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revision 1.9, Thu Nov 16 22:09:33 2006 UTC revision 1.26, Mon Jun 11 18:44:40 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    
13  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
14    
# Line 15  Line 16 
16    
17  The Custom SEED Attributes Manager allows the user to upload and retrieve  The Custom SEED Attributes Manager allows the user to upload and retrieve
18  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
19  store the attributes, which are implemented as multi-valued fields  store the attributes.
20  of ERDB entities.  
21    Attributes are organized by I<attribute key>. Attribute values are
22    assigned to I<objects>. In the real world, objects have types and IDs;
23    however, to the attribute database only the ID matters. This will create
24    a problem if we have a single ID that applies to two objects of different
25    types, but it is more consistent with the original attribute implementation
26    in the SEED (which this implementation replaces).
27    
28    The actual attribute values are stored as a relationship between the attribute
29    keys and the objects. There can be multiple values for a single key/object pair.
30    
31    =head3 Object IDs
32    
33    The object ID is normally represented as
34    
35        I<type>:I<id>
36    
37    where I<type> is the object type (C<Role>, C<Coupling>, etc.) and I<id> is
38    the actual object ID. Note that the object type must consist of only upper- and
39    lower-case letters! Thus, C<GenomeGroup> is a valid object type, but
40    C<genome_group> is not. Given that restriction, the object ID
41    
42        Family:aclame|cluster10
43    
44    would represent the FIG family C<aclame|cluster10>. For historical reasons,
45    there are three exceptions: subsystems, genomes, and features do not need
46    a type. So, for PEG 3361 of Streptomyces coelicolor A3(2), you simply code
47    
48        fig|100226.1.peg.3361
49    
50    The methods L</ParseID> and L</FormID> can be used to make this all seem
51    more consistent. Given any object ID string, L</ParseID> will convert it to an
52    object type and ID, and given any object type and ID, L</FormID> will
53    convert it to an object ID string. The attribute database is pretty
54    freewheeling about what it will allow for an ID; however, for best
55    results, the type should match an entity type from a Sprout genetics
56    database. If this rule is followed, then the database object
57    corresponding to an ID in the attribute database could be retrieved using
58    L</GetTargetObject> method.
59    
60        my $object = CustomAttributes::GetTargetObject($sprout, $idValue);
61    
62    =head3 Retrieval and Logging
63    
64  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
65  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
66  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
67  would code  would code
68    
69      my @values = $attrDB->GetAttributes([Feature => $fid], 'essential');      my @values = $attrDB->GetAttributes($fid, 'essential');
70    
71  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.  
72    
73  New attributes are introduced by updating the database definition at  Keys can be split into two pieces using the splitter value defined in the
74  run-time. Attribute values are stored by uploading data from files.  constructor (the default is C<::>). The first piece of the key is called
75  A web interface is provided for both these activities.  the I<real key>. This portion of the key must be defined using the
76    web interface (C<Attributes.cgi>). The second portion of the key is called
77    the I<sub key>, and can take any value.
78    
79    Major attribute activity is recorded in a log (C<attributes.log>) in the
80    C<$FIG_Config::var> directory. The log reports the user name, time, and
81    the details of the operation. The user name will almost always be unknown,
82    the exception being when it is specified in this object's constructor
83    (see L</new>).
84    
85  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
86    
# Line 76  Line 126 
126    
127  =back  =back
128    
 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.  
   
129  =head2 Public Methods  =head2 Public Methods
130    
131  =head3 new  =head3 new
132    
133  C<< my $attrDB = CustomAttributes->new($splitter); >>  C<< my $attrDB = CustomAttributes->new(%options); >>
134    
135  Construct a new CustomAttributes object. This object cannot be used to add or  Construct a new CustomAttributes object. The following options are
136  delete keys because that requires modifying the database design. To do that,  supported.
 you need to use the static L</StoreAttributeKey> or L</DeleteAttributeKey>  
 methods.  
137    
138  =over 4  =over 4
139    
140  =item splitter  =item splitter
141    
142  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
143  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
144  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
145  worry about this parameter.  
146    =item user
147    
148    Name of the current user. This will appear in the attribute log.
149    
150  =back  =back
151    
# Line 142  Line 153 
153    
154  sub new {  sub new {
155      # Get the parameters.      # Get the parameters.
156      my ($class, $splitter) = @_;      my ($class, %options) = @_;
157      # Connect to the database.      # Connect to the database.
158      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
159                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 152  Line 163 
163      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
164      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
165      # Store the splitter value.      # Store the splitter value.
166      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
167        # Store the user name.
168        $retVal->{user} = $options{user} || '<unknown>';
169        Trace("User $retVal->{user} selected for attribute object.") if T(3);
170      # Return the result.      # Return the result.
171      return $retVal;      return $retVal;
172  }  }
173    
174  =head3 StoreAttributeKey  =head3 StoreAttributeKey
175    
176  C<< my $attrDB = CustomAttributes::StoreAttributeKey($entityName, $attributeName, $type, $notes); >>  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>
177    
178  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.  
179    
180  =over 4  =over 4
181    
 =item entityName  
   
 Name of the entity containing the attribute. The entity must exist.  
   
182  =item attributeName  =item attributeName
183    
184  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.  
185    
186  =item type  =item type
187    
# Line 185  Line 191 
191    
192  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.
193    
194  =item RETURN  =item groups
195    
196  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.
197  error will be thrown.  This will replace any groups to which the attribute is currently attached.
198    
199  =back  =back
200    
# Line 196  Line 202 
202    
203  sub StoreAttributeKey {  sub StoreAttributeKey {
204      # Get the parameters.      # Get the parameters.
205      my ($entityName, $attributeName, $type, $notes) = @_;      my ($self, $attributeName, $type, $notes, $groups) = @_;
206      # Declare the return variable.      # Declare the return variable.
207      my $retVal;      my $retVal;
208      # Get the data type hash.      # Get the data type hash.
209      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
210      # Validate the initial input values.      # Validate the initial input values.
211      if (! ERDB::ValidateFieldName($attributeName)) {      if ($attributeName =~ /$self->{splitter}/) {
212          Confess("Invalid attribute name \"$attributeName\" specified.");          Confess("Invalid attribute name \"$attributeName\" specified.");
213      } elsif (! $notes || length($notes) < 25) {      } elsif (! $notes || length($notes) < 25) {
214          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing or incomplete description for $attributeName.");
215      } elsif (! exists $types{$type}) {      } elsif (! exists $types{$type}) {
216          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid data type \"$type\" for $attributeName.");
217        } else {
218            # Create a variable to hold the action to be displayed for the log (Add or Update).
219            my $action;
220            # Okay, we're ready to begin. See if this key exists.
221            my $attribute = $self->GetEntity('AttributeKey', $attributeName);
222            if (defined($attribute)) {
223                # It does, so we do an update.
224                $action = "Update Key";
225                $self->UpdateEntity('AttributeKey', $attributeName,
226                                    { description => $notes, 'data-type' => $type });
227                # Detach the key from its current groups.
228                $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
229            } else {
230                # It doesn't, so we do an insert.
231                $action = "Insert Key";
232                $self->InsertObject('AttributeKey', { id => $attributeName,
233                                    description => $notes, 'data-type' => $type });
234            }
235            # Attach the key to the specified groups. (We presume the groups already
236            # exist.)
237            for my $group (@{$groups}) {
238                $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
239                                                   'to-link'   => $group });
240      }      }
241      # Our next step is to read in the XML for the database defintion. We          # Log the operation.
242      # 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);  
         }  
243      }      }
     return $retVal;  
244  }  }
245    
 =head3 Refresh  
246    
247  C<< $attrDB->Refresh($fig); >>  =head3 DeleteAttributeKey
248    
249    C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
250    
251  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.  
252    
253  =over 4  =over 4
254    
255  =item fig  =item attributeName
256    
257    Name of the attribute to delete.
258    
259    =item RETURN
260    
261  FIG-like object that can be used to find genomes and features.  Returns a statistics object describing the effects of the deletion.
262    
263  =back  =back
264    
265  =cut  =cut
266    
267  sub Refresh {  sub DeleteAttributeKey {
268      # Get the parameters.      # Get the parameters.
269      my ($self, $fig) = @_;      my ($self, $attributeName) = @_;
270      # Create load objects for the genomes and the features.      # Delete the attribute key.
271      my $loadGenome = ERDBLoad->new($self, 'Genome', $FIG_Config::temp);      my $retVal = $self->Delete('AttributeKey', $attributeName);
272      my $loadFeature = ERDBLoad->new($self, 'Feature', $FIG_Config::temp);      # Log this operation.
273      # Get the genome list.      $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
274      my @genomes = $fig->genomes();      # Return the result.
275      # Loop through the genomes.      return $retVal;
276      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);  
         }  
277      }      }
278      # Get a variable for holding statistics objects.  
279      my $stats;  =head3 NewName
280      # Finish the genome load.  
281      Trace("Loading Genome relation.") if T(2);  C<< my $text = CustomAttributes::NewName(); >>
282      $stats = $loadGenome->FinishAndLoad();  
283      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.
284      # Finish the feature load.  
285      Trace("Loading Feature relation.") if T(2);  =cut
286      $stats = $loadFeature->FinishAndLoad();  
287      Trace("Feature table load statistics:\n" . $stats->Show()) if T(3);  sub NewName {
288        return "(new)";
289  }  }
290    
291  =head3 LoadAttributeKey  =head3 ControlForm
292    
293  C<< my $stats = $attrDB->LoadAttributeKey($entityName, $fieldName, $fh, $keyCol, $dataCol); >>  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
294    
295  Load the specified attribute from the specified file. The file should be a  Return a form that can be used to control the creation and modification of
296  tab-delimited file with internal tab and new-line characters escaped. This is  attributes. Only a subset of the attribute keys will be displayed, as
297  the typical TBL-style file used by most FIG applications. One of the columns  determined by the incoming list.
 in the input file must contain the appropriate key value and the other the  
 corresponding attribute value.  
298    
299  =over 4  =over 4
300    
301  =item entityName  =item cgi
302    
303    CGI query object used to create HTML.
304    
305    =item name
306    
307    Name to give to the form. This should be unique for the web page.
308    
309    =item keys
310    
311    Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
312    attribute's data type, its description, and a list of the groups in which it participates.
313    
314    =item RETURN
315    
316    Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script
317    for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
318    controls are generated. The form tags are left to the caller.
319    
320    =back
321    
322  Name of the entity containing the attribute.  =cut
323    
324  =item fieldName  sub ControlForm {
325        # Get the parameters.
326        my ($self, $cgi, $name, $keys) = @_;
327        # Declare the return list.
328        my @retVal = ();
329        # We'll put the controls in a table. Nothing else ever seems to look nice.
330        push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
331        # The first row is for selecting the field name.
332        push @retVal, $cgi->Tr($cgi->th("Select a Field"),
333                               $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
334                                                         new => 1,
335                                                         notes => "document.$name.notes.value",
336                                                         type => "document.$name.dataType.value",
337                                                         groups => "document.$name.groups")));
338        # Now we set up a dropdown for the data types. The values will be the
339        # data type names, and the labels will be the descriptions.
340        my %types = ERDB::GetDataTypes();
341        my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
342        my $typeMenu = $cgi->popup_menu(-name   => 'dataType',
343                                        -values => [sort keys %types],
344                                        -labels => \%labelMap,
345                                        -default => 'string');
346        # Allow the user to specify a new field name. This is required if the
347        # user has selected the "(new)" marker.
348        my $fieldField = "document.$name.fieldName";
349        my $newName = "\"" . NewName() . "\"";
350        push @retVal, $cgi->Tr($cgi->th("New Field Name"),
351                               $cgi->td($cgi->textfield(-name => 'newName',
352                                                        -size => 30,
353                                                        -value => "",
354                                                        -onFocus => "setIfEmpty($fieldField, $newName);")),
355                                        );
356        push @retVal, $cgi->Tr($cgi->th("Data type"),
357                               $cgi->td($typeMenu));
358        # The next row is for the notes.
359        push @retVal, $cgi->Tr($cgi->th("Description"),
360                               $cgi->td($cgi->textarea(-name => 'notes',
361                                                       -rows => 6,
362                                                       -columns => 80))
363                              );
364        # Now we have the groups, which are implemented as a checkbox group.
365        my @groups = $self->GetGroups();
366        push @retVal, $cgi->Tr($cgi->th("Groups"),
367                               $cgi->td($cgi->checkbox_group(-name=>'groups',
368                                        -values=> \@groups))
369                              );
370        # Now the four buttons: STORE, SHOW, ERASE, and DELETE.
371        push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
372                               $cgi->td({align => 'center'}, join(" ",
373                                        $cgi->submit(-name => 'Delete', -value => 'DELETE'),
374                                        $cgi->submit(-name => 'Store',  -value => 'STORE'),
375                                        $cgi->submit(-name => 'Erase',  -value => 'ERASE'),
376                                        $cgi->submit(-name => 'Show',   -value => 'SHOW')
377                                       ))
378                              );
379        # Close the table and the form.
380        push @retVal, $cgi->end_table();
381        # Return the assembled HTML.
382        return join("\n", @retVal, "");
383    }
384    
385  Name of the actual attribute.  =head3 LoadAttributesFrom
386    
387  =item fh  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
388    s
389    Load attributes from the specified tab-delimited file. Each line of the file must
390    contain an object ID in the first column, an attribute key name in the second
391    column, and attribute values in the remaining columns. The attribute values will
392    be assembled into a single value using the splitter code. In addition, the key names may
393    contain a splitter. If this is the case, the portion of the key after the splitter is
394    treated as a subkey.
395    
396  Open file handle for the input file.  =over 4
397    
398  =item keyCol  =item fileName
399    
400  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.
401  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
402    control.)
403    
404  =item dataCol  =item options
405    
406  Index (0-based) of the column containing the data value field.  Hash of options for modifying the load process.
407    
408  =item RETURN  =item RETURN
409    
410  Returns a statistics object for the load process.  Returns a statistics object describing the load.
411    
412    =back
413    
414    Permissible option values are as follows.
415    
416    =over 4
417    
418    =item append
419    
420    If TRUE, then the attributes will be appended to existing data; otherwise, the
421    first time a key name is encountered, it will be erased.
422    
423    =item archive
424    
425    If specified, the name of a file into which the incoming data file should be saved.
426    
427    =item objectType
428    
429    If specified, the specified object type will be prefixed to each object ID.
430    
431  =back  =back
432    
433  =cut  =cut
434    
435  sub LoadAttributeKey {  sub LoadAttributesFrom {
436      # Get the parameters.      # Get the parameters.
437      my ($self, $entityName, $fieldName, $fh, $keyCol, $dataCol) = @_;      my ($self, $fileName, %options) = @_;
438      # Create the return variable.      # Declare the return variable.
439      my $retVal;      my $retVal = Stats->new('keys', 'values');
440      # Insure the entity exists.      # Check for append mode.
441      my $found = grep { $_ eq $entityName } $self->GetEntityTypes();      my $append = ($options{append} ? 1 : 0);
442      if (! $found) {      # Create a hash of key names found.
443          Confess("Entity \"$entityName\" not found in database.");      my %keyHash = ();
444      } else {      # Open the file for input. Note we must anticipate the possibility of an
445          # Get the field structure for the named entity.      # open filehandle being passed in.
446          my $fieldHash = $self->GetFieldTable($entityName);      my $fh;
447          # Verify that the attribute exists.      if (ref $fileName) {
448          if (! exists $fieldHash->{$fieldName}) {          Trace("Using file opened by caller.") if T(3);
449              Confess("Attribute key \"$fieldName\" does not exist in entity $entityName.");          $fh = $fileName;
         } else {  
             # Create a loader for the specified attribute. We need the  
             # relation name first.  
             my $relName = $fieldHash->{$fieldName}->{relation};  
             my $loadAttribute = ERDBLoad->new($self, $relName, $FIG_Config::temp);  
             # Loop through the input file.  
             while (! eof $fh) {  
                 # Get the next line of the file.  
                 my @fields = Tracer::GetLine($fh);  
                 $loadAttribute->Add("lineIn");  
                 # Now we need to validate the line.  
                 if ($#fields < $dataCol) {  
                     $loadAttribute->Add("shortLine");  
                 } elsif (! $self->Exists($entityName, $fields[$keyCol])) {  
                     $loadAttribute->Add("badKey");  
450                  } else {                  } else {
451                      # It's valid,so send it to the loader.          Trace("Attributes will be loaded from $fileName.") if T(3);
452                      $loadAttribute->Put($fields[$keyCol], $fields[$dataCol]);          $fh = Open(undef, "<$fileName");
                     $loadAttribute->Add("lineUsed");  
453                  }                  }
454        # Now check to see if we need to archive.
455        my $ah;
456        if ($options{archive}) {
457            $ah = Open(undef, ">$options{archive}");
458            Trace("Load file will be archived to $options{archive}.") if T(3);
459        }
460        # Finally, open a database transaction.
461        $self->BeginTran();
462        # Insure we recover from errors. If an error occurs, we will delete the archive file and
463        # roll back the updates.
464        eval {
465            # Loop through the file.
466            while (! eof $fh) {
467                # Read the current line.
468                my ($id, $key, @values) = Tracer::GetLine($fh);
469                $retVal->Add(linesIn => 1);
470                # Check to see if we need to fix up the object ID.
471                if ($options{objectType}) {
472                    $id = "$options{objectType}:$id";
473                }
474                # Archive the line (if necessary).
475                if (defined $ah) {
476                    Tracer::PutLine($ah, [$id, $key, @values]);
477                }
478                # Do some validation.
479                if (! $id) {
480                    # We ignore blank lines.
481                    $retVal->Add(blankLines => 1);
482                } elsif (substr($id, 0, 1) eq '#') {
483                    # A line beginning with a pound sign is a comment.
484                    $retVal->Add(comments => 1);
485                } elsif (! defined($key)) {
486                    # An ID without a key is a serious error.
487                    my $lines = $retVal->Ask('linesIn');
488                    Confess("Line $lines in $fileName has no attribute key.");
489                } elsif (! @values) {
490                    # A line with no values is not allowed.
491                    my $lines = $retVal->Ask('linesIn');
492                    Trace("Line $lines for key $key has no attribute values.") if T(1);
493                    $retVal->Add(skipped => 1);
494                } else {
495                    # The key contains a real part and an optional sub-part. We need the real part.
496                    my ($realKey, $subKey) = $self->SplitKey($key);
497                    # Now we need to check for a new key.
498                    if (! exists $keyHash{$realKey}) {
499                        if (! $self->Exists('AttributeKey', $realKey)) {
500                            my $line = $retVal->Ask('linesIn');
501                            Confess("Attribute \"$realKey\" on line $line of $fileName not found in database.");
502                        } else {
503                            # Make sure we know this is no longer a new key.
504                            $keyHash{$realKey} = 1;
505                            $retVal->Add(keys => 1);
506                            # If this is NOT append mode, erase the key.
507                            if (! $append) {
508                                $self->EraseAttribute($realKey);
509                            }
510                        }
511                        Trace("Key $realKey found.") if T(3);
512                    }
513                    # Everything is all set up, so add the value.
514                    $self->AddAttribute($id, $key, @values);
515                    my $progress = $retVal->Add(values => 1);
516                    Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
517                }
518            }
519        };
520        # Check for an error.
521        if ($@) {
522            # Here we have an error. Roll back the transaction and delete the archive file.
523            my $message = $@;
524            Trace("Rolling back attribute updates due to error.") if T(1);
525            $self->RollbackTran();
526            if (defined $ah) {
527                Trace("Deleting archive file $options{archive}.") if T(1);
528                close $ah;
529                unlink $options{archive};
530              }              }
531              # Finish the load.          Confess("Error during attribute load: $message");
532              $retVal = $loadAttribute->FinishAndLoad();      } else {
533            # Here the load worked. Commit the transaction and close the archive file.
534            Trace("Committing attribute upload.") if T(2);
535            $self->CommitTran();
536            if (defined $ah) {
537                Trace("Closing archive file $options{archive}.") if T(2);
538                close $ah;
539          }          }
540      }      }
541      # Return the statistics.      # Return the result.
542      return $retVal;      return $retVal;
543  }  }
544    
545    =head3 BackupKeys
546    
547  =head3 DeleteAttributeKey  C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
   
 C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  
548    
549  Delete an attribute from the custom attributes database.  Backup the attribute key information from the attribute database.
550    
551  =over 4  =over 4
552    
553  =item entityName  =item fileName
554    
555  Name of the entity possessing the attribute.  Name of the output file.
556    
557  =item attributeName  =item options
558    
559  Name of the attribute to delete.  Options for modifying the backup process.
560    
561    =item RETURN
562    
563    Returns a statistics object for the backup.
564    
565    =back
566    
567    Currently there are no options. The backup is straight to a text file in
568    tab-delimited format. Each key is backup up to two lines. The first line
569    is all of the data from the B<AttributeKey> table. The second is a
570    tab-delimited list of all the groups.
571    
572    =cut
573    
574    sub BackupKeys {
575        # Get the parameters.
576        my ($self, $fileName, %options) = @_;
577        # Declare the return variable.
578        my $retVal = Stats->new();
579        # Open the output file.
580        my $fh = Open(undef, ">$fileName");
581        # Set up to read the keys.
582        my $keyQuery = $self->Get(['AttributeKey'], "", []);
583        # Loop through the keys.
584        while (my $keyData = $keyQuery->Fetch()) {
585            $retVal->Add(key => 1);
586            # Get the fields.
587            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
588                                                              'AttributeKey(description)']);
589            # Escape any tabs or new-lines in the description.
590            my $escapedDescription = Tracer::Escape($description);
591            # Write the key data to the output.
592            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
593            # Get the key's groups.
594            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
595                                        'IsInGroup(to-link)');
596            $retVal->Add(memberships => scalar(@groups));
597            # Write them to the output. Note we put a marker at the beginning to insure the line
598            # is nonempty.
599            Tracer::PutLine($fh, ['#GROUPS', @groups]);
600        }
601        # Log the operation.
602        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
603        # Return the result.
604        return $retVal;
605    }
606    
607    =head3 RestoreKeys
608    
609    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
610    
611    Restore the attribute keys and groups from a backup file.
612    
613    =over 4
614    
615    =item fileName
616    
617    Name of the file containing the backed-up keys. Each key has a pair of lines,
618    one containing the key data and one listing its groups.
619    
620  =back  =back
621    
622  =cut  =cut
623    
624  sub DeleteAttributeKey {  sub RestoreKeys {
625      # Get the parameters.      # Get the parameters.
626      my ($entityName, $attributeName) = @_;      my ($self, $fileName, %options) = @_;
627      # Read in the XML for the database defintion. We need to verify that      # Declare the return variable.
628      # the named entity exists and it has the named attribute.      my $retVal = Stats->new();
629      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Set up a hash to hold the group IDs.
630      my $entityHash = $metadata->{Entities};      my %groups = ();
631      if (! exists $entityHash->{$entityName}) {      # Open the file.
632          Confess("Entity \"$entityName\" not found.");      my $fh = Open(undef, "<$fileName");
633      } else {      # Loop until we're done.
634          # Get the field hash.      while (! eof $fh) {
635          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);          # Get a key record.
636          if (! exists $fieldHash->{$attributeName}) {          my ($id, $dataType, $description) = Tracer::GetLine($fh);
637              Confess("Attribute key \"$attributeName\" not found in entity $entityName.");          if ($id eq '#GROUPS') {
638          } else {              Confess("Group record found when key record expected.");
639              # Get the attribute's relation name.          } elsif (! defined($description)) {
640              my $relName = $fieldHash->{$attributeName}->{relation};              Confess("Invalid format found for key record.");
641              # Check for an index.          } else {
642              my $indexIdx = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);              $retVal->Add("keyIn" => 1);
643              if (defined($indexIdx)) {              # Add this key to the database.
644                  Trace("Index for $attributeName found at position $indexIdx for $entityName.") if T(3);              $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
645                  delete $entityHash->{$entityName}->{Indexes}->[$indexIdx];                                                    description => Tracer::UnEscape($description) });
646              }              Trace("Attribute $id stored.") if T(3);
647              # Delete the attribute from the field hash.              # Get the group line.
648              Trace("Deleting attribute $attributeName from $entityName.") if T(3);              my ($marker, @groups) = Tracer::GetLine($fh);
649              delete $fieldHash->{$attributeName};              if (! defined($marker)) {
650              # Write the XML back out.                  Confess("End of file found where group record expected.");
651              ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);              } elsif ($marker ne '#GROUPS') {
652              # Insure the relation does not exist in the database. This requires connecting                  Confess("Group record not found after key record.");
653              # since we may have to do a table drop.              } else {
654              my $attrDB = CustomAttributes->new();                  $retVal->Add(memberships => scalar(@groups));
655              Trace("Dropping table $relName.") if T(3);                  # Connect the groups.
656              $attrDB->DropRelation($relName);                  for my $group (@groups) {
657                        # Find out if this is a new group.
658                        if (! $groups{$group}) {
659                            $retVal->Add(newGroup => 1);
660                            # Add the group.
661                            $self->InsertObject('AttributeGroup', { id => $group });
662                            Trace("Group $group created.") if T(3);
663                            # Make sure we know it's not new.
664                            $groups{$group} = 1;
665                        }
666                        # Connect the group to our key.
667                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
668                    }
669                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
670                }
671          }          }
672      }      }
673        # Log the operation.
674        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
675        # Return the result.
676        return $retVal;
677  }  }
678    
679  =head3 ControlForm  =head3 ArchiveFileName
680    
681  C<< my $formHtml = $attrDB->ControlForm($cgi, $name); >>  C<< my $fileName = $ca->ArchiveFileName(); >>
682    
683  Return a form that can be used to control the creation and modification of  Compute a file name for archiving attribute input data. The file will be in the attribute log directory
684  attributes.  
685    =cut
686    
687    sub ArchiveFileName {
688        # Get the parameters.
689        my ($self) = @_;
690        # Declare the return variable.
691        my $retVal;
692        # We start by turning the timestamp into something usable as a file name.
693        my $now = Tracer::Now();
694        $now =~ tr/ :\//___/;
695        # Next we get the directory name.
696        my $dir = "$FIG_Config::var/attributes";
697        if (! -e $dir) {
698            Trace("Creating attribute file directory $dir.") if T(1);
699            mkdir $dir;
700        }
701        # Put it together with the field name and the time stamp.
702        $retVal = "$dir/upload.$now";
703        # Modify the file name to insure it's unique.
704        my $seq = 0;
705        while (-e "$retVal.$seq.tbl") { $seq++ }
706        # Use the computed sequence number to get the correct file name.
707        $retVal .= ".$seq.tbl";
708        # Return the result.
709        return $retVal;
710    }
711    
712    =head3 BackupAllAttributes
713    
714    C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
715    
716    Backup all of the attributes to a file. The attributes will be stored in a
717    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
718    
719  =over 4  =over 4
720    
721  =item cgi  =item fileName
722    
723  CGI query object used to create HTML.  Name of the file to which the attribute data should be backed up.
724    
725  =item name  =item options
726    
727  Name to give to the form. This should be unique for the web page.  Hash of options for the backup.
728    
729  =item RETURN  =item RETURN
730    
731  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.  
732    
733  =back  =back
734    
735    Currently there are no options defined.
736    
737  =cut  =cut
738    
739  sub ControlForm {  sub BackupAllAttributes {
740      # Get the parameters.      # Get the parameters.
741      my ($self, $cgi, $name) = @_;      my ($self, $fileName, %options) = @_;
742      # Declare the return list.      # Declare the return variable.
743      my @retVal = ();      my $retVal = Stats->new();
744      # Start the form. We use multipart to support the upload control.      # Get a list of the keys.
745      push @retVal, $cgi->start_multipart_form(-name => $name);      my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
746      # 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);
747      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      # Open the file for output.
748      # The first row is for selecting the field name.      my $fh = Open(undef, ">$fileName");
749      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      # Loop through the keys.
750                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,      for my $key (@keys) {
751                                                       "document.$name.notes.value",          Trace("Backing up attribute $key.") if T(3);
752                                                       "document.$name.dataType.value")));          $retVal->Add(keys => 1);
753      # Now we set up a dropdown for the data types. The values will be the          # Loop through this key's values.
754      # data type names, and the labels will be the descriptions.          my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
755      my %types = ERDB::GetDataTypes();          my $valuesFound = 0;
756      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;          while (my $line = $query->Fetch()) {
757      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',              $valuesFound++;
758                                      -values => [sort keys %types],              # Get this row's data.
759                                      -labels => \%labelMap);              my ($id, $key, $subKey, $value) = $line->Values(['HasValueFor(to-link)',
760      push @retVal, $cgi->Tr($cgi->th("Data type"),                                                               'HasValueFor(from-link)',
761                             $cgi->td($typeMenu));                                                               'HasValueFor(subkey)',
762      # The next row is for the notes.                                                               'HasValueFor(value)']);
763      push @retVal, $cgi->Tr($cgi->th("Description"),              # Check for a subkey.
764                             $cgi->td($cgi->textarea(-name => 'notes',              if ($subKey ne '') {
765                                                     -rows => 6,                  $key = "$key$self->{splitter}$subKey";
766                                                     -columns => 80))              }
767                            );              # Write it to the file.
768      # Allow the user to specify a new field name. This is required if the              Tracer::PutLine($fh, [$id, $key, $value]);
769      # user has selected one of the "(new)" markers.          }
770      push @retVal, $cgi->Tr($cgi->th("New Field Name"),          Trace("$valuesFound values backed up for key $key.") if T(3);
771                             $cgi->td($cgi->textfield(-name => 'newName',          $retVal->Add(values => $valuesFound);
772                                                      -size => 30)),      }
773                                      );      # Log the operation.
774      # If the user wants to upload new values for the field, then we have      $self->LogOperation("Backup Data", $fileName, $retVal->Display());
775      # an upload file name and column indicators.      # Return the result.
776      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, "");  
777  }  }
778    
779  =head3 FieldMenu  =head3 FieldMenu
780    
781  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
782    
783  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
784  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
785  CGI package, but actually looks like a list. The list will contain  CGI package, but actually looks like a list. The list will contain
786  one selectable row per field, grouped by entity.  one selectable row per field.
787    
788  =over 4  =over 4
789    
# Line 556  Line 800 
800  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
801  appear when the form is submitted.  appear when the form is submitted.
802    
803  =item newFlag (optional)  =item keys
804    
805    Reference to a hash mapping each attribute key name to a list reference,
806    the list itself consisting of the attribute data type, its description,
807    and a list of its groups.
808    
809    =item options
810    
811    Hash containing options that modify the generation of the menu.
812    
813    =item RETURN
814    
815    Returns the HTML to create a form field that can be used to select an
816    attribute from the custom attributes system.
817    
818    =back
819    
820    The permissible options are as follows.
821    
822    =over 4
823    
824    =item new
825    
826  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
827  a new attribute. In other words, the user can select an existing  a new attribute. In other words, the user can select an existing
828  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
829  be created in the parent entity.  be created in the parent entity.
830    
831  =item noteControl (optional)  =item notes
832    
833  If specified, the name of a variable for displaying the notes attached  If specified, the name of a variable for displaying the notes attached
834  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 839 
839  it is copied in. Specifying this parameter generates Javascript for  it is copied in. Specifying this parameter generates Javascript for
840  displaying the field description when a field is selected.  displaying the field description when a field is selected.
841    
842  =item typeControl (optional)  =item type
843    
844  If specified, the name of a variable for displaying the field's  If specified, the name of a variable for displaying the field's
845  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 847 
847  raw value is put into the specified variable. Otherwise, the same  raw value is put into the specified variable. Otherwise, the same
848  rules apply to this value that apply to I<$noteControl>.  rules apply to this value that apply to I<$noteControl>.
849    
850  =item RETURN  =item groups
851    
852  Returns the HTML to create a form field that can be used to select an  If specified, the name of a multiple-selection list control (also called
853  attribute from the custom attributes system.  a popup menu) which shall be used to display the selected groups.
854    
855  =back  =back
856    
# Line 593  Line 858 
858    
859  sub FieldMenu {  sub FieldMenu {
860      # Get the parameters.      # Get the parameters.
861      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self, $cgi, $height, $name, $keys, %options) = @_;
862      # These next two hashes make everything happen. "entities"      # Reformat the list of keys.
863      # maps each entity name to the list of values to be put into its      my %keys = %{$keys};
864      # option group. "labels" maps each entity name to a map from values      # Add the (new) key, if needed.
865      # to labels.      if ($options{new}) {
866      my @entityNames = sort ($self->GetEntityTypes());          $keys{NewName()} = ["string", ""];
867      my %entities = map { $_ => [] } @entityNames;      }
868      my %labels = map { $_ => { }} @entityNames;      # Get a sorted list of key.
869      # Loop through the entities, adding the existing attributes.      my @keys = sort keys %keys;
870      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  
871      # 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
872      # for the menu.      # for the menu.
873      my $changeName = "${name}_setNotes";      my $changeName = "${name}_setNotes";
874      my $retVal = $cgi->popup_menu({name => $name,      my $retVal = $cgi->popup_menu({name => $name,
875                                     size => $height,                                     size => $height,
876                                     onChange => "$changeName(this.value)",                                     onChange => "$changeName(this.value)",
877                                     values => [map { $cgi->optgroup(-name => $_,                                     values => \@keys,
878                                                                     -values => $entities{$_},                                    });
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
879      # Create the change function.      # Create the change function.
880      $retVal .= "\n<script language=\"javascript\">\n";      $retVal .= "\n<script language=\"javascript\">\n";
881      $retVal .= "    function $changeName(fieldValue) {\n";      $retVal .= "    function $changeName(fieldValue) {\n";
882      # The function only has a body if we have a notes control to store the description.      # The function only has a body if we have a control to store data about the
883      if ($noteControl || $typeControl) {      # attribute.
884        if ($options{notes} || $options{type} || $options{groups}) {
885          # 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.
886            my $noteControl = $options{notes};
887          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
888          # 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
889          # field description will be stored in the JavaScript variable "myText"          # field description will be stored in the JavaScript variable "myText"
# Line 652  Line 892 
892          $retVal .= "        var myText = \"\";\n";          $retVal .= "        var myText = \"\";\n";
893          $retVal .= "        var myType = \"string\";\n";          $retVal .= "        var myType = \"string\";\n";
894          $retVal .= "        switch (fieldValue) {\n";          $retVal .= "        switch (fieldValue) {\n";
895          # Loop through the entities.          # Loop through the keys.
896          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};  
897                      # Generate this case.                      # Generate this case.
898                      $retVal .= "        case \"$value\" :\n";              $retVal .= "        case \"$key\" :\n";
899                      # Here we either want to update the note display, the                      # Here we either want to update the note display, the
900                      # type display, or both.              # type display, the group list, or a combination of them.
901                my ($type, $notes, @groups) = @{$keys{$key}};
902                      if ($noteControl) {                      if ($noteControl) {
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
903                          # Insure it's in the proper form.                          # Insure it's in the proper form.
904                          if ($htmlMode) {                          if ($htmlMode) {
905                              $notes = ERDB::HTMLNote($notes);                              $notes = ERDB::HTMLNote($notes);
# Line 679  Line 909 
909                          $notes =~ s/"/\\"/g;                          $notes =~ s/"/\\"/g;
910                          $retVal .= "           myText = \"$notes\";\n";                          $retVal .= "           myText = \"$notes\";\n";
911                      }                      }
912                      if ($typeControl) {              if ($options{type}) {
913                          # Here we want the type updated.                          # Here we want the type updated.
                         my $type = $element->{type};  
914                          $retVal .= "           myType = \"$type\";\n";                          $retVal .= "           myType = \"$type\";\n";
915                      }                      }
916                if ($options{groups}) {
917                    # Here we want the groups shown. Get a list of this attribute's groups.
918                    # We'll search through this list for each group to see if it belongs with
919                    # our attribute.
920                    my $groupLiteral = "=" . join("=", @groups) . "=";
921                    # Now we need some variables containing useful code for the javascript. It's
922                    # worth knowing we go through a bit of pain to insure $groupField[i] isn't
923                    # parsed as an array element.
924                    my $groupField = $options{groups};
925                    my $currentField = $groupField . "[i]";
926                    # Do the javascript.
927                    $retVal .= "           var groupList = \"$groupLiteral\";\n";
928                    $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";
929                    $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";
930                    $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";
931                    $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";
932                    $retVal .= "           }\n";
933                }
934                      # Close this case.                      # Close this case.
935                      $retVal .= "           break;\n";                      $retVal .= "           break;\n";
936                  }                  }
             }  
         }  
937          # Close the CASE statement and make the appropriate assignments.          # Close the CASE statement and make the appropriate assignments.
938          $retVal .= "        }\n";          $retVal .= "        }\n";
939          if ($noteControl) {          if ($noteControl) {
940              $retVal .= "        $noteControl = myText;\n";              $retVal .= "        $noteControl = myText;\n";
941          }          }
942          if ($typeControl) {          if ($options{type}) {
943              $retVal .= "        $typeControl = myType;\n";              $retVal .= "        $options{type} = myType;\n";
944          }          }
945      }      }
946      # Terminate the change function.      # Terminate the change function.
# Line 705  Line 950 
950      return $retVal;      return $retVal;
951  }  }
952    
953  =head3 MatchSqlPattern  =head3 GetGroups
954    
955  C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>  C<< my @groups = $attrDB->GetGroups(); >>
956    
957  Determine whether or not a specified value matches an SQL pattern. An SQL  Return a list of the available groups.
 pattern has two wild card characters: C<%> that matches multiple characters,  
 and C<_> that matches a single character. These can be escaped using a  
 backslash (C<\>). We pull this off by converting the SQL pattern to a  
 PERL regular expression. As per SQL rules, the match is case-insensitive.  
958    
959  =over 4  =cut
960    
961  =item value  sub GetGroups {
962        # Get the parameters.
963        my ($self) = @_;
964        # Get the groups.
965        my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
966        # Return them.
967        return @retVal;
968    }
969    
970  Value to be matched against the pattern. Note that an undefined or empty  =head3 GetAttributeData
 value will not match anything.  
971    
972  =item pattern  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
973    
974  SQL pattern against which to match the value. An undefined or empty pattern will  Return attribute data for the selected attributes. The attribute
975  match everything.  data is a hash mapping each attribute key name to a n-tuple containing the
976    data type, the description, and the groups. This is the same format expected in
977    the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.
978    
979  =item RETURN  =over 4
980    
981  Returns TRUE if the value and pattern match, else FALSE.  =item type
982    
983  =back  Type of attribute criterion: C<name> for attributes whose names begin with the
984    specified string, or C<group> for attributes in the specified group.
985    
986    =item list
987    
988    List containing the names of the groups or keys for the desired attributes.
989    
990    =item RETURN
991    
992    Returns a hash mapping each attribute key name to its data type, description, and
993    parent groups.
994    
995    =back
996    
997  =cut  =cut
998    
999  sub MatchSqlPattern {  sub GetAttributeData {
1000      # Get the parameters.      # Get the parameters.
1001      my ($value, $pattern) = @_;      my ($self, $type, @list) = @_;
1002      # Declare the return variable.      # Set up a hash to store the attribute data.
1003      my $retVal;      my %retVal = ();
1004      # Insure we have a pattern.      # Loop through the list items.
1005      if (! defined($pattern) || $pattern eq "") {      for my $item (@list) {
1006          $retVal = 1;          # Set up a query for the desired attributes.
1007      } else {          my $query;
1008          # Break the pattern into pieces around the wildcard characters. Because we          if ($type eq 'name') {
1009          # 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
1010          # list elements for the delimiters as well as the rest of the string.              # on a %.
1011          my @pieces = split /([_%]|\\[_%])/, $pattern;              my $parm = $item;
1012          # Check some fast special cases.              $parm =~ s/_/\\_/g;
1013          if ($pattern eq '%') {              $parm =~ s/%/\\%/g;
1014              # A null pattern matches everything.              $parm .= "%";
1015              $retVal = 1;              # Ask for matching attributes. (Note that if the user passed in a null string
1016          } elsif (@pieces == 1) {              # he'll get everything.)
1017              # No wildcards, so we have a literal comparison. Note we're case-insensitive.              $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
1018              $retVal = (lc($value) eq lc($pattern));          } elsif ($type eq 'group') {
1019          } 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);  
1020                  } else {                  } else {
1021                      # Here we have raw text.              Confess("Unknown attribute query type \"$type\".");
                     $realPattern .= quotemeta($piece);  
1022                  }                  }
1023            while (my $row = $query->Fetch()) {
1024                # Get this attribute's data.
1025                my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
1026                                                         'AttributeKey(description)']);
1027                # If it's new, get its groups and add it to the return hash.
1028                if (! exists $retVal{$key}) {
1029                    my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
1030                                                [$key], 'IsInGroup(to-link)');
1031                    $retVal{$key} = [$type, $notes, @groups];
1032              }              }
             # Do the match.  
             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);  
1033          }          }
1034      }      }
1035      # Return the result.      # Return the result.
1036      return $retVal;      return %retVal;
1037  }  }
1038    
1039  =head3 MigrateAttributes  =head3 LogOperation
1040    
1041  C<< CustomAttributes::MigrateAttributes($fig); >>  C<< $ca->LogOperation($action, $target, $description); >>
1042    
1043  Migrate all the attributes data from the specified FIG instance. This is a long, slow  Write an operation description to the attribute activity log (C<$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.  
1044    
1045  =over 4  =over 4
1046    
1047  =item fig  =item action
1048    
1049    Action being logged (e.g. C<Delete Group> or C<Load Key>).
1050    
1051    =item target
1052    
1053    ID of the key or group affected.
1054    
1055    =item description
1056    
1057  A FIG object that can be used to retrieve attributes for migration purposes.  Short description of the action.
1058    
1059  =back  =back
1060    
1061  =cut  =cut
1062    
1063  sub MigrateAttributes {  sub LogOperation {
1064      # Get the parameters.      # Get the parameters.
1065      my ($fig) = @_;      my ($self, $action, $target, $description) = @_;
1066      # Get a list of the objects to migrate. This requires connecting. Note we      # Get the user ID.
1067      # will map each entity type to a file name. The file will contain a list      my $user = $self->{user};
1068      # of the object's IDs so we can get to them when we're not connected to      # Get a timestamp.
1069      # the database.      my $timeString = Tracer::Now();
1070      my $ca = CustomAttributes->new();      # Open the log file for appending.
1071      my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();      my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
1072      # Set up hash of the existing attribute keys for each entity type.      # Write the data to it.
1073      my %oldKeys = ();      Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
1074      # Finally, we have a hash that counts the IDs for each entity type.      # Close the log file.
1075      my %idCounts = map { $_ => 0 } keys %objects;      close $oh;
1076      # Loop through the list, creating key files to read back in.  }
1077      for my $entityType (keys %objects) {  
1078          Trace("Retrieving keys for $entityType.") if T(2);  =head2 Internal Utility Methods
1079          # Create the key file.  
1080          my $idFile = Open(undef, ">$objects{$entityType}");  =head3 _KeywordString
1081          # Loop through the keys.  
1082          my @ids = $ca->GetFlat([$entityType], "", [], "$entityType(id)");  C<< my $keywordString = $ca->_KeywordString($key, $value); >>
1083          for my $id (@ids) {  
1084              print $idFile "$id\n";  Compute the keyword string for a specified key/value pair. This consists of the
1085          }  key name and value converted to lower case with underscores translated to spaces.
1086          close $idFile;  
1087          # 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
1088          # in the database. This avoids a circularity problem that might occur if the $fig  insert a B<HasValueFor> record.
1089          # object is retrieving from the custom attributes database already.  
1090          my %fields = $ca->GetSecondaryFields($entityType);  =over 4
1091          $oldKeys{$entityType} = \%fields;  
1092          # Finally, we have the ID count.  =item key
1093          $idCounts{$entityType} = scalar @ids;  
1094      }  Name of the relevant attribute key.
1095      # Release the custom attributes database so we can add attributes.  
1096      undef $ca;  =item target
1097      # Loop through the objects.  
1098      for my $entityType (keys %objects) {  ID of the target object to which this key/value pair will be associated.
1099          # Get a hash of all the attributes already in this database. These are  
1100          # left untouched.  =item value
1101          my $myOldKeys = $oldKeys{$entityType};  
1102          # Create a hash to control the load file names for each attribute key we find.  The value to store for this key/object combination.
1103          my %keyHash = ();  
1104          # Set up some counters so we can trace our progress.  =item RETURN
1105          my ($totalIDs, $processedIDs, $keyCount, $valueCount) = ($idCounts{$entityType}, 0, 0, 0);  
1106          # Open this object's ID file.  Returns the value that should be stored as the keyword string for the specified
1107          Trace("Migrating data for $entityType. $totalIDs found.") if T(3);  key/value pair.
1108          my $keysIn = Open(undef, "<$objects{$entityType}");  
1109          while (my $id = <$keysIn>) {  =back
1110              # Remove the EOL characters.  
1111              chomp $id;  =cut
1112              # Get this object's attributes.  
1113              my @allData = $fig->get_attributes($id);  sub _KeywordString {
1114              Trace(scalar(@allData) . " attribute values found for $entityType($id).") if T(4);      # Get the parameters.
1115              # Loop through the attribute values one at a time.      my ($self, $key, $value) = @_;
1116              for my $dataTuple (@allData) {      # Get a copy of the key name and convert underscores to spaces.
1117                  # Get the key, value, and URL. We ignore the first element because that's the      my $keywordString = $key;
1118                  # object ID, and we already know the object ID.      $keywordString =~ s/_/ /g;
1119                  my (undef, $key, $value, $url) = @{$dataTuple};      # Add the value convert it all to lower case.
1120                  # Remove the buggy "1" for $url.      my $retVal = lc "$keywordString $value";
1121                  if ($url eq "1") {      # Return the result.
1122                      $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 $entityType.") if T(2);  
     }  
     # All keys for all entity types are now loaded.  
     Trace("Migration complete.") if T(2);  
1123  }  }
1124    
1125  =head3 ComputeObjectTypeFromID  =head3 _QueryResults
1126    
1127  C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>  C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1128    
1129  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
1130  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
1131  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
1132  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.  
1133    
1134  =over 4  =over 4
1135    
1136  =item objectID  =item query
1137    
1138    A query object that will return the desired B<HasValueFor> records.
1139    
1140  Object ID to examine.  =item values
1141    
1142    List of the desired attribute values, section by section. If C<undef>
1143    or an empty string is specified, all values in that section will match. A
1144    generic match can be requested by placing a percent sign (C<%>) at the end.
1145    In that case, all values that match up to and not including the percent sign
1146    will match. You may also specify a regular expression enclosed
1147    in slashes. All values that match the regular expression will be returned. For
1148    performance reasons, only values have this extra capability.
1149    
1150  =item RETURN  =item RETURN
1151    
1152  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
1153    second is an attribute key, and the remaining elements are the sections of
1154    the attribute value. All of the tuples will match the criteria set forth in
1155    the parameter list.
1156    
1157  =back  =back
1158    
1159  =cut  =cut
1160    
1161  sub ComputeObjectTypeFromID {  sub _QueryResults {
1162      # Get the parameters.      # Get the parameters.
1163      my ($objectID) = @_;      my ($self, $query, @values) = @_;
1164      # Declare the return variables.      # Declare the return value.
1165      my ($entityName, $id);      my @retVal = ();
1166      # 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.
1167      # pair of undefs.      my $sectionCount = scalar(@values);
1168      if ($objectID) {      # Loop through the assignments found.
1169          if (ref $objectID eq 'ARRAY') {      while (my $row = $query->Fetch()) {
1170              # Here we have the new-style list reference. Pull out its pieces.          # Get the current row's data.
1171              ($entityName, $id) = @{$objectID};          my ($id, $realKey, $subKey, $valueString) = $row->Values(['HasValueFor(to-link)',
1172          } else {                                                                    'HasValueFor(from-link)',
1173              # Here the ID is the outgoing ID, and we need to look at its structure                                                                    'HasValueFor(subkey)',
1174              # to determine the entity type.                                                                    'HasValueFor(value)'
1175              $id = $objectID;                                                                  ]);
1176              if ($objectID =~ /^\d+\.\d+/) {          # Form the key from the real key and the sub key.
1177                  # Digits with a single period is a genome.          my $key = $self->JoinKey($realKey, $subKey);
1178                  $entityName = 'Genome';          # Break the value into sections.
1179              } elsif ($objectID =~ /^fig\|/) {          my @sections = split($self->{splitter}, $valueString);
1180                  # The "fig|" prefix indicates a feature.          # Match each section against the incoming values. We'll assume we're
1181                  $entityName = 'Feature';          # okay unless we learn otherwise.
1182            my $matching = 1;
1183            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1184                # We need to check to see if this section is generic.
1185                my $value = $values[$i];
1186                Trace("Current value pattern is \"$value\".") if T(4);
1187                if (substr($value, -1, 1) eq '%') {
1188                    Trace("Generic match used.") if T(4);
1189                    # Here we have a generic match.
1190                    my $matchLen = length($values[$i]) - 1;
1191                    $matching = substr($sections[$i], 0, $matchLen) eq
1192                                substr($values[$i], 0, $matchLen);
1193                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1194                    Trace("Regular expression detected.") if T(4);
1195                    # Here we have a regular expression match.
1196                    my $section = $sections[$i];
1197                    $matching = eval("\$section =~ $value");
1198              } else {              } else {
1199                  # Anything else is illegal!                  # Here we have a strict match.
1200                  Confess("Invalid attribute ID specification \"$objectID\".");                  Trace("Strict match used.") if T(4);
1201                    $matching = ($sections[$i] eq $values[$i]);
1202              }              }
1203          }          }
1204            # If we match, output this row to the return list.
1205            if ($matching) {
1206                push @retVal, [$id, $key, @sections];
1207      }      }
1208      # Return the result.      }
1209      return ($entityName, $id);      # Return the rows found.
1210        return @retVal;
1211  }  }
1212    
1213  =head2 FIG Method Replacements  =head2 FIG Method Replacements
1214    
1215  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.
1216  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
1217  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
1218  capabilities were used in the old system.  capabilities were used in the old system.
1219    
# Line 993  Line 1221 
1221  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
1222  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.
1223    
1224  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,
1225  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
1226  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
1227  value of the splitter parameter on the constructor (L</new>). The default is double  is double colons C<::>.
 colons C<::>.  
1228    
1229  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
1230  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
1231  splitter value would be stored as  splitter value would be stored as
1232    
# Line 1010  Line 1237 
1237    
1238  =head3 GetAttributes  =head3 GetAttributes
1239    
1240  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1241    
1242  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1243  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
1244  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
1245  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1246  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.  
1247    
1248  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
1249  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
1250  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1251    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1252    of the parameters. So, for example,
1253    
1254      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1255    
1256  would return something like  would return something like
1257    
# Line 1033  Line 1260 
1260      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1261      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1262    
1263  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1264  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1265  matches any sequence of characters, and C<_>, which matches any single character.  
1266  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1267  underscore.)  
1268    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1269    features.
1270    
1271  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1272  values, so even  values, so even
1273    
1274      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1275    
1276  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.
1277    
1278  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
1279  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
1280  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
1281  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
1282  be written as  are stored in a single string. As a result, queries in which filter only on value end up
1283    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.  
1284    
1285  =over 4  =over 4
1286    
1287  =item objectID  =item objectID
1288    
1289  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
1290  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
1291  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
1292  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.  
1293    
1294  =item key  =item key
1295    
1296  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
1297  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
1298  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
1299  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.  
1300    
1301  =item valuePatterns  =item values
1302    
1303  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1304  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
1305    generic match can be requested by placing a percent sign (C<%>) at the end.
1306    In that case, all values that match up to and not including the percent sign
1307    will match. You may also specify a regular expression enclosed
1308    in slashes. All values that match the regular expression will be returned. For
1309    performance reasons, only values have this extra capability.
1310    
1311  =item RETURN  =item RETURN
1312    
# Line 1107  Line 1321 
1321    
1322  sub GetAttributes {  sub GetAttributes {
1323      # Get the parameters.      # Get the parameters.
1324      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1325      # Declare the return variable.      # This hash will map "HasValueFor" fields to patterns. We use it to build the
1326      my @retVal = ();      # SQL statement.
1327      # Determine the entity types for our search.      my %data;
1328      my @objects = ();      # Before we do anything else, we must parse the key. The key is treated by the
1329      my ($actualObjectID, $computedType);      # user as a single field, but to us it's actually a real key and a subkey.
1330      if (! $objectID) {      # If the key has no splitter and is exact, the real key is the original key
1331          push @objects, $self->GetEntityTypes();      # and the subkey is an empty string. If the key has a splitter, it is
1332      } else {      # split into two pieces and each piece is processed separately. If the key has
1333          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);      # no splitter and is generic, the real key is the incoming key and the subkey
1334          push @objects, $computedType;      # is allowed to be wild. Of course, this only matters if an actual key has
1335      }      # been specified.
1336      # Loop through the entity types.      if (defined $key) {
1337      for my $entityType (@objects) {          if ($key =~ /$self->{splitter}/) {
1338          # Now we need to find all the matching keys. The keys are actually stored in              # Here we have a two-part key, so we split it normally.
1339          # our database object, so this process is fast. Note that our              my ($realKey, $subKey) = $self->SplitKey($key);
1340          # MatchSqlPattern method              $data{'HasValueFor(from-link)'} = $realKey;
1341          my %secondaries = $self->GetSecondaryFields($entityType);              $data{'HasValueFor(subkey)'} = $subKey;
1342          my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;          } elsif (substr($key, -1, 1) eq '%') {
1343          # Now we figure out whether or not we need to filter by object. We will always              $data{'HasValueFor(from-link)'} = $key;
1344          # filter by key to a limited extent, so if we're filtering by object we need an          } else {
1345          # AND to join the object ID filter with the key filter.              $data{'HasValueFor(from-link)'} = $key;
1346          my $filter = "";              $data{'HasValueFor(subkey)'} = '';
1347          my @params = ();          }
1348          if (defined($actualObjectID)) {      }
1349              # Here the caller wants to filter on object ID. Check for a pattern.      # Add the object ID to the key information.
1350              my $comparator = ($actualObjectID =~ /%/ ? "LIKE" : "=");      $data{'HasValueFor(to-link)'} = $objectID;
1351              # Update the filter and the parameter list.      # The first value represents a problem, because we can search it using SQL, but not
1352              $filter = "$entityType(id) $comparator ? AND ";      # in the normal way. If the user specifies a generic search or exact match for
1353              push @params, $actualObjectID;      # every alternative value (remember, the values may be specified as a list),
1354          }      # then we can create SQL filtering for it. If any of the values are specified
1355          # 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
1356          # each attribute is actually a different field in the database. We know here that      # every value to verify a match.
1357          # all the keys we've collected are for the correct entity because we got them from      if (@values > 0) {
1358          # 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.
1359          for my $key (@fieldList) {          my $valueParm = $values[0];
1360              # Get all of the attribute values for this key.          my @valueList;
1361              my @dataRows = $self->GetAll([$entityType], "$filter$entityType($key) IS NOT NULL",          if (ref $valueParm eq 'ARRAY') {
1362                                           \@params, ["$entityType(id)", "$entityType($key)"]);              @valueList = @{$valueParm};
1363              # Process each value separately. We need to verify the values and reformat the          } else {
1364              # tuples. Note that GetAll will give us one row per matching object ID,              @valueList = ($valueParm);
1365              # with the ID first followed by a list of the data values. This is very          }
1366              # 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
1367              # per value.          # @valueList. We'll copy the values to a new array in which they have been
1368              for my $dataRow (@dataRows) {          # converted to generic requests. If we find a regular-expression match
1369                  # Get the object ID and the list of values.          # anywhere in the list, we toss the whole thing.
1370                  my ($rowObjectID, @dataValues) = @{$dataRow};          my @valuePatterns = ();
1371                  # Loop through the values. There will be one result row per attribute value.          my $okValues = 1;
1372                  for my $dataValue (@dataValues) {          for my $valuePattern (@valueList) {
1373                      # Separate this value into sections.              # Check the pattern type.
1374                      my @sections = split("::", $dataValue);              if (substr($valuePattern, 0, 1) eq '/') {
1375                      # Loop through the value patterns, looking for a mismatch. Note that                  # Regular expressions invalidate the entire process.
1376                      # since we're working through parallel arrays, we are using an index                  $okValues = 0;
1377                      # loop. As soon as a match fails we stop checking. This means that              } elsif (substr($valuePattern, -1, 1) eq '%') {
1378                      # if the value pattern list is longer than the number of sections,                  # A Generic pattern is passed in unmodified.
1379                      # we will fail as soon as we run out of sections.                  push @valuePatterns, $valuePattern;
1380                      my $match = 1;              } else {
1381                      for (my $i = 0; $i <= $#valuePatterns && $match; $i++) {                  # An exact match is converted to generic.
1382                          $match = MatchSqlPattern($sections[$i], $valuePatterns[$i]);                  push @valuePatterns, "$valuePattern%";
1383                      }              }
1384                      # If we match, we save this value in the output list.          }
1385                      if ($match) {          # If everything works, add the value data to the filtering hash.
1386                          push @retVal, [$rowObjectID, $key, @sections];          if ($okValues) {
1387                      }              $data{'HasValueFor(value)'} = \@valuePatterns;
1388                  }          }
1389                  # Here we've processed all the attribute values for the current object ID.      }
1390        # Create some lists to contain the filter fragments and parameter values.
1391        my @filter = ();
1392        my @parms = ();
1393        # This next loop goes through the different fields that can be specified in the
1394        # parameter list and generates filters for each. The %data hash that we built above
1395        # contains all the necessary information to do this.
1396        for my $field (keys %data) {
1397            # Accumulate filter information for this field. We will OR together all the
1398            # elements accumulated to create the final result.
1399            my @fieldFilter = ();
1400            # Get the specified data from the caller.
1401            my $fieldPattern = $data{$field};
1402            # Only proceed if the pattern is one that won't match everything.
1403            if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1404                # Convert the pattern to an array.
1405                my @patterns = ();
1406                if (ref $fieldPattern eq 'ARRAY') {
1407                    push @patterns, @{$fieldPattern};
1408                } else {
1409                    push @patterns, $fieldPattern;
1410                }
1411                # Only proceed if the array is nonempty. The loop will work fine if the
1412                # array is empty, but when we build the filter string at the end we'll
1413                # get "()" in the filter list, which will result in an SQL syntax error.
1414                if (@patterns) {
1415                    # Loop through the individual patterns.
1416                    for my $pattern (@patterns) {
1417                        # Check for a generic request.
1418                        if (substr($pattern, -1, 1) ne '%') {
1419                            # Here we have a normal request.
1420                            push @fieldFilter, "$field = ?";
1421                            push @parms, $pattern;
1422                        } else {
1423                            # Here we have a generic request, so we will use the LIKE operator to
1424                            # filter the field to this value pattern.
1425                            push @fieldFilter, "$field LIKE ?";
1426                            # We must convert the pattern value to an SQL match pattern. First
1427                            # we get a copy of it.
1428                            my $actualPattern = $pattern;
1429                            # Now we escape the underscores. Underscores are an SQL wild card
1430                            # character, but they are used frequently in key names and object IDs.
1431                            $actualPattern =~ s/_/\\_/g;
1432                            # Add the escaped pattern to the bound parameter list.
1433                            push @parms, $actualPattern;
1434                        }
1435                    }
1436                    # Form the filter for this field.
1437                    my $fieldFilterString = join(" OR ", @fieldFilter);
1438                    push @filter, "($fieldFilterString)";
1439              }              }
             # Here we've processed all the rows returned by GetAll. In general, there will  
             # be one row per object ID.  
1440          }          }
         # Here we've processed all the matching attribute keys.  
1441      }      }
1442      # 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
1443      # results.      # values to bind to them.
1444        my $actualFilter = join(" AND ", @filter);
1445        # Now we're ready to make our query.
1446        my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1447        # Format the results.
1448        my @retVal = $self->_QueryResults($query, @values);
1449        # Return the rows found.
1450      return @retVal;      return @retVal;
1451  }  }
1452    
# Line 1195  Line 1461 
1461    
1462  =item objectID  =item objectID
1463    
1464  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.  
1465    
1466  =item key  =item key
1467    
1468  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1469    
1470  =item values  =item values
1471    
# Line 1225  Line 1488 
1488      } elsif (! @values) {      } elsif (! @values) {
1489          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1490      } else {      } else {
1491          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1492          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1493          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1494          # Insert the value.          # Split up the key.
1495          $self->InsertValue($id, "$entityName($key)", $valueString);          my ($realKey, $subKey) = $self->SplitKey($key);
1496            # Connect the object to the key.
1497            $self->InsertObject('HasValueFor', { 'from-link' => $realKey,
1498                                                 'to-link'   => $objectID,
1499                                                 'subkey'    => $subKey,
1500                                                 'value'     => $valueString,
1501                                           });
1502      }      }
1503      # Return a one. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1504      return 1;      return 1;
1505  }  }
1506    
# Line 1243  Line 1510 
1510    
1511  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1512    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1513  =over 4  =over 4
1514    
1515  =item objectID  =item objectID
1516    
1517  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.  
1518    
1519  =item key  =item key
1520    
1521  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1522    
1523  =item values  =item values
1524    
1525  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
1526    will be deleted. Otherwise, only a matching value will be deleted.
1527    
1528  =back  =back
1529    
# Line 1275  Line 1537 
1537          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1538      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1539          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 $key.");  
1540      } else {      } else {
1541          # Now compute the object type and ID.          # Split the key into the real key and the subkey.
1542          my ($entityName, $id) = ComputeObjectTypeFromID($objectID);          my ($realKey, $subKey) = $self->SplitKey($key);
1543          # Form the values into a scalar.          if ($subKey eq '' && scalar(@values) == 0) {
1544                # Here we erase the entire key for this object.
1545                $self->DeleteRow('HasValueFor', $key, $objectID);
1546            } else {
1547                # Here we erase the matching values.
1548          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1549          # Delete the value.              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1550          $self->DeleteValue($entityName, $id, $key, $valueString);                               { subkey => $subKey, value => $valueString });
1551            }
1552      }      }
1553      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1554      return 1;      return 1;
1555  }  }
1556    
1557    =head3 DeleteMatchingAttributes
1558    
1559    C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>
1560    
1561    Delete all attributes that match the specified criteria. This is equivalent to
1562    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1563    row found.
1564    
1565    =over 4
1566    
1567    =item objectID
1568    
1569    ID of object whose attributes are to be deleted. If the attributes for multiple
1570    objects are to be deleted, this parameter can be specified as a list reference. If
1571    attributes are to be deleted for all objects, specify C<undef> or an empty string.
1572    Finally, you can delete attributes for a range of object IDs by putting a percent
1573    sign (C<%>) at the end.
1574    
1575    =item key
1576    
1577    Attribute key name. A value of C<undef> or an empty string will match all
1578    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1579    specified as a list reference. Finally, you can delete attributes for a range of
1580    keys by putting a percent sign (C<%>) at the end.
1581    
1582    =item values
1583    
1584    List of the desired attribute values, section by section. If C<undef>
1585    or an empty string is specified, all values in that section will match. A
1586    generic match can be requested by placing a percent sign (C<%>) at the end.
1587    In that case, all values that match up to and not including the percent sign
1588    will match. You may also specify a regular expression enclosed
1589    in slashes. All values that match the regular expression will be deleted. For
1590    performance reasons, only values have this extra capability.
1591    
1592    =item RETURN
1593    
1594    Returns a list of tuples for the attributes that were deleted, in the
1595    same form as L</GetAttributes>.
1596    
1597    =back
1598    
1599    =cut
1600    
1601    sub DeleteMatchingAttributes {
1602        # Get the parameters.
1603        my ($self, $objectID, $key, @values) = @_;
1604        # Get the matching attributes.
1605        my @retVal = $self->GetAttributes($objectID, $key, @values);
1606        # Loop through the attributes, deleting them.
1607        for my $tuple (@retVal) {
1608            $self->DeleteAttribute(@{$tuple});
1609        }
1610        # Log this operation.
1611        my $count = @retVal;
1612        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1613        # Return the deleted attributes.
1614        return @retVal;
1615    }
1616    
1617  =head3 ChangeAttribute  =head3 ChangeAttribute
1618    
1619  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>
# Line 1333  Line 1658 
1658      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1659          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1660      } else {      } else {
1661          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1662          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1663          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1664      }      }
# Line 1343  Line 1668 
1668    
1669  =head3 EraseAttribute  =head3 EraseAttribute
1670    
1671  C<< $attrDB->EraseAttribute($entityName, $key); >>  C<< $attrDB->EraseAttribute($key); >>
1672    
1673  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
1674  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
1675    
1676  =over 4  =over 4
1677    
 =item entityName  
   
 Name of the entity to which the key belongs. If undefined, all entities will be  
 examined for the desired key.  
   
1678  =item key  =item key
1679    
1680  Key to erase.  Key to erase. This must be a real key; that is, it cannot have a subkey
1681    component.
1682    
1683  =back  =back
1684    
# Line 1365  Line 1686 
1686    
1687  sub EraseAttribute {  sub EraseAttribute {
1688      # Get the parameters.      # Get the parameters.
1689      my ($self, $entityName, $key) = @_;      my ($self, $key) = @_;
1690      # Determine the relevant entity types.      # Delete everything connected to the key.
1691      my @objects = ();      $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1692      if (! $entityName) {      # Log the operation.
1693          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);  
         }  
     }  
1694      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1695      return 1;      return 1;
1696  }  }
1697    
1698  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1699    
1700  C<< my @keyList = $attrDB->GetAttributeKeys($entityName); >>  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1701    
1702  Return a list of the attribute keys for a particular entity type.  Return a list of the attribute keys for a particular group.
1703    
1704  =over 4  =over 4
1705    
1706  =item entityName  =item groupName
1707    
1708  Name of the entity whose keys are desired.  Name of the group whose keys are desired.
1709    
1710  =item RETURN  =item RETURN
1711    
1712  Returns a list of the attribute keys for the specified entity.  Returns a list of the attribute keys for the specified group.
1713    
1714  =back  =back
1715    
# Line 1408  Line 1717 
1717    
1718  sub GetAttributeKeys {  sub GetAttributeKeys {
1719      # Get the parameters.      # Get the parameters.
1720      my ($self, $entityName) = @_;      my ($self, $groupName) = @_;
1721      # Get the entity's secondary fields.      # Get the attributes for the specified group.
1722      my %keyList = $self->GetSecondaryFields($entityName);      my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1723                                    'IsInGroup(from-link)');
1724      # Return the keys.      # Return the keys.
1725      return sort keys %keyList;      return sort @groups;
1726    }
1727    
1728    =head3 QueryAttributes
1729    
1730    C<< my @attributeData = $ca->QueryAttributes($filter, $filterParms); >>
1731    
1732    Return the attribute data based on an SQL filter clause. In the filter clause,
1733    the name C<$object> should be used for the object ID, C<$key> should be used for
1734    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1735    
1736    =over 4
1737    
1738    =item filter
1739    
1740    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1741    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1742    and C<$value> for the value field. This abstraction enables us to hide the details of
1743    the database construction from the user.
1744    
1745    =item filterParms
1746    
1747    Parameters for the filter clause.
1748    
1749    =item RETURN
1750    
1751    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1752    one or more attribute values.
1753    
1754    =back
1755    
1756    =cut
1757    
1758    # This hash is used to drive the substitution process.
1759    my %AttributeParms = (object => 'HasValueFor(to-link)',
1760                          key    => 'HasValueFor(from-link)',
1761                          subkey => 'HasValueFor(subkey)',
1762                          value  => 'HasValueFor(value)');
1763    
1764    sub QueryAttributes {
1765        # Get the parameters.
1766        my ($self, $filter, $filterParms) = @_;
1767        # Declare the return variable.
1768        my @retVal = ();
1769        # Make sue we have filter parameters.
1770        my $realParms = (defined($filterParms) ? $filterParms : []);
1771        # Create the query by converting the filter.
1772        my $realFilter = $filter;
1773        for my $name (keys %AttributeParms) {
1774            $realFilter =~ s/\$$name/$AttributeParms{$name}/g;
1775        }
1776        my $query = $self->Get(['HasValueFor'], $realFilter, $realParms);
1777        # Loop through the results, forming the output attribute tuples.
1778        while (my $result = $query->Fetch()) {
1779            # Get the four values from this query result row.
1780            my ($objectID, $key, $subkey, $value) = $result->Values([$AttributeParms{object},
1781                                                                    $AttributeParms{key},
1782                                                                    $AttributeParms{subkey},
1783                                                                    $AttributeParms{value}]);
1784            # Combine the key and the subkey.
1785            my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1786            # Split the value.
1787            my @values = split $self->{splitter}, $value;
1788            # Output the result.
1789            push @retVal, [$objectID, $realKey, @values];
1790        }
1791        # Return the result.
1792        return @retVal;
1793    }
1794    
1795    =head2 Key and ID Manipulation Methods
1796    
1797    =head3 ParseID
1798    
1799    C<< my ($type, $id) = CustomAttributes::ParseID($idValue); >>
1800    
1801    Determine the type and object ID corresponding to an ID value from the attribute database.
1802    Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
1803    however, Genomes, Features, and Subsystems are not stored with a type name, so we need to
1804    deduce the type from the ID value structure.
1805    
1806    The theory here is that you can plug the ID and type directly into a Sprout database method, as
1807    follows
1808    
1809        my ($type, $id) = CustomAttributes::ParseID($attrList[$num]->[0]);
1810        my $target = $sprout->GetEntity($type, $id);
1811    
1812    =over 4
1813    
1814    =item idValue
1815    
1816    ID value taken from the attribute database.
1817    
1818    =item RETURN
1819    
1820    Returns a two-element list. The first element is the type of object indicated by the ID value,
1821    and the second element is the actual object ID.
1822    
1823    =back
1824    
1825    =cut
1826    
1827    sub ParseID {
1828        # Get the parameters.
1829        my ($idValue) = @_;
1830        # Declare the return variables.
1831        my ($type, $id);
1832        # Parse the incoming ID. We first check for the presence of an entity name. Entity names
1833        # can only contain letters, which helps to insure typed object IDs don't collide with
1834        # subsystem names (which are untyped).
1835        if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1836            # Here we have a typed ID.
1837            ($type, $id) = ($1, $2);
1838            # Fix the case sensitivity on PDB IDs.
1839            if ($type eq 'PDB') { $id = lc $id; }
1840        } elsif ($idValue =~ /fig\|/) {
1841            # Here we have a feature ID.
1842            ($type, $id) = (Feature => $idValue);
1843        } elsif ($idValue =~ /\d+\.\d+/) {
1844            # Here we have a genome ID.
1845            ($type, $id) = (Genome => $idValue);
1846        } else {
1847            # The default is a subsystem ID.
1848            ($type, $id) = (Subsystem => $idValue);
1849        }
1850        # Return the results.
1851        return ($type, $id);
1852    }
1853    
1854    =head3 FormID
1855    
1856    C<< my $idValue = CustomAttributes::FormID($type, $id); >>
1857    
1858    Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1859    genomes, and features are stored in the database without type information, but all other object IDs
1860    must be prefixed with the object type.
1861    
1862    =over 4
1863    
1864    =item type
1865    
1866    Relevant object type.
1867    
1868    =item id
1869    
1870    ID of the object in question.
1871    
1872    =item RETURN
1873    
1874    Returns a string that will be recognized as an object ID in the attribute database.
1875    
1876    =back
1877    
1878    =cut
1879    
1880    sub FormID {
1881        # Get the parameters.
1882        my ($type, $id) = @_;
1883        # Declare the return variable.
1884        my $retVal;
1885        # Compute the ID string from the type.
1886        if (grep { $type eq $_ } qw(Feature Genome Subsystem)) {
1887            $retVal = $id;
1888        } else {
1889            $retVal = "$type:$id";
1890        }
1891        # Return the result.
1892        return $retVal;
1893    }
1894    
1895    =head3 GetTargetObject
1896    
1897    C<< my $object = CustomAttributes::GetTargetObject($erdb, $idValue); >>
1898    
1899    Return the database object corresponding to the specified attribute object ID. The
1900    object type associated with the ID value must correspond to an entity name in the
1901    specified database.
1902    
1903    =over 4
1904    
1905    =item erdb
1906    
1907    B<ERDB> object for accessing the target database.
1908    
1909    =item idValue
1910    
1911    ID value retrieved from the attribute database.
1912    
1913    =item RETURN
1914    
1915    Returns a B<ERDBObject> for the attribute value's target object.
1916    
1917    =back
1918    
1919    =cut
1920    
1921    sub GetTargetObject {
1922        # Get the parameters.
1923        my ($erdb, $idValue) = @_;
1924        # Declare the return variable.
1925        my $retVal;
1926        # Get the type and ID for the target object.
1927        my ($type, $id) = ParseID($idValue);
1928        # Plug them into the GetEntity method.
1929        $retVal = $erdb->GetEntity($type, $id);
1930        # Return the resulting object.
1931        return $retVal;
1932    }
1933    
1934    =head3 SplitKey
1935    
1936    C<< my ($realKey, $subKey) = $ca->SplitKey($key); >>
1937    
1938    Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1939    The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
1940    then the sub key is presumed to be an empty string.
1941    
1942    =over 4
1943    
1944    =item key
1945    
1946    Incoming key to be split.
1947    
1948    =item RETURN
1949    
1950    Returns a two-element list, the first element of which is the real key and the second element of
1951    which is the sub key.
1952    
1953    =back
1954    
1955    =cut
1956    
1957    sub SplitKey {
1958        # Get the parameters.
1959        my ($self, $key) = @_;
1960        # Do the split.
1961        my ($realKey, $subKey) = split($self->{splitter}, $key, 2);
1962        # Insure the subkey has a value.
1963        if (! defined $subKey) {
1964            $subKey = '';
1965        }
1966        # Return the results.
1967        return ($realKey, $subKey);
1968    }
1969    
1970    =head3 JoinKey
1971    
1972    C<< my $key = $ca->JoinKey($realKey, $subKey); >>
1973    
1974    Join a real key and a subkey together to make an external key. The external key is the attribute key
1975    used by the caller. The real key and the subkey are how the keys are represented in the database. The
1976    real key is the key to the B<AttributeKey> entity. The subkey is an attribute of the B<HasValueFor>
1977    relationship.
1978    
1979    =over 4
1980    
1981    =item realKey
1982    
1983    The real attribute key.
1984    
1985    =item subKey
1986    
1987    The subordinate portion of the attribute key.
1988    
1989    =item RETURN
1990    
1991    Returns a single string representing both keys.
1992    
1993    =back
1994    
1995    =cut
1996    
1997    sub JoinKey {
1998        # Get the parameters.
1999        my ($self, $realKey, $subKey) = @_;
2000        # Declare the return variable.
2001        my $retVal;
2002        # Check for a subkey.
2003        if ($subKey eq '') {
2004            # No subkey, so the real key is the key.
2005            $retVal = $realKey;
2006        } else {
2007            # Subkey found, so the two pieces must be joined by a splitter.
2008            $retVal = "$realKey$self->{splitter}$subKey";
2009  }  }
2010        # Return the result.
2011        return $retVal;
2012    }
2013    
2014    
2015    =head3 AttributeTable
2016    
2017    C<< my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList); >>
2018    
2019    Format the attribute data into an HTML table.
2020    
2021    =over 4
2022    
2023    =item cgi
2024    
2025    CGI query object used to generate the HTML
2026    
2027    =item attrList
2028    
2029    List of attribute results, in the format returned by the L</GetAttributes> or
2030    L</QueryAttributes> methods.
2031    
2032    =item RETURN
2033    
2034    Returns an HTML table displaying the attribute keys and values.
2035    
2036    =back
2037    
2038    =cut
2039    
2040    sub AttributeTable {
2041        # Get the parameters.
2042        my ($cgi, @attrList) = @_;
2043        # Accumulate the table rows.
2044        my @html = ();
2045        for my $attrData (@attrList) {
2046            # Format the object ID and key.
2047            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
2048            # Now we format the values. These remain unchanged unless one of them is a URL.
2049            my $lastValue = scalar(@{$attrData}) - 1;
2050            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
2051            # Assemble the values into a table row.
2052            push @html, $cgi->Tr($cgi->td(\@columns));
2053        }
2054        # Format the table in the return variable.
2055        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
2056        # Return it.
2057        return $retVal;
2058    }
2059  1;  1;

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