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revision 1.5, Fri Nov 10 21:20:37 2006 UTC revision 1.33, Tue Aug 12 06:06:02 2008 UTC
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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 15  Line 18 
18    
19  The Custom SEED Attributes Manager allows the user to upload and retrieve  The Custom SEED Attributes Manager allows the user to upload and retrieve
20  custom data for SEED objects. It uses the B<ERDB> database system to  custom data for SEED objects. It uses the B<ERDB> database system to
21  store the attributes, which are implemented as multi-valued fields  store the attributes.
22  of ERDB entities.  
23    Attributes are organized by I<attribute key>. Attribute values are
24    assigned to I<objects>. In the real world, objects have types and IDs;
25    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
27    types, but it is more consistent with the original attribute implementation
28    in the SEED (which this implementation replaces).
29    
30    The actual attribute values are stored as a relationship between the attribute
31    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
68  the values of the attribute C<essential> in the B<Feature> entity, you  the values of the attribute C<essential> in a specified B<Feature>, you
69  would code  would code
70    
71      my @values = $attrDB->GetAttributeValues($fid, Feature => 'essential');      my @values = $attrDB->GetAttributes($fid, 'essential');
72    
73  where I<$fid> contains the ID of the desired feature. Each attribute has  where I<$fid> contains the ID of the desired feature.
 an alternate index to allow searching for attributes by value.  
74    
75  New attributes are introduced by updating the database definition at  Keys can be split into two pieces using the splitter value defined in the
76  run-time. Attribute values are stored by uploading data from files.  constructor (the default is C<::>). The first piece of the key is called
77  A web interface is provided for both these activities.  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 74  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  =back  =item attr_default_table
130    
131  =head2 Implementation Note  Name of the default relationship for attribute values. If not present,
132    C<HasValueFor> is used.
133    
134  The L</Refresh> method reloads the entities in the database. If new  =back
 entity types are added, that method will need to be adjusted accordingly.  
135    
136  =head2 Public Methods  =head2 Public Methods
137    
138  =head3 new  =head3 new
139    
140  C<< my $attrDB = CustomAttributes->new($splitter); >>      my $attrDB = CustomAttributes->new(%options);
141    
142  Construct a new CustomAttributes object. This object cannot be used to add or  Construct a new CustomAttributes object. The following options are
143  delete keys because that requires modifying the database design. To do that,  supported.
 you need to use the static L</StoreAttributeKey> or L</DeleteAttributeKey>  
 methods.  
144    
145  =over 4  =over 4
146    
147  =item splitter  =item splitter
148    
149  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
150  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
151  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
152  worry about this parameter.  
153    =item user
154    
155    Name of the current user. This will appear in the attribute log.
156    
157  =back  =back
158    
# Line 107  Line 160 
160    
161  sub new {  sub new {
162      # Get the parameters.      # Get the parameters.
163      my ($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 117  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        # Store the user name.
176        $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        # default is HasValueFor.
180        $retVal->{defaultRel} = $FIG_Config::attr_default_table || 'HasValueFor';
181      # Return the result.      # Return the result.
182      return $retVal;      return $retVal;
183  }  }
184    
185  =head3 StoreAttributeKey  =head3 StoreAttributeKey
186    
187  C<< my $attrDB = CustomAttributes::StoreAttributeKey($entityName, $attributeName, $type, $notes); >>      $attrDB->StoreAttributeKey($attributeName, $notes, \@groups, $table);
188    
189  Create or update an attribute for the database. This method will update the database definition  Create or update an attribute for the database.
 XML, but it will not create the table. It will connect to the database so that the caller  
 can upload the attribute values.  
190    
191  =over 4  =over 4
192    
 =item entityName  
   
 Name of the entity containing the attribute. The entity must exist.  
   
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    
199  Descriptive notes about the attribute. It is presumed to be raw text, not HTML.  Descriptive notes about the attribute. It is presumed to be raw text, not HTML.
200    
201  =item RETURN  =item groups
202    
203    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.
205    
206    =item table
207    
208  Returns a Custom Attribute Database object if successful. If unsuccessful, an  The name of the relationship in which the attribute's values are to be stored.
209  error will be thrown.  If empty or undefined, the default relationship (usually C<HasValueFor>) will be
210    assumed.
211    
212  =back  =back
213    
# Line 161  Line 215 
215    
216  sub StoreAttributeKey {  sub StoreAttributeKey {
217      # Get the parameters.      # Get the parameters.
218      my ($entityName, $attributeName, $type, $notes) = @_;      my ($self, $attributeName, $notes, $groups, $table) = @_;
219        # Declare the return variable.
220        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 {
235      # Our next step is to read in the XML for the database defintion. We          # Create a variable to hold the action to be displayed for the log (Add or Update).
236      # need to verify that the named entity exists.          my $action;
237      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);          # Okay, we're ready to begin. See if this key exists.
238      my $entityHash = $metadata->{Entities};          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
239      if (! exists $entityHash->{$entityName}) {          if (defined($attribute)) {
240          Confess("Entity $entityName not found.");              # It does, so we do an update.
241      } else {              $action = "Update Key";
242          # Okay, we're ready to begin. Get the entity hash and the field hash.              $self->UpdateEntity('AttributeKey', $attributeName,
243          my $entityData = $entityHash->{$entityName};                                  { description => $notes,
244          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);                                    'relationship-name' => $table});
245          # Compute the attribute's relation name.              # Detach the key from its current groups.
246          my $relName = join("", $entityName, map { ucfirst $_ } split(/-|_/, $attributeName));              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
247          # Store the attribute's field data. Note the use of the "content" hash for          } else {
248          # the notes. This is how the XML writer knows Notes is a text tag instead of              # It doesn't, so we do an insert.
249          # an attribute.              $action = "Insert Key";
250          $fieldHash->{$attributeName} = { type => $type, relation => $relName,              $self->InsertObject('AttributeKey', { id => $attributeName,
251                                           Notes => { content => $notes } };                                  description => $notes,
252          # Insure we have an index for this attribute.                                  'relationship-name' => $table});
253          my $index = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);          }
254          if (! defined($index)) {          # Attach the key to the specified groups. (We presume the groups already
255              push @{$entityData->{Indexes}}, { IndexFields => [ { name => $attributeName, order => 'ascending' } ],          # exist.)
256                                                Notes       => "Alternate index provided for access by $attributeName." };          for my $group (@{$groups}) {
257                $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
258                                                   'to-link'   => $group });
259          }          }
260          # Write the XML back out.          # Log the operation.
261          ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);          $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
262      }      }
     # Open a database with the new XML.  
     my $retVal = CustomAttributes->new();  
     return $retVal;  
263  }  }
264    
 =head3 Refresh  
265    
266  C<< $attrDB->Refresh($fig); >>  =head3 DeleteAttributeKey
267    
268        my $stats = $attrDB->DeleteAttributeKey($attributeName);
269    
270  Refresh the primary entity tables from the FIG data store. This method basically  Delete an attribute from the custom attributes database.
 drops and reloads the main tables of the custom attributes database.  
271    
272  =over 4  =over 4
273    
274  =item fig  =item attributeName
275    
276    Name of the attribute to delete.
277    
278    =item RETURN
279    
280  FIG-like object that can be used to find genomes and features.  Returns a statistics object describing the effects of the deletion.
281    
282  =back  =back
283    
284  =cut  =cut
285    
286  sub Refresh {  sub DeleteAttributeKey {
287      # Get the parameters.      # Get the parameters.
288      my ($self, $fig) = @_;      my ($self, $attributeName) = @_;
289      # Create load objects for the genomes and the features.      # Delete the attribute key.
290      my $loadGenome = ERDBLoad->new($self, 'Genome', $FIG_Config::temp);      my $retVal = $self->Delete('AttributeKey', $attributeName);
291      my $loadFeature = ERDBLoad->new($self, 'Feature', $FIG_Config::temp);      # Log this operation.
292      # Get the genome list.      $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
293      my @genomes = $fig->genomes();      # Return the result.
294      # Loop through the genomes.      return $retVal;
     for my $genomeID (@genomes) {  
         # Put this genome in the genome table.  
         $loadGenome->Put($genomeID);  
         Trace("Processing Genome $genomeID") if T(3);  
         # Put its features into the feature table. Note we have to use a hash to  
         # remove duplicates.  
         my %featureList = map { $_ => 1 } $fig->all_features($genomeID);  
         for my $fid (keys %featureList) {  
             $loadFeature->Put($fid);  
         }  
     }  
     # Get a variable for holding statistics objects.  
     my $stats;  
     # Finish the genome load.  
     Trace("Loading Genome relation.") if T(2);  
     $stats = $loadGenome->FinishAndLoad();  
     Trace("Genome table load statistics:\n" . $stats->Show()) if T(3);  
     # Finish the feature load.  
     Trace("Loading Feature relation.") if T(2);  
     $stats = $loadFeature->FinishAndLoad();  
     Trace("Feature table load statistics:\n" . $stats->Show()) if T(3);  
 }  
295    
296  =head3 LoadAttributeKey  }
297    
298  C<< my $stats = $attrDB->LoadAttributeKey($entityName, $fieldName, $fh, $keyCol, $dataCol); >>  =head3 NewName
299    
300  Load the specified attribute from the specified file. The file should be a      my $text = CustomAttributes::NewName();
 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 key value and the other the  
 corresponding attribute value.  
301    
302  =over 4  Return the string used to indicate the user wants to add a new attribute.
303    
304  =item entityName  =cut
305    
306  Name of the entity containing the attribute.  sub NewName {
307        return "(new)";
308    }
309    
310  =item fieldName  =head3 LoadAttributesFrom
311    
312  Name of the actual attribute.  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
313    
314  =item fh  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  Open file handle for the input file.  =over 4
322    
323  =item keyCol  =item fileName
324    
325  Index (0-based) of the column containing the key field. The key field should  Name of the file from which to load the attributes, or an open handle for the file.
326  contain the ID of an instance of the named entity.  (This last enables the method to be used in conjunction with the CGI form upload
327    control.)
328    
329  =item dataCol  =item options
330    
331  Index (0-based) of the column containing the data value field.  Hash of options for modifying the load process.
332    
333  =item RETURN  =item RETURN
334    
335  Returns a statistics object for the load process.  Returns a statistics object describing the load.
336    
337  =back  =back
338    
339  =cut  Permissible option values are as follows.
340    
341  sub LoadAttributeKey {  =over 4
     # Get the parameters.  
     my ($self, $entityName, $fieldName, $fh, $keyCol, $dataCol) = @_;  
     # Create the return variable.  
     my $retVal;  
     # Insure the entity exists.  
     my $found = grep { $_ eq $entityName } $self->GetEntityTypes();  
     if (! $found) {  
         Confess("Entity \"$entityName\" not found in database.");  
     } else {  
         # Get the field structure for the named entity.  
         my $fieldHash = $self->GetFieldTable($entityName);  
         # Verify that the attribute exists.  
         if (! exists $fieldHash->{$fieldName}) {  
             Confess("Attribute key \"$fieldName\" does not exist in entity $entityName.");  
         } else {  
             # Create a loader for the specified attribute. We need the  
             # relation name first.  
             my $relName = $fieldHash->{$fieldName}->{relation};  
             my $loadAttribute = ERDBLoad->new($self, $relName, $FIG_Config::temp);  
             # Loop through the input file.  
             while (! eof $fh) {  
                 # Get the next line of the file.  
                 my @fields = Tracer::GetLine($fh);  
                 $loadAttribute->Add("lineIn");  
                 # Now we need to validate the line.  
                 if ($#fields < $dataCol) {  
                     $loadAttribute->Add("shortLine");  
                 } elsif (! $self->Exists($entityName, $fields[$keyCol])) {  
                     $loadAttribute->Add("badKey");  
                 } else {  
                     # It's valid,so send it to the loader.  
                     $loadAttribute->Put($fields[$keyCol], $fields[$dataCol]);  
                     $loadAttribute->Add("lineUsed");  
                 }  
             }  
             # Finish the load.  
             $retVal = $loadAttribute->FinishAndLoad();  
         }  
     }  
     # Return the statistics.  
     return $retVal;  
 }  
342    
343    =item mode
344    
345  =head3 DeleteAttributeKey  Loading mode. Legal values are C<low_priority> (which reduces the task priority
346    of the load) and C<concurrent> (which reduces the locking cost of the load). The
347    default is a normal load.
348    
349  C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  =item append
350    
351  Delete an attribute from the custom attributes database.  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  =over 4  =item archive
355    
356  =item entityName  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  Name of the entity possessing the attribute.  =item objectType
361    
362  =item attributeName  If specified, the specified object type will be prefixed to each object ID.
363    
364  Name of the attribute to delete.  =item resume
365    
366    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    =item chunkSize
380    
381    Number of lines to load in each burst. The default is 10,000.
382    
383  =back  =back
384    
385  =cut  =cut
386    
387  sub DeleteAttributeKey {  sub LoadAttributesFrom {
388      # Get the parameters.      # Get the parameters.
389      my ($entityName, $attributeName) = @_;      my ($self, $fileName, %options) = @_;
390      # Read in the XML for the database defintion. We need to verify that      # Declare the return variable.
391      # the named entity exists and it has the named attribute.      my $retVal = Stats->new('keys', 'values', 'linesOut');
392      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Initialize the timers.
393      my $entityHash = $metadata->{Entities};      my ($eraseTime, $archiveTime, $checkTime) = (0, 0, 0);
394      if (! exists $entityHash->{$entityName}) {      # Check for append mode.
395          Confess("Entity \"$entityName\" not found.");      my $append = ($options{append} ? 1 : 0);
396      } else {      # Check for resume mode.
397          # Get the field hash.      my $resume = (defined($options{resume}) ? $options{resume} : 'none');
398          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);      # Create a hash of key names found.
399          if (! exists $fieldHash->{$attributeName}) {      my %keyHash = ();
400              Confess("Attribute key \"$attributeName\" not found in entity $entityName.");      # Create a hash of table names to files. Most attributes go into the HasValueFor
401          } else {      # table, but some are put into other tables. Each table name will be mapped
402              # Get the attribute's relation name.      # to a sub-hash with keys "fileName" (output file for the table) and "count"
403              my $relName = $fieldHash->{$attributeName}->{relation};      # (number of lines in the file).
404              # Check for an index.      my %tableHash = ();
405              my $indexIdx = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);      # Compute the chunk size.
406              if (defined($indexIdx)) {      my $chunkSize = ($options{chunkSize} ? $options{chunkSize} : 10000);
407                  Trace("Index for $attributeName found at position $indexIdx for $entityName.") if T(3);      # Open the file for input. Note we must anticipate the possibility of an
408                  delete $entityHash->{$entityName}->{Indexes}->[$indexIdx];      # open filehandle being passed in. This occurs when the user is submitting
409              }      # the load file over the web.
410              # Delete the attribute from the field hash.      my $fh;
411              Trace("Deleting attribute $attributeName from $entityName.") if T(3);      if (ref $fileName) {
412              delete $fieldHash->{$attributeName};          Trace("Using file opened by caller.") if T(3);
413              # Write the XML back out.          $fh = $fileName;
414              ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);      } else {
415              # Insure the relation does not exist in the database. This requires connecting          Trace("Attributes will be loaded from $fileName.") if T(3);
416              # since we may have to do a table drop.          $fh = Open(undef, "<$fileName");
417              my $attrDB = CustomAttributes->new();      }
418              Trace("Dropping table $relName.") if T(3);      # Trace the mode.
419              $attrDB->DropRelation($relName);      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); >>      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.  
613    
614  =over 4  =over 4
615    
616  =item cgi  =item fileName
617    
618  CGI query object used to create HTML.  Name of the output file.
619    
620  =item name  =item options
621    
622  Name to give to the form. This should be unique for the web page.  Options for modifying the backup process.
623    
624  =item RETURN  =item RETURN
625    
626  Returns the HTML for a form that submits instructions to the C<Attributes.cgi> script  Returns a statistics object for the backup.
 for loading, creating, or deleting an attribute.  
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, $name) = @_;      my ($self, $fileName, %options) = @_;
640      # Declare the return list.      # Declare the return variable.
641      my @retVal = ();      my $retVal = Stats->new();
642      # Start the form. We use multipart to support the upload control.      # Open the output file.
643      push @retVal, $cgi->start_multipart_form(-name => $name);      my $fh = Open(undef, ">$fileName");
644      # We'll put the controls in a table. Nothing else ever seems to look nice.      # Set up to read the keys.
645      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      my $keyQuery = $self->Get(['AttributeKey'], "", []);
646      # The first row is for selecting the field name.      # Loop through the keys.
647      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      while (my $keyData = $keyQuery->Fetch()) {
648                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,          $retVal->Add(key => 1);
649                                                       "document.$name.notes.value",          # Get the fields.
650                                                       "document.$name.dataType.value")));          my ($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      push @retVal, $cgi->Tr($cgi->th("Data type"),          my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
659                             $cgi->td($typeMenu));                                      'IsInGroup(to-link)');
660      # The next row is for the notes.          $retVal->Add(memberships => scalar(@groups));
661      push @retVal, $cgi->Tr($cgi->th("Description"),          # Write them to the output. Note we put a marker at the beginning to insure the line
662                             $cgi->td($cgi->textarea(-name => 'notes',          # is nonempty.
663                                                     -rows => 6,          Tracer::PutLine($fh, ['#GROUPS', @groups]);
664                                                     -columns => 80))      }
665                            );      # Log the operation.
666      # Allow the user to specify a new field name. This is required if the      $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
667      # user has selected one of the "(new)" markers.      # Return the result.
668      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      return $retVal;
669                             $cgi->td($cgi->textfield(-name => 'newName',  }
                                                     -size => 30)),  
                                     );  
     # 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 two buttons: UPDATE 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')  
                                    )  
                           );  
     # Close the table and the form.  
     push @retVal, $cgi->end_table();  
     push @retVal, $cgi->end_form();  
     # Return the assembled HTML.  
     return join("\n", @retVal, "");  
 }  
   
 =head3 FieldMenu  
   
 C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  
   
 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, grouped by entity.  
   
 =over 4  
   
 =item cgi  
   
 CGI query object used to generate HTML.  
   
 =item height  
670    
671  Number of lines to display in the list.  =head3 RestoreKeys
672    
673  =item name      my $stats = $attrDB->RestoreKeys($fileName, %options);
674    
675  Name to give to the menu. This is the name under which the value will  Restore the attribute keys and groups from a backup file.
 appear when the form is submitted.  
676    
677  =item newFlag (optional)  =over 4
678    
679  If TRUE, then extra rows will be provided to allow the user to select  =item fileName
 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.  
680    
681  =item noteControl (optional)  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  If specified, the name of a variable for displaying the notes attached  =back
 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.  
685    
686  =item typeControl (optional)  =cut
687    
688  If specified, the name of a variable for displaying the field's  sub RestoreKeys {
689  data type. Data types are a much more controlled vocabulary than      # Get the parameters.
690  notes, so there is no worry about HTML translation. Instead, the      my ($self, $fileName, %options) = @_;
691  raw value is put into the specified variable. Otherwise, the same      # Declare the return variable.
692  rules apply to this value that apply to I<$noteControl>.      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 RETURN  =head3 ArchiveFileName
745    
746  Returns the HTML to create a form field that can be used to select an      my $fileName = $ca->ArchiveFileName();
 attribute from the custom attributes system.  
747    
748  =back  Compute a file name for archiving attribute input data. The file will be in the attribute log directory
749    
750  =cut  =cut
751    
752  sub FieldMenu {  sub ArchiveFileName {
753      # Get the parameters.      # Get the parameters.
754      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self) = @_;
755      # These next two hashes make everything happen. "entities"      # Declare the return variable.
756      # maps each entity name to the list of values to be put into its      my $retVal;
757      # option group. "labels" maps each entity name to a map from values      # We start by turning the timestamp into something usable as a file name.
758      # to labels.      my $now = Tracer::Now();
759      my @entityNames = sort ($self->GetEntityTypes());      $now =~ tr/ :\//___/;
760      my %entities = map { $_ => [] } @entityNames;      # Next we get the directory name.
761      my %labels = map { $_ => { }} @entityNames;      my $dir = "$FIG_Config::var/attributes";
762      # Loop through the entities, adding the existing attributes.      if (! -e $dir) {
763      for my $entity (@entityNames) {          Trace("Creating attribute file directory $dir.") if T(1);
764          # Get this entity's field table.          mkdir $dir;
765          my $fieldHash = $self->GetFieldTable($entity);      }
766          # Get its field list in our local hashes.      # Put it together with the field name and the time stamp.
767          my $fieldList = $entities{$entity};      $retVal = "$dir/upload.$now";
768          my $labelList = $labels{$entity};      # Modify the file name to insure it's unique.
769          # Add the NEW fields if we want them.      my $seq = 0;
770          if ($newFlag) {      while (-e "$retVal.$seq.tbl") { $seq++ }
771              push @{$fieldList}, $entity;      # Use the computed sequence number to get the correct file name.
772              $labelList->{$entity} = "(new)";      $retVal .= ".$seq.tbl";
         }  
         # Loop through the fields in the hash. We only keep the ones with a  
         # secondary relation name. (In other words, the name of the relation  
         # in which the field appears cannot be the same as the entity name.)  
         for my $fieldName (sort keys %{$fieldHash}) {  
             if ($fieldHash->{$fieldName}->{relation} ne $entity) {  
                 my $value = "$entity/$fieldName";  
                 push @{$fieldList}, $value;  
                 $labelList->{$value} = $fieldName;  
             }  
         }  
     }  
     # Now we have a hash and a list for each entity, and they correspond  
     # exactly to what the $cgi->optgroup function expects.  
     # The last step is to create the name for the onChange function. This function  
     # 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 => [map { $cgi->optgroup(-name => $_,  
                                                                    -values => $entities{$_},  
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
     # Create the change function.  
     $retVal .= "\n<script language=\"javascript\">\n";  
     $retVal .= "    function $changeName(fieldValue) {\n";  
     # The function only has a body if we have a notes control to store the description.  
     if ($noteControl || $typeControl) {  
         # Check to see if we're storing HTML or text into the note control.  
         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";  
         # Loop through the entities.  
         for my $entity (@entityNames) {  
             # Get the entity's field hash. This has the notes in it.  
             my $fieldHash = $self->GetFieldTable($entity);  
             # Loop through the values we might see for this entity's fields.  
             my $fields = $entities{$entity};  
             for my $value (@{$fields}) {  
                 # Only proceed if we have an existing field.  
                 if ($value =~ m!/(.+)$!) {  
                     # Get the field's hash element.  
                     my $element = $fieldHash->{$1};  
                     # Generate this case.  
                     $retVal .= "        case \"$value\" :\n";  
                     # Here we either want to update the note display, the  
                     # type display, or both.  
                     if ($noteControl) {  
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
                         # Insure it's in the proper form.  
                         if ($htmlMode) {  
                             $notes = ERDB::HTMLNote($notes);  
                         }  
                         # Escape it for use as a string literal.  
                         $notes =~ s/\n/\\n/g;  
                         $notes =~ s/"/\\"/g;  
                         $retVal .= "           myText = \"$notes\";\n";  
                     }  
                     if ($typeControl) {  
                         # Here we want the type updated.  
                         my $type = $element->{type};  
                         $retVal .= "           myType = \"$type\";\n";  
                     }  
                     # Close this case.  
                     $retVal .= "           break;\n";  
                 }  
             }  
         }  
         # Close the CASE statement and make the appropriate assignments.  
         $retVal .= "        }\n";  
         if ($noteControl) {  
             $retVal .= "        $noteControl = myText;\n";  
         }  
         if ($typeControl) {  
             $retVal .= "        $typeControl = myType;\n";  
         }  
     }  
     # Terminate the change function.  
     $retVal .= "    }\n";  
     $retVal .= "</script>\n";  
773      # Return the result.      # Return the result.
774      return $retVal;      return $retVal;
775  }  }
776    
777  =head3 MatchSqlPattern  =head3 BackupAllAttributes
778    
779  C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>      my $stats = $attrDB->BackupAllAttributes($fileName, %options);
780    
781  Determine whether or not a specified value matches an SQL pattern. An SQL  Backup all of the attributes to a file. The attributes will be stored in a
782  pattern has two wild card characters: C<%> that matches multiple characters,  tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
 and C<_> that matches a single character. These can be escaped using a  
 backslash (C<\>). We pull this off by converting the SQL pattern to a  
 PERL regular expression. As per SQL rules, the match is case-insensitive.  
783    
784  =over 4  =over 4
785    
786  =item value  =item fileName
787    
788  Value to be matched against the pattern. Note that an undefined or empty  Name of the file to which the attribute data should be backed up.
 value will not match anything.  
789    
790  =item pattern  =item options
791    
792  SQL pattern against which to match the value. An undefined or empty pattern will  Hash of options for the backup.
 match everything.  
793    
794  =item RETURN  =item RETURN
795    
796  Returns TRUE if the value and pattern match, else FALSE.  Returns a statistics object describing the backup.
797    
798  =back  =back
799    
800    Currently there are no options defined.
801    
802  =cut  =cut
803    
804  sub MatchSqlPattern {  sub BackupAllAttributes {
805      # Get the parameters.      # Get the parameters.
806      my ($value, $pattern) = @_;      my ($self, $fileName, %options) = @_;
807      # Declare the return variable.      # Declare the return variable.
808      my $retVal;      my $retVal = Stats->new();
809      # Insure we have a pattern.      # Get a list of the keys.
810      if (! defined($pattern) || $pattern eq "") {      my %keys = map { $_->[0] => $_->[1] } $self->GetAll(['AttributeKey'],
811          $retVal = 1;                                                          "", [], ['AttributeKey(id)',
812      } else {                                                                    'AttributeKey(relationship-name)']);
813          # Break the pattern into pieces around the wildcard characters. Because we      Trace(scalar(keys %keys) . " keys found during backup.") if T(2);
814          # use parentheses in the split function's delimiter expression, we'll get      # Open the file for output.
815          # list elements for the delimiters as well as the rest of the string.      my $fh = Open(undef, ">$fileName");
816          my @pieces = split /([_%]|\\[_%])/, $pattern;      # Loop through the keys.
817          # Check some fast special cases.      for my $key (sort keys %keys) {
818          if ($pattern eq '%') {          Trace("Backing up attribute $key.") if T(3);
819              # A null pattern matches everything.          $retVal->Add(keys => 1);
820              $retVal = 1;          # Get the key's relevant relationship name.
821          } elsif (@pieces == 1) {          my $relName = $keys{$key};
822              # No wildcards, so we have a literal comparison. Note we're case-insensitive.          # Loop through this key's values.
823              $retVal = (lc($value) eq lc($pattern));          my $query = $self->Get([$relName], "$relName(from-link) = ?", [$key]);
824          } elsif (@pieces == 2 && $pieces[1] eq '%') {          my $valuesFound = 0;
825              # A wildcard at the end, so we have a substring match. This is also case-insensitive.          while (my $line = $query->Fetch()) {
826              $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));              $valuesFound++;
827          } else {              # Get this row's data.
828              # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.              my ($id, $key, $subKey, $value) = $line->Values(["$relName(to-link)",
829              my $realPattern = "";                                                               "$relName(from-link)",
830              for my $piece (@pieces) {                                                               "$relName(subkey)",
831                  # Determine the type of piece.                                                               "$relName(value)"]);
832                  if ($piece eq "") {              # Check for a subkey.
833                      # Empty pieces are ignored.              if ($subKey ne '') {
834                  } elsif ($piece eq "%") {                  $key = "$key$self->{splitter}$subKey";
                     # Here we have a multi-character wildcard. Note that it can match  
                     # zero or more characters.  
                     $realPattern .= ".*"  
                 } elsif ($piece eq "_") {  
                     # Here we have a single-character wildcard.  
                     $realPattern .= ".";  
                 } elsif ($piece eq "\\%" || $piece eq "\\_") {  
                     # This is an escape sequence (which is a rare thing, actually).  
                     $realPattern .= substr($piece, 1, 1);  
                 } else {  
                     # Here we have raw text.  
                     $realPattern .= quotemeta($piece);  
                 }  
835              }              }
836              # Do the match.              # Write it to the file.
837              $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);              Tracer::PutLine($fh, [$id, $key, Escape($value)]);
838          }          }
839            Trace("$valuesFound values backed up for key $key.") if T(3);
840            $retVal->Add(values => $valuesFound);
841      }      }
842        # Log the operation.
843        $self->LogOperation("Backup Data", $fileName, $retVal->Display());
844      # Return the result.      # Return the result.
845      return $retVal;      return $retVal;
846  }  }
847    
 =head3 MigrateAttributes  
848    
849  C<< CustomAttributes::MigrateAttributes($fig); >>  =head3 GetGroups
850    
851        my @groups = $attrDB->GetGroups();
852    
853    Return a list of the available groups.
854    
855    =cut
856    
857    sub GetGroups {
858        # Get the parameters.
859        my ($self) = @_;
860        # Get the groups.
861        my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
862        # Return them.
863        return @retVal;
864    }
865    
866    =head3 GetAttributeData
867    
868        my %keys = $attrDB->GetAttributeData($type, @list);
869    
870  Migrate all the attributes data from the specified FIG instance. This is a long, slow  Return attribute data for the selected attributes. The attribute
871  method used to convert the old attribute data to the new system. Only attribute  data is a hash mapping each attribute key name to a n-tuple containing the
872  keys that are not already in the database will be loaded, and only for entity instances  data type, the description, the table name, and the groups.
 current in the database. To get an accurate capture of the attributes in the given  
 instance, you may want to clear the database and the DBD before starting and  
 run L</Refresh> to populate the entities.  
873    
874  =over 4  =over 4
875    
876  =item fig  =item type
877    
878    Type of attribute criterion: C<name> for attributes whose names begin with the
879    specified string, or C<group> for attributes in the specified group.
880    
881    =item list
882    
883    List containing the names of the groups or keys for the desired attributes.
884    
885    =item RETURN
886    
887  A FIG object that can be used to retrieve attributes for migration purposes.  Returns a hash mapping each attribute key name to its description,
888    table name, and parent groups.
889    
890  =back  =back
891    
892  =cut  =cut
893    
894  sub MigrateAttributes {  sub GetAttributeData {
895      # Get the parameters.      # Get the parameters.
896      my ($fig) = @_;      my ($self, $type, @list) = @_;
897      # Get a list of the objects to migrate. This requires connecting. Note we      # Set up a hash to store the attribute data.
898      # will map each entity type to a file name. The file will contain a list      my %retVal = ();
899      # of the object's IDs so we can get to them when we're not connected to      # Loop through the list items.
900      # the database.      for my $item (@list) {
901      my $ca = CustomAttributes->new();          # Set up a query for the desired attributes.
902      my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();          my $query;
903      # Set up hash of the existing attribute keys for each entity type.          if ($type eq 'name') {
904      my %oldKeys = ();              # Here we're doing a generic name search. We need to escape it and then tack
905      # Finally, we have a hash that counts the IDs for each entity type.              # on a %.
906      my %idCounts = map { $_ => 0 } keys %objects;              my $parm = $item;
907      # Loop through the list, creating key files to read back in.              $parm =~ s/_/\\_/g;
908      for my $entityType (keys %objects) {              $parm =~ s/%/\\%/g;
909          Trace("Retrieving keys for $entityType.") if T(2);              $parm .= "%";
910          # Create the key file.              # Ask for matching attributes. (Note that if the user passed in a null string
911          my $idFile = Open(undef, ">$objects{$entityType}");              # he'll get everything.)
912          # Loop through the keys.              $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
913          my @ids = $ca->GetFlat([$entityType], "", [], "$entityType(id)");          } elsif ($type eq 'group') {
914          for my $id (@ids) {              $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
915              print $idFile "$id\n";          } else {
916          }              Confess("Unknown attribute query type \"$type\".");
917          close $idFile;          }
918          # In addition to the key file, we must get a list of attributes already          while (my $row = $query->Fetch()) {
919          # in the database. This avoids a circularity problem that might occur if the $fig              # Get this attribute's data.
920          # object is retrieving from the custom attributes database already.              my ($key, $relName, $notes) = $row->Values(['AttributeKey(id)',
921          my %fields = $ca->GetSecondaryFields($entityType);                                                       'AttributeKey(relationship-name)',
922          $oldKeys{$entityType} = \%fields;                                                       'AttributeKey(description)']);
923          # Finally, we have the ID count.              # If it's new, get its groups and add it to the return hash.
924          $idCounts{$entityType} = scalar @ids;              if (! exists $retVal{$key}) {
925      }                  my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
926      # Release the custom attributes database so we can add attributes.                                              [$key], 'IsInGroup(to-link)');
927      undef $ca;                  $retVal{$key} = [$relName, $notes, @groups];
     # Loop through the objects.  
     for my $entityType (keys %objects) {  
         # Get a hash of all the attributes already in this database. These are  
         # left untouched.  
         my $myOldKeys = $oldKeys{$entityType};  
         # Create a hash to control the load file names for each attribute key we find.  
         my %keyHash = ();  
         # Set up some counters so we can trace our progress.  
         my ($totalIDs, $processedIDs, $keyCount, $valueCount) = ($idCounts{$entityType}, 0, 0, 0);  
         # Open this object's ID file.  
         Trace("Migrating data for $entityType. $totalIDs found.") if T(3);  
         my $keysIn = Open(undef, "<$objects{$entityType}");  
         while (my $id = <$keysIn>) {  
             # Remove the EOL characters.  
             chomp $id;  
             # Get this object's attributes.  
             my @allData = $fig->get_attributes($id);  
             Trace(scalar(@allData) . " attribute values found for $entityType($id).") if T(4);  
             # Loop through the attribute values one at a time.  
             for my $dataTuple (@allData) {  
                 # Get the key, value, and URL. We ignore the first element because that's the  
                 # object ID, and we already know the object ID.  
                 my (undef, $key, $value, $url) = @{$dataTuple};  
                 # Only proceed if this is not an old key.  
                 if (! $myOldKeys->{$key}) {  
                     # See if we've run into this key before.  
                     if (! exists $keyHash{$key}) {  
                         # Here we need to create the attribute key in the database.  
                         StoreAttributeKey($entityType, $key, 'text',  
                                           "Key migrated automatically from the FIG system. " .  
                                           "Please replace these notes as soon as possible " .  
                                           "with useful text."  
                                          );  
                         # Compute the attribute's load file name and open it for output.  
                         my $fileName = "$FIG_Config::temp/$entityType.$key.load.tbl";  
                         my $fh = Open(undef, ">$fileName");  
                         # Store the file name and handle.  
                         $keyHash{$key} = {h => $fh, name => $fileName};  
                         # Count this key.  
                         $keyCount++;  
                     }  
                     # Smash the value and the URL together.  
                     if (defined($url) && length($url) > 0) {  
                         $value .= "::$url";  
                     }  
                     # Write the attribute value to the load file.  
                     Tracer::PutLine($keyHash{$key}->{h}, [$id, $value]);  
                     $valueCount++;  
                 }  
             }  
             # Now we've finished all the attributes for this object. Count and trace it.  
             $processedIDs++;  
             if ($processedIDs % 500 == 0) {  
                 Trace("$processedIDs of $totalIDs ${entityType}s processed.") if T(3);  
                 Trace("$entityType has $keyCount keys and $valueCount values so far.") if T(3);  
             }  
         }  
         # Now we've finished all the attributes for all objects of this type.  
         Trace("$processedIDs ${entityType}s processed, with $keyCount keys and $valueCount values.") if T(2);  
         # Loop through the files, loading the keys into the database.  
         Trace("Connecting to database.") if T(2);  
         my $objectCA = CustomAttributes->new();  
         Trace("Loading key files.") if T(2);  
         for my $key (sort keys %keyHash) {  
             # Close the key's load file.  
             close $keyHash{$key}->{h};  
             # Reopen it for input.  
             my $fileName = $keyHash{$key}->{name};  
             my $fh = Open(undef, "<$fileName");  
             Trace("Loading $key from $fileName.") if T(3);  
             my $stats = $objectCA->LoadAttributeKey($entityType, $key, $fh, 0, 1);  
             Trace("Statistics for $key of $entityType:\n" . $stats->Show()) if T(3);  
928          }          }
         # All the keys for this entity type are now loaded.  
         Trace("Key files loaded for $entityType.") if T(2);  
929      }      }
930      # All keys for all entity types are now loaded.      }
931      Trace("Migration complete.") if T(2);      # Return the result.
932        return %retVal;
933  }  }
934    
935  =head3 ComputeObjectTypeFromID  =head3 LogOperation
936    
937  C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>      $ca->LogOperation($action, $target, $description);
938    
939  This method will compute the entity type corresponding to a specified object ID.  Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
 If the object ID begins with C<fig|>, it is presumed to be a feature ID. If it  
 is all digits with a single period, it is presumed to by a genome ID. Otherwise,  
 it must be a list reference. In this last case the first list element will be  
 taken as the entity type and the second will be taken as the actual ID.  
940    
941  =over 4  =over 4
942    
943  =item objectID  =item action
944    
945  Object ID to examine.  Action being logged (e.g. C<Delete Group> or C<Load Key>).
946    
947  =item RETURN  =item target
948    
949    ID of the key or group affected.
950    
951    =item description
952    
953  Returns a 2-element list consisting of the entity type followed by the specified ID.  Short description of the action.
954    
955  =back  =back
956    
957  =cut  =cut
958    
959  sub ComputeObjectTypeFromID {  sub LogOperation {
960      # Get the parameters.      # Get the parameters.
961      my ($objectID) = @_;      my ($self, $action, $target, $description) = @_;
962      # Declare the return variables.      # Get the user ID.
963      my ($entityName, $id);      my $user = $self->{user};
964      # Only proceed if the object ID is defined. If it's not, we'll be returning a      # Get a timestamp.
965      # pair of undefs.      my $timeString = Tracer::Now();
966      if ($objectID) {      # Open the log file for appending.
967          if (ref $objectID eq 'ARRAY') {      my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
968              # Here we have the new-style list reference. Pull out its pieces.      # Write the data to it.
969              ($entityName, $id) = @{$objectID};      Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
970          } else {      # Close the log file.
971              # Here the ID is the outgoing ID, and we need to look at its structure      close $oh;
             # to determine the entity type.  
             $id = $objectID;  
             if ($objectID =~ /^\d+\.\d+/) {  
                 # Digits with a single period is a genome.  
                 $entityName = 'Genome';  
             } elsif ($objectID =~ /^fig\|/) {  
                 # The "fig|" prefix indicates a feature.  
                 $entityName = 'Feature';  
             } else {  
                 # Anything else is illegal!  
                 Confess("Invalid attribute ID specification \"$objectID\".");  
             }  
         }  
     }  
     # Return the result.  
     return ($entityName, $id);  
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.
977  Some of the old functionality is no longer present. Controlled vocabulary is no longer  Some of the old functionality is no longer present: controlled vocabulary is no longer
978  supported and there is no longer any searching by URL. Fortunately, neither of these  supported and there is no longer any searching by URL. Fortunately, neither of these
979  capabilities were used in the old system.  capabilities were used in the old system.
980    
# Line 942  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
992  splitter value would be stored as  splitter value would be stored as
993    
# Line 959  Line 998 
998    
999  =head3 GetAttributes  =head3 GetAttributes
1000    
1001  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>      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
1005  the attribute system as a whole, merely a convenience for the purpose of  the attribute system as a whole, merely a convenience for the purpose of
1006  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1007  object-based calls, the splitter will always be the default value of  is matched against the corresponding criterion in the I<@valuePatterns> list.
 double colons (C<::>). If a value has multiple sections, each section  
 is matched against the correspond criterion in the I<@valuePatterns> list.  
1008    
1009  This method returns a series of tuples that match the specified criteria. Each tuple  This method returns a series of tuples that match the specified criteria. Each tuple
1010  will contain an object ID, a key, and one or more values. The parameters to this  will contain an object ID, a key, and one or more values. The parameters to this
1011  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1012    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1013    of the parameters. So, for example,
1014    
1015      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1016    
1017  would return something like  would return something like
1018    
# Line 982  Line 1021 
1021      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1022      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1023    
1024  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1025  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1026  matches any sequence of characters, and C<_>, which matches any single character.  
1027  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1028  underscore.)  
1029    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1030    features.
1031    
1032  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1033  values, so even  values, so even
1034    
1035      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1036    
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  For reasons of backward compatability, we examine the structure of the object ID to  Value matching in this system works very poorly, because of the way multiple values are
1040  determine the entity type. In that case the only two types allowed are C<Genome> and  stored. For the object ID, key name, and first value, we create queries that filter for the
1041  C<Feature>. An alternative method is to use a list reference, with the list consisting  desired results. On any filtering by value, we must do a comparison after the attributes are
1042  of an entity type name and the actual ID. Thus, the above example could equivalently  retrieved from the database, since the database has no notion of the multiple values, which
1043  be written as  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.
     my @attributeList = GetAttributes([Feature => $peg], 'virulent');  
   
 The list-reference approach allows us to add attributes to other entity types in  
 the future. Doing so, however, will require modifying the L</Refresh> method and  
 updated the database design XML.  
   
 The list-reference approach also allows for a more fault-tolerant approach to  
 getting all objects with a particular attribute.  
   
     my @attributeList = GetAttributes([Feature => undef], 'virulent');  
   
 will only return feature attributes, while  
   
     my @attributeList = GetAttributes(undef, 'virulent');  
   
 could at some point in the future get you attributes for genomes or even subsystems  
 as well as features.  
1045    
1046  =over 4  =over 4
1047    
1048  =item objectID  =item objectID
1049    
1050  ID of the genome or feature whose attributes are desired. In general, an ID that  ID of object whose attributes are desired. If the attributes are desired for multiple
1051  starts with C<fig|> is treated as a feature ID, and an ID that is all digits with a  objects, this parameter can be specified as a list reference. If the attributes are
1052  single period is treated as a genome ID. For other entity types, use a list reference; in  desired for all objects, specify C<undef> or an empty string. Finally, you can specify
1053  this case the first list element is the entity type and the second is the ID. A value of  attributes for a range of object IDs by putting a percent sign (C<%>) at the end.
 C<undef> or an empty string here will match all objects.  
1054    
1055  =item key  =item key
1056    
1057  Attribute key name. Since attributes are stored as fields in the database with a  Attribute key name. A value of C<undef> or an empty string will match all
1058  field name equal to the key name, it is very fast to find a list of all the  attribute keys. If the values are desired for multiple keys, this parameter can be
1059  matching keys. Each key's values require a separate query, however, which may  specified as a list reference. Finally, you can specify attributes for a range of
1060  be a performance problem if the pattern matches a lot of keys. Wild cards are  keys by putting a percent sign (C<%>) at the end.
 acceptable here, and a value of C<undef> or an empty string will match all  
 attribute keys.  
1061    
1062  =item valuePatterns  =item values
1063    
1064  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1065  or an empty string is specified, all values in that section will match.  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.
1067    In that case, all values that match up to and not including the percent sign
1068    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 1056  Line 1082 
1082    
1083  sub GetAttributes {  sub GetAttributes {
1084      # Get the parameters.      # Get the parameters.
1085      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1086        # This hash will map value-table fields to patterns. We use it to build the
1087        # SQL statement.
1088        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, $subKey];
1161                }
1162            }
1163        }
1164      # Declare the return variable.      # Declare the return variable.
1165      my @retVal = ();      my @retVal = ();
1166      # Determine the entity types for our search.      # Now we loop through the tables of interest, performing queries.
1167      my @objects = ();      # Loop through the tables.
1168      my ($actualObjectID, $computedType);      for my $table (keys %tables) {
1169      if (! $objectID) {          # Get the key pairs for this table.
1170          push @objects, $self->GetEntityTypes();          my $pairs = $tables{$table};
1171      } else {          # Does this table have data? It does if there is no key specified or
1172          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);          # it has at least one key pair.
1173          push @objects, $computedType;          my $pairCount = scalar @{$pairs};
1174      }          Trace("Pair count for table $table is $pairCount.") if T(3);
1175      # Loop through the entity types.          if ($pairCount || ! $key) {
1176      for my $entityType (@objects) {              # Create some lists to contain the filter fragments and parameter values.
1177          # Now we need to find all the matching keys. The keys are actually stored in              my @filter = ();
1178          # our database object, so this process is fast. Note that our              my @parms = ();
1179          # MatchSqlPattern method              # This next loop goes through the different fields that can be specified in the
1180          my %secondaries = $self->GetSecondaryFields($entityType);              # parameter list and generates filters for each. The %data hash that we built above
1181          my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;              # contains most of the necessary information to do this. When we're done, we'll
1182          # Now we figure out whether or not we need to filter by object.              # paste on stuff for the key pairs.
1183          my $filter = "";              for my $field (keys %data) {
1184          my @params = ();                  # Accumulate filter information for this field. We will OR together all the
1185          if (defined($actualObjectID)) {                  # elements accumulated to create the final result.
1186              # Here the caller wants to filter on object ID.                  my @fieldFilter = ();
1187              $filter = "$entityType(id) = ?";                  # Get the specified filter for this field.
1188              push @params, $actualObjectID;                  my $fieldPattern = $data{$field};
1189          }                  # Only proceed if the pattern is one that won't match everything.
1190          # It's time to begin making queries. We process one attribute key at a time, because                  if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1191          # each attribute is actually a different field in the database. We know here that                      # Convert the pattern to an array.
1192          # all the keys we've collected are for the correct entity because we got them from                      my @patterns = ();
1193          # the DBD. That's a good thing, because an invalid key name will cause an SQL error.                      if (ref $fieldPattern eq 'ARRAY') {
1194          for my $key (@fieldList) {                          push @patterns, @{$fieldPattern};
1195              # Get all of the attribute values for this key.                      } else {
1196              my @dataRows = $self->GetAll([$entityType], $filter, \@params,                          push @patterns, $fieldPattern;
1197                                           ["$entityType(id)", "$entityType($key)"]);                      }
1198              # Process each value separately. We need to verify the values and reformat the                      # Only proceed if the array is nonempty. The loop will work fine if the
1199              # tuples. Note that GetAll will give us one row per matching object ID,                      # array is empty, but when we build the filter string at the end we'll
1200              # with the ID first followed by a list of the data values. This is very                      # get "()" in the filter list, which will result in an SQL syntax error.
1201              # different from the structure we'll be returning, which has one row                      if (@patterns) {
1202              # per value.                          # Loop through the individual patterns.
1203              for my $dataRow (@dataRows) {                          for my $pattern (@patterns) {
1204                  # Get the object ID and the list of values.                              my ($clause, $value) = _WherePart($table, $field, $pattern);
1205                  my ($rowObjectID, @dataValues) = @{$dataRow};                              push @fieldFilter, $clause;
1206                  # Loop through the values. There will be one result row per attribute value.                              push @parms, $value;
1207                  for my $dataValue (@dataValues) {                          }
1208                      # Separate this value into sections.                          # Form the filter for this field.
1209                      my @sections = split("::", $dataValue);                          my $fieldFilterString = join(" OR ", @fieldFilter);
1210                      # Loop through the value patterns, looking for a mismatch. Note that                          push @filter, "($fieldFilterString)";
1211                      # since we're working through parallel arrays, we are using an index                      }
                     # loop. As soon as a match fails we stop checking. This means that  
                     # if the value pattern list is longer than the number of sections,  
                     # we will fail as soon as we run out of sections.  
                     my $match = 1;  
                     for (my $i = 0; $i <= $#valuePatterns && $match; $i++) {  
                         $match = MatchSqlPattern($sections[$i], $valuePatterns[$i]);  
                     }  
                     # If we match, we save this value in the output list.  
                     if ($match) {  
                         push @retVal, [$rowObjectID, $key, @sections];  
                     }  
                 }  
                 # Here we've processed all the attribute values for the current object ID.  
1212              }              }
             # Here we've processed all the rows returned by GetAll. In general, there will  
             # be one row per object ID.  
1213          }          }
1214          # Here we've processed all the matching attribute keys.              # The final filter is for the key pairs. Only proceed if we have some.
1215                if ($pairCount) {
1216                    # We'll accumulate pair filter clauses in here.
1217                    my @pairFilters = ();
1218                    # Loop through the key pairs.
1219                    for my $pair (@$pairs) {
1220                        my ($realKey, $subKey) = @{$pair};
1221                        my ($realClause, $realValue) = _WherePart($table, 'from-link', $realKey);
1222                        if (! $subKey) {
1223                            # Here the subkey is wild, so only the real key matters.
1224                            push @pairFilters, $realClause;
1225                            push @parms, $realValue;
1226                        } else {
1227                            # Here we have to select on both keys.
1228                            my ($subClause, $subValue) = _WherePart($table, 'subkey', $subKey);
1229                            push @pairFilters, "($realClause AND $subClause)";
1230                            push @parms, $subValue;
1231                        }
1232                    }
1233                    # Join the pair filters together to make a giant key filter.
1234                    my $pairFilter = "(" . join(" OR ", @pairFilters) . ")";
1235                    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      # Here we've processed all the entity types. That means @retVal has all the matching      # The above loop ran the query for each necessary value table and merged the
1247      # results.      # 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 1140  Line 1259 
1259    
1260  =item objectID  =item objectID
1261    
1262  ID of the genome or feature to which the attribute is to be added. In general, an ID that  ID of the object to which the attribute is to be added.
 starts with C<fig|> is treated as a feature ID, and an ID that is all digits and periods  
 is treated as a genome ID. For IDs of other types, this parameter should be a reference  
 to a 2-tuple consisting of the entity type name followed by the object ID.  
1263    
1264  =item key  =item key
1265    
1266  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1267    
1268  =item values  =item values
1269    
# Line 1170  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 $key.");
1288      } else {      } else {
1289          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1290          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1291          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1292          # Insert the value.          # Split up the key.
1293          $self->InsertValue($id, "$entityName($key)", $valueString);          my ($realKey, $subKey) = $self->SplitKey($key);
1294            # Find the table containing the key.
1295            my $table = $self->_KeyTable($realKey);
1296            # Connect the object to the key.
1297            $self->InsertObject($table, { 'from-link' => $realKey,
1298                                                 'to-link'   => $objectID,
1299                                                 'subkey'    => $subKey,
1300                                                 'value'     => $valueString,
1301                                           });
1302      }      }
1303      # Return a one. 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    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1313  =over 4  =over 4
1314    
1315  =item objectID  =item objectID
1316    
1317  ID of the genome or feature to which the attribute is to be added. In general, an ID that  ID of the object whose attribute is to be deleted.
 starts with C<fig|> is treated as a feature ID, and an ID that is all digits and periods  
 is treated as a genome ID. For IDs of other types, this parameter should be a reference  
 to a 2-tuple consisting of the entity type name followed by the object ID.  
1318    
1319  =item key  =item key
1320    
1321  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1322    
1323  =item values  =item values
1324    
1325  One or more values to be associated with the key.  One or more values associated with the key. If no values are specified, then all values
1326    will be deleted. Otherwise, only a matching value will be deleted.
1327    
1328  =back  =back
1329    
# Line 1220  Line 1337 
1337          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1338      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1339          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
     } elsif (! @values) {  
         Confess("No values specified in DeleteAttribute call for key $key.");  
1340      } else {      } else {
1341          # Now compute the object type and ID.          # Split the key into the real key and the subkey.
1342          my ($entityName, $id) = ComputeObjectTypeFromID($objectID);          my ($realKey, $subKey) = $self->SplitKey($key);
1343          # Form the values into a scalar.          # Find the table containing the key's values.
1344            my $table = $self->_KeyTable($realKey);
1345            if ($subKey eq '' && scalar(@values) == 0) {
1346                # Here we erase the entire key for this object.
1347                $self->DeleteRow('HasValueFor', $key, $objectID);
1348            } else {
1349                # Here we erase the matching values.
1350          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1351          # Delete the value.              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1352          $self->DeleteValue($entityName, $id, $key, $valueString);                               { 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, $key, \@oldValues, \@newValues);
1422    
1423  Change the value of an attribute key/value pair for an object.  Change the value of an attribute key/value pair for an object.
1424    
# Line 1278  Line 1460 
1460      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1461          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1462      } else {      } else {
1463          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1464          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1465          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1466      }      }
# Line 1286  Line 1468 
1468      return 1;      return 1;
1469  }  }
1470    
1471    =head3 EraseAttribute
1472    
1473        $attrDB->EraseAttribute($key);
1474    
1475    Erase all values for the specified attribute key. This does not remove the
1476    key from the database; it merely removes all the values.
1477    
1478    =over 4
1479    
1480    =item key
1481    
1482    Key to erase. This must be a real key; that is, it cannot have a subkey
1483    component.
1484    
1485    =back
1486    
1487    =cut
1488    
1489    sub EraseAttribute {
1490        # Get the parameters.
1491        my ($self, $key) = @_;
1492        # Find the table containing the key.
1493        my $table = $self->_KeyTable($key);
1494        # 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.
1506        return 1;
1507    }
1508    
1509    =head3 GetAttributeKeys
1510    
1511        my @keyList = $attrDB->GetAttributeKeys($groupName);
1512    
1513    Return a list of the attribute keys for a particular group.
1514    
1515    =over 4
1516    
1517    =item groupName
1518    
1519    Name of the group whose keys are desired.
1520    
1521    =item RETURN
1522    
1523    Returns a list of the attribute keys for the specified group.
1524    
1525    =back
1526    
1527    =cut
1528    
1529    sub GetAttributeKeys {
1530        # Get the parameters.
1531        my ($self, $groupName) = @_;
1532        # Get the attributes for the specified group.
1533        my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1534                                    'IsInGroup(from-link)');
1535        # Return the keys.
1536        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        # Get the number of value sections we have to match.
1983        my $sectionCount = scalar(@values);
1984        # Loop through the assignments found.
1985        while (my $row = $query->Fetch()) {
1986            # Get the current row's data.
1987            my ($id, $realKey, $subKey, $valueString) = $row->Values(["$table(to-link)",
1988                                                                      "$table(from-link)",
1989                                                                      "$table(subkey)",
1990                                                                      "$table(value)"
1991                                                                    ]);
1992            # Form the key from the real key and the sub key.
1993            my $key = $self->JoinKey($realKey, $subKey);
1994            # Break the value into sections.
1995            my @sections = split($self->{splitter}, $valueString);
1996            # Match each section against the incoming values. We'll assume we're
1997            # okay unless we learn otherwise.
1998            my $matching = 1;
1999            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
2000                # We need to check to see if this section is generic.
2001                my $value = $values[$i];
2002                Trace("Current value pattern is \"$value\".") if T(4);
2003                if ($value =~ m#^/(.+)/[a-z]*$#) {
2004                    Trace("Regular expression detected.") if T(4);
2005                    # Here we have a regular expression match.
2006                    my $section = $sections[$i];
2007                    $matching = eval("\$section =~ $value");
2008                } else {
2009                    # Here we have a normal match.
2010                    Trace("SQL match used.") if T(4);
2011                    $matching = _CheckSQLPattern($values[$i], $sections[$i]);
2012                }
2013            }
2014            # If we match, output this row to the return list.
2015            if ($matching) {
2016                push @retVal, [$id, $key, @sections];
2017            }
2018        }
2019        # Return the rows found.
2020        return @retVal;
2021    }
2022    
2023    
2024    =head3 _LoadAttributeTable
2025    
2026        $attr->_LoadAttributeTable($tableName, $fileName, $stats, $mode);
2027    
2028    Load a file's data into an attribute table. This is an internal method
2029    provided for the convenience of L</LoadAttributesFrom>. It loads the
2030    specified file into the specified table and updates the statistics
2031    object.
2032    
2033    =over 4
2034    
2035    =item tableName
2036    
2037    Name of the table being loaded. This is usually C<HasValueFor>, but may
2038    be a different table for some specific attribute keys.
2039    
2040    =item fileName
2041    
2042    Name of the file containing a chunk of attribute data to load.
2043    
2044    =item stats
2045    
2046    Statistics object into which counts and times should be placed.
2047    
2048    =item mode
2049    
2050    Load mode for the file, usually C<low_priority>, C<concurrent>, or
2051    an empty string. The mode is used by some applications to control access
2052    to the table while it's being loaded. The default (empty string) is to lock the
2053    table until all the data's in place.
2054    
2055    =back
2056    
2057    =cut
2058    
2059    sub _LoadAttributeTable {
2060        # Get the parameters.
2061        my ($self, $tableName, $fileName, $stats, $mode) = @_;
2062        # Load the table from the file. Note that we don't do an analyze.
2063        # The analyze is done only after everything is complete.
2064        my $startTime = time();
2065        Trace("Loading attributes from $fileName: " . (-s $fileName) .
2066              " characters.") if T(3);
2067        my $loadStats = $self->LoadTable($fileName, $tableName,
2068                                         mode => $mode, partial => 1);
2069        # Record the load time.
2070        $stats->Add(insertTime => time() - $startTime);
2071        # Roll up the other statistics.
2072        $stats->Accumulate($loadStats);
2073    }
2074    
2075    
2076    =head3 _GetAllTables
2077    
2078        my @tables = $ca->_GetAllTables();
2079    
2080    Return a list of the names of all the tables used to store attribute
2081    values.
2082    
2083    =cut
2084    
2085    sub _GetAllTables {
2086        # Get the parameters.
2087        my ($self) = @_;
2088        # Start with the default table.
2089        my @retVal = $self->{defaultRel};
2090        # Add the tables named in the key hash. These tables are automatically
2091        # NOT the default, and each can only occur once, because alternate tables
2092        # are allocated on a per-key basis.
2093        my $keyHash = $self->_KeyTable();
2094        push @retVal, values %$keyHash;
2095        # Return the result.
2096        return @retVal;
2097    }
2098    
2099    
2100    =head3 _SplitKeyPattern
2101    
2102        my ($realKey, $subKey) = $ca->_SplitKeyPattern($keyChoice);
2103    
2104    Split a key pattern into the main part (the I<real key>) and a sub-part
2105    (the I<sub key>). This method differs from L</SplitKey> in that it treats
2106    the key as an SQL pattern instead of a raw string. Also, if there is no
2107    incoming sub-part, the sub-key will be undefined instead of an empty
2108    string.
2109    
2110    =over 4
2111    
2112    =item keyChoice
2113    
2114    SQL key pattern to be examined. This can either be a literal, an SQL pattern,
2115    a literal with an internal splitter code (usually C<::>) or an SQL pattern with
2116    an internal splitter. Note that the only SQL pattern we support is a percent
2117    sign (C<%>) at the end. This is the way we've declared things in the documentation,
2118    so users who try anything else will have problems.
2119    
2120    =item RETURN
2121    
2122    Returns a two-element list. The first element is the SQL pattern for the
2123    real key and the second is the SQL pattern for the sub-key. If the value
2124    for either one does not matter (e.g., the user wants a real key value of
2125    C<iedb> and doesn't care about the sub-key value), it will be undefined.
2126    
2127    =back
2128    
2129    =cut
2130    
2131    sub _SplitKeyPattern {
2132        # Get the parameters.
2133        my ($self, $keyChoice) = @_;
2134        # Declare the return variables.
2135        my ($realKey, $subKey);
2136        # Look for a splitter in the input.
2137        if ($keyChoice =~ /^(.*?)$self->{splitter}(.*)/) {
2138            # We found one. This means we can treat both sides of the
2139            # splitter as known patterns.
2140            ($realKey, $subKey) = ($1, $2);
2141        } elsif ($keyChoice =~ /%$/) {
2142            # Here we have a generic pattern for the whole key. The pattern
2143            # is treated as the correct pattern for the real key, but the
2144            # sub-key is considered to be wild.
2145            $realKey = $keyChoice;
2146        } else {
2147            # Here we have a literal pattern for the whole key. The pattern
2148            # is treated as the correct pattern for the real key, and the
2149            # sub-key is required to be blank.
2150            $realKey = $keyChoice;
2151            $subKey = '';
2152        }
2153        # Return the results.
2154        return ($realKey, $subKey);
2155    }
2156    
2157    
2158    =head3 _WherePart
2159    
2160        my ($sqlClause, $escapedValue) = _WherePart($tableName, $fieldName, $sqlPattern);
2161    
2162    Return the SQL clause and value for checking a field against the
2163    specified SQL pattern value. If the pattern is generic (ends in a C<%>),
2164    then a C<LIKE> expression is returned. Otherwise, an equality expression
2165    is returned. We take in information describing the field being checked,
2166    and the pattern we're checking against it. The output is a WHERE clause
2167    fragment for the comparison and a value to be used as a bound parameter
2168    value for the clause.
2169    
2170    =over 4
2171    
2172    =item tableName
2173    
2174    Name of the table containing the field we want checked by the clause.
2175    
2176    =item fieldName
2177    
2178    Name of the field to check in that table.
2179    
2180    =item sqlPattern
2181    
2182    Pattern to be compared against the field. If the last character is a percent sign
2183    (C<%>), it will be treated as a generic SQL pattern; otherwise, it will be treated
2184    as a literal.
2185    
2186    =item RETURN
2187    
2188    Returns a two-element list. The first element will be an SQL comparison expression
2189    and the second will be the value to be used as a bound parameter for the expression
2190    in order to
2191    
2192    =back
2193    
2194    =cut
2195    
2196    sub _WherePart {
2197        # Get the parameters.
2198        my ($tableName, $fieldName, $sqlPattern) = @_;
2199        # Declare the return variables.
2200        my ($sqlClause, $escapedValue);
2201        # Copy the pattern into the return area.
2202        $escapedValue = $sqlPattern;
2203        # Check the pattern. Is it generic or exact?
2204        if ($sqlPattern =~ /%$/) {
2205            # Yes, it is. We need a LIKE clause and we must escape the underscores
2206            # and percents in the pattern.
2207            $escapedValue =~ s/(%|_)/\\$1/g;
2208            $sqlClause = "$tableName($fieldName) LIKE ?";
2209        } else {
2210            # No, it isn't. We use an equality clause.
2211            $sqlClause = "$tableName($fieldName) = ?";
2212        }
2213        # Return the results.
2214        return ($sqlClause, $escapedValue);
2215    }
2216    
2217    
2218    =head3 _CheckSQLPattern
2219    
2220        my $flag = _CheckSQLPattern($pattern, $value);
2221    
2222    Return TRUE if the specified SQL pattern matches the specified value,
2223    else FALSE. The pattern is not a true full-blown SQL LIKE pattern: the
2224    only wild-carding allowed is a percent sign (C<%>) at the end.
2225    
2226    =over 4
2227    
2228    =item pattern
2229    
2230    SQL pattern to match against a value.
2231    
2232    =item value
2233    
2234    Value to match against an SQL pattern.
2235    
2236    =item RETURN
2237    
2238    Returns TRUE if the pattern matches the value, else FALSE.
2239    
2240    =back
2241    
2242    =cut
2243    
2244    sub _CheckSQLPattern {
2245        # Get the parameters.
2246        my ($pattern, $value) = @_;
2247        # Declare the return variable.
2248        my $retVal;
2249        # Check for a generic pattern.
2250        if ($pattern =~ /(.*)%$/) {
2251            # Here we have one. Do a substring match.
2252            $retVal = (substr($value, 0, length $1) eq $1);
2253        } else {
2254            # Here it's an exact match.
2255            $retVal = ($pattern eq $value);
2256        }
2257        # Return the result.
2258        return $retVal;
2259    }
2260    
2261  1;  1;

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