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

Reviewed-on: https://gitea.cect.org/MIRRI/mirri_utils/pulls/1

mirri/validation/error_logging/error_message.py

@@ -355,6 +355,12 @@ 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 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
@@ -376,7 +382,7 @@ 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."

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,
+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,
 # 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",
+                    {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',
         VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
         ROW_VALIDATION: [
-            {TYPE: NAGOYA, ERROR_CODE: "STRXXX"},
+            {TYPE: NAGOYA, ERROR_CODE: "STD46"},
         ],
         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 = {
@@ -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 = {