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revision 1.47, Thu Oct 20 12:02:43 2005 UTC revision 1.52, Mon Dec 12 21:48:57 2005 UTC
# Line 1176  Line 1176 
1176          # Get the annotation fields.          # Get the annotation fields.
1177          my ($timeStamp, $text, $user) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1178          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1179          my ($type, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1180          if ($type && ! exists $retVal{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1181              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1182              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1183              # return hash.              # return hash.
1184              $retVal{$user} = $function;              $retVal{$actualUser} = $function;
1185          }          }
1186      }      }
1187      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1259  Line 1259 
1259              }              }
1260          }          }
1261          # 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.
1262          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1263                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1264                                 [$featureID]);                                 [$featureID]);
1265          my $timeSelected = 0;          my $timeSelected = 0;
1266          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1267          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1268              # Get the annotation text.              # Get the annotation text.
1269              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1270                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1271              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1272              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1273              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1274                if ($actualUser) {
1275                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1276                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1277                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1278                      $retVal = $function;                      $retVal = $function;
1279                      $timeSelected = $time;                      $timeSelected = $time;
1280                  }                  }
# Line 1331  Line 1333 
1333          # users.          # users.
1334          my %trusteeTable = ();          my %trusteeTable = ();
1335          # 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.
1336          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1337                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1338                                 [$featureID]);                                 [$featureID]);
1339          my $timeSelected = 0;          my $timeSelected = 0;
1340          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1341          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1342              # Get the annotation text.              # Get the annotation text.
1343              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1344                                                                'Annotation(time)',
1345                                                                'MadeAnnotation(user)']);
1346              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1347              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1348              if ($user) {              if ($actualUser) {
1349                  # Here it is a functional assignment.                  # Here it is a functional assignment.
1350                  push @retVal, [$user, $function];                  push @retVal, [$actualUser, $function];
1351              }              }
1352          }          }
1353      } else {      } else {
1354          # 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
1355          # matter. We simply get the information from the External Alias Function          # matter. We simply get the information from the External Alias Function
1356          # table.          # table.
1357          push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);          my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1358                                                     ['ExternalAliasFunc(func)']);
1359            push @retVal, map { ['master', $_] } @assignments;
1360      }      }
1361      # Return the assignments found.      # Return the assignments found.
1362      return @retVal;      return @retVal;
# Line 1476  Line 1482 
1482      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1483      if ($genomeData) {      if ($genomeData) {
1484          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1485          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1486      }      }
1487      # Return the result.      # Return the result.
1488      return $retVal;      return $retVal;
# Line 3225  Line 3231 
3231    
3232  A functional assignment is always of the form  A functional assignment is always of the form
3233    
3234      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3235    
3236  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3237  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3238  same, but that is not always the case.  not always the case.
3239    
3240    In addition, the functional role may contain extra data that is stripped, such as
3241    terminating spaces or a comment separated from the rest of the text by a tab.
3242    
3243  This is a static method.  This is a static method.
3244    
3245  =over 4  =over 4
3246    
3247    =item user
3248    
3249    Name of the assigning user.
3250    
3251  =item text  =item text
3252    
3253  Text of the annotation.  Text of the annotation.
# Line 3250  Line 3263 
3263    
3264  sub _ParseAssignment {  sub _ParseAssignment {
3265      # Get the parameters.      # Get the parameters.
3266      my ($text) = @_;      my ($user, $text) = @_;
3267      # Declare the return value.      # Declare the return value.
3268      my @retVal = ();      my @retVal = ();
3269      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3270      my ($type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3271      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3272          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3273          # and the assigning user.          @retVal = ($user, $function);
3274        } elsif ($type =~ m/^set (\S+) function to$/i) {
3275            # Here we have an assignment with a user that is passed back to the caller.
3276          @retVal = ($1, $function);          @retVal = ($1, $function);
3277      }      }
3278        # If we have an assignment, we need to clean the function text. There may be
3279        # extra junk at the end added as a note from the user.
3280        if (@retVal) {
3281            $retVal[1] =~ s/(\t\S)?\s*$//;
3282        }
3283      # Return the result list.      # Return the result list.
3284      return @retVal;      return @retVal;
3285  }  }
# Line 3348  Line 3368 
3368  }  }
3369    
3370    
   
3371  1;  1;

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