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revision 1.41, Tue Oct 18 02:24:23 2005 UTC revision 1.49, Thu Oct 20 18:03:43 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) {              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 $trusteeTable{$user}) && ($time > $timeSelected)) {
# Line 1291  Line 1290 
1290      return $retVal;      return $retVal;
1291  }  }
1292    
1293    =head3 FunctionsOf
1294    
1295    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1296    
1297    Return the functional assignments of a particular feature.
1298    
1299    The functional assignment is handled differently depending on the type of feature. If
1300    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1301    assignment is a type of annotation. The format of an assignment is described in
1302    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1303    annotation itself because it's a text field; however, this is not a big problem because
1304    most features only have a small number of annotations.
1305    
1306    If the feature is B<not> identified by a FIG ID, then the functional assignment
1307    information is taken from the B<ExternalAliasFunc> table. If the table does
1308    not contain an entry for the feature, an empty list is returned.
1309    
1310    =over 4
1311    
1312    =item featureID
1313    
1314    ID of the feature whose functional assignments are desired.
1315    
1316    =item RETURN
1317    
1318    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1319    that user.
1320    
1321    =back
1322    
1323    =cut
1324    #: Return Type @@;
1325    sub FunctionsOf {
1326        # Get the parameters.
1327        my ($self, $featureID) = @_;
1328        # Declare the return value.
1329        my @retVal = ();
1330        # Determine the ID type.
1331        if ($featureID =~ m/^fig\|/) {
1332            # Here we have a FIG feature ID. We must build the list of trusted
1333            # users.
1334            my %trusteeTable = ();
1335            # Build a query for all of the feature's annotations, sorted by date.
1336            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1337                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1338                                   [$featureID]);
1339            my $timeSelected = 0;
1340            # Loop until we run out of annotations.
1341            while (my $annotation = $query->Fetch()) {
1342                # Get the annotation text.
1343                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1344                                                                'Annotation(time)',
1345                                                                'MadeAnnotation(user)']);
1346                # Check to see if this is a functional assignment for a trusted user.
1347                my ($actualUser, $function) = _ParseAssignment($user, $text);
1348                if ($actualUser) {
1349                    # Here it is a functional assignment.
1350                    push @retVal, [$actualUser, $function];
1351                }
1352            }
1353        } else {
1354            # 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
1356            # table.
1357            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1358                                                     ['ExternalAliasFunc(func)']);
1359            push @retVal, map { ['master', $_] } @assignments;
1360        }
1361        # Return the assignments found.
1362        return @retVal;
1363    }
1364    
1365  =head3 BBHList  =head3 BBHList
1366    
1367  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 2609  Line 2680 
2680                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2681      # Create the return value.      # Create the return value.
2682      my %retVal = ();      my %retVal = ();
2683        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2684        # in two spreadsheet cells.
2685        my %dupHash = ();
2686      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2687      for my $record (@subsystems) {      for my $record (@subsystems) {
2688            # Get this subsystem and role.
2689          my ($subsys, $role) = @{$record};          my ($subsys, $role) = @{$record};
2690          if (exists $retVal{$subsys}) {          # Insure it's the first time for both.
2691            my $dupKey = "$subsys\n$role";
2692            if (! exists $dupHash{"$subsys\n$role"}) {
2693                $dupHash{$dupKey} = 1;
2694              push @{$retVal{$subsys}}, $role;              push @{$retVal{$subsys}}, $role;
         } else {  
             $retVal{$subsys} = [$role];  
2695          }          }
2696      }      }
2697      # Return the hash.      # Return the hash.
# Line 3155  Line 3231 
3231    
3232  A functional assignment is always of the form  A functional assignment is always of the form
3233    
3234      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3235    
3236  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3237  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3238  same, but that is not always the case.  not always the case.
3239    
3240  This is a static method.  This is a static method.
3241    
3242  =over 4  =over 4
3243    
3244    =item user
3245    
3246    Name of the assigning user.
3247    
3248  =item text  =item text
3249    
3250  Text of the annotation.  Text of the annotation.
# Line 3180  Line 3260 
3260    
3261  sub _ParseAssignment {  sub _ParseAssignment {
3262      # Get the parameters.      # Get the parameters.
3263      my ($text) = @_;      my ($user, $text) = @_;
3264      # Declare the return value.      # Declare the return value.
3265      my @retVal = ();      my @retVal = ();
3266      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3267      my ($user, $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          @retVal = ($1, $function, $user);      } elsif ($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);
3274      }      }
3275      # Return the result list.      # Return the result list.
3276      return @retVal;      return @retVal;
# Line 3277  Line 3359 
3359      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3360  }  }
3361    
   
   
3362  1;  1;

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