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revision 1.11, Wed Nov 29 20:28:52 2006 UTC revision 1.28, Sun Sep 30 20:52:51 2007 UTC
# Line 8  Line 8 
8      use strict;      use strict;
9      use Tracer;      use Tracer;
10      use ERDBLoad;      use ERDBLoad;
11        use Stats;
12        use Time::HiRes qw(time);
13    
14  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
15    
# Line 27  Line 29 
29  The actual attribute values are stored as a relationship between the attribute  The actual attribute values are stored as a relationship between the attribute
30  keys and the objects. There can be multiple values for a single key/object pair.  keys and the objects. There can be multiple values for a single key/object pair.
31    
32    =head3 Object IDs
33    
34    The object ID is normally represented as
35    
36        I<type>:I<id>
37    
38    where I<type> is the object type (C<Role>, C<Coupling>, etc.) and I<id> is
39    the actual object ID. Note that the object type must consist of only upper- and
40    lower-case letters! Thus, C<GenomeGroup> is a valid object type, but
41    C<genome_group> is not. Given that restriction, the object ID
42    
43        Family:aclame|cluster10
44    
45    would represent the FIG family C<aclame|cluster10>. For historical reasons,
46    there are three exceptions: subsystems, genomes, and features do not need
47    a type. So, for PEG 3361 of Streptomyces coelicolor A3(2), you simply code
48    
49        fig|100226.1.peg.3361
50    
51    The methods L</ParseID> and L</FormID> can be used to make this all seem
52    more consistent. Given any object ID string, L</ParseID> will convert it to an
53    object type and ID, and given any object type and ID, L</FormID> will
54    convert it to an object ID string. The attribute database is pretty
55    freewheeling about what it will allow for an ID; however, for best
56    results, the type should match an entity type from a Sprout genetics
57    database. If this rule is followed, then the database object
58    corresponding to an ID in the attribute database could be retrieved using
59    L</GetTargetObject> method.
60    
61        my $object = CustomAttributes::GetTargetObject($sprout, $idValue);
62    
63    =head3 Retrieval and Logging
64    
65  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
66  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
67  the values of the attribute C<essential> in a specified B<Feature>, you  the values of the attribute C<essential> in a specified B<Feature>, you
# Line 36  Line 71 
71    
72  where I<$fid> contains the ID of the desired feature.  where I<$fid> contains the ID of the desired feature.
73    
74  New attribute keys must be defined before they can be used. A web interface  Keys can be split into two pieces using the splitter value defined in the
75  is provided for this purpose.  constructor (the default is C<::>). The first piece of the key is called
76    the I<real key>. This portion of the key must be defined using the
77    web interface (C<Attributes.cgi>). The second portion of the key is called
78    the I<sub key>, and can take any value.
79    
80    Major attribute activity is recorded in a log (C<attributes.log>) in the
81    C<$FIG_Config::var> directory. The log reports the user name, time, and
82    the details of the operation. The user name will almost always be unknown,
83    the exception being when it is specified in this object's constructor
84    (see L</new>).
85    
86  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
87    
# Line 87  Line 131 
131    
132  =head3 new  =head3 new
133    
134  C<< my $attrDB = CustomAttributes->new($splitter); >>  C<< my $attrDB = CustomAttributes->new(%options); >>
135    
136  Construct a new CustomAttributes object.  Construct a new CustomAttributes object. The following options are
137    supported.
138    
139  =over 4  =over 4
140    
141  =item splitter  =item splitter
142    
143  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
144  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
145  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
146  worry about this parameter.  
147    =item user
148    
149    Name of the current user. This will appear in the attribute log.
150    
151  =back  =back
152    
# Line 106  Line 154 
154    
155  sub new {  sub new {
156      # Get the parameters.      # Get the parameters.
157      my ($class, $splitter) = @_;      my ($class, %options) = @_;
158      # Connect to the database.      # Connect to the database.
159      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
160                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 116  Line 164 
164      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
165      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
166      # Store the splitter value.      # Store the splitter value.
167      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
168        # Store the user name.
169        $retVal->{user} = $options{user} || '<unknown>';
170        Trace("User $retVal->{user} selected for attribute object.") if T(3);
171      # Return the result.      # Return the result.
172      return $retVal;      return $retVal;
173  }  }
# Line 131  Line 182 
182    
183  =item attributeName  =item attributeName
184    
185  Name of the attribute. It must be a valid ERDB field name, consisting entirely of  Name of the attribute (the real key). If it does not exist already, it will be created.
 letters, digits, and hyphens, with a letter at the beginning. If it does not  
 exist already, it will be created.  
186    
187  =item type  =item type
188    
# Line 160  Line 209 
209      # Get the data type hash.      # Get the data type hash.
210      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
211      # Validate the initial input values.      # Validate the initial input values.
212      if (! ERDB::ValidateFieldName($attributeName)) {      if ($attributeName =~ /$self->{splitter}/) {
213          Confess("Invalid attribute name \"$attributeName\" specified.");          Confess("Invalid attribute name \"$attributeName\" specified.");
214      } elsif (! $notes || length($notes) < 25) {      } elsif (! $notes || length($notes) < 25) {
215          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing or incomplete description for $attributeName.");
216      } elsif (! exists $types{$type}) {      } elsif (! exists $types{$type}) {
217          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid data type \"$type\" for $attributeName.");
218      } else {      } else {
219            # Create a variable to hold the action to be displayed for the log (Add or Update).
220            my $action;
221          # Okay, we're ready to begin. See if this key exists.          # Okay, we're ready to begin. See if this key exists.
222          my $attribute = $self->GetEntity('AttributeKey', $attributeName);          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
223          if (defined($attribute)) {          if (defined($attribute)) {
224              # It does, so we do an update.              # It does, so we do an update.
225                $action = "Update Key";
226              $self->UpdateEntity('AttributeKey', $attributeName,              $self->UpdateEntity('AttributeKey', $attributeName,
227                                  { description => $notes, 'data-type' => $type });                                  { description => $notes, 'data-type' => $type });
228              # Detach the key from its current groups.              # Detach the key from its current groups.
229              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
230          } else {          } else {
231              # It doesn't, so we do an insert.              # It doesn't, so we do an insert.
232                $action = "Insert Key";
233              $self->InsertObject('AttributeKey', { id => $attributeName,              $self->InsertObject('AttributeKey', { id => $attributeName,
234                                  description => $notes, 'data-type' => $type });                                  description => $notes, 'data-type' => $type });
235          }          }
# Line 186  Line 239 
239              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
240                                                 'to-link'   => $group });                                                 'to-link'   => $group });
241          }          }
242            # Log the operation.
243            $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
244      }      }
245  }  }
246    
 =head3 LoadAttributeKey  
   
 C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>  
   
 Load the specified attribute from the specified file. The file should be a  
 tab-delimited file with internal tab and new-line characters escaped. This is  
 the typical TBL-style file used by most FIG applications. One of the columns  
 in the input file must contain the appropriate object id value and the other the  
 corresponding attribute value.  
   
 =over 4  
   
 =item keyName  
   
 Key of the attribute to load.  
   
 =item fh  
   
 Open file handle for the input file.  
   
 =item idCol  
   
 Index (0-based) of the column containing the ID field. The ID field should  
 contain the ID of an instance of the named entity.  
   
 =item dataCol  
   
 Index (0-based) of the column containing the data value field.  
   
 =item options  
   
 Hash specifying the options for this load.  
   
 =item RETURN  
   
 Returns a statistics object for the load process.  
   
 =back  
   
 The available options are as follows.  
   
 =over 4  
   
 =item erase  
   
 If TRUE, the key's values will all be erased before loading. (Doing so  
 makes for a faster load.)  
   
 =back  
   
 =cut  
   
 sub LoadAttributeKey {  
     # Get the parameters.  
     my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;  
     # Create the return variable.  
     my $retVal = Stats->new("lineIn", "shortLine", "newObject");  
     # Compute the minimum number of fields required in each input line.  
     my $minCols = ($idCol < $dataCol ? $idCol : $idCol) + 1;  
     # Insure the attribute key exists.  
     my $found = $self->GetEntity('AttributeKey', $keyName);  
     if (! defined $found) {  
         Confess("Attribute key \"$keyName\" not found in database.");  
     } else {  
         # Erase the key's current values.  
         $self->EraseAttribute($keyName);  
         # Save a list of the object IDs we need to add.  
         my %objectIDs = ();  
         # Loop through the input file.  
         while (! eof $fh) {  
             # Get the next line of the file.  
             my @fields = Tracer::GetLine($fh);  
             $retVal->Add(lineIn => 1);  
             # Now we need to validate the line.  
             if (scalar(@fields) < $minCols) {  
                 $retVal->Add(shortLine => 1);  
             } else {  
                 # It's valid, so get the ID and value.  
                 my ($id, $value) = ($fields[$idCol], $fields[$dataCol]);  
                 # Denote we're using this input line.  
                 $retVal->Add(lineUsed => 1);  
                 # Now the fun begins. Find out if we need to create a target object record for this object ID.  
                 if (! exists $objectIDs{$id}) {  
                     my $found = $self->Exists('TargetObject', $id);  
                     if (! $found) {  
                         $self->InsertObject('TargetObject', { id => $id });  
                     }  
                     $objectIDs{$id} = 1;  
                     $retVal->Add(newObject => 1);  
                 }  
                 # Now we insert the attribute.  
                 $self->InsertObject('HasValueFor', { from => $keyName, to => $id, value => $value });  
                 $retVal->Add(newValue => 1);  
             }  
         }  
     }  
     # Return the statistics.  
     return $retVal;  
 }  
   
247    
248  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
249    
# Line 315  Line 270 
270      my ($self, $attributeName) = @_;      my ($self, $attributeName) = @_;
271      # Delete the attribute key.      # Delete the attribute key.
272      my $retVal = $self->Delete('AttributeKey', $attributeName);      my $retVal = $self->Delete('AttributeKey', $attributeName);
273        # Log this operation.
274        $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
275      # Return the result.      # Return the result.
276      return $retVal;      return $retVal;
277    
# Line 388  Line 345 
345                                      -labels => \%labelMap,                                      -labels => \%labelMap,
346                                      -default => 'string');                                      -default => 'string');
347      # Allow the user to specify a new field name. This is required if the      # Allow the user to specify a new field name. This is required if the
348      # user has selected the "(new)" marker. We put a little scriptlet in here that      # user has selected the "(new)" marker.
     # selects the (new) marker when the user enters the field.  
     push @retVal, "<script language=\"javaScript\">";  
349      my $fieldField = "document.$name.fieldName";      my $fieldField = "document.$name.fieldName";
350      my $newName = "\"" . NewName() . "\"";      my $newName = "\"" . NewName() . "\"";
351      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      push @retVal, $cgi->Tr($cgi->th("New Field Name"),
# Line 413  Line 368 
368                             $cgi->td($cgi->checkbox_group(-name=>'groups',                             $cgi->td($cgi->checkbox_group(-name=>'groups',
369                                      -values=> \@groups))                                      -values=> \@groups))
370                            );                            );
371      # If the user wants to upload new values for the field, then we have      # Now the four buttons: STORE, SHOW, ERASE, and DELETE.
     # an upload file name and column indicators.  
     push @retVal, $cgi->Tr($cgi->th("Upload Values"),  
                            $cgi->td($cgi->filefield(-name => 'newValueFile',  
                                                     -size => 20) .  
                                     " Key&nbsp;" .  
                                     $cgi->textfield(-name => 'keyCol',  
                                                     -size => 3,  
                                                     -default => 0) .  
                                     " Value&nbsp;" .  
                                     $cgi->textfield(-name => 'valueCol',  
                                                     -size => 3,  
                                                     -default => 1)  
                                    ),  
                           );  
     # Now the three buttons: STORE, SHOW, and DELETE.  
372      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
373                             $cgi->td({align => 'center'},                             $cgi->td({align => 'center'}, join(" ",
374                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .                                      $cgi->submit(-name => 'Delete', -value => 'DELETE'),
375                                      $cgi->submit(-name => 'Store',  -value => 'STORE') . " " .                                      $cgi->submit(-name => 'Store',  -value => 'STORE'),
376                                        $cgi->submit(-name => 'Erase',  -value => 'ERASE'),
377                                      $cgi->submit(-name => 'Show',   -value => 'SHOW')                                      $cgi->submit(-name => 'Show',   -value => 'SHOW')
378                                     )                                     ))
379                            );                            );
380      # Close the table and the form.      # Close the table and the form.
381      push @retVal, $cgi->end_table();      push @retVal, $cgi->end_table();
# Line 445  Line 386 
386  =head3 LoadAttributesFrom  =head3 LoadAttributesFrom
387    
388  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
389    s
390  Load attributes from the specified tab-delimited file. Each line of the file must  Load attributes from the specified tab-delimited file. Each line of the file must
391  contain an object ID in the first column, an attribute key name in the second  contain an object ID in the first column, an attribute key name in the second
392  column, and attribute values in the remaining columns. The attribute values will  column, and attribute values in the remaining columns. The attribute values will
393  be assembled into a single value using the splitter code.  be assembled into a single value using the splitter code. In addition, the key names may
394    contain a splitter. If this is the case, the portion of the key after the splitter is
395    treated as a subkey.
396    
397  =over 4  =over 4
398    
399  =item fileName  =item fileName
400    
401  Name of the file from which to load the attributes.  Name of the file from which to load the attributes, or an open handle for the file.
402    (This last enables the method to be used in conjunction with the CGI form upload
403    control.)
404    
405  =item options  =item options
406    
# Line 476  Line 421 
421  If TRUE, then the attributes will be appended to existing data; otherwise, the  If TRUE, then the attributes will be appended to existing data; otherwise, the
422  first time a key name is encountered, it will be erased.  first time a key name is encountered, it will be erased.
423    
424    =item archive
425    
426    If specified, the name of a file into which the incoming data file should be saved.
427    
428    =item objectType
429    
430    If specified, the specified object type will be prefixed to each object ID.
431    
432    =item resume
433    
434    If specified, key-value pairs already in the database will not be reinserted.
435    
436  =back  =back
437    
438  =cut  =cut
# Line 485  Line 442 
442      my ($self, $fileName, %options) = @_;      my ($self, $fileName, %options) = @_;
443      # Declare the return variable.      # Declare the return variable.
444      my $retVal = Stats->new('keys', 'values');      my $retVal = Stats->new('keys', 'values');
445        # Initialize the timers.
446        my ($insertTime, $eraseTime, $archiveTime, $checkTime) = (0, 0, 0, 0);
447      # Check for append mode.      # Check for append mode.
448      my $append = ($options{append} ? 1 : 0);      my $append = ($options{append} ? 1 : 0);
449        # Check for resume mode.
450        my $resume = ($options{resume} ? 1 : 0);
451      # Create a hash of key names found.      # Create a hash of key names found.
452      my %keyHash = ();      my %keyHash = ();
453      # Open the file for input.      # Open the file for input. Note we must anticipate the possibility of an
454      my $fh = Open(undef, "<$fileName");      # open filehandle being passed in.
455        my $fh;
456        if (ref $fileName) {
457            Trace("Using file opened by caller.") if T(3);
458            $fh = $fileName;
459        } else {
460            Trace("Attributes will be loaded from $fileName.") if T(3);
461            $fh = Open(undef, "<$fileName");
462        }
463        # Now check to see if we need to archive.
464        my $ah;
465        if ($options{archive}) {
466            $ah = Open(undef, ">$options{archive}");
467            Trace("Load file will be archived to $options{archive}.") if T(3);
468        }
469        # Insure we recover from errors.
470        eval {
471      # Loop through the file.      # Loop through the file.
472      while (! eof $fh) {      while (! eof $fh) {
473                # Read the current line.
474          my ($id, $key, @values) = Tracer::GetLine($fh);          my ($id, $key, @values) = Tracer::GetLine($fh);
475          $retVal->Add(linesIn => 1);          $retVal->Add(linesIn => 1);
476                # Check to see if we need to fix up the object ID.
477                if ($options{objectType}) {
478                    $id = "$options{objectType}:$id";
479                }
480                # Archive the line (if necessary).
481                if (defined $ah) {
482                    my $startTime = time();
483                    Tracer::PutLine($ah, [$id, $key, @values]);
484                    $archiveTime += time() - $startTime;
485                }
486          # Do some validation.          # Do some validation.
487          if (! defined($id)) {              if (! $id) {
488              # We ignore blank lines.              # We ignore blank lines.
489              $retVal->Add(blankLines => 1);              $retVal->Add(blankLines => 1);
490                } elsif (substr($id, 0, 1) eq '#') {
491                    # A line beginning with a pound sign is a comment.
492                    $retVal->Add(comments => 1);
493          } elsif (! defined($key)) {          } elsif (! defined($key)) {
494              # An ID without a key is a serious error.              # An ID without a key is a serious error.
495              my $lines = $retVal->Ask('linesIn');              my $lines = $retVal->Ask('linesIn');
496              Confess("Line $lines in $fileName has no attribute key.");              Confess("Line $lines in $fileName has no attribute key.");
497                } elsif (! @values) {
498                    # A line with no values is not allowed.
499                    my $lines = $retVal->Ask('linesIn');
500                    Trace("Line $lines for key $key has no attribute values.") if T(1);
501                    $retVal->Add(skipped => 1);
502          } else {          } else {
503                    # The key contains a real part and an optional sub-part. We need the real part.
504                    my ($realKey, $subKey) = $self->SplitKey($key);
505              # Now we need to check for a new key.              # Now we need to check for a new key.
506              if (! exists $keyHash{$key}) {                  if (! exists $keyHash{$realKey}) {
507                  # This is a new key. Verify that it exists.                      if (! $self->Exists('AttributeKey', $realKey)) {
                 if (! $self->Exists('AttributeKey', $key)) {  
508                      my $line = $retVal->Ask('linesIn');                      my $line = $retVal->Ask('linesIn');
509                      Confess("Attribute \"$key\" on line $line of $fileName not found in database.");                          Confess("Attribute \"$realKey\" on line $line of $fileName not found in database.");
510                  } else {                  } else {
511                      # Make sure we know this is no longer a new key.                      # Make sure we know this is no longer a new key.
512                      $keyHash{$key} = 1;                          $keyHash{$realKey} = 1;
513                      $retVal->Add(keys => 1);                      $retVal->Add(keys => 1);
514                      # If this is NOT append mode, erase the key.                      # If this is NOT append mode, erase the key.
515                      if (! $append) {                      if (! $append) {
516                          $self->EraseAttribute($key);                              my $startTime = time();
517                      }                              $self->EraseAttribute($realKey);
518                  }                              $eraseTime += time() - $startTime;
519                  Trace("Key $key found.") if T(3);                              Trace("Attribute $realKey erased.") if T(3);
520              }                          }
521              # Now we know the key is valid. Add this value.                      }
522                        Trace("Key $realKey found.") if T(3);
523                    }
524                    # If we're in resume mode, check to see if this insert is redundant.
525                    my $ok = 1;
526                    if ($resume) {
527                        my $startTime = time();
528                        my $count = $self->GetAttributes($id, $key, @values);
529                        $ok = ! $count;
530                        $checkTime += time() - $startTime;
531                    }
532                    if ($ok) {
533                        # Everything is all set up, so add the value.
534                        my $startTime = time();
535              $self->AddAttribute($id, $key, @values);              $self->AddAttribute($id, $key, @values);
536                        $insertTime += time() - $startTime;
537                    } else {
538                        # Here we skipped because of resume mode.
539                        $retVal->Add(resumeSkip => 1);
540                    }
541    
542              my $progress = $retVal->Add(values => 1);              my $progress = $retVal->Add(values => 1);
543              Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);              Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
544                }
545            }
546            $retVal->Add(eraseTime   => $eraseTime);
547            $retVal->Add(insertTime  => $insertTime);
548            $retVal->Add(archiveTime => $archiveTime);
549            $retVal->Add(checkTime   => $checkTime);
550        };
551        # Check for an error.
552        if ($@) {
553            # Here we have an error. Display the error message.
554            my $message = $@;
555            Trace("Error during attribute load: $message") if T(0);
556            $retVal->AddMessage($message);
557        }
558        # Close the archive file, if any.
559        if (defined $ah) {
560            Trace("Closing archive file $options{archive}.") if T(2);
561            close $ah;
562        }
563        # Return the result.
564        return $retVal;
565    }
566    
567    =head3 BackupKeys
568    
569    C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
570    
571    Backup the attribute key information from the attribute database.
572    
573    =over 4
574    
575    =item fileName
576    
577    Name of the output file.
578    
579    =item options
580    
581    Options for modifying the backup process.
582    
583    =item RETURN
584    
585    Returns a statistics object for the backup.
586    
587    =back
588    
589    Currently there are no options. The backup is straight to a text file in
590    tab-delimited format. Each key is backup up to two lines. The first line
591    is all of the data from the B<AttributeKey> table. The second is a
592    tab-delimited list of all the groups.
593    
594    =cut
595    
596    sub BackupKeys {
597        # Get the parameters.
598        my ($self, $fileName, %options) = @_;
599        # Declare the return variable.
600        my $retVal = Stats->new();
601        # Open the output file.
602        my $fh = Open(undef, ">$fileName");
603        # Set up to read the keys.
604        my $keyQuery = $self->Get(['AttributeKey'], "", []);
605        # Loop through the keys.
606        while (my $keyData = $keyQuery->Fetch()) {
607            $retVal->Add(key => 1);
608            # Get the fields.
609            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
610                                                              'AttributeKey(description)']);
611            # Escape any tabs or new-lines in the description.
612            my $escapedDescription = Tracer::Escape($description);
613            # Write the key data to the output.
614            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
615            # Get the key's groups.
616            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
617                                        'IsInGroup(to-link)');
618            $retVal->Add(memberships => scalar(@groups));
619            # Write them to the output. Note we put a marker at the beginning to insure the line
620            # is nonempty.
621            Tracer::PutLine($fh, ['#GROUPS', @groups]);
622          }          }
623        # Log the operation.
624        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
625        # Return the result.
626        return $retVal;
627      }      }
628    
629    =head3 RestoreKeys
630    
631    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
632    
633    Restore the attribute keys and groups from a backup file.
634    
635    =over 4
636    
637    =item fileName
638    
639    Name of the file containing the backed-up keys. Each key has a pair of lines,
640    one containing the key data and one listing its groups.
641    
642    =back
643    
644    =cut
645    
646    sub RestoreKeys {
647        # Get the parameters.
648        my ($self, $fileName, %options) = @_;
649        # Declare the return variable.
650        my $retVal = Stats->new();
651        # Set up a hash to hold the group IDs.
652        my %groups = ();
653        # Open the file.
654        my $fh = Open(undef, "<$fileName");
655        # Loop until we're done.
656        while (! eof $fh) {
657            # Get a key record.
658            my ($id, $dataType, $description) = Tracer::GetLine($fh);
659            if ($id eq '#GROUPS') {
660                Confess("Group record found when key record expected.");
661            } elsif (! defined($description)) {
662                Confess("Invalid format found for key record.");
663            } else {
664                $retVal->Add("keyIn" => 1);
665                # Add this key to the database.
666                $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
667                                                      description => Tracer::UnEscape($description) });
668                Trace("Attribute $id stored.") if T(3);
669                # Get the group line.
670                my ($marker, @groups) = Tracer::GetLine($fh);
671                if (! defined($marker)) {
672                    Confess("End of file found where group record expected.");
673                } elsif ($marker ne '#GROUPS') {
674                    Confess("Group record not found after key record.");
675                } else {
676                    $retVal->Add(memberships => scalar(@groups));
677                    # Connect the groups.
678                    for my $group (@groups) {
679                        # Find out if this is a new group.
680                        if (! $groups{$group}) {
681                            $retVal->Add(newGroup => 1);
682                            # Add the group.
683                            $self->InsertObject('AttributeGroup', { id => $group });
684                            Trace("Group $group created.") if T(3);
685                            # Make sure we know it's not new.
686                            $groups{$group} = 1;
687                        }
688                        # Connect the group to our key.
689                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
690                    }
691                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
692                }
693            }
694        }
695        # Log the operation.
696        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
697        # Return the result.
698        return $retVal;
699    }
700    
701    =head3 ArchiveFileName
702    
703    C<< my $fileName = $ca->ArchiveFileName(); >>
704    
705    Compute a file name for archiving attribute input data. The file will be in the attribute log directory
706    
707    =cut
708    
709    sub ArchiveFileName {
710        # Get the parameters.
711        my ($self) = @_;
712        # Declare the return variable.
713        my $retVal;
714        # We start by turning the timestamp into something usable as a file name.
715        my $now = Tracer::Now();
716        $now =~ tr/ :\//___/;
717        # Next we get the directory name.
718        my $dir = "$FIG_Config::var/attributes";
719        if (! -e $dir) {
720            Trace("Creating attribute file directory $dir.") if T(1);
721            mkdir $dir;
722        }
723        # Put it together with the field name and the time stamp.
724        $retVal = "$dir/upload.$now";
725        # Modify the file name to insure it's unique.
726        my $seq = 0;
727        while (-e "$retVal.$seq.tbl") { $seq++ }
728        # Use the computed sequence number to get the correct file name.
729        $retVal .= ".$seq.tbl";
730      # Return the result.      # Return the result.
731      return $retVal;      return $retVal;
732  }  }
# Line 568  Line 767 
767      my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');      my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
768      Trace(scalar(@keys) . " keys found during backup.") if T(2);      Trace(scalar(@keys) . " keys found during backup.") if T(2);
769      # Open the file for output.      # Open the file for output.
770      my $fh = Open(undef, $fileName);      my $fh = Open(undef, ">$fileName");
771      # Loop through the keys.      # Loop through the keys.
772      for my $key (@keys) {      for my $key (@keys) {
773          Trace("Backing up attribute $key.") if T(3);          Trace("Backing up attribute $key.") if T(3);
774          $retVal->Add(keys => 1);          $retVal->Add(keys => 1);
775          # Loop through this key's values.          # Loop through this key's values.
776          my $query = $self->Get(['HasValueFor'], "HasValueFor(to-link) = ?", [$key]);          my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
777          my $valuesFound = 0;          my $valuesFound = 0;
778          while (my $line = $query->Fetch()) {          while (my $line = $query->Fetch()) {
779              $valuesFound++;              $valuesFound++;
780              # Get this row's data.              # Get this row's data.
781              my @row = $line->Values(['HasValueFor(from-link)', 'HasValueFor(to-link)',              my ($id, $key, $subKey, $value) = $line->Values(['HasValueFor(to-link)',
782                                                                 'HasValueFor(from-link)',
783                                                                 'HasValueFor(subkey)',
784                                       'HasValueFor(value)']);                                       'HasValueFor(value)']);
785                # Check for a subkey.
786                if ($subKey ne '') {
787                    $key = "$key$self->{splitter}$subKey";
788                }
789              # Write it to the file.              # Write it to the file.
790              Tracer::PutLine($fh, \@row);              Tracer::PutLine($fh, [$id, $key, $value]);
791          }          }
792          Trace("$valuesFound values backed up for key $key.") if T(3);          Trace("$valuesFound values backed up for key $key.") if T(3);
793          $retVal->Add(values => $valuesFound);          $retVal->Add(values => $valuesFound);
794      }      }
795        # Log the operation.
796        $self->LogOperation("Backup Data", $fileName, $retVal->Display());
797      # Return the result.      # Return the result.
798      return $retVal;      return $retVal;
799  }  }
# Line 851  Line 1058 
1058      return %retVal;      return %retVal;
1059  }  }
1060    
1061    =head3 LogOperation
1062    
1063    C<< $ca->LogOperation($action, $target, $description); >>
1064    
1065    Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
1066    
1067    =over 4
1068    
1069    =item action
1070    
1071    Action being logged (e.g. C<Delete Group> or C<Load Key>).
1072    
1073    =item target
1074    
1075    ID of the key or group affected.
1076    
1077    =item description
1078    
1079    Short description of the action.
1080    
1081    =back
1082    
1083    =cut
1084    
1085    sub LogOperation {
1086        # Get the parameters.
1087        my ($self, $action, $target, $description) = @_;
1088        # Get the user ID.
1089        my $user = $self->{user};
1090        # Get a timestamp.
1091        my $timeString = Tracer::Now();
1092        # Open the log file for appending.
1093        my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
1094        # Write the data to it.
1095        Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
1096        # Close the log file.
1097        close $oh;
1098    }
1099    
1100    =head2 Internal Utility Methods
1101    
1102    =head3 _KeywordString
1103    
1104    C<< my $keywordString = $ca->_KeywordString($key, $value); >>
1105    
1106    Compute the keyword string for a specified key/value pair. This consists of the
1107    key name and value converted to lower case with underscores translated to spaces.
1108    
1109    This method is for internal use only. It is called whenever we need to update or
1110    insert a B<HasValueFor> record.
1111    
1112    =over 4
1113    
1114    =item key
1115    
1116    Name of the relevant attribute key.
1117    
1118    =item target
1119    
1120    ID of the target object to which this key/value pair will be associated.
1121    
1122    =item value
1123    
1124    The value to store for this key/object combination.
1125    
1126    =item RETURN
1127    
1128    Returns the value that should be stored as the keyword string for the specified
1129    key/value pair.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub _KeywordString {
1136        # Get the parameters.
1137        my ($self, $key, $value) = @_;
1138        # Get a copy of the key name and convert underscores to spaces.
1139        my $keywordString = $key;
1140        $keywordString =~ s/_/ /g;
1141        # Add the value convert it all to lower case.
1142        my $retVal = lc "$keywordString $value";
1143        # Return the result.
1144        return $retVal;
1145    }
1146    
1147    =head3 _QueryResults
1148    
1149    C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1150    
1151    Match the results of a B<HasValueFor> query against value criteria and return
1152    the results. This is an internal method that splits the values coming back
1153    and matches the sections against the specified section patterns. It serves
1154    as the back end to L</GetAttributes> and L</FindAttributes>.
1155    
1156    =over 4
1157    
1158    =item query
1159    
1160    A query object that will return the desired B<HasValueFor> records.
1161    
1162    =item values
1163    
1164    List of the desired attribute values, section by section. If C<undef>
1165    or an empty string is specified, all values in that section will match. A
1166    generic match can be requested by placing a percent sign (C<%>) at the end.
1167    In that case, all values that match up to and not including the percent sign
1168    will match. You may also specify a regular expression enclosed
1169    in slashes. All values that match the regular expression will be returned. For
1170    performance reasons, only values have this extra capability.
1171    
1172    =item RETURN
1173    
1174    Returns a list of tuples. The first element in the tuple is an object ID, the
1175    second is an attribute key, and the remaining elements are the sections of
1176    the attribute value. All of the tuples will match the criteria set forth in
1177    the parameter list.
1178    
1179    =back
1180    
1181    =cut
1182    
1183    sub _QueryResults {
1184        # Get the parameters.
1185        my ($self, $query, @values) = @_;
1186        # Declare the return value.
1187        my @retVal = ();
1188        # Get the number of value sections we have to match.
1189        my $sectionCount = scalar(@values);
1190        # Loop through the assignments found.
1191        while (my $row = $query->Fetch()) {
1192            # Get the current row's data.
1193            my ($id, $realKey, $subKey, $valueString) = $row->Values(['HasValueFor(to-link)',
1194                                                                      'HasValueFor(from-link)',
1195                                                                      'HasValueFor(subkey)',
1196                                                                      'HasValueFor(value)'
1197                                                                    ]);
1198            # Form the key from the real key and the sub key.
1199            my $key = $self->JoinKey($realKey, $subKey);
1200            # Break the value into sections.
1201            my @sections = split($self->{splitter}, $valueString);
1202            # Match each section against the incoming values. We'll assume we're
1203            # okay unless we learn otherwise.
1204            my $matching = 1;
1205            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1206                # We need to check to see if this section is generic.
1207                my $value = $values[$i];
1208                Trace("Current value pattern is \"$value\".") if T(4);
1209                if (substr($value, -1, 1) eq '%') {
1210                    Trace("Generic match used.") if T(4);
1211                    # Here we have a generic match.
1212                    my $matchLen = length($values[$i]) - 1;
1213                    $matching = substr($sections[$i], 0, $matchLen) eq
1214                                substr($values[$i], 0, $matchLen);
1215                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1216                    Trace("Regular expression detected.") if T(4);
1217                    # Here we have a regular expression match.
1218                    my $section = $sections[$i];
1219                    $matching = eval("\$section =~ $value");
1220                } else {
1221                    # Here we have a strict match.
1222                    Trace("Strict match used.") if T(4);
1223                    $matching = ($sections[$i] eq $values[$i]);
1224                }
1225            }
1226            # If we match, output this row to the return list.
1227            if ($matching) {
1228                push @retVal, [$id, $key, @sections];
1229            }
1230        }
1231        # Return the rows found.
1232        return @retVal;
1233    }
1234    
1235  =head2 FIG Method Replacements  =head2 FIG Method Replacements
1236    
1237  The following methods are used by B<FIG.pm> to replace the previous attribute functionality.  The following methods are used by B<FIG.pm> to replace the previous attribute functionality.
# Line 862  Line 1243 
1243  The idea is that these methods represent attribute manipulation allowed by all users, while  The idea is that these methods represent attribute manipulation allowed by all users, while
1244  the others are only for privileged users with access to the attribute server.  the others are only for privileged users with access to the attribute server.
1245    
1246  In the previous implementation, an attribute had a value and a URL. In the new implementation,  In the previous implementation, an attribute had a value and a URL. In this implementation,
1247  there is only a value. In this implementation, each attribute has only a value. These  each attribute has only a value. These methods will treat the value as a list with the individual
1248  methods will treat the value as a list with the individual elements separated by the  elements separated by the value of the splitter parameter on the constructor (L</new>). The default
1249  value of the splitter parameter on the constructor (L</new>). The default is double  is double colons C<::>.
 colons C<::>.  
1250    
1251  So, for example, an old-style keyword with a value of C<essential> and a URL of  So, for example, an old-style keyword with a value of C<essential> and a URL of
1252  C<http://www.sciencemag.org/cgi/content/abstract/293/5538/2266> using the default  C<http://www.sciencemag.org/cgi/content/abstract/293/5538/2266> using the default
# Line 918  Line 1298 
1298  which has no wildcard in the key or the object ID, may return multiple tuples.  which has no wildcard in the key or the object ID, may return multiple tuples.
1299    
1300  Value matching in this system works very poorly, because of the way multiple values are  Value matching in this system works very poorly, because of the way multiple values are
1301  stored. For the object ID and key name, we create queries that filter for the desired  stored. For the object ID, key name, and first value, we create queries that filter for the
1302  results. For the values, we do a comparison after the attributes are retrieved from the  desired results. On any filtering by value, we must do a comparison after the attributes are
1303  database. As a result, queries in which filter only on value end up reading the entire  retrieved from the database, since the database has no notion of the multiple values, which
1304  attribute table to find the desired results.  are stored in a single string. As a result, queries in which filter only on value end up
1305    reading a lot more than they need to.
1306    
1307  =over 4  =over 4
1308    
# Line 945  Line 1326 
1326  or an empty string is specified, all values in that section will match. A  or an empty string is specified, all values in that section will match. A
1327  generic match can be requested by placing a percent sign (C<%>) at the end.  generic match can be requested by placing a percent sign (C<%>) at the end.
1328  In that case, all values that match up to and not including the percent sign  In that case, all values that match up to and not including the percent sign
1329  will match.  will match. You may also specify a regular expression enclosed
1330    in slashes. All values that match the regular expression will be returned. For
1331    performance reasons, only values have this extra capability.
1332    
1333  =item RETURN  =item RETURN
1334    
# Line 961  Line 1344 
1344  sub GetAttributes {  sub GetAttributes {
1345      # Get the parameters.      # Get the parameters.
1346      my ($self, $objectID, $key, @values) = @_;      my ($self, $objectID, $key, @values) = @_;
1347      # We will create one big honking query. The following hash will build the filter      # This hash will map "HasValueFor" fields to patterns. We use it to build the
1348      # clause and a parameter list.      # SQL statement.
1349      my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);      my %data;
1350        # Before we do anything else, we must parse the key. The key is treated by the
1351        # user as a single field, but to us it's actually a real key and a subkey.
1352        # If the key has no splitter and is exact, the real key is the original key
1353        # and the subkey is an empty string. If the key has a splitter, it is
1354        # split into two pieces and each piece is processed separately. If the key has
1355        # no splitter and is generic, the real key is the incoming key and the subkey
1356        # is allowed to be wild. Of course, this only matters if an actual key has
1357        # been specified.
1358        if (defined $key) {
1359            if ($key =~ /$self->{splitter}/) {
1360                # Here we have a two-part key, so we split it normally.
1361                my ($realKey, $subKey) = $self->SplitKey($key);
1362                $data{'HasValueFor(from-link)'} = $realKey;
1363                $data{'HasValueFor(subkey)'} = $subKey;
1364            } elsif (substr($key, -1, 1) eq '%') {
1365                $data{'HasValueFor(from-link)'} = $key;
1366            } else {
1367                $data{'HasValueFor(from-link)'} = $key;
1368                $data{'HasValueFor(subkey)'} = '';
1369            }
1370        }
1371        # Add the object ID to the key information.
1372        $data{'HasValueFor(to-link)'} = $objectID;
1373        # The first value represents a problem, because we can search it using SQL, but not
1374        # in the normal way. If the user specifies a generic search or exact match for
1375        # every alternative value (remember, the values may be specified as a list),
1376        # then we can create SQL filtering for it. If any of the values are specified
1377        # as a regular expression, however, that's a problem, because we need to read
1378        # every value to verify a match.
1379        if (@values > 0) {
1380            # Get the first value and put its alternatives in an array.
1381            my $valueParm = $values[0];
1382            my @valueList;
1383            if (ref $valueParm eq 'ARRAY') {
1384                @valueList = @{$valueParm};
1385            } else {
1386                @valueList = ($valueParm);
1387            }
1388            # Okay, now we have all the possible criteria for the first value in the list
1389            # @valueList. We'll copy the values to a new array in which they have been
1390            # converted to generic requests. If we find a regular-expression match
1391            # anywhere in the list, we toss the whole thing.
1392            my @valuePatterns = ();
1393            my $okValues = 1;
1394            for my $valuePattern (@valueList) {
1395                # Check the pattern type.
1396                if (substr($valuePattern, 0, 1) eq '/') {
1397                    # Regular expressions invalidate the entire process.
1398                    $okValues = 0;
1399                } elsif (substr($valuePattern, -1, 1) eq '%') {
1400                    # A Generic pattern is passed in unmodified.
1401                    push @valuePatterns, $valuePattern;
1402                } else {
1403                    # An exact match is converted to generic.
1404                    push @valuePatterns, "$valuePattern%";
1405                }
1406            }
1407            # If everything works, add the value data to the filtering hash.
1408            if ($okValues) {
1409                $data{'HasValueFor(value)'} = \@valuePatterns;
1410            }
1411        }
1412        # Create some lists to contain the filter fragments and parameter values.
1413      my @filter = ();      my @filter = ();
1414      my @parms = ();      my @parms = ();
1415      # This next loop goes through the different fields that can be specified in the      # This next loop goes through the different fields that can be specified in the
1416      # parameter list and generates filters for each.      # parameter list and generates filters for each. The %data hash that we built above
1417        # contains all the necessary information to do this.
1418      for my $field (keys %data) {      for my $field (keys %data) {
1419          # Accumulate filter information for this field. We will OR together all the          # Accumulate filter information for this field. We will OR together all the
1420          # elements accumulated to create the final result.          # elements accumulated to create the final result.
# Line 995  Line 1442 
1442                          push @fieldFilter, "$field = ?";                          push @fieldFilter, "$field = ?";
1443                          push @parms, $pattern;                          push @parms, $pattern;
1444                      } else {                      } else {
1445                          # Here we have a generate request, so we will use the LIKE operator to                          # Here we have a generic request, so we will use the LIKE operator to
1446                          # filter the field to this value pattern.                          # filter the field to this value pattern.
1447                          push @fieldFilter, "$field LIKE ?";                          push @fieldFilter, "$field LIKE ?";
1448                          # We must convert the pattern value to an SQL match pattern. First                          # We must convert the pattern value to an SQL match pattern. First
# Line 1017  Line 1464 
1464      # Now @filter contains one or more filter strings and @parms contains the parameter      # Now @filter contains one or more filter strings and @parms contains the parameter
1465      # values to bind to them.      # values to bind to them.
1466      my $actualFilter = join(" AND ", @filter);      my $actualFilter = join(" AND ", @filter);
     # Declare the return variable.  
     my @retVal = ();  
     # Get the number of value sections we have to match.  
     my $sectionCount = scalar(@values);  
1467      # Now we're ready to make our query.      # Now we're ready to make our query.
1468      my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);      my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1469      # Loop through the assignments found.      # Format the results.
1470      while (my $row = $query->Fetch()) {      my @retVal = $self->_QueryResults($query, @values);
         # Get the current row's data.  
         my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',  
                                                       'HasValueFor(value)']);  
         # Break the value into sections.  
         my @sections = split($self->{splitter}, $valueString);  
         # Match each section against the incoming values. We'll assume we're  
         # okay unless we learn otherwise.  
         my $matching = 1;  
         for (my $i = 0; $i < $sectionCount && $matching; $i++) {  
             # We need to check to see if this section is generic.  
             if (substr($values[$i], -1, 1) eq '%') {  
                 my $matchLen = length($values[$i] - 1);  
                 $matching = substr($sections[$i], 0, $matchLen) eq  
                             substr($values[$i], 0, $matchLen);  
             } else {  
                 $matching = ($sections[$i] eq $values[$i]);  
             }  
         }  
         # If we match, output this row to the return list.  
         if ($matching) {  
             push @retVal, [$id, $key, @sections];  
         }  
     }  
1471      # Return the rows found.      # Return the rows found.
1472      return @retVal;      return @retVal;
1473  }  }
# Line 1093  Line 1513 
1513          # Okay, now we have some reason to believe we can do this. Form the values          # Okay, now we have some reason to believe we can do this. Form the values
1514          # into a scalar.          # into a scalar.
1515          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1516            # Split up the key.
1517            my ($realKey, $subKey) = $self->SplitKey($key);
1518          # Connect the object to the key.          # Connect the object to the key.
1519          $self->InsertObject('HasValueFor', { 'from-link' => $key,          $self->InsertObject('HasValueFor', { 'from-link' => $realKey,
1520                                               'to-link'   => $objectID,                                               'to-link'   => $objectID,
1521                                                 'subkey'    => $subKey,
1522                                               'value'     => $valueString,                                               'value'     => $valueString,
1523                                         });                                         });
1524      }      }
# Line 1136  Line 1559 
1559          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1560      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1561          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1562      } elsif (scalar(@values) == 0) {      } else {
1563          # Here we erase the entire key.          # Split the key into the real key and the subkey.
1564          $self->EraseAttribute($key);          my ($realKey, $subKey) = $self->SplitKey($key);
1565            if ($subKey eq '' && scalar(@values) == 0) {
1566                # Here we erase the entire key for this object.
1567                $self->DeleteRow('HasValueFor', $key, $objectID);
1568      } else {      } else {
1569          # Here we erase the matching values.          # Here we erase the matching values.
1570          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1571          $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1572                                 { subkey => $subKey, value => $valueString });
1573            }
1574      }      }
1575      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1576      return 1;      return 1;
1577  }  }
1578    
1579    =head3 DeleteMatchingAttributes
1580    
1581    C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>
1582    
1583    Delete all attributes that match the specified criteria. This is equivalent to
1584    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1585    row found.
1586    
1587    =over 4
1588    
1589    =item objectID
1590    
1591    ID of object whose attributes are to be deleted. If the attributes for multiple
1592    objects are to be deleted, this parameter can be specified as a list reference. If
1593    attributes are to be deleted for all objects, specify C<undef> or an empty string.
1594    Finally, you can delete attributes for a range of object IDs by putting a percent
1595    sign (C<%>) at the end.
1596    
1597    =item key
1598    
1599    Attribute key name. A value of C<undef> or an empty string will match all
1600    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1601    specified as a list reference. Finally, you can delete attributes for a range of
1602    keys by putting a percent sign (C<%>) at the end.
1603    
1604    =item values
1605    
1606    List of the desired attribute values, section by section. If C<undef>
1607    or an empty string is specified, all values in that section will match. A
1608    generic match can be requested by placing a percent sign (C<%>) at the end.
1609    In that case, all values that match up to and not including the percent sign
1610    will match. You may also specify a regular expression enclosed
1611    in slashes. All values that match the regular expression will be deleted. For
1612    performance reasons, only values have this extra capability.
1613    
1614    =item RETURN
1615    
1616    Returns a list of tuples for the attributes that were deleted, in the
1617    same form as L</GetAttributes>.
1618    
1619    =back
1620    
1621    =cut
1622    
1623    sub DeleteMatchingAttributes {
1624        # Get the parameters.
1625        my ($self, $objectID, $key, @values) = @_;
1626        # Get the matching attributes.
1627        my @retVal = $self->GetAttributes($objectID, $key, @values);
1628        # Loop through the attributes, deleting them.
1629        for my $tuple (@retVal) {
1630            $self->DeleteAttribute(@{$tuple});
1631        }
1632        # Log this operation.
1633        my $count = @retVal;
1634        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1635        # Return the deleted attributes.
1636        return @retVal;
1637    }
1638    
1639  =head3 ChangeAttribute  =head3 ChangeAttribute
1640    
1641  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>
# Line 1211  Line 1699 
1699    
1700  =item key  =item key
1701    
1702  Key to erase.  Key to erase. This must be a real key; that is, it cannot have a subkey
1703    component.
1704    
1705  =back  =back
1706    
# Line 1220  Line 1709 
1709  sub EraseAttribute {  sub EraseAttribute {
1710      # Get the parameters.      # Get the parameters.
1711      my ($self, $key) = @_;      my ($self, $key) = @_;
1712      # Delete everything connected to the key. The "keepRoot" option keeps the key in the      # Delete everything connected to the key.
1713      # datanase while deleting everything attached to it.      $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1714      $self->Delete('AttributeKey', $key, keepRoot => 1);      # Log the operation.
1715        $self->LogOperation("Erase Data", $key);
1716      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1717      return 1;      return 1;
1718  }  }
# Line 1257  Line 1747 
1747      return sort @groups;      return sort @groups;
1748  }  }
1749    
1750    =head3 QueryAttributes
1751    
1752    C<< my @attributeData = $ca->QueryAttributes($filter, $filterParms); >>
1753    
1754    Return the attribute data based on an SQL filter clause. In the filter clause,
1755    the name C<$object> should be used for the object ID, C<$key> should be used for
1756    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1757    
1758    =over 4
1759    
1760    =item filter
1761    
1762    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1763    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1764    and C<$value> for the value field. This abstraction enables us to hide the details of
1765    the database construction from the user.
1766    
1767    =item filterParms
1768    
1769    Parameters for the filter clause.
1770    
1771    =item RETURN
1772    
1773    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1774    one or more attribute values.
1775    
1776    =back
1777    
1778    =cut
1779    
1780    # This hash is used to drive the substitution process.
1781    my %AttributeParms = (object => 'HasValueFor(to-link)',
1782                          key    => 'HasValueFor(from-link)',
1783                          subkey => 'HasValueFor(subkey)',
1784                          value  => 'HasValueFor(value)');
1785    
1786    sub QueryAttributes {
1787        # Get the parameters.
1788        my ($self, $filter, $filterParms) = @_;
1789        # Declare the return variable.
1790        my @retVal = ();
1791        # Make sue we have filter parameters.
1792        my $realParms = (defined($filterParms) ? $filterParms : []);
1793        # Create the query by converting the filter.
1794        my $realFilter = $filter;
1795        for my $name (keys %AttributeParms) {
1796            $realFilter =~ s/\$$name/$AttributeParms{$name}/g;
1797        }
1798        my $query = $self->Get(['HasValueFor'], $realFilter, $realParms);
1799        # Loop through the results, forming the output attribute tuples.
1800        while (my $result = $query->Fetch()) {
1801            # Get the four values from this query result row.
1802            my ($objectID, $key, $subkey, $value) = $result->Values([$AttributeParms{object},
1803                                                                    $AttributeParms{key},
1804                                                                    $AttributeParms{subkey},
1805                                                                    $AttributeParms{value}]);
1806            # Combine the key and the subkey.
1807            my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1808            # Split the value.
1809            my @values = split $self->{splitter}, $value;
1810            # Output the result.
1811            push @retVal, [$objectID, $realKey, @values];
1812        }
1813        # Return the result.
1814        return @retVal;
1815    }
1816    
1817    =head2 Key and ID Manipulation Methods
1818    
1819    =head3 ParseID
1820    
1821    C<< my ($type, $id) = CustomAttributes::ParseID($idValue); >>
1822    
1823    Determine the type and object ID corresponding to an ID value from the attribute database.
1824    Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
1825    however, Genomes, Features, and Subsystems are not stored with a type name, so we need to
1826    deduce the type from the ID value structure.
1827    
1828    The theory here is that you can plug the ID and type directly into a Sprout database method, as
1829    follows
1830    
1831        my ($type, $id) = CustomAttributes::ParseID($attrList[$num]->[0]);
1832        my $target = $sprout->GetEntity($type, $id);
1833    
1834    =over 4
1835    
1836    =item idValue
1837    
1838    ID value taken from the attribute database.
1839    
1840    =item RETURN
1841    
1842    Returns a two-element list. The first element is the type of object indicated by the ID value,
1843    and the second element is the actual object ID.
1844    
1845    =back
1846    
1847    =cut
1848    
1849    sub ParseID {
1850        # Get the parameters.
1851        my ($idValue) = @_;
1852        # Declare the return variables.
1853        my ($type, $id);
1854        # Parse the incoming ID. We first check for the presence of an entity name. Entity names
1855        # can only contain letters, which helps to insure typed object IDs don't collide with
1856        # subsystem names (which are untyped).
1857        if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1858            # Here we have a typed ID.
1859            ($type, $id) = ($1, $2);
1860            # Fix the case sensitivity on PDB IDs.
1861            if ($type eq 'PDB') { $id = lc $id; }
1862        } elsif ($idValue =~ /fig\|/) {
1863            # Here we have a feature ID.
1864            ($type, $id) = (Feature => $idValue);
1865        } elsif ($idValue =~ /\d+\.\d+/) {
1866            # Here we have a genome ID.
1867            ($type, $id) = (Genome => $idValue);
1868        } else {
1869            # The default is a subsystem ID.
1870            ($type, $id) = (Subsystem => $idValue);
1871        }
1872        # Return the results.
1873        return ($type, $id);
1874    }
1875    
1876    =head3 FormID
1877    
1878    C<< my $idValue = CustomAttributes::FormID($type, $id); >>
1879    
1880    Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1881    genomes, and features are stored in the database without type information, but all other object IDs
1882    must be prefixed with the object type.
1883    
1884    =over 4
1885    
1886    =item type
1887    
1888    Relevant object type.
1889    
1890    =item id
1891    
1892    ID of the object in question.
1893    
1894    =item RETURN
1895    
1896    Returns a string that will be recognized as an object ID in the attribute database.
1897    
1898    =back
1899    
1900    =cut
1901    
1902    sub FormID {
1903        # Get the parameters.
1904        my ($type, $id) = @_;
1905        # Declare the return variable.
1906        my $retVal;
1907        # Compute the ID string from the type.
1908        if (grep { $type eq $_ } qw(Feature Genome Subsystem)) {
1909            $retVal = $id;
1910        } else {
1911            $retVal = "$type:$id";
1912        }
1913        # Return the result.
1914        return $retVal;
1915    }
1916    
1917    =head3 GetTargetObject
1918    
1919    C<< my $object = CustomAttributes::GetTargetObject($erdb, $idValue); >>
1920    
1921    Return the database object corresponding to the specified attribute object ID. The
1922    object type associated with the ID value must correspond to an entity name in the
1923    specified database.
1924    
1925    =over 4
1926    
1927    =item erdb
1928    
1929    B<ERDB> object for accessing the target database.
1930    
1931    =item idValue
1932    
1933    ID value retrieved from the attribute database.
1934    
1935    =item RETURN
1936    
1937    Returns a B<ERDBObject> for the attribute value's target object.
1938    
1939    =back
1940    
1941    =cut
1942    
1943    sub GetTargetObject {
1944        # Get the parameters.
1945        my ($erdb, $idValue) = @_;
1946        # Declare the return variable.
1947        my $retVal;
1948        # Get the type and ID for the target object.
1949        my ($type, $id) = ParseID($idValue);
1950        # Plug them into the GetEntity method.
1951        $retVal = $erdb->GetEntity($type, $id);
1952        # Return the resulting object.
1953        return $retVal;
1954    }
1955    
1956    =head3 SplitKey
1957    
1958    C<< my ($realKey, $subKey) = $ca->SplitKey($key); >>
1959    
1960    Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1961    The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
1962    then the sub key is presumed to be an empty string.
1963    
1964    =over 4
1965    
1966    =item key
1967    
1968    Incoming key to be split.
1969    
1970    =item RETURN
1971    
1972    Returns a two-element list, the first element of which is the real key and the second element of
1973    which is the sub key.
1974    
1975    =back
1976    
1977    =cut
1978    
1979    sub SplitKey {
1980        # Get the parameters.
1981        my ($self, $key) = @_;
1982        # Do the split.
1983        my ($realKey, $subKey) = split($self->{splitter}, $key, 2);
1984        # Insure the subkey has a value.
1985        if (! defined $subKey) {
1986            $subKey = '';
1987        }
1988        # Return the results.
1989        return ($realKey, $subKey);
1990    }
1991    
1992    =head3 JoinKey
1993    
1994    C<< my $key = $ca->JoinKey($realKey, $subKey); >>
1995    
1996    Join a real key and a subkey together to make an external key. The external key is the attribute key
1997    used by the caller. The real key and the subkey are how the keys are represented in the database. The
1998    real key is the key to the B<AttributeKey> entity. The subkey is an attribute of the B<HasValueFor>
1999    relationship.
2000    
2001    =over 4
2002    
2003    =item realKey
2004    
2005    The real attribute key.
2006    
2007    =item subKey
2008    
2009    The subordinate portion of the attribute key.
2010    
2011    =item RETURN
2012    
2013    Returns a single string representing both keys.
2014    
2015    =back
2016    
2017    =cut
2018    
2019    sub JoinKey {
2020        # Get the parameters.
2021        my ($self, $realKey, $subKey) = @_;
2022        # Declare the return variable.
2023        my $retVal;
2024        # Check for a subkey.
2025        if ($subKey eq '') {
2026            # No subkey, so the real key is the key.
2027            $retVal = $realKey;
2028        } else {
2029            # Subkey found, so the two pieces must be joined by a splitter.
2030            $retVal = "$realKey$self->{splitter}$subKey";
2031        }
2032        # Return the result.
2033        return $retVal;
2034    }
2035    
2036    
2037    =head3 AttributeTable
2038    
2039    C<< my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList); >>
2040    
2041    Format the attribute data into an HTML table.
2042    
2043    =over 4
2044    
2045    =item cgi
2046    
2047    CGI query object used to generate the HTML
2048    
2049    =item attrList
2050    
2051    List of attribute results, in the format returned by the L</GetAttributes> or
2052    L</QueryAttributes> methods.
2053    
2054    =item RETURN
2055    
2056    Returns an HTML table displaying the attribute keys and values.
2057    
2058    =back
2059    
2060    =cut
2061    
2062    sub AttributeTable {
2063        # Get the parameters.
2064        my ($cgi, @attrList) = @_;
2065        # Accumulate the table rows.
2066        my @html = ();
2067        for my $attrData (@attrList) {
2068            # Format the object ID and key.
2069            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
2070            # Now we format the values. These remain unchanged unless one of them is a URL.
2071            my $lastValue = scalar(@{$attrData}) - 1;
2072            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
2073            # Assemble the values into a table row.
2074            push @html, $cgi->Tr($cgi->td(\@columns));
2075        }
2076        # Format the table in the return variable.
2077        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
2078        # Return it.
2079        return $retVal;
2080    }
2081  1;  1;
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