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revision 1.46, Thu Oct 20 11:52:36 2005 UTC revision 1.51, Thu Dec 8 18:02:52 2005 UTC
# Line 1163  Line 1163 
1163      # Get the parameters.      # Get the parameters.
1164      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1165      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1166      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1167                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1168                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170      # Declare the return hash.      # Declare the return hash.
1171      my %retVal;      my %retVal;
1172      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
# Line 1173  Line 1174 
1174      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1175      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1176          # Get the annotation fields.          # Get the annotation fields.
1177          my ($timeStamp, $text) = @{$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 ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1180          if ($user && ! 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 1258  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 1330  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 1475  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 $retVal;
# Line 3224  Line 3231 
3231    
3232  A functional assignment is always of the form  A functional assignment is always of the form
3233    
3234      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3235    
3236  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3237  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3238  same, but that is not always the case.  not always the case.
3239    
3240  This is a static method.  This is a static method.
3241    
3242  =over 4  =over 4
3243    
3244    =item user
3245    
3246    Name of the assigning user.
3247    
3248  =item text  =item text
3249    
3250  Text of the annotation.  Text of the annotation.
# Line 3249  Line 3260 
3260    
3261  sub _ParseAssignment {  sub _ParseAssignment {
3262      # Get the parameters.      # Get the parameters.
3263      my ($text) = @_;      my ($user, $text) = @_;
3264      # Declare the return value.      # Declare the return value.
3265      my @retVal = ();      my @retVal = ();
3266      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3267      my ($type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3268      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3269          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3270          # and the assigning user.          @retVal = ($user, $function);
3271        } elsif ($type =~ m/^set (\S+) function to$/i) {
3272            # Here we have an assignment with a user, that is passed back to the caller.
3273          @retVal = ($1, $function);          @retVal = ($1, $function);
3274      }      }
3275      # Return the result list.      # Return the result list.
# Line 3347  Line 3360 
3360  }  }
3361    
3362    
   
3363  1;  1;

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