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revision 1.10, Tue Nov 28 01:00:08 2006 UTC revision 1.35, Wed Sep 3 20:53:19 2008 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        use FIGRules;
14    
15  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
16    
# Line 22  Line 25 
25  however, to the attribute database only the ID matters. This will create  however, to the attribute database only the ID matters. This will create
26  a problem if we have a single ID that applies to two objects of different  a problem if we have a single ID that applies to two objects of different
27  types, but it is more consistent with the original attribute implementation  types, but it is more consistent with the original attribute implementation
28  in the SEED (which this implementation replaces.  in the SEED (which this implementation replaces).
29    
30  An I<assignment> relates a specific attribute key to a specific object.  The actual attribute values are stored as a relationship between the attribute
31  Each assignment contains one or more values.  keys and the objects. There can be multiple values for a single key/object pair.
32    
33    =head3 Object IDs
34    
35    The object ID is normally represented as
36    
37        I<type>:I<id>
38    
39    where I<type> is the object type (C<Role>, C<Coupling>, etc.) and I<id> is
40    the actual object ID. Note that the object type must consist of only upper- and
41    lower-case letters! Thus, C<GenomeGroup> is a valid object type, but
42    C<genome_group> is not. Given that restriction, the object ID
43    
44        Family:aclame|cluster10
45    
46    would represent the FIG family C<aclame|cluster10>. For historical reasons,
47    there are three exceptions: subsystems, genomes, and features do not need
48    a type. So, for PEG 3361 of Streptomyces coelicolor A3(2), you simply code
49    
50        fig|100226.1.peg.3361
51    
52    The methods L</ParseID> and L</FormID> can be used to make this all seem
53    more consistent. Given any object ID string, L</ParseID> will convert it to an
54    object type and ID, and given any object type and ID, L</FormID> will
55    convert it to an object ID string. The attribute database is pretty
56    freewheeling about what it will allow for an ID; however, for best
57    results, the type should match an entity type from a Sprout genetics
58    database. If this rule is followed, then the database object
59    corresponding to an ID in the attribute database could be retrieved using
60    L</GetTargetObject> method.
61    
62        my $object = CustomAttributes::GetTargetObject($sprout, $idValue);
63    
64    =head3 Retrieval and Logging
65    
66  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
67  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
# Line 36  Line 72 
72    
73  where I<$fid> contains the ID of the desired feature.  where I<$fid> contains the ID of the desired feature.
74    
75  New attribute keys must be defined before they can be used. A web interface  Keys can be split into two pieces using the splitter value defined in the
76  is provided for this purpose.  constructor (the default is C<::>). The first piece of the key is called
77    the I<real key>. This portion of the key must be defined using the
78    web interface (C<Attributes.cgi>). The second portion of the key is called
79    the I<sub key>, and can take any value.
80    
81    Major attribute activity is recorded in a log (C<attributes.log>) in the
82    C<$FIG_Config::var> directory. The log reports the user name, time, and
83    the details of the operation. The user name will almost always be unknown,
84    the exception being when it is specified in this object's constructor
85    (see L</new>).
86    
87  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
88    
# Line 81  Line 126 
126  functions as data to the attribute management process, so if the data is  functions as data to the attribute management process, so if the data is
127  moved, this file must go with it.  moved, this file must go with it.
128    
129    =item attr_default_table
130    
131    Name of the default relationship for attribute values. If not present,
132    C<HasValueFor> is used.
133    
134  =back  =back
135    
136  =head2 Public Methods  =head2 Public Methods
137    
138  =head3 new  =head3 new
139    
140  C<< my $attrDB = CustomAttributes->new($splitter); >>      my $attrDB = CustomAttributes->new(%options);
141    
142  Construct a new CustomAttributes object.  Construct a new CustomAttributes object. The following options are
143    supported.
144    
145  =over 4  =over 4
146    
147  =item splitter  =item splitter
148    
149  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
150  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
151  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
152  worry about this parameter.  
153    =item user
154    
155    Name of the current user. This will appear in the attribute log.
156    
157  =back  =back
158    
# Line 106  Line 160 
160    
161  sub new {  sub new {
162      # Get the parameters.      # Get the parameters.
163      my ($class, $splitter) = @_;      my ($class, %options) = @_;
164        # Get the name ofthe default table.
165      # Connect to the database.      # Connect to the database.
166      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
167                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 116  Line 171 
171      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
172      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
173      # Store the splitter value.      # Store the splitter value.
174      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
175      # Return the result.      # Store the user name.
176      return $retVal;      $retVal->{user} = $options{user} || '<unknown>';
177  }      Trace("User $retVal->{user} selected for attribute object.") if T(3);
178        # Compute the default value table name. If it's not overridden, the
179  =head3 AssignmentKey      # default is HasValueFor.
180        $retVal->{defaultRel} = $FIG_Config::attr_default_table || 'HasValueFor';
 C<< my $hashedValue = $attrDB->AssignmentKey($id, $keyName); >>  
   
 Return the hashed key used in the assignment table for the specified object ID and  
 key name.  
   
 =over 4  
   
 =item id  
   
 ID of the object relevant to the assignment.  
   
 =item keyName  
   
 Name of the key being assigned values.  
   
 =item RETURN  
   
 Returns the ID that would be used for an B<Assignment> instance representing this  
 key/id pair.  
   
 =back  
   
 =cut  
   
 sub AssignmentKey {  
     # Get the parameters.  
     my ($self, $id, $keyName) = @_;  
     # Compute the result.  
     my $retVal = $self->DigestKey("$keyName=$id");  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 GetAssignment  
   
 C<< my $assign = $attrDB->GetAssignment($id, $keyName); >>  
   
 Check for an assignment between the specified attribute key and the specified object ID.  
 If an assignment exists, a B<DBObject> for it will be returned. If it does not exist, an  
 undefined value will be returned.  
   
 =over 4  
   
 =item id  
   
 ID of the object relevant to the assignment.  
   
 =item keyName  
   
 Attribute key name for the attribute to which the assignment is to be made.  
   
 =item RETURN  
   
 Returns a B<DBObject> for the indicated assignment, or C<undef> if the assignment  
 does not exist.  
   
 =back  
   
 =cut  
   
 sub GetAssignment {  
     # Get the parameters.  
     my ($self, $id, $keyName) = @_;  
     # Compute the assignment key.  
     my $hashKey = $self->AssignmentKey($id, $keyName);  
     # Check for an assignment.  
     my $retVal = $self->GetEntity('Assignment', $hashKey);  
181      # Return the result.      # Return the result.
182      return $retVal;      return $retVal;
183  }  }
184    
185  =head3 StoreAttributeKey  =head3 StoreAttributeKey
186    
187  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>      $attrDB->StoreAttributeKey($attributeName, $notes, \@groups, $table);
188    
189  Create or update an attribute for the database.  Create or update an attribute for the database.
190    
# Line 204  Line 192 
192    
193  =item attributeName  =item attributeName
194    
195  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.  
   
 =item type  
   
 Data type of the attribute. This must be a valid ERDB data type name.  
196    
197  =item notes  =item notes
198    
# Line 221  Line 203 
203  Reference to a list of the groups to which the attribute should be associated.  Reference to a list of the groups to which the attribute should be associated.
204  This will replace any groups to which the attribute is currently attached.  This will replace any groups to which the attribute is currently attached.
205    
206    =item table
207    
208    The name of the relationship in which the attribute's values are to be stored.
209    If empty or undefined, the default relationship (usually C<HasValueFor>) will be
210    assumed.
211    
212  =back  =back
213    
214  =cut  =cut
215    
216  sub StoreAttributeKey {  sub StoreAttributeKey {
217      # Get the parameters.      # Get the parameters.
218      my ($self, $attributeName, $type, $notes, $groups) = @_;      my ($self, $attributeName, $notes, $groups, $table) = @_;
219      # Declare the return variable.      # Declare the return variable.
220      my $retVal;      my $retVal;
221        # Default the table name.
222        if (! $table) {
223            $table = $self->{defaultRel};
224        }
225      # Get the data type hash.      # Get the data type hash.
226      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
227      # Validate the initial input values.      # Validate the initial input values.
228      if (! ERDB::ValidateFieldName($attributeName)) {      if ($attributeName =~ /$self->{splitter}/) {
229          Confess("Invalid attribute name \"$attributeName\" specified.");          Confess("Invalid attribute name \"$attributeName\" specified.");
230      } elsif (! $notes || length($notes) < 25) {      } elsif (! $notes) {
231          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing description for $attributeName.");
232      } elsif (! exists $types{$type}) {      } elsif (! grep { $_ eq $table } $self->GetConnectingRelationships('AttributeKey')) {
233          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid relationship name \"$table\" specified as a custom attribute table.");
234      } else {      } else {
235            # Create a variable to hold the action to be displayed for the log (Add or Update).
236            my $action;
237          # Okay, we're ready to begin. See if this key exists.          # Okay, we're ready to begin. See if this key exists.
238          my $attribute = $self->GetEntity('AttributeKey', $attributeName);          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
239          if (defined($attribute)) {          if (defined($attribute)) {
240              # It does, so we do an update.              # It does, so we do an update.
241                $action = "Update Key";
242              $self->UpdateEntity('AttributeKey', $attributeName,              $self->UpdateEntity('AttributeKey', $attributeName,
243                                  { description => $notes, 'data-type' => $type });                                  { description => $notes,
244                                      'relationship-name' => $table});
245              # Detach the key from its current groups.              # Detach the key from its current groups.
246              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
247          } else {          } else {
248              # It doesn't, so we do an insert.              # It doesn't, so we do an insert.
249                $action = "Insert Key";
250              $self->InsertObject('AttributeKey', { id => $attributeName,              $self->InsertObject('AttributeKey', { id => $attributeName,
251                                  description => $notes, 'data-type' => $type });                                  description => $notes,
252                                    'relationship-name' => $table});
253          }          }
254          # Attach the key to the specified groups. (We presume the groups already          # Attach the key to the specified groups. (We presume the groups already
255          # exist.)          # exist.)
# Line 259  Line 257 
257              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
258                                                 'to-link'   => $group });                                                 'to-link'   => $group });
259          }          }
260            # Log the operation.
261            $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
262      }      }
263  }  }
264    
 =head3 LoadAttributeKey  
265    
266  C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>  =head3 DeleteAttributeKey
267    
268        my $stats = $attrDB->DeleteAttributeKey($attributeName);
269    
270  Load the specified attribute from the specified file. The file should be a  Delete an attribute from the custom attributes database.
 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.  
271    
272  =over 4  =over 4
273    
274  =item keyName  =item attributeName
275    
276  Key of the attribute to load.  Name of the attribute to delete.
277    
278  =item fh  =item RETURN
279    
280  Open file handle for the input file.  Returns a statistics object describing the effects of the deletion.
281    
282  =item idCol  =back
283    
284  Index (0-based) of the column containing the ID field. The ID field should  =cut
 contain the ID of an instance of the named entity.  
285    
286  =item dataCol  sub DeleteAttributeKey {
287        # Get the parameters.
288        my ($self, $attributeName) = @_;
289        # Delete the attribute key.
290        my $retVal = $self->Delete('AttributeKey', $attributeName);
291        # Log this operation.
292        $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
293        # Return the result.
294        return $retVal;
295    
296  Index (0-based) of the column containing the data value field.  }
297    
298  =item options  =head3 NewName
299    
300  Hash specifying the options for this load.      my $text = CustomAttributes::NewName();
301    
302  =item RETURN  Return the string used to indicate the user wants to add a new attribute.
303    
304  Returns a statistics object for the load process.  =cut
305    
306  =back  sub NewName {
307        return "(new)";
308    }
309    
310  The available options are as follows.  =head3 LoadAttributesFrom
311    
312  =over 4  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
313    
314  =item erase  Load attributes from the specified tab-delimited file. Each line of the file must
315    contain an object ID in the first column, an attribute key name in the second
316    column, and attribute values in the remaining columns. The attribute values must
317    be assembled into a single value using the splitter code. In addition, the key names may
318    contain a splitter. If this is the case, the portion of the key after the splitter is
319    treated as a subkey.
320    
321  If TRUE, the key's values will all be erased before loading. (Doing so  =over 4
 makes for a faster load.)  
322    
323  =back  =item fileName
324    
325  =cut  Name of the file from which to load the attributes, or an open handle for the file.
326    (This last enables the method to be used in conjunction with the CGI form upload
327    control.)
328    
329  sub LoadAttributeKey {  =item options
     # Get the parameters.  
     my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;  
     # Create the return variable.  
     my $retVal = Stats->new("lineIn", "shortLine", "lineUsed");  
     # 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 {  
         # We need three load files: one for "IsKeyOf", one for "Assignment", and  
         # one for "AssignmentValue".  
         my $isKeyOfFileName = "$FIG_Config::temp/IsKeyOf$$.dtx";  
         my $isKeyOfH = Open(undef, ">$isKeyOfFileName");  
         my $assignmentFileName = "$FIG_Config::temp/Assignment.dtx";  
         my $assignmentH = Open(undef, ">$assignmentFileName");  
         my $assignmentValueFileName = "$FIG_Config::temp/Assignment.dtx";  
         my $assignmentValueH = Open(undef, ">$assignmentValueFileName");  
         # We also need a hash to track the assignments we find.  
         my %assignHash = ();  
         # Find out if we intend to erase the key before loading.  
         my $erasing = $options{erase} || 0;  
         # 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 an assignment for this object ID.  
                 my $assignKey = "$keyName=$id";  
                 my $assignValue = $assignHash{$assignKey};  
                 if (! defined $assignValue) {  
                     # Here we have a new assignment. If we are using an erased key,  
                     # we will create an assignment object for it. Otherwise, we have  
                     # to check the database. First, we get the digested value.  
                     $assignValue = $self->AssignmentKey($id, $keyName);  
                     # If we're erasing, we always need to create an assignment, but if  
                     # we're not erasing we need to check the keys.  
                     if ($erasing || ! $self->Exists('Assignment', $assignValue)) {  
                         # Here we need to create the assignment.  
                         Tracer::PutLine($assignmentH, [$assignValue, $id]);  
                         Tracer::PutLine($isKeyOfH, [$keyName, $assignValue]);  
                         # Save the assignment key in the hash.  
                         $assignHash{$assignKey} = $assignValue;  
                         # Update the counter.  
                         $retVal->Add(newAssignment => 1);  
                     }  
                 }  
                 # Now we have the assignment ID, so we can attach the new value to the  
                 # assignment.  
                 Tracer::PutLine($assignmentValueH, [$assignValue, $value]);  
             }  
         }  
         # Close all the files.  
         close $assignmentH;  
         close $assignmentValueH;  
         close $isKeyOfH;  
         # If we are erasing, erase the old key values.  
         if ($erasing) {  
             $self->EraseAttribute($keyName);  
         }  
         # If there are new assignments, load them.  
         if ($retVal->Ask("newAssignment") > 0) {  
             my $ikoStats = $self->LoadTable($isKeyOfFileName, "IsKeyOf", 0);  
             $retVal->Accumulate($ikoStats);  
             my $aStats = $self->LoadTable($assignmentFileName, "Assignment", 0);  
             $retVal->Accumulate($aStats);  
         }  
         # Finally, load the values.  
         my $avStats = $self->LoadTable($assignmentValueFileName, "AssignmentValue", 0);  
         $retVal->Accumulate($avStats);  
     }  
     # Return the statistics.  
     return $retVal;  
 }  
330    
331    Hash of options for modifying the load process.
332    
333  =head3 DeleteAttributeKey  =item RETURN
334    
335  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>  Returns a statistics object describing the load.
336    
337  Delete an attribute from the custom attributes database.  =back
338    
339    Permissible option values are as follows.
340    
341  =over 4  =over 4
342    
343  =item attributeName  =item mode
344    
345  Name of the attribute to delete.  Loading mode. Legal values are C<low_priority> (which reduces the task priority
346    of the load) and C<concurrent> (which reduces the locking cost of the load). The
347    default is a normal load.
348    
349  =item RETURN  =item append
350    
351  Returns a statistics object describing the effects of the deletion.  If TRUE, then the attributes will be appended to existing data; otherwise, the
352    first time a key name is encountered, it will be erased.
353    
354  =back  =item archive
355    
356  =cut  If specified, the name of a file into which the incoming data should be saved.
357    If I<resume> is also specified, only the lines actually loaded will be put
358    into this file.
359    
360  sub DeleteAttributeKey {  =item objectType
     # Get the parameters.  
     my ($self, $attributeName) = @_;  
     # Delete the attribute key.  
     my $retVal = $self->Delete('AttributeKey', $attributeName);  
     # Return the result.  
     return $retVal;  
361    
362  }  If specified, the specified object type will be prefixed to each object ID.
363    
364  =head3 NewName  =item resume
365    
366  C<< my $text = CustomAttributes::NewName(); >>  If specified, key-value pairs already in the database will not be reinserted.
367    Specify a number to start checking after the specified number of lines and
368    then admit everything after the first line not yet loaded. Specify C<careful>
369    to check every single line. Specify C<none> to ignore this option. The default
370    is C<none>. So, if you believe that a previous load failed somewhere after 50000
371    lines, a resume value of C<50000> would skip 50000 lines in the file, then
372    check each line after that until it finds one not already in the database. The
373    first such line found and all lines after that will be loaded. On the other
374    hand, if you have a file of 100000 records, and some have been loaded and some
375    not, you would use the word C<careful>, so that every line would be checked before
376    it is inserted. A resume of C<0> will start checking the first line of the
377    input file and then begin loading once it finds a line not in the database.
378    
379  Return the string used to indicate the user wants to add a new attribute.  =item chunkSize
380    
381    Number of lines to load in each burst. The default is 10,000.
382    
383    =back
384    
385  =cut  =cut
386    
387  sub NewName {  sub LoadAttributesFrom {
388      return "(new)";      # Get the parameters.
389        my ($self, $fileName, %options) = @_;
390        # Declare the return variable.
391        my $retVal = Stats->new('keys', 'values', 'linesOut');
392        # Initialize the timers.
393        my ($eraseTime, $archiveTime, $checkTime) = (0, 0, 0);
394        # Check for append mode.
395        my $append = ($options{append} ? 1 : 0);
396        # Check for resume mode.
397        my $resume = (defined($options{resume}) ? $options{resume} : 'none');
398        # Create a hash of key names found.
399        my %keyHash = ();
400        # Create a hash of table names to files. Most attributes go into the HasValueFor
401        # table, but some are put into other tables. Each table name will be mapped
402        # to a sub-hash with keys "fileName" (output file for the table) and "count"
403        # (number of lines in the file).
404        my %tableHash = ();
405        # Compute the chunk size.
406        my $chunkSize = ($options{chunkSize} ? $options{chunkSize} : 10000);
407        # Open the file for input. Note we must anticipate the possibility of an
408        # open filehandle being passed in. This occurs when the user is submitting
409        # the load file over the web.
410        my $fh;
411        if (ref $fileName) {
412            Trace("Using file opened by caller.") if T(3);
413            $fh = $fileName;
414        } else {
415            Trace("Attributes will be loaded from $fileName.") if T(3);
416            $fh = Open(undef, "<$fileName");
417        }
418        # Trace the mode.
419        if (T(3)) {
420            if ($options{mode}) {
421                Trace("Mode is $options{mode}.")
422            } else {
423                Trace("No mode specified.")
424            }
425        }
426        # Now check to see if we need to archive.
427        my $ah;
428        if (exists $options{archive}) {
429            my $ah = Open(undef, ">$options{archive}");
430            Trace("Load file will be archived to $options{archive}.") if T(3);
431        }
432        # Insure we recover from errors.
433        eval {
434            # If we have a resume number, process it here.
435            if ($resume =~ /\d+/) {
436                Trace("Skipping $resume lines.") if T(2);
437                my $startTime = time();
438                # Skip the specified number of lines.
439                for (my $skipped = 0; ! eof($fh) && $skipped < $resume; $skipped++) {
440                    my $line = <$fh>;
441                    $retVal->Add(skipped => 1);
442                }
443                $checkTime += time() - $startTime;
444            }
445            # Loop through the file.
446            Trace("Starting load.") if T(2);
447            while (! eof $fh) {
448                # Read the current line.
449                my ($id, $key, @values) = Tracer::GetLine($fh);
450                $retVal->Add(linesIn => 1);
451                # Do some validation.
452                if (! $id) {
453                    # We ignore blank lines.
454                    $retVal->Add(blankLines => 1);
455                } elsif (substr($id, 0, 1) eq '#') {
456                    # A line beginning with a pound sign is a comment.
457                    $retVal->Add(comments => 1);
458                } elsif (! defined($key)) {
459                    # An ID without a key is a serious error.
460                    my $lines = $retVal->Ask('linesIn');
461                    Confess("Line $lines in $fileName has no attribute key.");
462                } elsif (! @values) {
463                    # A line with no values is not allowed.
464                    my $lines = $retVal->Ask('linesIn');
465                    Trace("Line $lines for key $key has no attribute values.") if T(1);
466                    $retVal->Add(skipped => 1);
467                } else {
468                    # Check to see if we need to fix up the object ID.
469                    if ($options{objectType}) {
470                        $id = "$options{objectType}:$id";
471                    }
472                    # The key contains a real part and an optional sub-part. We need the real part.
473                    my ($realKey, $subKey) = $self->SplitKey($key);
474                    # Now we need to check for a new key.
475                    if (! exists $keyHash{$realKey}) {
476                        my $keyObject = $self->GetEntity(AttributeKey => $realKey);
477                        if (! defined($keyObject)) {
478                            # Here the specified key does not exist, which is an error.
479                            my $line = $retVal->Ask('linesIn');
480                            Confess("Attribute \"$realKey\" on line $line of $fileName not found in database.");
481                        } else {
482                            # Make sure we know this is no longer a new key. We do this by putting
483                            # its table name in the key hash.
484                            $keyHash{$realKey} = $keyObject->PrimaryValue('AttributeKey(relationship-name)');
485                            $retVal->Add(keys => 1);
486                            # If this is NOT append mode, erase the key. This does not delete the key
487                            # itself; it just clears out all the values.
488                            if (! $append) {
489                                my $startTime = time();
490                                $self->EraseAttribute($realKey);
491                                $eraseTime += time() - $startTime;
492                                Trace("Attribute $realKey erased.") if T(3);
493                            }
494                        }
495                        Trace("Key $realKey found.") if T(3);
496                    }
497                    # If we're in resume mode, check to see if this insert is redundant.
498                    my $ok = 1;
499                    if ($resume ne 'none') {
500                        my $startTime = time();
501                        my $count = $self->GetAttributes($id, $key, @values);
502                        if ($count) {
503                            # Here the record is found, so we skip it.
504                            $ok = 0;
505                            $retVal->Add(skipped => 1);
506                        } else {
507                            # Here the record is not found. If we're in non-careful mode, we
508                            # stop resume checking at this point.
509                            if ($resume ne 'careful') {
510                                $resume = 'none';
511                            }
512                        }
513                        $checkTime += time() - $startTime;
514                    }
515                    if ($ok) {
516                        # We're in business. First, archive this row.
517                        if (defined $ah) {
518                            my $startTime = time();
519                            Tracer::PutLine($ah, [$id, $key, @values]);
520                            $archiveTime += time() - $startTime;
521                        }
522                        # We need to format the attribute data so it will work
523                        # as if it were a load file. This means we join the
524                        # values.
525                        my $valueString = join('::', @values);
526                        # Now we need to get access to the key's load file. Check for it in the
527                        # table hash.
528                        my $keyTable = $keyHash{$realKey};
529                        if (! exists $tableHash{$keyTable}) {
530                            # This is a new table, so we need to set it up. First, we get
531                            # a temporary file for it.
532                            my $tempFileName = FIGRules::GetTempFileName(sessionID => $$ . $keyTable,
533                                                                         extension => 'dtx');
534                            my $oh = Open(undef, ">$tempFileName");
535                            # Now we create its descriptor in the table hash.
536                            $tableHash{$keyTable} = {fileName => $tempFileName, handle => $oh, count => 0};
537                        }
538                        # Everything is all set up, so we put the value in the temporary file and
539                        # count it.
540                        my $tableData = $tableHash{$keyTable};
541                        my $startTime = time();
542                        Tracer::PutLine($tableData->{handle}, [$realKey, $id, $subKey, $valueString]);
543                        $archiveTime += time() - $startTime;
544                        $retVal->Add(linesOut => 1);
545                        $tableData->{count}++;
546                        # See if it's time to load a chunk.
547                        if ($tableData->{count} >= $chunkSize) {
548                            # We've filled a chunk, so it's time.
549                            close $tableData->{handle};
550                            $self->_LoadAttributeTable($keyTable, $tableData->{fileName}, $retVal);
551                            # Reset for the next chunk.
552                            $tableData->{count} = 0;
553                            $tableData->{handle} = Open(undef, ">$tableData->{fileName}");
554                        }
555                    } else {
556                        # Here we skipped because of resume mode.
557                        $retVal->Add(resumeSkip => 1);
558                    }
559                    Trace($retVal->Ask('values') . " values processed.") if $retVal->Check(values => 1000) && T(3);
560                }
561            }
562            # Now we close the archive file. Note we undefine the handle so the error methods know
563            # not to worry.
564            if (defined $ah) {
565                close $ah;
566                undef $ah;
567            }
568            # Now we load the residual from the temporary files (if any). This time we'll do an
569            # analyze as well.
570            for my $tableName (keys %tableHash) {
571                # Get the data for this table.
572                my $tableData = $tableHash{$tableName};
573                # Close the handle. ERDB will re-open it for input later.
574                close $tableData->{handle};
575                # Check to see if there's anything left to load.
576                if ($tableData->{count} > 0) {
577                    # Yes, load the data.
578                    $self->_LoadAttributeTable($tableName, $tableData->{fileName}, $retVal);
579                }
580                # Regardless of whether additional loading was required, we need to
581                # analyze the table for performance.
582                my $startTime = time();
583                $self->Analyze($tableName);
584                $retVal->Add(analyzeTime => time() - $startTime);
585            }
586            Trace("Attribute load successful.") if T(2);
587        };
588        # Check for an error.
589        if ($@) {
590            # Here we have an error. Display the error message.
591            my $message = $@;
592            Trace("Error during attribute load: $message") if T(0);
593            $retVal->AddMessage($message);
594            # Close the archive file if it's open. The archive file can sometimes provide
595            # clues as to what happened.
596            if (defined $ah) {
597                close $ah;
598            }
599        }
600        # Store the timers.
601        $retVal->Add(eraseTime   => $eraseTime);
602        $retVal->Add(archiveTime => $archiveTime);
603        $retVal->Add(checkTime   => $checkTime);
604        # Return the result.
605        return $retVal;
606  }  }
607    
608  =head3 ControlForm  =head3 BackupKeys
609    
610  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>      my $stats = $attrDB->BackupKeys($fileName, %options);
611    
612  Return a form that can be used to control the creation and modification of  Backup the attribute key information from the attribute database.
 attributes. Only a subset of the attribute keys will be displayed, as  
 determined by the incoming list.  
613    
614  =over 4  =over 4
615    
616  =item cgi  =item fileName
   
 CGI query object used to create HTML.  
   
 =item name  
617    
618  Name to give to the form. This should be unique for the web page.  Name of the output file.
619    
620  =item keys  =item options
621    
622  Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the  Options for modifying the backup process.
 attribute's data type, its description, and a list of the groups in which it participates.  
623    
624  =item RETURN  =item RETURN
625    
626  Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script  Returns a statistics object for the backup.
 for loading, creating, displaying, changing, or deleting an attribute. Note that only the form  
 controls are generated. The form tags are left to the caller.  
627    
628  =back  =back
629    
630    Currently there are no options. The backup is straight to a text file in
631    tab-delimited format. Each key is backup up to two lines. The first line
632    is all of the data from the B<AttributeKey> table. The second is a
633    tab-delimited list of all the groups.
634    
635  =cut  =cut
636    
637  sub ControlForm {  sub BackupKeys {
638      # Get the parameters.      # Get the parameters.
639      my ($self, $cgi, $name, $keys) = @_;      my ($self, $fileName, %options) = @_;
640      # Declare the return list.      # Declare the return variable.
641      my @retVal = ();      my $retVal = Stats->new();
642      # We'll put the controls in a table. Nothing else ever seems to look nice.      # Open the output file.
643      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      my $fh = Open(undef, ">$fileName");
644      # The first row is for selecting the field name.      # Set up to read the keys.
645      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      my $keyQuery = $self->Get(['AttributeKey'], "", []);
646                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,      # Loop through the keys.
647                                                       new => 1,      while (my $keyData = $keyQuery->Fetch()) {
648                                                       notes => "document.$name.notes.value",          $retVal->Add(key => 1);
649                                                       type => "document.$name.dataType.value",          # Get the fields.
650                                                       groups => "document.$name.groups")));          my ($id, $type, $tableName, $description) =
651      # Now we set up a dropdown for the data types. The values will be the              $keyData->Values(['AttributeKey(id)', 'AttributeKey(relationship-name)',
652      # data type names, and the labels will be the descriptions.                                'AttributeKey(description)']);
653      my %types = ERDB::GetDataTypes();          # Escape any tabs or new-lines in the description.
654      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;          my $escapedDescription = Tracer::Escape($description);
655      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',          # Write the key data to the output.
656                                      -values => [sort keys %types],          Tracer::PutLine($fh, [$id, $type, $tableName, $escapedDescription]);
657                                      -labels => \%labelMap,          # Get the key's groups.
658                                      -default => 'string');          my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
659      # Allow the user to specify a new field name. This is required if the                                      'IsInGroup(to-link)');
660      # user has selected the "(new)" marker. We put a little scriptlet in here that          $retVal->Add(memberships => scalar(@groups));
661      # selects the (new) marker when the user enters the field.          # Write them to the output. Note we put a marker at the beginning to insure the line
662      push @retVal, "<script language=\"javaScript\">";          # is nonempty.
663      my $fieldField = "document.$name.fieldName";          Tracer::PutLine($fh, ['#GROUPS', @groups]);
664      my $newName = "\"" . NewName() . "\"";      }
665      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      # Log the operation.
666                             $cgi->td($cgi->textfield(-name => 'newName',      $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
667                                                      -size => 30,      # Return the result.
668                                                      -value => "",      return $retVal;
669                                                      -onFocus => "setIfEmpty($fieldField, $newName);")),  }
                                     );  
     push @retVal, $cgi->Tr($cgi->th("Data type"),  
                            $cgi->td($typeMenu));  
     # The next row is for the notes.  
     push @retVal, $cgi->Tr($cgi->th("Description"),  
                            $cgi->td($cgi->textarea(-name => 'notes',  
                                                    -rows => 6,  
                                                    -columns => 80))  
                           );  
     # Now we have the groups, which are implemented as a checkbox group.  
     my @groups = $self->GetGroups();  
     push @retVal, $cgi->Tr($cgi->th("Groups"),  
                            $cgi->td($cgi->checkbox_group(-name=>'groups',  
                                     -values=> \@groups))  
                           );  
     # If the user wants to upload new values for the field, then we have  
     # 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.  
     push @retVal, $cgi->Tr($cgi->th("&nbsp;"),  
                            $cgi->td({align => 'center'},  
                                     $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .  
                                     $cgi->submit(-name => 'Store',  -value => 'STORE') . " " .  
                                     $cgi->submit(-name => 'Show',   -value => 'SHOW')  
                                    )  
                           );  
     # Close the table and the form.  
     push @retVal, $cgi->end_table();  
     # Return the assembled HTML.  
     return join("\n", @retVal, "");  
 }  
   
 =head3 FieldMenu  
   
 C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>  
   
 Return the HTML for a menu to select an attribute field. The menu will  
 be a standard SELECT/OPTION thing which is called "popup menu" in the  
 CGI package, but actually looks like a list. The list will contain  
 one selectable row per field.  
670    
671  =over 4  =head3 RestoreKeys
672    
673  =item cgi      my $stats = $attrDB->RestoreKeys($fileName, %options);
674    
675  CGI query object used to generate HTML.  Restore the attribute keys and groups from a backup file.
676    
677  =item height  =over 4
678    
679  Number of lines to display in the list.  =item fileName
680    
681  =item name  Name of the file containing the backed-up keys. Each key has a pair of lines,
682    one containing the key data and one listing its groups.
683    
684  Name to give to the menu. This is the name under which the value will  =back
 appear when the form is submitted.  
685    
686  =item keys  =cut
687    
688  Reference to a hash mapping each attribute key name to a list reference,  sub RestoreKeys {
689  the list itself consisting of the attribute data type, its description,      # Get the parameters.
690  and a list of its groups.      my ($self, $fileName, %options) = @_;
691        # Declare the return variable.
692        my $retVal = Stats->new();
693        # Set up a hash to hold the group IDs.
694        my %groups = ();
695        # Open the file.
696        my $fh = Open(undef, "<$fileName");
697        # Loop until we're done.
698        while (! eof $fh) {
699            # Get a key record.
700            my ($id, $tableName, $description) = Tracer::GetLine($fh);
701            if ($id eq '#GROUPS') {
702                Confess("Group record found when key record expected.");
703            } elsif (! defined($description)) {
704                Confess("Invalid format found for key record.");
705            } else {
706                $retVal->Add("keyIn" => 1);
707                # Add this key to the database.
708                $self->InsertObject('AttributeKey', { id => $id,
709                                                      description => Tracer::UnEscape($description),
710                                                      'relationship-name' => $tableName});
711                Trace("Attribute $id stored.") if T(3);
712                # Get the group line.
713                my ($marker, @groups) = Tracer::GetLine($fh);
714                if (! defined($marker)) {
715                    Confess("End of file found where group record expected.");
716                } elsif ($marker ne '#GROUPS') {
717                    Confess("Group record not found after key record.");
718                } else {
719                    $retVal->Add(memberships => scalar(@groups));
720                    # Connect the groups.
721                    for my $group (@groups) {
722                        # Find out if this is a new group.
723                        if (! $groups{$group}) {
724                            $retVal->Add(newGroup => 1);
725                            # Add the group.
726                            $self->InsertObject('AttributeGroup', { id => $group });
727                            Trace("Group $group created.") if T(3);
728                            # Make sure we know it's not new.
729                            $groups{$group} = 1;
730                        }
731                        # Connect the group to our key.
732                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
733                    }
734                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
735                }
736            }
737        }
738        # Log the operation.
739        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
740        # Return the result.
741        return $retVal;
742    }
743    
744  =item options  =head3 ArchiveFileName
745    
746  Hash containing options that modify the generation of the menu.      my $fileName = $ca->ArchiveFileName();
747    
748  =item RETURN  Compute a file name for archiving attribute input data. The file will be in the attribute log directory
749    
750  Returns the HTML to create a form field that can be used to select an  =cut
 attribute from the custom attributes system.  
751    
752  =back  sub ArchiveFileName {
753        # Get the parameters.
754        my ($self) = @_;
755        # Declare the return variable.
756        my $retVal;
757        # We start by turning the timestamp into something usable as a file name.
758        my $now = Tracer::Now();
759        $now =~ tr/ :\//___/;
760        # Next we get the directory name.
761        my $dir = "$FIG_Config::var/attributes";
762        if (! -e $dir) {
763            Trace("Creating attribute file directory $dir.") if T(1);
764            mkdir $dir;
765        }
766        # Put it together with the field name and the time stamp.
767        $retVal = "$dir/upload.$now";
768        # Modify the file name to insure it's unique.
769        my $seq = 0;
770        while (-e "$retVal.$seq.tbl") { $seq++ }
771        # Use the computed sequence number to get the correct file name.
772        $retVal .= ".$seq.tbl";
773        # Return the result.
774        return $retVal;
775    }
776    
777  The permissible options are as follows.  =head3 BackupAllAttributes
778    
779  =over 4      my $stats = $attrDB->BackupAllAttributes($fileName, %options);
780    
781  =item new  Backup all of the attributes to a file. The attributes will be stored in a
782    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
783    
784  If TRUE, then extra rows will be provided to allow the user to select  =over 4
 a new attribute. In other words, the user can select an existing  
 attribute, or can choose a C<(new)> marker to indicate a field to  
 be created in the parent entity.  
785    
786  =item notes  =item fileName
787    
788  If specified, the name of a variable for displaying the notes attached  Name of the file to which the attribute data should be backed up.
 to the field. This must be in Javascript form ready for assignment.  
 So, for example, if you have a variable called C<notes> that  
 represents a paragraph element, you should code C<notes.innerHTML>.  
 If it actually represents a form field you should code C<notes.value>.  
 If an C<innerHTML> coding is used, the text will be HTML-escaped before  
 it is copied in. Specifying this parameter generates Javascript for  
 displaying the field description when a field is selected.  
789    
790  =item type  =item options
791    
792  If specified, the name of a variable for displaying the field's  Hash of options for the backup.
 data type. Data types are a much more controlled vocabulary than  
 notes, so there is no worry about HTML translation. Instead, the  
 raw value is put into the specified variable. Otherwise, the same  
 rules apply to this value that apply to I<$noteControl>.  
793    
794  =item groups  =item RETURN
795    
796  If specified, the name of a multiple-selection list control (also called  Returns a statistics object describing the backup.
 a popup menu) which shall be used to display the selected groups.  
797    
798  =back  =back
799    
800    Currently there are no options defined.
801    
802  =cut  =cut
803    
804  sub FieldMenu {  sub BackupAllAttributes {
805      # Get the parameters.      # Get the parameters.
806      my ($self, $cgi, $height, $name, $keys, %options) = @_;      my ($self, $fileName, %options) = @_;
807      # Reformat the list of keys.      # Declare the return variable.
808      my %keys = %{$keys};      my $retVal = Stats->new();
809      # Add the (new) key, if needed.      # Get a list of the keys.
810      if ($options{new}) {      my %keys = map { $_->[0] => $_->[1] } $self->GetAll(['AttributeKey'],
811          $keys{NewName()} = ["string", ""];                                                          "", [], ['AttributeKey(id)',
812      }                                                                    'AttributeKey(relationship-name)']);
813      # Get a sorted list of key.      Trace(scalar(keys %keys) . " keys found during backup.") if T(2);
814      my @keys = sort keys %keys;      # Open the file for output.
815      # We need to create the name for the onChange function. This function      my $fh = Open(undef, ">$fileName");
     # may not do anything, but we need to know the name to generate the HTML  
     # for the menu.  
     my $changeName = "${name}_setNotes";  
     my $retVal = $cgi->popup_menu({name => $name,  
                                    size => $height,  
                                    onChange => "$changeName(this.value)",  
                                    values => \@keys,  
                                   });  
     # Create the change function.  
     $retVal .= "\n<script language=\"javascript\">\n";  
     $retVal .= "    function $changeName(fieldValue) {\n";  
     # The function only has a body if we have a control to store data about the  
     # attribute.  
     if ($options{notes} || $options{type} || $options{groups}) {  
         # Check to see if we're storing HTML or text into the note control.  
         my $noteControl = $options{notes};  
         my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);  
         # We use a CASE statement based on the newly-selected field value. The  
         # field description will be stored in the JavaScript variable "myText"  
         # and the data type in "myType". Note the default data type is a normal  
         # string, but the default notes is an empty string.  
         $retVal .= "        var myText = \"\";\n";  
         $retVal .= "        var myType = \"string\";\n";  
         $retVal .= "        switch (fieldValue) {\n";  
816          # Loop through the keys.          # Loop through the keys.
817          for my $key (@keys) {      for my $key (sort keys %keys) {
818              # Generate this case.          Trace("Backing up attribute $key.") if T(3);
819              $retVal .= "        case \"$key\" :\n";          $retVal->Add(keys => 1);
820              # Here we either want to update the note display, the          # Get the key's relevant relationship name.
821              # type display, the group list, or a combination of them.          my $relName = $keys{$key};
822              my ($type, $notes, @groups) = @{$keys{$key}};          # Loop through this key's values.
823              if ($noteControl) {          my $query = $self->Get([$relName], "$relName(from-link) = ?", [$key]);
824                  # Insure it's in the proper form.          my $valuesFound = 0;
825                  if ($htmlMode) {          while (my $line = $query->Fetch()) {
826                      $notes = ERDB::HTMLNote($notes);              $valuesFound++;
827                  }              # Get this row's data.
828                  # Escape it for use as a string literal.              my ($id, $key, $subKey, $value) = $line->Values(["$relName(to-link)",
829                  $notes =~ s/\n/\\n/g;                                                               "$relName(from-link)",
830                  $notes =~ s/"/\\"/g;                                                               "$relName(subkey)",
831                  $retVal .= "           myText = \"$notes\";\n";                                                               "$relName(value)"]);
832              }              # Check for a subkey.
833              if ($options{type}) {              if ($subKey ne '') {
834                  # Here we want the type updated.                  $key = "$key$self->{splitter}$subKey";
835                  $retVal .= "           myType = \"$type\";\n";              }
836              }              # Write it to the file.
837              if ($options{groups}) {              Tracer::PutLine($fh, [$id, $key, Escape($value)]);
838                  # Here we want the groups shown. Get a list of this attribute's groups.          }
839                  # We'll search through this list for each group to see if it belongs with          Trace("$valuesFound values backed up for key $key.") if T(3);
840                  # our attribute.          $retVal->Add(values => $valuesFound);
841                  my $groupLiteral = "=" . join("=", @groups) . "=";      }
842                  # Now we need some variables containing useful code for the javascript. It's      # Log the operation.
843                  # worth knowing we go through a bit of pain to insure $groupField[i] isn't      $self->LogOperation("Backup Data", $fileName, $retVal->Display());
                 # parsed as an array element.  
                 my $groupField = $options{groups};  
                 my $currentField = $groupField . "[i]";  
                 # Do the javascript.  
                 $retVal .= "           var groupList = \"$groupLiteral\";\n";  
                 $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";  
                 $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";  
                 $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";  
                 $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";  
                 $retVal .= "           }\n";  
             }  
             # Close this case.  
             $retVal .= "           break;\n";  
         }  
         # Close the CASE statement and make the appropriate assignments.  
         $retVal .= "        }\n";  
         if ($noteControl) {  
             $retVal .= "        $noteControl = myText;\n";  
         }  
         if ($options{type}) {  
             $retVal .= "        $options{type} = myType;\n";  
         }  
     }  
     # Terminate the change function.  
     $retVal .= "    }\n";  
     $retVal .= "</script>\n";  
844      # Return the result.      # Return the result.
845      return $retVal;      return $retVal;
846  }  }
847    
848    
849  =head3 GetGroups  =head3 GetGroups
850    
851  C<< my @groups = $attrDB->GetGroups(); >>      my @groups = $attrDB->GetGroups();
852    
853  Return a list of the available groups.  Return a list of the available groups.
854    
# Line 745  Line 865 
865    
866  =head3 GetAttributeData  =head3 GetAttributeData
867    
868  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>      my %keys = $attrDB->GetAttributeData($type, @list);
869    
870  Return attribute data for the selected attributes. The attribute  Return attribute data for the selected attributes. The attribute
871  data is a hash mapping each attribute key name to a n-tuple containing the  data is a hash mapping each attribute key name to a n-tuple containing the
872  data type, the description, and the groups. This is the same format expected in  data type, the description, the table name, and the groups.
 the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.  
873    
874  =over 4  =over 4
875    
# Line 765  Line 884 
884    
885  =item RETURN  =item RETURN
886    
887  Returns a hash mapping each attribute key name to its data type, description, and  Returns a hash mapping each attribute key name to its description,
888  parent groups.  table name, and parent groups.
889    
890  =back  =back
891    
# Line 798  Line 917 
917          }          }
918          while (my $row = $query->Fetch()) {          while (my $row = $query->Fetch()) {
919              # Get this attribute's data.              # Get this attribute's data.
920              my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',              my ($key, $relName, $notes) = $row->Values(['AttributeKey(id)',
921                                                         'AttributeKey(relationship-name)',
922                                                       'AttributeKey(description)']);                                                       'AttributeKey(description)']);
923              # If it's new, get its groups and add it to the return hash.              # If it's new, get its groups and add it to the return hash.
924              if (! exists $retVal{$key}) {              if (! exists $retVal{$key}) {
925                  my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",                  my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
926                                              [$key], 'IsInGroup(to-link)');                                              [$key], 'IsInGroup(to-link)');
927                  $retVal{$key} = [$type, $notes, @groups];                  $retVal{$key} = [$relName, $notes, @groups];
928              }              }
929          }          }
930      }      }
# Line 812  Line 932 
932      return %retVal;      return %retVal;
933  }  }
934    
935    =head3 LogOperation
936    
937        $ca->LogOperation($action, $target, $description);
938    
939    Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
940    
941    =over 4
942    
943    =item action
944    
945    Action being logged (e.g. C<Delete Group> or C<Load Key>).
946    
947    =item target
948    
949    ID of the key or group affected.
950    
951    =item description
952    
953    Short description of the action.
954    
955    =back
956    
957    =cut
958    
959    sub LogOperation {
960        # Get the parameters.
961        my ($self, $action, $target, $description) = @_;
962        # Get the user ID.
963        my $user = $self->{user};
964        # Get a timestamp.
965        my $timeString = Tracer::Now();
966        # Open the log file for appending.
967        my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
968        # Write the data to it.
969        Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
970        # Close the log file.
971        close $oh;
972    }
973    
974  =head2 FIG Method Replacements  =head2 FIG Method Replacements
975    
976  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 823  Line 982 
982  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
983  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.
984    
985  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,
986  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
987  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
988  value of the splitter parameter on the constructor (L</new>). The default is double  is double colons C<::>.
 colons C<::>.  
989    
990  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
991  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 840  Line 998 
998    
999  =head3 GetAttributes  =head3 GetAttributes
1000    
1001  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>      my @attributeList = $attrDB->GetAttributes($objectID, $key, @values);
1002    
1003  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1004  value specified in the constructor (L</new>). This is not a requirement of  value specified in the constructor (L</new>). This is not a requirement of
# Line 879  Line 1037 
1037  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.
1038    
1039  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
1040  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
1041  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
1042  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
1043  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
1044    reading a lot more than they need to.
1045    
1046  =over 4  =over 4
1047    
# Line 906  Line 1065 
1065  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
1066  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.
1067  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
1068  will match.  will match. You may also specify a regular expression enclosed
1069    in slashes. All values that match the regular expression will be returned. For
1070    performance reasons, only values have this extra capability.
1071    
1072  =item RETURN  =item RETURN
1073    
# Line 922  Line 1083 
1083  sub GetAttributes {  sub GetAttributes {
1084      # Get the parameters.      # Get the parameters.
1085      my ($self, $objectID, $key, @values) = @_;      my ($self, $objectID, $key, @values) = @_;
1086      # We will create one big honking query. The following hash will build the filter      # This hash will map value-table fields to patterns. We use it to build the
1087      # clause and a parameter list.      # SQL statement.
1088      my %data = ('IsKeyOf(from-link)' => $key, 'Assignment(object-id)' => $objectID);      my %data;
1089        # Add the object ID to the key information.
1090        $data{'to-link'} = $objectID;
1091        # The first value represents a problem, because we can search it using SQL, but not
1092        # in the normal way. If the user specifies a generic search or exact match for
1093        # every alternative value (remember, the values may be specified as a list),
1094        # then we can create SQL filtering for it. If any of the values are specified
1095        # as a regular expression, however, that's a problem, because we need to read
1096        # every value to verify a match.
1097        if (@values > 0) {
1098            # Get the first value and put its alternatives in an array.
1099            my $valueParm = $values[0];
1100            my @valueList;
1101            if (ref $valueParm eq 'ARRAY') {
1102                @valueList = @{$valueParm};
1103            } else {
1104                @valueList = ($valueParm);
1105            }
1106            # Okay, now we have all the possible criteria for the first value in the list
1107            # @valueList. We'll copy the values to a new array in which they have been
1108            # converted to generic requests. If we find a regular-expression match
1109            # anywhere in the list, we toss the whole thing.
1110            my @valuePatterns = ();
1111            my $okValues = 1;
1112            for my $valuePattern (@valueList) {
1113                # Check the pattern type.
1114                if (substr($valuePattern, 0, 1) eq '/') {
1115                    # Regular expressions invalidate the entire process.
1116                    $okValues = 0;
1117                } elsif (substr($valuePattern, -1, 1) eq '%') {
1118                    # A Generic pattern is passed in unmodified.
1119                    push @valuePatterns, $valuePattern;
1120                } else {
1121                    # An exact match is converted to generic.
1122                    push @valuePatterns, "$valuePattern%";
1123                }
1124            }
1125            # If everything works, add the value data to the filtering hash.
1126            if ($okValues) {
1127                $data{value} = \@valuePatterns;
1128            }
1129        }
1130        # Now comes the really tricky part, which is key handling. The key is
1131        # actually split in two parts: the real key and a sub-key. The real key
1132        # determines which value table contains the relevant values. The information
1133        # we need is kept in here.
1134        my %tables = map { $_ => [] } $self->_GetAllTables();
1135        # See if we have any key filtering to worry about.
1136        if ($key) {
1137            # Here we have either a single key or a list. We convert both cases to a list.
1138            my $keyList = (ref $key ne 'ARRAY' ? [$key] : $key);
1139            # Get easy access to the key/table hash.
1140            my $keyTableHash = $self->_KeyTable();
1141            # Loop through the keys, discovering tables.
1142            for my $keyChoice (@$keyList) {
1143                # Now we have to start thinking about the real key and the subkeys.
1144                my ($realKey, $subKey) = $self->_SplitKeyPattern($keyChoice);
1145                # Find the matches for the real key in the key hash. For each of
1146                # these, we memorize the table name in the hash below.
1147                my %tableNames = ();
1148                for my $keyInTable (keys %{$keyTableHash}) {
1149                    if ($self->_CheckSQLPattern($realKey, $keyInTable)) {
1150                        $tableNames{$keyTableHash->{$key}} = 1;
1151                    }
1152                }
1153                # If the key is generic, or didn't match anything, add
1154                # the default table to the mix.
1155                if (keys %tableNames == 0 || $keyChoice =~ /%/) {
1156                    $tableNames{$self->{defaultRel}} = 1;
1157                }
1158                # Now we add this key combination to the key list for each relevant table.
1159                for my $tableName (keys %tableNames) {
1160                    push @{$tables{$tableName}}, [$realKey, $subKey];
1161                }
1162            }
1163        }
1164        # Declare the return variable.
1165        my @retVal = ();
1166        # Now we loop through the tables of interest, performing queries.
1167        # Loop through the tables.
1168        for my $table (keys %tables) {
1169            # Get the key pairs for this table.
1170            my $pairs = $tables{$table};
1171            # Does this table have data? It does if there is no key specified or
1172            # it has at least one key pair.
1173            my $pairCount = scalar @{$pairs};
1174            Trace("Pair count for table $table is $pairCount.") if T(3);
1175            if ($pairCount || ! $key) {
1176                # Create some lists to contain the filter fragments and parameter values.
1177      my @filter = ();      my @filter = ();
1178      my @parms = ();      my @parms = ();
1179      # 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
1180      # parameter list and generates filters for each.              # parameter list and generates filters for each. The %data hash that we built above
1181                # contains most of the necessary information to do this. When we're done, we'll
1182                # paste on stuff for the key pairs.
1183      for my $field (keys %data) {      for my $field (keys %data) {
1184          # Accumulate filter information for this field. We will OR together all the          # Accumulate filter information for this field. We will OR together all the
1185          # elements accumulated to create the final result.          # elements accumulated to create the final result.
1186          my @fieldFilter = ();          my @fieldFilter = ();
1187          # Get the specified data from the caller.                  # Get the specified filter for this field.
1188          my $fieldPattern = $data{$field};          my $fieldPattern = $data{$field};
1189          # Only proceed if the pattern is one that won't match everything.          # Only proceed if the pattern is one that won't match everything.
1190          if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {          if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
# Line 950  Line 1201 
1201              if (@patterns) {              if (@patterns) {
1202                  # Loop through the individual patterns.                  # Loop through the individual patterns.
1203                  for my $pattern (@patterns) {                  for my $pattern (@patterns) {
1204                      # Check for a generic request.                              my ($clause, $value) = _WherePart($table, $field, $pattern);
1205                      if (substr($pattern, -1, 1) ne '%') {                              push @fieldFilter, $clause;
1206                          # Here we have a normal request.                              push @parms, $value;
                         push @fieldFilter, "$field = ?";  
                         push @parms, $pattern;  
                     } else {  
                         # Here we have a generate request, so we will use the LIKE operator to  
                         # filter the field to this value pattern.  
                         push @fieldFilter, "$field LIKE ?";  
                         # We must convert the pattern value to an SQL match pattern. First  
                         # we chop off the percent sign. (Note that I eschew chop because I  
                         # want a copy of the string.  
                         my $actualPattern = substr($pattern, 0, -1);  
                         # Now we escape the underscores. Underscores are an SQL wild card  
                         # character, but they are used frequently in key names and object IDs.  
                         $actualPattern = s/_/\\_/g;  
                         # Add the escaped pattern to the bound parameter list.  
                         push @parms, $actualPattern;  
                     }  
1207                  }                  }
1208                  # Form the filter for this field.                  # Form the filter for this field.
1209                  my $fieldFilterString = join(" OR ", @fieldFilter);                  my $fieldFilterString = join(" OR ", @fieldFilter);
# Line 976  Line 1211 
1211              }              }
1212          }          }
1213      }      }
1214      # Now @filter contains one or more filter strings and @parms contains the parameter              # The final filter is for the key pairs. Only proceed if we have some.
1215      # values to bind to them.              if ($pairCount) {
1216      my $actualFilter = join(" AND ", @filter);                  # We'll accumulate pair filter clauses in here.
1217      # Declare the return variable.                  my @pairFilters = ();
1218      my @retVal = ();                  # Loop through the key pairs.
1219      # Get the number of value sections we have to match.                  for my $pair (@$pairs) {
1220      my $sectionCount = scalar(@values);                      my ($realKey, $subKey) = @{$pair};
1221      # Now we're ready to make our query.                      my ($realClause, $realValue) = _WherePart($table, 'from-link', $realKey);
1222      my $query = $self->Get(['IsKeyOf', 'Assignment'], $actualFilter, \@parms);                      if (! $subKey) {
1223      # Loop through the assignments found.                          # Here the subkey is wild, so only the real key matters.
1224      while (my $row = $query->Fetch()) {                          push @pairFilters, $realClause;
1225          # Get the current row's data.                          push @parms, $realValue;
         my ($id, $key, @valueStrings) = $row->Values(['Assignment(object-id)', 'IsKeyOf(from-link)',  
                                                       'Assignment(value)']);  
         # Process each value string individually.  
         for my $valueString (@valueStrings) {  
             # Break the value into sections.  
             my @sections = split($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);  
1226                  } else {                  } else {
1227                      $matching = ($sections[$i] eq $values[$i]);                          # Here we have to select on both keys.
1228                            my ($subClause, $subValue) = _WherePart($table, 'subkey', $subKey);
1229                            push @pairFilters, "($realClause AND $subClause)";
1230                            push @parms, $subValue;
1231                  }                  }
1232              }              }
1233              # If we match, output this row to the return list.                  # Join the pair filters together to make a giant key filter.
1234              if ($matching) {                  my $pairFilter = "(" . join(" OR ", @pairFilters) . ")";
1235                  push @retVal, [$id, $key, @sections];                  push @filter, $pairFilter;
1236              }              }
1237                # At this point, @filter contains one or more filter strings and @parms
1238                # contains the parameter values to bind to them.
1239                my $actualFilter = join(" AND ", @filter);
1240                # Now we're ready to make our query.
1241                my $query = $self->Get([$table], $actualFilter, \@parms);
1242                # Format the results.
1243                push @retVal, $self->_QueryResults($query, $table, @values);
1244          }          }
1245      }      }
1246      # Return the rows found.      # The above loop ran the query for each necessary value table and merged the
1247        # results into @retVal. Now we return the rows found.
1248      return @retVal;      return @retVal;
1249  }  }
1250    
1251  =head3 AddAttribute  =head3 AddAttribute
1252    
1253  C<< $attrDB->AddAttribute($objectID, $key, @values); >>      $attrDB->AddAttribute($objectID, $key, @values);
1254    
1255  Add an attribute key/value pair to an object. This method cannot add a new key, merely  Add an attribute key/value pair to an object. This method cannot add a new key, merely
1256  add a value to an existing key. Use L</StoreAttributeKey> to create a new key.  add a value to an existing key. Use L</StoreAttributeKey> to create a new key.
# Line 1055  Line 1286 
1286      } elsif (! @values) {      } elsif (! @values) {
1287          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1288      } else {      } else {
1289          # Okay, now we have some reason to believe we can do this. Get the key for          # Okay, now we have some reason to believe we can do this. Form the values
1290          # the relevant assignment.          # into a scalar.
         my $assignKey = $self->AssignmentKey($objectID, $key);  
         # Form the values into a scalar.  
1291          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1292          # See if the assignment exists.          # Split up the key.
1293          my $found = $self->Exists('Assignment', $assignKey);          my ($realKey, $subKey) = $self->SplitKey($key);
1294          if (! $found) {          # Find the table containing the key.
1295              # Here we have a new assignment. Insure that the key is valid.          my $table = $self->_KeyTable($realKey);
1296              $found = $self->Exists('AttributeKey', $key);          # Connect the object to the key.
1297              if (! $found) {          $self->InsertObject($table, { 'from-link' => $realKey,
1298                  Confess("Attribute key \"$key\" not found in database.");                                               'to-link'   => $objectID,
1299              } else {                                               'subkey'    => $subKey,
1300                  # The key is valid, so we can create a new assignment.                                               'value'     => $valueString,
                 $self->InsertObject('Assignment', { id => $assignKey,  
                                                     'object-id' => $objectID,  
                                                     value => [$valueString],  
                                                   });  
                 # Connect the assignment to the key.  
                 $self->InsertObject('IsKeyOf', { 'from-link' => $key,  
                                                  'to-link' => $assignKey,  
1301                                                 });                                                 });
1302              }              }
         } else {  
             # An assignment already exists. Add the new value to it.  
             $self->InsertValue($assignKey, 'Assignment(value)', $valueString);  
         }  
     }  
1303      # Return a one, indicating success. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1304      return 1;      return 1;
1305  }  }
1306    
1307  =head3 DeleteAttribute  =head3 DeleteAttribute
1308    
1309  C<< $attrDB->DeleteAttribute($objectID, $key, @values); >>      $attrDB->DeleteAttribute($objectID, $key, @values);
1310    
1311  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1312    
# Line 1121  Line 1338 
1338      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1339          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1340      } else {      } else {
1341          # Get the assignment key for this object/attribute pair.          # Split the key into the real key and the subkey.
1342          my $assignKey = $self->AssignmentKey($objectID, $key);          my ($realKey, $subKey) = $self->SplitKey($key);
1343          # Only proceed if it exists.          # Find the table containing the key's values.
1344          my $found = $self->Exists('Assignment', $assignKey);          my $table = $self->_KeyTable($realKey);
1345          if ($found && ! @values) {          if ($subKey eq '' && scalar(@values) == 0) {
1346              # Here the caller wants to delete the entire assignment.              # Here we erase the entire key for this object.
1347              $self->Delete('Assignment', $assignKey);              $self->DeleteRow('HasValueFor', $key, $objectID);
         } else {  
             # Here we're looking to delete only the one value. First, we get all  
             # the values currently present.  
             my @currentValues = $self->GetFlat(['Assignment'], "Assignment(id) = ?",  
                                                [$assignKey], 'Assignment(value)');  
             # Find our value amongst them.  
             my $valueString = join($self->{splitter}, @values);  
             my @matches = grep { $_ eq $valueString } @currentValues;  
             # Only proceed if we found it.  
             if (@matches) {  
                 # Find out if it's the only value.  
                 if (scalar(@matches) == scalar(@currentValues)) {  
                     # It is, so delete the assignment.  
                     $self->Delete('Assignment', $assignKey);  
1348                  } else {                  } else {
1349                      # It's not, so only delete the value itself.              # Here we erase the matching values.
1350                      $self->DeleteValue('Assignment', $assignKey, 'value', $valueString);              my $valueString = join($self->{splitter}, @values);
1351                  }              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1352              }                               { subkey => $subKey, value => $valueString });
1353          }          }
1354      }      }
1355      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1356      return 1;      return 1;
1357  }  }
1358    
1359    =head3 DeleteMatchingAttributes
1360    
1361        my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values);
1362    
1363    Delete all attributes that match the specified criteria. This is equivalent to
1364    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1365    row found.
1366    
1367    =over 4
1368    
1369    =item objectID
1370    
1371    ID of object whose attributes are to be deleted. If the attributes for multiple
1372    objects are to be deleted, this parameter can be specified as a list reference. If
1373    attributes are to be deleted for all objects, specify C<undef> or an empty string.
1374    Finally, you can delete attributes for a range of object IDs by putting a percent
1375    sign (C<%>) at the end.
1376    
1377    =item key
1378    
1379    Attribute key name. A value of C<undef> or an empty string will match all
1380    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1381    specified as a list reference. Finally, you can delete attributes for a range of
1382    keys by putting a percent sign (C<%>) at the end.
1383    
1384    =item values
1385    
1386    List of the desired attribute values, section by section. If C<undef>
1387    or an empty string is specified, all values in that section will match. A
1388    generic match can be requested by placing a percent sign (C<%>) at the end.
1389    In that case, all values that match up to and not including the percent sign
1390    will match. You may also specify a regular expression enclosed
1391    in slashes. All values that match the regular expression will be deleted. For
1392    performance reasons, only values have this extra capability.
1393    
1394    =item RETURN
1395    
1396    Returns a list of tuples for the attributes that were deleted, in the
1397    same form as L</GetAttributes>.
1398    
1399    =back
1400    
1401    =cut
1402    
1403    sub DeleteMatchingAttributes {
1404        # Get the parameters.
1405        my ($self, $objectID, $key, @values) = @_;
1406        # Get the matching attributes.
1407        my @retVal = $self->GetAttributes($objectID, $key, @values);
1408        # Loop through the attributes, deleting them.
1409        for my $tuple (@retVal) {
1410            $self->DeleteAttribute(@{$tuple});
1411        }
1412        # Log this operation.
1413        my $count = @retVal;
1414        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1415        # Return the deleted attributes.
1416        return @retVal;
1417    }
1418    
1419  =head3 ChangeAttribute  =head3 ChangeAttribute
1420    
1421  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>      $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues);
1422    
1423  Change the value of an attribute key/value pair for an object.  Change the value of an attribute key/value pair for an object.
1424    
# Line 1207  Line 1470 
1470    
1471  =head3 EraseAttribute  =head3 EraseAttribute
1472    
1473  C<< $attrDB->EraseAttribute($entityName, $key); >>      $attrDB->EraseAttribute($key);
1474    
1475  Erase all values for the specified attribute key. This does not remove the  Erase all values for the specified attribute key. This does not remove the
1476  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
# Line 1216  Line 1479 
1479    
1480  =item key  =item key
1481    
1482  Key to erase.  Key to erase. This must be a real key; that is, it cannot have a subkey
1483    component.
1484    
1485  =back  =back
1486    
# Line 1225  Line 1489 
1489  sub EraseAttribute {  sub EraseAttribute {
1490      # Get the parameters.      # Get the parameters.
1491      my ($self, $key) = @_;      my ($self, $key) = @_;
1492      # Delete everything connected to the key. The "keepRoot" option keeps the key in the      # Find the table containing the key.
1493      # datanase while deleting everything attached to it.      my $table = $self->_KeyTable($key);
1494      $self->Delete('AttributeKey', $key, keepRoot => 1);      # Is it the default table?
1495        if ($table eq $self->{defaultRel}) {
1496            # Yes, so the key is mixed in with other keys.
1497            # Delete everything connected to it.
1498            $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1499        } else {
1500            # No. Drop and re-create the table.
1501            $self->TruncateTable($table);
1502        }
1503        # Log the operation.
1504        $self->LogOperation("Erase Data", $key);
1505      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1506      return 1;      return 1;
1507  }  }
1508    
1509  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1510    
1511  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>      my @keyList = $attrDB->GetAttributeKeys($groupName);
1512    
1513  Return a list of the attribute keys for a particular group.  Return a list of the attribute keys for a particular group.
1514    
# Line 1262  Line 1536 
1536      return sort @groups;      return sort @groups;
1537  }  }
1538    
1539    =head3 QueryAttributes
1540    
1541        my @attributeData = $ca->QueryAttributes($filter, $filterParms);
1542    
1543    Return the attribute data based on an SQL filter clause. In the filter clause,
1544    the name C<$object> should be used for the object ID, C<$key> should be used for
1545    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1546    
1547    =over 4
1548    
1549    =item filter
1550    
1551    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1552    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1553    and C<$value> for the value field. This abstraction enables us to hide the details of
1554    the database construction from the user.
1555    
1556    =item filterParms
1557    
1558    Parameters for the filter clause.
1559    
1560    =item RETURN
1561    
1562    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1563    one or more attribute values.
1564    
1565    =back
1566    
1567    =cut
1568    
1569    # This hash is used to drive the substitution process.
1570    my %AttributeParms = (object => 'to-link',
1571                          key    => 'from-link',
1572                          subkey => 'subkey',
1573                          value  => 'value');
1574    
1575    sub QueryAttributes {
1576        # Get the parameters.
1577        my ($self, $filter, $filterParms) = @_;
1578        # Declare the return variable.
1579        my @retVal = ();
1580        # Make sue we have filter parameters.
1581        my $realParms = (defined($filterParms) ? $filterParms : []);
1582        # Loop through all the value tables.
1583        for my $table ($self->_GetAllTables()) {
1584            # Create the query for this table by converting the filter.
1585            my $realFilter = $filter;
1586            for my $name (keys %AttributeParms) {
1587                $realFilter =~ s/\$$name/$table($AttributeParms{$name})/g;
1588            }
1589            my $query = $self->Get([$table], $realFilter, $realParms);
1590            # Loop through the results, forming the output attribute tuples.
1591            while (my $result = $query->Fetch()) {
1592                # Get the four values from this query result row.
1593                my ($objectID, $key, $subkey, $value) = $result->Values(["$table($AttributeParms{object})",
1594                                                                        "$table($AttributeParms{key})",
1595                                                                        "$table($AttributeParms{subkey})",
1596                                                                        "$table($AttributeParms{value})"]);
1597                # Combine the key and the subkey.
1598                my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1599                # Split the value.
1600                my @values = split $self->{splitter}, $value;
1601                # Output the result.
1602                push @retVal, [$objectID, $realKey, @values];
1603            }
1604        }
1605        # Return the result.
1606        return @retVal;
1607    }
1608    
1609    =head2 Key and ID Manipulation Methods
1610    
1611    =head3 ParseID
1612    
1613        my ($type, $id) = CustomAttributes::ParseID($idValue);
1614    
1615    Determine the type and object ID corresponding to an ID value from the attribute database.
1616    Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
1617    however, Genomes, Features, and Subsystems are not stored with a type name, so we need to
1618    deduce the type from the ID value structure.
1619    
1620    The theory here is that you can plug the ID and type directly into a Sprout database method, as
1621    follows
1622    
1623        my ($type, $id) = CustomAttributes::ParseID($attrList[$num]->[0]);
1624        my $target = $sprout->GetEntity($type, $id);
1625    
1626    =over 4
1627    
1628    =item idValue
1629    
1630    ID value taken from the attribute database.
1631    
1632    =item RETURN
1633    
1634    Returns a two-element list. The first element is the type of object indicated by the ID value,
1635    and the second element is the actual object ID.
1636    
1637    =back
1638    
1639    =cut
1640    
1641    sub ParseID {
1642        # Get the parameters.
1643        my ($idValue) = @_;
1644        # Declare the return variables.
1645        my ($type, $id);
1646        # Parse the incoming ID. We first check for the presence of an entity name. Entity names
1647        # can only contain letters, which helps to insure typed object IDs don't collide with
1648        # subsystem names (which are untyped).
1649        if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1650            # Here we have a typed ID.
1651            ($type, $id) = ($1, $2);
1652            # Fix the case sensitivity on PDB IDs.
1653            if ($type eq 'PDB') { $id = lc $id; }
1654        } elsif ($idValue =~ /fig\|/) {
1655            # Here we have a feature ID.
1656            ($type, $id) = (Feature => $idValue);
1657        } elsif ($idValue =~ /\d+\.\d+/) {
1658            # Here we have a genome ID.
1659            ($type, $id) = (Genome => $idValue);
1660        } else {
1661            # The default is a subsystem ID.
1662            ($type, $id) = (Subsystem => $idValue);
1663        }
1664        # Return the results.
1665        return ($type, $id);
1666    }
1667    
1668    =head3 FormID
1669    
1670        my $idValue = CustomAttributes::FormID($type, $id);
1671    
1672    Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1673    genomes, and features are stored in the database without type information, but all other object IDs
1674    must be prefixed with the object type.
1675    
1676    =over 4
1677    
1678    =item type
1679    
1680    Relevant object type.
1681    
1682    =item id
1683    
1684    ID of the object in question.
1685    
1686    =item RETURN
1687    
1688    Returns a string that will be recognized as an object ID in the attribute database.
1689    
1690    =back
1691    
1692    =cut
1693    
1694    sub FormID {
1695        # Get the parameters.
1696        my ($type, $id) = @_;
1697        # Declare the return variable.
1698        my $retVal;
1699        # Compute the ID string from the type.
1700        if (grep { $type eq $_ } qw(Feature Genome Subsystem)) {
1701            $retVal = $id;
1702        } else {
1703            $retVal = "$type:$id";
1704        }
1705        # Return the result.
1706        return $retVal;
1707    }
1708    
1709    =head3 GetTargetObject
1710    
1711        my $object = CustomAttributes::GetTargetObject($erdb, $idValue);
1712    
1713    Return the database object corresponding to the specified attribute object ID. The
1714    object type associated with the ID value must correspond to an entity name in the
1715    specified database.
1716    
1717    =over 4
1718    
1719    =item erdb
1720    
1721    B<ERDB> object for accessing the target database.
1722    
1723    =item idValue
1724    
1725    ID value retrieved from the attribute database.
1726    
1727    =item RETURN
1728    
1729    Returns a B<ERDBObject> for the attribute value's target object.
1730    
1731    =back
1732    
1733    =cut
1734    
1735    sub GetTargetObject {
1736        # Get the parameters.
1737        my ($erdb, $idValue) = @_;
1738        # Declare the return variable.
1739        my $retVal;
1740        # Get the type and ID for the target object.
1741        my ($type, $id) = ParseID($idValue);
1742        # Plug them into the GetEntity method.
1743        $retVal = $erdb->GetEntity($type, $id);
1744        # Return the resulting object.
1745        return $retVal;
1746    }
1747    
1748    =head3 SplitKey
1749    
1750        my ($realKey, $subKey) = $ca->SplitKey($key);
1751    
1752    Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1753    The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
1754    then the sub key is presumed to be an empty string.
1755    
1756    =over 4
1757    
1758    =item key
1759    
1760    Incoming key to be split.
1761    
1762    =item RETURN
1763    
1764    Returns a two-element list, the first element of which is the real key and the second element of
1765    which is the sub key.
1766    
1767    =back
1768    
1769    =cut
1770    
1771    sub SplitKey {
1772        # Get the parameters.
1773        my ($self, $key) = @_;
1774        # Do the split.
1775        my ($realKey, $subKey) = split($self->{splitter}, $key, 2);
1776        # Insure the subkey has a value.
1777        if (! defined $subKey) {
1778            $subKey = '';
1779        }
1780        # Return the results.
1781        return ($realKey, $subKey);
1782    }
1783    
1784    
1785    =head3 JoinKey
1786    
1787        my $key = $ca->JoinKey($realKey, $subKey);
1788    
1789    Join a real key and a subkey together to make an external key. The external key is the attribute key
1790    used by the caller. The real key and the subkey are how the keys are represented in the database. The
1791    real key is the key to the B<AttributeKey> entity. The subkey is an attribute of the B<HasValueFor>
1792    relationship.
1793    
1794    =over 4
1795    
1796    =item realKey
1797    
1798    The real attribute key.
1799    
1800    =item subKey
1801    
1802    The subordinate portion of the attribute key.
1803    
1804    =item RETURN
1805    
1806    Returns a single string representing both keys.
1807    
1808    =back
1809    
1810    =cut
1811    
1812    sub JoinKey {
1813        # Get the parameters.
1814        my ($self, $realKey, $subKey) = @_;
1815        # Declare the return variable.
1816        my $retVal;
1817        # Check for a subkey.
1818        if ($subKey eq '') {
1819            # No subkey, so the real key is the key.
1820            $retVal = $realKey;
1821        } else {
1822            # Subkey found, so the two pieces must be joined by a splitter.
1823            $retVal = "$realKey$self->{splitter}$subKey";
1824        }
1825        # Return the result.
1826        return $retVal;
1827    }
1828    
1829    
1830    =head3 AttributeTable
1831    
1832        my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList);
1833    
1834    Format the attribute data into an HTML table.
1835    
1836    =over 4
1837    
1838    =item cgi
1839    
1840    CGI query object used to generate the HTML
1841    
1842    =item attrList
1843    
1844    List of attribute results, in the format returned by the L</GetAttributes> or
1845    L</QueryAttributes> methods.
1846    
1847    =item RETURN
1848    
1849    Returns an HTML table displaying the attribute keys and values.
1850    
1851    =back
1852    
1853    =cut
1854    
1855    sub AttributeTable {
1856        # Get the parameters.
1857        my ($cgi, @attrList) = @_;
1858        # Accumulate the table rows.
1859        my @html = ();
1860        for my $attrData (@attrList) {
1861            # Format the object ID and key.
1862            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
1863            # Now we format the values. These remain unchanged unless one of them is a URL.
1864            my $lastValue = scalar(@{$attrData}) - 1;
1865            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
1866            # Assemble the values into a table row.
1867            push @html, $cgi->Tr($cgi->td(\@columns));
1868        }
1869        # Format the table in the return variable.
1870        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
1871        # Return it.
1872        return $retVal;
1873    }
1874    
1875    
1876    =head2 Internal Utility Methods
1877    
1878    =head3 _KeyTable
1879    
1880        my $tableName = $ca->_KeyTable($keyName);
1881    
1882    Return the name of the table that contains the attribute values for the
1883    specified key.
1884    
1885    Most attribute values are stored in the default table (usually C<HasValueFor>).
1886    Some, however, are placed in private tables by themselves for performance reasons.
1887    
1888    =over 4
1889    
1890    =item keyName (optional)
1891    
1892    Name of the attribute key whose table name is desired. If not specified, the
1893    entire key/table hash is returned.
1894    
1895    =item RETURN
1896    
1897    Returns the name of the table containing the specified attribute key's values,
1898    or a reference to a hash that maps key names to table names.
1899    
1900    =back
1901    
1902    =cut
1903    
1904    sub _KeyTable {
1905        # Get the parameters.
1906        my ($self, $keyName) = @_;
1907        # Declare the return variable.
1908        my $retVal;
1909        # Insure the key table hash is present.
1910        if (! exists $self->{keyTables}) {
1911            $self->{keyTables} = { map { $_->[0] => $_->[1] } $self->GetAll(['AttributeKey'],
1912                                                    "AttributeKey(relationship-name) <> ?",
1913                                                    [$self->{defaultRel}],
1914                                                    ['AttributeKey(id)', 'AttributeKey(relationship-name)']) };
1915        }
1916        # Get the key hash.
1917        my $keyHash = $self->{keyTables};
1918        # Does the user want a specific table or the whole thing?
1919        if ($keyName) {
1920            # Here we want a specific table. Is this key in the hash?
1921            if (exists $keyHash->{$keyName}) {
1922                # It's there, so return the specified table.
1923                $retVal = $keyHash->{$keyName};
1924            } else {
1925                # No, return the default table name.
1926                $retVal = $self->{defaultRel};
1927            }
1928        } else {
1929            # Here we want the whole hash.
1930            $retVal = $keyHash;
1931        }
1932        # Return the result.
1933        return $retVal;
1934    }
1935    
1936    
1937    =head3 _QueryResults
1938    
1939        my @attributeList = $attrDB->_QueryResults($query, $table, @values);
1940    
1941    Match the results of a query against value criteria and return
1942    the results. This is an internal method that splits the values coming back
1943    and matches the sections against the specified section patterns. It serves
1944    as the back end to L</GetAttributes> and L</FindAttributes>.
1945    
1946    =over 4
1947    
1948    =item query
1949    
1950    A query object that will return the desired records.
1951    
1952    =item table
1953    
1954    Name of the value table for the query.
1955    
1956    =item values
1957    
1958    List of the desired attribute values, section by section. If C<undef>
1959    or an empty string is specified, all values in that section will match. A
1960    generic match can be requested by placing a percent sign (C<%>) at the end.
1961    In that case, all values that match up to and not including the percent sign
1962    will match. You may also specify a regular expression enclosed
1963    in slashes. All values that match the regular expression will be returned. For
1964    performance reasons, only values have this extra capability.
1965    
1966    =item RETURN
1967    
1968    Returns a list of tuples. The first element in the tuple is an object ID, the
1969    second is an attribute key, and the remaining elements are the sections of
1970    the attribute value. All of the tuples will match the criteria set forth in
1971    the parameter list.
1972    
1973    =back
1974    
1975    =cut
1976    
1977    sub _QueryResults {
1978        # Get the parameters.
1979        my ($self, $query, $table, @values) = @_;
1980        # Declare the return value.
1981        my @retVal = ();
1982        # We use this hash to check for duplicates.
1983        my %dupHash = ();
1984        # Get the number of value sections we have to match.
1985        my $sectionCount = scalar(@values);
1986        # Loop through the assignments found.
1987        while (my $row = $query->Fetch()) {
1988            # Get the current row's data.
1989            my ($id, $realKey, $subKey, $valueString) = $row->Values(["$table(to-link)",
1990                                                                      "$table(from-link)",
1991                                                                      "$table(subkey)",
1992                                                                      "$table(value)"
1993                                                                    ]);
1994            # Form the key from the real key and the sub key.
1995            my $key = $self->JoinKey($realKey, $subKey);
1996            # Check for a duplicate.
1997            my $wholeThing = join($self->{splitter}, $id, $key, $valueString);
1998            if (! $dupHash{$wholeThing}) {
1999                # It's okay, we're not a duplicate. Insure we don't duplicate this result.
2000                $dupHash{$wholeThing} = 1;
2001                # Break the value into sections.
2002                my @sections = split($self->{splitter}, $valueString);
2003                # Match each section against the incoming values. We'll assume we're
2004                # okay unless we learn otherwise.
2005                my $matching = 1;
2006                for (my $i = 0; $i < $sectionCount && $matching; $i++) {
2007                    # We need to check to see if this section is generic.
2008                    my $value = $values[$i];
2009                    Trace("Current value pattern is \"$value\".") if T(4);
2010                    if ($value =~ m#^/(.+)/[a-z]*$#) {
2011                        Trace("Regular expression detected.") if T(4);
2012                        # Here we have a regular expression match.
2013                        my $section = $sections[$i];
2014                        $matching = eval("\$section =~ $value");
2015                    } else {
2016                        # Here we have a normal match.
2017                        Trace("SQL match used.") if T(4);
2018                        $matching = _CheckSQLPattern($values[$i], $sections[$i]);
2019                    }
2020                }
2021                # If we match, output this row to the return list.
2022                if ($matching) {
2023                    push @retVal, [$id, $key, @sections];
2024                }
2025            }
2026        }
2027        # Return the rows found.
2028        return @retVal;
2029    }
2030    
2031    
2032    =head3 _LoadAttributeTable
2033    
2034        $attr->_LoadAttributeTable($tableName, $fileName, $stats, $mode);
2035    
2036    Load a file's data into an attribute table. This is an internal method
2037    provided for the convenience of L</LoadAttributesFrom>. It loads the
2038    specified file into the specified table and updates the statistics
2039    object.
2040    
2041    =over 4
2042    
2043    =item tableName
2044    
2045    Name of the table being loaded. This is usually C<HasValueFor>, but may
2046    be a different table for some specific attribute keys.
2047    
2048    =item fileName
2049    
2050    Name of the file containing a chunk of attribute data to load.
2051    
2052    =item stats
2053    
2054    Statistics object into which counts and times should be placed.
2055    
2056    =item mode
2057    
2058    Load mode for the file, usually C<low_priority>, C<concurrent>, or
2059    an empty string. The mode is used by some applications to control access
2060    to the table while it's being loaded. The default (empty string) is to lock the
2061    table until all the data's in place.
2062    
2063    =back
2064    
2065    =cut
2066    
2067    sub _LoadAttributeTable {
2068        # Get the parameters.
2069        my ($self, $tableName, $fileName, $stats, $mode) = @_;
2070        # Load the table from the file. Note that we don't do an analyze.
2071        # The analyze is done only after everything is complete.
2072        my $startTime = time();
2073        Trace("Loading attributes from $fileName: " . (-s $fileName) .
2074              " characters.") if T(3);
2075        my $loadStats = $self->LoadTable($fileName, $tableName,
2076                                         mode => $mode, partial => 1);
2077        # Record the load time.
2078        $stats->Add(insertTime => time() - $startTime);
2079        # Roll up the other statistics.
2080        $stats->Accumulate($loadStats);
2081    }
2082    
2083    
2084    =head3 _GetAllTables
2085    
2086        my @tables = $ca->_GetAllTables();
2087    
2088    Return a list of the names of all the tables used to store attribute
2089    values.
2090    
2091    =cut
2092    
2093    sub _GetAllTables {
2094        # Get the parameters.
2095        my ($self) = @_;
2096        # Start with the default table.
2097        my @retVal = $self->{defaultRel};
2098        # Add the tables named in the key hash. These tables are automatically
2099        # NOT the default, and each can only occur once, because alternate tables
2100        # are allocated on a per-key basis.
2101        my $keyHash = $self->_KeyTable();
2102        push @retVal, values %$keyHash;
2103        # Return the result.
2104        return @retVal;
2105    }
2106    
2107    
2108    =head3 _SplitKeyPattern
2109    
2110        my ($realKey, $subKey) = $ca->_SplitKeyPattern($keyChoice);
2111    
2112    Split a key pattern into the main part (the I<real key>) and a sub-part
2113    (the I<sub key>). This method differs from L</SplitKey> in that it treats
2114    the key as an SQL pattern instead of a raw string. Also, if there is no
2115    incoming sub-part, the sub-key will be undefined instead of an empty
2116    string.
2117    
2118    =over 4
2119    
2120    =item keyChoice
2121    
2122    SQL key pattern to be examined. This can either be a literal, an SQL pattern,
2123    a literal with an internal splitter code (usually C<::>) or an SQL pattern with
2124    an internal splitter. Note that the only SQL pattern we support is a percent
2125    sign (C<%>) at the end. This is the way we've declared things in the documentation,
2126    so users who try anything else will have problems.
2127    
2128    =item RETURN
2129    
2130    Returns a two-element list. The first element is the SQL pattern for the
2131    real key and the second is the SQL pattern for the sub-key. If the value
2132    for either one does not matter (e.g., the user wants a real key value of
2133    C<iedb> and doesn't care about the sub-key value), it will be undefined.
2134    
2135    =back
2136    
2137    =cut
2138    
2139    sub _SplitKeyPattern {
2140        # Get the parameters.
2141        my ($self, $keyChoice) = @_;
2142        # Declare the return variables.
2143        my ($realKey, $subKey);
2144        # Look for a splitter in the input.
2145        if ($keyChoice =~ /^(.*?)$self->{splitter}(.*)/) {
2146            # We found one. This means we can treat both sides of the
2147            # splitter as known patterns.
2148            ($realKey, $subKey) = ($1, $2);
2149        } elsif ($keyChoice =~ /%$/) {
2150            # Here we have a generic pattern for the whole key. The pattern
2151            # is treated as the correct pattern for the real key, but the
2152            # sub-key is considered to be wild.
2153            $realKey = $keyChoice;
2154        } else {
2155            # Here we have a literal pattern for the whole key. The pattern
2156            # is treated as the correct pattern for the real key, and the
2157            # sub-key is required to be blank.
2158            $realKey = $keyChoice;
2159            $subKey = '';
2160        }
2161        # Return the results.
2162        return ($realKey, $subKey);
2163    }
2164    
2165    
2166    =head3 _WherePart
2167    
2168        my ($sqlClause, $escapedValue) = _WherePart($tableName, $fieldName, $sqlPattern);
2169    
2170    Return the SQL clause and value for checking a field against the
2171    specified SQL pattern value. If the pattern is generic (ends in a C<%>),
2172    then a C<LIKE> expression is returned. Otherwise, an equality expression
2173    is returned. We take in information describing the field being checked,
2174    and the pattern we're checking against it. The output is a WHERE clause
2175    fragment for the comparison and a value to be used as a bound parameter
2176    value for the clause.
2177    
2178    =over 4
2179    
2180    =item tableName
2181    
2182    Name of the table containing the field we want checked by the clause.
2183    
2184    =item fieldName
2185    
2186    Name of the field to check in that table.
2187    
2188    =item sqlPattern
2189    
2190    Pattern to be compared against the field. If the last character is a percent sign
2191    (C<%>), it will be treated as a generic SQL pattern; otherwise, it will be treated
2192    as a literal.
2193    
2194    =item RETURN
2195    
2196    Returns a two-element list. The first element will be an SQL comparison expression
2197    and the second will be the value to be used as a bound parameter for the expression
2198    in order to
2199    
2200    =back
2201    
2202    =cut
2203    
2204    sub _WherePart {
2205        # Get the parameters.
2206        my ($tableName, $fieldName, $sqlPattern) = @_;
2207        # Declare the return variables.
2208        my ($sqlClause, $escapedValue);
2209        # Copy the pattern into the return area.
2210        $escapedValue = $sqlPattern;
2211        # Check the pattern. Is it generic or exact?
2212        if ($sqlPattern =~ /(.+)%$/) {
2213            # Yes, it is. We need a LIKE clause and we must escape the underscores
2214            # and percents in the pattern (except for the last one, of course).
2215            $escapedValue = $1;
2216            $escapedValue =~ s/(%|_)/\\$1/g;
2217            $escapedValue .= "%";
2218            $sqlClause = "$tableName($fieldName) LIKE ?";
2219        } else {
2220            # No, it isn't. We use an equality clause.
2221            $sqlClause = "$tableName($fieldName) = ?";
2222        }
2223        # Return the results.
2224        return ($sqlClause, $escapedValue);
2225    }
2226    
2227    
2228    =head3 _CheckSQLPattern
2229    
2230        my $flag = _CheckSQLPattern($pattern, $value);
2231    
2232    Return TRUE if the specified SQL pattern matches the specified value,
2233    else FALSE. The pattern is not a true full-blown SQL LIKE pattern: the
2234    only wild-carding allowed is a percent sign (C<%>) at the end.
2235    
2236    =over 4
2237    
2238    =item pattern
2239    
2240    SQL pattern to match against a value.
2241    
2242    =item value
2243    
2244    Value to match against an SQL pattern.
2245    
2246    =item RETURN
2247    
2248    Returns TRUE if the pattern matches the value, else FALSE.
2249    
2250    =back
2251    
2252    =cut
2253    
2254    sub _CheckSQLPattern {
2255        # Get the parameters.
2256        my ($pattern, $value) = @_;
2257        # Declare the return variable.
2258        my $retVal;
2259        # Check for a generic pattern.
2260        if ($pattern =~ /(.*)%$/) {
2261            # Here we have one. Do a substring match.
2262            $retVal = (substr($value, 0, length $1) eq $1);
2263        } else {
2264            # Here it's an exact match.
2265            $retVal = ($pattern eq $value);
2266        }
2267        # Return the result.
2268        return $retVal;
2269    }
2270    
2271  1;  1;

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