| java.lang.Object
 org.griphyn.vdl.dbschema.DatabaseSchema
org.griphyn.vdl.dbschema.AnnotationSchema
| AnnotationSchema | | public class AnnotationSchema extends DatabaseSchema implements Advanced,Annotation(Code) | | This class provides basic functionalities to interact with the
backend database, such as insertion, deletion, and search.
While the main database layout for storing definitions is derived
from the "chunk" schema with minor improvements, the database
layout of the annotations is shown in the following figure:
The central five elements that can receive annotations, all depend
on the same sequence generator for their primary key. Their secondary
key references the definition in question, or otherwise qualifies the
element to annotate. Note that logical filenames can be annotated
outside of any definitions.
Grouped along the outer edges, five primary data type tables store
annotations efficiently. The distinction into separate data types is
necessary to enable efficient searches and appropriate operations.
Their primary key is also a foreign key referencing the five central
elements.
author:
Jens-S. Vöckler
author:
Yong Zhao
version:
$Revision: 50 $ |
| Field Summary | |
| final protected static String[] | c_lfn_names
Name of the four parameter tables in human readable format. | | protected Cache | m_cache
A cache for definitions to avoid reloading from the database. | | protected boolean | m_deferDeleteCommit
Communication between saveDefinition and deleteDefinition in
update mode. |
| Method Summary | |
| public ResultSet | backdoor(String query)
A too generic method to search annotation (and anything) in
the database. | | public boolean | containsDefinition(Definition definition)
Search the database for the existence of a definition. | | public boolean | deleteAnnotation(String primary, Object secondary, int kind, String key)
Deletes an annotation with the specified key.
Parameters:
primary - is the primary object specifier for the class. | | public boolean | deleteAnnotationCall(String fqdi, int index, String key)
Deletes a specific key for a call statement. | | public boolean | deleteAnnotationDeclare(String fqdi, String farg, String key)
Deletes a specific key in an annotated formal argument. | | public boolean | deleteAnnotationDerivation(String fqdi, String key)
Deletes a specific key in an annotated derivation. | | public boolean | deleteAnnotationFilename(String filename, String key)
Deletes a specific key in an annotated filename. | | public boolean | deleteAnnotationTransformation(String fqdi, String key)
Deletes a specific key in an annotated transformation. | | public boolean | deleteDefinition(Definition definition)
Delete a specific Definition objects from the database. | | public java.util.List | deleteDefinition(String namespace, String name, String version, int type)
Delete Definition objects from the database. | | public java.util.List | deleteDefinitionEx(String namespace, String name, String version, int type)
Delete one or more definitions from the backend database. | | protected Long | getDefinitionId(Definition d)
Obtains the primary key id for a given definition. | | protected java.util.List | getDefinitionId(String namespace, String name, String version, int type)
Obtains the list of primary key ids for a matching definitions.
This method allows for wildcards in the usual fashion. | | protected java.util.List | getDefinitionIdEx(String namespace, String name, String version, int type)
Obtains the list of primary key ids for a matching definitions.
This method allows for wildcards in the usual fashion. | | public java.util.List | getFQDNList(int type)
Searches the database for a list of fully-qualified names of
the definitions sorted in ascending order. | | public java.util.List | getNamespaceList(int type)
Searches the database for a list of namespaces of the definitions
Sorted in ascending order. | | protected Long | getSpecificDefinitionId(String namespace, String name, String version, int type)
Obtains the primary key id for a given definition. | | public Tuple | loadAnnotation(String primary, Object secondary, int kind, String key)
Retrieves a specific annotation from an annotatable classes with
the specified tuple. | | public java.util.List | loadAnnotation(String primary, Object secondary, int kind)
Retrieves all annotations from an annotatable classes with
the specified tuple. | | public Tuple | loadAnnotationCall(String fqdi, int index, String key)
Obtains the value to a specific key for a call statement. | | public java.util.List | loadAnnotationCall(String fqdi, int index)
Lists all annotations for a call statement.
Parameters:
fqdi - is the FQDI of the transformation
Parameters:
index - is the number of the call to annotate. | | public Tuple | loadAnnotationDeclare(String fqdi, String farg, String key)
Obtains the value to a specific key in an annotated formal argument. | | public java.util.List | loadAnnotationDeclare(String fqdi, String farg)
Lists all annotations for a formal argument. | | public Tuple | loadAnnotationDerivation(String fqdi, String key)
Obtains the value to a specific key in an annotated derivation. | | public java.util.List | loadAnnotationDerivation(String fqdi)
Lists all annotations for a derivation. | | public Tuple | loadAnnotationFilename(String filename, String key)
Obtains the value to a specific key in an annotated filename. | | public java.util.List | loadAnnotationFilename(String filename)
Lists all annotations for a logical filename.
Parameters:
filename - is the logical filename. | | public Tuple | loadAnnotationTransformation(String fqdi, String key)
Obtains the value to a specific key in an annotated transformation. | | public java.util.List | loadAnnotationTransformation(String fqdi)
Lists all annotations for a transformation. | | public Definition | loadDefinition(String namespace, String name, String version, int type)
Loads a single Definition from the backend database into an Java object.
This method does not allow wildcarding!
Parameters:
namespace - namespace, null will be converted into empty string
Parameters:
name - name, null will be converted into empty string
Parameters:
version - version, null will be converted into empty string
Parameters:
type - type of the definition (TR or DV), must not be -1. | | public long | saveAnnotation(String primary, Object secondary, int kind, Tuple annotation, boolean overwrite)
Annotates any of the annotatable classes with the specified tuple.
This is an interface method to the various class-specific methods.
Parameters:
primary - is the primary object specifier for the class. | | public long | saveAnnotationCall(String fqdi, int index, Tuple annotation, boolean overwrite)
Annotates a transformation call with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
index - is the number of the call to annotate.
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. | | public long | saveAnnotationDeclare(String fqdi, String formalname, Tuple annotation, boolean overwrite)
Annotates a transformation argument with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
formalname - is the name of the formal argument to annotoate.
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. | | public long | saveAnnotationDerivation(String fqdi, Tuple annotation, boolean overwrite)
Annotates a derivation with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. | | public long | saveAnnotationFilename(String filename, Tuple annotation, boolean overwrite)
Annotates a logical filename with a tuple.
Parameters:
filename - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. | | public long | saveAnnotationTransformation(String fqdi, Tuple annotation, boolean overwrite)
Annotates a transformation with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. | | public boolean | saveDefinition(Definition definition, boolean overwrite)
Saves a Definition, that is either a Transformation or Derivation,
into the backend database. | | public java.util.List | searchAnnotation(int kind, Object arg, QueryTree tree)
Search for LFNs or Definitions that has certain annotations
Parameters:
kind - defines the kind/class of object annotated.
Parameters:
arg - is used only for TR ARG and TR CALL. | | public ResultSet | searchAnnotation(java.util.List select, String table, java.util.Map where, String order)
A not very generic method to search annotation (and anything) in
the database. | | public java.util.List | searchDefinition(String namespace, String name, String version, int type)
Search the database for definitions by ns::name:version triple
and by type (either Transformation or Derivation). | | public java.util.List | searchDefinitionEx(String namespace, String name, String version, int type)
Search the database for definitions by ns::name:version triple
and by type (either Transformation or Derivation). | | public java.util.List | searchFilename(String lfn, int link)
Searches the database for all derivations that contain a certain LFN.
The linkage is an additional constraint. | | public java.util.List | searchLFN(String lfn, int link)
Searches the database for all LFNs that match a certain pattern.
The linkage is an additional constraint. |
| c_lfn_names | | final protected static String[] c_lfn_names(Code) | | Name of the four parameter tables in human readable format.
|
| m_cache | | protected Cache m_cache(Code) | | A cache for definitions to avoid reloading from the database.
|
| m_deferDeleteCommit | | protected boolean m_deferDeleteCommit(Code) | | Communication between saveDefinition and deleteDefinition in
update mode.
|
| backdoor | | public ResultSet backdoor(String query) throws SQLException(Code) | | A too generic method to search annotation (and anything) in
the database. This method is also responsible for breaking
any no-database-based backends.
WARNING: This is a method for internal use only.
Parameters:
query - is an SQL query statement. something to search for results in.
exception:
SQLException - if something goes wrong with the database. |
| containsDefinition | | public boolean containsDefinition(Definition definition) throws SQLException(Code) | | Search the database for the existence of a definition.
Parameters:
definition - the definition object to search for true, if the definition exists, false if not found |
| deleteAnnotation | | public boolean deleteAnnotation(String primary, Object secondary, int kind, String key) throws SQLException, IllegalArgumentException(Code) | | Deletes an annotation with the specified key.
Parameters:
primary - is the primary object specifier for the class. According to the type, this is either the FQDI, or the filename.
Parameters:
secondary - is a helper argument for annotations to callsand formal arguments, and should be null for all other classes.For calls, the argument must be packed into java.lang.Integer.
Parameters:
kind - defines the kind/class of object to annotate.
Parameters:
key - is the annotation key. true, if the database was modified, false otherwise.
exception:
SQLException - , if something went wrong during databaseaccess. |
| deleteAnnotationCall | | public boolean deleteAnnotationCall(String fqdi, int index, String key) throws SQLException, IllegalArgumentException(Code) | | Deletes a specific key for a call statement.
Parameters:
fqdi - is the FQDI of the transformation
Parameters:
index - is the number of the call to annotate.
Parameters:
key - is the key to search for true, if the database was modified, false otherwise.
See Also: org.griphyn.vdl.classes.Call |
| deleteDefinition | | public java.util.List deleteDefinition(String namespace, String name, String version, int type) throws SQLException(Code) | | Delete Definition objects from the database. This method allows for
wildcards in the usual fashion. Use null for strings as wildcards,
and -1 for the type wildcard. For efficiency reasons, this method
will return an empty list.
Parameters:
namespace - namespace, null to match any namespace
Parameters:
name - name, null to match any name
Parameters:
version - version, null to match any version
Parameters:
type - definition type (TR or DV) a list containing all Definitions that were deleted
See Also: org.griphyn.vdl.classes.Definition.TRANSFORMATION
See Also: org.griphyn.vdl.classes.Definition.DERIVATION
See Also: |
| getDefinitionIdEx | | protected java.util.List getDefinitionIdEx(String namespace, String name, String version, int type) throws SQLException(Code) | | Obtains the list of primary key ids for a matching definitions.
This method allows for wildcards in the usual fashion. Use null for
strings as wildcards, and -1 for the type wildcard. It also allows
special characters '%' and '_' in strings. This method may
return an empty list, but it will not return null. This is an
internal helper function.
Parameters:
namespace - namespace, null to match any namespace
Parameters:
name - name, null to match any name
Parameters:
version - version, null to match any version
Parameters:
type - definition type (TR or DV) a possibly empty list containing all matchingdefinition ids as Longs.
See Also: org.griphyn.vdl.classes.Definition.TRANSFORMATION
See Also: org.griphyn.vdl.classes.Definition.DERIVATION
See Also:
See Also: AnnotationSchema.getDefinitionId(Definition)
See Also: |
| getSpecificDefinitionId | | protected Long getSpecificDefinitionId(String namespace, String name, String version, int type) throws SQLException(Code) | | Obtains the primary key id for a given definition. "Fake" definitions
are NOT permissable. This is an internal helper function.
Parameters:
namespace - is the specific namespace, null will be mapped to ""
Parameters:
name - is the specific name, null will be mapped to ""
Parameters:
version - is the specific version, null will be mapped to ""
Parameters:
type - is the type identifier, -1 is not allowed. the id of the definition, or null if not found.
See Also: AnnotationSchema.getDefinitionId(String,String,String,int) |
| loadAnnotation | | public Tuple loadAnnotation(String primary, Object secondary, int kind, String key) throws SQLException, IllegalArgumentException(Code) | | Retrieves a specific annotation from an annotatable classes with
the specified tuple. This is an interface method to the various
class-specific methods.
Parameters:
primary - is the primary object specifier for the class. According to the type, this is either the FQDI, or the filename.
Parameters:
secondary - is a helper argument for annotations to callsand formal arguments, and should be null for all other classes.For calls, the argument must be packed into java.lang.Integer.
Parameters:
kind - defines the kind/class of object to annotate.
Parameters:
key - is the key to look for. null if not found, otherwise the annotation tuple.
See Also: AnnotationSchema.loadAnnotationTransformation(String,String)
See Also: AnnotationSchema.loadAnnotationDerivation(String,String)
See Also: AnnotationSchema.loadAnnotationCall(String,int,String)
See Also: AnnotationSchema.loadAnnotationDeclare(String,String,String)
See Also: AnnotationSchema.loadAnnotationFilename(String,String) |
| loadAnnotation | | public java.util.List loadAnnotation(String primary, Object secondary, int kind) throws SQLException, IllegalArgumentException(Code) | | Retrieves all annotations from an annotatable classes with
the specified tuple. This is an interface method to the various
class-specific methods.
Parameters:
primary - is the primary object specifier for the class. According to the type, this is either the FQDI, or the filename.
Parameters:
secondary - is a helper argument for annotations to callsand formal arguments, and should be null for all other classes.For calls, the argument must be packed into java.lang.Integer.
Parameters:
kind - defines the kind/class of object to annotate. null if not found, otherwise the annotation tuple.
See Also: AnnotationSchema.loadAnnotationTransformation(String)
See Also: AnnotationSchema.loadAnnotationDerivation(String)
See Also: AnnotationSchema.loadAnnotationCall(String,int)
See Also: AnnotationSchema.loadAnnotationDeclare(String,String)
See Also: AnnotationSchema.loadAnnotationFilename(String) |
| saveAnnotation | | public long saveAnnotation(String primary, Object secondary, int kind, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates any of the annotatable classes with the specified tuple.
This is an interface method to the various class-specific methods.
Parameters:
primary - is the primary object specifier for the class. According to the type, this is either the FQDI, or the filename.
Parameters:
secondary - is a helper argument for annotations to callsand formal arguments, and should be null for all other classes.For calls, the argument must be packed into java.lang.Integer.
Parameters:
kind - defines the kind/class of object to annotate.
Parameters:
annotation - is the value to place into the class.
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: AnnotationSchema.saveAnnotationTransformation(String,Tuple,boolean)
See Also: AnnotationSchema.saveAnnotationDerivation(String,Tuple,boolean)
See Also: AnnotationSchema.saveAnnotationCall(String,int,Tuple,boolean)
See Also: AnnotationSchema.saveAnnotationDeclare(String,String,Tuple,boolean)
See Also: AnnotationSchema.saveAnnotationFilename(String,Tuple,boolean) |
| saveAnnotationCall | | public long saveAnnotationCall(String fqdi, int index, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates a transformation call with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
index - is the number of the call to annotate.
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: org.griphyn.vdl.classes.Call |
| saveAnnotationDeclare | | public long saveAnnotationDeclare(String fqdi, String formalname, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates a transformation argument with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
formalname - is the name of the formal argument to annotoate.
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: org.griphyn.vdl.classes.Declare |
| saveAnnotationDerivation | | public long saveAnnotationDerivation(String fqdi, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates a derivation with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: org.griphyn.vdl.classes.Derivation |
| saveAnnotationFilename | | public long saveAnnotationFilename(String filename, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates a logical filename with a tuple.
Parameters:
filename - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: org.griphyn.vdl.classes.LFN |
| saveAnnotationTransformation | | public long saveAnnotationTransformation(String fqdi, Tuple annotation, boolean overwrite) throws SQLException, IllegalArgumentException(Code) | | Annotates a transformation with a tuple.
Parameters:
fqdi - is the FQDI to annotate
Parameters:
annotation - is the value to place
Parameters:
overwrite - is a predicate on replace or maintain. the insertion id, or -1, if the database was untouched
See Also: org.griphyn.vdl.classes.Transformation |
| saveDefinition | | public boolean saveDefinition(Definition definition, boolean overwrite) throws SQLException(Code) | | Saves a Definition, that is either a Transformation or Derivation,
into the backend database. This method, of course, does not allow
wildcarding. The definition has to be completely specified and
valid.
Please note that updating a definition will remove all the meta-
data that was defined for the definition.
Parameters:
definition - is the new Definition to store.
Parameters:
overwrite - true, if existing defitions will be overwritten bynew ones with the same primary (or secondary) key (-set), or false,if a new definition will be rejected on key matches. true, if the backend database was changed, orfalse, if the definition was not accepted into the backend.
See Also: org.griphyn.vdl.classes.Definition
See Also: org.griphyn.vdl.classes.Transformation
See Also: org.griphyn.vdl.classes.Derivation
See Also: AnnotationSchema.loadDefinition(String,String,String,int) |
| searchAnnotation | | public java.util.List searchAnnotation(int kind, Object arg, QueryTree tree) throws SQLException(Code) | | Search for LFNs or Definitions that has certain annotations
Parameters:
kind - defines the kind/class of object annotated.
Parameters:
arg - is used only for TR ARG and TR CALL. For the formerit is the name of the argument (String), for the latter the position of the call (Integer).
Parameters:
tree - stores the query tree to query the annotation a list of LFNs if search for filenames, otherwise a list ofdefinitions.
exception:
SQLException - if something goes wrong with the database.
See Also: org.griphyn.vdl.annotation.QueryTree |
| searchAnnotation | | public ResultSet searchAnnotation(java.util.List select, String table, java.util.Map where, String order) throws SQLException(Code) | | A not very generic method to search annotation (and anything) in
the database. Selects any rows in one or more colums from one or
more tables restricted by some condition, possibly ordered.
WARNING: This is a method for internal use only.
Parameters:
select - is the ordered set of column names to select, orsimply a one-value list with an asterisk.
Parameters:
table - is the name of the table to select from.
Parameters:
where - is a collection of column names and values they must equal.
Parameters:
order - is an optional ordering string. something to search for results in.
exception:
SQLException - if something goes wrong with the database.
See Also: org.griphyn.vdl.dbdriver.DatabaseDriver.select(java.util.ListStringjava.util.MapString) |
| searchDefinitionEx | | public java.util.List searchDefinitionEx(String namespace, String name, String version, int type) throws SQLException(Code) | | Search the database for definitions by ns::name:version triple
and by type (either Transformation or Derivation). This version
of the search allows for jokers expressed as null value
Parameters:
namespace - namespace, null to match any namespace
Parameters:
name - name, null to match any name
Parameters:
version - version, null to match any version
Parameters:
type - type of definition, see below, or -1 as wildcard a list of Definition items, which may be empty
See Also: org.griphyn.vdl.classes.Definition.TRANSFORMATION
See Also: org.griphyn.vdl.classes.Definition.DERIVATION
See Also: AnnotationSchema.loadDefinition(String,String,String,int) |
| Methods inherited from org.griphyn.vdl.dbschema.DatabaseSchema | public boolean cachingMakesSense()(Code)(Java Doc)
public void close() throws SQLException(Code)(Java Doc)
protected void finalize() throws Throwable(Code)(Java Doc)
public static DatabaseSchema loadSchema(String dbSchemaName, String propertyPrefix, Object[] arguments) throws ClassNotFoundException, IOException, NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException(Code)(Java Doc)
public static DatabaseSchema loadSchema(String propertyPrefix) throws ClassNotFoundException, IOException, NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException(Code)(Java Doc)
protected void longOrNull(PreparedStatement ps, int pos, long l) throws SQLException(Code)(Java Doc)
protected String makeNotNull(String s)(Code)(Java Doc)
protected void stringOrNull(PreparedStatement ps, int pos, String s) throws SQLException(Code)(Java Doc)
|
|
|