public class BioAssaySetUtil
extends java.lang.Object
BioAssaySet
.Constructor and Description |
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BioAssaySetUtil() |
Modifier and Type | Method and Description |
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static Expression |
createJepExpression(DbControl dc,
java.lang.String formula,
DynamicQuery query)
Parse a JEP expression and create a restrictions that is suitable to
be used in a dynamic query.
|
static Restriction |
createJepRestriction(DbControl dc,
java.lang.String formula,
DynamicQuery query)
Parse a JEP expression and create a restrictions that is suitable to
be used in a dynamic query.
|
static java.util.Set<?> |
getAnnotationValues(DbControl dc,
SnapshotManager snapshotManager,
BioAssay bioAssay,
AnnotationType annotationType)
Find the annotation values for a given annotation type on a bioassay.
|
static java.util.Set<java.lang.Object> |
getParentProperties(DbControl dc,
BioAssay bioAssay,
Metadata.PropertyPath<RawBioAssay,?> property)
Find the values of parent properties for a given bioassay.
|
public static java.util.Set<?> getAnnotationValues(DbControl dc, SnapshotManager snapshotManager, BioAssay bioAssay, AnnotationType annotationType)
Since a bioassay may have more than one parent raw bioassay and each annotation may have multiple values it is possible that the set contains multiple values. Each value is only present once regardless of how many times it appears in the annotations.
dc
- The DbControl for database accesssnapshotManager
- A snapshot manager that is used for loading the annotations
from either the database or the file cache (if null, an internal, non-reusable
snapshot manager is used)bioAssay
- The bioassay to get the annotations forannotationType
- The annotation type of the annotationspublic static java.util.Set<java.lang.Object> getParentProperties(DbControl dc, BioAssay bioAssay, Metadata.PropertyPath<RawBioAssay,?> property)
Metadata.PropertyPath
object to find the value of the given property for that raw bioassay.
Since a bioassay may have more than one parent raw bioassay and it is possible that the set contains multiple values. Each value is only present once regardless of how many times it appears among the parents.
Examples of property paths:
dc
- The DbControl for database accessbioAssay
- The bioassay to get the annotations forproperty
- The property to get the value forpublic static Restriction createJepRestriction(DbControl dc, java.lang.String formula, DynamicQuery query)
Jep.getFunctions()
) this method can use additional
functions. The extra functions are defined by the query. See
AbstractSqlQuery.getJepFunctions(DbControl, boolean)
and it's subclasses
for detailed information. Here are some useful functions:
createJepExpression(DbControl,
String, DynamicQuery)
method
dc
- DbControl to use when accessing the database.formula
- The formula to parse. Must not be null.query
- The query where the restriction will be used, it is not
recommended to use the expression in a different query since it may
generate incorrect SQLInvalidDataException
- If any of required parameters are null.BaseException
- If creating the restriction fails.Jep
public static Expression createJepExpression(DbControl dc, java.lang.String formula, DynamicQuery query)
Jep.getFunctions()
) this method can use additional
functions. The extra functions are defined by the query. See
AbstractSqlQuery.getJepFunctions(DbControl, boolean)
and it's subclasses
for detailed information. Here are some useful functions:
DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean)
flag controls this.
ReporterData
in the
specified ReporterList
(numeric or external ID)
ExtraValue
(numeric ID or the external ID of the ExtraValueType
)
dc
- The DbControl to use when accessing the database.formula
- The formula that should be parsed. Must not be null.query
- The query where the expression will be used, it is not
recommended to use the expression in a different query since it may
generate incorrect SQLInvalidDataException
- If any of required parameters are null.BaseException
- If creating the expression fails.Jep