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2    
3  =head1 Load Sprout Tables  =head1 Load Sprout Tables
4    
5  Create the load files for a group of Sprout tables. The parameters are the names of  =head2 Introduction
6  the table groups whose data is to be created. The legal table group names are given below.  
7    The Sprout database reflects a snapshot of the SEED taken at a particular point in
8    time. At some point in the future, it will be possible to add annotations to the
9    Sprout data. All records added to Sprout after the snapshot is taken are
10    specially-marked so that the changes can be copied to the SEED. The SEED remains
11    the live version of the data.
12    
13    The snapshot is produced by reading the SEED data and writing it to sequential
14    files. There is one file per Sprout table, and each such file's name consists of
15    the table name with the suffix C<dtx>. Thus, the file for the C<Genome> table
16    would be named C<Genome.dtx>. These files are used to load the actual Sprout
17    database and to generate Glimpse indices.
18    
19    To load all the Sprout tables and then validate the result, you need to issue three
20    commands.
21    
22        LoadSproutTables -dbLoad -dbCreate "*"
23        TestSproutLoad [genomeID] ...
24        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
30    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
32    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
34    load of the B<MadeAnnotation> and B<Compound> tables, you would need to run
35    
36        LoadSproutTables -dbLoad Annotation Reaction
37    
38    because B<MadeAnnotation> is in the C<Annotation> group, and B<Compound> is in the
39    C<Reaction> group. A list of the groups is given below.
40    
41    You can omit the C<dbLoad> option to create the load files without
42    loading the database, and you can add a C<trace> option to change the trace level.
43    The command below creates the Genome-related load files with a trace level of 3 and
44    does not load them into the Sprout database.
45    
46        LoadSproutTables -trace=3 Genome
47    
48    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.
50    
51    =head2 The NMPDR Web Site
52    
53    Sprout is the database engine for the NMPDR web site. The NMPDR web site consists of two
54    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
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  =over 4
65    
66  =item Genome  =item sproutData
67    
68  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.  Name of the data directory for the Sprout load files.
69    
70  =item Coupling  =item var
71    
72  Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  Name of the directory to contain cached NMPDR pages. The most important file in
73  B<UsesAsEvidence>.  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
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
115    
116    Type
117    
118        nohup LoadSproutTables -dbLoad -user=you -background "*" >null &
119    
120    where C<you> is your user ID, and press ENTER.
121    
122    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 the load fails at some point and you are able to correct the problem, use the
128    C<resume> option to restart it. For example, if the load failed while doing the
129    Feature load group, you would resume it using
130    
131        nohup LoadSproutTables -dbLoad -dbCreate -user=you -resume -background Feature >null &
132    
133    =item 2
134    
135    Type
136    
137        index_sprout_lucene
138    
139     and press ENTER. This will create the Lucene indexes for the Sprout data.
140    
141    =back
142    
143    =head2 LoadSproutTables Command
144    
145    C<LoadSproutTables> creates the load files for Sprout tables and optionally loads them.
146    The parameters are the names of the table groups whose data is to be created.
147    The legal table group names are given below.
148    
149    =over 4
150    
151    =item Genome
152    
153    Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
154    
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>,
168  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>.  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
169    B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
170    B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
171    B<RoleOccursIn>.
172    
173  =item Annotation  =item Annotation
174    
175  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
176  B<MadeAnnotation>.  B<MadeAnnotation>.
177    
 =item Diagram  
   
 Loads B<Diagram>, B<RoleOccursIn>.  
   
178  =item Property  =item Property
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 55  Line 191 
191    
192  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.
193    
194    =item Reaction
195    
196    Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
197    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 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    
215  Loads all of the above tables.  Loads all of the above tables.
216    
217  =back  =back
218    
219  There are two command-line options, given below. Note that in the command line, spaces  The command-line options are given below.
 inside parameters should be represented by C<\b>.  
220    
221  =over 4  =over 4
222    
# Line 71  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 82  Line 237 
237    
238  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
239    
240    =item user
241    
242    Suffix to use for trace, output, and error files created.
243    
244    =item dbLoad
245    
246    If TRUE, the database tables will be loaded automatically from the load files created.
247    
248    =item dbCreate
249    
250    If TRUE, the database will be created. If the database exists already, it will be
251    dropped. Use the function with caution.
252    
253    =item loadOnly
254    
255    If TRUE, the database tables will be loaded from existing load files. Load files
256    will not be created. This option is useful if you are setting up a copy of Sprout
257    and have load files already set up from the original version.
258    
259    =item primaryOnly
260    
261    If TRUE, only the group's primary entity will be loaded.
262    
263    =item background
264    
265    Redirect the standard and error output to files in the FIG temporary directory.
266    
267    =item resume
268    
269    Resume an interrupted load, starting with the load group specified in the first
270    positional parameter.
271    
272    =item sql
273    
274    Trace SQL statements.
275    
276    =item phone
277    
278    Phone number to message when the load finishes.
279    
280  =back  =back
281    
282  =cut  =cut
# Line 96  Line 291 
291  use File::Path;  use File::Path;
292  use SproutLoad;  use SproutLoad;
293  use Stats;  use Stats;
294    use SFXlate;
295    
296  # Get the command-line parameters and options.  # Get the command-line parameters and options.
297  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
298                                                      trace => 3 },                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
299                                                { geneFile => ["", "name of the genome list file"],
300                                                  subsysFile => ["", "name of the trusted subsystem file"],
301                                                  dbLoad => [0, "load the database from generated files"],
302                                                  dbCreate => [0, "drop and re-create the database"],
303                                                  loadOnly => [0, "load the database from previously generated files"],
304                                                  primaryOnly => [0, "only process the group's main entity"],
305                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
306                                                  phone => ["", "phone number (international format) to call when load finishes"],
307                                                },
308                                                "<group1> <group2> ...",
309                                                                 @ARGV);                                                                 @ARGV);
310  # Set up tracing.  # If we're doing a load-only, turn on loading.
311  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");  if ($options->{loadOnly}) {
312  # Create the sprout loader object.      $options->{dbLoad} = 1
313    }
314    if ($options->{dbCreate}) {
315        # Here we want to drop and re-create the database.
316        my $db = $FIG_Config::sproutDB;
317        DBKernel::CreateDB($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
325    # 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();  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
328  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile},  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
329                            $options->{subsysFile});  # Insure we have an output directory.
330    FIG::verify_dir($FIG_Config::sproutData);
331    # If we're resuming, we only want to have 1 parameter.
332    my $resume = $options->{resume};
333    if ($resume && @parameters > 1) {
334        Confess("If resume=1, only one load group can be specified.");
335    } elsif (! @parameters) {
336        Trace("No load groups were specified.") if T(0);
337    }
338    # Set a variable to contain return type information.
339    my $rtype;
340    # Insure we catch errors.
341    eval {
342  # Process the parameters.  # Process the parameters.
343  for my $group (@parameters) {  for my $group (@parameters) {
344      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
345      my $stats;      my $stats;
346      if ($group eq 'Genome' || $group eq '*') {      if ($group eq 'Genome' || $group eq '*') {
347          $spl->LoadGenomeData();          $spl->LoadGenomeData();
348                $group = ResumeCheck($resume, $group);
349      }      }
350      if ($group eq 'Feature' || $group eq '*') {      if ($group eq 'Feature' || $group eq '*') {
351          $spl->LoadFeatureData();          $spl->LoadFeatureData();
352                $group = ResumeCheck($resume, $group);
353      }      }
354      if ($group eq 'Coupling' || $group eq '*') {      if ($group eq 'Coupling' || $group eq '*') {
355          $spl->LoadCouplingData();          $spl->LoadCouplingData();
356                $group = ResumeCheck($resume, $group);
357      }      }
358      if ($group eq 'Subsystem' || $group eq '*') {      if ($group eq 'Subsystem' || $group eq '*') {
359          $spl->LoadSubsystemData();          $spl->LoadSubsystemData();
360                $group = ResumeCheck($resume, $group);
361      }      }
362      if ($group eq 'Property' || $group eq '*') {      if ($group eq 'Property' || $group eq '*') {
363          $spl->LoadPropertyData();          $spl->LoadPropertyData();
364      }              $group = ResumeCheck($resume, $group);
     if ($group eq 'Diagram' || $group eq '*') {  
         $spl->LoadDiagramData();  
365      }      }
366      if ($group eq 'Annotation' || $group eq '*') {      if ($group eq 'Annotation' || $group eq '*') {
367          $spl->LoadAnnotationData();          $spl->LoadAnnotationData();
368      }              $group = ResumeCheck($resume, $group);
     if ($group eq 'BBH' || $group eq '*') {  
         $spl->LoadBBHData();  
369      }      }
370      if ($group eq 'Group' || $group eq '*') {      if ($group eq 'Group' || $group eq '*') {
371          $spl->LoadGroupData();          $spl->LoadGroupData();
372                $group = ResumeCheck($resume, $group);
373      }      }
374      if ($group eq 'Source' || $group eq '*') {      if ($group eq 'Source' || $group eq '*') {
375          $spl->LoadSourceData();          $spl->LoadSourceData();
376                $group = ResumeCheck($resume, $group);
377      }      }
378      if ($group eq 'External' || $group eq '*') {      if ($group eq 'External' || $group eq '*') {
379          $spl->LoadExternalData();          $spl->LoadExternalData();
380                $group = ResumeCheck($resume, $group);
381            }
382            if ($group eq 'Reaction' || $group eq '*') {
383                $spl->LoadReactionData();
384                $group = ResumeCheck($resume, $group);
385            }
386            if ($group eq 'Synonym' || $group eq '*') {
387                $spl->LoadSynonymData();
388                $group = ResumeCheck($resume, $group);
389            }
390            if ($group eq 'Family' || $group eq '*') {
391                $spl->LoadFamilyData();
392                $group = ResumeCheck($resume, $group);
393            }
394    #        if ($group eq 'Drug' || $group eq '*') {
395    #            $spl->LoadDrugData();
396    #            $group = ResumeCheck($resume, $group);
397    #        }
398        }
399    };
400    if ($@) {
401        Trace("Load failed with error: $@") if T(0);
402        $rtype = "error";
403    } else {
404        Trace("Load complete.") if T(2);
405        $rtype = "no error";
406    }
407    if ($options->{phone}) {
408        my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
409        if ($msgID) {
410            Trace("Phone message sent with ID $msgID.") if T(2);
411        } else {
412            Trace("Phone message not sent.") if T(2);
413        }
414      }      }
415    
416    # If the resume flag is set, return "*", else return "".
417    sub ResumeCheck {
418        my ($resume, $group) = @_;
419        return ($resume ? "*" : $group);
420  }  }
 Trace("Load complete.") if T(2);  
421    
422  1;  1;

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