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revision 1.9, Thu Nov 16 22:09:33 2006 UTC revision 1.28, Sun Sep 30 20:52:51 2007 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    
14  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
15    
# Line 15  Line 17 
17    
18  The Custom SEED Attributes Manager allows the user to upload and retrieve  The Custom SEED Attributes Manager allows the user to upload and retrieve
19  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
20  store the attributes, which are implemented as multi-valued fields  store the attributes.
21  of ERDB entities.  
22    Attributes are organized by I<attribute key>. Attribute values are
23    assigned to I<objects>. In the real world, objects have types and IDs;
24    however, to the attribute database only the ID matters. This will create
25    a problem if we have a single ID that applies to two objects of different
26    types, but it is more consistent with the original attribute implementation
27    in the SEED (which this implementation replaces).
28    
29    The actual attribute values are stored as a relationship between the attribute
30    keys and the objects. There can be multiple values for a single key/object pair.
31    
32    =head3 Object IDs
33    
34    The object ID is normally represented as
35    
36        I<type>:I<id>
37    
38    where I<type> is the object type (C<Role>, C<Coupling>, etc.) and I<id> is
39    the actual object ID. Note that the object type must consist of only upper- and
40    lower-case letters! Thus, C<GenomeGroup> is a valid object type, but
41    C<genome_group> is not. Given that restriction, the object ID
42    
43        Family:aclame|cluster10
44    
45    would represent the FIG family C<aclame|cluster10>. For historical reasons,
46    there are three exceptions: subsystems, genomes, and features do not need
47    a type. So, for PEG 3361 of Streptomyces coelicolor A3(2), you simply code
48    
49        fig|100226.1.peg.3361
50    
51    The methods L</ParseID> and L</FormID> can be used to make this all seem
52    more consistent. Given any object ID string, L</ParseID> will convert it to an
53    object type and ID, and given any object type and ID, L</FormID> will
54    convert it to an object ID string. The attribute database is pretty
55    freewheeling about what it will allow for an ID; however, for best
56    results, the type should match an entity type from a Sprout genetics
57    database. If this rule is followed, then the database object
58    corresponding to an ID in the attribute database could be retrieved using
59    L</GetTargetObject> method.
60    
61        my $object = CustomAttributes::GetTargetObject($sprout, $idValue);
62    
63    =head3 Retrieval and Logging
64    
65  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
66  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
67  the values of the attribute C<essential> in a specified B<Feature>, you  the values of the attribute C<essential> in a specified B<Feature>, you
68  would code  would code
69    
70      my @values = $attrDB->GetAttributes([Feature => $fid], 'essential');      my @values = $attrDB->GetAttributes($fid, 'essential');
71    
72  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.  
73    
74  New attributes are introduced by updating the database definition at  Keys can be split into two pieces using the splitter value defined in the
75  run-time. Attribute values are stored by uploading data from files.  constructor (the default is C<::>). The first piece of the key is called
76  A web interface is provided for both these activities.  the I<real key>. This portion of the key must be defined using the
77    web interface (C<Attributes.cgi>). The second portion of the key is called
78    the I<sub key>, and can take any value.
79    
80    Major attribute activity is recorded in a log (C<attributes.log>) in the
81    C<$FIG_Config::var> directory. The log reports the user name, time, and
82    the details of the operation. The user name will almost always be unknown,
83    the exception being when it is specified in this object's constructor
84    (see L</new>).
85    
86  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
87    
# Line 76  Line 127 
127    
128  =back  =back
129    
 The DBD file is critical, and must have reasonable contents before we can  
 begin using the system. In the old system, attributes were only provided  
 for Genomes and Features, so the initial XML file was the following.  
   
     <Database>  
       <Title>SEED Custom Attribute Database</Title>  
       <Entities>  
         <Entity name="Feature" keyType="id-string">  
           <Notes>A [i]feature[/i] is a part of the genome  
           that is of special interest. Features may be spread  
           across multiple contigs of a genome, but never across  
           more than one genome. Features can be assigned to roles  
           via spreadsheet cells, and are the targets of  
           annotation.</Notes>  
         </Entity>  
         <Entity name="Genome" keyType="name-string">  
           <Notes>A [i]genome[/i] describes a particular individual  
           organism's DNA.</Notes>  
         </Entity>  
       </Entities>  
     </Database>  
   
 It is not necessary to put any tables into the database; however, you should  
 run  
   
     AttrDBRefresh  
   
 periodically to insure it has the correct Genomes and Features in it. When  
 converting from the old system, use  
   
     AttrDBRefresh -migrate  
   
 to initialize the database and migrate the legacy data. You should only need  
 to do that once.  
   
 =head2 Implementation Note  
   
 The L</Refresh> method reloads the entities in the database. If new  
 entity types are added, that method will need to be adjusted accordingly.  
   
130  =head2 Public Methods  =head2 Public Methods
131    
132  =head3 new  =head3 new
133    
134  C<< my $attrDB = CustomAttributes->new($splitter); >>  C<< my $attrDB = CustomAttributes->new(%options); >>
135    
136  Construct a new CustomAttributes object. This object cannot be used to add or  Construct a new CustomAttributes object. The following options are
137  delete keys because that requires modifying the database design. To do that,  supported.
 you need to use the static L</StoreAttributeKey> or L</DeleteAttributeKey>  
 methods.  
138    
139  =over 4  =over 4
140    
141  =item splitter  =item splitter
142    
143  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
144  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
145  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
146  worry about this parameter.  
147    =item user
148    
149    Name of the current user. This will appear in the attribute log.
150    
151  =back  =back
152    
# Line 142  Line 154 
154    
155  sub new {  sub new {
156      # Get the parameters.      # Get the parameters.
157      my ($class, $splitter) = @_;      my ($class, %options) = @_;
158      # Connect to the database.      # Connect to the database.
159      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
160                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 152  Line 164 
164      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
165      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
166      # Store the splitter value.      # Store the splitter value.
167      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
168        # Store the user name.
169        $retVal->{user} = $options{user} || '<unknown>';
170        Trace("User $retVal->{user} selected for attribute object.") if T(3);
171      # Return the result.      # Return the result.
172      return $retVal;      return $retVal;
173  }  }
174    
175  =head3 StoreAttributeKey  =head3 StoreAttributeKey
176    
177  C<< my $attrDB = CustomAttributes::StoreAttributeKey($entityName, $attributeName, $type, $notes); >>  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>
178    
179  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.  
180    
181  =over 4  =over 4
182    
 =item entityName  
   
 Name of the entity containing the attribute. The entity must exist.  
   
183  =item attributeName  =item attributeName
184    
185  Name of the attribute. It must be a valid ERDB field name, consisting entirely of  Name of the attribute (the real key). If it does not exist already, it will be created.
 letters, digits, and hyphens, with a letter at the beginning. If it does not  
 exist already, it will be created.  
186    
187  =item type  =item type
188    
# Line 185  Line 192 
192    
193  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.
194    
195  =item RETURN  =item groups
196    
197  Returns a Custom Attribute Database object if successful. If unsuccessful, an  Reference to a list of the groups to which the attribute should be associated.
198  error will be thrown.  This will replace any groups to which the attribute is currently attached.
199    
200  =back  =back
201    
# Line 196  Line 203 
203    
204  sub StoreAttributeKey {  sub StoreAttributeKey {
205      # Get the parameters.      # Get the parameters.
206      my ($entityName, $attributeName, $type, $notes) = @_;      my ($self, $attributeName, $type, $notes, $groups) = @_;
207      # Declare the return variable.      # Declare the return variable.
208      my $retVal;      my $retVal;
209      # Get the data type hash.      # Get the data type hash.
210      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
211      # Validate the initial input values.      # Validate the initial input values.
212      if (! ERDB::ValidateFieldName($attributeName)) {      if ($attributeName =~ /$self->{splitter}/) {
213          Confess("Invalid attribute name \"$attributeName\" specified.");          Confess("Invalid attribute name \"$attributeName\" specified.");
214      } elsif (! $notes || length($notes) < 25) {      } elsif (! $notes || length($notes) < 25) {
215          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing or incomplete description for $attributeName.");
216      } elsif (! exists $types{$type}) {      } elsif (! exists $types{$type}) {
217          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid data type \"$type\" for $attributeName.");
218        } else {
219            # Create a variable to hold the action to be displayed for the log (Add or Update).
220            my $action;
221            # Okay, we're ready to begin. See if this key exists.
222            my $attribute = $self->GetEntity('AttributeKey', $attributeName);
223            if (defined($attribute)) {
224                # It does, so we do an update.
225                $action = "Update Key";
226                $self->UpdateEntity('AttributeKey', $attributeName,
227                                    { description => $notes, 'data-type' => $type });
228                # Detach the key from its current groups.
229                $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
230            } else {
231                # It doesn't, so we do an insert.
232                $action = "Insert Key";
233                $self->InsertObject('AttributeKey', { id => $attributeName,
234                                    description => $notes, 'data-type' => $type });
235            }
236            # Attach the key to the specified groups. (We presume the groups already
237            # exist.)
238            for my $group (@{$groups}) {
239                $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
240                                                   'to-link'   => $group });
241      }      }
242      # Our next step is to read in the XML for the database defintion. We          # Log the operation.
243      # need to verify that the named entity exists.          $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
     my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);  
     my $entityHash = $metadata->{Entities};  
     if (! exists $entityHash->{$entityName}) {  
         Confess("Entity $entityName not found.");  
     } else {  
         # Okay, we're ready to begin. Get the entity hash and the field hash.  
         my $entityData = $entityHash->{$entityName};  
         my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);  
         # Compare the old attribute data to the new data.  
         my $bigChange = 1;  
         if (exists $fieldHash->{$attributeName} && $fieldHash->{$attributeName}->{type} eq $type) {  
             $bigChange = 0;  
         }  
         # Compute the attribute's relation name.  
         my $relName = join("", $entityName, map { ucfirst $_ } split(/-|_/, $attributeName));  
         # Store the attribute's field data. Note the use of the "content" hash for  
         # the notes. This is how the XML writer knows Notes is a text tag instead of  
         # an attribute.  
         $fieldHash->{$attributeName} = { type => $type, relation => $relName,  
                                          Notes => { content => $notes } };  
         # Insure we have an index for this attribute.  
         my $index = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);  
         if (! defined($index)) {  
             push @{$entityData->{Indexes}}, { IndexFields => [ { name => $attributeName, order => 'ascending' } ],  
                                               Notes       => "Alternate index provided for access by $attributeName." };  
         }  
         # Write the XML back out.  
         ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);  
         # Open a database with the new XML.  
         $retVal = CustomAttributes->new();  
         # Create the table if there has been a significant change.  
         if ($bigChange) {  
             $retVal->CreateTable($relName);  
         }  
244      }      }
     return $retVal;  
245  }  }
246    
 =head3 Refresh  
247    
248  C<< $attrDB->Refresh($fig); >>  =head3 DeleteAttributeKey
249    
250    C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
251    
252  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.  
253    
254  =over 4  =over 4
255    
256  =item fig  =item attributeName
257    
258    Name of the attribute to delete.
259    
260    =item RETURN
261    
262  FIG-like object that can be used to find genomes and features.  Returns a statistics object describing the effects of the deletion.
263    
264  =back  =back
265    
266  =cut  =cut
267    
268  sub Refresh {  sub DeleteAttributeKey {
269      # Get the parameters.      # Get the parameters.
270      my ($self, $fig) = @_;      my ($self, $attributeName) = @_;
271      # Create load objects for the genomes and the features.      # Delete the attribute key.
272      my $loadGenome = ERDBLoad->new($self, 'Genome', $FIG_Config::temp);      my $retVal = $self->Delete('AttributeKey', $attributeName);
273      my $loadFeature = ERDBLoad->new($self, 'Feature', $FIG_Config::temp);      # Log this operation.
274      # Get the genome list.      $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
275      my @genomes = $fig->genomes();      # Return the result.
276      # Loop through the genomes.      return $retVal;
277      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);  
         }  
278      }      }
279      # Get a variable for holding statistics objects.  
280      my $stats;  =head3 NewName
281      # Finish the genome load.  
282      Trace("Loading Genome relation.") if T(2);  C<< my $text = CustomAttributes::NewName(); >>
283      $stats = $loadGenome->FinishAndLoad();  
284      Trace("Genome table load statistics:\n" . $stats->Show()) if T(3);  Return the string used to indicate the user wants to add a new attribute.
285      # Finish the feature load.  
286      Trace("Loading Feature relation.") if T(2);  =cut
287      $stats = $loadFeature->FinishAndLoad();  
288      Trace("Feature table load statistics:\n" . $stats->Show()) if T(3);  sub NewName {
289        return "(new)";
290  }  }
291    
292  =head3 LoadAttributeKey  =head3 ControlForm
293    
294  C<< my $stats = $attrDB->LoadAttributeKey($entityName, $fieldName, $fh, $keyCol, $dataCol); >>  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
295    
296  Load the specified attribute from the specified file. The file should be a  Return a form that can be used to control the creation and modification of
297  tab-delimited file with internal tab and new-line characters escaped. This is  attributes. Only a subset of the attribute keys will be displayed, as
298  the typical TBL-style file used by most FIG applications. One of the columns  determined by the incoming list.
 in the input file must contain the appropriate key value and the other the  
 corresponding attribute value.  
299    
300  =over 4  =over 4
301    
302  =item entityName  =item cgi
303    
304    CGI query object used to create HTML.
305    
306    =item name
307    
308    Name to give to the form. This should be unique for the web page.
309    
310    =item keys
311    
312    Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
313    attribute's data type, its description, and a list of the groups in which it participates.
314    
315    =item RETURN
316    
317    Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script
318    for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
319    controls are generated. The form tags are left to the caller.
320    
321    =back
322    
323  Name of the entity containing the attribute.  =cut
324    
325  =item fieldName  sub ControlForm {
326        # Get the parameters.
327        my ($self, $cgi, $name, $keys) = @_;
328        # Declare the return list.
329        my @retVal = ();
330        # We'll put the controls in a table. Nothing else ever seems to look nice.
331        push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
332        # The first row is for selecting the field name.
333        push @retVal, $cgi->Tr($cgi->th("Select a Field"),
334                               $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
335                                                         new => 1,
336                                                         notes => "document.$name.notes.value",
337                                                         type => "document.$name.dataType.value",
338                                                         groups => "document.$name.groups")));
339        # Now we set up a dropdown for the data types. The values will be the
340        # data type names, and the labels will be the descriptions.
341        my %types = ERDB::GetDataTypes();
342        my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
343        my $typeMenu = $cgi->popup_menu(-name   => 'dataType',
344                                        -values => [sort keys %types],
345                                        -labels => \%labelMap,
346                                        -default => 'string');
347        # Allow the user to specify a new field name. This is required if the
348        # user has selected the "(new)" marker.
349        my $fieldField = "document.$name.fieldName";
350        my $newName = "\"" . NewName() . "\"";
351        push @retVal, $cgi->Tr($cgi->th("New Field Name"),
352                               $cgi->td($cgi->textfield(-name => 'newName',
353                                                        -size => 30,
354                                                        -value => "",
355                                                        -onFocus => "setIfEmpty($fieldField, $newName);")),
356                                        );
357        push @retVal, $cgi->Tr($cgi->th("Data type"),
358                               $cgi->td($typeMenu));
359        # The next row is for the notes.
360        push @retVal, $cgi->Tr($cgi->th("Description"),
361                               $cgi->td($cgi->textarea(-name => 'notes',
362                                                       -rows => 6,
363                                                       -columns => 80))
364                              );
365        # Now we have the groups, which are implemented as a checkbox group.
366        my @groups = $self->GetGroups();
367        push @retVal, $cgi->Tr($cgi->th("Groups"),
368                               $cgi->td($cgi->checkbox_group(-name=>'groups',
369                                        -values=> \@groups))
370                              );
371        # Now the four buttons: STORE, SHOW, ERASE, and DELETE.
372        push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
373                               $cgi->td({align => 'center'}, join(" ",
374                                        $cgi->submit(-name => 'Delete', -value => 'DELETE'),
375                                        $cgi->submit(-name => 'Store',  -value => 'STORE'),
376                                        $cgi->submit(-name => 'Erase',  -value => 'ERASE'),
377                                        $cgi->submit(-name => 'Show',   -value => 'SHOW')
378                                       ))
379                              );
380        # Close the table and the form.
381        push @retVal, $cgi->end_table();
382        # Return the assembled HTML.
383        return join("\n", @retVal, "");
384    }
385    
386  Name of the actual attribute.  =head3 LoadAttributesFrom
387    
388  =item fh  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
389    s
390    Load attributes from the specified tab-delimited file. Each line of the file must
391    contain an object ID in the first column, an attribute key name in the second
392    column, and attribute values in the remaining columns. The attribute values will
393    be assembled into a single value using the splitter code. In addition, the key names may
394    contain a splitter. If this is the case, the portion of the key after the splitter is
395    treated as a subkey.
396    
397  Open file handle for the input file.  =over 4
398    
399  =item keyCol  =item fileName
400    
401  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.
402  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
403    control.)
404    
405  =item dataCol  =item options
406    
407  Index (0-based) of the column containing the data value field.  Hash of options for modifying the load process.
408    
409  =item RETURN  =item RETURN
410    
411  Returns a statistics object for the load process.  Returns a statistics object describing the load.
412    
413    =back
414    
415    Permissible option values are as follows.
416    
417    =over 4
418    
419    =item append
420    
421    If TRUE, then the attributes will be appended to existing data; otherwise, the
422    first time a key name is encountered, it will be erased.
423    
424    =item archive
425    
426    If specified, the name of a file into which the incoming data file should be saved.
427    
428    =item objectType
429    
430    If specified, the specified object type will be prefixed to each object ID.
431    
432    =item resume
433    
434    If specified, key-value pairs already in the database will not be reinserted.
435    
436  =back  =back
437    
438  =cut  =cut
439    
440  sub LoadAttributeKey {  sub LoadAttributesFrom {
441      # Get the parameters.      # Get the parameters.
442      my ($self, $entityName, $fieldName, $fh, $keyCol, $dataCol) = @_;      my ($self, $fileName, %options) = @_;
443      # Create the return variable.      # Declare the return variable.
444      my $retVal;      my $retVal = Stats->new('keys', 'values');
445      # Insure the entity exists.      # Initialize the timers.
446      my $found = grep { $_ eq $entityName } $self->GetEntityTypes();      my ($insertTime, $eraseTime, $archiveTime, $checkTime) = (0, 0, 0, 0);
447      if (! $found) {      # Check for append mode.
448          Confess("Entity \"$entityName\" not found in database.");      my $append = ($options{append} ? 1 : 0);
449      } else {      # Check for resume mode.
450          # Get the field structure for the named entity.      my $resume = ($options{resume} ? 1 : 0);
451          my $fieldHash = $self->GetFieldTable($entityName);      # Create a hash of key names found.
452          # Verify that the attribute exists.      my %keyHash = ();
453          if (! exists $fieldHash->{$fieldName}) {      # Open the file for input. Note we must anticipate the possibility of an
454              Confess("Attribute key \"$fieldName\" does not exist in entity $entityName.");      # open filehandle being passed in.
455          } else {      my $fh;
456              # Create a loader for the specified attribute. We need the      if (ref $fileName) {
457              # relation name first.          Trace("Using file opened by caller.") if T(3);
458              my $relName = $fieldHash->{$fieldName}->{relation};          $fh = $fileName;
459              my $loadAttribute = ERDBLoad->new($self, $relName, $FIG_Config::temp);      } else {
460              # Loop through the input file.          Trace("Attributes will be loaded from $fileName.") if T(3);
461            $fh = Open(undef, "<$fileName");
462        }
463        # Now check to see if we need to archive.
464        my $ah;
465        if ($options{archive}) {
466            $ah = Open(undef, ">$options{archive}");
467            Trace("Load file will be archived to $options{archive}.") if T(3);
468        }
469        # Insure we recover from errors.
470        eval {
471            # Loop through the file.
472              while (! eof $fh) {              while (! eof $fh) {
473                  # Get the next line of the file.              # Read the current line.
474                  my @fields = Tracer::GetLine($fh);              my ($id, $key, @values) = Tracer::GetLine($fh);
475                  $loadAttribute->Add("lineIn");              $retVal->Add(linesIn => 1);
476                  # Now we need to validate the line.              # Check to see if we need to fix up the object ID.
477                  if ($#fields < $dataCol) {              if ($options{objectType}) {
478                      $loadAttribute->Add("shortLine");                  $id = "$options{objectType}:$id";
479                  } elsif (! $self->Exists($entityName, $fields[$keyCol])) {              }
480                      $loadAttribute->Add("badKey");              # Archive the line (if necessary).
481                if (defined $ah) {
482                    my $startTime = time();
483                    Tracer::PutLine($ah, [$id, $key, @values]);
484                    $archiveTime += time() - $startTime;
485                }
486                # Do some validation.
487                if (! $id) {
488                    # We ignore blank lines.
489                    $retVal->Add(blankLines => 1);
490                } elsif (substr($id, 0, 1) eq '#') {
491                    # A line beginning with a pound sign is a comment.
492                    $retVal->Add(comments => 1);
493                } elsif (! defined($key)) {
494                    # An ID without a key is a serious error.
495                    my $lines = $retVal->Ask('linesIn');
496                    Confess("Line $lines in $fileName has no attribute key.");
497                } elsif (! @values) {
498                    # A line with no values is not allowed.
499                    my $lines = $retVal->Ask('linesIn');
500                    Trace("Line $lines for key $key has no attribute values.") if T(1);
501                    $retVal->Add(skipped => 1);
502                } else {
503                    # The key contains a real part and an optional sub-part. We need the real part.
504                    my ($realKey, $subKey) = $self->SplitKey($key);
505                    # Now we need to check for a new key.
506                    if (! exists $keyHash{$realKey}) {
507                        if (! $self->Exists('AttributeKey', $realKey)) {
508                            my $line = $retVal->Ask('linesIn');
509                            Confess("Attribute \"$realKey\" on line $line of $fileName not found in database.");
510                  } else {                  } else {
511                      # It's valid,so send it to the loader.                          # Make sure we know this is no longer a new key.
512                      $loadAttribute->Put($fields[$keyCol], $fields[$dataCol]);                          $keyHash{$realKey} = 1;
513                      $loadAttribute->Add("lineUsed");                          $retVal->Add(keys => 1);
514                            # If this is NOT append mode, erase the key.
515                            if (! $append) {
516                                my $startTime = time();
517                                $self->EraseAttribute($realKey);
518                                $eraseTime += time() - $startTime;
519                                Trace("Attribute $realKey erased.") if T(3);
520                            }
521                        }
522                        Trace("Key $realKey found.") if T(3);
523                    }
524                    # If we're in resume mode, check to see if this insert is redundant.
525                    my $ok = 1;
526                    if ($resume) {
527                        my $startTime = time();
528                        my $count = $self->GetAttributes($id, $key, @values);
529                        $ok = ! $count;
530                        $checkTime += time() - $startTime;
531                    }
532                    if ($ok) {
533                        # Everything is all set up, so add the value.
534                        my $startTime = time();
535                        $self->AddAttribute($id, $key, @values);
536                        $insertTime += time() - $startTime;
537                    } else {
538                        # Here we skipped because of resume mode.
539                        $retVal->Add(resumeSkip => 1);
540                  }                  }
541    
542                    my $progress = $retVal->Add(values => 1);
543                    Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
544              }              }
             # Finish the load.  
             $retVal = $loadAttribute->FinishAndLoad();  
545          }          }
546            $retVal->Add(eraseTime   => $eraseTime);
547            $retVal->Add(insertTime  => $insertTime);
548            $retVal->Add(archiveTime => $archiveTime);
549            $retVal->Add(checkTime   => $checkTime);
550        };
551        # Check for an error.
552        if ($@) {
553            # Here we have an error. Display the error message.
554            my $message = $@;
555            Trace("Error during attribute load: $message") if T(0);
556            $retVal->AddMessage($message);
557        }
558        # Close the archive file, if any.
559        if (defined $ah) {
560            Trace("Closing archive file $options{archive}.") if T(2);
561            close $ah;
562      }      }
563      # Return the statistics.      # Return the result.
564      return $retVal;      return $retVal;
565  }  }
566    
567    =head3 BackupKeys
568    
569  =head3 DeleteAttributeKey  C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
   
 C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  
570    
571  Delete an attribute from the custom attributes database.  Backup the attribute key information from the attribute database.
572    
573  =over 4  =over 4
574    
575  =item entityName  =item fileName
576    
577  Name of the entity possessing the attribute.  Name of the output file.
578    
579  =item attributeName  =item options
580    
581  Name of the attribute to delete.  Options for modifying the backup process.
582    
583    =item RETURN
584    
585    Returns a statistics object for the backup.
586    
587  =back  =back
588    
589    Currently there are no options. The backup is straight to a text file in
590    tab-delimited format. Each key is backup up to two lines. The first line
591    is all of the data from the B<AttributeKey> table. The second is a
592    tab-delimited list of all the groups.
593    
594  =cut  =cut
595    
596  sub DeleteAttributeKey {  sub BackupKeys {
597        # Get the parameters.
598        my ($self, $fileName, %options) = @_;
599        # Declare the return variable.
600        my $retVal = Stats->new();
601        # Open the output file.
602        my $fh = Open(undef, ">$fileName");
603        # Set up to read the keys.
604        my $keyQuery = $self->Get(['AttributeKey'], "", []);
605        # Loop through the keys.
606        while (my $keyData = $keyQuery->Fetch()) {
607            $retVal->Add(key => 1);
608            # Get the fields.
609            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
610                                                              'AttributeKey(description)']);
611            # Escape any tabs or new-lines in the description.
612            my $escapedDescription = Tracer::Escape($description);
613            # Write the key data to the output.
614            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
615            # Get the key's groups.
616            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
617                                        'IsInGroup(to-link)');
618            $retVal->Add(memberships => scalar(@groups));
619            # Write them to the output. Note we put a marker at the beginning to insure the line
620            # is nonempty.
621            Tracer::PutLine($fh, ['#GROUPS', @groups]);
622        }
623        # Log the operation.
624        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
625        # Return the result.
626        return $retVal;
627    }
628    
629    =head3 RestoreKeys
630    
631    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
632    
633    Restore the attribute keys and groups from a backup file.
634    
635    =over 4
636    
637    =item fileName
638    
639    Name of the file containing the backed-up keys. Each key has a pair of lines,
640    one containing the key data and one listing its groups.
641    
642    =back
643    
644    =cut
645    
646    sub RestoreKeys {
647      # Get the parameters.      # Get the parameters.
648      my ($entityName, $attributeName) = @_;      my ($self, $fileName, %options) = @_;
649      # Read in the XML for the database defintion. We need to verify that      # Declare the return variable.
650      # the named entity exists and it has the named attribute.      my $retVal = Stats->new();
651      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Set up a hash to hold the group IDs.
652      my $entityHash = $metadata->{Entities};      my %groups = ();
653      if (! exists $entityHash->{$entityName}) {      # Open the file.
654          Confess("Entity \"$entityName\" not found.");      my $fh = Open(undef, "<$fileName");
655      } else {      # Loop until we're done.
656          # Get the field hash.      while (! eof $fh) {
657          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);          # Get a key record.
658          if (! exists $fieldHash->{$attributeName}) {          my ($id, $dataType, $description) = Tracer::GetLine($fh);
659              Confess("Attribute key \"$attributeName\" not found in entity $entityName.");          if ($id eq '#GROUPS') {
660          } else {              Confess("Group record found when key record expected.");
661              # Get the attribute's relation name.          } elsif (! defined($description)) {
662              my $relName = $fieldHash->{$attributeName}->{relation};              Confess("Invalid format found for key record.");
663              # Check for an index.          } else {
664              my $indexIdx = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);              $retVal->Add("keyIn" => 1);
665              if (defined($indexIdx)) {              # Add this key to the database.
666                  Trace("Index for $attributeName found at position $indexIdx for $entityName.") if T(3);              $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
667                  delete $entityHash->{$entityName}->{Indexes}->[$indexIdx];                                                    description => Tracer::UnEscape($description) });
668              }              Trace("Attribute $id stored.") if T(3);
669              # Delete the attribute from the field hash.              # Get the group line.
670              Trace("Deleting attribute $attributeName from $entityName.") if T(3);              my ($marker, @groups) = Tracer::GetLine($fh);
671              delete $fieldHash->{$attributeName};              if (! defined($marker)) {
672              # Write the XML back out.                  Confess("End of file found where group record expected.");
673              ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);              } elsif ($marker ne '#GROUPS') {
674              # Insure the relation does not exist in the database. This requires connecting                  Confess("Group record not found after key record.");
675              # since we may have to do a table drop.              } else {
676              my $attrDB = CustomAttributes->new();                  $retVal->Add(memberships => scalar(@groups));
677              Trace("Dropping table $relName.") if T(3);                  # Connect the groups.
678              $attrDB->DropRelation($relName);                  for my $group (@groups) {
679                        # Find out if this is a new group.
680                        if (! $groups{$group}) {
681                            $retVal->Add(newGroup => 1);
682                            # Add the group.
683                            $self->InsertObject('AttributeGroup', { id => $group });
684                            Trace("Group $group created.") if T(3);
685                            # Make sure we know it's not new.
686                            $groups{$group} = 1;
687                        }
688                        # Connect the group to our key.
689                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
690          }          }
691                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
692                }
693            }
694        }
695        # Log the operation.
696        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
697        # Return the result.
698        return $retVal;
699      }      }
700    
701    =head3 ArchiveFileName
702    
703    C<< my $fileName = $ca->ArchiveFileName(); >>
704    
705    Compute a file name for archiving attribute input data. The file will be in the attribute log directory
706    
707    =cut
708    
709    sub ArchiveFileName {
710        # Get the parameters.
711        my ($self) = @_;
712        # Declare the return variable.
713        my $retVal;
714        # We start by turning the timestamp into something usable as a file name.
715        my $now = Tracer::Now();
716        $now =~ tr/ :\//___/;
717        # Next we get the directory name.
718        my $dir = "$FIG_Config::var/attributes";
719        if (! -e $dir) {
720            Trace("Creating attribute file directory $dir.") if T(1);
721            mkdir $dir;
722        }
723        # Put it together with the field name and the time stamp.
724        $retVal = "$dir/upload.$now";
725        # Modify the file name to insure it's unique.
726        my $seq = 0;
727        while (-e "$retVal.$seq.tbl") { $seq++ }
728        # Use the computed sequence number to get the correct file name.
729        $retVal .= ".$seq.tbl";
730        # Return the result.
731        return $retVal;
732  }  }
733    
734  =head3 ControlForm  =head3 BackupAllAttributes
735    
736  C<< my $formHtml = $attrDB->ControlForm($cgi, $name); >>  C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
737    
738  Return a form that can be used to control the creation and modification of  Backup all of the attributes to a file. The attributes will be stored in a
739  attributes.  tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
740    
741  =over 4  =over 4
742    
743  =item cgi  =item fileName
744    
745  CGI query object used to create HTML.  Name of the file to which the attribute data should be backed up.
746    
747  =item name  =item options
748    
749  Name to give to the form. This should be unique for the web page.  Hash of options for the backup.
750    
751  =item RETURN  =item RETURN
752    
753  Returns the HTML for a form that submits instructions to the C<Attributes.cgi> script  Returns a statistics object describing the backup.
 for loading, creating, or deleting an attribute.  
754    
755  =back  =back
756    
757    Currently there are no options defined.
758    
759  =cut  =cut
760    
761  sub ControlForm {  sub BackupAllAttributes {
762      # Get the parameters.      # Get the parameters.
763      my ($self, $cgi, $name) = @_;      my ($self, $fileName, %options) = @_;
764      # Declare the return list.      # Declare the return variable.
765      my @retVal = ();      my $retVal = Stats->new();
766      # Start the form. We use multipart to support the upload control.      # Get a list of the keys.
767      push @retVal, $cgi->start_multipart_form(-name => $name);      my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
768      # We'll put the controls in a table. Nothing else ever seems to look nice.      Trace(scalar(@keys) . " keys found during backup.") if T(2);
769      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      # Open the file for output.
770      # The first row is for selecting the field name.      my $fh = Open(undef, ">$fileName");
771      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      # Loop through the keys.
772                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,      for my $key (@keys) {
773                                                       "document.$name.notes.value",          Trace("Backing up attribute $key.") if T(3);
774                                                       "document.$name.dataType.value")));          $retVal->Add(keys => 1);
775      # Now we set up a dropdown for the data types. The values will be the          # Loop through this key's values.
776      # data type names, and the labels will be the descriptions.          my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
777      my %types = ERDB::GetDataTypes();          my $valuesFound = 0;
778      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;          while (my $line = $query->Fetch()) {
779      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',              $valuesFound++;
780                                      -values => [sort keys %types],              # Get this row's data.
781                                      -labels => \%labelMap);              my ($id, $key, $subKey, $value) = $line->Values(['HasValueFor(to-link)',
782      push @retVal, $cgi->Tr($cgi->th("Data type"),                                                               'HasValueFor(from-link)',
783                             $cgi->td($typeMenu));                                                               'HasValueFor(subkey)',
784      # The next row is for the notes.                                                               'HasValueFor(value)']);
785      push @retVal, $cgi->Tr($cgi->th("Description"),              # Check for a subkey.
786                             $cgi->td($cgi->textarea(-name => 'notes',              if ($subKey ne '') {
787                                                     -rows => 6,                  $key = "$key$self->{splitter}$subKey";
788                                                     -columns => 80))              }
789                            );              # Write it to the file.
790      # Allow the user to specify a new field name. This is required if the              Tracer::PutLine($fh, [$id, $key, $value]);
791      # user has selected one of the "(new)" markers.          }
792      push @retVal, $cgi->Tr($cgi->th("New Field Name"),          Trace("$valuesFound values backed up for key $key.") if T(3);
793                             $cgi->td($cgi->textfield(-name => 'newName',          $retVal->Add(values => $valuesFound);
794                                                      -size => 30)),      }
795                                      );      # Log the operation.
796      # If the user wants to upload new values for the field, then we have      $self->LogOperation("Backup Data", $fileName, $retVal->Display());
797      # an upload file name and column indicators.      # Return the result.
798      push @retVal, $cgi->Tr($cgi->th("Upload Values"),      return $retVal;
                            $cgi->td($cgi->filefield(-name => 'newValueFile',  
                                                     -size => 20) .  
                                     " Key&nbsp;" .  
                                     $cgi->textfield(-name => 'keyCol',  
                                                     -size => 3,  
                                                     -default => 0) .  
                                     " Value&nbsp;" .  
                                     $cgi->textfield(-name => 'valueCol',  
                                                     -size => 3,  
                                                     -default => 1)  
                                    ),  
                           );  
     # Now the three buttons: UPDATE, SHOW, and DELETE.  
     push @retVal, $cgi->Tr($cgi->th("&nbsp;"),  
                            $cgi->td({align => 'center'},  
                                     $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .  
                                     $cgi->submit(-name => 'Store',  -value => 'STORE') . " " .  
                                     $cgi->submit(-name => 'Show',   -value => 'SHOW')  
                                    )  
                           );  
     # Close the table and the form.  
     push @retVal, $cgi->end_table();  
     push @retVal, $cgi->end_form();  
     # Return the assembled HTML.  
     return join("\n", @retVal, "");  
799  }  }
800    
801  =head3 FieldMenu  =head3 FieldMenu
802    
803  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
804    
805  Return the HTML for a menu to select an attribute field. The menu will  Return the HTML for a menu to select an attribute field. The menu will
806  be a standard SELECT/OPTION thing which is called "popup menu" in the  be a standard SELECT/OPTION thing which is called "popup menu" in the
807  CGI package, but actually looks like a list. The list will contain  CGI package, but actually looks like a list. The list will contain
808  one selectable row per field, grouped by entity.  one selectable row per field.
809    
810  =over 4  =over 4
811    
# Line 556  Line 822 
822  Name to give to the menu. This is the name under which the value will  Name to give to the menu. This is the name under which the value will
823  appear when the form is submitted.  appear when the form is submitted.
824    
825  =item newFlag (optional)  =item keys
826    
827    Reference to a hash mapping each attribute key name to a list reference,
828    the list itself consisting of the attribute data type, its description,
829    and a list of its groups.
830    
831    =item options
832    
833    Hash containing options that modify the generation of the menu.
834    
835    =item RETURN
836    
837    Returns the HTML to create a form field that can be used to select an
838    attribute from the custom attributes system.
839    
840    =back
841    
842    The permissible options are as follows.
843    
844    =over 4
845    
846    =item new
847    
848  If TRUE, then extra rows will be provided to allow the user to select  If TRUE, then extra rows will be provided to allow the user to select
849  a new attribute. In other words, the user can select an existing  a new attribute. In other words, the user can select an existing
850  attribute, or can choose a C<(new)> marker to indicate a field to  attribute, or can choose a C<(new)> marker to indicate a field to
851  be created in the parent entity.  be created in the parent entity.
852    
853  =item noteControl (optional)  =item notes
854    
855  If specified, the name of a variable for displaying the notes attached  If specified, the name of a variable for displaying the notes attached
856  to the field. This must be in Javascript form ready for assignment.  to the field. This must be in Javascript form ready for assignment.
# Line 574  Line 861 
861  it is copied in. Specifying this parameter generates Javascript for  it is copied in. Specifying this parameter generates Javascript for
862  displaying the field description when a field is selected.  displaying the field description when a field is selected.
863    
864  =item typeControl (optional)  =item type
865    
866  If specified, the name of a variable for displaying the field's  If specified, the name of a variable for displaying the field's
867  data type. Data types are a much more controlled vocabulary than  data type. Data types are a much more controlled vocabulary than
# Line 582  Line 869 
869  raw value is put into the specified variable. Otherwise, the same  raw value is put into the specified variable. Otherwise, the same
870  rules apply to this value that apply to I<$noteControl>.  rules apply to this value that apply to I<$noteControl>.
871    
872  =item RETURN  =item groups
873    
874  Returns the HTML to create a form field that can be used to select an  If specified, the name of a multiple-selection list control (also called
875  attribute from the custom attributes system.  a popup menu) which shall be used to display the selected groups.
876    
877  =back  =back
878    
# Line 593  Line 880 
880    
881  sub FieldMenu {  sub FieldMenu {
882      # Get the parameters.      # Get the parameters.
883      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self, $cgi, $height, $name, $keys, %options) = @_;
884      # These next two hashes make everything happen. "entities"      # Reformat the list of keys.
885      # maps each entity name to the list of values to be put into its      my %keys = %{$keys};
886      # option group. "labels" maps each entity name to a map from values      # Add the (new) key, if needed.
887      # to labels.      if ($options{new}) {
888      my @entityNames = sort ($self->GetEntityTypes());          $keys{NewName()} = ["string", ""];
889      my %entities = map { $_ => [] } @entityNames;      }
890      my %labels = map { $_ => { }} @entityNames;      # Get a sorted list of key.
891      # Loop through the entities, adding the existing attributes.      my @keys = sort keys %keys;
892      for my $entity (@entityNames) {      # We need to create the name for the onChange function. This function
         # Get this entity's field table.  
         my $fieldHash = $self->GetFieldTable($entity);  
         # Get its field list in our local hashes.  
         my $fieldList = $entities{$entity};  
         my $labelList = $labels{$entity};  
         # Add the NEW fields if we want them.  
         if ($newFlag) {  
             push @{$fieldList}, $entity;  
             $labelList->{$entity} = "(new)";  
         }  
         # 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  
893      # may not do anything, but we need to know the name to generate the HTML      # may not do anything, but we need to know the name to generate the HTML
894      # for the menu.      # for the menu.
895      my $changeName = "${name}_setNotes";      my $changeName = "${name}_setNotes";
896      my $retVal = $cgi->popup_menu({name => $name,      my $retVal = $cgi->popup_menu({name => $name,
897                                     size => $height,                                     size => $height,
898                                     onChange => "$changeName(this.value)",                                     onChange => "$changeName(this.value)",
899                                     values => [map { $cgi->optgroup(-name => $_,                                     values => \@keys,
900                                                                     -values => $entities{$_},                                    });
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
901      # Create the change function.      # Create the change function.
902      $retVal .= "\n<script language=\"javascript\">\n";      $retVal .= "\n<script language=\"javascript\">\n";
903      $retVal .= "    function $changeName(fieldValue) {\n";      $retVal .= "    function $changeName(fieldValue) {\n";
904      # The function only has a body if we have a notes control to store the description.      # The function only has a body if we have a control to store data about the
905      if ($noteControl || $typeControl) {      # attribute.
906        if ($options{notes} || $options{type} || $options{groups}) {
907          # Check to see if we're storing HTML or text into the note control.          # Check to see if we're storing HTML or text into the note control.
908            my $noteControl = $options{notes};
909          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
910          # We use a CASE statement based on the newly-selected field value. The          # We use a CASE statement based on the newly-selected field value. The
911          # field description will be stored in the JavaScript variable "myText"          # field description will be stored in the JavaScript variable "myText"
# Line 652  Line 914 
914          $retVal .= "        var myText = \"\";\n";          $retVal .= "        var myText = \"\";\n";
915          $retVal .= "        var myType = \"string\";\n";          $retVal .= "        var myType = \"string\";\n";
916          $retVal .= "        switch (fieldValue) {\n";          $retVal .= "        switch (fieldValue) {\n";
917          # Loop through the entities.          # Loop through the keys.
918          for my $entity (@entityNames) {          for my $key (@keys) {
             # 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};  
919                      # Generate this case.                      # Generate this case.
920                      $retVal .= "        case \"$value\" :\n";              $retVal .= "        case \"$key\" :\n";
921                      # Here we either want to update the note display, the                      # Here we either want to update the note display, the
922                      # type display, or both.              # type display, the group list, or a combination of them.
923                my ($type, $notes, @groups) = @{$keys{$key}};
924                      if ($noteControl) {                      if ($noteControl) {
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
925                          # Insure it's in the proper form.                          # Insure it's in the proper form.
926                          if ($htmlMode) {                          if ($htmlMode) {
927                              $notes = ERDB::HTMLNote($notes);                              $notes = ERDB::HTMLNote($notes);
# Line 679  Line 931 
931                          $notes =~ s/"/\\"/g;                          $notes =~ s/"/\\"/g;
932                          $retVal .= "           myText = \"$notes\";\n";                          $retVal .= "           myText = \"$notes\";\n";
933                      }                      }
934                      if ($typeControl) {              if ($options{type}) {
935                          # Here we want the type updated.                          # Here we want the type updated.
                         my $type = $element->{type};  
936                          $retVal .= "           myType = \"$type\";\n";                          $retVal .= "           myType = \"$type\";\n";
937                      }                      }
938                if ($options{groups}) {
939                    # Here we want the groups shown. Get a list of this attribute's groups.
940                    # We'll search through this list for each group to see if it belongs with
941                    # our attribute.
942                    my $groupLiteral = "=" . join("=", @groups) . "=";
943                    # Now we need some variables containing useful code for the javascript. It's
944                    # worth knowing we go through a bit of pain to insure $groupField[i] isn't
945                    # parsed as an array element.
946                    my $groupField = $options{groups};
947                    my $currentField = $groupField . "[i]";
948                    # Do the javascript.
949                    $retVal .= "           var groupList = \"$groupLiteral\";\n";
950                    $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";
951                    $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";
952                    $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";
953                    $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";
954                    $retVal .= "           }\n";
955                }
956                      # Close this case.                      # Close this case.
957                      $retVal .= "           break;\n";                      $retVal .= "           break;\n";
958                  }                  }
             }  
         }  
959          # Close the CASE statement and make the appropriate assignments.          # Close the CASE statement and make the appropriate assignments.
960          $retVal .= "        }\n";          $retVal .= "        }\n";
961          if ($noteControl) {          if ($noteControl) {
962              $retVal .= "        $noteControl = myText;\n";              $retVal .= "        $noteControl = myText;\n";
963          }          }
964          if ($typeControl) {          if ($options{type}) {
965              $retVal .= "        $typeControl = myType;\n";              $retVal .= "        $options{type} = myType;\n";
966          }          }
967      }      }
968      # Terminate the change function.      # Terminate the change function.
# Line 705  Line 972 
972      return $retVal;      return $retVal;
973  }  }
974    
975  =head3 MatchSqlPattern  =head3 GetGroups
976    
977  C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>  C<< my @groups = $attrDB->GetGroups(); >>
978    
979  Determine whether or not a specified value matches an SQL pattern. An SQL  Return a list of the available groups.
 pattern has two wild card characters: C<%> that matches multiple characters,  
 and C<_> that matches a single character. These can be escaped using a  
 backslash (C<\>). We pull this off by converting the SQL pattern to a  
 PERL regular expression. As per SQL rules, the match is case-insensitive.  
980    
981  =over 4  =cut
982    
983  =item value  sub GetGroups {
984        # Get the parameters.
985        my ($self) = @_;
986        # Get the groups.
987        my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
988        # Return them.
989        return @retVal;
990    }
991    
992  Value to be matched against the pattern. Note that an undefined or empty  =head3 GetAttributeData
 value will not match anything.  
993    
994  =item pattern  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
995    
996  SQL pattern against which to match the value. An undefined or empty pattern will  Return attribute data for the selected attributes. The attribute
997  match everything.  data is a hash mapping each attribute key name to a n-tuple containing the
998    data type, the description, and the groups. This is the same format expected in
999    the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.
1000    
1001  =item RETURN  =over 4
1002    
1003  Returns TRUE if the value and pattern match, else FALSE.  =item type
1004    
1005    Type of attribute criterion: C<name> for attributes whose names begin with the
1006    specified string, or C<group> for attributes in the specified group.
1007    
1008    =item list
1009    
1010    List containing the names of the groups or keys for the desired attributes.
1011    
1012    =item RETURN
1013    
1014    Returns a hash mapping each attribute key name to its data type, description, and
1015    parent groups.
1016    
1017  =back  =back
1018    
1019  =cut  =cut
1020    
1021  sub MatchSqlPattern {  sub GetAttributeData {
1022      # Get the parameters.      # Get the parameters.
1023      my ($value, $pattern) = @_;      my ($self, $type, @list) = @_;
1024      # Declare the return variable.      # Set up a hash to store the attribute data.
1025      my $retVal;      my %retVal = ();
1026      # Insure we have a pattern.      # Loop through the list items.
1027      if (! defined($pattern) || $pattern eq "") {      for my $item (@list) {
1028          $retVal = 1;          # Set up a query for the desired attributes.
1029      } else {          my $query;
1030          # Break the pattern into pieces around the wildcard characters. Because we          if ($type eq 'name') {
1031          # use parentheses in the split function's delimiter expression, we'll get              # Here we're doing a generic name search. We need to escape it and then tack
1032          # list elements for the delimiters as well as the rest of the string.              # on a %.
1033          my @pieces = split /([_%]|\\[_%])/, $pattern;              my $parm = $item;
1034          # Check some fast special cases.              $parm =~ s/_/\\_/g;
1035          if ($pattern eq '%') {              $parm =~ s/%/\\%/g;
1036              # A null pattern matches everything.              $parm .= "%";
1037              $retVal = 1;              # Ask for matching attributes. (Note that if the user passed in a null string
1038          } elsif (@pieces == 1) {              # he'll get everything.)
1039              # No wildcards, so we have a literal comparison. Note we're case-insensitive.              $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
1040              $retVal = (lc($value) eq lc($pattern));          } elsif ($type eq 'group') {
1041          } elsif (@pieces == 2 && $pieces[1] eq '%') {              $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
             # A wildcard at the end, so we have a substring match. This is also case-insensitive.  
             $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));  
         } else {  
             # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.  
             my $realPattern = "";  
             for my $piece (@pieces) {  
                 # Determine the type of piece.  
                 if ($piece eq "") {  
                     # Empty pieces are ignored.  
                 } elsif ($piece eq "%") {  
                     # 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);  
1042                  } else {                  } else {
1043                      # Here we have raw text.              Confess("Unknown attribute query type \"$type\".");
                     $realPattern .= quotemeta($piece);  
1044                  }                  }
1045            while (my $row = $query->Fetch()) {
1046                # Get this attribute's data.
1047                my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
1048                                                         'AttributeKey(description)']);
1049                # If it's new, get its groups and add it to the return hash.
1050                if (! exists $retVal{$key}) {
1051                    my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
1052                                                [$key], 'IsInGroup(to-link)');
1053                    $retVal{$key} = [$type, $notes, @groups];
1054              }              }
             # Do the match.  
             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);  
1055          }          }
1056      }      }
1057      # Return the result.      # Return the result.
1058      return $retVal;      return %retVal;
1059  }  }
1060    
1061  =head3 MigrateAttributes  =head3 LogOperation
1062    
1063  C<< CustomAttributes::MigrateAttributes($fig); >>  C<< $ca->LogOperation($action, $target, $description); >>
1064    
1065  Migrate all the attributes data from the specified FIG instance. This is a long, slow  Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
 method used to convert the old attribute data to the new system. Only attribute  
 keys that are not already in the database will be loaded, and only for entity instances  
 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.  
1066    
1067  =over 4  =over 4
1068    
1069  =item fig  =item action
1070    
1071    Action being logged (e.g. C<Delete Group> or C<Load Key>).
1072    
1073    =item target
1074    
1075    ID of the key or group affected.
1076    
1077    =item description
1078    
1079  A FIG object that can be used to retrieve attributes for migration purposes.  Short description of the action.
1080    
1081  =back  =back
1082    
1083  =cut  =cut
1084    
1085  sub MigrateAttributes {  sub LogOperation {
1086      # Get the parameters.      # Get the parameters.
1087      my ($fig) = @_;      my ($self, $action, $target, $description) = @_;
1088      # Get a list of the objects to migrate. This requires connecting. Note we      # Get the user ID.
1089      # will map each entity type to a file name. The file will contain a list      my $user = $self->{user};
1090      # of the object's IDs so we can get to them when we're not connected to      # Get a timestamp.
1091      # the database.      my $timeString = Tracer::Now();
1092      my $ca = CustomAttributes->new();      # Open the log file for appending.
1093      my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();      my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
1094      # Set up hash of the existing attribute keys for each entity type.      # Write the data to it.
1095      my %oldKeys = ();      Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
1096      # Finally, we have a hash that counts the IDs for each entity type.      # Close the log file.
1097      my %idCounts = map { $_ => 0 } keys %objects;      close $oh;
1098      # Loop through the list, creating key files to read back in.  }
1099      for my $entityType (keys %objects) {  
1100          Trace("Retrieving keys for $entityType.") if T(2);  =head2 Internal Utility Methods
1101          # Create the key file.  
1102          my $idFile = Open(undef, ">$objects{$entityType}");  =head3 _KeywordString
1103          # Loop through the keys.  
1104          my @ids = $ca->GetFlat([$entityType], "", [], "$entityType(id)");  C<< my $keywordString = $ca->_KeywordString($key, $value); >>
1105          for my $id (@ids) {  
1106              print $idFile "$id\n";  Compute the keyword string for a specified key/value pair. This consists of the
1107          }  key name and value converted to lower case with underscores translated to spaces.
1108          close $idFile;  
1109          # In addition to the key file, we must get a list of attributes already  This method is for internal use only. It is called whenever we need to update or
1110          # in the database. This avoids a circularity problem that might occur if the $fig  insert a B<HasValueFor> record.
1111          # object is retrieving from the custom attributes database already.  
1112          my %fields = $ca->GetSecondaryFields($entityType);  =over 4
1113          $oldKeys{$entityType} = \%fields;  
1114          # Finally, we have the ID count.  =item key
1115          $idCounts{$entityType} = scalar @ids;  
1116      }  Name of the relevant attribute key.
1117      # Release the custom attributes database so we can add attributes.  
1118      undef $ca;  =item target
1119      # Loop through the objects.  
1120      for my $entityType (keys %objects) {  ID of the target object to which this key/value pair will be associated.
1121          # Get a hash of all the attributes already in this database. These are  
1122          # left untouched.  =item value
1123          my $myOldKeys = $oldKeys{$entityType};  
1124          # Create a hash to control the load file names for each attribute key we find.  The value to store for this key/object combination.
1125          my %keyHash = ();  
1126          # Set up some counters so we can trace our progress.  =item RETURN
1127          my ($totalIDs, $processedIDs, $keyCount, $valueCount) = ($idCounts{$entityType}, 0, 0, 0);  
1128          # Open this object's ID file.  Returns the value that should be stored as the keyword string for the specified
1129          Trace("Migrating data for $entityType. $totalIDs found.") if T(3);  key/value pair.
1130          my $keysIn = Open(undef, "<$objects{$entityType}");  
1131          while (my $id = <$keysIn>) {  =back
1132              # Remove the EOL characters.  
1133              chomp $id;  =cut
1134              # Get this object's attributes.  
1135              my @allData = $fig->get_attributes($id);  sub _KeywordString {
1136              Trace(scalar(@allData) . " attribute values found for $entityType($id).") if T(4);      # Get the parameters.
1137              # Loop through the attribute values one at a time.      my ($self, $key, $value) = @_;
1138              for my $dataTuple (@allData) {      # Get a copy of the key name and convert underscores to spaces.
1139                  # Get the key, value, and URL. We ignore the first element because that's the      my $keywordString = $key;
1140                  # object ID, and we already know the object ID.      $keywordString =~ s/_/ /g;
1141                  my (undef, $key, $value, $url) = @{$dataTuple};      # Add the value convert it all to lower case.
1142                  # Remove the buggy "1" for $url.      my $retVal = lc "$keywordString $value";
1143                  if ($url eq "1") {      # Return the result.
1144                      $url = undef;      return $retVal;
                 }  
                 # 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);  
         }  
         # All the keys for this entity type are now loaded.  
         Trace("Key files loaded for $entityType.") if T(2);  
     }  
     # All keys for all entity types are now loaded.  
     Trace("Migration complete.") if T(2);  
1145  }  }
1146    
1147  =head3 ComputeObjectTypeFromID  =head3 _QueryResults
1148    
1149  C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>  C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1150    
1151  This method will compute the entity type corresponding to a specified object ID.  Match the results of a B<HasValueFor> query against value criteria and return
1152  If the object ID begins with C<fig|>, it is presumed to be a feature ID. If it  the results. This is an internal method that splits the values coming back
1153  is all digits with a single period, it is presumed to by a genome ID. Otherwise,  and matches the sections against the specified section patterns. It serves
1154  it must be a list reference. In this last case the first list element will be  as the back end to L</GetAttributes> and L</FindAttributes>.
 taken as the entity type and the second will be taken as the actual ID.  
1155    
1156  =over 4  =over 4
1157    
1158  =item objectID  =item query
1159    
1160    A query object that will return the desired B<HasValueFor> records.
1161    
1162  Object ID to examine.  =item values
1163    
1164    List of the desired attribute values, section by section. If C<undef>
1165    or an empty string is specified, all values in that section will match. A
1166    generic match can be requested by placing a percent sign (C<%>) at the end.
1167    In that case, all values that match up to and not including the percent sign
1168    will match. You may also specify a regular expression enclosed
1169    in slashes. All values that match the regular expression will be returned. For
1170    performance reasons, only values have this extra capability.
1171    
1172  =item RETURN  =item RETURN
1173    
1174  Returns a 2-element list consisting of the entity type followed by the specified ID.  Returns a list of tuples. The first element in the tuple is an object ID, the
1175    second is an attribute key, and the remaining elements are the sections of
1176    the attribute value. All of the tuples will match the criteria set forth in
1177    the parameter list.
1178    
1179  =back  =back
1180    
1181  =cut  =cut
1182    
1183  sub ComputeObjectTypeFromID {  sub _QueryResults {
1184      # Get the parameters.      # Get the parameters.
1185      my ($objectID) = @_;      my ($self, $query, @values) = @_;
1186      # Declare the return variables.      # Declare the return value.
1187      my ($entityName, $id);      my @retVal = ();
1188      # Only proceed if the object ID is defined. If it's not, we'll be returning a      # Get the number of value sections we have to match.
1189      # pair of undefs.      my $sectionCount = scalar(@values);
1190      if ($objectID) {      # Loop through the assignments found.
1191          if (ref $objectID eq 'ARRAY') {      while (my $row = $query->Fetch()) {
1192              # Here we have the new-style list reference. Pull out its pieces.          # Get the current row's data.
1193              ($entityName, $id) = @{$objectID};          my ($id, $realKey, $subKey, $valueString) = $row->Values(['HasValueFor(to-link)',
1194          } else {                                                                    'HasValueFor(from-link)',
1195              # Here the ID is the outgoing ID, and we need to look at its structure                                                                    'HasValueFor(subkey)',
1196              # to determine the entity type.                                                                    'HasValueFor(value)'
1197              $id = $objectID;                                                                  ]);
1198              if ($objectID =~ /^\d+\.\d+/) {          # Form the key from the real key and the sub key.
1199                  # Digits with a single period is a genome.          my $key = $self->JoinKey($realKey, $subKey);
1200                  $entityName = 'Genome';          # Break the value into sections.
1201              } elsif ($objectID =~ /^fig\|/) {          my @sections = split($self->{splitter}, $valueString);
1202                  # The "fig|" prefix indicates a feature.          # Match each section against the incoming values. We'll assume we're
1203                  $entityName = 'Feature';          # okay unless we learn otherwise.
1204            my $matching = 1;
1205            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1206                # We need to check to see if this section is generic.
1207                my $value = $values[$i];
1208                Trace("Current value pattern is \"$value\".") if T(4);
1209                if (substr($value, -1, 1) eq '%') {
1210                    Trace("Generic match used.") if T(4);
1211                    # Here we have a generic match.
1212                    my $matchLen = length($values[$i]) - 1;
1213                    $matching = substr($sections[$i], 0, $matchLen) eq
1214                                substr($values[$i], 0, $matchLen);
1215                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1216                    Trace("Regular expression detected.") if T(4);
1217                    # Here we have a regular expression match.
1218                    my $section = $sections[$i];
1219                    $matching = eval("\$section =~ $value");
1220              } else {              } else {
1221                  # Anything else is illegal!                  # Here we have a strict match.
1222                  Confess("Invalid attribute ID specification \"$objectID\".");                  Trace("Strict match used.") if T(4);
1223                    $matching = ($sections[$i] eq $values[$i]);
1224              }              }
1225          }          }
1226            # If we match, output this row to the return list.
1227            if ($matching) {
1228                push @retVal, [$id, $key, @sections];
1229      }      }
1230      # Return the result.      }
1231      return ($entityName, $id);      # Return the rows found.
1232        return @retVal;
1233  }  }
1234    
1235  =head2 FIG Method Replacements  =head2 FIG Method Replacements
1236    
1237  The following methods are used by B<FIG.pm> to replace the previous attribute functionality.  The following methods are used by B<FIG.pm> to replace the previous attribute functionality.
1238  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
1239  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
1240  capabilities were used in the old system.  capabilities were used in the old system.
1241    
# Line 993  Line 1243 
1243  The idea is that these methods represent attribute manipulation allowed by all users, while  The idea is that these methods represent attribute manipulation allowed by all users, while
1244  the others are only for privileged users with access to the attribute server.  the others are only for privileged users with access to the attribute server.
1245    
1246  In the previous implementation, an attribute had a value and a URL. In the new implementation,  In the previous implementation, an attribute had a value and a URL. In this implementation,
1247  there is only a value. In this implementation, each attribute has only a value. These  each attribute has only a value. These methods will treat the value as a list with the individual
1248  methods will treat the value as a list with the individual elements separated by the  elements separated by the value of the splitter parameter on the constructor (L</new>). The default
1249  value of the splitter parameter on the constructor (L</new>). The default is double  is double colons C<::>.
 colons C<::>.  
1250    
1251  So, for example, an old-style keyword with a /value of C<essential> and a URL of  So, for example, an old-style keyword with a value of C<essential> and a URL of
1252  C<http://www.sciencemag.org/cgi/content/abstract/293/5538/2266> using the default  C<http://www.sciencemag.org/cgi/content/abstract/293/5538/2266> using the default
1253  splitter value would be stored as  splitter value would be stored as
1254    
# Line 1010  Line 1259 
1259    
1260  =head3 GetAttributes  =head3 GetAttributes
1261    
1262  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1263    
1264  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1265  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
1266  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
1267  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1268  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.  
1269    
1270  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
1271  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
1272  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1273    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1274    of the parameters. So, for example,
1275    
1276      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1277    
1278  would return something like  would return something like
1279    
# Line 1033  Line 1282 
1282      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1283      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1284    
1285  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1286  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1287  matches any sequence of characters, and C<_>, which matches any single character.  
1288  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1289  underscore.)  
1290    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1291    features.
1292    
1293  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1294  values, so even  values, so even
1295    
1296      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1297    
1298  which has no wildcard in the key or the object ID, may return multiple tuples.  which has no wildcard in the key or the object ID, may return multiple tuples.
1299    
1300  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
1301  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
1302  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
1303  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
1304  be written as  are stored in a single string. As a result, queries in which filter only on value end up
1305    reading a lot more than they need to.
     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.  
1306    
1307  =over 4  =over 4
1308    
1309  =item objectID  =item objectID
1310    
1311  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
1312  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
1313  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
1314  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.  
1315    
1316  =item key  =item key
1317    
1318  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
1319  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
1320  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
1321  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.  
1322    
1323  =item valuePatterns  =item values
1324    
1325  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1326  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
1327    generic match can be requested by placing a percent sign (C<%>) at the end.
1328    In that case, all values that match up to and not including the percent sign
1329    will match. You may also specify a regular expression enclosed
1330    in slashes. All values that match the regular expression will be returned. For
1331    performance reasons, only values have this extra capability.
1332    
1333  =item RETURN  =item RETURN
1334    
# Line 1107  Line 1343 
1343    
1344  sub GetAttributes {  sub GetAttributes {
1345      # Get the parameters.      # Get the parameters.
1346      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1347      # Declare the return variable.      # This hash will map "HasValueFor" fields to patterns. We use it to build the
1348      my @retVal = ();      # SQL statement.
1349      # Determine the entity types for our search.      my %data;
1350      my @objects = ();      # Before we do anything else, we must parse the key. The key is treated by the
1351      my ($actualObjectID, $computedType);      # user as a single field, but to us it's actually a real key and a subkey.
1352      if (! $objectID) {      # If the key has no splitter and is exact, the real key is the original key
1353          push @objects, $self->GetEntityTypes();      # and the subkey is an empty string. If the key has a splitter, it is
1354      } else {      # split into two pieces and each piece is processed separately. If the key has
1355          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);      # no splitter and is generic, the real key is the incoming key and the subkey
1356          push @objects, $computedType;      # is allowed to be wild. Of course, this only matters if an actual key has
1357      }      # been specified.
1358      # Loop through the entity types.      if (defined $key) {
1359      for my $entityType (@objects) {          if ($key =~ /$self->{splitter}/) {
1360          # Now we need to find all the matching keys. The keys are actually stored in              # Here we have a two-part key, so we split it normally.
1361          # our database object, so this process is fast. Note that our              my ($realKey, $subKey) = $self->SplitKey($key);
1362          # MatchSqlPattern method              $data{'HasValueFor(from-link)'} = $realKey;
1363          my %secondaries = $self->GetSecondaryFields($entityType);              $data{'HasValueFor(subkey)'} = $subKey;
1364          my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;          } elsif (substr($key, -1, 1) eq '%') {
1365          # Now we figure out whether or not we need to filter by object. We will always              $data{'HasValueFor(from-link)'} = $key;
1366          # filter by key to a limited extent, so if we're filtering by object we need an          } else {
1367          # AND to join the object ID filter with the key filter.              $data{'HasValueFor(from-link)'} = $key;
1368          my $filter = "";              $data{'HasValueFor(subkey)'} = '';
1369          my @params = ();          }
1370          if (defined($actualObjectID)) {      }
1371              # Here the caller wants to filter on object ID. Check for a pattern.      # Add the object ID to the key information.
1372              my $comparator = ($actualObjectID =~ /%/ ? "LIKE" : "=");      $data{'HasValueFor(to-link)'} = $objectID;
1373              # Update the filter and the parameter list.      # The first value represents a problem, because we can search it using SQL, but not
1374              $filter = "$entityType(id) $comparator ? AND ";      # in the normal way. If the user specifies a generic search or exact match for
1375              push @params, $actualObjectID;      # every alternative value (remember, the values may be specified as a list),
1376          }      # then we can create SQL filtering for it. If any of the values are specified
1377          # It's time to begin making queries. We process one attribute key at a time, because      # as a regular expression, however, that's a problem, because we need to read
1378          # each attribute is actually a different field in the database. We know here that      # every value to verify a match.
1379          # all the keys we've collected are for the correct entity because we got them from      if (@values > 0) {
1380          # the DBD. That's a good thing, because an invalid key name will cause an SQL error.          # Get the first value and put its alternatives in an array.
1381          for my $key (@fieldList) {          my $valueParm = $values[0];
1382              # Get all of the attribute values for this key.          my @valueList;
1383              my @dataRows = $self->GetAll([$entityType], "$filter$entityType($key) IS NOT NULL",          if (ref $valueParm eq 'ARRAY') {
1384                                           \@params, ["$entityType(id)", "$entityType($key)"]);              @valueList = @{$valueParm};
1385              # Process each value separately. We need to verify the values and reformat the          } else {
1386              # tuples. Note that GetAll will give us one row per matching object ID,              @valueList = ($valueParm);
1387              # with the ID first followed by a list of the data values. This is very          }
1388              # different from the structure we'll be returning, which has one row          # Okay, now we have all the possible criteria for the first value in the list
1389              # per value.          # @valueList. We'll copy the values to a new array in which they have been
1390              for my $dataRow (@dataRows) {          # converted to generic requests. If we find a regular-expression match
1391                  # Get the object ID and the list of values.          # anywhere in the list, we toss the whole thing.
1392                  my ($rowObjectID, @dataValues) = @{$dataRow};          my @valuePatterns = ();
1393                  # Loop through the values. There will be one result row per attribute value.          my $okValues = 1;
1394                  for my $dataValue (@dataValues) {          for my $valuePattern (@valueList) {
1395                      # Separate this value into sections.              # Check the pattern type.
1396                      my @sections = split("::", $dataValue);              if (substr($valuePattern, 0, 1) eq '/') {
1397                      # Loop through the value patterns, looking for a mismatch. Note that                  # Regular expressions invalidate the entire process.
1398                      # since we're working through parallel arrays, we are using an index                  $okValues = 0;
1399                      # loop. As soon as a match fails we stop checking. This means that              } elsif (substr($valuePattern, -1, 1) eq '%') {
1400                      # if the value pattern list is longer than the number of sections,                  # A Generic pattern is passed in unmodified.
1401                      # we will fail as soon as we run out of sections.                  push @valuePatterns, $valuePattern;
1402                      my $match = 1;              } else {
1403                      for (my $i = 0; $i <= $#valuePatterns && $match; $i++) {                  # An exact match is converted to generic.
1404                          $match = MatchSqlPattern($sections[$i], $valuePatterns[$i]);                  push @valuePatterns, "$valuePattern%";
1405                      }              }
1406                      # If we match, we save this value in the output list.          }
1407                      if ($match) {          # If everything works, add the value data to the filtering hash.
1408                          push @retVal, [$rowObjectID, $key, @sections];          if ($okValues) {
1409                      }              $data{'HasValueFor(value)'} = \@valuePatterns;
1410                  }          }
1411                  # Here we've processed all the attribute values for the current object ID.      }
1412        # Create some lists to contain the filter fragments and parameter values.
1413        my @filter = ();
1414        my @parms = ();
1415        # This next loop goes through the different fields that can be specified in the
1416        # parameter list and generates filters for each. The %data hash that we built above
1417        # contains all the necessary information to do this.
1418        for my $field (keys %data) {
1419            # Accumulate filter information for this field. We will OR together all the
1420            # elements accumulated to create the final result.
1421            my @fieldFilter = ();
1422            # Get the specified data from the caller.
1423            my $fieldPattern = $data{$field};
1424            # Only proceed if the pattern is one that won't match everything.
1425            if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1426                # Convert the pattern to an array.
1427                my @patterns = ();
1428                if (ref $fieldPattern eq 'ARRAY') {
1429                    push @patterns, @{$fieldPattern};
1430                } else {
1431                    push @patterns, $fieldPattern;
1432                }
1433                # Only proceed if the array is nonempty. The loop will work fine if the
1434                # array is empty, but when we build the filter string at the end we'll
1435                # get "()" in the filter list, which will result in an SQL syntax error.
1436                if (@patterns) {
1437                    # Loop through the individual patterns.
1438                    for my $pattern (@patterns) {
1439                        # Check for a generic request.
1440                        if (substr($pattern, -1, 1) ne '%') {
1441                            # Here we have a normal request.
1442                            push @fieldFilter, "$field = ?";
1443                            push @parms, $pattern;
1444                        } else {
1445                            # Here we have a generic request, so we will use the LIKE operator to
1446                            # filter the field to this value pattern.
1447                            push @fieldFilter, "$field LIKE ?";
1448                            # We must convert the pattern value to an SQL match pattern. First
1449                            # we get a copy of it.
1450                            my $actualPattern = $pattern;
1451                            # Now we escape the underscores. Underscores are an SQL wild card
1452                            # character, but they are used frequently in key names and object IDs.
1453                            $actualPattern =~ s/_/\\_/g;
1454                            # Add the escaped pattern to the bound parameter list.
1455                            push @parms, $actualPattern;
1456                        }
1457                    }
1458                    # Form the filter for this field.
1459                    my $fieldFilterString = join(" OR ", @fieldFilter);
1460                    push @filter, "($fieldFilterString)";
1461              }              }
             # Here we've processed all the rows returned by GetAll. In general, there will  
             # be one row per object ID.  
1462          }          }
         # Here we've processed all the matching attribute keys.  
1463      }      }
1464      # Here we've processed all the entity types. That means @retVal has all the matching      # Now @filter contains one or more filter strings and @parms contains the parameter
1465      # results.      # values to bind to them.
1466        my $actualFilter = join(" AND ", @filter);
1467        # Now we're ready to make our query.
1468        my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1469        # Format the results.
1470        my @retVal = $self->_QueryResults($query, @values);
1471        # Return the rows found.
1472      return @retVal;      return @retVal;
1473  }  }
1474    
# Line 1195  Line 1483 
1483    
1484  =item objectID  =item objectID
1485    
1486  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.  
1487    
1488  =item key  =item key
1489    
1490  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1491    
1492  =item values  =item values
1493    
# Line 1225  Line 1510 
1510      } elsif (! @values) {      } elsif (! @values) {
1511          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1512      } else {      } else {
1513          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1514          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1515          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1516          # Insert the value.          # Split up the key.
1517          $self->InsertValue($id, "$entityName($key)", $valueString);          my ($realKey, $subKey) = $self->SplitKey($key);
1518            # Connect the object to the key.
1519            $self->InsertObject('HasValueFor', { 'from-link' => $realKey,
1520                                                 'to-link'   => $objectID,
1521                                                 'subkey'    => $subKey,
1522                                                 'value'     => $valueString,
1523                                           });
1524      }      }
1525      # Return a one. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1526      return 1;      return 1;
1527  }  }
1528    
# Line 1243  Line 1532 
1532    
1533  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1534    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1535  =over 4  =over 4
1536    
1537  =item objectID  =item objectID
1538    
1539  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.  
1540    
1541  =item key  =item key
1542    
1543  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1544    
1545  =item values  =item values
1546    
1547  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
1548    will be deleted. Otherwise, only a matching value will be deleted.
1549    
1550  =back  =back
1551    
# Line 1275  Line 1559 
1559          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1560      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1561          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
     } elsif (! @values) {  
         Confess("No values specified in DeleteAttribute call for key $key.");  
1562      } else {      } else {
1563          # Now compute the object type and ID.          # Split the key into the real key and the subkey.
1564          my ($entityName, $id) = ComputeObjectTypeFromID($objectID);          my ($realKey, $subKey) = $self->SplitKey($key);
1565          # Form the values into a scalar.          if ($subKey eq '' && scalar(@values) == 0) {
1566                # Here we erase the entire key for this object.
1567                $self->DeleteRow('HasValueFor', $key, $objectID);
1568            } else {
1569                # Here we erase the matching values.
1570          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1571          # Delete the value.              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1572          $self->DeleteValue($entityName, $id, $key, $valueString);                               { subkey => $subKey, value => $valueString });
1573            }
1574      }      }
1575      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1576      return 1;      return 1;
1577  }  }
1578    
1579    =head3 DeleteMatchingAttributes
1580    
1581    C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>
1582    
1583    Delete all attributes that match the specified criteria. This is equivalent to
1584    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1585    row found.
1586    
1587    =over 4
1588    
1589    =item objectID
1590    
1591    ID of object whose attributes are to be deleted. If the attributes for multiple
1592    objects are to be deleted, this parameter can be specified as a list reference. If
1593    attributes are to be deleted for all objects, specify C<undef> or an empty string.
1594    Finally, you can delete attributes for a range of object IDs by putting a percent
1595    sign (C<%>) at the end.
1596    
1597    =item key
1598    
1599    Attribute key name. A value of C<undef> or an empty string will match all
1600    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1601    specified as a list reference. Finally, you can delete attributes for a range of
1602    keys by putting a percent sign (C<%>) at the end.
1603    
1604    =item values
1605    
1606    List of the desired attribute values, section by section. If C<undef>
1607    or an empty string is specified, all values in that section will match. A
1608    generic match can be requested by placing a percent sign (C<%>) at the end.
1609    In that case, all values that match up to and not including the percent sign
1610    will match. You may also specify a regular expression enclosed
1611    in slashes. All values that match the regular expression will be deleted. For
1612    performance reasons, only values have this extra capability.
1613    
1614    =item RETURN
1615    
1616    Returns a list of tuples for the attributes that were deleted, in the
1617    same form as L</GetAttributes>.
1618    
1619    =back
1620    
1621    =cut
1622    
1623    sub DeleteMatchingAttributes {
1624        # Get the parameters.
1625        my ($self, $objectID, $key, @values) = @_;
1626        # Get the matching attributes.
1627        my @retVal = $self->GetAttributes($objectID, $key, @values);
1628        # Loop through the attributes, deleting them.
1629        for my $tuple (@retVal) {
1630            $self->DeleteAttribute(@{$tuple});
1631        }
1632        # Log this operation.
1633        my $count = @retVal;
1634        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1635        # Return the deleted attributes.
1636        return @retVal;
1637    }
1638    
1639  =head3 ChangeAttribute  =head3 ChangeAttribute
1640    
1641  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>
# Line 1333  Line 1680 
1680      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1681          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1682      } else {      } else {
1683          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1684          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1685          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1686      }      }
# Line 1343  Line 1690 
1690    
1691  =head3 EraseAttribute  =head3 EraseAttribute
1692    
1693  C<< $attrDB->EraseAttribute($entityName, $key); >>  C<< $attrDB->EraseAttribute($key); >>
1694    
1695  Erase all values for the specified attribute key. This does not remove the  Erase all values for the specified attribute key. This does not remove the
1696  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
1697    
1698  =over 4  =over 4
1699    
 =item entityName  
   
 Name of the entity to which the key belongs. If undefined, all entities will be  
 examined for the desired key.  
   
1700  =item key  =item key
1701    
1702  Key to erase.  Key to erase. This must be a real key; that is, it cannot have a subkey
1703    component.
1704    
1705  =back  =back
1706    
# Line 1365  Line 1708 
1708    
1709  sub EraseAttribute {  sub EraseAttribute {
1710      # Get the parameters.      # Get the parameters.
1711      my ($self, $entityName, $key) = @_;      my ($self, $key) = @_;
1712      # Determine the relevant entity types.      # Delete everything connected to the key.
1713      my @objects = ();      $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1714      if (! $entityName) {      # Log the operation.
1715          push @objects, $self->GetEntityTypes();      $self->LogOperation("Erase Data", $key);
     } else {  
         push @objects, $entityName;  
     }  
     # Loop through the entity types.  
     for my $entityType (@objects) {  
         # Now check for this key in this entity.  
         my %secondaries = $self->GetSecondaryFields($entityType);  
         if (exists $secondaries{$key}) {  
             # We found it, so delete all the values of the key.  
             $self->DeleteValue($entityType, undef, $key);  
         }  
     }  
1716      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1717      return 1;      return 1;
1718  }  }
1719    
1720  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1721    
1722  C<< my @keyList = $attrDB->GetAttributeKeys($entityName); >>  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1723    
1724  Return a list of the attribute keys for a particular entity type.  Return a list of the attribute keys for a particular group.
1725    
1726  =over 4  =over 4
1727    
1728  =item entityName  =item groupName
1729    
1730  Name of the entity whose keys are desired.  Name of the group whose keys are desired.
1731    
1732  =item RETURN  =item RETURN
1733    
1734  Returns a list of the attribute keys for the specified entity.  Returns a list of the attribute keys for the specified group.
1735    
1736  =back  =back
1737    
# Line 1408  Line 1739 
1739    
1740  sub GetAttributeKeys {  sub GetAttributeKeys {
1741      # Get the parameters.      # Get the parameters.
1742      my ($self, $entityName) = @_;      my ($self, $groupName) = @_;
1743      # Get the entity's secondary fields.      # Get the attributes for the specified group.
1744      my %keyList = $self->GetSecondaryFields($entityName);      my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1745                                    'IsInGroup(from-link)');
1746      # Return the keys.      # Return the keys.
1747      return sort keys %keyList;      return sort @groups;
1748    }
1749    
1750    =head3 QueryAttributes
1751    
1752    C<< my @attributeData = $ca->QueryAttributes($filter, $filterParms); >>
1753    
1754    Return the attribute data based on an SQL filter clause. In the filter clause,
1755    the name C<$object> should be used for the object ID, C<$key> should be used for
1756    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1757    
1758    =over 4
1759    
1760    =item filter
1761    
1762    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1763    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1764    and C<$value> for the value field. This abstraction enables us to hide the details of
1765    the database construction from the user.
1766    
1767    =item filterParms
1768    
1769    Parameters for the filter clause.
1770    
1771    =item RETURN
1772    
1773    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1774    one or more attribute values.
1775    
1776    =back
1777    
1778    =cut
1779    
1780    # This hash is used to drive the substitution process.
1781    my %AttributeParms = (object => 'HasValueFor(to-link)',
1782                          key    => 'HasValueFor(from-link)',
1783                          subkey => 'HasValueFor(subkey)',
1784                          value  => 'HasValueFor(value)');
1785    
1786    sub QueryAttributes {
1787        # Get the parameters.
1788        my ($self, $filter, $filterParms) = @_;
1789        # Declare the return variable.
1790        my @retVal = ();
1791        # Make sue we have filter parameters.
1792        my $realParms = (defined($filterParms) ? $filterParms : []);
1793        # Create the query by converting the filter.
1794        my $realFilter = $filter;
1795        for my $name (keys %AttributeParms) {
1796            $realFilter =~ s/\$$name/$AttributeParms{$name}/g;
1797        }
1798        my $query = $self->Get(['HasValueFor'], $realFilter, $realParms);
1799        # Loop through the results, forming the output attribute tuples.
1800        while (my $result = $query->Fetch()) {
1801            # Get the four values from this query result row.
1802            my ($objectID, $key, $subkey, $value) = $result->Values([$AttributeParms{object},
1803                                                                    $AttributeParms{key},
1804                                                                    $AttributeParms{subkey},
1805                                                                    $AttributeParms{value}]);
1806            # Combine the key and the subkey.
1807            my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1808            # Split the value.
1809            my @values = split $self->{splitter}, $value;
1810            # Output the result.
1811            push @retVal, [$objectID, $realKey, @values];
1812        }
1813        # Return the result.
1814        return @retVal;
1815    }
1816    
1817    =head2 Key and ID Manipulation Methods
1818    
1819    =head3 ParseID
1820    
1821    C<< my ($type, $id) = CustomAttributes::ParseID($idValue); >>
1822    
1823    Determine the type and object ID corresponding to an ID value from the attribute database.
1824    Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
1825    however, Genomes, Features, and Subsystems are not stored with a type name, so we need to
1826    deduce the type from the ID value structure.
1827    
1828    The theory here is that you can plug the ID and type directly into a Sprout database method, as
1829    follows
1830    
1831        my ($type, $id) = CustomAttributes::ParseID($attrList[$num]->[0]);
1832        my $target = $sprout->GetEntity($type, $id);
1833    
1834    =over 4
1835    
1836    =item idValue
1837    
1838    ID value taken from the attribute database.
1839    
1840    =item RETURN
1841    
1842    Returns a two-element list. The first element is the type of object indicated by the ID value,
1843    and the second element is the actual object ID.
1844    
1845    =back
1846    
1847    =cut
1848    
1849    sub ParseID {
1850        # Get the parameters.
1851        my ($idValue) = @_;
1852        # Declare the return variables.
1853        my ($type, $id);
1854        # Parse the incoming ID. We first check for the presence of an entity name. Entity names
1855        # can only contain letters, which helps to insure typed object IDs don't collide with
1856        # subsystem names (which are untyped).
1857        if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1858            # Here we have a typed ID.
1859            ($type, $id) = ($1, $2);
1860            # Fix the case sensitivity on PDB IDs.
1861            if ($type eq 'PDB') { $id = lc $id; }
1862        } elsif ($idValue =~ /fig\|/) {
1863            # Here we have a feature ID.
1864            ($type, $id) = (Feature => $idValue);
1865        } elsif ($idValue =~ /\d+\.\d+/) {
1866            # Here we have a genome ID.
1867            ($type, $id) = (Genome => $idValue);
1868        } else {
1869            # The default is a subsystem ID.
1870            ($type, $id) = (Subsystem => $idValue);
1871        }
1872        # Return the results.
1873        return ($type, $id);
1874    }
1875    
1876    =head3 FormID
1877    
1878    C<< my $idValue = CustomAttributes::FormID($type, $id); >>
1879    
1880    Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1881    genomes, and features are stored in the database without type information, but all other object IDs
1882    must be prefixed with the object type.
1883    
1884    =over 4
1885    
1886    =item type
1887    
1888    Relevant object type.
1889    
1890    =item id
1891    
1892    ID of the object in question.
1893    
1894    =item RETURN
1895    
1896    Returns a string that will be recognized as an object ID in the attribute database.
1897    
1898    =back
1899    
1900    =cut
1901    
1902    sub FormID {
1903        # Get the parameters.
1904        my ($type, $id) = @_;
1905        # Declare the return variable.
1906        my $retVal;
1907        # Compute the ID string from the type.
1908        if (grep { $type eq $_ } qw(Feature Genome Subsystem)) {
1909            $retVal = $id;
1910        } else {
1911            $retVal = "$type:$id";
1912        }
1913        # Return the result.
1914        return $retVal;
1915    }
1916    
1917    =head3 GetTargetObject
1918    
1919    C<< my $object = CustomAttributes::GetTargetObject($erdb, $idValue); >>
1920    
1921    Return the database object corresponding to the specified attribute object ID. The
1922    object type associated with the ID value must correspond to an entity name in the
1923    specified database.
1924    
1925    =over 4
1926    
1927    =item erdb
1928    
1929    B<ERDB> object for accessing the target database.
1930    
1931    =item idValue
1932    
1933    ID value retrieved from the attribute database.
1934    
1935    =item RETURN
1936    
1937    Returns a B<ERDBObject> for the attribute value's target object.
1938    
1939    =back
1940    
1941    =cut
1942    
1943    sub GetTargetObject {
1944        # Get the parameters.
1945        my ($erdb, $idValue) = @_;
1946        # Declare the return variable.
1947        my $retVal;
1948        # Get the type and ID for the target object.
1949        my ($type, $id) = ParseID($idValue);
1950        # Plug them into the GetEntity method.
1951        $retVal = $erdb->GetEntity($type, $id);
1952        # Return the resulting object.
1953        return $retVal;
1954    }
1955    
1956    =head3 SplitKey
1957    
1958    C<< my ($realKey, $subKey) = $ca->SplitKey($key); >>
1959    
1960    Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1961    The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
1962    then the sub key is presumed to be an empty string.
1963    
1964    =over 4
1965    
1966    =item key
1967    
1968    Incoming key to be split.
1969    
1970    =item RETURN
1971    
1972    Returns a two-element list, the first element of which is the real key and the second element of
1973    which is the sub key.
1974    
1975    =back
1976    
1977    =cut
1978    
1979    sub SplitKey {
1980        # Get the parameters.
1981        my ($self, $key) = @_;
1982        # Do the split.
1983        my ($realKey, $subKey) = split($self->{splitter}, $key, 2);
1984        # Insure the subkey has a value.
1985        if (! defined $subKey) {
1986            $subKey = '';
1987        }
1988        # Return the results.
1989        return ($realKey, $subKey);
1990    }
1991    
1992    =head3 JoinKey
1993    
1994    C<< my $key = $ca->JoinKey($realKey, $subKey); >>
1995    
1996    Join a real key and a subkey together to make an external key. The external key is the attribute key
1997    used by the caller. The real key and the subkey are how the keys are represented in the database. The
1998    real key is the key to the B<AttributeKey> entity. The subkey is an attribute of the B<HasValueFor>
1999    relationship.
2000    
2001    =over 4
2002    
2003    =item realKey
2004    
2005    The real attribute key.
2006    
2007    =item subKey
2008    
2009    The subordinate portion of the attribute key.
2010    
2011    =item RETURN
2012    
2013    Returns a single string representing both keys.
2014    
2015    =back
2016    
2017    =cut
2018    
2019    sub JoinKey {
2020        # Get the parameters.
2021        my ($self, $realKey, $subKey) = @_;
2022        # Declare the return variable.
2023        my $retVal;
2024        # Check for a subkey.
2025        if ($subKey eq '') {
2026            # No subkey, so the real key is the key.
2027            $retVal = $realKey;
2028        } else {
2029            # Subkey found, so the two pieces must be joined by a splitter.
2030            $retVal = "$realKey$self->{splitter}$subKey";
2031  }  }
2032        # Return the result.
2033        return $retVal;
2034    }
2035    
2036    
2037    =head3 AttributeTable
2038    
2039    C<< my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList); >>
2040    
2041    Format the attribute data into an HTML table.
2042    
2043    =over 4
2044    
2045    =item cgi
2046    
2047    CGI query object used to generate the HTML
2048    
2049    =item attrList
2050    
2051    List of attribute results, in the format returned by the L</GetAttributes> or
2052    L</QueryAttributes> methods.
2053    
2054    =item RETURN
2055    
2056    Returns an HTML table displaying the attribute keys and values.
2057    
2058    =back
2059    
2060    =cut
2061    
2062    sub AttributeTable {
2063        # Get the parameters.
2064        my ($cgi, @attrList) = @_;
2065        # Accumulate the table rows.
2066        my @html = ();
2067        for my $attrData (@attrList) {
2068            # Format the object ID and key.
2069            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
2070            # Now we format the values. These remain unchanged unless one of them is a URL.
2071            my $lastValue = scalar(@{$attrData}) - 1;
2072            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
2073            # Assemble the values into a table row.
2074            push @html, $cgi->Tr($cgi->td(\@columns));
2075        }
2076        # Format the table in the return variable.
2077        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
2078        # Return it.
2079        return $retVal;
2080    }
2081  1;  1;

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