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revision 1.46, Thu Dec 6 14:58:03 2007 UTC revision 1.49, Tue Sep 16 18:53:28 2008 UTC
# Line 104  Line 104 
104    
105  =back  =back
106    
 =over 4  
   
107  Most of the above preparation is performed by the B<NMPDRSetup> utility.  Most of the above preparation is performed by the B<NMPDRSetup> utility.
108  NMPDRSetup prints the instructions for completing the process, including  NMPDRSetup prints the instructions for completing the process, including
109  loading the Sprout database. The specific procedure for loading  loading the Sprout database. The specific procedure for loading
110  the Sprout data, however, is as follows.  the Sprout data, however, is as follows.
111    
 =item 1  
   
 Type  
   
     nohup LoadSproutTables -dbLoad -user=you -background "*" >null &  
   
 where C<you> is your user ID, and press ENTER.  
   
 The above command line runs the load in the background. The standard output,  
 standard error, and trace output will be directed to files in the FIG temporary  
 directory. If your user name is C<Bruce> then the files will be named  
 C<outBruce.log>, C<errBruce.log>, and C<traceBruce.log> respectively.  
   
 If the load fails at some point and you are able to correct the problem, use the  
 C<resume> option to restart it. For example, if the load failed while doing the  
 Feature load group, you would resume it using  
   
     nohup LoadSproutTables -dbLoad -dbCreate -user=you -resume -background Feature >null &  
   
 =item 2  
   
 Type  
   
     index_sprout_lucene  
   
  and press ENTER. This will create the Lucene indexes for the Sprout data.  
   
 =back  
   
112  =head2 LoadSproutTables Command  =head2 LoadSproutTables Command
113    
114  C<LoadSproutTables> creates the load files for Sprout tables and optionally loads them.  C<LoadSproutTables> creates the load files for Sprout tables and optionally loads them.
# Line 152  Line 121 
121    
122  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
123    
 =item Feature  
   
 Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  
 B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,  
 B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,  
 B<CDD>, and B<IsPresentOnProteinOf>  
   
124  =item Subsystem  =item Subsystem
125    
126  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
127  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
128  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,  B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
129  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
130  B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>,  B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>, and
131  B<ContainsFeature>.  B<ContainsFeature>.
132    
133  =item Annotation  =item Annotation
134    
135  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>, and
136  B<MadeAnnotation>.  B<MadeAnnotation>.
137    
138  =item Property  =item Property
139    
140  Loads B<Property>, B<HasProperty>.  Loads B<Property>, and B<HasProperty>.
   
 =item Group  
   
 Loads B<GenomeGroups>.  
141    
142  =item Source  =item Source
143    
144  Loads B<Source>, B<ComesFrom>, B<SourceURL>.  Loads B<Source>, B<ComesFrom>, and B<SourceURL>.
   
 =item External  
   
 Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  
145    
146  =item Reaction  =item Reaction
147    
148  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
149  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>, B<Scenario>, B<IsInputFor>,
150    B<IsOutputOf>, B<IsOnDiagram>, and B<Catalyzes>.
151    
152  =item Synonym  =item Synonym
153    
# Line 206  Line 161 
161    
162  Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.  Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.
163    
164    =item Feature
165    
166    Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
167    B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,
168    B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,
169    B<CDD>, B<IsPresentOnProteinOf>, and B<Keyword>.
170    
171  =item *  =item *
172    
173  Loads all of the above tables.  Loads all of the above tables.
# Line 275  Line 237 
237    
238  use strict;  use strict;
239  use Tracer;  use Tracer;
 use DocUtils;  
240  use Cwd;  use Cwd;
241  use FIG;  use FIG;
242  use SFXlate;  use SFXlate;
# Line 287  Line 248 
248    
249  # This is a list of the load groups in their natural order. We'll go through these in sequence, processing  # This is a list of the load groups in their natural order. We'll go through these in sequence, processing
250  # the ones the user asks for.  # the ones the user asks for.
251  my @LoadGroups = qw(Genome Feature Subsystem Property Annotation Source External Reaction Synonym Family Drug);  my @LoadGroups = qw(Genome Subsystem Property Annotation Source Reaction Synonym Family Drug Feature);
252    
253  # Get the command-line parameters and options.  # Get the command-line parameters and options.
254  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
# Line 299  Line 260 
260                                                loadOnly => [0, "load the database from previously generated files"],                                                loadOnly => [0, "load the database from previously generated files"],
261                                                resume => [0, "resume a complete load starting with the first group specified in the parameter list"],                                                resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
262                                                phone => ["", "phone number (international format) to call when load finishes"],                                                phone => ["", "phone number (international format) to call when load finishes"],
263                                                  trace => [3, "trace level"],
264                                              },                                              },
265                                              "<group1> <group2> ...",                                              "<group1> <group2> ...",
266                                              @ARGV);                                              @ARGV);

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