Package net.sf.basedb.util.overview
Class Validator
java.lang.Object
net.sf.basedb.util.overview.Validator
- All Implemented Interfaces:
Action
,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
Modifier and TypeFieldDescriptionstatic final Validator
Validator rule that checks if a cloned annotation value is in sync with the source annotation.static final Validator
Validator rule that checks if a cloned annotation value has lost the reference to the parent item.static final Validator
Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.static final Validator
Validator rule that checks if an inherited annotation value is inherited from a parent item.static final Validator
Validator rule that checks if two or more inherited annotations have the same annotation type.static final Validator
Validator rule that checks if an annotation is not valid for the current item type.static final Validator
Validator rule that checks if an annotation value is invalid according to annotation type specification.static final Validator
Validator rule that checks if an annotation is a protocol parameter.static final Validator
Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow.static final Validator
Validator rule that checks for circular references among pooled items.static final Validator
Validator rule that checks if a data file is valid.static final Validator
Validator rule that checks if a data file can be used on the current item type.static final Validator
Validator rule that checks if a file is registered with a platform/item subtype or not.static final Validator
Validator rule that checks if a data file has been validated or not.static final Validator
Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files.private Severity
static final Validator
Validator rule that checks for denied access to an annotation type.static final Validator
Validator rule that checks for denied access the referenced item in an any-to-any link.static final Validator
Validator rule that checks for denied access to an array batch.static final Validator
Validator rule that checks for denied access to an array design.static final Validator
Validator rule that checks for denied access to array slides.static final Validator
Validator rule that checks for denied access to a bioplate.static final Validator
Validator rule that checks for denied access to biosource.static final Validator
Validator rule that checks for denied access to data file types.static final Validator
Validator rule that checks for denied access to derived bioassay.static final Validator
Validator rule that checks for denied access to extracts.static final Validator
Validator rule that checks for denied access to (data) files.static final Validator
Validator rule that checks for denied access to hardware.static final Validator
Validator rule that checks for denied access to kit.static final Validator
Validator rule that checks for denied access to physical bioassay.static final Validator
Validator rule that checks for denied access to platform.static final Validator
Validator rule that checks for denied access to protocols.static final Validator
Validator rule that checks for denied access to samples.static final Validator
Validator rule that checks for denied access to software.static final Validator
Validator rule that checks for denied access to tags.private String
static final Validator
Validator rule that checks if the parent to a tagged extract has a different tag.private String
private String
static final Validator
Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay.static final Validator
Validator that checks if the biomaterial on a bioplate is of the correct item type.static final Validator
Validator that checks if the parent biosource of a sample has the expected subtype.static final Validator
Validator that checks if a derived bioassay has the expected subtype.static final Validator
Validator that checks if the parent extract of a extract/bioassay has the expected subtype.static final Validator
Validator rule that checks if the file attached to an item has a correct file type.static final Validator
Validator rule that checks if the hardware attached to an item has a correct hardware type.static final Validator
Validator rule that checks if the kit attached to an item has a correct kit type.static final Validator
Validator that checks if a physical bioassay has the expected subtype.static final Validator
Validator rule that checks if the protocol attached to an item has a correct protocol type.static final Validator
Validator that checks if the parent sample of a sample/extract has the expected subtype.static final Validator
Validator rule that checks if the software attached to an item has a correct software type.static final Validator
Validator rule that checks if the tag attached to an extract has a correct subtype.static final Validator
Validator rule that checks if a kit has been used after it's exiration date.static final Validator
Validator rule that checks for a missing reference in an any-to-any link.static final Validator
Validator rule that checks for missing array batch.static final Validator
Validator rule that checks for missing array design.static final Validator
Validator rule that checks for missing array slide.static final Validator
Validator rule that checks for missing bioplate location.static final Validator
Validator rule that checks for missing biosource.static final Validator
Validator rule that checks if all files required by the platform are present or not.static final Validator
Validator rule that checks for missing parent derived bioassay.static final Validator
Validator rule that checks for missing extract.static final Validator
Validator rule that checks for missing experimental factor value.static final Validator
Validator rule that checks for denied access to (data) files.static final Validator
Validator rule that checks for missing hardware.static final Validator
Validator rule that checks for missing kits.static final Validator
Validator rule that checks for missing "Required for MIAME" annotation.static final Validator
Validator rule that checks for missing protocol parameter values.static final Validator
Validator rule that checks for missing physical bioassay.static final Validator
Validator rule that checks for missing protocols.static final Validator
Validator rule that checks for missing sample.static final Validator
Validator rule that checks for missing software.static final Validator
Validator rule that checks for missing tag.static final Validator
Validator rule that checks if all raw bioassays in an experiment uses the same array design.static final Validator
Validator rule that checks if an item uses a different array design than specified by the project default.static final Validator
Validator rule that checks if an item uses a different hardware than specified by the project default.static final Validator
Validator rule that checks if an item uses a different platform / variant than specified by the project default.static final Validator
Validator rule that checks if an item uses a different protocol than specified by the project default.static final Validator
Validator rule that checks if an item uses a different raw data type than specified by the project default.static final Validator
Validator rule that checks if an item uses a different software than specified by the project default.static final Validator
Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold).static final Validator
Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay.static final Validator
Validator rule that checks if two items of the same type has the same name.static final Validator
Validator rule that checks if two items of different type has the same name.static final Validator
Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position.static final Validator
Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.static final Validator
Validator rule that checks if the parent to a non-tagged extract has a tag.private String
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Constructor Summary
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Method Summary
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Field Details
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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
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DENIED_KIT
Validator rule that checks for denied access to kit. Default severity level is WARNING.- Since:
- 3.7
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MISSING_PHYSICALBIOASSAY
Validator rule that checks for missing physical bioassay. Default severity level is WARNING.- Since:
- 3.0
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DENIED_PHYSICALBIOASSAY
Validator rule that checks for denied access to physical bioassay. Default severity level is WARNING.- Since:
- 3.0
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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
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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
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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
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MISSING_BIOPLATE
Validator rule that checks for missing bioplate location. Default severity level is IGNORE.- Since:
- 3.2
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DENIED_BIOPLATE
Validator rule that checks for denied access to a bioplate. Default severity level is WARNING.- Since:
- 3.2
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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
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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
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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
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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
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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
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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
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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
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INCORRECT_PHYSICALBIOASSAY_TYPE
Validator that checks if a physical bioassay has the expected subtype. Default severity level is WARNING.- Since:
- 3.0
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INCORRECT_DERIVEDBIOASSAY_TYPE
Validator that checks if a derived bioassay has the expected subtype. Default severity level is WARNING.- Since:
- 3.0
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
-
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
-
getDefaultSeverity
Get the default severity level.- Specified by:
getDefaultSeverity
in interfaceValidationRuleAction
-