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2    
3  =head1 Load Sprout Tables  =head1 Load Sprout Tables
4    
5  Load a group of Sprout tables from the command line. The parameters are the names of  =head2 Introduction
6  the table groups to load. 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
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
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  =over 4
150    
# Line 11  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    
155    =item Feature
156    
157    Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
158    B<IsLocatedIn>, B<FeatureLink>.
159    
160  =item Coupling  =item Coupling
161    
162  Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,
163  B<UsesAsEvidence>.  B<UsesAsEvidence>.
164    
165  =item Feature  =item Subsystem
166    
167  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
168  B<IsLocatedIn>, B<IsBidirectionalBestHitOf>, B<FeatureLink>.  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 Subsystem  =item Annotation
174    
175    Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
176    B<MadeAnnotation>.
177    
178    =item Property
179    
180    Loads B<Property>, B<HasProperty>.
181    
182    =item Group
183    
184    Loads B<GenomeGroups>.
185    
186    =item Source
187    
188    Loads B<Source>, B<ComesFrom>, B<SourceURL>.
189    
190    =item External
191    
192    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<Subsystem>, B<Role>, B<SSCell>, B<Diagram>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Family> and B<IsFamilyForFeature>.
206  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>.  
207    =item *
208    
209    Loads all of the above tables.
210    
211  =back  =back
212    
213  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>.  
214    
215  =over 4  =over 4
216    
# Line 38  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 49  Line 231 
231    
232  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
233    
234    =item user
235    
236    Suffix to use for trace, output, and error files created.
237    
238    =item dbLoad
239    
240    If TRUE, the database tables will be loaded automatically from the load files created.
241    
242    =item dbCreate
243    
244    If TRUE, the database will be created. If the database exists already, it will be
245    dropped. Use the function with caution.
246    
247    =item loadOnly
248    
249    If TRUE, the database tables will be loaded from existing load files. Load files
250    will not be created. This option is useful if you are setting up a copy of Sprout
251    and have load files already set up from the original version.
252    
253    =item primaryOnly
254    
255    If TRUE, only the group's primary entity will be loaded.
256    
257    =item background
258    
259    Redirect the standard and error output to files in the FIG temporary directory.
260    
261    =item resume
262    
263    Resume an interrupted load, starting with the load group specified in the first
264    positional parameter.
265    
266    =item sql
267    
268    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 56  Line 278 
278  use strict;  use strict;
279  use Tracer;  use Tracer;
280  use DocUtils;  use DocUtils;
 use TestUtils;  
281  use Cwd;  use Cwd;
282  use FIG;  use FIG;
283  use SFXlate;  use SFXlate;
# Line 64  Line 285 
285  use File::Path;  use File::Path;
286  use SproutLoad;  use SproutLoad;
287  use Stats;  use Stats;
288    use SFXlate;
289    
290  # Get the command-line parameters and options.  # Get the command-line parameters and options.
291  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
292                                                      trace => 3 },                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
293                                                { geneFile => ["", "name of the genome list file"],
294                                                  subsysFile => ["", "name of the trusted subsystem file"],
295                                                  dbLoad => [0, "load the database from generated files"],
296                                                  dbCreate => [0, "drop and re-create the database"],
297                                                  loadOnly => [0, "load the database from previously generated files"],
298                                                  primaryOnly => [0, "only process the group's main entity"],
299                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
300                                                  phone => ["", "phone number (international format) to call when load finishes"],
301                                                },
302                                                "<group1> <group2> ...",
303                                                                 @ARGV);                                                                 @ARGV);
304  # Set up tracing.  # If we're doing a load-only, turn on loading.
305  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Tracer Load", "+>$FIG_Config::temp/trace.log");  if ($options->{loadOnly}) {
306  # Create the sprout loader object.      $options->{dbLoad} = 1
307    }
308    if ($options->{dbCreate}) {
309        # Here we want to drop and re-create the database.
310        my $db = $FIG_Config::sproutDB;
311        DBKernel::CreateDB($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
319    # 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();  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
322  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile},  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
323                            $options->{subsysFile});  # Insure we have an output directory.
324    FIG::verify_dir($FIG_Config::sproutData);
325    # If we're resuming, we only want to have 1 parameter.
326    my $resume = $options->{resume};
327    if ($resume && @parameters > 1) {
328        Confess("If resume=1, only one load group can be specified.");
329    } elsif (! @parameters) {
330        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);
339      my $stats;      my $stats;
340      if ($group eq 'Genome') {          if ($group eq 'Genome' || $group eq '*') {
341          $spl->LoadGenomeData();          $spl->LoadGenomeData();
342      } elsif ($group eq 'Feature') {              $group = ResumeCheck($resume, $group);
343            }
344            if ($group eq 'Feature' || $group eq '*') {
345          $spl->LoadFeatureData();          $spl->LoadFeatureData();
346      } elsif ($group eq 'Coupling') {              $group = ResumeCheck($resume, $group);
347            }
348            if ($group eq 'Coupling' || $group eq '*') {
349          $spl->LoadCouplingData();          $spl->LoadCouplingData();
350      } elsif ($group eq 'Subsystem') {              $group = ResumeCheck($resume, $group);
351            }
352            if ($group eq 'Subsystem' || $group eq '*') {
353          $spl->LoadSubsystemData();          $spl->LoadSubsystemData();
354      } elsif ($group eq 'Property') {              $group = ResumeCheck($resume, $group);
355            }
356            if ($group eq 'Property' || $group eq '*') {
357          $spl->LoadPropertyData();          $spl->LoadPropertyData();
358      } else {              $group = ResumeCheck($resume, $group);
         Confess("Invalid group name $group.");  
359      }      }
360            if ($group eq 'Annotation' || $group eq '*') {
361                $spl->LoadAnnotationData();
362                $group = ResumeCheck($resume, $group);
363  }  }
364            #if ($group eq 'BBH' || $group eq '*') {
365            #    $spl->LoadBBHData();
366            #    $group = ResumeCheck($resume, $group);
367            #}
368            if ($group eq 'Group' || $group eq '*') {
369                $spl->LoadGroupData();
370                $group = ResumeCheck($resume, $group);
371            }
372            if ($group eq 'Source' || $group eq '*') {
373                $spl->LoadSourceData();
374                $group = ResumeCheck($resume, $group);
375            }
376            if ($group eq 'External' || $group eq '*') {
377                $spl->LoadExternalData();
378                $group = ResumeCheck($resume, $group);
379            }
380            if ($group eq 'Reaction' || $group eq '*') {
381                $spl->LoadReactionData();
382                $group = ResumeCheck($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 $msgID.") if T(2);
405        } else {
406            Trace("Phone message not sent.") if T(2);
407        }
408    }
409    
410    # If the resume flag is set, return "*", else return "".
411    sub ResumeCheck {
412        my ($resume, $group) = @_;
413        return ($resume ? "*" : $group);
414    }
415    
416  1;  1;

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