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revision 1.1, Wed Jul 27 20:05:24 2005 UTC revision 1.6, Sun Sep 11 17:34:05 2005 UTC
# Line 2  Line 2 
2    
3  =head1 Load Sprout Tables  =head1 Load Sprout Tables
4    
5  Load a group of Sprout tables from the command line. The parameters are the names of  Create the load files for a group of Sprout tables. The parameters are the names of
6  the table groups to load. The legal table group names are given below.  the table groups whose data is to be created. The legal table group names are given below.
7    
8  =over 4  =over 4
9    
# Line 19  Line 19 
19  =item Feature  =item Feature
20    
21  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
22  B<IsLocatedIn>, B<IsBidirectionalBestHitOf>, B<FeatureLink>.  B<IsLocatedIn>, B<FeatureLink>.
23    
24  =item Subsystem  =item Subsystem
25    
26  Loads B<Subsystem>, B<Role>, B<SSCell>, B<Diagram>, 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    
29    =item Annotation
30    
31    Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
32    B<MadeAnnotation>.
33    
34    =item Diagram
35    
36    Loads B<Diagram>, B<RoleOccursIn>.
37    
38    =item Property
39    
40    Loads B<Property>, B<HasProperty>.
41    
42    =item BBH
43    
44    Loads B<IsBidirectionalBestHitOf>.
45    
46    =item Group
47    
48    Loads B<GenomeGroups>.
49    
50    =item Source
51    
52    Loads B<Source>, B<ComesFrom>, B<SourceURL>.
53    
54    =item External
55    
56    Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.
57    
58    =item *
59    
60    Loads all of the above tables.
61    
62  =back  =back
63    
64  There are two command-line options, given below. Note that in the command line, spaces  There are two command-line options, given below. Note that in the command line, spaces
# Line 56  Line 89 
89  use strict;  use strict;
90  use Tracer;  use Tracer;
91  use DocUtils;  use DocUtils;
 use TestUtils;  
92  use Cwd;  use Cwd;
93  use FIG;  use FIG;
94  use SFXlate;  use SFXlate;
# Line 70  Line 102 
102                                                      trace => 3 },                                                      trace => 3 },
103                                                                 @ARGV);                                                                 @ARGV);
104  # Set up tracing.  # Set up tracing.
105  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Tracer Load", "+>$FIG_Config::temp/trace.log");  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");
106  # Create the sprout loader object.  # Create the sprout loader object.
107  my $fig = FIG->new();  my $fig = FIG->new();
108  my $sprout = SFXlate->new_sprout_only();  my $sprout = Sprout->new($FIG_Config::sproutDB, { noDBOpen => 1 });
109  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile},  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile});
                           $options->{subsysFile});  
110  # Process the parameters.  # Process the parameters.
111  for my $group (@parameters) {  for my $group (@parameters) {
112      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
113      my $stats;      my $stats;
114      if ($group eq 'Genome') {      if ($group eq 'Genome' || $group eq '*') {
115          $spl->LoadGenomeData();          $spl->LoadGenomeData();
116      } elsif ($group eq 'Feature') {      }
117        if ($group eq 'Feature' || $group eq '*') {
118          $spl->LoadFeatureData();          $spl->LoadFeatureData();
119      } elsif ($group eq 'Coupling') {      }
120        if ($group eq 'Coupling' || $group eq '*') {
121          $spl->LoadCouplingData();          $spl->LoadCouplingData();
122      } elsif ($group eq 'Subsystem') {      }
123        if ($group eq 'Subsystem' || $group eq '*') {
124          $spl->LoadSubsystemData();          $spl->LoadSubsystemData();
125      } elsif ($group eq 'Property') {      }
126        if ($group eq 'Property' || $group eq '*') {
127          $spl->LoadPropertyData();          $spl->LoadPropertyData();
     } else {  
         Confess("Invalid group name $group.");  
128      }      }
129        if ($group eq 'Diagram' || $group eq '*') {
130            $spl->LoadDiagramData();
131        }
132        if ($group eq 'Annotation' || $group eq '*') {
133            $spl->LoadAnnotationData();
134        }
135        if ($group eq 'BBH' || $group eq '*') {
136            $spl->LoadBBHData();
137        }
138        if ($group eq 'Group' || $group eq '*') {
139            $spl->LoadGroupData();
140        }
141        if ($group eq 'Source' || $group eq '*') {
142            $spl->LoadSourceData();
143        }
144        if ($group eq 'External' || $group eq '*') {
145            $spl->LoadExternalData();
146        }
147    
148  }  }
149  Trace("Load complete.") if T(2);  Trace("Load complete.") if T(2);
150    

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