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revision 1.4, Sun Sep 11 17:06:21 2005 UTC revision 1.11, Wed Nov 2 21:45:08 2005 UTC
# Line 24  Line 24 
24  =item Subsystem  =item Subsystem
25    
26  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
27  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>.  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
28    B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
29    B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>
30    
31  =item Annotation  =item Annotation
32    
# Line 55  Line 57 
57    
58  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.
59    
60    =item Reaction
61    
62    Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
63    B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
64    
65  =item *  =item *
66    
67  Loads all of the above tables.  Loads all of the above tables.
68    
69  =back  =back
70    
71  There are two command-line options, given below. Note that in the command line, spaces  The command-line options are given below.
 inside parameters should be represented by C<\b>.  
72    
73  =over 4  =over 4
74    
# Line 82  Line 88 
88    
89  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
90    
91    =item limitedFeatures
92    
93    Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.
94    
95    =item dbLoad
96    
97    If TRUE, the database tables will be loaded automatically from the load files created.
98    
99  =back  =back
100    
101  =cut  =cut
# Line 96  Line 110 
110  use File::Path;  use File::Path;
111  use SproutLoad;  use SproutLoad;
112  use Stats;  use Stats;
113    use SFXlate;
114    
115  # Get the command-line parameters and options.  # Get the command-line parameters and options.
116  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",
117                                                      trace => 3 },                                                      trace => 3, limitedFeatures => 0,
118                                                                 @ARGV);                                                      dbLoad => 0 }, @ARGV);
119  # Set up tracing.  # Set up tracing.
120  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");
121  # Create the sprout loader object.  # Create the sprout loader object. Note that the Sprout object does not
122    # open the database unless the "dbLoad" option is turned on.
123  my $fig = FIG->new();  my $fig = FIG->new();
124  my $sprout = SFXlate->new_sprout_only();  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
125  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile},  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);
                           $options->{subsysFile});  
126  # Process the parameters.  # Process the parameters.
127  for my $group (@parameters) {  for my $group (@parameters) {
128      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
# Line 145  Line 160 
160      if ($group eq 'External' || $group eq '*') {      if ($group eq 'External' || $group eq '*') {
161          $spl->LoadExternalData();          $spl->LoadExternalData();
162      }      }
163        if ($group eq 'Reaction' || $group eq '*') {
164            $spl->LoadReactionData();
165        }
166    
167  }  }
168  Trace("Load complete.") if T(2);  Trace("Load complete.") if T(2);

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