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revision 1.47, Thu Oct 20 12:02:43 2005 UTC revision 1.55, Mon Apr 3 18:33:58 2006 UTC
# Line 92  Line 92 
92                                                          # database type                                                          # database type
93                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
94                                                          # data file directory                                                          # data file directory
95                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$FIG_Config::fig/SproutDBD.xml",
96                                                          # database definition file name                                                          # database definition file name
97                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                          # user name and password                                                          # user name and password
# Line 740  Line 740 
740  should be of the form returned by L</featureLocation> when in a list context. In other words,  should be of the form returned by L</featureLocation> when in a list context. In other words,
741  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.
742    
743    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
744    between positions 1401 and 1532, inclusive.
745    
746        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
747    
748  =over 4  =over 4
749    
750  =item locationList  =item locationList
751    
752  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
753  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
754    
755  =item RETURN  =item RETURN
756    
# Line 1176  Line 1181 
1181          # Get the annotation fields.          # Get the annotation fields.
1182          my ($timeStamp, $text, $user) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1183          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1184          my ($type, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1185          if ($type && ! exists $retVal{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1186              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1187              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1188              # return hash.              # return hash.
1189              $retVal{$user} = $function;              $retVal{$actualUser} = $function;
1190          }          }
1191      }      }
1192      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1259  Line 1264 
1264              }              }
1265          }          }
1266          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1267          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1268                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1269                                 [$featureID]);                                 [$featureID]);
1270          my $timeSelected = 0;          my $timeSelected = 0;
1271          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1272          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1273              # Get the annotation text.              # Get the annotation text.
1274              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1275                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1276              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1277              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1278              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1279                if ($actualUser) {
1280                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1281                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1282                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1283                      $retVal = $function;                      $retVal = $function;
1284                      $timeSelected = $time;                      $timeSelected = $time;
1285                  }                  }
# Line 1331  Line 1338 
1338          # users.          # users.
1339          my %trusteeTable = ();          my %trusteeTable = ();
1340          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1341          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1342                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1343                                 [$featureID]);                                 [$featureID]);
1344          my $timeSelected = 0;          my $timeSelected = 0;
1345          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1346          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1347              # Get the annotation text.              # Get the annotation text.
1348              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1349                                                                'Annotation(time)',
1350                                                                'MadeAnnotation(user)']);
1351              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1352              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1353              if ($user) {              if ($actualUser) {
1354                  # Here it is a functional assignment.                  # Here it is a functional assignment.
1355                  push @retVal, [$user, $function];                  push @retVal, [$actualUser, $function];
1356              }              }
1357          }          }
1358      } else {      } else {
1359          # Here we have a non-FIG feature ID. In this case the user ID does not          # Here we have a non-FIG feature ID. In this case the user ID does not
1360          # matter. We simply get the information from the External Alias Function          # matter. We simply get the information from the External Alias Function
1361          # table.          # table.
1362          push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);          my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1363                                                     ['ExternalAliasFunc(func)']);
1364            push @retVal, map { ['master', $_] } @assignments;
1365      }      }
1366      # Return the assignments found.      # Return the assignments found.
1367      return @retVal;      return @retVal;
# Line 1476  Line 1487 
1487      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1488      if ($genomeData) {      if ($genomeData) {
1489          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1490          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1491      }      }
1492      # Return the result.      # Return the result.
1493      return $retVal;      return $retVal;
# Line 3215  Line 3226 
3226      return $retVal;      return $retVal;
3227  }  }
3228    
3229    =head3 DeleteGenome
3230    
3231    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3232    
3233    Delete a genome from the database.
3234    
3235    =over 4
3236    
3237    =item genomeID
3238    
3239    ID of the genome to delete
3240    
3241    =item testFlag
3242    
3243    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3244    
3245    =item RETURN
3246    
3247    Returns a statistics object describing the rows deleted.
3248    
3249    =back
3250    
3251    =cut
3252    #: Return Type $%;
3253    sub DeleteGenome {
3254        # Get the parameters.
3255        my ($self, $genomeID, $testFlag) = @_;
3256        # Perform the delete for the genome's features.
3257        my $retVal = $self->{_erdb}->Delete('Feature', "fig|$genomeID.%", $testFlag);
3258        # Perform the delete for the primary genome data.
3259        my $stats = $self->{_erdb}->Delete('Genome', $genomeID, $testFlag);
3260        $retVal->Accumulate($stats);
3261        # Return the result.
3262        return $retVal;
3263    }
3264    
3265  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3266    
3267  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3225  Line 3272 
3272    
3273  A functional assignment is always of the form  A functional assignment is always of the form
3274    
3275      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3276    
3277  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3278  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3279  same, but that is not always the case.  not always the case.
3280    
3281    In addition, the functional role may contain extra data that is stripped, such as
3282    terminating spaces or a comment separated from the rest of the text by a tab.
3283    
3284  This is a static method.  This is a static method.
3285    
3286  =over 4  =over 4
3287    
3288    =item user
3289    
3290    Name of the assigning user.
3291    
3292  =item text  =item text
3293    
3294  Text of the annotation.  Text of the annotation.
# Line 3250  Line 3304 
3304    
3305  sub _ParseAssignment {  sub _ParseAssignment {
3306      # Get the parameters.      # Get the parameters.
3307      my ($text) = @_;      my ($user, $text) = @_;
3308      # Declare the return value.      # Declare the return value.
3309      my @retVal = ();      my @retVal = ();
3310      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3311      my ($type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3312      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3313          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3314          # and the assigning user.          @retVal = ($user, $function);
3315        } elsif ($type =~ m/^set (\S+) function to$/i) {
3316            # Here we have an assignment with a user that is passed back to the caller.
3317          @retVal = ($1, $function);          @retVal = ($1, $function);
3318      }      }
3319        # If we have an assignment, we need to clean the function text. There may be
3320        # extra junk at the end added as a note from the user.
3321        if (@retVal) {
3322            $retVal[1] =~ s/(\t\S)?\s*$//;
3323        }
3324      # Return the result list.      # Return the result list.
3325      return @retVal;      return @retVal;
3326  }  }
# Line 3348  Line 3409 
3409  }  }
3410    
3411    
   
3412  1;  1;

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