674 lines
18 KiB
Python
674 lines
18 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, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE,
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UNIQUE,VERSION,
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VALIDATION, VALUES, BIBLIO, DOMINIO, URL_DOMINIO,ISO, JUST_URL, URL_TITLE, TITLE, HISTORY,NAGOYA1)
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from mirri.settings import (ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO,
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STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET, MARKERS, CONTROL_SHEET,)
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# GEOGRAPHIC_ORIGIN
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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: "accessionNumber",
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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: "useRestrictions",
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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: "mirriAccessionNumber",
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VALIDATION: [
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{TYPE: UNIQUE, ERROR_CODE: 'STD51'},
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{TYPE: REGEXP, MATCH: "^MIRRI[0-9]{7}$", ERROR_CODE: "STD52"},
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],
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},
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{
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FIELD: "nagoyaConditions",
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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: "absFile",
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VALIDATION: [
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{TYPE: TITLE, ERROR_CODE: "STD59"},
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{TYPE: URL_TITLE, ERROR_CODE: "STD60",
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MULTIPLE: True, SEPARATOR: ";"},
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],
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},
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{
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FIELD: "siteLinks",
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VALIDATION: [
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{TYPE: DOMINIO, ERROR_CODE: "STD53",
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MULTIPLE: False, SEPARATOR: ";"},
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{TYPE: URL_DOMINIO, ERROR_CODE: "STD56",
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MULTIPLE: False, SEPARATOR: ";"},
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],
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},
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{
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FIELD: "mtaFile",
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VALIDATION: [
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{TYPE: JUST_URL, ERROR_CODE: "STD58",
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MULTIPLE: True, SEPARATOR: ";"},
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],
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},
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{
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FIELD: "otherCollectionNumbers",
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VALIDATION: [
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{TYPE: REGEXP, MATCH: "([^ ]* [^ ]*)(; [^ ]* [^ ]*)*$", ERROR_CODE: "STD63",
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MULTIPLE: True, SEPARATOR: ';'},
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#{TYPE: CROSSREF, CROSSREF_NAME: "Strains", ERROR_CODE: "STD64"},
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]
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},
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{
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FIELD: "registeredCollection",
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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: "type",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"], ERROR_CODE: "STD64"},
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]
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},
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{
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FIELD: "riskGroup",
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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: "dualUse",
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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: "euQuarantine",
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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: "axenicCulture",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["Axenic", "Not axenic"],
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ERROR_CODE: "STD50"}
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]
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},
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{
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FIELD: "organismType",
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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", "Filamentous fungi",
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"Yeast", "Microalgae",
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"1", "2", "3", "4", "5", "6", "7"],
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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: "speciesName",
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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: "infrasubspecificNames",
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VALIDATION: []
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},
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{
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FIELD: "taxonomyComments",
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VALIDATION: []
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},
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{
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FIELD: "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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VALIDATION: [
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{TYPE: REGEXP, MATCH: "^(type of|neotype of|holotype of |epitype of) ([a-zA-Z .'-]+)$", ERROR_CODE: "STD65"},
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]
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},
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{
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FIELD: "depositHistory",
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VALIDATION: [
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{TYPE: HISTORY, ERROR_CODE: 'STD24'},
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]
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},
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{
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FIELD: "depositor",
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VALIDATION: []
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},
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{
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FIELD: "depositDate",
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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: "accessionDate",
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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: "collector",
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VALIDATION: []
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},
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{
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FIELD: "substrate",
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VALIDATION: []
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},
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{
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FIELD: "temperatureGrowthRange",
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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: "recommendedTemperature",
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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: "supplyForms",
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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: "otherDenomination",
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VALIDATION: []
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},
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{
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FIELD: "geographicCoordinates",
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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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# value can be in the cell or in another sheet. Don't configure this
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FIELD: "geographicOrigin",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD68"},
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{TYPE: MISSING, ERROR_CODE: "STD69"},
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{TYPE: CROSSREF, CROSSREF_NAME: "Geographic origin", ERROR_CODE: "STD46"},
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]
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},
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{
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FIELD: "isolationHabitat",
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VALIDATION: []
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},
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{
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FIELD: "ontobiotopeTerms",
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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: "qps",
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VALIDATION: [
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{TYPE: CHOICES, VALUES: ["1", "2"],
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ERROR_CODE: "STD49"}
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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: "gmoConstruction",
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VALIDATION: []
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},
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{
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FIELD: "mutant",
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VALIDATION: []
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},
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{
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FIELD: "genotype",
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VALIDATION: []
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},
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{
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FIELD: "Plant pathogenicity code",
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VALIDATION: []
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},
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{
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FIELD: "sexualState",
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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: ["1", "2", "3", "4", "5", "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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VALIDATION: []
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},
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{
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FIELD: "plasmidCollections",
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VALIDATION: [
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{TYPE: REGEXP, MATCH: "([a-zA-Z .'-]+)\(([a-zA-Z .'-]+) (\d+)\)(;([a-zA-Z .'-]+)\(([a-zA-Z .'-]+) (\d+)\))*$",
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ERROR_CODE: "STD62"}
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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: "identificationLiterature",
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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: "pathogenicity",
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VALIDATION: []
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},
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{
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FIELD: "enzymes",
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VALIDATION: []
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},
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{
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FIELD: "metabolites",
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VALIDATION: []
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},
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{
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FIELD: "applications",
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VALIDATION: []
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},
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{
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FIELD: "remarks",
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VALIDATION: []
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},
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{
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FIELD: "sequenceLiterature",
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VALIDATION: [
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{TYPE: REGEXP, MATCH: "^\d+(;?\s*\d+)*$", ERROR_CODE: "STD61"},
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]
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},
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{
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FIELD: "recommendedMedium",
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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: "country",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "STD54"},
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{TYPE: MISSING, ERROR_CODE: "STD55"},
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{TYPE: ISO, ERROR_CODE: "STD57"},
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#{TYPE: CROSSREF, CROSSREF_NAME: COUNTRY_CODES_SHEET, ERROR_CODE: "STD57"}
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]
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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: CROSSREF, CROSSREF_NAME: MARKERS, ERROR_CODE: "GID06"}
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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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{TYPE: REGEXP, MATCH: "^[A-Z]{2}[0-9]{6}$", ERROR_CODE: "GID11"},
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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': 'accessionNumber',
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VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
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ROW_VALIDATION: [],
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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: "PMID",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID18"},
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]
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},
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{
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FIELD: "DOI",
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VALIDATION: [
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{TYPE: MANDATORY, ERROR_CODE: "LID20"},
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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: [
|
|
{TYPE: MANDATORY, ERROR_CODE: "LID13"},
|
|
]
|
|
},
|
|
{
|
|
FIELD: "Issue",
|
|
VALIDATION: []
|
|
},
|
|
{
|
|
FIELD: "First page",
|
|
VALIDATION: [
|
|
{TYPE: MANDATORY, ERROR_CODE: "LID15"},
|
|
]
|
|
},
|
|
{
|
|
FIELD: "Last page",
|
|
VALIDATION: []
|
|
},
|
|
{
|
|
FIELD: "Book title",
|
|
VALIDATION: []
|
|
},
|
|
{
|
|
FIELD: "Editors",
|
|
VALIDATION: []
|
|
},
|
|
{
|
|
FIELD: "Publisher",
|
|
VALIDATION: []
|
|
}
|
|
],
|
|
},
|
|
# SEXUAL_STATE_SHEET: {"acronym": "SSD", COLUMNS: []},
|
|
# RESOURCE_TYPES_VALUES: {"acronym": "RTD", COLUMNS: []},
|
|
# FORM_OF_SUPPLY_SHEET: {"acronym": "FSD", COLUMNS: []},
|
|
# PLOIDY_SHEET: {"acronym": "PLD", COLUMNS: []},
|
|
ONTOBIOTOPE: {
|
|
"acronym": "OTD",
|
|
"id_field": "ID",
|
|
VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS06"},
|
|
COLUMNS: [
|
|
{
|
|
FIELD: "ID",
|
|
VALIDATION: [
|
|
{TYPE: MANDATORY, ERROR_CODE: "OTD01"},
|
|
{TYPE: MISSING, ERROR_CODE: "OTD02"},
|
|
]
|
|
},
|
|
{
|
|
FIELD: "Name",
|
|
VALIDATION: []
|
|
},
|
|
]
|
|
},
|
|
|
|
|
|
|
|
|
|
|
|
CONTROL_SHEET: {
|
|
"acronym": "CTR",
|
|
"id_field": "Version",
|
|
VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS09"},
|
|
COLUMNS: [
|
|
{
|
|
FIELD: "Version",
|
|
VALIDATION: [
|
|
{TYPE: MANDATORY, ERROR_CODE: "CTR01"},
|
|
{TYPE: MISSING, ERROR_CODE: "CTR02"},
|
|
{TYPE: VERSION, ERROR_CODE: "CTR05"},
|
|
]
|
|
},
|
|
{
|
|
FIELD: "Date",
|
|
VALIDATION: [
|
|
{TYPE: MANDATORY, ERROR_CODE: "CTR03"},
|
|
{TYPE: MISSING, ERROR_CODE: "CTR04"},
|
|
]
|
|
},
|
|
]
|
|
},
|
|
|
|
MARKERS: {
|
|
"acronym": "MKD",
|
|
"id_field": "Acronym",
|
|
COLUMNS: [
|
|
{
|
|
FIELD: "Acronym",
|
|
VALIDATION: []
|
|
},
|
|
{
|
|
FIELD: "Marker",
|
|
VALIDATION: []
|
|
},
|
|
],
|
|
},
|
|
}
|
|
|
|
|
|
CROSS_REF_CONF = {
|
|
ONTOBIOTOPE: ['ID'],
|
|
LITERATURE_SHEET: ['ID', 'DOI', 'PMID', 'Full reference', 'Authors', 'Title', 'Journal', 'Year', 'Volume', 'First page'],
|
|
LOCATIONS: ['ID', 'Locality'],
|
|
GROWTH_MEDIA: ['Acronym'],
|
|
STRAINS: ["accessionNumber"],
|
|
SEXUAL_STATE_SHEET: [],
|
|
MARKERS: ["Acronym"],
|
|
|
|
}
|
|
|
|
MIRRI_12052023_VALLIDATION_CONF = {
|
|
'sheet_schema': SHEETS_SCHEMA,
|
|
'cross_ref_conf': CROSS_REF_CONF,
|
|
'keep_sheets_in_memory': [
|
|
{'sheet_name': LOCATIONS, 'indexed_by': 'Locality'}]
|
|
}
|
|
|
|
version_config = {
|
|
'5.1.2': MIRRI_12052023_VALLIDATION_CONF,
|
|
'date': '12/05/2023'
|
|
|
|
}
|
|
|