: "STD40"},
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]
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},
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{
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# value can be in the cell or in another sheet. Don't configure this
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FIELD: "Geographic origin",
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},
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{
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FIELD: "Isolation habitat",
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},
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{
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FIELD: "Ontobiotope term for the isolation habitat",
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VALIDATION: [
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{TYPE: CROSSREF, CROSSREF_NAME: "Ontobiotope",
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MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD41"}
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]
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},
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{
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FIELD: "GMO",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD42"}
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]
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},
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{
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FIELD: "GMO construction information",
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},
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{
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FIELD: "Mutant information",
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},
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{
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FIELD: "Genotype",
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},
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{
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FIELD: "Sexual state",
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VALIDATION: [
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{TYPE: CROSSREF, CROSSREF_NAME: SEXUAL_STATE_SHEET,
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ERROR_CODE: "STD43"}
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# {TYPE: CHOICES, VALUES: ["Mata", "Matalpha", "Mata/Matalpha",
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# "Matb", "Mata/Matb", "MTLa", "MTLalpha", "MTLa/MTLalpha",
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# "MAT1-1", "MAT1-2", "MAT1", "MAT2", "MT+", "MT-"],
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# ERROR_CODE: "STD43"}
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]
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},
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{
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FIELD: "Ploidy",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["0", "1", "2", "3", "4", "9"],
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ERROR_CODE: "STD44"}
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]
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},
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{
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FIELD: "Plasmids",
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},
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{
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FIELD: "Plasmids collections fields",
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},
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{
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# value can be in the cell or in another sheet. Don't configure this
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FIELD: "Literature",
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VALIDATION: [
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{TYPE: CROSSREF, CROSSREF_NAME: LITERATURE_SHEET,
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MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD45"}
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]
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},
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{
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FIELD: "Plant pathogenicity code",
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},
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{
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FIELD: "Pathogenicity",
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},
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{
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FIELD: "Enzyme production",
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},
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{
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FIELD: "Production of metabolites",
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},
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{
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FIELD: "Applications",
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},
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{
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FIELD: "Remarks"
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},
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{
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FIELD: "Literature linked to the sequence/genome",
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},
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]
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SHEETS_SCHEMA = {
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LOCATIONS: {
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"acronym": "GOD",
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"id_field": "ID",
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS02"},
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COLUMNS: [
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{
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FIELD: "ID",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GOD01"},
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{TYPE: MISSING, ERROR_CODE: "GOD02"},
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]
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},
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{
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FIELD: "Country",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GOD03"},
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{TYPE: MISSING, ERROR_CODE: "GOD04"}
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]
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},
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{
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FIELD: "Region",
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VALIDATION: []
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},
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{
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FIELD: "City",
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VALIDATION: []
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},
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{
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FIELD: "Locality",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GOD06"},
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{TYPE: MISSING, ERROR_CODE: "GOD07"}
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]
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}
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],
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},
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GROWTH_MEDIA: {
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"acronym": "GMD",
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"id_field": "Acronym",
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS01"},
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COLUMNS: [
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{
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FIELD: "Acronym",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GMD01"},
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{TYPE: MISSING, ERROR_CODE: "GMD02"}
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]
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},
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{
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FIELD: "Description",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GMD03"},
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{TYPE: MISSING, ERROR_CODE: "GMD04"}
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]
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},
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{
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FIELD: "Full description",
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VALIDATION: []
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},
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],
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},
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GENOMIC_INFO: {
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"acronym": "GID",
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"id_field": "Strain AN",
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS08"},
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COLUMNS: [
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{
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FIELD: "Strain AN",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GID01"},
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{TYPE: MISSING, ERROR_CODE: "GID02"},
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{TYPE: CROSSREF, CROSSREF_NAME: "Strains",
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ERROR_CODE: "GID03"},
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]
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},
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{
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FIELD: "Marker",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GID04"},
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{TYPE: MISSING, ERROR_CODE: "GID05"},
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{TYPE: CHOICES, ERROR_CODE: "GID06",
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VALUES: ['16S rRNA', 'ACT', 'CaM', 'EF-1α', 'ITS',
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'LSU', 'RPB1', 'RPB2', 'TUBB']}
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]
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},
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{
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FIELD: "INSDC AN",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "GID07"},
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{TYPE: MISSING, ERROR_CODE: "GID08"},
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]
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},
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{
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FIELD: "Sequence",
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VALIDATION: []
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},
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],
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},
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STRAINS: {
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"acronym": "STD",
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'id_field': 'Accession number',
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
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ROW_VALIDATION: [
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{TYPE: NAGOYA, ERROR_CODE: "STRXXX"},
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],
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COLUMNS: STRAIN_FIELDS,
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},
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LITERATURE_SHEET: {
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"acronym": "LID",
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'id_field': 'ID',
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS03"},
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ROW_VALIDATION: [
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{TYPE: BIBLIO, ERROR_CODE: 'LID17'}
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],
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COLUMNS: [
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{
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FIELD: "ID",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID01"},
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{TYPE: MISSING, ERROR_CODE: "LID02"},
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]
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},
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{
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FIELD: "Full reference",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID03"},
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]
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},
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{
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FIELD: "Authors",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID05"},
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]
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},
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{
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FIELD: "Title",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID07"},
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]
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},
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{
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FIELD: "Journal",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID09"},
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]
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},
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{
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FIELD: "Year",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID11"},
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]
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},
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{
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FIELD: "Volume",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID13"},
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]
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},
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{
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FIELD: "Issue",
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VALIDATION: []
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},
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{
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FIELD: "First page",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID15"},
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{TYPE: MISSING, ERROR_CODE: "LID16"},
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]
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},
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{
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FIELD: "Last page",
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VALIDATION: []
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},
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{
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FIELD: "Book title",
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VALIDATION: []
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},
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{
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FIELD: "Editors",
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VALIDATION: []
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},
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{
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FIELD: "Publisher",
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VALIDATION: []
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}
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],
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},
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# SEXUAL_STATE_SHEET: {"acronym": "SSD", COLUMNS: []},
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# RESOURCE_TYPES_VALUES: {"acronym": "RTD", COLUMNS: []},
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# FORM_OF_SUPPLY_SHEET: {"acronym": "FSD", COLUMNS: []},
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# PLOIDY_SHEET: {"acronym": "PLD", COLUMNS: []},
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ONTOBIOTOPE: {
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"acronym": "OTD",
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"id_field": "ID",
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS06"},
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COLUMNS: [
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{
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FIELD: "ID",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "OTD01"},
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{TYPE: MISSING, ERROR_CODE: "OTD02"},
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]
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},
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{
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FIELD: "Name",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "OTD03"},
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{TYPE: MISSING, ERROR_CODE: "OTD04"},
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]
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},
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]
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},
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# MARKERS: {
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# "acronym": "MKD",
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# "id_field": "",
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# COLUMNS: [
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# {
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# FIELD: "Acronym",
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# VALIDATION: []
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# },
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# {
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# FIELD: "Marker",
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# VALIDATION: []
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# },
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# ],
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# },
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}
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CROSS_REF_CONF = {
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ONTOBIOTOPE: ['ID', 'Name'],
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LITERATURE_SHEET: ['ID'],
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LOCATIONS: ['Locality'],
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GROWTH_MEDIA: ['Acronym'],
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STRAINS: ["Accession number"],
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SEXUAL_STATE_SHEET: []
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}
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MIRRI_20200601_VALLIDATION_CONF = {
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'sheet_schema': SHEETS_SCHEMA,
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'cross_ref_conf': CROSS_REF_CONF,
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'keep_sheets_in_memory': [
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{'sheet_name': LOCATIONS, 'indexed_by': 'Locality'}]
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}
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