Package net.sf.basedb.util.overview
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 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
-
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 placeString
getFailureSummary()
Get a short summary that is displayed when the validation failsString
getId()
Get the unique ID of this validator.String
getTitle()
Get the title of this validator.
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Field Details
-
MISSING_PROTOCOL
Validator rule that checks for missing protocols. Default severity level is WARNING. -
DENIED_PROTOCOL
Validator rule that checks for denied access to protocols. Default severity level is WARNING. -
MISSING_DERIVEDBIOASSAY
Validator rule that checks for missing parent derived bioassay. Default severity level is WARNING.- Since:
- 3.0
-
DENIED_DERIVEDBIOASSAY
Validator rule that checks for denied access to derived bioassay. Default severity level is WARNING.- Since:
- 3.0
-
DENIED_PLATFORM
Validator rule that checks for denied access to platform. Default severity level is WARNING. -
DENIED_FILE
Validator rule that checks for denied access to (data) files. Default severity level is WARNING. -
MISSING_FILE
Validator rule that checks for denied access to (data) files. Default severity level is WARNING.- Since:
- 3.17
-
DENIED_DATAFILETYPE
Validator rule that checks for denied access to data file types. Default severity level is WARNING. -
MISSING_SOFTWARE
Validator rule that checks for missing software. Default severity level is WARNING. -
DENIED_SOFTWARE
Validator rule that checks for denied access to software. Default severity level is WARNING. -
MISSING_HARDWARE
Validator rule that checks for missing hardware. Default severity level is WARNING. -
DENIED_HARDWARE
Validator rule that checks for denied access to hardware. Default severity level is WARNING. -
MISSING_KIT
Validator rule that checks for missing kits. Default severity level is WARNING.- Since:
- 3.7
-
DENIED_KIT
Validator rule that checks for denied access to kit. Default severity level is WARNING.- Since:
- 3.7
-
MISSING_PHYSICALBIOASSAY
Validator rule that checks for missing physical bioassay. Default severity level is WARNING.- Since:
- 3.0
-
DENIED_PHYSICALBIOASSAY
Validator rule that checks for denied access to physical bioassay. Default severity level is WARNING.- Since:
- 3.0
-
MISSING_ARRAYSLIDE
Validator rule that checks for missing array slide. Default severity level is WARNING. -
DENIED_ARRAYSLIDE
Validator rule that checks for denied access to array slides. Default severity level is WARNING. -
MISSING_EXTRACT
Validator rule that checks for missing extract. Default severity level is WARNING. -
DENIED_EXTRACT
Validator rule that checks for denied access to extracts. Default severity level is WARNING. -
MISSING_SAMPLE
Validator rule that checks for missing sample. Default severity level is WARNING. -
DENIED_SAMPLE
Validator rule that checks for denied access to samples. Default severity level is WARNING. -
MISSING_BIOSOURCE
Validator rule that checks for missing biosource. Default severity level is WARNING. -
DENIED_BIOSOURCE
Validator rule that checks for denied access to biosource. Default severity level is WARNING. -
MISSING_TAG
Validator rule that checks for missing tag. Default severity level is WARNING. -
DENIED_TAG
Validator rule that checks for denied access to tags. Default severity level is WARNING.- Since:
- 3.0
-
MISSING_ARRAYDESIGN
Validator rule that checks for missing array design. Default severity level is WARNING. -
DENIED_ARRAYDESIGN
Validator rule that checks for denied access to an array design. Default severity level is WARNING. -
MISSING_ARRAYBATCH
Validator rule that checks for missing array batch. Default severity level is WARNING. -
DENIED_ARRAYBATCH
Validator rule that checks for denied access to an array batch. Default severity level is WARNING. -
MISSING_FACTORVALUE
Validator rule that checks for missing experimental factor value. Default severity level is ERROR. -
MISSING_PARAMETER
Validator rule that checks for missing protocol parameter values. Default severity level is ERROR. -
MISSING_MIAME_ANNOTATION
Validator rule that checks for missing "Required for MIAME" annotation. Default severity level is ERROR. -
DENIED_ANNOTATIONTYPE
Validator rule that checks for denied access to an annotation type. Default severity level is WARNING. -
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
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
Validator rule that checks for missing bioplate location. Default severity level is IGNORE.- Since:
- 3.2
-
DENIED_BIOPLATE
Validator rule that checks for denied access to a bioplate. Default severity level is WARNING.- Since:
- 3.2
-
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
Validator rule that checks if an item uses a different protocol than specified by the project default. Default severity level is WARNING. -
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
Validator rule that checks if an item uses a different software than specified by the project default. Default severity level is WARNING. -
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
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
Validator rule that checks if all raw bioassays in an experiment uses the same array design. Default severity level is WARNING. -
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
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
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
Validator rule that checks if the protocol attached to an item has a correct protocol type. Default severity level is WARNING. -
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
Validator rule that checks if the hardware attached to an item has a correct hardware type. Default severity level is WARNING. -
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
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
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
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
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
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
Validator that checks if a physical bioassay has the expected subtype. Default severity level is WARNING.- Since:
- 3.0
-
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
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
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
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
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
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
Validator rule that checks if two items of the same type has the same name. Default severity level is ERROR. -
NONUNIQUE_NAME_GLOBAL
Validator rule that checks if two items of different type has the same name. Default severity level is IGNORE. -
CIRCULAR_REFERENCE
Validator rule that checks for circular references among pooled items. Default severity level is ERROR. -
ANNOTATION_IS_PARAMETER
Validator rule that checks if an annotation is a protocol parameter. Default severity level is WARNING. -
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
Validator rule that checks if an annotation value is invalid according to annotation type specification. Default severity level is ERROR. -
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
Validator rule that checks if an inherited annotation value is inherited from a parent item. Default severity level is ERROR. -
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
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
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
Validator rule that checks if two or more inherited annotations have the same annotation type. Default severity level is ERROR. -
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
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
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
Validator rule that checks if all files required by the platform are present or not. Default severity level is ERROR. -
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
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
Validator rule that checks if a kit has been used after it's exiration date. Default severity level is WARNING.- Since:
- 3.7
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id
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title
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description
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failureSummary
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defaultSeverity
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Constructor Details
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Validator
public Validator(String id, String title, String description, String failureSummary, Severity defaultSeverity)Create a new validator.- Parameters:
id
- A unique ID among all validatorstitle
- The title for the validation ruledescription
- A lengthier description of the validation that takes placefailureSummary
- A short summary that is displayed when the validation failsdefaultSeverity
- The default severity level of the validation
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-
Method Details
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getId
Get the unique ID of this validator.- Specified by:
getId
in interfaceValidationRuleAction
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getTitle
Get the title of this validator.- Specified by:
getTitle
in interfaceValidationRuleAction
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getDescription
Get a lengthier description of the validation that takes place- Specified by:
getDescription
in interfaceValidationRuleAction
-
getFailureSummary
Get a short summary that is displayed when the validation fails- Specified by:
getFailureSummary
in interfaceValidationRuleAction
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getDefaultSeverity
Get the default severity level.- Specified by:
getDefaultSeverity
in interfaceValidationRuleAction
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