net.sf.basedb.util.overview
Class Validator

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

public class Validator
extends Object

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: 2010-11-22 09:02:13 +0100 (Mon, 22 Nov 2010) $

Field Summary

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	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 all files required by the platform are present or not.
static Validator	DATAFILE_NOTVALIDATED Validator rule that checks if a data file has been validated or not.
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_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_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_HYBRIDIZATION Validator rule that checks for denied access to hybridization.
static Validator	DENIED_LABEL Validator rule that checks for denied access to labels.
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_SCAN Validator rule that checks for denied access to scans.
static Validator	DENIED_SOFTWARE Validator rule that checks for denied access to software.
private String	description
static Validator	DIFFERENT_LABEL Validator rule that checks if a parent to a pooled labeled extract has the same lebel.
static Validator	DUPLICATE_ARRAY_NUM Validator rule that checks if the same sub-array index is used on more than one raw bioassay from the same scan.
private String	failureSummary
private String	id
static Validator	INCORRECT_ARRAY_NUM Validator rule that checks if the sub-array index on a raw bioassay or labeled extract is between 1 and the number of sub-arrays on the hybridization.
static Validator	INCORRECT_HARDWARETYPE Validator rule that checks if the hardware attached to an item has a correct hardware type.
static Validator	INCORRECT_NUM_LABELEDEXTRACTS Validator rule that checks if the number of labeled extracts attached to a hybridization matches the number of channels in the experiment.
static Validator	INCORRECT_PROTOCOLTYPE Validator rule that checks if the protocol attached to an item has a correct protocol type.
static Validator	INCORRECT_SOFTWARETYPE Validator rule that checks if the software attached to an item has a correct software type.
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_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_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_HYBRIDIZATION Validator rule that checks for missing hybridization.
static Validator	MISSING_LABELED_EXTRACT Validator rule that checks for missing labeled extract.
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_PROTOCOL Validator rule that checks for missing protocols.
static Validator	MISSING_SAMPLE Validator rule that checks for missing sample.
static Validator	MISSING_SCAN Validator rule that checks for missing scan.
static Validator	MISSING_SOFTWARE Validator rule that checks for missing software.
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 hybridization.
static Validator	NONUNIQUE_LABEL Validator rule that checks if a hybridization has more than one labeled extract with the same label.
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.
private String	title

Constructor Summary

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

Method Summary

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 Detail

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_SCAN

public static final Validator MISSING_SCAN

Validator rule that checks for missing scan. Default severity level is WARNING.

DENIED_SCAN

public static final Validator DENIED_SCAN

Validator rule that checks for denied access to scans. Default severity level is WARNING.

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.

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_HYBRIDIZATION

public static final Validator MISSING_HYBRIDIZATION

Validator rule that checks for missing hybridization. Default severity level is WARNING.

DENIED_HYBRIDIZATION

public static final Validator DENIED_HYBRIDIZATION

Validator rule that checks for denied access to hybridization. Default severity level is WARNING.

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_LABELED_EXTRACT

public static final Validator MISSING_LABELED_EXTRACT

Validator rule that checks for missing labeled extract. 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.

DENIED_LABEL

public static final Validator DENIED_LABEL

Validator rule that checks for denied access to labels. Default severity level is WARNING.

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

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 hybridization. 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_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_ARRAY_NUM

public static final Validator INCORRECT_ARRAY_NUM

Validator rule that checks if the sub-array index on a raw bioassay or labeled extract is between 1 and the number of sub-arrays on the hybridization. Default severity level is WARNING.

DUPLICATE_ARRAY_NUM

public static final Validator DUPLICATE_ARRAY_NUM

Validator rule that checks if the same sub-array index is used on more than one raw bioassay from the same scan. Default severity level is WARNING.

INCORRECT_NUM_LABELEDEXTRACTS

public static final Validator INCORRECT_NUM_LABELEDEXTRACTS

Validator rule that checks if the number of labeled extracts attached to a hybridization matches the number of channels in the experiment. Default severity level is ERROR.

NONUNIQUE_LABEL

public static final Validator NONUNIQUE_LABEL

Validator rule that checks if a hybridization has more than one labeled extract with the same label. Default severity level is WARNING.

DIFFERENT_LABEL

public static final Validator DIFFERENT_LABEL

Validator rule that checks if a parent to a pooled labeled extract has the same lebel. Default severity level is WARNING.

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_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_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 all files required by the platform are present or not. Default severity level is WARNING.

id

private String id

title

private String title

description

private String description

failureSummary

private String failureSummary

defaultSeverity

private Severity defaultSeverity

Constructor Detail

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 Detail

getId

public String getId()

Get the unique ID of this validator.

getTitle

public String getTitle()

Get the title of this validator.

getDescription

public String getDescription()

Get a lengthier description of the validation that takes place

getFailureSummary

public String getFailureSummary()

Get a short summary that is displayed when the validation fails

getDefaultSeverity

public Severity getDefaultSeverity()

Get the default severity level.