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revision 1.29, Sat May 13 14:51:39 2006 UTC revision 1.40, Wed Sep 13 04:27:38 2006 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 214  Line 152 
152    
153  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
154    
 =item Coupling  
   
 Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  
 B<UsesAsEvidence>.  
   
155  =item Feature  =item Feature
156    
157  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
158  B<IsLocatedIn>, B<FeatureLink>.  B<IsLocatedIn>, B<FeatureLink>.
159    
160    =item Coupling
161    
162    Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,
163    B<UsesAsEvidence>.
164    
165  =item Subsystem  =item Subsystem
166    
167  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
# 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 262  Line 196 
196  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
197  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
198    
199    =item Synonym
200    
201    Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
202    
203    =item Family
204    
205    Loads B<Family> and B<IsFamilyForFeature>.
206    
207  =item *  =item *
208    
209  Loads all of the above tables.  Loads all of the above tables.
# Line 277  Line 219 
219  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
220  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
221  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
222  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
223    default gene file-- C<genes.tbl> in the C<SproutData> directory.
224    
225  =item subsysFile  =item subsysFile
226    
# Line 290  Line 233 
233    
234  =item user  =item user
235    
236  Suffix to use for trace, output, and error files created in  Suffix to use for trace, output, and error files created.
237    
238  =item dbLoad  =item dbLoad
239    
# Line 324  Line 267 
267    
268  Trace SQL statements.  Trace SQL statements.
269    
270    =item phone
271    
272    Phone number to message when the load finishes.
273    
274  =back  =back
275    
276  =cut  =cut
# Line 350  Line 297 
297                                                loadOnly => [0, "load the database from previously generated files"],                                                loadOnly => [0, "load the database from previously generated files"],
298                                                primaryOnly => [0, "only process the group's main entity"],                                                primaryOnly => [0, "only process the group's main entity"],
299                                                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"],
300                                                  phone => ["", "phone number (international format) to call when load finishes"],
301                                              },                                              },
302                                              "<group1> <group2> ...",                                              "<group1> <group2> ...",
303                                              @ARGV);                                              @ARGV);
# Line 362  Line 310 
310      my $db = $FIG_Config::sproutDB;      my $db = $FIG_Config::sproutDB;
311      DBKernel::CreateDB($db);      DBKernel::CreateDB($db);
312  }  }
313    # Compute the gene file name.
314    my $geneFile = $options->{geneFile};
315    if ($geneFile eq 'default') {
316        $geneFile = "$FIG_Config::sproutData/genes.tbl";
317    }
318  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
319  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
320  my $fig = FIG->new();  my $fig = FIG->new();
321  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
322  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
323  # Insure we have an output directory.  # Insure we have an output directory.
324  FIG::verify_dir($FIG_Config::sproutData);  FIG::verify_dir($FIG_Config::sproutData);
325  # If we're resuming, we only want to have 1 parameter.  # If we're resuming, we only want to have 1 parameter.
# Line 374  Line 327 
327  if ($resume && @parameters > 1) {  if ($resume && @parameters > 1) {
328      Confess("If resume=1, only one load group can be specified.");      Confess("If resume=1, only one load group can be specified.");
329  } elsif (! @parameters) {  } elsif (! @parameters) {
330      Confess("No load groups were specified.");      Trace("No load groups were specified.") if T(0);
331  }  }
332    # Set a variable to contain return type information.
333    my $rtype;
334    # Insure we catch errors.
335    eval {
336  # Process the parameters.  # Process the parameters.
337  for my $group (@parameters) {  for my $group (@parameters) {
338      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
# Line 404  Line 361 
361          $spl->LoadAnnotationData();          $spl->LoadAnnotationData();
362          $group = ResumeCheck($resume, $group);          $group = ResumeCheck($resume, $group);
363      }      }
364      if ($group eq 'BBH' || $group eq '*') {          #if ($group eq 'BBH' || $group eq '*') {
365          $spl->LoadBBHData();          #    $spl->LoadBBHData();
366          $group = ResumeCheck($resume, $group);          #    $group = ResumeCheck($resume, $group);
367      }          #}
368      if ($group eq 'Group' || $group eq '*') {      if ($group eq 'Group' || $group eq '*') {
369          $spl->LoadGroupData();          $spl->LoadGroupData();
370          $group = ResumeCheck($resume, $group);          $group = ResumeCheck($resume, $group);
# Line 424  Line 381 
381          $spl->LoadReactionData();          $spl->LoadReactionData();
382          $group = ResumeCheck($resume, $group);          $group = ResumeCheck($resume, $group);
383      }      }
384            if ($group eq 'Synonym' || $group eq '*') {
385                $spl->LoadSynonymData();
386                $group = ResumeCheck($resume, $group);
387            }
388            if ($group eq 'Family' || $group eq '*') {
389                $spl->LoadFamilyData();
390                $group = ResumeCheck($resume, $group);
391            }
392  }  }
393    };
394    if ($@) {
395        Trace("Load failed with error: $@") if T(0);
396        $rtype = "error";
397    } else {
398  Trace("Load complete.") if T(2);  Trace("Load complete.") if T(2);
399        $rtype = "no error";
400    }
401    if ($options->{phone}) {
402        my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
403        if ($msgID) {
404            Trace("Phone message sent with ID $msgID.") if T(2);
405        } else {
406            Trace("Phone message not sent.") if T(2);
407        }
408    }
409    
410  # If the resume flag is set, return "*", else return "".  # If the resume flag is set, return "*", else return "".
411  sub ResumeCheck {  sub ResumeCheck {

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