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revision 1.24, Fri Mar 31 18:38:35 2006 UTC revision 1.37, Sun Jul 30 01:23:47 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 46  Line 49 
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  Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load
52  against the FIG data. Again, the end of the C<trace.log> file will contain a summary  against the FIG data. The end of the trace log file will contain statistics on
53  of the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming  the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming
54  script, so you may want to set the trace level to 3 to see visible progress.  script, so you may want to set the trace level to 3 to see visible progress.
55    
56      TestSproutLoad -trace=3      TestSproutLoad -trace=3 [genomeID] ...
57    
58    The I<[genomeID]> specifies zero or more IDs of genomes to receive more thorough
59    testing. So, for example,
60    
61        TestSproutLoad -trace=3 100226.1 83333.1
62    
63    would do thorough testing of I<Streptomyces coelicolor A3-2> (100226.1) and
64    I<Escherichia coli K12> (83333.1).
65    
66  Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are  Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are
67  mixed in with the trace messages. They are all, however, marked with a trace type  mixed in with the trace messages. They are all, however, marked with a trace type
# Line 68  Line 79 
79  The test may reveal that some tables need to be reloaded, or that a software  The test may reveal that some tables need to be reloaded, or that a software
80  problem has crept into the Sprout.  problem has crept into the Sprout.
81    
82  Once all the tables have the correct data, C<index_sprout> can be run to create the  Once all the tables have the correct data, C<index_sprout_lucene> can be run to create the
83  Glimpse indexes.  Lucene search indexes. Lucene is a web site search engine produced by the Apache project.
84    It is written in Java, and in order to run it you must have the B<LuceneSearch> and
85    B<NmpdrConfigs> projects checked out from CVS and made.
86    
87    =head2 The NMPDR Web Site
88    
89    Sprout is the database engine for the NMPDR web site. The NMPDR web site consists of two
90    pieces that run on two different machines. The B<WEB> machine contains HTML pages
91    generated by a Content Management Tool.
92    
93  =head2 Procedure For Loading Sprout  =head2 Procedure For Loading Sprout
94    
95    In order to load the Sprout, you need to have the B<Sprout>, B<NmpdrConfigs>, and
96    B<LuceneSearch> projects checked out from CVS in addition to the standard FIG
97    projects. You must also set up the following B<FIG_Config.pm> variables in addition
98    to the normal ones.
99    
100    =over 4
101    
102    =item sproutData
103    
104    Name of the data directory for the Sprout load files.
105    
106    =item var
107    
108    Name of the directory to contain cached NMPDR pages. The most important file in
109    this directory is C<nmpdr_page_template.html>, which contains a skeleton page
110    from the main NMPDR web site. This skeleton page is used to generate output
111    pages that look like the other NMPDR pages.
112    
113    =item java
114    
115    Path to the Java runtime environment.
116    
117    =item sproutDB
118    
119    Name of the Sprout database
120    
121    =item dbuser
122    
123    User name for logging into the Sprout database.
124    
125    =item dbpass
126    
127    Password for logging into the Sprout database.
128    
129    =item nmpdr_site_url
130    
131    URL for the NMPDR cover pages. The NMPDR cover pages are informational and text
132    pages that serve as the entry point to the NMPDR web site. They are generated by
133    a Content Management tool, and some Sprout scripts need to know where to find
134    them.
135    
136    =item nmpdr_site_template_id
137    
138    Page number for the template page used to generate results that look like they're
139    part of the NMPDR web site.
140    
141    =back
142    
143  =over 4  =over 4
144    
145    The procedure for loading Sprout is as follows.
146    
147  =item 1  =item 1
148    
149  Type C<LoadSproutTables -dbLoad -dbCreate "*"> and press ENTER. This will create  Type
150  the C<dtx> files and load them. You may be asked for a password. If this is the  
151  case, simply press ENTER. If that does not work, use the C<dbpass> value specified      nohup LoadSproutTables -dbLoad -dbCreate -user=you -background "*" >null &
152  in your C<FIG_Config.pm> file.  
153    where C<you> is your user ID, and press ENTER. This will create the C<dtx> files
154    and load them. You may be asked for a password. If this is the case, simply
155    press ENTER. If that does not work, use the C<dbpass> value specified in
156    your C<FIG_Config.pm> file.
157    
158    The above command line runs the load in the background. The standard output,
159    standard error, and trace output will be directed to files in the FIG temporary
160    directory. If your user name is C<Bruce> then the files will be named
161    C<outBruce.log>, C<errBruce.log>, and C<traceBruce.log> respectively.
162    
163    If the load fails at some point and you are able to correct the problem, use the
164    C<resume> option to restart it. For example, if the load failed while doing the
165    Feature load group, you would resume it using
166    
167        nohup LoadSproutTables -dbLoad -dbCreate -user=you -resume -background Feature >null &
168    
169  =item 2  =item 2
170    
171  Type C<TestSproutLoad 100226.1 83333.1> and press ENTER. This will validate  Type
172  the Sprout database against the SEED data.  
173        nohup TestSproutLoad -user=you -background >null &100226.1 83333.1>
174    
175    and press ENTER. This will validate the Sprout database against the SEED data.
176    
177  =item 3  =item 3
178    
# Line 95  Line 182 
182    
183  =item 4  =item 4
184    
185  Type C<index_sprout> and press ENTER. This will create the Glimpse indexes  Type
186  for the Sprout data.  
187        index_sprout_lucene
188    
189     and press ENTER. This will create the Lucene indexes for the Sprout data.
190    
191    =item 5
192    
193    Change to the B<SproutData/Indexes> directory under B<FIGdisk> and look for the
194    directory created by C<index_sprout_lucene>. The directory name will be
195    something like C<Lucene.20060412-154112>. The numbers indicate the date and time
196    the index was created. In this case it was 04/12/2006 03:41:12pm. Type
197    
198        ln -sf directory Lucene
199    
200    where C<directory> is the new directory name, to point the C<Lucene> directory to the
201    new search index.
202    
203  =back  =back
204    
# Line 112  Line 214 
214    
215  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
216    
 =item Coupling  
   
 Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  
 B<UsesAsEvidence>.  
   
217  =item Feature  =item Feature
218    
219  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
220  B<IsLocatedIn>, B<FeatureLink>.  B<IsLocatedIn>, B<FeatureLink>.
221    
222    =item Coupling
223    
224    Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,
225    B<UsesAsEvidence>.
226    
227  =item Subsystem  =item Subsystem
228    
229  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
# Line 160  Line 262 
262  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
263  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
264    
265    =item Synonym
266    
267    Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
268    
269    =item Family
270    
271    Loads B<Family> and B<ContainsFeature>.
272    
273  =item *  =item *
274    
275  Loads all of the above tables.  Loads all of the above tables.
# Line 186  Line 296 
296    
297  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
298    
299    =item user
300    
301    Suffix to use for trace, output, and error files created.
302    
303  =item dbLoad  =item dbLoad
304    
305  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 205  Line 319 
319    
320  If TRUE, only the group's primary entity will be loaded.  If TRUE, only the group's primary entity will be loaded.
321    
322    =item background
323    
324    Redirect the standard and error output to files in the FIG temporary directory.
325    
326    =item resume
327    
328    Resume an interrupted load, starting with the load group specified in the first
329    positional parameter.
330    
331    =item sql
332    
333    Trace SQL statements.
334    
335    =item phone
336    
337    Phone number to message when the load finishes.
338    
339  =back  =back
340    
341  =cut  =cut
# Line 223  Line 354 
354    
355  # Get the command-line parameters and options.  # Get the command-line parameters and options.
356  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
357                                              'ERDB', 'Load', 'Sprout'],                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
358                                              { geneFile => ["", "name of the genome list file"],                                              { geneFile => ["", "name of the genome list file"],
359                                                subsysFile => ["", "name of the trusted subsystem file"],                                                subsysFile => ["", "name of the trusted subsystem file"],
360                                                dbLoad => [0, "load the database from generated files"],                                                dbLoad => [0, "load the database from generated files"],
# Line 231  Line 362 
362                                                loadOnly => [0, "load the database from previously generated files"],                                                loadOnly => [0, "load the database from previously generated files"],
363                                                primaryOnly => [0, "only process the group's main entity"],                                                primaryOnly => [0, "only process the group's main entity"],
364                                                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"],
365                                                  phone => ["", "phone number (international format) to call when load finishes"],
366                                              },                                              },
367                                              "<group1> <group2> ...",                                              "<group1> <group2> ...",
368                                              @ARGV);                                              @ARGV);
# Line 255  Line 387 
387  if ($resume && @parameters > 1) {  if ($resume && @parameters > 1) {
388      Confess("If resume=1, only one load group can be specified.");      Confess("If resume=1, only one load group can be specified.");
389  } elsif (! @parameters) {  } elsif (! @parameters) {
390      Confess("No load groups were specified.");      Trace("No load groups were specified.") if T(0);
391  }  }
392    # Set a variable to contain return type information.
393    my $rtype;
394    # Insure we catch errors.
395    eval {
396  # Process the parameters.  # Process the parameters.
397  for my $group (@parameters) {  for my $group (@parameters) {
398      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
399      my $stats;      my $stats;
400      if ($group eq 'Genome' || $group eq '*') {      if ($group eq 'Genome' || $group eq '*') {
401          $spl->LoadGenomeData();          $spl->LoadGenomeData();
402          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
403      }      }
404      if ($group eq 'Feature' || $group eq '*') {      if ($group eq 'Feature' || $group eq '*') {
405          $spl->LoadFeatureData();          $spl->LoadFeatureData();
406          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
407      }      }
408      if ($group eq 'Coupling' || $group eq '*') {      if ($group eq 'Coupling' || $group eq '*') {
409          $spl->LoadCouplingData();          $spl->LoadCouplingData();
410          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
411      }      }
412      if ($group eq 'Subsystem' || $group eq '*') {      if ($group eq 'Subsystem' || $group eq '*') {
413          $spl->LoadSubsystemData();          $spl->LoadSubsystemData();
414          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
415      }      }
416      if ($group eq 'Property' || $group eq '*') {      if ($group eq 'Property' || $group eq '*') {
417          $spl->LoadPropertyData();          $spl->LoadPropertyData();
418          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
419      }      }
420      if ($group eq 'Annotation' || $group eq '*') {      if ($group eq 'Annotation' || $group eq '*') {
421          $spl->LoadAnnotationData();          $spl->LoadAnnotationData();
422          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
423      }      }
424      if ($group eq 'BBH' || $group eq '*') {      if ($group eq 'BBH' || $group eq '*') {
425          $spl->LoadBBHData();          $spl->LoadBBHData();
426          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
427      }      }
428      if ($group eq 'Group' || $group eq '*') {      if ($group eq 'Group' || $group eq '*') {
429          $spl->LoadGroupData();          $spl->LoadGroupData();
430          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
431      }      }
432      if ($group eq 'Source' || $group eq '*') {      if ($group eq 'Source' || $group eq '*') {
433          $spl->LoadSourceData();          $spl->LoadSourceData();
434          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
435      }      }
436      if ($group eq 'External' || $group eq '*') {      if ($group eq 'External' || $group eq '*') {
437          $spl->LoadExternalData();          $spl->LoadExternalData();
438          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
439      }      }
440      if ($group eq 'Reaction' || $group eq '*') {      if ($group eq 'Reaction' || $group eq '*') {
441          $spl->LoadReactionData();          $spl->LoadReactionData();
442          $group = ResumeCheck($resume);              $group = ResumeCheck($resume, $group);
     }  
   
443  }  }
444            if ($group eq 'Synonym' || $group eq '*') {
445                $spl->LoadSynonymData();
446                $group = ResumeCheck($resume, $group);
447            }
448            if ($group eq 'Family' || $group eq '*') {
449                $spl->LoadFamilyData();
450                $group = ResumeCheck($resume, $group);
451            }
452        }
453    };
454    if ($@) {
455        Trace("Load failed with error: $@") if T(0);
456        $rtype = "error";
457    } else {
458  Trace("Load complete.") if T(2);  Trace("Load complete.") if T(2);
459        $rtype = "no error";
460    }
461    if ($options->{phone}) {
462        my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
463        if ($msgID) {
464            Trace("Phone message sent with ID $msgID.") if T(2);
465        } else {
466            Trace("Phone message not sent.") if T(2);
467        }
468    }
469    
470  # If the resume flag is set, return "*", else return "".  # If the resume flag is set, return "*", else return "".
471  sub ResumeCheck {  sub ResumeCheck {
472      my ($resume) = @_;      my ($resume, $group) = @_;
473      return ($resume ? "*" : "");      return ($resume ? "*" : $group);
474  }  }
475    
476  1;  1;

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