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 Summary

Fields
Modifier and Type	Field	Description
`static Validator`	`ANNOTATION_CLONE_OUTOFSYNC`	Validator rule that checks if a cloned annotation value is in sync with the source annotation.
`static Validator`	`ANNOTATION_CLONED_FROM_UNKNOWNPARENT`	Validator rule that checks if a cloned annotation value has lost the reference to the parent item.
`static 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.
`static Validator`	`ANNOTATION_INHERIT_FROM_NONPARENT`	Validator rule that checks if an inherited annotation value is inherited from a parent item.
`static Validator`	`ANNOTATION_INHERIT_MULTIPLE`	Validator rule that checks if two or more inherited annotations have the same annotation type.
`static Validator`	`ANNOTATION_INVALID_ITEM`	Validator rule that checks if an annotation is not valid for the current item type.
`static Validator`	`ANNOTATION_INVALID_VALUE`	Validator rule that checks if an annotation value is invalid according to annotation type specification.
`static Validator`	`ANNOTATION_IS_PARAMETER`	Validator rule that checks if an annotation is a protocol parameter.
`static 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.
`static Validator`	`CIRCULAR_REFERENCE`	Validator rule that checks for circular references among pooled items.
`static Validator`	`DATAFILE_INVALID`	Validator rule that checks if a data file is valid.
`static Validator`	`DATAFILE_INVALID_ITEM`	Validator rule that checks if a data file can be used on the current item type.
`static Validator`	`DATAFILE_NOTPLATFORM`	Validator rule that checks if a file is registered with a platform/item subtype or not.
`static Validator`	`DATAFILE_NOTVALIDATED`	Validator rule that checks if a data file has been validated or not.
`static Validator`	`DATAFILE_TOOMANYFILES`	Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files.
`private Severity`	`defaultSeverity`
`static Validator`	`DENIED_ANNOTATIONTYPE`	Validator rule that checks for denied access to an annotation type.
`static Validator`	`DENIED_ANYTOANY`	Validator rule that checks for denied access the referenced item in an any-to-any link.
`static Validator`	`DENIED_ARRAYBATCH`	Validator rule that checks for denied access to an array batch.
`static Validator`	`DENIED_ARRAYDESIGN`	Validator rule that checks for denied access to an array design.
`static Validator`	`DENIED_ARRAYSLIDE`	Validator rule that checks for denied access to array slides.
`static Validator`	`DENIED_BIOPLATE`	Validator rule that checks for denied access to a bioplate.
`static Validator`	`DENIED_BIOSOURCE`	Validator rule that checks for denied access to biosource.
`static Validator`	`DENIED_DATAFILETYPE`	Validator rule that checks for denied access to data file types.
`static Validator`	`DENIED_DERIVEDBIOASSAY`	Validator rule that checks for denied access to derived bioassay.
`static Validator`	`DENIED_EXTRACT`	Validator rule that checks for denied access to extracts.
`static Validator`	`DENIED_FILE`	Validator rule that checks for denied access to (data) files.
`static Validator`	`DENIED_HARDWARE`	Validator rule that checks for denied access to hardware.
`static Validator`	`DENIED_KIT`	Validator rule that checks for denied access to kit.
`static Validator`	`DENIED_PHYSICALBIOASSAY`	Validator rule that checks for denied access to physical bioassay.
`static Validator`	`DENIED_PLATFORM`	Validator rule that checks for denied access to platform.
`static Validator`	`DENIED_PROTOCOL`	Validator rule that checks for denied access to protocols.
`static Validator`	`DENIED_SAMPLE`	Validator rule that checks for denied access to samples.
`static Validator`	`DENIED_SOFTWARE`	Validator rule that checks for denied access to software.
`static Validator`	`DENIED_TAG`	Validator rule that checks for denied access to tags.
`private String`	`description`
`static Validator`	`DIFFERENT_TAG`	Validator rule that checks if the parent to a tagged extract has a different tag.
`private String`	`failureSummary`
`private String`	`id`
`static 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.
`static Validator`	`INCORRECT_BIOMATERIAL_TYPE`	Validator that checks if the biomaterial on a bioplate is of the correct item type.
`static Validator`	`INCORRECT_BIOSOURCE_TYPE`	Validator that checks if the parent biosource of a sample has the expected subtype.
`static Validator`	`INCORRECT_DERIVEDBIOASSAY_TYPE`	Validator that checks if a derived bioassay has the expected subtype.
`static Validator`	`INCORRECT_EXTRACT_TYPE`	Validator that checks if the parent extract of a extract/bioassay has the expected subtype.
`static Validator`	`INCORRECT_FILETYPE`	Validator rule that checks if the file attached to an item has a correct file type.
`static Validator`	`INCORRECT_HARDWARETYPE`	Validator rule that checks if the hardware attached to an item has a correct hardware type.
`static Validator`	`INCORRECT_KITTYPE`	Validator rule that checks if the kit attached to an item has a correct kit type.
`static Validator`	`INCORRECT_PHYSICALBIOASSAY_TYPE`	Validator that checks if a physical bioassay has the expected subtype.
`static Validator`	`INCORRECT_PROTOCOLTYPE`	Validator rule that checks if the protocol attached to an item has a correct protocol type.
`static Validator`	`INCORRECT_SAMPLE_TYPE`	Validator that checks if the parent sample of a sample/extract has the expected subtype.
`static Validator`	`INCORRECT_SOFTWARETYPE`	Validator rule that checks if the software attached to an item has a correct software type.
`static Validator`	`INCORRECT_TAGTYPE`	Validator rule that checks if the tag attached to an extract has a correct subtype.
`static Validator`	`KIT_USED_AFTER_EXPIRATIONDATE`	Validator rule that checks if a kit has been used after it's exiration date.
`static Validator`	`MISSING_ANYTOANY`	Validator rule that checks for a missing reference in an any-to-any link.
`static Validator`	`MISSING_ARRAYBATCH`	Validator rule that checks for missing array batch.
`static Validator`	`MISSING_ARRAYDESIGN`	Validator rule that checks for missing array design.
`static Validator`	`MISSING_ARRAYSLIDE`	Validator rule that checks for missing array slide.
`static Validator`	`MISSING_BIOPLATE`	Validator rule that checks for missing bioplate location.
`static Validator`	`MISSING_BIOSOURCE`	Validator rule that checks for missing biosource.
`static Validator`	`MISSING_DATAFILE`	Validator rule that checks if all files required by the platform are present or not.
`static Validator`	`MISSING_DERIVEDBIOASSAY`	Validator rule that checks for missing parent derived bioassay.
`static Validator`	`MISSING_EXTRACT`	Validator rule that checks for missing extract.
`static Validator`	`MISSING_FACTORVALUE`	Validator rule that checks for missing experimental factor value.
`static Validator`	`MISSING_FILE`	Validator rule that checks for denied access to (data) files.
`static Validator`	`MISSING_HARDWARE`	Validator rule that checks for missing hardware.
`static Validator`	`MISSING_KIT`	Validator rule that checks for missing kits.
`static Validator`	`MISSING_MIAME_ANNOTATION`	Validator rule that checks for missing "Required for MIAME" annotation.
`static Validator`	`MISSING_PARAMETER`	Validator rule that checks for missing protocol parameter values.
`static Validator`	`MISSING_PHYSICALBIOASSAY`	Validator rule that checks for missing physical bioassay.
`static Validator`	`MISSING_PROTOCOL`	Validator rule that checks for missing protocols.
`static Validator`	`MISSING_SAMPLE`	Validator rule that checks for missing sample.
`static Validator`	`MISSING_SOFTWARE`	Validator rule that checks for missing software.
`static Validator`	`MISSING_TAG`	Validator rule that checks for missing tag.
`static Validator`	`MULTIPLE_ARRAYDESIGNS`	Validator rule that checks if all raw bioassays in an experiment uses the same array design.
`static Validator`	`NONDEFAULT_ARRAYDESIGN`	Validator rule that checks if an item uses a different array design than specified by the project default.
`static Validator`	`NONDEFAULT_HARDWARE`	Validator rule that checks if an item uses a different hardware than specified by the project default.
`static Validator`	`NONDEFAULT_PLATFORM`	Validator rule that checks if an item uses a different platform / variant than specified by the project default.
`static Validator`	`NONDEFAULT_PROTOCOL`	Validator rule that checks if an item uses a different protocol than specified by the project default.
`static Validator`	`NONDEFAULT_RAWDATATYPE`	Validator rule that checks if an item uses a different raw data type than specified by the project default.
`static Validator`	`NONDEFAULT_SOFTWARE`	Validator rule that checks if an item uses a different software than specified by the project default.
`static 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).
`static Validator`	`NONMATHCING_ARRAYDESIGN`	Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay.
`static Validator`	`NONUNIQUE_NAME_FOR_TYPE`	Validator rule that checks if two items of the same type has the same name.
`static Validator`	`NONUNIQUE_NAME_GLOBAL`	Validator rule that checks if two items of different type has the same name.
`static Validator`	`NONUNIQUE_TAG`	Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position.
`static Validator`	`PARENT_EXTRACT_MISMATCH`	Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.
`static Validator`	`TAGGED_PARENT`	Validator rule that checks if the parent to a non-tagged extract has a tag.
`private String`	`title`

Constructor Summary

Constructors

Constructor Description

Validator(String id, String title, String description, String failureSummary, Severity defaultSeverity)
Create a new validator.

Method Summary

Modifier and Type	Method	Description
`Severity`	`getDefaultSeverity()`	Get the default severity level.
`String`	`getDescription()`	Get a lengthier description of the validation that takes place
`String`	`getFailureSummary()`	Get a short summary that is displayed when the validation fails
`String`	`getId()`	Get the unique ID of this validator.
`String`	`getTitle()`	Get the title of this validator.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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
- getId
  
  public String getId()
  
  Get the unique ID of this validator.
  
  Specified by:
  
  getId in interface ValidationRuleAction
- getTitle
  
  public String getTitle()
  
  Get the title of this validator.
  
  Specified by:
  
  getTitle in interface ValidationRuleAction
- getDescription
  
  public String getDescription()
  
  Get a lengthier description of the validation that takes place
  
  Specified by:
  
  getDescription in interface ValidationRuleAction
- getFailureSummary
  
  public String getFailureSummary()
  
  Get a short summary that is displayed when the validation fails
  
  Specified by:
  
  getFailureSummary in interface ValidationRuleAction
- getDefaultSeverity
  
  public Severity getDefaultSeverity()
  
  Get the default severity level.
  
  Specified by:
  
  getDefaultSeverity in interface ValidationRuleAction

Class Validator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

MISSING_PROTOCOL

DENIED_PROTOCOL

MISSING_DERIVEDBIOASSAY

DENIED_DERIVEDBIOASSAY

DENIED_PLATFORM

DENIED_FILE

MISSING_FILE

DENIED_DATAFILETYPE

MISSING_SOFTWARE

DENIED_SOFTWARE

MISSING_HARDWARE

DENIED_HARDWARE

MISSING_KIT

DENIED_KIT

MISSING_PHYSICALBIOASSAY

DENIED_PHYSICALBIOASSAY

MISSING_ARRAYSLIDE

DENIED_ARRAYSLIDE

MISSING_EXTRACT

DENIED_EXTRACT

MISSING_SAMPLE

DENIED_SAMPLE

MISSING_BIOSOURCE

DENIED_BIOSOURCE

MISSING_TAG

DENIED_TAG

MISSING_ARRAYDESIGN

DENIED_ARRAYDESIGN

MISSING_ARRAYBATCH

DENIED_ARRAYBATCH

MISSING_FACTORVALUE

MISSING_PARAMETER

MISSING_MIAME_ANNOTATION

DENIED_ANNOTATIONTYPE

MISSING_ANYTOANY

DENIED_ANYTOANY

MISSING_BIOPLATE

DENIED_BIOPLATE

NONDEFAULT_PLATFORM

NONDEFAULT_PROTOCOL

NONDEFAULT_HARDWARE

NONDEFAULT_SOFTWARE

NONDEFAULT_ARRAYDESIGN

NONDEFAULT_RAWDATATYPE

MULTIPLE_ARRAYDESIGNS

NONMATHCING_ARRAYDESIGN

NONMATCHING_SPOTCOUNT

INCORRECT_TAGTYPE

INCORRECT_PROTOCOLTYPE

INCORRECT_SOFTWARETYPE

INCORRECT_HARDWARETYPE

INCORRECT_KITTYPE

INCORRECT_FILETYPE

INCORRECT_BIOSOURCE_TYPE

INCORRECT_SAMPLE_TYPE

INCORRECT_EXTRACT_TYPE

INCORRECT_BIOMATERIAL_TYPE

INCORRECT_PHYSICALBIOASSAY_TYPE

INCORRECT_DERIVEDBIOASSAY_TYPE

INCORRECT_BIOASSAY_POSITION

NONUNIQUE_TAG

DIFFERENT_TAG

TAGGED_PARENT

PARENT_EXTRACT_MISMATCH

NONUNIQUE_NAME_FOR_TYPE

NONUNIQUE_NAME_GLOBAL

CIRCULAR_REFERENCE

ANNOTATION_IS_PARAMETER

ANNOTATION_INVALID_ITEM

ANNOTATION_INVALID_VALUE

ANNOTATION_TOO_MANY_VALUES

ANNOTATION_INHERIT_FROM_NONPARENT

ANNOTATION_CLONED_FROM_UNKNOWNPARENT

ANNOTATION_CLONE_OUTOFSYNC