Class Validator

  • All Implemented Interfaces:
    Action, ValidationRuleAction

    public class Validator
    extends Object
    implements ValidationRuleAction
    Placeholder for a validation rule. An object instance contains a name and description of the validation and a default severity level.

    The actual validation takes place in the overview generating code. See implementations of NodeValidator interface.

    Version:
    2.2
    Author:
    Nicklas
    Last modified
    $Date: 2020-10-21 07:39:15 +0200 (Wed, 21 Oct 2020) $
    • Field Detail

      • MISSING_PROTOCOL

        public static final Validator MISSING_PROTOCOL
        Validator rule that checks for missing protocols. Default severity level is WARNING.
      • DENIED_PROTOCOL

        public static final Validator DENIED_PROTOCOL
        Validator rule that checks for denied access to protocols. Default severity level is WARNING.
      • MISSING_DERIVEDBIOASSAY

        public static final Validator MISSING_DERIVEDBIOASSAY
        Validator rule that checks for missing parent derived bioassay. Default severity level is WARNING.
        Since:
        3.0
      • DENIED_DERIVEDBIOASSAY

        public static final Validator DENIED_DERIVEDBIOASSAY
        Validator rule that checks for denied access to derived bioassay. Default severity level is WARNING.
        Since:
        3.0
      • DENIED_PLATFORM

        public static final Validator DENIED_PLATFORM
        Validator rule that checks for denied access to platform. Default severity level is WARNING.
      • DENIED_FILE

        public static final Validator DENIED_FILE
        Validator rule that checks for denied access to (data) files. Default severity level is WARNING.
      • MISSING_FILE

        public static final Validator MISSING_FILE
        Validator rule that checks for denied access to (data) files. Default severity level is WARNING.
        Since:
        3.17
      • DENIED_DATAFILETYPE

        public static final Validator DENIED_DATAFILETYPE
        Validator rule that checks for denied access to data file types. Default severity level is WARNING.
      • MISSING_SOFTWARE

        public static final Validator MISSING_SOFTWARE
        Validator rule that checks for missing software. Default severity level is WARNING.
      • DENIED_SOFTWARE

        public static final Validator DENIED_SOFTWARE
        Validator rule that checks for denied access to software. Default severity level is WARNING.
      • MISSING_HARDWARE

        public static final Validator MISSING_HARDWARE
        Validator rule that checks for missing hardware. Default severity level is WARNING.
      • DENIED_HARDWARE

        public static final Validator DENIED_HARDWARE
        Validator rule that checks for denied access to hardware. Default severity level is WARNING.
      • MISSING_KIT

        public static final Validator MISSING_KIT
        Validator rule that checks for missing kits. Default severity level is WARNING.
        Since:
        3.7
      • DENIED_KIT

        public static final Validator DENIED_KIT
        Validator rule that checks for denied access to kit. Default severity level is WARNING.
        Since:
        3.7
      • MISSING_PHYSICALBIOASSAY

        public static final Validator MISSING_PHYSICALBIOASSAY
        Validator rule that checks for missing physical bioassay. Default severity level is WARNING.
        Since:
        3.0
      • DENIED_PHYSICALBIOASSAY

        public static final Validator DENIED_PHYSICALBIOASSAY
        Validator rule that checks for denied access to physical bioassay. Default severity level is WARNING.
        Since:
        3.0
      • MISSING_ARRAYSLIDE

        public static final Validator MISSING_ARRAYSLIDE
        Validator rule that checks for missing array slide. Default severity level is WARNING.
      • DENIED_ARRAYSLIDE

        public static final Validator DENIED_ARRAYSLIDE
        Validator rule that checks for denied access to array slides. Default severity level is WARNING.
      • MISSING_EXTRACT

        public static final Validator MISSING_EXTRACT
        Validator rule that checks for missing extract. Default severity level is WARNING.
      • DENIED_EXTRACT

        public static final Validator DENIED_EXTRACT
        Validator rule that checks for denied access to extracts. Default severity level is WARNING.
      • MISSING_SAMPLE

        public static final Validator MISSING_SAMPLE
        Validator rule that checks for missing sample. Default severity level is WARNING.
      • DENIED_SAMPLE

        public static final Validator DENIED_SAMPLE
        Validator rule that checks for denied access to samples. Default severity level is WARNING.
      • MISSING_BIOSOURCE

        public static final Validator MISSING_BIOSOURCE
        Validator rule that checks for missing biosource. Default severity level is WARNING.
      • DENIED_BIOSOURCE

        public static final Validator DENIED_BIOSOURCE
        Validator rule that checks for denied access to biosource. Default severity level is WARNING.
      • MISSING_TAG

        public static final Validator MISSING_TAG
        Validator rule that checks for missing tag. Default severity level is WARNING.
      • DENIED_TAG

        public static final Validator DENIED_TAG
        Validator rule that checks for denied access to tags. Default severity level is WARNING.
        Since:
        3.0
      • MISSING_ARRAYDESIGN

        public static final Validator MISSING_ARRAYDESIGN
        Validator rule that checks for missing array design. Default severity level is WARNING.
      • DENIED_ARRAYDESIGN

        public static final Validator DENIED_ARRAYDESIGN
        Validator rule that checks for denied access to an array design. Default severity level is WARNING.
      • MISSING_ARRAYBATCH

        public static final Validator MISSING_ARRAYBATCH
        Validator rule that checks for missing array batch. Default severity level is WARNING.
      • DENIED_ARRAYBATCH

        public static final Validator DENIED_ARRAYBATCH
        Validator rule that checks for denied access to an array batch. Default severity level is WARNING.
      • MISSING_FACTORVALUE

        public static final Validator MISSING_FACTORVALUE
        Validator rule that checks for missing experimental factor value. Default severity level is ERROR.
      • MISSING_PARAMETER

        public static final Validator MISSING_PARAMETER
        Validator rule that checks for missing protocol parameter values. Default severity level is ERROR.
      • MISSING_MIAME_ANNOTATION

        public static final Validator MISSING_MIAME_ANNOTATION
        Validator rule that checks for missing "Required for MIAME" annotation. Default severity level is ERROR.
      • DENIED_ANNOTATIONTYPE

        public static final Validator DENIED_ANNOTATIONTYPE
        Validator rule that checks for denied access to an annotation type. Default severity level is WARNING.
      • MISSING_ANYTOANY

        public static final Validator MISSING_ANYTOANY
        Validator rule that checks for a missing reference in an any-to-any link. Eg. due to the non-relational nature an any-to-any entry may point to an item that has been deleted. Default severity level is WARNING.
        Since:
        2.17
      • DENIED_ANYTOANY

        public static final Validator DENIED_ANYTOANY
        Validator rule that checks for denied access the referenced item in an any-to-any link. Default severity level is WARNING.
        Since:
        2.17
      • MISSING_BIOPLATE

        public static final Validator MISSING_BIOPLATE
        Validator rule that checks for missing bioplate location. Default severity level is IGNORE.
        Since:
        3.2
      • DENIED_BIOPLATE

        public static final Validator DENIED_BIOPLATE
        Validator rule that checks for denied access to a bioplate. Default severity level is WARNING.
        Since:
        3.2
      • NONDEFAULT_PLATFORM

        public static final Validator NONDEFAULT_PLATFORM
        Validator rule that checks if an item uses a different platform / variant than specified by the project default. Default severity level is WARNING.
      • NONDEFAULT_PROTOCOL

        public static final Validator NONDEFAULT_PROTOCOL
        Validator rule that checks if an item uses a different protocol than specified by the project default. Default severity level is WARNING.
      • NONDEFAULT_HARDWARE

        public static final Validator NONDEFAULT_HARDWARE
        Validator rule that checks if an item uses a different hardware than specified by the project default. Default severity level is WARNING.
      • NONDEFAULT_SOFTWARE

        public static final Validator NONDEFAULT_SOFTWARE
        Validator rule that checks if an item uses a different software than specified by the project default. Default severity level is WARNING.
      • NONDEFAULT_ARRAYDESIGN

        public static final Validator NONDEFAULT_ARRAYDESIGN
        Validator rule that checks if an item uses a different array design than specified by the project default. Default severity level is WARNING.
      • NONDEFAULT_RAWDATATYPE

        public static final Validator NONDEFAULT_RAWDATATYPE
        Validator rule that checks if an item uses a different raw data type than specified by the project default. Default severity level is WARNING.
      • MULTIPLE_ARRAYDESIGNS

        public static final Validator MULTIPLE_ARRAYDESIGNS
        Validator rule that checks if all raw bioassays in an experiment uses the same array design. Default severity level is WARNING.
      • NONMATHCING_ARRAYDESIGN

        public static final Validator NONMATHCING_ARRAYDESIGN
        Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay. Default severity level is WARNING.
      • NONMATCHING_SPOTCOUNT

        public static final Validator NONMATCHING_SPOTCOUNT
        Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold). Default severity level is WARNING.
      • INCORRECT_TAGTYPE

        public static final Validator INCORRECT_TAGTYPE
        Validator rule that checks if the tag attached to an extract has a correct subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_PROTOCOLTYPE

        public static final Validator INCORRECT_PROTOCOLTYPE
        Validator rule that checks if the protocol attached to an item has a correct protocol type. Default severity level is WARNING.
      • INCORRECT_SOFTWARETYPE

        public static final Validator INCORRECT_SOFTWARETYPE
        Validator rule that checks if the software attached to an item has a correct software type. Default severity level is WARNING.
      • INCORRECT_HARDWARETYPE

        public static final Validator INCORRECT_HARDWARETYPE
        Validator rule that checks if the hardware attached to an item has a correct hardware type. Default severity level is WARNING.
      • INCORRECT_KITTYPE

        public static final Validator INCORRECT_KITTYPE
        Validator rule that checks if the kit attached to an item has a correct kit type. Default severity level is WARNING.
        Since:
        3.7
      • INCORRECT_FILETYPE

        public static final Validator INCORRECT_FILETYPE
        Validator rule that checks if the file attached to an item has a correct file type. Default severity level is WARNING.
        Since:
        3.17
      • INCORRECT_BIOSOURCE_TYPE

        public static final Validator INCORRECT_BIOSOURCE_TYPE
        Validator that checks if the parent biosource of a sample has the expected subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_SAMPLE_TYPE

        public static final Validator INCORRECT_SAMPLE_TYPE
        Validator that checks if the parent sample of a sample/extract has the expected subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_EXTRACT_TYPE

        public static final Validator INCORRECT_EXTRACT_TYPE
        Validator that checks if the parent extract of a extract/bioassay has the expected subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_BIOMATERIAL_TYPE

        public static final Validator INCORRECT_BIOMATERIAL_TYPE
        Validator that checks if the biomaterial on a bioplate is of the correct item type. Default severity level is ERROR.
        Since:
        3.2
      • INCORRECT_PHYSICALBIOASSAY_TYPE

        public static final Validator INCORRECT_PHYSICALBIOASSAY_TYPE
        Validator that checks if a physical bioassay has the expected subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_DERIVEDBIOASSAY_TYPE

        public static final Validator INCORRECT_DERIVEDBIOASSAY_TYPE
        Validator that checks if a derived bioassay has the expected subtype. Default severity level is WARNING.
        Since:
        3.0
      • INCORRECT_BIOASSAY_POSITION

        public static final Validator INCORRECT_BIOASSAY_POSITION
        Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay. Default severity level is WARNING.
        Since:
        3.0
      • NONUNIQUE_TAG

        public static final Validator NONUNIQUE_TAG
        Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position. Default severity level is ERROR.
        Since:
        3.0
      • DIFFERENT_TAG

        public static final Validator DIFFERENT_TAG
        Validator rule that checks if the parent to a tagged extract has a different tag. Default severity level is WARNING.
        Since:
        3.0
      • TAGGED_PARENT

        public static final Validator TAGGED_PARENT
        Validator rule that checks if the parent to a non-tagged extract has a tag. Default severity level is WARNING.
        Since:
        3.0
      • PARENT_EXTRACT_MISMATCH

        public static final Validator PARENT_EXTRACT_MISMATCH
        Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.
        Since:
        3.0
      • NONUNIQUE_NAME_FOR_TYPE

        public static final Validator NONUNIQUE_NAME_FOR_TYPE
        Validator rule that checks if two items of the same type has the same name. Default severity level is ERROR.
      • NONUNIQUE_NAME_GLOBAL

        public static final Validator NONUNIQUE_NAME_GLOBAL
        Validator rule that checks if two items of different type has the same name. Default severity level is IGNORE.
      • CIRCULAR_REFERENCE

        public static final Validator CIRCULAR_REFERENCE
        Validator rule that checks for circular references among pooled items. Default severity level is ERROR.
      • ANNOTATION_IS_PARAMETER

        public static final Validator ANNOTATION_IS_PARAMETER
        Validator rule that checks if an annotation is a protocol parameter. Default severity level is WARNING.
      • ANNOTATION_INVALID_ITEM

        public static final Validator ANNOTATION_INVALID_ITEM
        Validator rule that checks if an annotation is not valid for the current item type. Default severity level is WARNING.
      • ANNOTATION_INVALID_VALUE

        public static final Validator ANNOTATION_INVALID_VALUE
        Validator rule that checks if an annotation value is invalid according to annotation type specification. Default severity level is ERROR.
      • ANNOTATION_TOO_MANY_VALUES

        public static final Validator ANNOTATION_TOO_MANY_VALUES
        Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow. Default severity level is WANRING.
        Since:
        3.2
      • ANNOTATION_INHERIT_FROM_NONPARENT

        public static final Validator ANNOTATION_INHERIT_FROM_NONPARENT
        Validator rule that checks if an inherited annotation value is inherited from a parent item. Default severity level is ERROR.
      • ANNOTATION_CLONED_FROM_UNKNOWNPARENT

        public static final Validator ANNOTATION_CLONED_FROM_UNKNOWNPARENT
        Validator rule that checks if a cloned annotation value has lost the reference to the parent item. Default severity level is WARNING.
        Since:
        3.6
      • ANNOTATION_CLONE_OUTOFSYNC

        public static final Validator ANNOTATION_CLONE_OUTOFSYNC
        Validator rule that checks if a cloned annotation value is in sync with the source annotation. Default severity level is WARNING.
        Since:
        3.6
      • ANNOTATION_INHERIT_FROM_DENIEDPARENT

        public static final Validator ANNOTATION_INHERIT_FROM_DENIEDPARENT
        Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value. Default severity level is WARNING.
        Since:
        2.10
      • ANNOTATION_INHERIT_MULTIPLE

        public static final Validator ANNOTATION_INHERIT_MULTIPLE
        Validator rule that checks if two or more inherited annotations have the same annotation type. Default severity level is ERROR.
      • DATAFILE_INVALID_ITEM

        public static final Validator DATAFILE_INVALID_ITEM
        Validator rule that checks if a data file can be used on the current item type. Default severity level is WARNING.
      • DATAFILE_NOTVALIDATED

        public static final Validator DATAFILE_NOTVALIDATED
        Validator rule that checks if a data file has been validated or not. Default severity level is WARNING, but this rule is not checked if the data file type doesn't have a validator.
      • DATAFILE_INVALID

        public static final Validator DATAFILE_INVALID
        Validator rule that checks if a data file is valid. Default severity level is ERROR, but this rule is not checked if the data file hasn't been validated.
      • MISSING_DATAFILE

        public static final Validator MISSING_DATAFILE
        Validator rule that checks if all files required by the platform are present or not. Default severity level is ERROR.
      • DATAFILE_NOTPLATFORM

        public static final Validator DATAFILE_NOTPLATFORM
        Validator rule that checks if a file is registered with a platform/item subtype or not. Default severity level is WARNING.
      • DATAFILE_TOOMANYFILES

        public static final Validator DATAFILE_TOOMANYFILES
        Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files. Default severity level is WARNING.
        Since:
        3.0
      • KIT_USED_AFTER_EXPIRATIONDATE

        public static final Validator KIT_USED_AFTER_EXPIRATIONDATE
        Validator rule that checks if a kit has been used after it's exiration date. Default severity level is WARNING.
        Since:
        3.7
      • description

        private String description
      • failureSummary

        private String failureSummary
      • defaultSeverity

        private Severity defaultSeverity
    • Constructor Detail

      • Validator

        public Validator​(String id,
                         String title,
                         String description,
                         String failureSummary,
                         Severity defaultSeverity)
        Create a new validator.
        Parameters:
        id - A unique ID among all validators
        title - The title for the validation rule
        description - A lengthier description of the validation that takes place
        failureSummary - A short summary that is displayed when the validation fails
        defaultSeverity - The default severity level of the validation