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Merge pull request 'Bugfix' (#1) from dev into master

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Reviewed-on: https://gitea.cect.org/MIRRI/mirri_utils/pulls/1
This commit is contained in:
avara 2022-05-19 10:21:24 +00:00
commit bd8093a720
2 changed files with 28 additions and 25 deletions
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8
mirri/validation/error_logging/error_message.py
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@ -355,6 +355,12 @@ class ErrorMessage():
msg += "If the those values are Pubmed ids or DOIs, please ignore this messsage" msg += "If the those values are Pubmed ids or DOIs, please ignore this messsage"
return msg return msg
def STD46(self):
msg = f"If date of collection/isolation/deposit/inclusion in the catalog is after 2014," \
f" the value of column Geographic Origin must be provided and associated with a country in the " \
f"Geographic Origin sheet. The value is missing or not associated with a country for strain {self.pk}."
return msg
""" """
Genomic Information Error Codes Genomic Information Error Codes
@ -376,7 +382,7 @@ class ErrorMessage():
return f"The 'Marker' for genomic information with Strain AN {self.pk} is missing." return f"The 'Marker' for genomic information with Strain AN {self.pk} is missing."
def GID06(self): def GID06(self):
return f"The 'Marker' for genomic information with Strain AN {self.pk} is incorrect." return f"The value of 'Marker' {self.value} is not in the Markers sheet."
def GID07(self): def GID07(self):
return f"The 'INSDC AN' column is a mandatory field in the Genomic Information Sheet. The column can not be empty." return f"The 'INSDC AN' column is a mandatory field in the Genomic Information Sheet. The column can not be empty."

45
mirri/validation/validation_conf_20200601.py
View File

@ -3,9 +3,9 @@ from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROS
MISSING, MULTIPLE, NAGOYA, NUMBER, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE, MISSING, MULTIPLE, NAGOYA, NUMBER, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE,
UNIQUE, UNIQUE,
VALIDATION, VALUES, BIBLIO) VALIDATION, VALUES, BIBLIO)
from mirri.settings import (GEOGRAPHIC_ORIGIN, ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO, from mirri.settings import (ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO,
STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET) STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET, MARKERS)
# MARKERS, # GEOGRAPHIC_ORIGIN
# SEXUAL_STATE_SHEET, # SEXUAL_STATE_SHEET,
# RESOURCE_TYPES_VALUES, # RESOURCE_TYPES_VALUES,
# FORM_OF_SUPPLY_SHEET, # FORM_OF_SUPPLY_SHEET,
@ -64,7 +64,6 @@ STRAIN_FIELDS = [
}, },
{ {
FIELD: "Risk Group", FIELD: "Risk Group",
VALIDATION: [ VALIDATION: [
{TYPE: MANDATORY, ERROR_CODE: "STD12"}, {TYPE: MANDATORY, ERROR_CODE: "STD12"},
{TYPE: MISSING, ERROR_CODE: "STD13"}, {TYPE: MISSING, ERROR_CODE: "STD13"},
@ -382,9 +381,7 @@ SHEETS_SCHEMA = {
VALIDATION: [ VALIDATION: [
{TYPE: MANDATORY, ERROR_CODE: "GID04"}, {TYPE: MANDATORY, ERROR_CODE: "GID04"},
{TYPE: MISSING, ERROR_CODE: "GID05"}, {TYPE: MISSING, ERROR_CODE: "GID05"},
{TYPE: CHOICES, ERROR_CODE: "GID06", {TYPE: CROSSREF, CROSSREF_NAME: MARKERS, ERROR_CODE: "GID06"}
VALUES: ['16S rRNA', 'ACT', 'CaM', 'EF-1α', 'ITS',
'LSU', 'RPB1', 'RPB2', 'TUBB']}
] ]
}, },
{ {
@ -405,7 +402,7 @@ SHEETS_SCHEMA = {
'id_field': 'Accession number', 'id_field': 'Accession number',
VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"}, VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
ROW_VALIDATION: [ ROW_VALIDATION: [
{TYPE: NAGOYA, ERROR_CODE: "STRXXX"}, {TYPE: NAGOYA, ERROR_CODE: "STD46"},
], ],
COLUMNS: STRAIN_FIELDS, COLUMNS: STRAIN_FIELDS,
}, },
@ -514,20 +511,20 @@ SHEETS_SCHEMA = {
}, },
] ]
}, },
# MARKERS: { MARKERS: {
# "acronym": "MKD", "acronym": "MKD",
# "id_field": "", "id_field": "Acronym",
# COLUMNS: [ COLUMNS: [
# { {
# FIELD: "Acronym", FIELD: "Acronym",
# VALIDATION: [] VALIDATION: []
# }, },
# { {
# FIELD: "Marker", FIELD: "Marker",
# VALIDATION: [] VALIDATION: []
# }, },
# ], ],
# }, },
} }
CROSS_REF_CONF = { CROSS_REF_CONF = {
@ -536,8 +533,8 @@ CROSS_REF_CONF = {
LOCATIONS: ['Locality'], LOCATIONS: ['Locality'],
GROWTH_MEDIA: ['Acronym'], GROWTH_MEDIA: ['Acronym'],
STRAINS: ["Accession number"], STRAINS: ["Accession number"],
SEXUAL_STATE_SHEET: [] SEXUAL_STATE_SHEET: [],
MARKERS: ["Acronym"],
} }
MIRRI_20200601_VALLIDATION_CONF = { MIRRI_20200601_VALLIDATION_CONF = {