Generic function to validate an object which represents a dmdScheme

This function validates an object representing a dmdScheme. The result can be used as a basis for a report by running report() on the resultiung object of class dmdScheme_validation.

Usage

validate(x, path = ".", validateData = TRUE, errorIfStructFalse = TRUE)

# S3 method for character
validate(x, path = ".", validateData = TRUE, errorIfStructFalse = TRUE)

# S3 method for dmdSchemeSet_raw
validate(x, path = ".", validateData = TRUE, errorIfStructFalse = TRUE)

Arguments

x: object referring to a dmdScheme to be validatedof class dmdSchemeSet_raw as returned from read_excel( keepData = FALSE, raw = TRUE) or file name of an xlsx file containing the metadata.
path: path to the data files
validateData: if TRUE data is validated as well; the structure is always validated
errorIfStructFalse: if TRUE an error will be raised if the schemes are not identical, i.e. there are structural differences.

Value

return the dmdScheme_validation object

Methods (by class)

validate(character): validate a character object referring to a spreadsheet file which contains the metadata.
validate(dmdSchemeSet_raw): validate a dmdSchemeSet_raw object

Examples

## validata an Excel file containing the metadata
validate(
    x = scheme_path_xlsx()
)
#> Validating Experiment
#> Validating MdBibliometric
#> Validating MdAuthors
#> Validating Genus
#> Validating Treatments
#> Validating Measurement
#> Validating DataExtraction
#> Validating DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#> [1] NA
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">Overall MetaData - error</span>**"
#> 
#> $description
#> [1] "The result of the overall validation of the data."
#> 
#> $descriptionDetails
#> [1] "The details contain the different validations of the metadata as a hierarchical list. errors propagate towards the root, i.e., if the 'worst' is a 'warning' in a validation in `details` the error here will be a 'warning' as well."
#> 
#> $comment
#> [1] ""
#> 
#> $structure
#> $error
#> [1] 0
#> 
#> $details
#> [1] TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Structural / Formal validity - OK</span>**"
#> 
#> $description
#> [1] "Test if the structure of the metadata is correct.  This includes column names, required info, ...  Should normally be OK, if no modification has been done."
#> 
#> $descriptionDetails
#> [1] ""
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Experiment
#> $error
#> [1] 0
#> 
#> $details
#>   Module errorCode isOK
#> 1  types        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Experiment - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **Experiment** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   name temperature light humidity incubator container microcosmVolume mediaType
#> 1 TRUE        TRUE  TRUE     TRUE      TRUE      TRUE            TRUE      TRUE
#>   mediaConcentration cultureConditions comunityType mediaAdditions duration
#> 1               TRUE              TRUE         TRUE           TRUE     TRUE
#>   comment
#> 1    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdBibliometric
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues        OK  TRUE
#> 4         IDField     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdBibliometric - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdBibliometric ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE TRUE            TRUE  TRUE        TRUE    <NA>     TRUE     TRUE
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       <NA> <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         <NA>             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 3
#> 
#> $details
#>                         hasIDField  isOK
#> 1 tab has ID field in first column FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">ID Field present and in the first column - error</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdAuthors
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues     error FALSE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdAuthors - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdAuthors ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 2     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 2     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 3
#> 
#> $details
#>   authorID familyName givenName affiliation orcid  role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> FALSE
#> 2     <NA>       <NA>      <NA>        <NA>  <NA>  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">values in allowedValues - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Genus
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Genus - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Genus ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      TRUE   TRUE    TRUE            TRUE    TRUE
#> 2      TRUE   TRUE    <NA>            TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>   FALSE            TRUE    <NA>
#> 2      <NA>   <NA>    TRUE           FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>    <NA>            <NA>    <NA>
#> 2      <NA>   <NA>    <NA>            <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Treatments
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Treatments - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Treatments ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        TRUE                 TRUE    <NA>
#> 2        TRUE                 TRUE    <NA>
#> 3        TRUE                 TRUE    <NA>
#> 4        TRUE                 TRUE    <NA>
#> 5        TRUE                 TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1       FALSE                FALSE    <NA>
#> 2       FALSE                FALSE    <NA>
#> 3       FALSE                FALSE    <NA>
#> 4       FALSE                FALSE    <NA>
#> 5       FALSE                FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        <NA>                 <NA>    <NA>
#> 2        <NA>                 <NA>    <NA>
#> 3        <NA>                 <NA>    <NA>
#> 4        <NA>                 <NA>    <NA>
#> 5        <NA>                 <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Measurement
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Measurement - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Measurement ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 2          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 3          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 4          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           TRUE             TRUE         TRUE    <NA>
#> 2           TRUE             TRUE         TRUE    <NA>
#> 3           TRUE             TRUE         TRUE    <NA>
#> 4           TRUE             TRUE         TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   measurementID variable method  unit object noOfSamplesInTimeSeries
#> 1          <NA>    FALSE   TRUE  TRUE   TRUE                    <NA>
#> 2          <NA>     TRUE  FALSE  TRUE   TRUE                    <NA>
#> 3          <NA>    FALSE  FALSE FALSE   TRUE                    <NA>
#> 4          <NA>     TRUE  FALSE FALSE  FALSE                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 2          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 3          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 4          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataExtraction
#> $error
#> [1] 0
#> 
#> $details
#>            Module errorCode isOK
#> 1           types        OK TRUE
#> 2 suggestedValues        OK TRUE
#> 3   allowedValues        OK TRUE
#> 4         IDField        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">DataExtraction - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** DataExtraction ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             TRUE   <NA>      <NA>  <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   TRUE      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   <NA>      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#>           Module errorCode  isOK
#> 1          types        OK  TRUE
#> 2  allowedValues        OK  TRUE
#> 3 dataFilesExist     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">DataFileMetaData - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **DataExtraction** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 3          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 7          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 8          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 11         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 12         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 13         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 14         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 16         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 18         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 19         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 3          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 7          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 8          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 11         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 12         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 13         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 14         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 16         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 18         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 19         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $dataFilesExist
#> $error
#> [1] 3
#> 
#> $details
#>                    dataFileName  IsOK
#> 1 dissolved_oxygen_measures.csv FALSE
#> 2                     smell.csv FALSE
#> 3                abundances.csv FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">`dataFile` exists in path - error</span>**"
#> 
#> $description
#> [1] "Test if all `dataFile` exist in the given `path`. The `error` can have the following values apart from `OK`:\n \n    error   : If not all `dataFile` exist in the given `path`\n \n"
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique `variable` The following values are possible for the column `isTRUE`:\n \n    TRUE : If `dataFile` exist in the given `path`\n    FALSE: If `dataFile` does not exist in the given `path`\n    NA   : empty cell\n \n One or more FALSE or missing values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                

## validate a `dmdScheme_raw object`
validate(
   x = dmdScheme_raw()
)
#> Validating Experiment
#> Validating MdBibliometric
#> Validating MdAuthors
#> Validating Genus
#> Validating Treatments
#> Validating Measurement
#> Validating DataExtraction
#> Validating DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#> [1] NA
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">Overall MetaData - error</span>**"
#> 
#> $description
#> [1] "The result of the overall validation of the data."
#> 
#> $descriptionDetails
#> [1] "The details contain the different validations of the metadata as a hierarchical list. errors propagate towards the root, i.e., if the 'worst' is a 'warning' in a validation in `details` the error here will be a 'warning' as well."
#> 
#> $comment
#> [1] ""
#> 
#> $structure
#> $error
#> [1] 0
#> 
#> $details
#> [1] TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Structural / Formal validity - OK</span>**"
#> 
#> $description
#> [1] "Test if the structure of the metadata is correct.  This includes column names, required info, ...  Should normally be OK, if no modification has been done."
#> 
#> $descriptionDetails
#> [1] ""
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Experiment
#> $error
#> [1] 0
#> 
#> $details
#>   Module errorCode isOK
#> 1  types        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Experiment - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **Experiment** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   name temperature light humidity incubator container microcosmVolume mediaType
#> 1 TRUE        TRUE  TRUE     TRUE      TRUE      TRUE            TRUE      TRUE
#>   mediaConcentration cultureConditions comunityType mediaAdditions duration
#> 1               TRUE              TRUE         TRUE           TRUE     TRUE
#>   comment
#> 1    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdBibliometric
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues        OK  TRUE
#> 4         IDField     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdBibliometric - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdBibliometric ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE TRUE            TRUE  TRUE        TRUE    <NA>     TRUE     TRUE
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       <NA> <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         <NA>             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 3
#> 
#> $details
#>                         hasIDField  isOK
#> 1 tab has ID field in first column FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">ID Field present and in the first column - error</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdAuthors
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues     error FALSE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdAuthors - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdAuthors ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 2     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 2     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 3
#> 
#> $details
#>   authorID familyName givenName affiliation orcid  role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> FALSE
#> 2     <NA>       <NA>      <NA>        <NA>  <NA>  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">values in allowedValues - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Genus
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Genus - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Genus ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      TRUE   TRUE    TRUE            TRUE    TRUE
#> 2      TRUE   TRUE    <NA>            TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>   FALSE            TRUE    <NA>
#> 2      <NA>   <NA>    TRUE           FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>    <NA>            <NA>    <NA>
#> 2      <NA>   <NA>    <NA>            <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Treatments
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Treatments - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Treatments ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        TRUE                 TRUE    <NA>
#> 2        TRUE                 TRUE    <NA>
#> 3        TRUE                 TRUE    <NA>
#> 4        TRUE                 TRUE    <NA>
#> 5        TRUE                 TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1       FALSE                FALSE    <NA>
#> 2       FALSE                FALSE    <NA>
#> 3       FALSE                FALSE    <NA>
#> 4       FALSE                FALSE    <NA>
#> 5       FALSE                FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        <NA>                 <NA>    <NA>
#> 2        <NA>                 <NA>    <NA>
#> 3        <NA>                 <NA>    <NA>
#> 4        <NA>                 <NA>    <NA>
#> 5        <NA>                 <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Measurement
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Measurement - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Measurement ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 2          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 3          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 4          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           TRUE             TRUE         TRUE    <NA>
#> 2           TRUE             TRUE         TRUE    <NA>
#> 3           TRUE             TRUE         TRUE    <NA>
#> 4           TRUE             TRUE         TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   measurementID variable method  unit object noOfSamplesInTimeSeries
#> 1          <NA>    FALSE   TRUE  TRUE   TRUE                    <NA>
#> 2          <NA>     TRUE  FALSE  TRUE   TRUE                    <NA>
#> 3          <NA>    FALSE  FALSE FALSE   TRUE                    <NA>
#> 4          <NA>     TRUE  FALSE FALSE  FALSE                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 2          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 3          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 4          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataExtraction
#> $error
#> [1] 0
#> 
#> $details
#>            Module errorCode isOK
#> 1           types        OK TRUE
#> 2 suggestedValues        OK TRUE
#> 3   allowedValues        OK TRUE
#> 4         IDField        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">DataExtraction - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** DataExtraction ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             TRUE   <NA>      <NA>  <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   TRUE      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   <NA>      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#>           Module errorCode  isOK
#> 1          types        OK  TRUE
#> 2  allowedValues        OK  TRUE
#> 3 dataFilesExist     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">DataFileMetaData - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **DataExtraction** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 3          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 7          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 8          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 11         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 12         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 13         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 14         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 16         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 18         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 19         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 3          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 7          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 8          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 11         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 12         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 13         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 14         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 16         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 18         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 19         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $dataFilesExist
#> $error
#> [1] 3
#> 
#> $details
#>                    dataFileName  IsOK
#> 1 dissolved_oxygen_measures.csv FALSE
#> 2                     smell.csv FALSE
#> 3                abundances.csv FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">`dataFile` exists in path - error</span>**"
#> 
#> $description
#> [1] "Test if all `dataFile` exist in the given `path`. The `error` can have the following values apart from `OK`:\n \n    error   : If not all `dataFile` exist in the given `path`\n \n"
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique `variable` The following values are possible for the column `isTRUE`:\n \n    TRUE : If `dataFile` exist in the given `path`\n    FALSE: If `dataFile` does not exist in the given `path`\n    NA   : empty cell\n \n One or more FALSE or missing values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                

## use `read_raw()` to read an Excel spreadsheet into a `dmdScheme_raw` object
x <- read_excel_raw( scheme_path_xlsx() )
validate( x = x )
#> Validating Experiment
#> Validating MdBibliometric
#> Validating MdAuthors
#> Validating Genus
#> Validating Treatments
#> Validating Measurement
#> Validating DataExtraction
#> Validating DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#> [1] NA
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">Overall MetaData - error</span>**"
#> 
#> $description
#> [1] "The result of the overall validation of the data."
#> 
#> $descriptionDetails
#> [1] "The details contain the different validations of the metadata as a hierarchical list. errors propagate towards the root, i.e., if the 'worst' is a 'warning' in a validation in `details` the error here will be a 'warning' as well."
#> 
#> $comment
#> [1] ""
#> 
#> $structure
#> $error
#> [1] 0
#> 
#> $details
#> [1] TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Structural / Formal validity - OK</span>**"
#> 
#> $description
#> [1] "Test if the structure of the metadata is correct.  This includes column names, required info, ...  Should normally be OK, if no modification has been done."
#> 
#> $descriptionDetails
#> [1] ""
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Experiment
#> $error
#> [1] 0
#> 
#> $details
#>   Module errorCode isOK
#> 1  types        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">Experiment - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **Experiment** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   name temperature light humidity incubator container microcosmVolume mediaType
#> 1 TRUE        TRUE  TRUE     TRUE      TRUE      TRUE            TRUE      TRUE
#>   mediaConcentration cultureConditions comunityType mediaAdditions duration
#> 1               TRUE              TRUE         TRUE           TRUE     TRUE
#>   comment
#> 1    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdBibliometric
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues        OK  TRUE
#> 4         IDField     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdBibliometric - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdBibliometric ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE TRUE            TRUE  TRUE        TRUE    <NA>     TRUE     TRUE
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       <NA> <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         <NA>             <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   uploadType  doi publicationDate title description version language keywords
#> 1       TRUE <NA>            <NA>  <NA>        <NA>    <NA>     <NA>     <NA>
#>   additionalNotes accessRights accessRightsInfo license
#> 1            <NA>         TRUE             <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 3
#> 
#> $details
#>                         hasIDField  isOK
#> 1 tab has ID field in first column FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">ID Field present and in the first column - error</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $MdAuthors
#> $error
#> [1] 3
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues        OK  TRUE
#> 3   allowedValues     error FALSE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">MdAuthors - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** MdAuthors ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 2     TRUE       TRUE      TRUE        TRUE  <NA> TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   authorID familyName givenName affiliation orcid role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 2     <NA>       <NA>      <NA>        <NA>  <NA> <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 3
#> 
#> $details
#>   authorID familyName givenName affiliation orcid  role
#> 1     <NA>       <NA>      <NA>        <NA>  <NA> FALSE
#> 2     <NA>       <NA>      <NA>        <NA>  <NA>  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">values in allowedValues - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Genus
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Genus - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Genus ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      TRUE   TRUE    TRUE            TRUE    TRUE
#> 2      TRUE   TRUE    <NA>            TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>   FALSE            TRUE    <NA>
#> 2      <NA>   <NA>    TRUE           FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   speciesID colour density functionalGroup comment
#> 1      <NA>   <NA>    <NA>            <NA>    <NA>
#> 2      <NA>   <NA>    <NA>            <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Treatments
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Treatments - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Treatments ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        TRUE                 TRUE    <NA>
#> 2        TRUE                 TRUE    <NA>
#> 3        TRUE                 TRUE    <NA>
#> 4        TRUE                 TRUE    <NA>
#> 5        TRUE                 TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1       FALSE                FALSE    <NA>
#> 2       FALSE                FALSE    <NA>
#> 3       FALSE                FALSE    <NA>
#> 4       FALSE                FALSE    <NA>
#> 5       FALSE                FALSE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   treatmentID treatmentLevelHeight comment
#> 1        <NA>                 <NA>    <NA>
#> 2        <NA>                 <NA>    <NA>
#> 3        <NA>                 <NA>    <NA>
#> 4        <NA>                 <NA>    <NA>
#> 5        <NA>                 <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $Measurement
#> $error
#> [1] 1
#> 
#> $details
#>            Module errorCode  isOK
#> 1           types        OK  TRUE
#> 2 suggestedValues      note FALSE
#> 3   allowedValues        OK  TRUE
#> 4         IDField        OK  TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">Measurement - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** Measurement ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 2          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 3          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#> 4          TRUE     TRUE   TRUE TRUE   TRUE                    TRUE
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           TRUE             TRUE         TRUE    <NA>
#> 2           TRUE             TRUE         TRUE    <NA>
#> 3           TRUE             TRUE         TRUE    <NA>
#> 4           TRUE             TRUE         TRUE    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 1
#> 
#> $details
#>   measurementID variable method  unit object noOfSamplesInTimeSeries
#> 1          <NA>    FALSE   TRUE  TRUE   TRUE                    <NA>
#> 2          <NA>     TRUE  FALSE  TRUE   TRUE                    <NA>
#> 3          <NA>    FALSE  FALSE FALSE   TRUE                    <NA>
#> 4          <NA>     TRUE  FALSE FALSE  FALSE                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#55AA00\">values in suggestedValues - note</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   measurementID variable method unit object noOfSamplesInTimeSeries
#> 1          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 2          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 3          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#> 4          <NA>     <NA>   <NA> <NA>   <NA>                    <NA>
#>   samplingVolume dataExtractionID measuredFrom comment
#> 1           <NA>             <NA>         <NA>    <NA>
#> 2           <NA>             <NA>         <NA>    <NA>
#> 3           <NA>             <NA>         <NA>    <NA>
#> 4           <NA>             <NA>         <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataExtraction
#> $error
#> [1] 0
#> 
#> $details
#>            Module errorCode isOK
#> 1           types        OK TRUE
#> 2 suggestedValues        OK TRUE
#> 3   allowedValues        OK TRUE
#> 4         IDField        OK TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">DataExtraction - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning ** DataExtraction ** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             TRUE   <NA>      <NA>  <NA>    TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $suggestedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   TRUE      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in suggestedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the suggestedValues list.\n    TRUE : If the cell value is contained in the suggestedValues list.\n    NA   : empty cell or no suggested values specified\n \n One or more FALSE values will result in a WARNING."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>   dataExtractionID method parameter value comment
#> 1             <NA>   <NA>      <NA>  <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $IDField
#> $error
#> [1] 0
#> 
#> $details
#>                         hasIDField isOK
#> 1 tab has ID field in first column TRUE
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">ID Field present and in the first column - OK</span>**"
#> 
#> $description
#> [1] "Check if the tab's first column contains an ID field, named as `...ID`. This function does not check for uniqueness of this ID field!"
#> 
#> $descriptionDetails
#> [1] "Returns a boolean value, with the following possible values:\n \n    TRUE  : The tab's first column is an ID field\n    FALSE : The tab's first column is not an ID field\n \n FALSE will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $DataFileMetaData
#> $error
#> [1] 3
#> 
#> $details
#>           Module errorCode  isOK
#> 1          types        OK  TRUE
#> 2  allowedValues        OK  TRUE
#> 3 dataFilesExist     error FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">DataFileMetaData - error</span>**"
#> 
#> $description
#> [1] "Test if the metadata concerning **DataExtraction** is correct.  This includes column names, required info, ... "
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique validation.\n The column `Module` contains the name of the validation,\n The column `error` contains the actual error of the validation.\n The following values are possible for the column `isTRUE`:\n \n    TRUE : If the validation was `OK`.\n    FALSE: If the validation was an `error`, `warning` or `note`.\n    NA   : If at least one v alidation resulted in `NA\n \n One or more FALSE or missing values values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> $types
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 3          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 7          TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 8          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 11         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 12         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 13         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 14         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         TRUE       <NA>       TRUE          TRUE TRUE        <NA>    <NA>
#> 16         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         TRUE       TRUE       TRUE          <NA> TRUE        TRUE    <NA>
#> 18         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 19         TRUE       TRUE       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         TRUE       TRUE       TRUE          TRUE TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">conversion of values into specified type lossless possible - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered follows the type for the column, i.e. integer, characterd, .... The validation is done by verifying if the column can be losslessly converted from character to the columnb type specified. the value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell contains an error, i.e. can not be losslessly converted.\n    TRUE : If the cell can be losslessly converted and is OK.\n    NA   : empty cell\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $allowedValues
#> $error
#> [1] 0
#> 
#> $details
#>    dataFileName columnName columnData mappingColumn type description comment
#> 1          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 2          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 3          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 4          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 5          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 6          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 7          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 8          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 9          <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 10         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 11         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 12         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 13         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 14         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 15         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 16         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 17         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 18         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 19         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 20         <NA>       <NA>       TRUE          <NA> TRUE        <NA>    <NA>
#> 
#> $header
#> [1] "**<span style=\"color:#00FF00\">values in allowedValues - OK</span>**"
#> 
#> $description
#> [1] "Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided."
#> 
#> $descriptionDetails
#> [1] "The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:\n \n    FALSE: If the cell value is not contained in the allowedValues list.\n    TRUE : If the cell value is contained in the allowedValues list.\n    NA   : empty cell or no allowed values specified\n \n One or more FALSE values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> $dataFilesExist
#> $error
#> [1] 3
#> 
#> $details
#>                    dataFileName  IsOK
#> 1 dissolved_oxygen_measures.csv FALSE
#> 2                     smell.csv FALSE
#> 3                abundances.csv FALSE
#> 
#> $header
#> [1] "**<span style=\"color:#FF0000\">`dataFile` exists in path - error</span>**"
#> 
#> $description
#> [1] "Test if all `dataFile` exist in the given `path`. The `error` can have the following values apart from `OK`:\n \n    error   : If not all `dataFile` exist in the given `path`\n \n"
#> 
#> $descriptionDetails
#> [1] "The details are a table with one row per unique `variable` The following values are possible for the column `isTRUE`:\n \n    TRUE : If `dataFile` exist in the given `path`\n    FALSE: If `dataFile` does not exist in the given `path`\n    NA   : empty cell\n \n One or more FALSE or missing values will result in an ERROR."
#> 
#> $comment
#> [1] ""
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"                
#> 
#> attr(,"class")
#> [1] "dmdScheme_validation" "list"