Mirri 5.1.2

2023-06-10 14:49:33 +01:00
parent e2278fd509
commit 322ed203d8
102 changed files with 1978 additions and 3356 deletions
@@ -0,0 +1,3 @@
+from .error import Entity, Error
+from .error_message import ErrorMessage
+from .error_log import ErrorLog
@@ -0,0 +1,119 @@
+from typing import Optional
+from .error_message import ErrorMessage
+
+
+class Entity():
+    """Entity information
+
+    Args:
+        acronym: acronym of the entity. Must be a 3-characters captalized string
+    """
+
+    def __init__(self, acronym: str) -> None:
+        self.acronym = acronym
+
+    def __str__(self) -> str:
+        return f"Entity {self.acronym}: {self.name}"
+
+    @property
+    def _acronyms(self) -> list:
+        return [
+            func
+            for func in dir(self)
+            if func.isupper() and
+            callable(getattr(self, func)) and
+            not func.startswith("__")
+        ]
+
+    @property
+    def _names(self) -> dict:
+        return {acr: getattr(self, acr)() for acr in self._acronyms}
+
+    @property
+    def name(self) -> str:
+        try:
+            return self._names[self.acronym]
+        except KeyError:
+            raise KeyError(f'Unknown acronym {self.acronym}.')
+
+    @property
+    def acronym(self) -> str:
+        return self._acronym
+
+    @acronym.setter
+    def acronym(self, acronym: str) -> None:
+        self._acronym = acronym
+
+    def EFS(self) -> str:
+        return 'Excel File Structure'
+
+    def GMD(self) -> str:
+        return 'Growth Media'
+
+    def GOD(self) -> str:
+        return 'Geographic Origin'
+
+    def LID(self) -> str:
+        return 'Literature'
+
+    def STD(self) -> str:
+        return 'Strains'
+
+    def GID(self) -> str:
+        return 'Genomic Information'
+
+    def OTD(self) -> str:
+        return 'Ontobiotope'
+
+    def UCT(self) -> str:
+        return 'Uncategorized'
+
+
+class Error():
+    """Error information
+
+        Args:
+            message (str): Error message
+            entity (Entity, optional): Entity related to the error. If None will default to Uncategorized. Defaults to None.
+            data (str, optional): Data used for sorting the messages. Defaults to None.
+    """
+
+    def __init__(self, code: str, pk: Optional[str] = None, data: Optional[str] = None) -> None:
+        self.code = code.upper()
+        self.pk = pk
+        self.data = data
+
+    def __str__(self):
+        return f"Error {self._code}: {self.message}"
+
+    @property
+    def code(self) -> str:
+        return self._code
+
+    @code.setter
+    def code(self, code: str) -> None:
+        self._code = code.upper()
+
+    @property
+    def pk(self) -> Optional[str]:
+        return self._pk
+
+    @pk.setter
+    def pk(self, pk: Optional[str] = None) -> None:
+        self._pk = pk
+
+    @property
+    def data(self) -> Optional[str]:
+        return self._data
+
+    @data.setter
+    def data(self, data: Optional[str]):
+        self._data = data
+
+    @property
+    def entity(self) -> Entity:
+        return Entity(self.code[:3])
+
+    @property
+    def message(self) -> str:
+        return ErrorMessage(self.code, self.pk, self.data).message
@@ -0,0 +1,77 @@
+from typing import Optional, Union
+from datetime import datetime
+from .error import Error
+
+
+class ErrorLog():
+    def __init__(self, input_filename: str, cc: Optional[str] = None, date: Optional[Union[str, datetime]] = None, limit: int = 100):
+        """
+        Logger for Error instances.
+
+        Args:
+            input_filename (str): name of the file to be logged
+            cc (str, optional): name of the curator. Defaults to None.
+            date (str, optional): date (e.g. created, last modified) associated with the file. Useful for versioning. Defaults to None.
+            limit (int, optional): limit of errors to print to the report. Defaults to 100.
+        """
+        self._input_filename = input_filename
+        self._cc = cc
+        self._date = date
+        self._errors = {}
+        self.limit = limit
+        self._counter = 0
+
+    def __str__(self) -> str:
+        output = f"""Error Log for file {self._input_filename}\nENTITY | CODE   | MESSAGE"""
+        for acronym, error_list in self.get_errors().items():
+            for error in error_list:
+                output += f"\n{acronym:6} | {error.code:6} | {error.message[:100]}"
+        return output
+
+    @property
+    def input_filename(self) -> str:
+        return self._input_filename
+
+    @input_filename.setter
+    def input_filename(self, input_filename: str) -> None:
+        self._input_filename = input_filename
+
+    @property
+    def cc(self) -> Optional[str]:
+        return self._cc
+
+    @cc.setter
+    def cc(self, cc: Optional[str]) -> None:
+        self._cc = cc
+
+    @property
+    def date(self) -> Optional[Union[str, datetime]]:
+        return self._date
+
+    @date.setter
+    def date(self, date: Optional[Union[str, datetime]] = None) -> None:
+        if isinstance(date, str):
+            self._date = datetime.strptime(date, r'%d-%m-%Y')
+        else:
+            self._date = date
+
+    def get_errors(self) -> dict:
+        """
+        Get all errors
+
+        Returns:
+            dict: Error intances grouped by entity acronym.
+        """
+        return self._errors
+
+    def add_error(self, error: Error) -> None:
+        """
+        Add an error.
+
+        Args:
+            error (Error): Error instance.
+        """
+        if error.entity.acronym not in self._errors:
+            self._errors[error.entity.acronym] = [error]
+        else:
+            self._errors[error.entity.acronym].append(error)
@@ -0,0 +1,552 @@
+from typing import Optional
+
+
+class ErrorMessage():
+    """Error message
+
+    Args:
+        code (str): Error code.
+        pk (str | optional): The instance's primary key that triggered the error. Defaults to None.
+        value (str | optional): The instance's value that triggered the error. Defaults to None.
+    """
+
+    def __init__(self, code: str, pk: Optional[str] = None, value: Optional[str] = None):
+        self.code = code.upper()
+        self.pk = pk
+        self.value = value
+
+    @property
+    def _codes(self) -> list:
+        return [
+            func
+            for func in dir(self)
+            if func.isupper() and
+            callable(getattr(self, func)) and
+            not func.startswith("__")
+        ]
+
+    @property
+    def _messages(self) -> dict:
+        return {code: getattr(self, code) for code in self._codes}
+
+    @property
+    def message(self) -> str:
+        if not self._validate_code():
+            raise ValueError(f"{self.code} not found")
+        return self._messages[self.code]()
+
+    @property
+    def code(self) -> str:
+        return self._code
+
+    @code.setter
+    def code(self, code: str) -> None:
+        self._code = code.upper()
+
+    def _validate_code(self) -> bool:
+        return self.code in self._codes
+
+    @property
+    def pk(self) -> str:
+        return self._pk
+
+    @pk.setter
+    def pk(self, pk: str) -> None:
+        self._pk = pk
+
+    @property
+    def value(self) -> str:
+        return self._value
+
+    @value.setter
+    def value(self, value: str) -> None:
+        self._value = value
+
+    """
+        Excel File Structure Error Codes
+    """
+
+    def EXL00(self):
+        return f"The provided file '{self.pk}' is not an excel(xlsx) file"
+
+    def EFS01(self):
+        return "The 'Growth media' sheet is missing. Please check the provided excel template."
+
+    def EFS02(self):
+        return "The 'Geographic origin' sheet is missing. Please check the provided excel template."
+
+    def EFS03(self):
+        return "The 'Literature' sheet is missing. Please check the provided excel template."
+
+    def EFS04(self):
+        return "The 'Sexual state' sheet is missing. Please check the provided excel template."
+
+    def EFS05(self):
+        return "The 'Strains' sheet is missing. Please check the provided excel template."
+
+    def EFS06(self):
+        return "The 'Ontobiotope' sheet is missing. Please check the provided excel template."
+
+    def EFS07(self):
+        return "The 'Markers' sheet is missing. Please check the provided excel template."
+
+    def EFS08(self):
+        return "The 'Genomic information' sheet is missing. Please check the provided excel template."
+    
+    def EFS09(self):
+        return "The 'Version' sheet is missing. Please check the provided excel template."
+
+    """
+        Growth Media Error Codes
+    """
+
+    def GMD01(self):
+        return "The 'Acronym' column is a mandatory field in the Growth Media sheet."
+
+    def GMD02(self):
+        return "The 'Acronym' column is empty or has missing values."
+
+    def GMD03(self):
+        return "The 'Description' column is a mandatory field in the Growth Media sheet. The column can not be empty."
+
+    def GMD04(self):
+        return f"The 'Description' for growth media with Acronym {self.pk} is missing."
+
+    """
+        Geographic Origin Error Codes
+    """
+
+    def GOD01(self):
+        return "The 'ID' column is a mandatory field in the Geographic Origin sheet."
+
+    def GOD02(self):
+        return "The 'ID' column is empty or has missing values."
+
+    def GOD03(self):
+        return "The 'Country' column is a mandatory field in the Geographic Origin sheet. The column can not be empty."
+
+    def GOD04(self):
+        return f"The 'Country' for geographic origin with ID {self.pk} is missing."
+
+    def GOD05(self):
+        return f"The 'Country' for geographic origin with ID {self.pk} is incorrect."
+
+    def GOD06(self):
+        return f"The 'Locality' column is a mandatory field in the Geographic Origin sheet. The column can not be empty."
+
+    def GOD07(self):
+        return f"The 'Locality' for geographic origin with ID {self.pk} is missing."
+
+    """
+        Literature Error Codes
+    """
+
+    def LID01(self):
+        return "The 'ID' column is a mandatory field in the Literature sheet."
+
+    def LID02(self):
+        return "The 'ID' column empty or missing values."
+
+    def LID03(self):
+        return "The 'Full reference' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    #def LID04(self):
+        #return f"The 'Full reference' for literature with ID {self.pk} is missing."
+
+    def LID05(self):
+        return "The 'Authors' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    #def LID06(self):
+        #return f"The 'Authors' for literature with ID {self.pk} is missing."
+
+    def LID07(self):
+        return "The 'Title' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    #def LID08(self):
+        #return f"The 'Title' for literature with ID {self.pk} is missing."
+
+    def LID09(self):
+        return "The 'Journal' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    #def LID10(self):
+        #return f"The 'Journal' for literature with ID {self.pk} is missing."
+
+    def LID11(self):
+        return "The 'Year' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    def LID12(self,):
+        return f"The 'Year' for literature with ID {self.pk} is missing."
+
+    def LID13(self):
+        return "The 'Volume' column is a mandatory field in the Literature sheet. The column can not be empty."
+
+    def LID14(self):
+        return f"The 'Volume' for literature with ID {self.pk} is missing."
+
+    def LID15(self):
+        return "The 'First page' column is a mandatory field. The column can not be empty."
+
+    def LID16(self):
+        return f"The 'First page' for literature with ID {self.pk} is missing."
+
+    def LID17(self):
+        return( f"There are four types of ways to fill in the 'Literature' sheet.",
+                "1st- Columns 'ID' and 'DOI' must be obrigatory.",
+                "2nd-Columns 'ID' and 'PMID' are obrigatory.",
+                "3rd-Columns 'ID' and 'Full reference' are obrigatory.",
+                "In the alternative of these three types of forms not being filled in, we have:",
+                "4th-Columns 'ID', 'Authors', 'Title', 'Journal', 'Year', 'Volume', 'First page'.")
+        
+    def LID18(self):
+        return "The 'PMID' column is a mandatory field. The column can not be empty."
+
+    #def LID19(self):
+        #return f"PMID for literature with ID {self.pk} is missing."
+    
+    def LID20(self):
+        return "The 'DOI' column is a mandatory field. The column can not be empty."
+
+    #def LID21(self):
+        #return f"DOI for literature with ID {self.pk} is missing."
+
+    """
+        Strains Error Codes
+    """
+    def STD01(self):
+        return "The 'accessionNumber' column is a mandatory field in the Strains sheet."
+
+    def STD02(self):
+        return "The 'accessionNumber' column is empty or has missing values."
+
+    def STD03(self):
+        return f"The 'accessionNumber' must be unique. The '{self.value}' is repeated."
+
+    def STD04(self):
+        return (f"The 'accessionNumber' {self.pk} is not according to the specification."
+                " The value must be of the format '<Sequence of characters> <sequence of characters>'.")
+
+    def STD05(self):
+        return f"The 'useRestrictions' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD06(self):
+        return f"The 'useRestrictions' for strain with accessionNumber {self.pk} is missing."
+
+    def STD07(self):
+        return (f"The 'useRestrictions' for strain with accessionNumber {self.pk} is not according to the specification."
+                f" Your value is {self.value} and the accepted values are 1, 2, 3.")
+
+    def STD08(self):
+        return f"The 'nagoyaConditions' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD09(self):
+        return f"The 'nagoyaConditions' for strain with accessionNumber {self.pk} is missing."
+
+    def STD10(self):
+        return (f"The 'nagoyaConditions' for strain with accessionNumber {self.pk} is not according to the specification."
+                f" Your value is {self.value} and the accepted values are 1, 2, 3.")
+
+    def STD11(self):
+        return (f"The 'registeredCollection' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2, 3.")
+
+    def STD12(self):
+        return "The 'riskGroup' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD13(self):
+        return f"The 'riskGroup' for strain with accessionNumber {self.pk} is missing."
+
+    def STD14(self):
+        return (f"The 'riskGroup' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2, 3, 4.")
+
+    def STD15(self):
+        return (f"The 'dualUse' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2.")
+
+    def STD16(self):
+        return (f"The “euQuarantine” for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2.")
+
+    def STD17(self):
+        return f"The 'organismType' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD18(self):
+        return f"The 'organismType' for strain with accessionNumber {self.pk} is missing."
+
+    def STD19(self):
+        return (f"The 'organismType' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 'Algae', 'Archaea', 'Bacteria', 'Cyanobacteria', "
+                "'Filamentous Fungi',  'Phage', 'Plasmid', 'Virus', 'Yeast', 1, 2, 3, 4, 5, 6, 7, 8, 9.")
+
+    def STD20(self):
+        return f"The 'speciesName' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD21(self):
+        return f"The 'speciesName' for strain with accessionNumber {self.pk} is missing."
+
+    def STD22(self):
+        return f"The 'speciesName' for strain with accessionNumber {self.pk} is incorrect."
+
+    def STD23(self):
+        return (f"The 'hybrid' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2.")
+
+    def STD24(self):
+        return (f"The 'depositHistory' for strain with accessionNumber {self.pk} is incorrect."
+                "The field includes entries separated by '<' meaning 'received from'."
+                "Entries may include persons or CCs. The name of the CC should be followed by"
+                "the month, when available, and year of the acquisition. Between parentheses,"
+                "the strain designation or CC numbers and/or a name can also be entered when "
+                "a name change has occurred.")
+
+    def STD25(self):
+        return (f"The 'depositDate' for strain with accessionNumber {self.pk} is incorrect."
+                " The allowed formats are 'YYYY-MM-DD', 'YYYYMMDD', 'YYYYMM', and 'YYYY'.")
+
+    def STD26(self):
+        return (f"The 'accessionDate' for strain with accessionNumber {self.pk} is incorrect."
+                " The allowed formats are 'YYYY-MM-DD', 'YYYYMMDD', 'YYYYMM', and 'YYYY'.")
+
+    def STD27(self):
+        return (f"The 'collectionDate' for strain with accessionNumber {self.pk} is incorrect."
+                " The allowed formats are 'YYYY-MM-DD', 'YYYYMMDD', 'YYYYMM', and 'YYYY'.")
+
+    def STD28(self):
+        return (f"The 'isolationDate' for strain with accessionNumber {self.pk} is incorrect."
+                " The allowed formats are 'YYYY-MM-DD', 'YYYYMMDD', 'YYYYMM', and 'YYYY'.")
+
+    def STD29(self):
+        return (f"The 'temperatureGrowthRange' for strain with accessionNumber {self.pk} is incorrect."
+                " It must have two decimal numbers separated by ','")
+
+    def STD30(self):
+        return f"The 'temperatureGrowthRange' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD31(self):
+        return f"The 'temperatureGrowthRange' for strain with accessionNumber {self.pk} is missing."
+
+    def STD32(self):
+        return (f"The 'temperatureGrowthRange' for strain with accessionNumber {self.pk} is incorrect."
+                " It must have two decimal numbers separated by ','.")
+
+    def STD33(self):
+        return ("The 'recommendedTemperature' column is a mandatory field in the Strains Sheet. The column can not be empty.")
+
+    def STD34(self):
+        return f"The 'recommendedTemperature' for strain with accessionNumber {self.pk} is missing."
+
+    def STD35(self):
+        return f"The value of 'recommendedTemperature' for strain with accessionNumber {self.pk} is not in the Growth Media Sheet."
+
+    def STD36(self):
+        return f"The 'supplyForms' column is a mandatory field in the Strains Sheet. The column can not be empty."
+
+    def STD37(self):
+        return f"The 'supplyForms' for strain with accessionNumber {self.pk} is missing."
+
+    def STD38(self):
+        return f"The value of 'supplyForms' for strain with accessionNumber {self.pk} is not in the Forms of Supply Sheet."
+
+    def STD39(self):
+        return (f"The 'geographicCoordinates' column for strain with accessionNumber {self.pk} is incorrect."
+                "The allowed formats are two, three or four decimal numbers separated by ','. Moreover, the first number must be."
+                "between [-90, 90], the second between [-180, 180], and the third and fourth refers to the precision and altitude, defined by decimal numbers." 
+                "Put a question mark for lack of precision or altitude when one of them is missing. Leave the values blank when both are missing. ")
+
+    def STD40(self):
+        return (f"The 'country' column for strain with accessionNumber {self.pk} is incorrect."
+                "The allowed formats are one decimal number between [-200, 8000].")
+    def STD54(self):
+        return (f"The 'country'column is a mandatory field in the Strains Sheet. The column can not be empty.")
+    def STD55(self):
+        return (f"The 'country' for strain with accessionNumber {self.pk} is missing.")
+
+    def STD41(self):
+        return f"The value of 'ontobiotopeTerms' for strain with accessionNumber {self.pk} is not in the Ontobiotope Sheet."
+
+    def STD42(self):
+        return (f"The 'gmo' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 1, 2")
+
+    def STD43(self):
+        return (f"The 'sexualState' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 'Mata', 'Matalpha', 'Mata/Matalpha', "
+                "'Matb', 'Mata/Matb', 'MTLa', 'MTLalpha', 'MTLa/MTLalpha', 'MAT1-1', 'MAT1-2', 'MAT1', 'MAT2', 'MT+', 'MT-'")
+
+    def STD44(self):
+        return (f"The 'ploidy' for strain with accessionNumber {self.pk} is not according to specification."
+                f" Your value is {self.value} and the accepted values are 0, 1, 2, 3, 4, 9")
+
+    def STD45(self):
+        msg = f"At least one of the values '{self.value}' of the literature field for strain {self.pk} are not in the literature sheet. "
+        msg += "If the those values are Pubmed ids or DOIs, please ignore this messsage"
+        return msg
+
+    def STD46(self):
+       return (f"The 'geographicOrigin' for strain with accessionNumber {self.pk} is not according to specification."
+           f"The 'geographicOrigin' column must consist of the ID's associated with the Geographic origin sheet.")
+
+    def STD47(self):
+        return "The 'country' column is a mandatory field in the Strains sheet."
+
+    def STD48(self):
+        return "The 'country' column is empty or has missing values."
+
+    def STD49(self):
+        return (f"The “qps” for strain with accessionNumber {self.pk} is not according to specification."
+            f" Your value is {self.value} and the accepted values are 1, 2.")
+        
+    def STD50(self):
+        return (f"The “axenicCulture” for strain with accessionNumber {self.pk} is not according to specification."
+        f" Your value is {self.value} and the accepted values are 'Axenic', 'Not axenic'.")    
+
+    def STD51(self):
+        return f"The 'mirriAccessionNumber' must be unique. The '{self.pk}' is repeated."
+    
+    def STD52(self): 
+        return (f"The 'mirriAccessionNumber' for strain with accessionNumber {self.pk} is incorrect."
+                " It must have the expression MIRRI followed by 7 digits")
+    
+    def STD53(self): 
+        return (f"The 'siteLinks' for strain with accessionNumber {self.pk} is incorrect."
+                " The displayed expression it should be composed of: site name ';' website url." )
+    
+    def STD56(self): 
+        return (f"The 'siteLinks' for strain with accessionNumber {self.pk} is incorrect."
+                " The url must be valid. " )    
+    def STD57(self): 
+        return (f"The 'country' for strain with accessionNumber {self.pk} is incorrect."
+                "This information must be expressed by using the ISO-3166 standard for country" 
+                "codes. The preferred set is ISO 3166-1 alpha-2 (two letters code), but ISO 3166-"
+                "1 alpha-3 (three letters code) is also accepted. Former country codes must" 
+                "follow standard’s part three ISO 3166-3 (four letters code). Only one code can" 
+                "be included." )    
+    def STD58(self): 
+        return (f"The 'mtaFile' for strain with accessionNumber {self.pk} is incorrect."
+                " The url must be valid. " )    
+    def STD59(self): 
+        return (f"The 'absFile' for strain with accessionNumber {self.pk} is incorrect."
+                "The displayed expression it should be composed of: name ';' website url."
+                "When only one URL is provided, the title may be omitted. In this case, the URL" 
+                "will be shown in clear to users." ) 
+    def STD60(self): 
+        return (f"The 'absFile' for strain with accessionNumber {self.pk} is incorrect."
+                 " The url must be valid. ")              
+    def STD61(self): 
+        return (f"The 'sequenceLiterature' for strain with accessionNumber {self.pk} is incorrect."
+                 "Numeric identifiers separated by a semicolon ';'.")   
+    
+    def STD62(self): 
+        return (f"The 'plasmidCollections' for strain with accessionNumber {self.pk} is incorrect."
+                "It should include the name of the plasmid followed by the CC number in"
+                "parentheses. More than one plasmid can be reported, separated by ';'. "
+                "Plasmid names should be provided as free text."
+                "CC numbers should be composed by the CC acronym followed by a number"
+                "separated by a space'. Numeric identifiers separated by a semicolon ';'.")  
+              
+    def STD63(self): 
+        return (f"The 'otherCollectionNumbers' for strain with accessionNumber {self.pk} is incorrect."
+                " The value must be of the format '<Sequence of characters> <sequence of characters>'.")
+        
+    def STD64(self): 
+        return (f"The 'type' for strain with accessionNumber {self.pk} is incorrect."
+              f"Your value is {self.value} and the accepted values are 1, 2.")
+        
+    def STD64(self): 
+        return (f"The 'status' for strain with accessionNumber {self.pk} is incorrect."
+                "When the type equal 2 the status must contain the type," 
+                "if the type equal 2 the status must have a null value.")
+        
+    def STD65(self): 
+        return (f"The 'status' for strain with accessionNumber {self.pk} is incorrect."
+                "The structure should be 'type of <character string>.")
+        
+    def STD68(self):
+        return (f"The 'geographicOrigin'column is a mandatory field in the Strains Sheet. The column can not be empty.")
+    
+    def STD69(self):
+        return (f"The 'geographicOrigin' for strain with accessionNumber {self.pk} is missing.")
+            
+    """
+        Genomic Information Error Codes
+    """
+
+    def GID01(self):
+        return f"The 'Strain accessionNumber' (Strain AN) column is a mandatory field in the Genomic Information Sheet."
+
+    def GID02(self):
+        return f"The 'Strain accessionNumber' (Strain AN) column is empty or has missing values."
+
+    def GID03(self):
+        return f"The value of 'Strain accessionNumber' (Strain AN) {self.value} is not in the Strains sheet."
+
+    def GID04(self):
+        return f"The 'Marker' column is a mandatory field in the Genomic Information Sheet. The column can not be empty."
+
+    def GID05(self):
+        return f"The 'Marker' for genomic information with Strain AN {self.pk} is missing."
+
+    def GID06(self):
+        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."
+
+    def GID08(self):
+        return f"The 'INSDC AN' for genomic information with Strain AN {self.pk} is missing."
+
+    def GID09(self):
+        return f"The 'INSDC AN' for genomic information with Strain AN {self.pk} is incorrect."
+
+    def GID10(self):
+        return (f"The 'Sequence' for genomic information with Strain AN {self.pk} is incorrect."
+                " It must be a sequence of 'G', 'T', 'A', 'C' characteres of any length and without white spaces.")
+
+    def GID11(self):
+        return (f"The 'Sequence' for genomic information with Strain AN {self.pk} is incorrect."
+                "An INSDC accession number is an alphanumeric"
+                "code made by a fixed number of letters followed by a fixed number of digits," 
+                "without any separation. For sequences, the code is currently made of two" 
+                "letters followed by six numbers.")
+
+
+    """
+    Ontobiotope Error Codes
+    """
+
+    def CTR01(self):
+        return "The 'Version' columns is a mandatory field in the Version Sheet."
+
+    def CTR02(self):
+        return "The 'Version' columns is empty or has missing values."
+    
+    def CTR03(self):
+        return "The 'Date' columns is a mandatory field in the Control Sheet."
+
+    def CTR04(self):
+        return "The 'Date' columns is empty or has missing values."
+
+    def CTR05(self):
+        return f"The version {self.value} is the only one to be used."
+
+
+
+    """
+        Ontobiotope Error Codes
+    """
+
+    def OTD01(self):
+        return "The 'ID' columns is a mandatory field in the Ontobiotope Sheet."
+
+    def OTD02(self):
+        return "The 'ID' columns is empty or has missing values."
+
+    #def OTD03(self):
+        return "The 'Name' columns is a mandatory field in the Ontobiotope Sheet. The column can not be empty."
+
+    #def OTD04(self):
+        return f"The 'Name' for ontobiotope with ID {self.pk} is missing."
+
+    
+
+    
@@ -0,0 +1,671 @@
+import re
+from pathlib import Path
+from io import BytesIO
+from zipfile import BadZipfile
+from datetime import datetime
+from calendar import monthrange
+import requests
+from openpyxl import load_workbook
+import pycountry
+
+from mirri.io.parsers.excel import workbook_sheet_reader, get_all_cell_data_from_sheet
+from mirri.validation.error_logging import ErrorLog, Error
+from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROSSREF_NAME, DATE,
+                                   ERROR_CODE, FIELD, MANDATORY, MATCH,
+                                   MISSING, MULTIPLE, NAGOYA, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON,
+                                   TYPE, UNIQUE, VALIDATION, VALUES, BIBLIO, DOMINIO,URL_DOMINIO, ISO, URL_TITLE,JUST_URL,TITLE,
+                                   HISTORY,NAGOYA1, VERSION)
+from mirri.settings import LOCATIONS, SUBTAXAS
+from mirri.settings_v1 import LOCATIONS, SUBTAXAS
+from mirri.validation.validation_conf_12052023 import version_config
+
+
+def validate_mirri_excel(fhand, version="", date=""):
+    configuration = version_config.get(version)
+    if configuration is None:
+        raise NotImplementedError("Unsupported version: " + version)
+    configuration["date"] = date or configuration.get("date")  
+    if configuration["date"] != "12/05/2023":
+        raise ValueError("Invalid date. Expected: 12/05/2023")
+    return validate_excel(fhand, configuration)
+ 
+    
+def version(value , validation_conf=None):
+    if value is None:
+        return True
+    try: 
+        for version in version_config:
+            if value == version :
+                return True
+    except:
+        return False    
+    
+        
+def validate_country_code(value,validation_conf=None):
+    if value is None:
+        return True
+    try:  
+        if pycountry.countries.get(alpha_2=value) or pycountry.countries.get(alpha_3=value) or pycountry.historic_countries.get(alpha_4 = value):
+            return True
+    except:
+        return False
+
+
+def validate_excel(fhand, configuration):
+    validation_conf = configuration['sheet_schema']
+    cross_ref_conf = configuration['cross_ref_conf']
+    in_memory_sheet_conf = configuration['keep_sheets_in_memory']
+    excel_name = Path(fhand.name).stem
+    error_log = ErrorLog(excel_name)
+
+    try:
+        workbook = load_workbook(filename=BytesIO(
+            fhand.read()), read_only=True, data_only=True)
+    except (BadZipfile, IOError):
+        error = Error('EXL00', fhand.name, fhand.name)
+        error_log.add_error(error)
+        return error_log
+
+    # excel structure errors
+    structure_errors = list(validate_excel_structure(workbook, validation_conf))
+    if structure_errors:
+        for error in structure_errors:
+            error = Error(error[ERROR_CODE], pk=error['id'],
+                          data=error['value'])
+            error_log.add_error(error)
+
+        return error_log
+
+    crossrefs = get_all_crossrefs(workbook, cross_ref_conf)
+    in_memory_sheets = get_all_in_memory_sheet(workbook, in_memory_sheet_conf)
+    content_errors = validate_content(workbook, validation_conf,
+                                      crossrefs, in_memory_sheets)
+
+    for error in content_errors:
+        # if error[ERROR_CODE] == 'STD43':
+        #     continue
+        error = Error(error[ERROR_CODE], pk=error['id'], data=error['value'])
+
+        error_log.add_error(error)
+    return error_log
+
+
+def validate_excel_structure(workbook, validation_conf):
+    for sheet_name, sheet_conf in validation_conf.items():
+        mandatory = sheet_conf.get(VALIDATION, {}).get(TYPE, None)
+        mandatory = mandatory == MANDATORY
+
+        error_code = sheet_conf.get(VALIDATION, {}).get(ERROR_CODE, False)
+        try:
+            sheet = workbook[sheet_name]
+        except KeyError:
+            sheet = None
+
+        if sheet is None:
+            if mandatory:
+                yield {'id': None, 'sheet': sheet_name, 'field': None,
+                       'error_code': error_code, 'value': None}
+            continue
+
+        headers = _get_sheet_headers(sheet)
+        for column in sheet_conf.get(COLUMNS):
+            field = column[FIELD]
+            for step in column.get(VALIDATION, []):
+                if step[TYPE] == MANDATORY and field not in headers:
+                    yield {'id': None, 'sheet': sheet_name, 'field': field,
+                           'error_code': step[ERROR_CODE], 'value': None}
+
+
+def _get_sheet_headers(sheet):
+    first_row = next(sheet.iter_rows(min_row=1, max_row=1))
+    return [c.value for c in first_row]
+
+
+def _get_values_from_columns(workbook, sheet_name, columns):
+    indexed_values = {}
+    for row in workbook_sheet_reader(workbook, sheet_name):
+        for col in columns:
+            indexed_values[str(row.get(col))] = ""
+
+    return indexed_values
+
+
+def get_all_crossrefs(workbook, cross_refs_names):
+    crossrefs = {}
+    for ref_name, columns in cross_refs_names.items():
+        if columns:
+            crossrefs[ref_name] = _get_values_from_columns(workbook, ref_name,
+                                                               columns)
+        else:
+            try:
+                crossrefs[ref_name] = get_all_cell_data_from_sheet(workbook, ref_name)
+            except ValueError as error:
+                if 'sheet is missing' in str(error):
+                    crossrefs[ref_name] = []
+                else:
+                    raise
+
+    return crossrefs
+
+
+def get_all_in_memory_sheet(workbook, in_memory_sheet_conf):
+    in_memory_sheets = {}
+    for sheet_conf in in_memory_sheet_conf:
+        sheet_name = sheet_conf['sheet_name']
+        indexed_by = sheet_conf['indexed_by']
+        rows = workbook_sheet_reader(workbook, sheet_name)
+        indexed_rows = {row[indexed_by]: row for row in rows}
+        in_memory_sheets[sheet_name] = indexed_rows
+
+    return in_memory_sheets
+
+
+def validate_content(workbook, validation_conf, crossrefs, in_memory_sheets):
+    for sheet_name in validation_conf.keys():
+        sheet_conf = validation_conf[sheet_name]
+        sheet_id_column = sheet_conf['id_field']
+        shown_values = {}
+        row_validation_steps = sheet_conf.get(ROW_VALIDATION, None)
+        for row in workbook_sheet_reader(workbook, sheet_name):
+            id_ = row.get(sheet_id_column, None)
+            if id_ is None:
+                error_code = _get_missing_row_id_error(sheet_id_column,
+                                                       sheet_conf)
+                yield {'id': id_, 'sheet': sheet_name,
+                       'field': sheet_id_column,
+                       'error_code': error_code, 'value': None}
+                continue
+            do_have_cell_error = False
+            for column in sheet_conf[COLUMNS]:
+                label = column[FIELD]
+                validation_steps = column.get(VALIDATION, None)
+                value = row.get(label, None)
+                if validation_steps:
+                    error_code = validate_cell(value, validation_steps,
+                                               crossrefs, shown_values, label)
+                    if error_code is not None:
+                        do_have_cell_error = True
+                        yield {'id': id_, 'sheet': sheet_name, 'field': label,
+                               'error_code': error_code, 'value': value}
+
+            if not do_have_cell_error and row_validation_steps:
+                error_code = validate_row(
+                    row, row_validation_steps, in_memory_sheets)
+                if error_code is not None:
+                    yield {'id': id_, 'sheet': sheet_name, 'field': 'row',
+                           'error_code': error_code, 'value': 'row'}
+
+
+def _get_missing_row_id_error(sheet_id_column, sheet_conf):
+    error_code = None
+    for column in sheet_conf[COLUMNS]:
+        if column[FIELD] == sheet_id_column:
+            error_code = [step[ERROR_CODE]
+                          for step in column[VALIDATION] if step[TYPE] == MISSING][0]
+    return error_code
+
+
+def validate_row(row, validation_steps, in_memory_sheets):
+    for validation_step in validation_steps:
+        kind = validation_step[TYPE]
+        error_code = validation_step[ERROR_CODE]
+        if kind == NAGOYA:
+            if not is_valid_nagoya_v20200601(row, in_memory_sheets):
+                return error_code
+            if not is_valid_nagoya_v12052023(row, in_memory_sheets):
+                return error_code
+        elif kind == BIBLIO:
+            if not is_valid_pub(row):
+                return error_code
+        elif kind == NAGOYA1:
+            if not is_valid_nago(row):
+                return error_code    
+        else:
+            msg = f'{kind} is not a recognized row validation type method'
+            raise NotImplementedError(msg)
+
+
+def validate_cell(value, validation_steps, crossrefs, shown_values, label):
+
+    for step_conf in validation_steps:
+        if step_conf[TYPE] == MANDATORY:
+            continue
+        step_conf['crossrefs_pointer'] = crossrefs
+        step_conf['shown_values'] = shown_values
+        step_conf['label'] = label
+        error_code = validate_value(value, step_conf)
+
+        if error_code is not None:
+            return error_code
+   
+def is_valid_pub(row):
+    pub_id = row.get('ID', None)
+    pub_pmid = row.get('PMID', None)
+    pub_doi = row.get('DOI', None)
+    title = row.get('Title', None)
+    full_reference = row.get('Full reference', None)
+    authors = row.get('Authors', None)
+    journal = row.get('Journal', None)
+    year = row.get('Year', None)
+    volumen = row.get('Volume', None)
+    first_page = row.get('First page', None)
+    book_title = row.get('Book title', None)
+    editors = row.get('Editors', None)
+    publishers = row.get('Publishers', None)
+
+    if (pub_id != None and pub_doi != None) or (pub_id != None and pub_pmid != None) or (pub_id != None and full_reference != None) or (pub_id != None and authors != None and title != None and journal != None and year != None and volumen != None and first_page != None) :
+        return True
+    is_journal = bool(title)
+
+   # if (is_journal and (not authors  or not journal or not not year or
+    #                    not volumen or not first_page)):
+     #   return False
+    #if (not is_journal and (not authors or not year or
+     #                       not editors or not publishers or not book_title)):
+      #  return False
+
+    return False
+
+def is_valid_nago(row):
+    if not row:
+        return True
+    status = row.get("status", None)
+    type = row.get("type", None)
+    regex = r'^[a-zA-Z\s.\'-]+$'
+    
+    if status != None and type != None:
+        if (re.match(regex, status) and type==1):
+            return False
+    if (type == 2 and status is None):
+        return False
+    return True
+
+def parsee_mirri_excel(row, in_memory_sheets, version=""):
+    if version == "20200601":
+        return is_valid_nagoya_v20200601 (row, in_memory_sheets)
+    elif version == "12052023":
+        return is_valid_nagoya_v12052023 (row, in_memory_sheets)            
+    else:
+        raise NotImplementedError("Only versions 20200601 and 12052023 are implemented")
+
+def is_valid_nagoya_v20200601(row, in_memory_sheets):  # sourcery skip: return-identity
+    location_index = row.get('Geographic origin', None)
+    if location_index is None:
+        country = None
+    else:
+        geo_origin = in_memory_sheets[LOCATIONS].get(location_index, {})
+        country = geo_origin.get('Country', None)
+
+    _date = row.get("Date of collection", None)
+    if _date is None:
+        _date = row.get("Date of isolation", None)
+    if _date is None:
+        _date = row.get("Date of deposit", None)
+    if _date is None:
+        _date = row.get("Date of inclusion in the catalogue", None)
+    if _date is not None:
+        year = _date.year if isinstance(_date, datetime) else int(str(_date)[:4])
+    else:
+        year = None
+
+    if year is not None and year >= 2014 and country is None:
+        return False
+    
+ 
+
+    return True
+
+def is_valid_nagoya_v12052023(row, in_memory_sheets):  # sourcery skip: return-identity
+    location_index = row.get('geographicOrigin', None)
+    if location_index is None:
+        country = None
+    else:
+        geo_origin = in_memory_sheets[LOCATIONS].get(location_index, {})
+        country = geo_origin.get('Country', None)
+
+    _date = row.get("collectionDate", None)
+    if _date is None:
+        _date = row.get("isolationDate", None)
+    if _date is None:
+        _date = row.get("depositDate", None)
+    if _date is None:
+        _date = row.get("accessionDate", None)
+    if _date is not None:
+        year = _date.year if isinstance(_date, datetime) else int(str(_date)[:4])
+    else:
+        year = None
+
+    if year is not None and year >= 2014 and country is None:
+        return False
+
+        
+    return True
+
+def is_valid_regex(value, validation_conf):
+    if value is None:
+        return True
+    value = str(value)
+    regexp = validation_conf[MATCH]
+    multiple = validation_conf.get(MULTIPLE, False)
+    separator = validation_conf.get(SEPARATOR, None)
+
+    values = [v.strip() for v in value.split(
+        separator)] if multiple else [value]
+
+    for value in values:
+        matches_regexp = re.fullmatch(regexp, value)
+        if not matches_regexp:
+            return False
+    return True
+
+
+def is_valid_crossrefs(value, validation_conf):
+    crossref_name = validation_conf[CROSSREF_NAME]
+    crossrefs = validation_conf['crossrefs_pointer']
+    choices = crossrefs[crossref_name]
+    if value is None or not choices:
+        return True
+    value = str(value)
+
+    multiple = validation_conf.get(MULTIPLE, False)
+    separator = validation_conf.get(SEPARATOR, None)
+    if value is None:
+        return True
+    if multiple:
+        values = [v.strip() for v in value.split(separator)]
+    else:
+        values = [value.strip()]
+
+    return all(value in choices for value in values)
+
+
+def is_valid_choices(value, validation_conf):
+    if value is None:
+        return True
+    choices = validation_conf[VALUES]
+    multiple = validation_conf.get(MULTIPLE, False)
+    separator = validation_conf.get(SEPARATOR, None)
+
+    if multiple:
+        values = [v.strip() for v in str(value).split(separator)]
+    else:
+        values = [str(value).strip()]
+    sorted_values = sorted(values)
+    if sorted_values != values:
+        return False
+    return all(value in choices for value in values)
+
+
+def is_valid_date(value, validation_conf):
+    if value is None:
+        return True
+    if isinstance(value, datetime):
+        year = value.year
+        month = value.month
+        day = value.day
+    elif isinstance(value, int):
+        year = value
+        month = None
+        day = None
+    elif isinstance(value, str):
+        value = value.replace('-', '')
+        value = value.replace('/', '')
+        month = None
+        day = None
+        try:
+            year = int(value[: 4])
+            if len(value) >= 6:
+                month = int(value[4: 6])
+                if len(value) >= 8:
+                    day = int(value[6: 8])
+
+        except (IndexError, TypeError, ValueError):
+            return False
+    else:
+        return False
+
+    if year < 1700 or year > datetime.now().year:
+        return False
+    if month is not None:
+        if month < 1 or month > 13:
+            return False
+        if day is not None and (day < 1 or day > monthrange(year, month)[1]):
+            return False
+    return True
+
+
+def is_valid_dominio(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split(";")]
+        if len(items) >1:
+            for i in range(0, len(items),2):
+                nameSite = str(items[i])
+                urlSite = str(items[i+1])
+                dominio = urlSite.split(".")[-2]
+                if nameSite.lower() != dominio:
+                    return False
+        
+        return True
+    except:
+        return False  
+
+def is_valid_title(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split(";")]
+        if len(items) >1:
+            for i in range(0, len(items),2):
+                nameSite = (items[i])
+                urlSite = str(items[i+1])
+                regex = r'^(http|https):\/\/[a-z0-9\-\.]+\.[a-z]{2,}([/a-z0-9\-\.]*)*$'
+                if  re.match(regex, nameSite)  or isinstance(nameSite, int) or nameSite == '':
+                    return False
+        return True
+    except:
+        return False  
+    
+def is_valid_url_title(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split(";")]
+        if len(items) ==1:
+            urlSite = str(items[0])
+            response = requests.head(urlSite)
+            if response.status_code != 200:
+                return False
+            
+        else:
+            items = [i.strip() for i in value.split(";")]
+            for i in range(0, len(items),2):
+                nameSite = (items[i])
+                urlSite = str(items[i+1])
+                response = requests.head(urlSite)
+                if response.status_code != 200:
+                    return False
+               
+                    
+        return True
+    except:
+        return False     
+    
+    
+def is_valid_url_dominio(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split(";")]
+        for i in range(0, len(items),2):
+            nameSite = str(items[i])
+            urlSite = str(items[i+1])
+            response = requests.head(urlSite)
+            if response.status_code != 200:
+                return False
+        
+        return True
+    except:
+        return False        
+     
+    
+def is_valid_just_url(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split(";")]
+        for i in items:
+            nameSite = str(items[0])
+            response = requests.head(i)
+            if response.status_code != 200:
+                return False
+        
+        return True
+    except:
+        return False 
+     
+    
+def is_valid_history(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+        items = [i.strip() for i in value.split("<")]
+        for i in items:   
+            regex1 = r'^[a-zA-Z &,;.''-]+, ((19|20)\d{2})'
+            regex2 =  r'^[a-zA-Z &,;.''-]+, [a-zA-Z &,;.''-] (19|20)\d{2}\s\([a-zA-Z &,;.''-]+\)'
+            regex3 = r'^[a-zA-Z &,;.''-]+\, [a-zA-Z &,;.''-]'
+            regex4 = r'^[a-zA-Z &,;.''-]+, (19|20)\d{2}\s\([a-zA-Z .''-,;&]+\)'
+            regex5 = r'^[a-zA-Z &,;.''-]+, \([a-zA-Z &,;.''-]+\) (19|20)\d{2}'
+            if re.match(regex1, i):
+                return True
+            elif re.match(regex2, i):
+                return True
+            elif re.match(regex3, i):
+                return True
+            elif re.match(regex4, i):
+                return True
+            elif re.match(regex5, i):
+                return True
+            else:
+                return False
+    except:
+        return False  
+        
+
+def is_valid_coords(value, validation_conf=None):
+    if value is None:
+        return True
+    try:
+              
+        regex1 = r'^-?(90(\.0+)?|[1-8]?\d(\.\d+)?);-?(180(\.0+)?|((1[0-7]\d)|(\d{1,2}))(\.\d+)?)$'
+        regex2 = r'^-?(90(\.0+)?|[1-8]?\d(\.\d+)?);-?(180(\.0+)?|((1[0-7]\d)|(\d{1,2}))(\.\d+)?);(\d+\.\d+|\?);(\d+\.\d+|\?)$|^(\d+\.\d+|\?)$|^;$'
+
+        if not re.match(regex1, value) and not re.match(regex2, value):
+            return False
+    
+        return True
+    except:
+        return False    
+
+
+def is_valid_missing(value, validation_conf=None):
+    return value is not None
+
+
+def is_valid_taxon(value, validation_conf=None):
+    multiple = validation_conf.get(MULTIPLE, False)
+    separator = validation_conf.get(SEPARATOR, ';')
+
+    value = value.split(separator) if multiple else [value]
+    for taxon in value:
+        taxon = taxon.strip()
+        if not _is_valid_taxon(taxon):
+            return False
+    return True
+
+
+def _is_valid_taxon(value):
+    value = value.strip()
+    if not value:
+        return True
+
+    items = re.split(r" +", value)
+    genus = items[0]
+
+    if len(items) > 1:
+        species = items[1]
+        if species in ("sp", "spp", ".sp", "sp."):
+            return False
+
+        if len(items) > 2:
+            for index in range(0, len(items[2:]), 2):
+                rank = SUBTAXAS.get(items[index + 2], None)
+                if rank is None:
+                    print(value)
+                    return False
+
+    return True
+
+
+def is_valid_unique(value, validation_conf):
+    if not value:
+        return True
+    label = validation_conf['label']
+    shown_values = validation_conf['shown_values']
+    if label not in shown_values:
+        shown_values[label] = {}
+
+    already_in_file = shown_values[label]
+    if value in already_in_file:
+        return False
+
+    # NOTE: what's the use of this?
+    # What is the expected format for value and shown_values?
+    shown_values[label][value] = None
+
+    return True
+
+def is_valid_file(path):
+    try:
+        with path.open("rb") as fhand:
+            error_log = validate_mirri_excel(fhand)
+            if "EXL" in error_log.get_errors():
+                return False
+    except:
+        return False
+
+    return True
+
+
+VALIDATION_FUNCTIONS = {
+    MISSING: is_valid_missing,
+    REGEXP: is_valid_regex,
+    CHOICES: is_valid_choices,
+    CROSSREF: is_valid_crossrefs,
+    DATE: is_valid_date,
+    COORDINATES: is_valid_coords,
+    TAXON: is_valid_taxon,
+    TITLE: is_valid_title,
+    DOMINIO: is_valid_dominio,
+    URL_TITLE: is_valid_url_title,
+    URL_DOMINIO: is_valid_url_dominio,
+    JUST_URL: is_valid_just_url,
+    ISO: validate_country_code,
+    HISTORY: is_valid_history,
+    VERSION: version,
+    UNIQUE: is_valid_unique}
+
+
+def validate_value(value, step_conf):
+    kind = step_conf[TYPE]
+    try:
+        is_value_valid = VALIDATION_FUNCTIONS[kind]
+    except KeyError:
+        msg = f'This validation type {kind} is not implemented'
+        raise NotImplementedError(msg)
+
+    error_code = step_conf[ERROR_CODE]
+
+    if not is_value_valid(value, step_conf):
+        return error_code
@@ -0,0 +1,35 @@
+MANDATORY = "mandatory"
+REGEXP = "regexp"
+CHOICES = "choices"
+CROSSREF = 'crossref'
+CROSSREF_NAME = 'crossref_name'
+MISSING = "missing"
+VALIDATION = 'validation'
+ERROR_CODE = 'error_code'
+FIELD = 'field'
+MULTIPLE = 'multiple'
+TYPE = 'type'
+COLUMNS = 'columns'
+SOURCE = "sources"
+SEPARATOR = "separator"
+MATCH = 'match'
+VALUES = 'values'
+DATE = 'date'
+COORDINATES = 'coord'
+COORDINATES1 = 'coord1'
+NUMBER = 'number'
+TAXON = 'taxon'
+UNIQUE = 'unique'
+ROW_VALIDATION = 'row_validation'
+NAGOYA = 'nagoya'
+BIBLIO = 'bibliography'
+DOMINIO= 'is_valid_dominio'
+TITLE= 'is_valid_title'
+URL_DOMINIO = 'urll_valid_dominio'
+URL_TITLE= 'is_valid_url_title'
+ISO = 'validate_country_code'
+JUST_URL= 'is_valid_just_url'
+HISTORY= 'is_valid_history'
+MEU='is_valid_crossrefs_meu'
+NAGOYA1 = 'nayoga1'
+VERSION = 'version'
@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+import pandas as pd
+import sys
+from pathlib import Path
+import warnings    
+warnings.simplefilter("ignore")
+from mirri.validation.excel_validator import validate_mirri_excel
+
+def main():
+    path = Path(sys.argv[1])
+    version = str(sys.argv[2])
+    date = str(sys.argv[3])
+    try:
+
+        error_log = validate_mirri_excel(path.open("rb"), version=version, date=date)
+        
+    except NotImplementedError as e:
+        print(e)    
+
+    for errors in error_log.get_errors().values():
+        for error in errors:
+            print(error.pk, error.message, error.code)
+
+
+if __name__ == "__main__":
+    main()
@@ -0,0 +1,675 @@
+from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROSSREF_NAME, DATE,
+                                   ERROR_CODE, FIELD, MANDATORY, MATCH,
+                                   MISSING, MULTIPLE, NAGOYA, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE,
+                                   UNIQUE,VERSION,
+                                   VALIDATION, VALUES, BIBLIO, DOMINIO, URL_DOMINIO,ISO, JUST_URL, URL_TITLE, TITLE, HISTORY,NAGOYA1)
+from mirri.settings import (ONTOBIOTOPE, LOCATIONS, GROWTH_MEDIA, GENOMIC_INFO,
+                            STRAINS, LITERATURE_SHEET, SEXUAL_STATE_SHEET, MARKERS,  CONTROL_SHEET,)
+
+
+
+# GEOGRAPHIC_ORIGIN
+# SEXUAL_STATE_SHEET,
+# RESOURCE_TYPES_VALUES,
+# FORM_OF_SUPPLY_SHEET,
+# PLOIDY_SHEET)
+
+
+
+
+STRAIN_FIELDS = [
+       
+    {
+        FIELD: "accessionNumber",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: 'STD01'},
+            {TYPE: UNIQUE, ERROR_CODE: 'STD03'},
+            {TYPE: MISSING, ERROR_CODE: "STD02"},
+            {TYPE: REGEXP, MATCH: "[^ ]* [^ ]*", ERROR_CODE: "STD04"}
+        ]
+    },
+    {
+        FIELD: "useRestrictions",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD05"},
+           {TYPE: MISSING, ERROR_CODE: "STD06"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3"],
+             MULTIPLE: False, ERROR_CODE: "STD07"}
+        ]
+    },
+     {
+        FIELD: "mirriAccessionNumber",
+        VALIDATION: [
+            {TYPE: UNIQUE, ERROR_CODE: 'STD51'},
+            {TYPE: REGEXP, MATCH: "^MIRRI[0-9]{7}$", ERROR_CODE: "STD52"},
+            ],
+    },
+    
+    {
+        FIELD: "nagoyaConditions",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD08"},
+            {TYPE: MISSING, ERROR_CODE: "STD09"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3"],
+             MULTIPLE: False, ERROR_CODE: "STD10"}
+        ]
+    },
+    {
+        FIELD: "absFile",
+        VALIDATION: [
+        {TYPE: TITLE, ERROR_CODE: "STD59"},
+        {TYPE: URL_TITLE, ERROR_CODE: "STD60", 
+         MULTIPLE: True, SEPARATOR: ";"},
+            ],
+    },
+    
+    {
+        FIELD: "siteLinks", 
+        VALIDATION: [
+        {TYPE: DOMINIO, ERROR_CODE: "STD53", 
+         MULTIPLE: False, SEPARATOR: ";"},
+        {TYPE: URL_DOMINIO, ERROR_CODE: "STD56", 
+         MULTIPLE: False, SEPARATOR: ";"},
+    ],
+    },
+    {
+        FIELD: "mtaFile",
+        VALIDATION: [
+        {TYPE: JUST_URL, ERROR_CODE: "STD58", 
+         MULTIPLE: True, SEPARATOR: ";"},
+            ],
+    },
+    {
+        FIELD: "otherCollectionNumbers",
+         VALIDATION: [
+            {TYPE: REGEXP, MATCH: "([^ ]* [^ ]*)(; [^ ]* [^ ]*)*$", ERROR_CODE: "STD63"},
+             #{TYPE: CROSSREF, CROSSREF_NAME: "Strains", ERROR_CODE: "STD64"},
+        ]
+    },
+    {
+        FIELD: "registeredCollection",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD11"}
+        ]
+    },
+     {
+        FIELD: "type",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"], ERROR_CODE: "STD64"},
+        ]
+    },
+    {
+        FIELD: "riskGroup",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD12"},
+            {TYPE: MISSING, ERROR_CODE: "STD13"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3", "4"],
+             MULTIPLE: False, ERROR_CODE: "STD14"}
+        ]
+    },
+    {
+        FIELD: "dualUse",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD15"}
+        ]
+    },
+    {
+        FIELD: "euQuarantine",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD16"}
+        ]
+    },
+     {
+        FIELD: "axenicCulture",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["Axenic", "Not axenic"],
+             ERROR_CODE: "STD50"}
+        ]
+    },
+    
+    {
+        FIELD: "organismType",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD17"},
+            {TYPE: MISSING, ERROR_CODE: "STD18"},
+            {TYPE: CHOICES, VALUES: ["Algae", "Archaea", "Bacteria",
+                                     "Cyanobacteria", "Filamentous Fungi", "Filamentous fungi",
+                                      "Yeast", "Microalgae",
+                                     "1", "2", "3", "4", "5", "6", "7"],
+             MULTIPLE: True, SEPARATOR: ";",  ERROR_CODE: "STD19"}
+        ]
+    },
+    {
+        FIELD: "speciesName",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD20"},
+            {TYPE: MISSING, ERROR_CODE: "STD21"},
+            {TYPE: TAXON, ERROR_CODE: "STD22", MULTIPLE: True,
+             SEPARATOR: ';'}
+        ]
+    },
+    {
+        FIELD: "infrasubspecificNames",
+        VALIDATION: []
+    },
+    {
+        FIELD: "taxonomyComments",
+        VALIDATION: []
+    },
+    {
+        FIELD: "hybrid",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD23"}
+        ]
+    },
+    {
+        FIELD: "status",
+        VALIDATION: [
+            {TYPE: REGEXP, MATCH: "^(type of|neotype of|holotype of |epitype of) ([a-zA-Z .'-]+)$", ERROR_CODE: "STD65"},
+            
+        ]
+        
+    },
+    {
+        FIELD: "depositHistory",
+        VALIDATION: [
+             {TYPE: HISTORY, ERROR_CODE: 'STD24'},
+        ]
+    },
+    {
+        FIELD: "depositor",
+        VALIDATION: []
+    },
+    {
+        FIELD: "depositDate",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD25"},
+        ]
+    },
+    {
+        FIELD: "accessionDate",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD26"},
+        ]
+    },
+    {
+        FIELD: "collector",
+        VALIDATION: []
+    },
+    
+    
+    {
+        FIELD: "substrate",
+        VALIDATION: []
+    },
+    {
+        FIELD: "temperatureGrowthRange",
+        VALIDATION: [
+            {TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
+             ERROR_CODE: "STD29", MULTIPLE: True, SEPARATOR: ";"}
+        ]
+    },
+    {
+        FIELD: "recommendedTemperature",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD30"},
+            {TYPE: MISSING, ERROR_CODE: "STD31"},
+            {TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
+             ERROR_CODE: "STD32",
+             MULTIPLE: True, SEPARATOR: ";"}
+        ]
+    },
+   
+    {
+        FIELD: "supplyForms",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD36"},
+            {TYPE: MISSING, ERROR_CODE: "STD37"},
+            {TYPE: CHOICES, VALUES: ['Agar', 'Cryo', 'Dry Ice', 'Liquid Culture Medium',
+                                     'Lyo', 'Oil', 'Water'],
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD38"}
+        ]
+    },
+    {
+        FIELD: "otherDenomination",
+        VALIDATION: []
+    },
+    {
+        FIELD: "geographicCoordinates",
+        VALIDATION: [
+            {TYPE: COORDINATES, ERROR_CODE: "STD39"},
+            
+        ]
+    },
+    
+    {
+        # value can be in the cell or in another sheet. Don't configure this
+        FIELD: "geographicOrigin",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD68"},
+           {TYPE: MISSING, ERROR_CODE: "STD69"},
+            {TYPE: CROSSREF, CROSSREF_NAME: "Geographic origin", ERROR_CODE: "STD46"},
+        ]
+    },
+    
+    {
+        FIELD: "isolationHabitat",
+        VALIDATION: []
+    },
+    {
+        FIELD: "ontobiotopeTerms",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: "Ontobiotope",
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD41"}
+        ]
+    },
+      {
+        FIELD: "qps",
+         VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD49"}
+        ]
+    },
+    {
+        FIELD: "gmo",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD42"}
+        ]
+    },
+    {
+        FIELD: "gmoConstruction",
+        VALIDATION: []
+    },
+    {
+        FIELD: "mutant",
+        VALIDATION: []
+    },
+    {
+        FIELD: "genotype",
+        VALIDATION: []
+    },
+    {
+        FIELD: "Plant pathogenicity code",
+        VALIDATION: []
+    },
+    {
+        FIELD: "sexualState",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: SEXUAL_STATE_SHEET,
+             ERROR_CODE: "STD43"}
+            # {TYPE: CHOICES, VALUES: ["Mata", "Matalpha", "Mata/Matalpha",
+            #                          "Matb", "Mata/Matb", "MTLa", "MTLalpha", "MTLa/MTLalpha",
+            #                          "MAT1-1", "MAT1-2", "MAT1", "MAT2", "MT+", "MT-"],
+            #  ERROR_CODE: "STD43"}
+        ]
+    },
+    {
+        FIELD: "ploidy",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2", "3", "4", "5", "9"],
+             ERROR_CODE: "STD44"}
+        ]
+    },
+    {
+        FIELD: "plasmids",
+        VALIDATION: []
+    },
+    {
+        FIELD: "plasmidCollections",
+         VALIDATION: [
+            {TYPE: REGEXP, MATCH: "([a-zA-Z .'-]+)\(([a-zA-Z .'-]+) (\d+)\)(; ([a-zA-Z .'-]+)\(([a-zA-Z .'-]+) (\d+)\))*$",
+             ERROR_CODE: "STD62"}
+         ]
+    },
+    {
+        # value can be in the cell or in another sheet. Don't configure this
+        FIELD: "identificationLiterature",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: LITERATURE_SHEET,
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD45"}
+        ]
+    },
+    {
+        FIELD: "pathogenicity",
+        VALIDATION: []
+    },
+    {
+        FIELD: "enzymes",
+        VALIDATION: []
+    },
+    {
+        FIELD: "metabolites",
+        VALIDATION: []
+    },
+    {
+        FIELD: "applications",
+        VALIDATION: []
+    },
+    {
+        FIELD: "remarks",
+        VALIDATION: []
+    },
+    {
+        FIELD: "sequenceLiterature",
+        VALIDATION: [
+             {TYPE: REGEXP, MATCH: "^\d+(; \d+)*$", ERROR_CODE: "STD61"},
+        ]
+
+    },
+
+ {
+        FIELD: "recommendedMedium",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD33"},
+            {TYPE: MISSING, ERROR_CODE: "STD34"},
+            {TYPE: CROSSREF, CROSSREF_NAME: "Growth media",
+             MULTIPLE: True, SEPARATOR: "/", ERROR_CODE: "STD35"}
+        ]
+    },
+
+
+ {
+        FIELD: "country",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD54"},
+            {TYPE: MISSING, ERROR_CODE: "STD55"},
+            {TYPE: ISO, ERROR_CODE: "STD57"},
+            #{TYPE: CROSSREF, CROSSREF_NAME: COUNTRY_CODES_SHEET, ERROR_CODE: "STD57"}
+        ]
+    },
+]
+SHEETS_SCHEMA = {
+    LOCATIONS: {
+        "acronym": "GOD",
+        "id_field": "ID",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS02"},
+        COLUMNS: [
+            {
+                FIELD: "ID",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD01"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD02"},
+                ]
+            },
+            {
+                FIELD: "Country",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD03"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD04"},
+                ]
+            },
+            {
+                FIELD: "Region",
+                VALIDATION: []
+            },
+            {
+                FIELD: "City",
+                VALIDATION: []
+            },
+            {
+                FIELD: "Locality",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD06"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD07"}
+                ]
+            }
+        ],
+    },
+    GROWTH_MEDIA: {
+        "acronym": "GMD",
+        "id_field": "Acronym",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS01"},
+        COLUMNS: [
+            {
+                FIELD: "Acronym",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GMD01"},
+                    {TYPE: MISSING, ERROR_CODE: "GMD02"}
+                ]
+            },
+            {
+                FIELD: "Description",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GMD03"},
+                    {TYPE: MISSING, ERROR_CODE: "GMD04"}
+                ]
+            },
+            {
+                FIELD: "Full description",
+                VALIDATION: []
+            },
+        ],
+    },
+    GENOMIC_INFO: {
+        "acronym": "GID",
+        "id_field": "Strain AN",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS08"},
+        COLUMNS: [
+            {
+                FIELD: "Strain AN",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID01"},
+                    {TYPE: MISSING, ERROR_CODE: "GID02"},
+                    {TYPE: CROSSREF, CROSSREF_NAME: "Strains",
+                     ERROR_CODE: "GID03"},
+                ]
+            },
+            {
+                FIELD: "Marker",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID04"},
+                    {TYPE: MISSING, ERROR_CODE: "GID05"},
+                    {TYPE: CROSSREF, CROSSREF_NAME: MARKERS, ERROR_CODE: "GID06"}
+                ]
+            },
+            {
+                FIELD: "INSDC AN",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID07"},
+                    {TYPE: MISSING, ERROR_CODE: "GID08"},
+                    {TYPE: REGEXP, MATCH: "^[A-Z]{2}[0-9]{6}$", ERROR_CODE: "GID11"},
+                ]
+            },
+            {
+                FIELD: "Sequence",
+                VALIDATION: []
+            },
+        ],
+    },
+    STRAINS: {
+        "acronym": "STD",
+        'id_field': 'accessionNumber',
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
+        ROW_VALIDATION: [
+            #{TYPE: NAGOYA, ERROR_CODE: "STD46"},
+            {TYPE: NAGOYA1, ERROR_CODE: "STD64"}
+        ],
+        COLUMNS: STRAIN_FIELDS,
+    },
+    LITERATURE_SHEET: {
+        "acronym": "LID",
+        'id_field': 'ID',
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS03"},
+        ROW_VALIDATION: [
+            {TYPE: BIBLIO, ERROR_CODE: 'LID17'}
+        ], 
+        COLUMNS: [
+            {
+                FIELD: "ID",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID01"},
+                    {TYPE: MISSING, ERROR_CODE: "LID02"},
+                ]
+            },
+            {
+                FIELD: "PMID",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID18"},
+                ]
+            },
+            {
+                FIELD: "DOI",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID20"},
+                ]
+            },
+            {
+                FIELD: "Full reference",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID03"},
+                ]
+            },
+            {
+                FIELD: "Authors",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID05"},
+                ]
+            },
+            {
+                FIELD: "Title",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID07"},
+                ]
+            },
+            {
+                FIELD: "Journal",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID09"},
+                ]
+            },
+            {
+                FIELD: "Year",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID11"},
+                ]
+            },
+            {
+                FIELD: "Volume",
+                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'
+
+}
+
@@ -0,0 +1,545 @@
+from mirri.validation.tags import (CHOICES, COLUMNS, COORDINATES, CROSSREF, CROSSREF_NAME, DATE,
+                                   ERROR_CODE, FIELD, MANDATORY, MATCH,
+                                   MISSING, MULTIPLE, NAGOYA, NUMBER, REGEXP, ROW_VALIDATION, SEPARATOR, TAXON, TYPE,
+                                   UNIQUE,
+                                   VALIDATION, VALUES, BIBLIO)
+from mirri.settings_v1 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,
+# PLOIDY_SHEET)
+
+
+STRAIN_FIELDS = [
+    {
+        FIELD: "Accession number",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: 'STD01'},
+            {TYPE: UNIQUE, ERROR_CODE: 'STD03'},
+            {TYPE: MISSING, ERROR_CODE: "STD02"},
+            {TYPE: REGEXP, MATCH: "[^ ]* [^ ]*", ERROR_CODE: "STD04"}
+        ]
+    },
+    {
+        FIELD: "Restrictions on use",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD05"},
+            {TYPE: MISSING, ERROR_CODE: "STD06"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3"],
+             MULTIPLE: False, ERROR_CODE: "STD07"}
+        ]
+    },
+    {
+        FIELD: "Nagoya protocol restrictions and compliance conditions",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD08"},
+            {TYPE: MISSING, ERROR_CODE: "STD09"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3"],
+             MULTIPLE: False, ERROR_CODE: "STD10"}
+        ]
+    },
+    {
+        FIELD: "ABS related files",
+        VALIDATION: [],
+    },
+    {
+        FIELD: "MTA file",
+        VALIDATION: [],
+    },
+    {
+        FIELD: "Other culture collection numbers",
+        # VALIDATION: [
+        #     {TYPE: REGEXP, "match": "[^ ]* [^ ]*", ERROR_CODE: "STD07",
+        #      MULTIPLE: True, SEPARATOR: ";"}
+        # ]
+    },
+    {
+        FIELD: "Strain from a registered collection",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD11"}
+        ]
+    },
+    {
+        FIELD: "Risk Group",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD12"},
+            {TYPE: MISSING, ERROR_CODE: "STD13"},
+            {TYPE: CHOICES, VALUES: ["1", "2", "3", "4"],
+             MULTIPLE: False, ERROR_CODE: "STD14"}
+        ]
+    },
+    {
+        FIELD: "Dual use",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD15"}
+        ]
+    },
+    {
+        FIELD: "Quarantine in Europe",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD16"}
+        ]
+    },
+    {
+        FIELD: "Organism type",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD17"},
+            {TYPE: MISSING, ERROR_CODE: "STD18"},
+            {TYPE: CHOICES, VALUES: ["Algae", "Archaea", "Bacteria",
+                                     "Cyanobacteria", "Filamentous Fungi",
+                                     "Phage", "Plasmid", "Virus", "Yeast",
+                                     "1", "2", "3", "4", "5", "6", "7", "8", "9"],
+             MULTIPLE: True, SEPARATOR: ";",  ERROR_CODE: "STD19"}
+        ]
+    },
+    {
+        FIELD: "Taxon name",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD20"},
+            {TYPE: MISSING, ERROR_CODE: "STD21"},
+            {TYPE: TAXON, ERROR_CODE: "STD22", MULTIPLE: True,
+             SEPARATOR: ';'}
+        ]
+    },
+    {
+        FIELD: "Infrasubspecific names",
+    },
+    {
+        FIELD: "Comment on taxonomy",
+    },
+    {
+        FIELD: "Interspecific hybrid",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD23"}
+        ]
+    },
+    {
+        FIELD: "Status",
+    },
+    {
+        FIELD: "History of deposit",
+        VALIDATION: [
+            # {TYPE: REGEXP, "match": "[^ ]* [^ ]*", ERROR_CODE: "STD24",  # modify the regex
+            #  MULTIPLE: True, SEPARATOR: ";"}
+        ]
+    },
+    {
+        FIELD: "Depositor"
+    },
+    {
+        FIELD: "Date of deposit",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD25"},
+        ]
+    },
+    {
+        FIELD: "Date of inclusion in the catalogue",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD26"},
+        ]
+    },
+    {
+        FIELD: "Collected by",
+    },
+    {
+        FIELD: "Date of collection",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD27"},
+        ]
+    },
+    {
+        FIELD: "Isolated by",
+    },
+    {
+        FIELD: "Date of isolation",
+        VALIDATION: [
+            {TYPE: DATE, ERROR_CODE: "STD28"},
+        ]
+    },
+    {
+        FIELD: "Substrate/host of isolation",
+    },
+    {
+        FIELD: "Tested temperature growth range",
+        VALIDATION: [
+            {TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
+             ERROR_CODE: "STD29", MULTIPLE: True, SEPARATOR: ";"}
+        ]
+    },
+    {
+        FIELD: "Recommended growth temperature",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD30"},
+            {TYPE: MISSING, ERROR_CODE: "STD31"},
+            {TYPE: REGEXP, "match": r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?',
+             ERROR_CODE: "STD32",
+             MULTIPLE: True, SEPARATOR: ";"}
+        ]
+    },
+    {
+        FIELD: "Recommended medium for growth",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD33"},
+            {TYPE: MISSING, ERROR_CODE: "STD34"},
+            {TYPE: CROSSREF, CROSSREF_NAME: "Growth media",
+             MULTIPLE: True, SEPARATOR: "/", ERROR_CODE: "STD35"}
+        ]
+    },
+    {
+        FIELD: "Form of supply",
+        VALIDATION: [
+            {TYPE: MANDATORY, ERROR_CODE: "STD36"},
+            {TYPE: MISSING, ERROR_CODE: "STD37"},
+            {TYPE: CHOICES, VALUES: ['Agar', 'Cryo', 'Dry Ice', 'Liquid Culture Medium',
+                                     'Lyo', 'Oil', 'Water'],
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD38"}
+        ]
+    },
+    {
+        FIELD: "Other denomination",
+    },
+    {
+        FIELD: "Coordinates of geographic origin",
+        VALIDATION: [
+            {TYPE: COORDINATES, ERROR_CODE: "STD39"},
+        ]
+    },
+    {
+        FIELD: "Altitude of geographic origin",
+        VALIDATION: [
+            {TYPE: NUMBER, 'max': 8000, 'min': -200, ERROR_CODE: "STD40"},
+        ]
+    },
+    {
+        # value can be in the cell or in another sheet. Don't configure this
+        FIELD: "Geographic origin",
+    },
+    {
+        FIELD: "Isolation habitat",
+    },
+    {
+        FIELD: "Ontobiotope term for the isolation habitat",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: "Ontobiotope",
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD41"}
+        ]
+    },
+    {
+        FIELD: "GMO",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["1", "2"],
+             ERROR_CODE: "STD42"}
+        ]
+    },
+    {
+        FIELD: "GMO construction information",
+    },
+    {
+        FIELD: "Mutant information",
+    },
+    {
+        FIELD: "Genotype",
+    },
+    {
+        FIELD: "Sexual state",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: SEXUAL_STATE_SHEET,
+             ERROR_CODE: "STD43"}
+            # {TYPE: CHOICES, VALUES: ["Mata", "Matalpha", "Mata/Matalpha",
+            #                          "Matb", "Mata/Matb", "MTLa", "MTLalpha", "MTLa/MTLalpha",
+            #                          "MAT1-1", "MAT1-2", "MAT1", "MAT2", "MT+", "MT-"],
+            #  ERROR_CODE: "STD43"}
+        ]
+    },
+    {
+        FIELD: "Ploidy",
+        VALIDATION: [
+            {TYPE: CHOICES, VALUES: ["0", "1", "2", "3", "4", "9"],
+             ERROR_CODE: "STD44"}
+        ]
+    },
+    {
+        FIELD: "Plasmids",
+    },
+    {
+        FIELD: "Plasmids collections fields",
+    },
+    {
+        # value can be in the cell or in another sheet. Don't configure this
+        FIELD: "Literature",
+        VALIDATION: [
+            {TYPE: CROSSREF, CROSSREF_NAME: LITERATURE_SHEET,
+             MULTIPLE: True, SEPARATOR: ";", ERROR_CODE: "STD45"}
+        ]
+    },
+    {
+        FIELD: "Plant pathogenicity code",
+    },
+    {
+        FIELD: "Pathogenicity",
+    },
+    {
+        FIELD: "Enzyme production",
+    },
+    {
+        FIELD: "Production of metabolites",
+    },
+    {
+        FIELD: "Applications",
+    },
+    {
+        FIELD: "Remarks"
+    },
+    {
+        FIELD: "Literature linked to the sequence/genome",
+    },
+]
+SHEETS_SCHEMA = {
+    LOCATIONS: {
+        "acronym": "GOD",
+        "id_field": "ID",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS02"},
+        COLUMNS: [
+            {
+                FIELD: "ID",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD01"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD02"},
+                ]
+            },
+            {
+                FIELD: "Country",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD03"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD04"}
+                ]
+            },
+            {
+                FIELD: "Region",
+                VALIDATION: []
+            },
+            {
+                FIELD: "City",
+                VALIDATION: []
+            },
+            {
+                FIELD: "Locality",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GOD06"},
+                    {TYPE: MISSING, ERROR_CODE: "GOD07"}
+                ]
+            }
+        ],
+    },
+    GROWTH_MEDIA: {
+        "acronym": "GMD",
+        "id_field": "Acronym",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS01"},
+        COLUMNS: [
+            {
+                FIELD: "Acronym",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GMD01"},
+                    {TYPE: MISSING, ERROR_CODE: "GMD02"}
+                ]
+            },
+            {
+                FIELD: "Description",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GMD03"},
+                    {TYPE: MISSING, ERROR_CODE: "GMD04"}
+                ]
+            },
+            {
+                FIELD: "Full description",
+                VALIDATION: []
+            },
+        ],
+    },
+    GENOMIC_INFO: {
+        "acronym": "GID",
+        "id_field": "Strain AN",
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS08"},
+        COLUMNS: [
+            {
+                FIELD: "Strain AN",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID01"},
+                    {TYPE: MISSING, ERROR_CODE: "GID02"},
+                    {TYPE: CROSSREF, CROSSREF_NAME: "Strains",
+                     ERROR_CODE: "GID03"},
+                ]
+            },
+            {
+                FIELD: "Marker",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID04"},
+                    {TYPE: MISSING, ERROR_CODE: "GID05"},
+                    {TYPE: CROSSREF, CROSSREF_NAME: MARKERS, ERROR_CODE: "GID06"}
+                ]
+            },
+            {
+                FIELD: "INSDC AN",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "GID07"},
+                    {TYPE: MISSING, ERROR_CODE: "GID08"},
+                ]
+            },
+            {
+                FIELD: "Sequence",
+                VALIDATION: []
+            },
+        ],
+    },
+    STRAINS: {
+        "acronym": "STD",
+        'id_field': 'Accession number',
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS05"},
+        ROW_VALIDATION: [
+            {TYPE: NAGOYA, ERROR_CODE: "STD46"},
+        ],
+        COLUMNS: STRAIN_FIELDS,
+    },
+    LITERATURE_SHEET: {
+        "acronym": "LID",
+        'id_field': 'ID',
+        VALIDATION: {TYPE: MANDATORY, ERROR_CODE: "EFS03"},
+        ROW_VALIDATION: [
+            {TYPE: BIBLIO, ERROR_CODE: 'LID17'}
+        ],
+        COLUMNS: [
+            {
+                FIELD: "ID",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID01"},
+                    {TYPE: MISSING, ERROR_CODE: "LID02"},
+                ]
+            },
+            {
+                FIELD: "Full reference",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID03"},
+                ]
+            },
+            {
+                FIELD: "Authors",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID05"},
+                ]
+            },
+            {
+                FIELD: "Title",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID07"},
+                ]
+            },
+            {
+                FIELD: "Journal",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID09"},
+                ]
+            },
+            {
+                FIELD: "Year",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID11"},
+                ]
+            },
+            {
+                FIELD: "Volume",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID13"},
+                ]
+            },
+            {
+                FIELD: "Issue",
+                VALIDATION: []
+            },
+            {
+                FIELD: "First page",
+                VALIDATION: [
+                    {TYPE: MANDATORY, ERROR_CODE: "LID15"},
+                    {TYPE: MISSING, ERROR_CODE: "LID16"},
+                ]
+            },
+            {
+                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: [
+                    {TYPE: MANDATORY, ERROR_CODE: "OTD03"},
+                    {TYPE: MISSING, ERROR_CODE: "OTD04"},
+                ]
+            },
+        ]
+    },
+    MARKERS: {
+         "acronym": "MKD",
+         "id_field": "Acronym",
+         COLUMNS: [
+             {
+                 FIELD: "Acronym",
+                 VALIDATION: []
+             },
+             {
+                 FIELD: "Marker",
+                 VALIDATION: []
+             },
+         ],
+     },
+}
+
+CROSS_REF_CONF = {
+    ONTOBIOTOPE: ['ID', 'Name'],
+    LITERATURE_SHEET: ['ID'],
+    LOCATIONS: ['Locality'],
+    GROWTH_MEDIA: ['Acronym'],
+    STRAINS: ["Accession number"],
+    SEXUAL_STATE_SHEET: [],
+    MARKERS: ["Acronym"],
+}
+
+MIRRI_20200601_VALLIDATION_CONF = {
+    'sheet_schema': SHEETS_SCHEMA,
+    'cross_ref_conf': CROSS_REF_CONF,
+    'keep_sheets_in_memory': [
+        {'sheet_name': LOCATIONS, 'indexed_by': 'Locality'}]
+}