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revision 1.11, Wed Nov 2 21:45:08 2005 UTC revision 1.47, Tue Feb 5 05:04:26 2008 UTC
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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 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 Coupling  =item java
78    
79  Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  Path to the Java runtime environment.
80  B<UsesAsEvidence>.  
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    Most of the above preparation is performed by the B<NMPDRSetup> utility.
108    NMPDRSetup prints the instructions for completing the process, including
109    loading the Sprout database. The specific procedure for loading
110    the Sprout data, however, is as follows.
111    
112    =head2 LoadSproutTables Command
113    
114    C<LoadSproutTables> creates the load files for Sprout tables and optionally loads them.
115    The parameters are the names of the table groups whose data is to be created.
116    The legal table group names are given below.
117    
118    =over 4
119    
120    =item Genome
121    
122    Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
123    
124  =item Feature  =item Feature
125    
126  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
127  B<IsLocatedIn>, B<FeatureLink>.  B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,
128    B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,
129    B<CDD>, and B<IsPresentOnProteinOf>
130    
131  =item Subsystem  =item Subsystem
132    
133  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
134  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
135  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
136  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
137    B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>,
138    B<ContainsFeature>.
139    
140  =item Annotation  =item Annotation
141    
142  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
143  B<MadeAnnotation>.  B<MadeAnnotation>.
144    
 =item Diagram  
   
 Loads B<Diagram>, B<RoleOccursIn>.  
   
145  =item Property  =item Property
146    
147  Loads B<Property>, B<HasProperty>.  Loads B<Property>, B<HasProperty>.
148    
 =item BBH  
   
 Loads B<IsBidirectionalBestHitOf>.  
   
149  =item Group  =item Group
150    
151  Loads B<GenomeGroups>.  Loads B<GenomeGroups>.
# Line 62  Line 163 
163  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
164  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
165    
166    =item Synonym
167    
168    Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
169    
170    =item Family
171    
172    Loads B<Family> and B<IsFamilyForFeature>.
173    
174    =item Drug
175    
176    Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.
177    
178  =item *  =item *
179    
180  Loads all of the above tables.  Loads all of the above tables.
# Line 77  Line 190 
190  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
191  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
192  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
193  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
194    default gene file-- C<genes.tbl> in the C<SproutData> directory.
195    
196  =item subsysFile  =item subsysFile
197    
# Line 88  Line 202 
202    
203  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
204    
205  =item limitedFeatures  =item user
206    
207  Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.  Suffix to use for trace, output, and error files created.
208    
209  =item dbLoad  =item dbLoad
210    
211  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.
212    
213    =item dbCreate
214    
215    If TRUE, the database will be created. If the database exists already, it will be
216    dropped. Use the function with caution.
217    
218    =item loadOnly
219    
220    If TRUE, the database tables will be loaded from existing load files. Load files
221    will not be created. This option is useful if you are setting up a copy of Sprout
222    and have load files already set up from the original version.
223    
224    =item background
225    
226    Redirect the standard and error output to files in the FIG temporary directory.
227    
228    =item resume
229    
230    Resume an interrupted load, starting with the load group specified in the first
231    positional parameter.
232    
233    =item sql
234    
235    Trace SQL statements.
236    
237    =item phone
238    
239    Phone number to message when the load finishes.
240    
241  =back  =back
242    
243  =cut  =cut
244    
245  use strict;  use strict;
246  use Tracer;  use Tracer;
 use DocUtils;  
247  use Cwd;  use Cwd;
248  use FIG;  use FIG;
249  use SFXlate;  use SFXlate;
# Line 112  Line 253 
253  use Stats;  use Stats;
254  use SFXlate;  use SFXlate;
255    
256    # This is a list of the load groups in their natural order. We'll go through these in sequence, processing
257    # the ones the user asks for.
258    my @LoadGroups = qw(Genome Feature Subsystem Property Annotation Source External Reaction Synonym Family Drug);
259    
260  # Get the command-line parameters and options.  # Get the command-line parameters and options.
261  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
262                                                      trace => 3, limitedFeatures => 0,                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
263                                                      dbLoad => 0 }, @ARGV);                                              { geneFile => ["", "name of the genome list file"],
264  # Set up tracing.                                                subsysFile => ["", "name of the trusted subsystem file"],
265  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");                                                dbLoad => [0, "load the database from generated files"],
266                                                  dbCreate => [0, "drop and re-create the database"],
267                                                  loadOnly => [0, "load the database from previously generated files"],
268                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
269                                                  phone => ["", "phone number (international format) to call when load finishes"],
270                                                },
271                                                "<group1> <group2> ...",
272                                                @ARGV);
273    # If we're doing a load-only, turn on loading.
274    if ($options->{loadOnly}) {
275        $options->{dbLoad} = 1
276    }
277    if ($options->{dbCreate}) {
278        # Here we want to drop and re-create the database.
279        my $db = $FIG_Config::sproutDB;
280        DBKernel::CreateDB($db);
281    }
282    # Compute the gene file name.
283    my $geneFile = $options->{geneFile};
284    if ($geneFile eq 'default') {
285        $geneFile = "$FIG_Config::sproutData/genes.tbl";
286    }
287  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
288  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
289  my $fig = FIG->new();  my $fig = FIG->new();
290  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
291  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
292    # Insure we have an output directory.
293    FIG::verify_dir($FIG_Config::sproutData);
294    # Check for the "*" option.
295    if ($parameters[0] eq '*') {
296        @parameters = @LoadGroups;
297    }
298    # If we're resuming, we only want to have 1 parameter.
299    my $resume = $options->{resume};
300    if ($resume && @parameters > 1) {
301        Confess("If resume=1, only one load group can be specified.");
302    } elsif (! @parameters) {
303        Trace("No load groups were specified.") if T(0);
304    }
305    # Process the resume option here. We modify the incoming parameters to
306    # contain the resume group and everything after it.
307    if ($resume) {
308        # Save the starting group.
309        my $resumeGroup = $parameters[0];
310        # Copy the load group list into the parameter array.
311        @parameters = @LoadGroups;
312        # Shift out the groups until we reach our desired starting point.
313        while (scalar(@parameters) && $parameters[0] ne $resumeGroup) {
314            shift @parameters;
315        }
316        if (! @parameters) {
317            Confess("Resume group \"$resumeGroup\" not found.");
318        }
319    }
320    # Set a variable to contain return type information.
321    my $rtype;
322    # Set up a statistics object for statistics about the entire load.
323    my $totalStats = Stats->new();
324    # Insure we catch errors.
325    eval {
326  # Process the parameters.  # Process the parameters.
327  for my $group (@parameters) {  for my $group (@parameters) {
328      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
329      my $stats;          # Compute the string we want to execute.
330      if ($group eq 'Genome' || $group eq '*') {          my $code = "\$spl->Load${group}Data()";
331          $spl->LoadGenomeData();          # Load this group.
332      }          my $stats = eval($code);
333      if ($group eq 'Feature' || $group eq '*') {          if ($@) {
334          $spl->LoadFeatureData();              Confess("Load group error: $@");
335      }          }
336      if ($group eq 'Coupling' || $group eq '*') {          # Merge the statistics into the master.
337          $spl->LoadCouplingData();          $totalStats->Accumulate($stats);
338      }      }
339      if ($group eq 'Subsystem' || $group eq '*') {      # Compute the statistical display.
340          $spl->LoadSubsystemData();      my $statDisplay = $totalStats->Show();
341      }      # Display it.
342      if ($group eq 'Property' || $group eq '*') {      Trace("Statistics for this load:\n$statDisplay") if T(2);
343          $spl->LoadPropertyData();      # Check for a "table load failed" message. If we find one, we want
344      }      # to end with an error.
345      if ($group eq 'Diagram' || $group eq '*') {      if ($statDisplay =~ /table load failed/i) {
346          $spl->LoadDiagramData();          Confess("One or more table loads failed.");
347      }      }
348      if ($group eq 'Annotation' || $group eq '*') {  };
349          $spl->LoadAnnotationData();  if ($@) {
350      }      Trace("Load failed with error: $@") if T(0);
351      if ($group eq 'BBH' || $group eq '*') {      $rtype = "error";
352          $spl->LoadBBHData();  } else {
353      }      Trace("Load complete.") if T(2);
354      if ($group eq 'Group' || $group eq '*') {      $rtype = "no error";
         $spl->LoadGroupData();  
     }  
     if ($group eq 'Source' || $group eq '*') {  
         $spl->LoadSourceData();  
     }  
     if ($group eq 'External' || $group eq '*') {  
         $spl->LoadExternalData();  
355      }      }
356      if ($group eq 'Reaction' || $group eq '*') {  if ($options->{phone}) {
357          $spl->LoadReactionData();      my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
358        if ($msgID) {
359            Trace("Phone message sent with ID $msgID.") if T(2);
360        } else {
361            Trace("Phone message not sent.") if T(2);
362      }      }
   
363  }  }
 Trace("Load complete.") if T(2);  
364    
365  1;  1;

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