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revision 1.4, Sun Sep 11 17:06:21 2005 UTC revision 1.44, Mon Jul 16 20:05:55 2007 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 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  =item Coupling  =head2 LoadSproutTables Command
144    
145  Loads B<Coupling>, B<IsEvidencedBy>, B<PCH>, B<ParticipatesInCoupling>,  C<LoadSproutTables> creates the load files for Sprout tables and optionally loads them.
146  B<UsesAsEvidence>.  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>, B<IsAliasOf>, B<CDD>, B<HasFeature>,
159    B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,
160    B<CDD>, and B<IsPresentOnProteinOf>
161    
162  =item Subsystem  =item Subsystem
163    
164  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
165  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>.  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
166    B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
167    B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
168    B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>,
169    B<ContainsFeature>.
170    
171  =item Annotation  =item Annotation
172    
173  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,
174  B<MadeAnnotation>.  B<MadeAnnotation>.
175    
 =item Diagram  
   
 Loads B<Diagram>, B<RoleOccursIn>.  
   
176  =item Property  =item Property
177    
178  Loads B<Property>, B<HasProperty>.  Loads B<Property>, B<HasProperty>.
179    
 =item BBH  
   
 Loads B<IsBidirectionalBestHitOf>.  
   
180  =item Group  =item Group
181    
182  Loads B<GenomeGroups>.  Loads B<GenomeGroups>.
# Line 55  Line 189 
189    
190  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.
191    
192    =item Reaction
193    
194    Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
195    B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
196    
197    =item Synonym
198    
199    Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
200    
201    =item Family
202    
203    Loads B<Family> and B<IsFamilyForFeature>.
204    
205    =item Drug
206    
207    Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.
208    
209  =item *  =item *
210    
211  Loads all of the above tables.  Loads all of the above tables.
212    
213  =back  =back
214    
215  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>.  
216    
217  =over 4  =over 4
218    
# Line 71  Line 221 
221  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
222  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
223  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
224  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
225    default gene file-- C<genes.tbl> in the C<SproutData> directory.
226    
227  =item subsysFile  =item subsysFile
228    
# Line 82  Line 233 
233    
234  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
235    
236    =item user
237    
238    Suffix to use for trace, output, and error files created.
239    
240    =item dbLoad
241    
242    If TRUE, the database tables will be loaded automatically from the load files created.
243    
244    =item dbCreate
245    
246    If TRUE, the database will be created. If the database exists already, it will be
247    dropped. Use the function with caution.
248    
249    =item loadOnly
250    
251    If TRUE, the database tables will be loaded from existing load files. Load files
252    will not be created. This option is useful if you are setting up a copy of Sprout
253    and have load files already set up from the original version.
254    
255    =item background
256    
257    Redirect the standard and error output to files in the FIG temporary directory.
258    
259    =item resume
260    
261    Resume an interrupted load, starting with the load group specified in the first
262    positional parameter.
263    
264    =item sql
265    
266    Trace SQL statements.
267    
268    =item phone
269    
270    Phone number to message when the load finishes.
271    
272  =back  =back
273    
274  =cut  =cut
# Line 96  Line 283 
283  use File::Path;  use File::Path;
284  use SproutLoad;  use SproutLoad;
285  use Stats;  use Stats;
286    use SFXlate;
287    
288    # This is a list of the load groups in their natural order. We'll go through these in sequence, processing
289    # the ones the user asks for.
290    my @LoadGroups = qw(Genome Feature Subsystem Property Annotation Source External Reaction Synonym Family Drug);
291    
292  # Get the command-line parameters and options.  # Get the command-line parameters and options.
293  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
294                                                      trace => 3 },                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
295                                                { geneFile => ["", "name of the genome list file"],
296                                                  subsysFile => ["", "name of the trusted subsystem file"],
297                                                  dbLoad => [0, "load the database from generated files"],
298                                                  dbCreate => [0, "drop and re-create the database"],
299                                                  loadOnly => [0, "load the database from previously generated files"],
300                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
301                                                  phone => ["", "phone number (international format) to call when load finishes"],
302                                                },
303                                                "<group1> <group2> ...",
304                                                                 @ARGV);                                                                 @ARGV);
305  # Set up tracing.  # If we're doing a load-only, turn on loading.
306  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");  if ($options->{loadOnly}) {
307  # Create the sprout loader object.      $options->{dbLoad} = 1
308    }
309    if ($options->{dbCreate}) {
310        # Here we want to drop and re-create the database.
311        my $db = $FIG_Config::sproutDB;
312        DBKernel::CreateDB($db);
313    }
314    # Compute the gene file name.
315    my $geneFile = $options->{geneFile};
316    if ($geneFile eq 'default') {
317        $geneFile = "$FIG_Config::sproutData/genes.tbl";
318    }
319    # Create the sprout loader object. Note that the Sprout object does not
320    # open the database unless the "dbLoad" option is turned on.
321  my $fig = FIG->new();  my $fig = FIG->new();
322  my $sprout = SFXlate->new_sprout_only();  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
323  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile},  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
324                            $options->{subsysFile});  # Insure we have an output directory.
325    FIG::verify_dir($FIG_Config::sproutData);
326    # If we're resuming, we only want to have 1 parameter.
327    my $resume = $options->{resume};
328    if ($resume && @parameters > 1) {
329        Confess("If resume=1, only one load group can be specified.");
330    } elsif (! @parameters) {
331        Trace("No load groups were specified.") if T(0);
332    }
333    # Process the resume option here. We modify the incoming parameters to
334    # contain the resume group and everything after it.
335    if ($resume) {
336        # Save the starting group.
337        my $resumeGroup = $parameters[0];
338        # Copy the load group list into the parameter array.
339        @parameters = @LoadGroups;
340        push @parameters, @LoadGroups;
341        # Shift out the groups until we reach our desired starting point.
342        while (scalar(@parameters) && $parameters[0] ne $resumeGroup) {
343            shift @parameters;
344        }
345        if (! @parameters) {
346            Confess("Resume group \"$resumeGroup\" not found.");
347        }
348    }
349    # Set a variable to contain return type information.
350    my $rtype;
351    # Set up a statistics object for statistics about the entire load.
352    my $totalStats = Stats->new();
353    # Insure we catch errors.
354    eval {
355  # Process the parameters.  # Process the parameters.
356  for my $group (@parameters) {  for my $group (@parameters) {
357      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
358      my $stats;          # Compute the string we want to execute.
359      if ($group eq 'Genome' || $group eq '*') {          my $code = "\$spl->Load${group}Data()";
360          $spl->LoadGenomeData();          # Load this group.
361      }          my $stats = eval($code);
362      if ($group eq 'Feature' || $group eq '*') {          # Merge the statistics into the master.
363          $spl->LoadFeatureData();          $totalStats->Accumulate($stats);
364      }      }
365      if ($group eq 'Coupling' || $group eq '*') {      # Compute the statistical display.
366          $spl->LoadCouplingData();      my $statDisplay = $totalStats->Show();
367      }      # Display it.
368      if ($group eq 'Subsystem' || $group eq '*') {      Trace("Statistics for this load:\n$statDisplay") if T(2);
369          $spl->LoadSubsystemData();      # Check for a "table load failed" message. If we find one, we want
370      }      # to end with an error.
371      if ($group eq 'Property' || $group eq '*') {      if ($statDisplay =~ /table load failed/i) {
372          $spl->LoadPropertyData();          Confess("One or more table loads failed.");
373      }      }
374      if ($group eq 'Diagram' || $group eq '*') {  };
375          $spl->LoadDiagramData();  if ($@) {
376      }      Trace("Load failed with error: $@") if T(0);
377      if ($group eq 'Annotation' || $group eq '*') {      $rtype = "error";
378          $spl->LoadAnnotationData();  } else {
379      }      Trace("Load complete.") if T(2);
380      if ($group eq 'BBH' || $group eq '*') {      $rtype = "no error";
         $spl->LoadBBHData();  
     }  
     if ($group eq 'Group' || $group eq '*') {  
         $spl->LoadGroupData();  
     }  
     if ($group eq 'Source' || $group eq '*') {  
         $spl->LoadSourceData();  
381      }      }
382      if ($group eq 'External' || $group eq '*') {  if ($options->{phone}) {
383          $spl->LoadExternalData();      my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
384        if ($msgID) {
385            Trace("Phone message sent with ID $msgID.") if T(2);
386        } else {
387            Trace("Phone message not sent.") if T(2);
388      }      }
   
389  }  }
 Trace("Load complete.") if T(2);  
390    
391  1;  1;

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