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revision 1.21, Mon Feb 13 09:45:07 2006 UTC revision 1.39, Wed Aug 30 15:00:42 2006 UTC
# Line 20  Line 20 
20  commands.  commands.
21    
22      LoadSproutTables -dbLoad -dbCreate "*"      LoadSproutTables -dbLoad -dbCreate "*"
23      TestSproutLoad      TestSproutLoad [genomeID] ...
24      index_sprout      index_sprout_lucene
25    
26    where I<[genomeID]> is one or more genome IDs. These genomes will be tested more
27    thoroughly than the others.
28    
29  All three commands send output to the console. In addition, C<LoadSproutTables> and  All three commands send output to the console. In addition, C<LoadSproutTables> and
30  C<TestSproutLoad> write tracing information to C<trace.log> in the FIG temporary  C<TestSproutLoad> write tracing information to a trace log in the FIG temporary
31  directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete  directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete
32  list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected  list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected
33  and the offending table group reloaded. So, for example, if there are errors in the  and the offending table group reloaded. So, for example, if there are errors in the
# Line 45  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    
51  Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load  =head2 The NMPDR Web Site
 against the FIG data. Again, the end of the C<trace.log> file will contain a summary  
 of 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  
   
 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.  
52    
53  Once all the tables have the correct data, C<index_sprout> can be run to create the  Sprout is the database engine for the NMPDR web site. The NMPDR web site consists of two
54  Glimpse indexes.  pieces that run on two different machines. The B<WEB> machine contains HTML pages
55    generated by a Content Management Tool.
56    
57  =head2 Procedure For Loading Sprout  =head2 Procedure For Loading Sprout
58    
59    In order to load the Sprout, you need to have the B<Sprout>, B<NmpdrConfigs>, and
60    B<LuceneSearch> projects checked out from CVS in addition to the standard FIG
61    projects. You must also set up the following B<FIG_Config.pm> variables in addition
62    to the normal ones.
63    
64    =over 4
65    
66    =item sproutData
67    
68    Name of the data directory for the Sprout load files.
69    
70    =item var
71    
72    Name of the directory to contain cached NMPDR pages. The most important file in
73    this directory is C<nmpdr_page_template.html>, which contains a skeleton page
74    from the main NMPDR web site. This skeleton page is used to generate output
75    pages that look like the other NMPDR pages.
76    
77    =item java
78    
79    Path to the Java runtime environment.
80    
81    =item sproutDB
82    
83    Name of the Sprout database
84    
85    =item dbuser
86    
87    User name for logging into the Sprout database.
88    
89    =item dbpass
90    
91    Password for logging into the Sprout database.
92    
93    =item nmpdr_site_url
94    
95    URL for the NMPDR cover pages. The NMPDR cover pages are informational and text
96    pages that serve as the entry point to the NMPDR web site. They are generated by
97    a Content Management tool, and some Sprout scripts need to know where to find
98    them.
99    
100    =item nmpdr_site_template_id
101    
102    Page number for the template page used to generate results that look like they're
103    part of the NMPDR web site.
104    
105    =back
106    
107  =over 4  =over 4
108    
109    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 C<LoadSproutTables -dbLoad -dbCreate "*"> and press ENTER. This will create  Type
 the C<dtx> files and load them.  
117    
118  =item 2      nohup LoadSproutTables -dbLoad -user=you -background "*" >null &
119    
120  Type C<TestSproutLoad 100226.1 83333.1> and press ENTER. This will validate  where C<you> is your user ID, and press ENTER.
 the Sprout database against the SEED data.  
121    
122  =item 3  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
124    directory. If your user name is C<Bruce> then the files will be named
125    C<outBruce.log>, C<errBruce.log>, and C<traceBruce.log> respectively.
126    
127  If any errors are detected in step (2), it is most likely due to a change in  If the load fails at some point and you are able to correct the problem, use the
128  SEED that did not make it to Sprout. Contact Bruce Parrello or Robert Olson  C<resume> option to restart it. For example, if the load failed while doing the
129  to get the code updated properly.  Feature load group, you would resume it using
130    
131  =item 4      nohup LoadSproutTables -dbLoad -dbCreate -user=you -resume -background Feature >null &
132    
133    =item 2
134    
135  Type C<index_sprout> and press ENTER. This will create the Glimpse indexes  Type
136  for the Sprout data.  
137        index_sprout_lucene
138    
139     and press ENTER. This will create the Lucene indexes for the Sprout data.
140    
141  =back  =back
142    
# Line 110  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 158  Line 200 
200  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
201  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
202    
203    =item Synonym
204    
205    Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
206    
207    =item Family
208    
209    Loads B<Family> and B<IsFamilyForFeature>.
210    
211  =item *  =item *
212    
213  Loads all of the above tables.  Loads all of the above tables.
# Line 173  Line 223 
223  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
224  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
225  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
226  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
227    default gene file-- C<genes.tbl> in the C<SproutData> directory.
228    
229  =item subsysFile  =item subsysFile
230    
# Line 184  Line 235 
235    
236  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
237    
238    =item user
239    
240    Suffix to use for trace, output, and error files created.
241    
242  =item dbLoad  =item dbLoad
243    
244  If TRUE, the database tables will be loaded automatically from the load files created.  If TRUE, the database tables will be loaded automatically from the load files created.
# Line 203  Line 258 
258    
259  If TRUE, only the group's primary entity will be loaded.  If TRUE, only the group's primary entity will be loaded.
260    
261    =item background
262    
263    Redirect the standard and error output to files in the FIG temporary directory.
264    
265    =item resume
266    
267    Resume an interrupted load, starting with the load group specified in the first
268    positional parameter.
269    
270    =item sql
271    
272    Trace SQL statements.
273    
274    =item phone
275    
276    Phone number to message when the load finishes.
277    
278  =back  =back
279    
280  =cut  =cut
# Line 221  Line 293 
293    
294  # Get the command-line parameters and options.  # Get the command-line parameters and options.
295  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
296                                              'ERDB', 'Load', 'Sprout'],                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
297                                              { geneFile => ["", "name of the genome list file"],                                              { geneFile => ["", "name of the genome list file"],
298                                                subsysFile => ["", "name of the trusted subsystem file"],                                                subsysFile => ["", "name of the trusted subsystem file"],
299                                                dbLoad => [0, "load the database from generated files"],                                                dbLoad => [0, "load the database from generated files"],
300                                                dbCreate => [0, "drop and re-create the database"],                                                dbCreate => [0, "drop and re-create the database"],
301                                                loadOnly => [0, "load the database from previously generated files"],                                                loadOnly => [0, "load the database from previously generated files"],
302                                                primaryOnly => [0, "only process the group's main entity"]                                                primaryOnly => [0, "only process the group's main entity"],
303                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
304                                                  phone => ["", "phone number (international format) to call when load finishes"],
305                                              },                                              },
306                                              "<group1> <group2> ...",                                              "<group1> <group2> ...",
307                                              @ARGV);                                              @ARGV);
# Line 240  Line 314 
314      my $db = $FIG_Config::sproutDB;      my $db = $FIG_Config::sproutDB;
315      DBKernel::CreateDB($db);      DBKernel::CreateDB($db);
316  }  }
317    # Compute the gene file name.
318    my $geneFile = $options->{geneFile};
319    if ($geneFile eq 'default') {
320        $geneFile = "$FIG_Config::sproutData/genes.tbl";
321    }
322  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
323  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
324  my $fig = FIG->new();  my $fig = FIG->new();
325  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
326  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
327  # Insure we have an output directory.  # Insure we have an output directory.
328  FIG::verify_dir($FIG_Config::sproutData);  FIG::verify_dir($FIG_Config::sproutData);
329    # If we're resuming, we only want to have 1 parameter.
330    my $resume = $options->{resume};
331    if ($resume && @parameters > 1) {
332        Confess("If resume=1, only one load group can be specified.");
333    } elsif (! @parameters) {
334        Trace("No load groups were specified.") if T(0);
335    }
336    # Set a variable to contain return type information.
337    my $rtype;
338    # Insure we catch errors.
339    eval {
340  # Process the parameters.  # Process the parameters.
341  for my $group (@parameters) {  for my $group (@parameters) {
342      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
343      my $stats;      my $stats;
344      if ($group eq 'Genome' || $group eq '*') {      if ($group eq 'Genome' || $group eq '*') {
345          $spl->LoadGenomeData();          $spl->LoadGenomeData();
346                $group = ResumeCheck($resume, $group);
347      }      }
348      if ($group eq 'Feature' || $group eq '*') {      if ($group eq 'Feature' || $group eq '*') {
349          $spl->LoadFeatureData();          $spl->LoadFeatureData();
350                $group = ResumeCheck($resume, $group);
351      }      }
352      if ($group eq 'Coupling' || $group eq '*') {      if ($group eq 'Coupling' || $group eq '*') {
353          $spl->LoadCouplingData();          $spl->LoadCouplingData();
354                $group = ResumeCheck($resume, $group);
355      }      }
356      if ($group eq 'Subsystem' || $group eq '*') {      if ($group eq 'Subsystem' || $group eq '*') {
357          $spl->LoadSubsystemData();          $spl->LoadSubsystemData();
358                $group = ResumeCheck($resume, $group);
359      }      }
360      if ($group eq 'Property' || $group eq '*') {      if ($group eq 'Property' || $group eq '*') {
361          $spl->LoadPropertyData();          $spl->LoadPropertyData();
362                $group = ResumeCheck($resume, $group);
363      }      }
364      if ($group eq 'Annotation' || $group eq '*') {      if ($group eq 'Annotation' || $group eq '*') {
365          $spl->LoadAnnotationData();          $spl->LoadAnnotationData();
366                $group = ResumeCheck($resume, $group);
367      }      }
368      if ($group eq 'BBH' || $group eq '*') {      if ($group eq 'BBH' || $group eq '*') {
369          $spl->LoadBBHData();          $spl->LoadBBHData();
370                $group = ResumeCheck($resume, $group);
371      }      }
372      if ($group eq 'Group' || $group eq '*') {      if ($group eq 'Group' || $group eq '*') {
373          $spl->LoadGroupData();          $spl->LoadGroupData();
374                $group = ResumeCheck($resume, $group);
375      }      }
376      if ($group eq 'Source' || $group eq '*') {      if ($group eq 'Source' || $group eq '*') {
377          $spl->LoadSourceData();          $spl->LoadSourceData();
378                $group = ResumeCheck($resume, $group);
379      }      }
380      if ($group eq 'External' || $group eq '*') {      if ($group eq 'External' || $group eq '*') {
381          $spl->LoadExternalData();          $spl->LoadExternalData();
382                $group = ResumeCheck($resume, $group);
383      }      }
384      if ($group eq 'Reaction' || $group eq '*') {      if ($group eq 'Reaction' || $group eq '*') {
385          $spl->LoadReactionData();          $spl->LoadReactionData();
386                $group = ResumeCheck($resume, $group);
387            }
388            if ($group eq 'Synonym' || $group eq '*') {
389                $spl->LoadSynonymData();
390                $group = ResumeCheck($resume, $group);
391            }
392            if ($group eq 'Family' || $group eq '*') {
393                $spl->LoadFamilyData();
394                $group = ResumeCheck($resume, $group);
395            }
396        }
397    };
398    if ($@) {
399        Trace("Load failed with error: $@") if T(0);
400        $rtype = "error";
401    } else {
402        Trace("Load complete.") if T(2);
403        $rtype = "no error";
404    }
405    if ($options->{phone}) {
406        my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
407        if ($msgID) {
408            Trace("Phone message sent with ID $msgID.") if T(2);
409        } else {
410            Trace("Phone message not sent.") if T(2);
411        }
412      }      }
413    
414    # If the resume flag is set, return "*", else return "".
415    sub ResumeCheck {
416        my ($resume, $group) = @_;
417        return ($resume ? "*" : $group);
418  }  }
 Trace("Load complete.") if T(2);  
419    
420  1;  1;

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