public class Validator extends java.lang.Object implements ValidationRuleAction
The actual validation takes place in the overview generating code.
See implementations of NodeValidator
interface.
Modifier and Type | Field and 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 java.lang.String |
description |
static Validator |
DIFFERENT_TAG
Validator rule that checks if the parent to a tagged extract has
a different tag.
|
private java.lang.String |
failureSummary |
private java.lang.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_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_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 java.lang.String |
title |
Constructor and Description |
---|
Validator(java.lang.String id,
java.lang.String title,
java.lang.String description,
java.lang.String failureSummary,
Severity defaultSeverity)
Create a new validator.
|
Modifier and Type | Method and Description |
---|---|
Severity |
getDefaultSeverity()
Get the default severity level.
|
java.lang.String |
getDescription()
Get a lengthier description of the validation that takes place
|
java.lang.String |
getFailureSummary()
Get a short summary that is displayed when the validation fails
|
java.lang.String |
getId()
Get the unique ID of this validator.
|
java.lang.String |
getTitle()
Get the title of this validator.
|
public static final Validator MISSING_PROTOCOL
public static final Validator DENIED_PROTOCOL
public static final Validator MISSING_DERIVEDBIOASSAY
public static final Validator DENIED_DERIVEDBIOASSAY
public static final Validator DENIED_PLATFORM
public static final Validator DENIED_FILE
public static final Validator DENIED_DATAFILETYPE
public static final Validator MISSING_SOFTWARE
public static final Validator DENIED_SOFTWARE
public static final Validator MISSING_HARDWARE
public static final Validator DENIED_HARDWARE
public static final Validator MISSING_KIT
public static final Validator DENIED_KIT
public static final Validator MISSING_PHYSICALBIOASSAY
public static final Validator DENIED_PHYSICALBIOASSAY
public static final Validator MISSING_ARRAYSLIDE
public static final Validator DENIED_ARRAYSLIDE
public static final Validator MISSING_EXTRACT
public static final Validator DENIED_EXTRACT
public static final Validator MISSING_SAMPLE
public static final Validator DENIED_SAMPLE
public static final Validator MISSING_BIOSOURCE
public static final Validator DENIED_BIOSOURCE
public static final Validator MISSING_TAG
public static final Validator DENIED_TAG
public static final Validator MISSING_ARRAYDESIGN
public static final Validator DENIED_ARRAYDESIGN
public static final Validator MISSING_ARRAYBATCH
public static final Validator DENIED_ARRAYBATCH
public static final Validator MISSING_FACTORVALUE
public static final Validator MISSING_PARAMETER
public static final Validator MISSING_MIAME_ANNOTATION
public static final Validator DENIED_ANNOTATIONTYPE
public static final Validator MISSING_ANYTOANY
public static final Validator DENIED_ANYTOANY
public static final Validator MISSING_BIOPLATE
public static final Validator DENIED_BIOPLATE
public static final Validator NONDEFAULT_PLATFORM
public static final Validator NONDEFAULT_PROTOCOL
public static final Validator NONDEFAULT_HARDWARE
public static final Validator NONDEFAULT_SOFTWARE
public static final Validator NONDEFAULT_ARRAYDESIGN
public static final Validator NONDEFAULT_RAWDATATYPE
public static final Validator MULTIPLE_ARRAYDESIGNS
public static final Validator NONMATHCING_ARRAYDESIGN
public static final Validator NONMATCHING_SPOTCOUNT
public static final Validator INCORRECT_TAGTYPE
public static final Validator INCORRECT_PROTOCOLTYPE
public static final Validator INCORRECT_SOFTWARETYPE
public static final Validator INCORRECT_HARDWARETYPE
public static final Validator INCORRECT_KITTYPE
public static final Validator INCORRECT_BIOSOURCE_TYPE
public static final Validator INCORRECT_SAMPLE_TYPE
public static final Validator INCORRECT_EXTRACT_TYPE
public static final Validator INCORRECT_BIOMATERIAL_TYPE
public static final Validator INCORRECT_PHYSICALBIOASSAY_TYPE
public static final Validator INCORRECT_DERIVEDBIOASSAY_TYPE
public static final Validator INCORRECT_BIOASSAY_POSITION
public static final Validator NONUNIQUE_TAG
public static final Validator DIFFERENT_TAG
public static final Validator TAGGED_PARENT
public static final Validator PARENT_EXTRACT_MISMATCH
public static final Validator NONUNIQUE_NAME_FOR_TYPE
public static final Validator NONUNIQUE_NAME_GLOBAL
public static final Validator CIRCULAR_REFERENCE
public static final Validator ANNOTATION_IS_PARAMETER
public static final Validator ANNOTATION_INVALID_ITEM
public static final Validator ANNOTATION_INVALID_VALUE
public static final Validator ANNOTATION_TOO_MANY_VALUES
public static final Validator ANNOTATION_INHERIT_FROM_NONPARENT
public static final Validator ANNOTATION_CLONED_FROM_UNKNOWNPARENT
public static final Validator ANNOTATION_CLONE_OUTOFSYNC
public static final Validator ANNOTATION_INHERIT_FROM_DENIEDPARENT
public static final Validator ANNOTATION_INHERIT_MULTIPLE
public static final Validator DATAFILE_INVALID_ITEM
public static final Validator DATAFILE_NOTVALIDATED
public static final Validator DATAFILE_INVALID
public static final Validator MISSING_DATAFILE
public static final Validator DATAFILE_NOTPLATFORM
public static final Validator DATAFILE_TOOMANYFILES
public static final Validator KIT_USED_AFTER_EXPIRATIONDATE
private java.lang.String id
private java.lang.String title
private java.lang.String description
private java.lang.String failureSummary
private Severity defaultSeverity
public Validator(java.lang.String id, java.lang.String title, java.lang.String description, java.lang.String failureSummary, Severity defaultSeverity)
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 validationpublic java.lang.String getId()
getId
in interface ValidationRuleAction
public java.lang.String getTitle()
getTitle
in interface ValidationRuleAction
public java.lang.String getDescription()
getDescription
in interface ValidationRuleAction
public java.lang.String getFailureSummary()
getFailureSummary
in interface ValidationRuleAction
public Severity getDefaultSeverity()
getDefaultSeverity
in interface ValidationRuleAction