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revision 1.13, Sat Nov 12 03:42:48 2005 UTC revision 1.49, Tue Sep 16 18:53:28 2008 UTC
# Line 4  Line 4 
4    
5  =head2 Introduction  =head2 Introduction
6    
7  This script creates the load files for Sprout tables and optionally loads them.  The Sprout database reflects a snapshot of the SEED taken at a particular point in
8  The parameters are the names of the table groups whose data is to be created.  time. At some point in the future, it will be possible to add annotations to the
9  The legal table group names are given below.  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 Feature  =item java
78    
79  Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  Path to the Java runtime environment.
80  B<IsLocatedIn>, B<FeatureLink>.  
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 Subsystem  =item Subsystem
125    
126  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
127  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
128  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,  B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
129  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
130  B<RoleOccursIn>.  B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>, and
131    B<ContainsFeature>.
132    
133  =item Annotation  =item Annotation
134    
135  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>, and
136  B<MadeAnnotation>.  B<MadeAnnotation>.
137    
138  =item Property  =item Property
139    
140  Loads B<Property>, B<HasProperty>.  Loads B<Property>, and B<HasProperty>.
141    
142  =item BBH  =item Source
143    
144  Loads B<IsBidirectionalBestHitOf>.  Loads B<Source>, B<ComesFrom>, and B<SourceURL>.
145    
146  =item Group  =item Reaction
147    
148  Loads B<GenomeGroups>.  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
149    B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>, B<Scenario>, B<IsInputFor>,
150    B<IsOutputOf>, B<IsOnDiagram>, and B<Catalyzes>.
151    
152  =item Source  =item Synonym
153    
154  Loads B<Source>, B<ComesFrom>, B<SourceURL>.  Loads B<SynonymGroup> and B<IsSynonymGroupFor>.
155    
156  =item External  =item Family
157    
158  Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  Loads B<Family> and B<IsFamilyForFeature>.
159    
160  =item Reaction  =item Drug
161    
162  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.
163  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  
164    =item Feature
165    
166    Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
167    B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,
168    B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,
169    B<CDD>, B<IsPresentOnProteinOf>, and B<Keyword>.
170    
171  =item *  =item *
172    
# Line 77  Line 183 
183  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
184  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
185  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
186  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
187    default gene file-- C<genes.tbl> in the C<SproutData> directory.
188    
189  =item subsysFile  =item subsysFile
190    
# Line 88  Line 195 
195    
196  Desired tracing level. The default is 3.  Desired tracing level. The default is 3.
197    
198  =item limitedFeatures  =item user
199    
200  Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.  Suffix to use for trace, output, and error files created.
201    
202  =item dbLoad  =item dbLoad
203    
204  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.
205    
206  =back  =item dbCreate
207    
208  =head2 Usage  If TRUE, the database will be created. If the database exists already, it will be
209    dropped. Use the function with caution.
210    
211  To load all the Sprout tables and then validate the result, you need to issue three  =item loadOnly
 commands.  
212    
213      LoadSproutTables -dbLoad "*"  If TRUE, the database tables will be loaded from existing load files. Load files
214      TestSproutLoad  will not be created. This option is useful if you are setting up a copy of Sprout
215      index_sprout  and have load files already set up from the original version.
216    
217  All three commands send output to the console. In addition, C<LoadSproutTables> and  =item background
 C<TestSproutLoad> write tracing information to C<trace.log> in the FIG temporary  
 directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete  
 list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected  
 and the offending table group reloaded. So, for example, if there are errors in the  
 load of the B<MadeAnnotation> and B<Compound> tables, you would need to run  
218    
219      LoadSproutTables -dbLoad Annotation Reaction  Redirect the standard and error output to files in the FIG temporary directory.
220    
221  because B<MadeAnnotation> is in the C<Annotation> group, and B<Compound> is in the  =item resume
 C<Reaction> group. You can omit the C<dbLoad> option to create the load files without  
 loading the database, and you can add a C<trace> option to change the trace level.  
 The command below creates the Genome-related load files with a trace level of 3 and  
 does not load them into the Sprout database.  
222    
223      LoadSproutTables -trace=3 Genome  Resume an interrupted load, starting with the load group specified in the first
224    positional parameter.
225    
226  C<LoadSproutTables> takes a long time to run, so setting the trace level to 3 helps  =item sql
227  to give you an idea of the progress.  
228    Trace SQL statements.
229    
230  Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load  =item phone
 against the FIG data. Again, the end of the C<trace.log> file will contain a summary  
 of the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming  
 script, so you may want to set the trace level to 3 to see visible progress.  
   
     TestSproutLoad -trace=3  
   
 Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are  
 mixed in with the trace messages. They are all, however, marked with a trace type  
 of B<Problem>, as shown in the fragment below.  
   
     11/02/2005 19:15:16 <main>: Processing feature fig|100226.1.peg.7742.  
     11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7741.  
     11/02/2005 19:15:17 <Problem>: assignment "Short-chain dehydrodenase ...  
     11/02/2005 19:15:17 <Problem>: assignment "putative oxidoreductase." ...  
     11/02/2005 19:15:17 <Problem>: Incorrect assignment for fig|100226.1.peg.7741...  
     11/02/2005 19:15:17 <Problem>: Incorrect number of annotations found in ...  
     11/02/2005 19:15:17 <main>: Processing feature fig|100226.1.peg.7740.  
     11/02/2005 19:15:18 <main>: Processing feature fig|100226.1.peg.7739.  
231    
232  The test may reveal that some tables need to be reloaded, or that a software  Phone number to message when the load finishes.
 problem has crept into the Sprout.  
233    
234  Once all the tables have the correct data, C<index_sprout> can be run to create the  =back
 Glimpse indexes.  
235    
236  =cut  =cut
237    
238  use strict;  use strict;
239  use Tracer;  use Tracer;
 use DocUtils;  
240  use Cwd;  use Cwd;
241  use FIG;  use FIG;
242  use SFXlate;  use SFXlate;
# Line 167  Line 246 
246  use Stats;  use Stats;
247  use SFXlate;  use SFXlate;
248    
249    # This is a list of the load groups in their natural order. We'll go through these in sequence, processing
250    # the ones the user asks for.
251    my @LoadGroups = qw(Genome Subsystem Property Annotation Source Reaction Synonym Family Drug Feature);
252    
253  # Get the command-line parameters and options.  # Get the command-line parameters and options.
254  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
255                                                      trace => 3, limitedFeatures => 0,                                              'ERDB', 'Load', 'Sprout', 'Subsystem'],
256                                                      dbLoad => 0 }, @ARGV);                                              { geneFile => ["", "name of the genome list file"],
257  # Set up tracing.                                                subsysFile => ["", "name of the trusted subsystem file"],
258  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");                                                dbLoad => [0, "load the database from generated files"],
259                                                  dbCreate => [0, "drop and re-create the database"],
260                                                  loadOnly => [0, "load the database from previously generated files"],
261                                                  resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
262                                                  phone => ["", "phone number (international format) to call when load finishes"],
263                                                  trace => [3, "trace level"],
264                                                },
265                                                "<group1> <group2> ...",
266                                                @ARGV);
267    # If we're doing a load-only, turn on loading.
268    if ($options->{loadOnly}) {
269        $options->{dbLoad} = 1
270    }
271    if ($options->{dbCreate}) {
272        # Here we want to drop and re-create the database.
273        my $db = $FIG_Config::sproutDB;
274        DBKernel::CreateDB($db);
275    }
276    # Compute the gene file name.
277    my $geneFile = $options->{geneFile};
278    if ($geneFile eq 'default') {
279        $geneFile = "$FIG_Config::sproutData/genes.tbl";
280    }
281  # Create the sprout loader object. Note that the Sprout object does not  # Create the sprout loader object. Note that the Sprout object does not
282  # open the database unless the "dbLoad" option is turned on.  # open the database unless the "dbLoad" option is turned on.
283  my $fig = FIG->new();  my $fig = FIG->new();
284  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
285  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $geneFile, $options->{subsysFile}, $options);
286    # Insure we have an output directory.
287    FIG::verify_dir($FIG_Config::sproutData);
288    # Check for the "*" option.
289    if ($parameters[0] eq '*') {
290        @parameters = @LoadGroups;
291    }
292    # If we're resuming, we only want to have 1 parameter.
293    my $resume = $options->{resume};
294    if ($resume && @parameters > 1) {
295        Confess("If resume=1, only one load group can be specified.");
296    } elsif (! @parameters) {
297        Trace("No load groups were specified.") if T(0);
298    }
299    # Process the resume option here. We modify the incoming parameters to
300    # contain the resume group and everything after it.
301    if ($resume) {
302        # Save the starting group.
303        my $resumeGroup = $parameters[0];
304        # Copy the load group list into the parameter array.
305        @parameters = @LoadGroups;
306        # Shift out the groups until we reach our desired starting point.
307        while (scalar(@parameters) && $parameters[0] ne $resumeGroup) {
308            shift @parameters;
309        }
310        if (! @parameters) {
311            Confess("Resume group \"$resumeGroup\" not found.");
312        }
313    }
314    # Set a variable to contain return type information.
315    my $rtype;
316    # Set up a statistics object for statistics about the entire load.
317    my $totalStats = Stats->new();
318    # Insure we catch errors.
319    eval {
320  # Process the parameters.  # Process the parameters.
321  for my $group (@parameters) {  for my $group (@parameters) {
322      Trace("Processing load group $group.") if T(2);      Trace("Processing load group $group.") if T(2);
323      my $stats;          # Compute the string we want to execute.
324      if ($group eq 'Genome' || $group eq '*') {          my $code = "\$spl->Load${group}Data()";
325          $spl->LoadGenomeData();          # Load this group.
326      }          my $stats = eval($code);
327      if ($group eq 'Feature' || $group eq '*') {          if ($@) {
328          $spl->LoadFeatureData();              Confess("Load group error: $@");
329      }          }
330      if ($group eq 'Coupling' || $group eq '*') {          # Merge the statistics into the master.
331          $spl->LoadCouplingData();          $totalStats->Accumulate($stats);
332      }      }
333      if ($group eq 'Subsystem' || $group eq '*') {      # Compute the statistical display.
334          $spl->LoadSubsystemData();      my $statDisplay = $totalStats->Show();
335      }      # Display it.
336      if ($group eq 'Property' || $group eq '*') {      Trace("Statistics for this load:\n$statDisplay") if T(2);
337          $spl->LoadPropertyData();      # Check for a "table load failed" message. If we find one, we want
338      }      # to end with an error.
339      if ($group eq 'Annotation' || $group eq '*') {      if ($statDisplay =~ /table load failed/i) {
340          $spl->LoadAnnotationData();          Confess("One or more table loads failed.");
341      }      }
342      if ($group eq 'BBH' || $group eq '*') {  };
343          $spl->LoadBBHData();  if ($@) {
344      }      Trace("Load failed with error: $@") if T(0);
345      if ($group eq 'Group' || $group eq '*') {      $rtype = "error";
346          $spl->LoadGroupData();  } else {
347      }      Trace("Load complete.") if T(2);
348      if ($group eq 'Source' || $group eq '*') {      $rtype = "no error";
         $spl->LoadSourceData();  
     }  
     if ($group eq 'External' || $group eq '*') {  
         $spl->LoadExternalData();  
349      }      }
350      if ($group eq 'Reaction' || $group eq '*') {  if ($options->{phone}) {
351          $spl->LoadReactionData();      my $msgID = Tracer::SendSMS($options->{phone}, "Sprout load terminated with $rtype.");
352        if ($msgID) {
353            Trace("Phone message sent with ID $msgID.") if T(2);
354        } else {
355            Trace("Phone message not sent.") if T(2);
356      }      }
   
357  }  }
 Trace("Load complete.") if T(2);  
358    
359  1;  1;

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