Print method for dmdScheme_validation
object
Source: R/print.dmdScheme_validation.R
print.dmdScheme_validation.Rd
When using different values for format
, different outputs are generated:
"default"print
x
aslist
"summary"print the description and errors of
x
as structured output, using the format as specified in the argumentformat
"details"print the details of
x
as structured output, using the format as specified in the argumentformat
Arguments
- x
object of class
dmdScheme_validation
- level
level at which the header structure should start
- listLevel
level at which the elements should be represented as lists and not headers anymore
- type
type of output, can be either
"default"
,"summary"
or"details"
. Default is"default"
- format
format in which the details tables should be printed. All values as used in
knitr::kable()
are allowed.- error
numeric v ector, containing error levels to print. Default is all error levels.
- ...
additional arguments for the function
knitr::kable()
function to format the table.
Examples
x <- validate(dmdScheme_raw())
#> Validating Experiment
#> Validating MdBibliometric
#> Validating MdAuthors
#> Validating Genus
#> Validating Treatments
#> Validating Measurement
#> Validating DataExtraction
#> Validating DataFileMetaData
## default printout as list
x
#> $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"
## the same as
print(x, type = "default")
#> $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"
## the summary
print(x, type = "summary")
#>
#> # **<span style="color:#FF0000">Overall MetaData - error</span>**
#>
#> The result of the overall validation of the data.
#>
#>
#> ## **<span style="color:#00FF00">Structural / Formal validity - OK</span>**
#>
#> 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.
#>
#>
#> ## **<span style="color:#00FF00">Experiment - OK</span>**
#>
#> Test if the metadata concerning **Experiment** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#>
#> ## **<span style="color:#FF0000">MdBibliometric - error</span>**
#>
#> Test if the metadata concerning ** MdBibliometric ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#FF0000">ID Field present and in the first column - error</span>**
#> 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!
#>
#>
#> ## **<span style="color:#FF0000">MdAuthors - error</span>**
#>
#> Test if the metadata concerning ** MdAuthors ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#FF0000">values in allowedValues - error</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> 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!
#>
#>
#> ## **<span style="color:#55AA00">Genus - note</span>**
#>
#> Test if the metadata concerning ** Genus ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> 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!
#>
#>
#> ## **<span style="color:#55AA00">Treatments - note</span>**
#>
#> Test if the metadata concerning ** Treatments ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> 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!
#>
#>
#> ## **<span style="color:#55AA00">Measurement - note</span>**
#>
#> Test if the metadata concerning ** Measurement ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> 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!
#>
#>
#> ## **<span style="color:#00FF00">DataExtraction - OK</span>**
#>
#> Test if the metadata concerning ** DataExtraction ** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> Test if the metadata entered is ion the suggestedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> 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!
#>
#>
#> ## **<span style="color:#FF0000">DataFileMetaData - error</span>**
#>
#> Test if the metadata concerning **DataExtraction** is correct. This includes column names, required info, ...
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> 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.
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> Test if the metadata entered is ion the allowedValues list. The value NA is allowed in all column types, empty cells should be avoided.
#>
#> - **<span style="color:#FF0000">`dataFile` exists in path - error</span>**
#> Test if all `dataFile` exist in the given `path`. The `error` can have the following values apart from `OK`:
#>
#> error : If not all `dataFile` exist in the given `path`
#>
#>
#>
## and the details
print(x, type = "details")
#>
#> # **<span style="color:#FF0000">Overall MetaData - error</span>**
#>
#> 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.
#>
#>
#>
#> |x |
#> |:--|
#> |NA |
#>
#>
#> ## **<span style="color:#00FF00">Structural / Formal validity - OK</span>**
#>
#>
#>
#>
#>
#> |x |
#> |:----|
#> |TRUE |
#>
#>
#> ## **<span style="color:#00FF00">Experiment - OK</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:------|:---------|:----|
#> |types |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |name |temperature |light |humidity |incubator |container |microcosmVolume |mediaType |mediaConcentration |cultureConditions |comunityType |mediaAdditions |duration |comment |
#> |:----|:-----------|:-----|:--------|:---------|:---------|:---------------|:---------|:------------------|:-----------------|:------------|:--------------|:--------|:-------|
#> |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |NA |
#>
#>
#> ## **<span style="color:#FF0000">MdBibliometric - error</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:-----|
#> |types |OK |TRUE |
#> |suggestedValues |OK |TRUE |
#> |allowedValues |OK |TRUE |
#> |IDField |error |FALSE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |uploadType |doi |publicationDate |title |description |version |language |keywords |additionalNotes |accessRights |accessRightsInfo |license |
#> |:----------|:----|:---------------|:-----|:-----------|:-------|:--------|:--------|:---------------|:------------|:----------------|:-------|
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |TRUE |TRUE |NA |TRUE |NA |TRUE |
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |uploadType |doi |publicationDate |title |description |version |language |keywords |additionalNotes |accessRights |accessRightsInfo |license |
#> |:----------|:---|:---------------|:-----|:-----------|:-------|:--------|:--------|:---------------|:------------|:----------------|:-------|
#> |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |TRUE |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |uploadType |doi |publicationDate |title |description |version |language |keywords |additionalNotes |accessRights |accessRightsInfo |license |
#> |:----------|:---|:---------------|:-----|:-----------|:-------|:--------|:--------|:---------------|:------------|:----------------|:-------|
#> |TRUE |NA |NA |NA |NA |NA |NA |NA |NA |TRUE |NA |NA |
#>
#> - **<span style="color:#FF0000">ID Field present and in the first column - error</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:-----|
#> |tab has ID field in first column |FALSE |
#>
#>
#> ## **<span style="color:#FF0000">MdAuthors - error</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:-----|
#> |types |OK |TRUE |
#> |suggestedValues |OK |TRUE |
#> |allowedValues |error |FALSE |
#> |IDField |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |authorID |familyName |givenName |affiliation |orcid |role |
#> |:--------|:----------|:---------|:-----------|:-----|:----|
#> |TRUE |TRUE |TRUE |TRUE |NA |TRUE |
#> |TRUE |TRUE |TRUE |TRUE |NA |TRUE |
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |authorID |familyName |givenName |affiliation |orcid |role |
#> |:--------|:----------|:---------|:-----------|:-----|:----|
#> |NA |NA |NA |NA |NA |NA |
#> |NA |NA |NA |NA |NA |NA |
#>
#> - **<span style="color:#FF0000">values in allowedValues - error</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |authorID |familyName |givenName |affiliation |orcid |role |
#> |:--------|:----------|:---------|:-----------|:-----|:-----|
#> |NA |NA |NA |NA |NA |FALSE |
#> |NA |NA |NA |NA |NA |TRUE |
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:----|
#> |tab has ID field in first column |TRUE |
#>
#>
#> ## **<span style="color:#55AA00">Genus - note</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:-----|
#> |types |OK |TRUE |
#> |suggestedValues |note |FALSE |
#> |allowedValues |OK |TRUE |
#> |IDField |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |speciesID |colour |density |functionalGroup |comment |
#> |:---------|:------|:-------|:---------------|:-------|
#> |TRUE |TRUE |TRUE |TRUE |TRUE |
#> |TRUE |TRUE |NA |TRUE |NA |
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |speciesID |colour |density |functionalGroup |comment |
#> |:---------|:------|:-------|:---------------|:-------|
#> |NA |NA |FALSE |TRUE |NA |
#> |NA |NA |TRUE |FALSE |NA |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |speciesID |colour |density |functionalGroup |comment |
#> |:---------|:------|:-------|:---------------|:-------|
#> |NA |NA |NA |NA |NA |
#> |NA |NA |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:----|
#> |tab has ID field in first column |TRUE |
#>
#>
#> ## **<span style="color:#55AA00">Treatments - note</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:-----|
#> |types |OK |TRUE |
#> |suggestedValues |note |FALSE |
#> |allowedValues |OK |TRUE |
#> |IDField |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |treatmentID |treatmentLevelHeight |comment |
#> |:-----------|:--------------------|:-------|
#> |TRUE |TRUE |NA |
#> |TRUE |TRUE |NA |
#> |TRUE |TRUE |NA |
#> |TRUE |TRUE |NA |
#> |TRUE |TRUE |NA |
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |treatmentID |treatmentLevelHeight |comment |
#> |:-----------|:--------------------|:-------|
#> |FALSE |FALSE |NA |
#> |FALSE |FALSE |NA |
#> |FALSE |FALSE |NA |
#> |FALSE |FALSE |NA |
#> |FALSE |FALSE |NA |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |treatmentID |treatmentLevelHeight |comment |
#> |:-----------|:--------------------|:-------|
#> |NA |NA |NA |
#> |NA |NA |NA |
#> |NA |NA |NA |
#> |NA |NA |NA |
#> |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:----|
#> |tab has ID field in first column |TRUE |
#>
#>
#> ## **<span style="color:#55AA00">Measurement - note</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:-----|
#> |types |OK |TRUE |
#> |suggestedValues |note |FALSE |
#> |allowedValues |OK |TRUE |
#> |IDField |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |measurementID |variable |method |unit |object |noOfSamplesInTimeSeries |samplingVolume |dataExtractionID |measuredFrom |comment |
#> |:-------------|:--------|:------|:----|:------|:-----------------------|:--------------|:----------------|:------------|:-------|
#> |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |TRUE |NA |
#>
#> - **<span style="color:#55AA00">values in suggestedValues - note</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |measurementID |variable |method |unit |object |noOfSamplesInTimeSeries |samplingVolume |dataExtractionID |measuredFrom |comment |
#> |:-------------|:--------|:------|:-----|:------|:-----------------------|:--------------|:----------------|:------------|:-------|
#> |NA |FALSE |TRUE |TRUE |TRUE |NA |NA |NA |NA |NA |
#> |NA |TRUE |FALSE |TRUE |TRUE |NA |NA |NA |NA |NA |
#> |NA |FALSE |FALSE |FALSE |TRUE |NA |NA |NA |NA |NA |
#> |NA |TRUE |FALSE |FALSE |FALSE |NA |NA |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |measurementID |variable |method |unit |object |noOfSamplesInTimeSeries |samplingVolume |dataExtractionID |measuredFrom |comment |
#> |:-------------|:--------|:------|:----|:------|:-----------------------|:--------------|:----------------|:------------|:-------|
#> |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |
#> |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |
#> |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |
#> |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:----|
#> |tab has ID field in first column |TRUE |
#>
#>
#> ## **<span style="color:#00FF00">DataExtraction - OK</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:---------------|:---------|:----|
#> |types |OK |TRUE |
#> |suggestedValues |OK |TRUE |
#> |allowedValues |OK |TRUE |
#> |IDField |OK |TRUE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |dataExtractionID |method |parameter |value |comment |
#> |:----------------|:------|:---------|:-----|:-------|
#> |TRUE |NA |NA |NA |TRUE |
#>
#> - **<span style="color:#00FF00">values in suggestedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the suggestedValues list.
#> TRUE : If the cell value is contained in the suggestedValues list.
#> NA : empty cell or no suggested values specified
#>
#> One or more FALSE values will result in a WARNING.
#>
#>
#> |dataExtractionID |method |parameter |value |comment |
#> |:----------------|:------|:---------|:-----|:-------|
#> |NA |TRUE |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |dataExtractionID |method |parameter |value |comment |
#> |:----------------|:------|:---------|:-----|:-------|
#> |NA |NA |NA |NA |NA |
#>
#> - **<span style="color:#00FF00">ID Field present and in the first column - OK</span>**
#> Returns a boolean value, with the following possible values:
#>
#> TRUE : The tab's first column is an ID field
#> FALSE : The tab's first column is not an ID field
#>
#> FALSE will result in an ERROR.
#>
#>
#> |hasIDField |isOK |
#> |:--------------------------------|:----|
#> |tab has ID field in first column |TRUE |
#>
#>
#> ## **<span style="color:#FF0000">DataFileMetaData - error</span>**
#>
#> The details are a table with one row per unique validation.
#> The column `Module` contains the name of the validation,
#> The column `error` contains the actual error of the validation.
#> The following values are possible for the column `isTRUE`:
#>
#> TRUE : If the validation was `OK`.
#> FALSE: If the validation was an `error`, `warning` or `note`.
#> NA : If at least one v alidation resulted in `NA
#>
#> One or more FALSE or missing values values will result in an ERROR.
#>
#>
#>
#> |Module |errorCode |isOK |
#> |:--------------|:---------|:-----|
#> |types |OK |TRUE |
#> |allowedValues |OK |TRUE |
#> |dataFilesExist |error |FALSE |
#>
#> - **<span style="color:#00FF00">conversion of values into specified type lossless possible - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell contains an error, i.e. can not be losslessly converted.
#> TRUE : If the cell can be losslessly converted and is OK.
#> NA : empty cell
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |dataFileName |columnName |columnData |mappingColumn |type |description |comment |
#> |:------------|:----------|:----------|:-------------|:----|:-----------|:-------|
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |NA |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |NA |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |TRUE |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |NA |TRUE |NA |NA |
#> |TRUE |TRUE |TRUE |TRUE |TRUE |NA |NA |
#>
#> - **<span style="color:#00FF00">values in allowedValues - OK</span>**
#> The details are a table of the same dimension as the input (green) area of the meatadata sheet. The following values are possible:
#>
#> FALSE: If the cell value is not contained in the allowedValues list.
#> TRUE : If the cell value is contained in the allowedValues list.
#> NA : empty cell or no allowed values specified
#>
#> One or more FALSE values will result in an ERROR.
#>
#>
#> |dataFileName |columnName |columnData |mappingColumn |type |description |comment |
#> |:------------|:----------|:----------|:-------------|:----|:-----------|:-------|
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#> |NA |NA |TRUE |NA |TRUE |NA |NA |
#>
#> - **<span style="color:#FF0000">`dataFile` exists in path - error</span>**
#> The details are a table with one row per unique `variable` The following values are possible for the column `isTRUE`:
#>
#> TRUE : If `dataFile` exist in the given `path`
#> FALSE: If `dataFile` does not exist in the given `path`
#> NA : empty cell
#>
#> One or more FALSE or missing values will result in an ERROR.
#>
#>
#> |dataFileName |IsOK |
#> |:-----------------------------|:-----|
#> |dissolved_oxygen_measures.csv |FALSE |
#> |smell.csv |FALSE |
#> |abundances.csv |FALSE |
#>
## can be used in a Rmd file like:
# ```{r, results = "asis"}
# print(result, level = 2, listLevel = 20, type = "summary")
# ```