From 192bf4a6214ca782f27c00971eb79c29df1ea09e Mon Sep 17 00:00:00 2001 From: Arthur Matta Date: Mon, 16 May 2022 09:48:04 +0100 Subject: [PATCH 1/3] Fixed missing error message --- mirri/validation/error_logging/error_message.py | 5 +++++ mirri/validation/validation_conf_20200601.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/mirri/validation/error_logging/error_message.py b/mirri/validation/error_logging/error_message.py index 7e958bf..1e68ca4 100644 --- a/mirri/validation/error_logging/error_message.py +++ b/mirri/validation/error_logging/error_message.py @@ -355,6 +355,11 @@ class ErrorMessage(): msg += "If the those values are Pubmed ids or DOIs, please ignore this messsage" return msg + def STD46(self): + msg = f"If date of collection/isolation/deposit/inclusion in the catalog is after 2014," \ + f" the value of Geographic Origin must be provided. It is missing for strain {self.pk}." + return msg + """ Genomic Information Error Codes diff --git a/mirri/validation/validation_conf_20200601.py b/mirri/validation/validation_conf_20200601.py index b8f5a8b..1487d6e 100644 --- a/mirri/validation/validation_conf_20200601.py +++ b/mirri/validation/validation_conf_20200601.py @@ -405,7 +405,7 @@ SHEETS_SCHEMA = { 'id_field': 'Accession number', VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"}, ROW_VALIDATION: [ - {TYPE: NAGOYA, ERROR_CODE: "STRXXX"}, + {TYPE: NAGOYA, ERROR_CODE: "STD46"}, ], COLUMNS: STRAIN_FIELDS, }, From e24dda2df3ad5e7e69b45196232bbb367097e19f Mon Sep 17 00:00:00 2001 From: Arthur Matta Date: Mon, 16 May 2022 11:27:10 +0100 Subject: [PATCH 2/3] Changed GID marker validation --- .../validation/error_logging/error_message.py | 2 +- mirri/validation/validation_conf_20200601.py | 43 +++++++++---------- 2 files changed, 21 insertions(+), 24 deletions(-) diff --git a/mirri/validation/error_logging/error_message.py b/mirri/validation/error_logging/error_message.py index 1e68ca4..a940e35 100644 --- a/mirri/validation/error_logging/error_message.py +++ b/mirri/validation/error_logging/error_message.py @@ -381,7 +381,7 @@ class ErrorMessage(): return f"The 'Marker' for genomic information with Strain AN {self.pk} is missing." 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): return f"The 'INSDC AN' column is a mandatory field in the Genomic Information Sheet. The column can not be empty." diff --git a/mirri/validation/validation_conf_20200601.py b/mirri/validation/validation_conf_20200601.py index 1487d6e..1d9752c 100644 --- a/mirri/validation/validation_conf_20200601.py +++ b/mirri/validation/validation_conf_20200601.py @@ -3,9 +3,9 @@ from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROS MISSING, MULTIPLE, NAGOYA, NUMBER, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE, UNIQUE, VALIDATION, VALUES, BIBLIO) -from mirri.settings import (GEOGRAPHIC_ORIGIN, ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO, - STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET) -# MARKERS, +from mirri.settings import (ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO, + STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET, MARKERS) +# GEOGRAPHIC_ORIGIN # SEXUAL_STATE_SHEET, # RESOURCE_TYPES_VALUES, # FORM_OF_SUPPLY_SHEET, @@ -64,7 +64,6 @@ STRAIN_FIELDS = [ }, { FIELD: "Risk Group", - VALIDATION: [ {TYPE: MANDATORY, ERROR_CODE: "STD12"}, {TYPE: MISSING, ERROR_CODE: "STD13"}, @@ -382,9 +381,7 @@ SHEETS_SCHEMA = { VALIDATION: [ {TYPE: MANDATORY, ERROR_CODE: "GID04"}, {TYPE: MISSING, ERROR_CODE: "GID05"}, - {TYPE: CHOICES, ERROR_CODE: "GID06", - VALUES: ['16S rRNA', 'ACT', 'CaM', 'EF-1α', 'ITS', - 'LSU', 'RPB1', 'RPB2', 'TUBB']} + {TYPE: CROSSREF, CROSSREF_NAME: MARKERS, ERROR_CODE: "GID06"} ] }, { @@ -514,20 +511,20 @@ SHEETS_SCHEMA = { }, ] }, - # MARKERS: { - # "acronym": "MKD", - # "id_field": "", - # COLUMNS: [ - # { - # FIELD: "Acronym", - # VALIDATION: [] - # }, - # { - # FIELD: "Marker", - # VALIDATION: [] - # }, - # ], - # }, + MARKERS: { + "acronym": "MKD", + "id_field": "Acronym", + COLUMNS: [ + { + FIELD: "Acronym", + VALIDATION: [] + }, + { + FIELD: "Marker", + VALIDATION: [] + }, + ], + }, } CROSS_REF_CONF = { @@ -536,8 +533,8 @@ CROSS_REF_CONF = { LOCATIONS: ['Locality'], GROWTH_MEDIA: ['Acronym'], STRAINS: ["Accession number"], - SEXUAL_STATE_SHEET: [] - + SEXUAL_STATE_SHEET: [], + MARKERS: ["Acronym"], } MIRRI_20200601_VALLIDATION_CONF = { From 038635999fda988def98b4e964888b28c1a3459e Mon Sep 17 00:00:00 2001 From: Arthur Matta Date: Mon, 16 May 2022 11:59:08 +0100 Subject: [PATCH 3/3] Updated error message STD46 --- mirri/validation/error_logging/error_message.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mirri/validation/error_logging/error_message.py b/mirri/validation/error_logging/error_message.py index a940e35..7188a9b 100644 --- a/mirri/validation/error_logging/error_message.py +++ b/mirri/validation/error_logging/error_message.py @@ -357,7 +357,8 @@ class ErrorMessage(): def STD46(self): msg = f"If date of collection/isolation/deposit/inclusion in the catalog is after 2014," \ - f" the value of Geographic Origin must be provided. It is missing for strain {self.pk}." + 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