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revision 1.15, Wed Dec 7 01:19:00 2005 UTC revision 1.22, Sun Mar 26 17:28:20 2006 UTC
# Line 78  Line 78 
78  =item 1  =item 1
79    
80  Type C<LoadSproutTables -dbLoad -dbCreate "*"> and press ENTER. This will create  Type C<LoadSproutTables -dbLoad -dbCreate "*"> and press ENTER. This will create
81  the C<dtx> files and load them.  the C<dtx> files and load them. You may be asked for a password. If this is the
82    case, simply press ENTER. If that does not work, use the C<dbpass> value specified
83    in your C<FIG_Config.pm> file.
84    
85  =item 2  =item 2
86    
87  Type C<TestSproutLoad> and press ENTER. This will validate the Sprout database  Type C<TestSproutLoad 100226.1 83333.1> and press ENTER. This will validate
88  against the SEED data.  the Sprout database against the SEED data.
89    
90  =item 3  =item 3
91    
# Line 184  Line 186 
186    
187  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
188    
 =item limitedFeatures  
   
 Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.  
   
189  =item dbLoad  =item dbLoad
190    
191  If TRUE, the database tables will be loaded automatically from the load files created.  If TRUE, the database tables will be loaded automatically from the load files created.
# Line 197  Line 195 
195  If TRUE, the database will be created. If the database exists already, it will be  If TRUE, the database will be created. If the database exists already, it will be
196  dropped. Use the function with caution.  dropped. Use the function with caution.
197    
198    =item loadOnly
199    
200    If TRUE, the database tables will be loaded from existing load files. Load files
201    will not be created. This option is useful if you are setting up a copy of Sprout
202    and have load files already set up from the original version.
203    
204    =item primaryOnly
205    
206    If TRUE, only the group's primary entity will be loaded.
207    
208  =back  =back
209    
210  =cut  =cut
# Line 214  Line 222 
222  use SFXlate;  use SFXlate;
223    
224  # Get the command-line parameters and options.  # Get the command-line parameters and options.
225  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
226                                                      trace => 3, limitedFeatures => 0,                                              'ERDB', 'Load', 'Sprout'],
227                                                      dbLoad => 0, dbCreate => 0 }, @ARGV);                                              { geneFile => ["", "name of the genome list file"],
228  # Set up tracing.                                                subsysFile => ["", "name of the trusted subsystem file"],
229  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");                                                dbLoad => [0, "load the database from generated files"],
230                                                  dbCreate => [0, "drop and re-create the database"],
231                                                  loadOnly => [0, "load the database from previously generated files"],
232                                                  primaryOnly => [0, "only process the group's main entity"]
233                                                },
234                                                "<group1> <group2> ...",
235                                                @ARGV);
236    # If we're doing a load-only, turn on loading.
237    if ($options->{loadOnly}) {
238        $options->{dbLoad} = 1
239    }
240  if ($options->{dbCreate}) {  if ($options->{dbCreate}) {
241      # Here we want to drop and re-create the database.      # Here we want to drop and re-create the database.
242      my $db = $FIG_Config::sproutDB;      my $db = $FIG_Config::sproutDB;
243      if ($FIG_Config::dbms eq "Pg") {      DBKernel::CreateDB($db);
         my $dbport = $FIG_Config::dbport;  
         my $dbuser = $FIG_Config::dbuser;  
         Trace("Dropping old database (failure is okay).") if T(2);  
         system("dropdb -p $dbport -U $dbuser $db");  
         Trace("Dropping old database (failure is okay).") if T(2);  
         &FIG::run("createdb -p $dbport -U $dbuser $db");  
     } elsif ($FIG_Config::dbms eq "mysql") {  
         Trace("Dropping old database (failure is okay).") if T(2);  
         system("mysqladmin -u $FIG_Config::dbuser -p drop $db");  
         &FIG::run("mysqladmin -u $FIG_Config::dbuser -p create $db");  
         Trace("Dropping old database (failure is okay).") if T(2);  
     }  
   
244  }  }
245  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
246  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
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