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revision 1.42, Tue Oct 18 06:58:09 2005 UTC revision 1.48, Thu Oct 20 12:33:00 2005 UTC
# Line 389  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
395  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 1153  Line 1153 
1153    
1154  =item RETURN  =item RETURN
1155    
1156  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
# 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)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170      # Declare the return hash.      # Declare the return hash.
1171      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1172      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1173      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
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 $timeHash{$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              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1185          }          }
1186      }      }
1187      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1200  Line 1197 
1197  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1198  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1199  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1200  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1201  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1202  most features only have a small number of annotations.  most features only have a small number of annotations.
1203    
# Line 1262  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) {              if ($actualUser) {
1274                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1275                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1276                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {
# Line 1291  Line 1289 
1289      return $retVal;      return $retVal;
1290  }  }
1291    
1292    =head3 FunctionsOf
1293    
1294    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1295    
1296    Return the functional assignments of a particular feature.
1297    
1298    The functional assignment is handled differently depending on the type of feature. If
1299    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1300    assignment is a type of annotation. The format of an assignment is described in
1301    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1302    annotation itself because it's a text field; however, this is not a big problem because
1303    most features only have a small number of annotations.
1304    
1305    If the feature is B<not> identified by a FIG ID, then the functional assignment
1306    information is taken from the B<ExternalAliasFunc> table. If the table does
1307    not contain an entry for the feature, an empty list is returned.
1308    
1309    =over 4
1310    
1311    =item featureID
1312    
1313    ID of the feature whose functional assignments are desired.
1314    
1315    =item RETURN
1316    
1317    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1318    that user.
1319    
1320    =back
1321    
1322    =cut
1323    #: Return Type @@;
1324    sub FunctionsOf {
1325        # Get the parameters.
1326        my ($self, $featureID) = @_;
1327        # Declare the return value.
1328        my @retVal = ();
1329        # Determine the ID type.
1330        if ($featureID =~ m/^fig\|/) {
1331            # Here we have a FIG feature ID. We must build the list of trusted
1332            # users.
1333            my %trusteeTable = ();
1334            # Build a query for all of the feature's annotations, sorted by date.
1335            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1336                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1337                                   [$featureID]);
1338            my $timeSelected = 0;
1339            # Loop until we run out of annotations.
1340            while (my $annotation = $query->Fetch()) {
1341                # Get the annotation text.
1342                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1343                                                                'Annotation(time)',
1344                                                                'MadeAnnotation(user)']);
1345                # Check to see if this is a functional assignment for a trusted user.
1346                my ($actualUser, $function) = _ParseAssignment($user, $text);
1347                if ($actualUser) {
1348                    # Here it is a functional assignment.
1349                    push @retVal, [$actualUser, $function];
1350                }
1351            }
1352        } else {
1353            # Here we have a non-FIG feature ID. In this case the user ID does not
1354            # matter. We simply get the information from the External Alias Function
1355            # table.
1356            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1357                                                     ['ExternalAliasFunc(func)']);
1358            push @retVal, map { ['master', $_] } @assignments;
1359        }
1360        # Return the assignments found.
1361        return @retVal;
1362    }
1363    
1364  =head3 BBHList  =head3 BBHList
1365    
1366  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 3160  Line 3230 
3230    
3231  A functional assignment is always of the form  A functional assignment is always of the form
3232    
3233      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3234    
3235  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,
3236  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
3237  same, but that is not always the case.  not always the case.
3238    
3239  This is a static method.  This is a static method.
3240    
3241  =over 4  =over 4
3242    
3243    =item user
3244    
3245    Name of the assigning user.
3246    
3247  =item text  =item text
3248    
3249  Text of the annotation.  Text of the annotation.
# Line 3185  Line 3259 
3259    
3260  sub _ParseAssignment {  sub _ParseAssignment {
3261      # Get the parameters.      # Get the parameters.
3262      my ($text) = @_;      my ($user, $text) = @_;
3263      # Declare the return value.      # Declare the return value.
3264      my @retVal = ();      my @retVal = ();
3265      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3266      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3267      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3268          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3269          # and the assigning user.          @retVal = ($user, $function);
3270          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
3271            # Here we have an assignment with a user, that is passed back to the caller.
3272            @retVal = ($1, $function);
3273      }      }
3274      # Return the result list.      # Return the result list.
3275      return @retVal;      return @retVal;
# Line 3282  Line 3358 
3358      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3359  }  }
3360    
   
   
3361  1;  1;

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