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revision 1.37, Sun Jul 30 01:23:47 2006 UTC revision 1.43, Fri May 11 06:23:51 2007 UTC
# Line 48  Line 48 
48  C<LoadSproutTables> takes a long time to run, so setting the trace level to 3 helps  C<LoadSproutTables> takes a long time to run, so setting the trace level to 3 helps
49  to give you an idea of the progress.  to give you an idea of the progress.
50    
 Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load  
 against the FIG data. The end of the trace log file will contain statistics on  
 the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming  
 script, so you may want to set the trace level to 3 to see visible progress.  
   
     TestSproutLoad -trace=3 [genomeID] ...  
   
 The I<[genomeID]> specifies zero or more IDs of genomes to receive more thorough  
 testing. So, for example,  
   
     TestSproutLoad -trace=3 100226.1 83333.1  
   
 would do thorough testing of I<Streptomyces coelicolor A3-2> (100226.1) and  
 I<Escherichia coli K12> (83333.1).  
   
 Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are  
 mixed in with the trace messages. They are all, however, marked with a trace type  
 of B<Problem>, as shown in the fragment below.  
   
     11/02/2005 19:15:16 <main>: Processing feature fig|100226.1.peg.7742.  
     11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7741.  
     11/02/2005 19:15:17 <Problem>: assignment "Short-chain dehydrodenase ...  
     11/02/2005 19:15:17 <Problem>: assignment "putative oxidoreductase." ...  
     11/02/2005 19:15:17 <Problem>: Incorrect assignment for fig|100226.1.peg.7741...  
     11/02/2005 19:15:17 <Problem>: Incorrect number of annotations found in ...  
     11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7740.  
     11/02/2005 19:15:18 <main>: Processing feature fig|100226.1.peg.7739.  
   
 The test may reveal that some tables need to be reloaded, or that a software  
 problem has crept into the Sprout.  
   
 Once all the tables have the correct data, C<index_sprout_lucene> can be run to create the  
 Lucene search indexes. Lucene is a web site search engine produced by the Apache project.  
 It is written in Java, and in order to run it you must have the B<LuceneSearch> and  
 B<NmpdrConfigs> projects checked out from CVS and made.  
   
51  =head2 The NMPDR Web Site  =head2 The NMPDR Web Site
52    
53  Sprout is the database engine for the NMPDR web site. The NMPDR web site consists of two  Sprout is the database engine for the NMPDR web site. The NMPDR web site consists of two
# Line 142  Line 106 
106    
107  =over 4  =over 4
108    
109  The procedure for loading Sprout is as follows.  Most of the above preparation is performed by the B<NMPDRSetup> utility.
110    NMPDRSetup prints the instructions for completing the process, including
111    loading the Sprout database. The specific procedure for loading
112    the Sprout data, however, is as follows.
113    
114  =item 1  =item 1
115    
116  Type  Type
117    
118      nohup LoadSproutTables -dbLoad -dbCreate -user=you -background "*" >null &      nohup LoadSproutTables -dbLoad -user=you -background "*" >null &
119    
120  where C<you> is your user ID, and press ENTER. This will create the C<dtx> files  where C<you> is your user ID, and press ENTER.
 and load them. You may be asked for a password. If this is the case, simply  
 press ENTER. If that does not work, use the C<dbpass> value specified in  
 your C<FIG_Config.pm> file.  
121    
122  The above command line runs the load in the background. The standard output,  The above command line runs the load in the background. The standard output,
123  standard error, and trace output will be directed to files in the FIG temporary  standard error, and trace output will be directed to files in the FIG temporary
# Line 170  Line 134 
134    
135  Type  Type
136    
     nohup TestSproutLoad -user=you -background >null &100226.1 83333.1>  
   
 and press ENTER. This will validate the Sprout database against the SEED data.  
   
 =item 3  
   
 If any errors are detected in step (2), it is most likely due to a change in  
 SEED that did not make it to Sprout. Contact Bruce Parrello or Robert Olson  
 to get the code updated properly.  
   
 =item 4  
   
 Type  
   
137      index_sprout_lucene      index_sprout_lucene
138    
139   and press ENTER. This will create the Lucene indexes for the Sprout data.   and press ENTER. This will create the Lucene indexes for the Sprout data.
140    
 =item 5  
   
 Change to the B<SproutData/Indexes> directory under B<FIGdisk> and look for the  
 directory created by C<index_sprout_lucene>. The directory name will be  
 something like C<Lucene.20060412-154112>. The numbers indicate the date and time  
 the index was created. In this case it was 04/12/2006 03:41:12pm. Type  
   
     ln -sf directory Lucene  
   
 where C<directory> is the new directory name, to point the C<Lucene> directory to the  
 new search index.  
   
141  =back  =back
142    
143  =head2 LoadSproutTables Command  =head2 LoadSproutTables Command
# Line 241  Line 179 
179    
180  Loads B<Property>, B<HasProperty>.  Loads B<Property>, B<HasProperty>.
181    
 =item BBH  
   
 Loads B<IsBidirectionalBestHitOf>.  
   
182  =item Group  =item Group
183    
184  Loads B<GenomeGroups>.  Loads B<GenomeGroups>.
# Line 268  Line 202 
202    
203  =item Family  =item Family
204    
205  Loads B<Family> and B<ContainsFeature>.  Loads B<Family> and B<IsFamilyForFeature>.
206    
207    =item Drug
208    
209    Loads B<DrugProject>, B<ContainsTopic>, B<DrugTopic>, B<ContainsAnalysisOf>,
210    B<PDB>, B<IncludesBound>, B<PDB>, B<IsBoundIn>, B<BindsWith>, B<Ligand>,
211    B<DescribesProteinForFeature>, and B<FeatureConservation>.
212    
213  =item *  =item *
214    
# Line 285  Line 225 
225  The name of the file containing the genomes and their associated access codes. The  The name of the file containing the genomes and their associated access codes. The
226  file should have one line per genome, each line consisting of the genome ID followed  file should have one line per genome, each line consisting of the genome ID followed
227  by the access code, separated by a tab. If no file is specified, all complete genomes  by the access code, separated by a tab. If no file is specified, all complete genomes
228  will be processed and the access code will be 1.  will be processed and the access code will be 1. Specify C<default> to use the
229    default gene file-- C<genes.tbl> in the C<SproutData> directory.
230    
231  =item subsysFile  =item subsysFile
232    
# Line 375  Line 316 
316      my $db = $FIG_Config::sproutDB;      my $db = $FIG_Config::sproutDB;
317      DBKernel::CreateDB($db);      DBKernel::CreateDB($db);
318  }  }
319    # Compute the gene file name.
320    my $geneFile = $options->{geneFile};
321    if ($geneFile eq 'default') {
322        $geneFile = "$FIG_Config::sproutData/genes.tbl";
323    }
324  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
325  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
326  my $fig = FIG->new();  my $fig = FIG->new();
327  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
328  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
329  # Insure we have an output directory.  # Insure we have an output directory.
330  FIG::verify_dir($FIG_Config::sproutData);  FIG::verify_dir($FIG_Config::sproutData);
331  # If we're resuming, we only want to have 1 parameter.  # If we're resuming, we only want to have 1 parameter.
# Line 421  Line 367 
367              $spl->LoadAnnotationData();              $spl->LoadAnnotationData();
368              $group = ResumeCheck($resume, $group);              $group = ResumeCheck($resume, $group);
369          }          }
         if ($group eq 'BBH' || $group eq '*') {  
             $spl->LoadBBHData();  
             $group = ResumeCheck($resume, $group);  
         }  
370          if ($group eq 'Group' || $group eq '*') {          if ($group eq 'Group' || $group eq '*') {
371              $spl->LoadGroupData();              $spl->LoadGroupData();
372              $group = ResumeCheck($resume, $group);              $group = ResumeCheck($resume, $group);
# Line 449  Line 391 
391              $spl->LoadFamilyData();              $spl->LoadFamilyData();
392              $group = ResumeCheck($resume, $group);              $group = ResumeCheck($resume, $group);
393          }          }
394            if ($group eq 'Drug' || $group eq '*') {
395                $spl->LoadDrugData();
396                $group = ResumeCheck($resume, $group);
397            }
398      }      }
399  };  };
400  if ($@) {  if ($@) {

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