Class Validator

java.lang.Object
net.sf.basedb.util.overview.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 Details

    • 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
    • id

      private String id
    • title

      private String title
    • description

      private String description
    • failureSummary

      private String failureSummary
    • defaultSeverity

      private Severity defaultSeverity
  • Constructor Details

    • 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
  • Method Details