Package edu.isi.pegasus.planner.catalog.replica.impl

Class JDBCRC

  • All Implemented Interfaces:
    Catalog, ReplicaCatalog
    public class JDBCRC
extends java.lang.Object
implements ReplicaCatalog
    This class implements a replica catalog on top of a simple table in a JDBC database. This enables a variety of replica catalog implementations in a transactionally safe, concurrent environment. The table must be defined using the statements appropriate for your database - they are part of the setup in $PEGASUS_HOME/sql/. If you chose to use an unsupported database, please check, if your database either supports sequence number, or if it supports auto increment columns. If your database supports sequences (e.g. PostGreSQL), you can use a setup similar to the following (for Oracle, the autoinc can be implemented via a trigger). 
     create sequence rc_lfn_id;

 create table rc_lfn (
   id      bigint default nextval('rc_lfn_id'::text),
   lfn     varchar(255) not null,
   pfn     varchar(255) not null,
   site    varchar(245),

   constraint pk_rc_lfn primary key(id),
   constraint sk_rc_lfn unique(lfn,pfn,site)
 );

 create index idx_rc_lfn on rc_lfn(lfn);

 create table rc_attr (
   id      bigint,
   name    varchar(64) not null,
   value   varchar(255) not null,

   constraint pk_rc_attr primary key(id,name),
   constraint fk_rc_attr foreign key(id) references rc_lfn(id) on delete cascade
 );

 create index idx_rc_attr on rc_attr(name);
    In case of databases that do not support sequences (e.g. MySQL), do not specify the create sequence, and use an auto-increment column for the primary key instead, e.g.: 
     create table rc_lfn (
   id      bigint default null auto_increment,
   lfn     varchar(255) not null,
   pfn     varchar(255) not null,
   site    varchar(245),

   constraint pk_rc_lfn primary key(id),
   constraint sk_rc_lfn unique(lfn,pfn,site)
 );

 create index idx_rc_lfn on rc_lfn(lfn);

 create table rc_attr (
   id      bigint,
   name    varchar(64) not null,
   value   varchar(255) not null,

   constraint pk_rc_attr primary key(id,name),
   constraint fk_rc_attr foreign key id references rc_lfn(id) on delete cascade
 );

 create index idx_rc_attr on rc_attr(name);
    The site attribute should be specified whenever possible. For the shell planner, it will always be of value "local".
    Version:
    $Revision$
    Author:
    Jens-S. Vöckler, Yong Zhao

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private static java.lang.String c_error
      This message is sent whenever one of the member function is executed which relies on an established database context.
      private boolean m_autoinc
      Remembers if obtaining generated keys will work or not.
      protected java.sql.Connection mConnection
      Maintains the connection to the database over the lifetime of this instance.
      private static java.lang.String[] mCStatements
      The statement to prepare to slurp attributes.
      protected LogManager mLogger
      The handle to the logging object.
      protected java.sql.PreparedStatement[] mStatements
      Maintains an essential set of prepared statement, ready to use.

    • Constructor Summary

      Constructors 
      Constructor Description
      JDBCRC()
      Default empty constructor creates an object that is not yet connected to any database.
      JDBCRC​(java.lang.String jdbc, java.lang.String url, java.lang.String username, java.lang.String password)
      Convenience c'tor: Establishes the connection to the replica catalog database.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private java.lang.String addItem​(java.lang.Object value, java.lang.String obj, boolean where)
      Helper function to assemble various pieces.
      private java.util.Map attributes​(java.lang.String id, java.lang.String handle)
      Slurps all attributes from related to a mapping into a map.
      int clear()
      Removes everything.
      void close()
      Explicitely free resources before the garbage collection hits.
      void connect​(java.lang.String url, java.lang.String username, java.lang.String password)
      Connects to the database.
      boolean connect​(java.util.Properties props)
      Establishes a connection to the database from the properties.
      int delete​(java.lang.String lfn, ReplicaCatalogEntry tuple)
      Deletes a very specific mapping from the replica catalog.
      int delete​(java.lang.String lfn, java.lang.String pfn)
      Deletes a specific mapping from the replica catalog.
      int delete​(java.lang.String lfn, java.lang.String name, java.lang.Object value)
      Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
      int delete​(java.util.Map x, boolean matchAttributes)
      Deletes multiple mappings into the replica catalog.
      int deleteByResource​(java.lang.String lfn, java.lang.String handle)
      Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
      protected java.sql.PreparedStatement getStatement​(int i)
      Singleton manager for prepared statements.
      int insert​(java.lang.String lfn, ReplicaCatalogEntry tuple)
      Inserts a new mapping into the replica catalog.
      int insert​(java.lang.String lfn, java.lang.String pfn, java.lang.String handle)
      Inserts a new mapping into the replica catalog.
      int insert​(java.util.Map x)
      Inserts multiple mappings into the replica catalog.
      boolean isClosed()
      Predicate to check, if the connection with the catalog's implementation is still active.
      java.util.Set list()
      Lists all logical filenames in the catalog.
      java.util.Set list​(java.lang.String constraint)
      Lists a subset of all logical filenames in the catalog.
      java.util.Collection lookup​(java.lang.String lfn)
      Retrieves all entries for a given LFN from the replica catalog.
      java.lang.String lookup​(java.lang.String lfn, java.lang.String handle)
      Retrieves the entry for a given filename and site handle from the replica catalog.
      java.util.Map lookup​(java.util.Map constraints)
      Retrieves multiple entries for a given logical filename, up to the complete catalog.
      java.util.Map lookup​(java.util.Set lfns)
      Retrieves multiple entries for a given logical filename, up to the complete catalog.
      java.util.Map lookup​(java.util.Set lfns, java.lang.String handle)
      Retrieves multiple entries for a given logical filename, up to the complete catalog.
      java.util.Set lookupNoAttributes​(java.lang.String lfn)
      Retrieves all entries for a given LFN from the replica catalog.
      java.util.Map lookupNoAttributes​(java.util.Set lfns)
      Retrieves multiple entries for a given logical filename, up to the complete catalog.
      java.util.Map lookupNoAttributes​(java.util.Set lfns, java.lang.String handle)
      Retrieves multiple entries for a given logical filename, up to the complete catalog.
      protected java.lang.String quote​(java.lang.String s)
      Quotes a string that may contain special SQL characters.
      int remove​(java.lang.String lfn)
      Removes all mappings for an LFN from the replica catalog.
      int remove​(java.util.Set lfns)
      Removes all mappings for a set of LFNs.
      int removeByAttribute​(java.lang.String handle)
      Removes all entries associated with a particular resource handle.
      int removeByAttribute​(java.lang.String name, java.lang.Object value)
      Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • c_error

        private static final java.lang.String c_error
        This message is sent whenever one of the member function is executed which relies on an established database context.
        See Also:
        Constant Field Values

      • mConnection

        protected java.sql.Connection mConnection
        Maintains the connection to the database over the lifetime of this instance.

      • mStatements

        protected java.sql.PreparedStatement[] mStatements
        Maintains an essential set of prepared statement, ready to use.

      • mLogger

        protected LogManager mLogger
        The handle to the logging object.

      • mCStatements

        private static final java.lang.String[] mCStatements
        The statement to prepare to slurp attributes.

      • m_autoinc

        private boolean m_autoinc
        Remembers if obtaining generated keys will work or not.

    • Constructor Detail

      • JDBCRC

        public JDBCRC​(java.lang.String jdbc,
              java.lang.String url,
              java.lang.String username,
              java.lang.String password)
       throws java.lang.LinkageError,
              java.lang.ExceptionInInitializerError,
              java.lang.ClassNotFoundException,
              java.sql.SQLException
        Convenience c'tor: Establishes the connection to the replica catalog database. The usual suspects for the class name include: 
         org.postgresql.Driver
 com.mysql.jdbc.Driver
 com.microsoft.jdbc.sqlserver.SQLServerDriver
 SQLite.JDBCDriver
 sun.jdbc.odbc.JdbcOdbcDriver
        Parameters:
        jdbc - is a string containing the full name of the java class that must be dynamically loaded. This is usually an external jar file which contains the Java database driver.
        url - is the database driving URL. This string is database specific, and tell the JDBC driver, at which host and port the database listens, permits additional arguments, and selects the database inside the rDBMS to connect to. Please refer to your JDBC driver documentation for the format and permitted values.
        username - is the database user account name to connect with.
        password - is the database account password to use.
        Throws:
        java.lang.LinkageError - if linking the dynamically loaded driver fails. This is a run-time error, and does not need to be caught.
        java.lang.ExceptionInInitializerError - if the initialization function of the driver's instantiation threw an exception itself. This is a run-time error, and does not need to be caught.
        java.lang.ClassNotFoundException - if the class in your jdbc parameter cannot be found in your given CLASSPATH environment. Callers must catch this exception.
        java.sql.SQLException - if something goes awry with the database. Callers must catch this exception.

      • JDBCRC

        public JDBCRC()
        Default empty constructor creates an object that is not yet connected to any database. You must use support methods to connect before this instance becomes usable.
        See Also:
        connect( String, String, String )

    • Method Detail

      • connect

        public void connect​(java.lang.String url,
                    java.lang.String username,
                    java.lang.String password)
             throws java.sql.SQLException
        Connects to the database. This is effectively an accessor to initialize the internal connection instance variable. Warning! You must call Class.forName( String ) yourself to load the database JDBC driver jar!
        Parameters:
        url - is the database driving URL. This string is database specific, and tell the JDBC driver, at which host and port the database listens, permits additional arguments, and selects the database inside the rDBMS to connect to. Please refer to your JDBC driver documentation for the format and permitted values.
        username - is the database user account name to connect with.
        password - is the database account password to use.
        Throws:
        java.sql.SQLException - if something goes awry with the database. Callers must catch this exception.
        See Also:
        JDBCRC( String, String, String, String ), DriverManager.getConnection( String, String, String )

      • connect

        public boolean connect​(java.util.Properties props)
        Establishes a connection to the database from the properties. You can specify a driver property to contain the class name of the JDBC driver for your database. This property will be removed before attempting to connect. You must speficy a url property to describe the connection. It will be removed before attempting to connect.
        Specified by:
        connect in interface Catalog
        Parameters:
        props - is the property table with sufficient settings to establish a link with the database. The minimum key required key is "url", and possibly "driver". Any other keys depend on the database driver.
        Returns:
        true if connected, false if failed to connect.
        Throws:
        java.lang.Error - subclasses for runtime errors in the class loader.
        See Also:
        DriverManager.getConnection( String, Properties )

      • close

        public void close()
        Explicitely free resources before the garbage collection hits.
        Specified by:
        close in interface Catalog

      • isClosed

        public boolean isClosed()
        Predicate to check, if the connection with the catalog's implementation is still active. This helps determining, if it makes sense to call close().
        Specified by:
        isClosed in interface Catalog
        Returns:
        true, if the implementation is disassociated, false otherwise.
        See Also:
        close()

      • quote

        protected java.lang.String quote​(java.lang.String s)
        Quotes a string that may contain special SQL characters.
        Parameters:
        s - is the raw string.
        Returns:
        the quoted string, which may be just the input string.

      • getStatement

        protected java.sql.PreparedStatement getStatement​(int i)
                                           throws java.sql.SQLException
        Singleton manager for prepared statements. This instruction checks that a prepared statement is ready to use, and will create an instance of the prepared statement, if it was unused previously.
        Parameters:
        i - is the index which prepared statement to check.
        Returns:
        a handle to the prepared statement.
        Throws:
        java.sql.SQLException

      • lookup

        public java.lang.String lookup​(java.lang.String lfn,
                               java.lang.String handle)
        Retrieves the entry for a given filename and site handle from the replica catalog.
        Specified by:
        lookup in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to obtain information for.
        handle - is the resource handle to obtain entries for.
        Returns:
        the (first) matching physical filename, or null if no match was found.

      • attributes

        private java.util.Map attributes​(java.lang.String id,
                                 java.lang.String handle)
                          throws java.sql.SQLException
        Slurps all attributes from related to a mapping into a map.
        Parameters:
        id - is the reference id to slurp from as string. Especially Postgres's indexing mechanism goes from tables scans to btrees, if the numeric key is represented as a string. Strings should be safe for other databases, too.
        Returns:
        a Map with the attributes, which may be empty.
        Throws:
        java.sql.SQLException

      • lookup

        public java.util.Collection lookup​(java.lang.String lfn)
        Retrieves all entries for a given LFN from the replica catalog. Each entry in the result set is a tuple of a PFN and all its attributes.
        Specified by:
        lookup in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to obtain information for.
        Returns:
        a collection of replica catalog entries
        See Also:
        ReplicaCatalogEntry

      • lookupNoAttributes

        public java.util.Set lookupNoAttributes​(java.lang.String lfn)
        Retrieves all entries for a given LFN from the replica catalog. Each entry in the result set is just a PFN string. Duplicates are reduced through the set paradigm.
        Specified by:
        lookupNoAttributes in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to obtain information for.
        Returns:
        a set of PFN strings

      • lookup

        public java.util.Map lookup​(java.util.Set lfns)
        Retrieves multiple entries for a given logical filename, up to the complete catalog. Retrieving full catalogs should be harmful, but may be helpful in an online display or portal.
        Specified by:
        lookup in interface ReplicaCatalog
        Parameters:
        lfns - is a set of logical filename strings to look up.
        Returns:
        a map indexed by the LFN. Each value is a collection of replica catalog entries for the LFN.
        See Also:
        org.griphyn.common.catalog.ReplicaCatalogEntry

      • lookupNoAttributes

        public java.util.Map lookupNoAttributes​(java.util.Set lfns)
        Retrieves multiple entries for a given logical filename, up to the complete catalog. Retrieving full catalogs should be harmful, but may be helpful in an online display or portal.
        Specified by:
        lookupNoAttributes in interface ReplicaCatalog
        Parameters:
        lfns - is a set of logical filename strings to look up.
        Returns:
        a map indexed by the LFN. Each value is a set of PFN strings.

      • lookup

        public java.util.Map lookup​(java.util.Set lfns,
                            java.lang.String handle)
        Retrieves multiple entries for a given logical filename, up to the complete catalog. Retrieving full catalogs should be harmful, but may be helpful in online display or portal.

        Specified by:
        lookup in interface ReplicaCatalog
        Parameters:
        lfns - is a set of logical filename strings to look up.
        handle - is the resource handle, restricting the LFNs.
        Returns:
        a map indexed by the LFN. Each value is a collection of replica catalog entries (all attributes).
        See Also:
        ReplicaCatalogEntry

      • lookupNoAttributes

        public java.util.Map lookupNoAttributes​(java.util.Set lfns,
                                        java.lang.String handle)
        Retrieves multiple entries for a given logical filename, up to the complete catalog. Retrieving full catalogs should be harmful, but may be helpful in online display or portal.

        Specified by:
        lookupNoAttributes in interface ReplicaCatalog
        Parameters:
        lfns - is a set of logical filename strings to look up.
        handle - is the resource handle, restricting the LFNs.
        Returns:
        a map indexed by the LFN. Each value is a set of physical filenames.

      • addItem

        private java.lang.String addItem​(java.lang.Object value,
                                 java.lang.String obj,
                                 boolean where)
        Helper function to assemble various pieces.
        Parameters:
        value - is the value of the object from the map.
        obj - is the name of the table column
        where - is the decision, if we had a previous WHERE clause or not.
        See Also:
        lookup( Map )

      • lookup

        public java.util.Map lookup​(java.util.Map constraints)
        Retrieves multiple entries for a given logical filename, up to the complete catalog. Retrieving full catalogs should be harmful, but may be helpful in online display or portal.
        Specified by:
        lookup in interface ReplicaCatalog
        Parameters:
        constraints - is mapping of keys 'lfn', 'pfn', or any attribute name, e.g. the resource handle 'site', to a string that has some meaning to the implementing system. This can be a SQL wildcard for queries, or a regular expression for Java-based memory collections. Unknown keys are ignored. Using an empty map requests the complete catalog.
        Returns:
        a map indexed by the LFN. Each value is a collection of replica catalog entries.
        See Also:
        ReplicaCatalogEntry

      • list

        public java.util.Set list()
        Lists all logical filenames in the catalog.
        Specified by:
        list in interface ReplicaCatalog
        Returns:
        A set of all logical filenames known to the catalog.

      • list

        public java.util.Set list​(java.lang.String constraint)
        Lists a subset of all logical filenames in the catalog.
        Specified by:
        list in interface ReplicaCatalog
        Parameters:
        constraint - is a constraint for the logical filename only. It is a string that has some meaning to the implementing system. This can be a SQL wildcard for queries, or a regular expression for Java-based memory collections.
        Returns:
        A set of logical filenames that match. The set may be empty

      • insert

        public int insert​(java.lang.String lfn,
                  ReplicaCatalogEntry tuple)
        Inserts a new mapping into the replica catalog.
        Specified by:
        insert in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename under which to book the entry.
        tuple - is the physical filename and associated PFN attributes.
        Returns:
        number of insertions, should always be 1. On failure, throw an exception, don't use zero.

      • insert

        public int insert​(java.lang.String lfn,
                  java.lang.String pfn,
                  java.lang.String handle)
        Inserts a new mapping into the replica catalog. This is a convenience function exposing the resource handle. Internally, the ReplicaCatalogEntry element will be contructed, and passed to the appropriate insert function.
        Specified by:
        insert in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename under which to book the entry.
        pfn - is the physical filename associated with it.
        handle - is a resource handle where the PFN resides.
        Returns:
        number of insertions, should always be 1. On failure, throw an exception, don't use zero.
        See Also:
        insert( String, ReplicaCatalogEntry ), ReplicaCatalogEntry

      • insert

        public int insert​(java.util.Map x)
        Inserts multiple mappings into the replica catalog. The input is a map indexed by the LFN. The value for each LFN key is a collection of replica catalog entries.
        Specified by:
        insert in interface ReplicaCatalog
        Parameters:
        x - is a map from logical filename string to list of replica catalog entries.
        Returns:
        the number of insertions.
        See Also:
        org.griphyn.common.catalog.ReplicaCatalogEntry

      • delete

        public int delete​(java.util.Map x,
                  boolean matchAttributes)
        Deletes multiple mappings into the replica catalog. The input is a map indexed by the LFN. The value for each LFN key is a collection of replica catalog entries. On setting matchAttributes to false, all entries having matching lfn pfn mapping to an entry in the Map are deleted. However, upon removal of an entry, all attributes associated with the pfn also evaporate (cascaded deletion).
        Specified by:
        delete in interface ReplicaCatalog
        Parameters:
        x - is a map from logical filename string to list of replica catalog entries.
        matchAttributes - whether mapping should be deleted only if all attributes match.
        Returns:
        the number of deletions.
        See Also:
        ReplicaCatalogEntry

      • delete

        public int delete​(java.lang.String lfn,
                  java.lang.String pfn)
        Deletes a specific mapping from the replica catalog. We don't care about the resource handle. More than one entry could theoretically be removed. Upon removal of an entry, all attributes associated with the PFN also evaporate (cascading deletion).
        Specified by:
        delete in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename in the tuple.
        pfn - is the physical filename in the tuple.
        Returns:
        the number of removed entries.

      • delete

        public int delete​(java.lang.String lfn,
                  ReplicaCatalogEntry tuple)
        Deletes a very specific mapping from the replica catalog. The LFN must be matches, the PFN, and all PFN attributes specified in the replica catalog entry. More than one entry could theoretically be removed. Upon removal of an entry, all attributes associated with the PFN also evaporate (cascading deletion).
        Specified by:
        delete in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename in the tuple.
        tuple - is a description of the PFN and its attributes.
        Returns:
        the number of removed entries, either 0 or 1.

      • delete

        public int delete​(java.lang.String lfn,
                  java.lang.String name,
                  java.lang.Object value)
        Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value. This method may be useful to remove all replica entries that have a certain MD5 sum associated with them. It may also be harmful overkill.
        Specified by:
        delete in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to look for.
        name - is the PFN attribute name to look for.
        value - is an exact match of the attribute value to match.
        Returns:
        the number of removed entries.

      • deleteByResource

        public int deleteByResource​(java.lang.String lfn,
                            java.lang.String handle)
        Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found. Karan requested this convenience method, which can be coded like 
          delete( lfn, RESOURCE_HANDLE, handle )
        Specified by:
        deleteByResource in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to look for.
        handle - is the resource handle
        Returns:
        the number of entries removed.

      • remove

        public int remove​(java.lang.String lfn)
        Removes all mappings for an LFN from the replica catalog.
        Specified by:
        remove in interface ReplicaCatalog
        Parameters:
        lfn - is the logical filename to remove all mappings for.
        Returns:
        the number of removed entries.

      • remove

        public int remove​(java.util.Set lfns)
        Removes all mappings for a set of LFNs.
        Specified by:
        remove in interface ReplicaCatalog
        Parameters:
        lfns - is a set of logical filename to remove all mappings for.
        Returns:
        the number of removed entries.

      • removeByAttribute

        public int removeByAttribute​(java.lang.String name,
                             java.lang.Object value)
        Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
        Specified by:
        removeByAttribute in interface ReplicaCatalog
        Parameters:
        name - is the PFN attribute name to look for.
        value - is an exact match of the attribute value to match.
        Returns:
        the number of removed entries.

      • removeByAttribute

        public int removeByAttribute​(java.lang.String handle)
        Removes all entries associated with a particular resource handle. This is useful, if a site goes offline. It is a convenience method, which calls the generic removeByAttribute method.
        Specified by:
        removeByAttribute in interface ReplicaCatalog
        Parameters:
        handle - is the site handle to remove all entries for.
        Returns:
        the number of removed entries.
        See Also:
        removeByAttribute( String, Object )

      • clear

        public int clear()
        Removes everything. Use with caution!
        Specified by:
        clear in interface ReplicaCatalog
        Returns:
        the number of removed entries.