Daylight Worksheet - Creating a database -- with HINTS

Creating a database means creating the empty files which are in the format required by the Daylight database servers. These files must then be loaded with data to be useful. When creating a database, the following must be specified: (1) a datatypes database, (2) primary hash table size, (3) cross-reference hash table size. Also, the path of the database directory must be known. This is normally referenced by $DY_THORDB.

• Creating a database with sthorman -
  1. Launch sthorman and select the databases menu. Create a "regular" database and specify a handy datatypes database (e.g., medchem98demo_datatypes).

     
     
     % sthorman
     Version: sthorman 4.62
      
               ....................................................
               .  STHORMAN -- Serial THOR Manager Program.        .
               .                                                  .
               .  Enter "?" for help at any prompt.               .
               .  The menu selection "." goes to top-level menu.  .
               ....................................................
      
     STHORMAN needs to be connected to a server.
      
     Enter machine the server is running on: ("norte") 
     Enter port (service) of server: ("thor") 
     Enter username: ("jj") 
     Enter server username's password: 
      
      
     Connected to new server.
     Current service:  norte:thor
      
     SERVER MENU (TOP LEVEL MENU):
     1) Connect to a new server
     2) List server's version
     3) List current users
     4) Change server security...
     5) Databases...
     6) Send message to users...
     7) Evict user...
     0) Quit
     Enter menu selection (or '?'): 5
      
     DATABASE MENU:
      1) List known databases
      2) Change database search-path...
      3) Get database information...
      4) Create   a database...
      5) Load     a database
      6) Dump     a database
      7) Crunch   a database
      8) Change   a database's configuration...
      9) Destroy  a database
     10) Send message to users of a database...
     11) Evict users of a database...
      0) Go back to server menu
     Enter menu selection (or '?'): 4
      
     DATABASE CREATION MENU:
     1) Create a datatypes database
     2) Create a indirect-reference database
     3) Create a monomer-table database
     4) Create a regular database
     0) Go back to database menu
     Enter menu selection (or '?'): 4
      
     Enter name of regular database to create: $DY_THORDB/test
      
     Existing datatypes databases:
       1) 
       2)  /daylight/thordb/ccr972demo_datatypes
       3)  /daylight/thordb/chemsynth97demo_datatypes
       4)  /daylight/thordb/ic97demo_datatypes
       5)  /daylight/thordb/maybridge97demo_datatypes
       6)  /daylight/thordb/medchem98demo_datatypes
       7)  /daylight/thordb/mix97demo_datatypes
       8)  /daylight/thordb/spresi95demo_datatypes
       9)  /daylight/thordb/spresirxn98demo_datatypes
       10)  /daylight/thordb/wdi981demo_datatypes
     Enter number of existing datatypes database: 6
      
     Existing indirect-reference databases:
       1) 
       2) 
       3)  /daylight/thordb/ccr972demo_indirect
       4)  /daylight/thordb/chemsynth97demo_indirect
       5)  /daylight/thordb/ic97demo_indirect
       6)  /daylight/thordb/medchem98demo_indirect
       7)  /daylight/thordb/spresi95demo_indirect
       8)  /daylight/thordb/spresirxn98demo_indirect
     Enter number of existing indirect database: 2
      
     Existing monomer-table databases:
       1) 
       2) 
       3)  /daylight/thordb/mix97demo_monomers
     Enter number of existing monomer-table database: 2
     Enter size for primary hash-table: 200
     Enter size for cross-reference hash-table: 200
     Enter  new READ password: 
      
     Verify new READ password: 
      
     Enter  new WRITE password: 
      
     Verify new WRITE password: 
      
     Enter  new EXECUTIVE password: 
      
     Verify new EXECUTIVE password: 
      
      
     The executive password for a database is needed to change passwords.
     No executive password has been specified; anybody can change any
     password.
     Is this ok? ("yes") 
      
     Database ............................ $DY_THORDB/test
     Database type ....................... regular
     Datatypes database ..................
     /daylight/thordb/medchem98demo_datatypes.THOR
     Indirect reference database ......... 
     Monomer-definitions database ........ 
     Primary hash-table size ............. 200
     Cross-ref. hash-table size .......... 200
      
     Create above database? ("yes") 
      
     Database created.
      
     

  2. Test that the database exists and is healthy by using the thordbping command and verifying that no error is reported.

     
     % thordbping test
     

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• Creating a database with thormake -
  1. thormake requires that all parameters are specified on the command line. Here is an example:

     thormake \
'$DY_THORDB/test' 100 400 \
-DATATYPES_DATABASE 'test_datatypes'


  2. Again test that the database exists and is healthy by using the thordbping command.

  ---

• Destroying a database with thordestroy -
  1. thordestroy is a client program which instructs the server to delete all files associated with the specified database.

     thordestroy '$DY_THORDB/test'


  2. Verify that the database has been destroyed by using the thordbping command. Also examine the database directory for files.