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revision 1.9, Thu Nov 16 22:09:33 2006 UTC revision 1.14, Wed Dec 20 20:04:23 2006 UTC
# Line 8  Line 8 
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  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
32  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
33  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
34  would code  would code
35    
36      my @values = $attrDB->GetAttributes([Feature => $fid], 'essential');      my @values = $attrDB->GetAttributes($fid, 'essential');
37    
38  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.  
39    
40  New attributes are introduced by updating the database definition at  New attribute keys must be defined before they can be used. A web interface
41  run-time. Attribute values are stored by uploading data from files.  is provided for this purpose.
 A web interface is provided for both these activities.  
42    
43  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
44    
# Line 76  Line 84 
84    
85  =back  =back
86    
 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.  
   
87  =head2 Public Methods  =head2 Public Methods
88    
89  =head3 new  =head3 new
90    
91  C<< my $attrDB = CustomAttributes->new($splitter); >>  C<< my $attrDB = CustomAttributes->new($splitter); >>
92    
93  Construct a new CustomAttributes object. This object cannot be used to add or  Construct a new CustomAttributes object.
 delete keys because that requires modifying the database design. To do that,  
 you need to use the static L</StoreAttributeKey> or L</DeleteAttributeKey>  
 methods.  
94    
95  =over 4  =over 4
96    
# Line 159  Line 124 
124    
125  =head3 StoreAttributeKey  =head3 StoreAttributeKey
126    
127  C<< my $attrDB = CustomAttributes::StoreAttributeKey($entityName, $attributeName, $type, $notes); >>  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>
128    
129  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.  
130    
131  =over 4  =over 4
132    
 =item entityName  
   
 Name of the entity containing the attribute. The entity must exist.  
   
133  =item attributeName  =item attributeName
134    
135  Name of the attribute. It must be a valid ERDB field name, consisting entirely of  Name of the attribute. It must be a valid ERDB field name, consisting entirely of
# Line 185  Line 144 
144    
145  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.
146    
147  =item RETURN  =item groups
148    
149  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.
150  error will be thrown.  This will replace any groups to which the attribute is currently attached.
151    
152  =back  =back
153    
# Line 196  Line 155 
155    
156  sub StoreAttributeKey {  sub StoreAttributeKey {
157      # Get the parameters.      # Get the parameters.
158      my ($entityName, $attributeName, $type, $notes) = @_;      my ($self, $attributeName, $type, $notes, $groups) = @_;
159      # Declare the return variable.      # Declare the return variable.
160      my $retVal;      my $retVal;
161      # Get the data type hash.      # Get the data type hash.
# Line 208  Line 167 
167          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing or incomplete description for $attributeName.");
168      } elsif (! exists $types{$type}) {      } elsif (! exists $types{$type}) {
169          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid data type \"$type\" for $attributeName.");
     }  
     # Our next step is to read in the XML for the database defintion. We  
     # need to verify that the named entity exists.  
     my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);  
     my $entityHash = $metadata->{Entities};  
     if (! exists $entityHash->{$entityName}) {  
         Confess("Entity $entityName not found.");  
170      } else {      } else {
171          # Okay, we're ready to begin. Get the entity hash and the field hash.          # Okay, we're ready to begin. See if this key exists.
172          my $entityData = $entityHash->{$entityName};          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
173          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);          if (defined($attribute)) {
174          # Compare the old attribute data to the new data.              # It does, so we do an update.
175          my $bigChange = 1;              $self->UpdateEntity('AttributeKey', $attributeName,
176          if (exists $fieldHash->{$attributeName} && $fieldHash->{$attributeName}->{type} eq $type) {                                  { description => $notes, 'data-type' => $type });
177              $bigChange = 0;              # Detach the key from its current groups.
178          }              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
179          # Compute the attribute's relation name.          } else {
180          my $relName = join("", $entityName, map { ucfirst $_ } split(/-|_/, $attributeName));              # It doesn't, so we do an insert.
181          # Store the attribute's field data. Note the use of the "content" hash for              $self->InsertObject('AttributeKey', { id => $attributeName,
182          # the notes. This is how the XML writer knows Notes is a text tag instead of                                  description => $notes, 'data-type' => $type });
183          # an attribute.          }
184          $fieldHash->{$attributeName} = { type => $type, relation => $relName,          # Attach the key to the specified groups. (We presume the groups already
185                                           Notes => { content => $notes } };          # exist.)
186          # Insure we have an index for this attribute.          for my $group (@{$groups}) {
187          my $index = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
188          if (! defined($index)) {                                                 'to-link'   => $group });
             push @{$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);  
         }  
189      }      }
     return $retVal;  
190  }  }
   
 =head3 Refresh  
   
 C<< $attrDB->Refresh($fig); >>  
   
 Refresh the primary entity tables from the FIG data store. This method basically  
 drops and reloads the main tables of the custom attributes database.  
   
 =over 4  
   
 =item fig  
   
 FIG-like object that can be used to find genomes and features.  
   
 =back  
   
 =cut  
   
 sub Refresh {  
     # Get the parameters.  
     my ($self, $fig) = @_;  
     # Create load objects for the genomes and the features.  
     my $loadGenome = ERDBLoad->new($self, 'Genome', $FIG_Config::temp);  
     my $loadFeature = ERDBLoad->new($self, 'Feature', $FIG_Config::temp);  
     # Get the genome list.  
     my @genomes = $fig->genomes();  
     # Loop through the genomes.  
     for my $genomeID (@genomes) {  
         # Put this genome in the genome table.  
         $loadGenome->Put($genomeID);  
         Trace("Processing Genome $genomeID") if T(3);  
         # Put its features into the feature table. Note we have to use a hash to  
         # remove duplicates.  
         my %featureList = map { $_ => 1 } $fig->all_features($genomeID);  
         for my $fid (keys %featureList) {  
             $loadFeature->Put($fid);  
         }  
     }  
     # Get a variable for holding statistics objects.  
     my $stats;  
     # Finish the genome load.  
     Trace("Loading Genome relation.") if T(2);  
     $stats = $loadGenome->FinishAndLoad();  
     Trace("Genome table load statistics:\n" . $stats->Show()) if T(3);  
     # Finish the feature load.  
     Trace("Loading Feature relation.") if T(2);  
     $stats = $loadFeature->FinishAndLoad();  
     Trace("Feature table load statistics:\n" . $stats->Show()) if T(3);  
191  }  }
192    
193  =head3 LoadAttributeKey  =head3 LoadAttributeKey
194    
195  C<< my $stats = $attrDB->LoadAttributeKey($entityName, $fieldName, $fh, $keyCol, $dataCol); >>  C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>
196    
197  Load the specified attribute from the specified file. The file should be a  Load the specified attribute from the specified file. The file should be a
198  tab-delimited file with internal tab and new-line characters escaped. This is  tab-delimited file with internal tab and new-line characters escaped. This is
199  the typical TBL-style file used by most FIG applications. One of the columns  the typical TBL-style file used by most FIG applications. One of the columns
200  in the input file must contain the appropriate key value and the other the  in the input file must contain the appropriate object id value and the other the
201  corresponding attribute value.  corresponding attribute value.
202    
203  =over 4  =over 4
204    
205  =item entityName  =item keyName
   
 Name of the entity containing the attribute.  
206    
207  =item fieldName  Key of the attribute to load.
   
 Name of the actual attribute.  
208    
209  =item fh  =item fh
210    
211  Open file handle for the input file.  Open file handle for the input file.
212    
213  =item keyCol  =item idCol
214    
215  Index (0-based) of the column containing the key field. The key field should  Index (0-based) of the column containing the ID field. The ID field should
216  contain the ID of an instance of the named entity.  contain the ID of an instance of the named entity.
217    
218  =item dataCol  =item dataCol
219    
220  Index (0-based) of the column containing the data value field.  Index (0-based) of the column containing the data value field.
221    
222    =item options
223    
224    Hash specifying the options for this load.
225    
226  =item RETURN  =item RETURN
227    
228  Returns a statistics object for the load process.  Returns a statistics object for the load process.
229    
230  =back  =back
231    
232    The available options are as follows.
233    
234    =over 4
235    
236    =item erase
237    
238    If TRUE, the key's values will all be erased before loading. (Doing so
239    makes for a faster load.)
240    
241    =back
242    
243  =cut  =cut
244    
245  sub LoadAttributeKey {  sub LoadAttributeKey {
246      # Get the parameters.      # Get the parameters.
247      my ($self, $entityName, $fieldName, $fh, $keyCol, $dataCol) = @_;      my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;
248      # Create the return variable.      # Create the return variable.
249      my $retVal;      my $retVal = Stats->new("lineIn", "shortLine", "newObject");
250      # Insure the entity exists.      # Compute the minimum number of fields required in each input line.
251      my $found = grep { $_ eq $entityName } $self->GetEntityTypes();      my $minCols = ($idCol < $dataCol ? $idCol : $idCol) + 1;
252      if (! $found) {      # Insure the attribute key exists.
253          Confess("Entity \"$entityName\" not found in database.");      my $found = $self->GetEntity('AttributeKey', $keyName);
254      } else {      if (! defined $found) {
255          # Get the field structure for the named entity.          Confess("Attribute key \"$keyName\" not found in database.");
         my $fieldHash = $self->GetFieldTable($entityName);  
         # Verify that the attribute exists.  
         if (! exists $fieldHash->{$fieldName}) {  
             Confess("Attribute key \"$fieldName\" does not exist in entity $entityName.");  
256          } else {          } else {
257              # Create a loader for the specified attribute. We need the          # Erase the key's current values.
258              # relation name first.          $self->EraseAttribute($keyName);
259              my $relName = $fieldHash->{$fieldName}->{relation};          # Save a list of the object IDs we need to add.
260              my $loadAttribute = ERDBLoad->new($self, $relName, $FIG_Config::temp);          my %objectIDs = ();
261              # Loop through the input file.              # Loop through the input file.
262              while (! eof $fh) {              while (! eof $fh) {
263                  # Get the next line of the file.                  # Get the next line of the file.
264                  my @fields = Tracer::GetLine($fh);                  my @fields = Tracer::GetLine($fh);
265                  $loadAttribute->Add("lineIn");              $retVal->Add(lineIn => 1);
266                  # Now we need to validate the line.                  # Now we need to validate the line.
267                  if ($#fields < $dataCol) {              if (scalar(@fields) < $minCols) {
268                      $loadAttribute->Add("shortLine");                  $retVal->Add(shortLine => 1);
                 } elsif (! $self->Exists($entityName, $fields[$keyCol])) {  
                     $loadAttribute->Add("badKey");  
269                  } else {                  } else {
270                      # It's valid,so send it to the loader.                  # It's valid, so get the ID and value.
271                      $loadAttribute->Put($fields[$keyCol], $fields[$dataCol]);                  my ($id, $value) = ($fields[$idCol], $fields[$dataCol]);
272                      $loadAttribute->Add("lineUsed");                  # Denote we're using this input line.
273                    $retVal->Add(lineUsed => 1);
274                    # Now the fun begins. Find out if we need to create a target object record for this object ID.
275                    if (! exists $objectIDs{$id}) {
276                        my $found = $self->Exists('TargetObject', $id);
277                        if (! $found) {
278                            $self->InsertObject('TargetObject', { id => $id });
279                  }                  }
280                        $objectIDs{$id} = 1;
281                        $retVal->Add(newObject => 1);
282                    }
283                    # Now we insert the attribute.
284                    $self->InsertObject('HasValueFor', { from => $keyName, to => $id, value => $value });
285                    $retVal->Add(newValue => 1);
286              }              }
             # Finish the load.  
             $retVal = $loadAttribute->FinishAndLoad();  
287          }          }
288      }      }
289      # Return the statistics.      # Return the statistics.
# Line 386  Line 293 
293    
294  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
295    
296  C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
297    
298  Delete an attribute from the custom attributes database.  Delete an attribute from the custom attributes database.
299    
300  =over 4  =over 4
301    
 =item entityName  
   
 Name of the entity possessing the attribute.  
   
302  =item attributeName  =item attributeName
303    
304  Name of the attribute to delete.  Name of the attribute to delete.
305    
306    =item RETURN
307    
308    Returns a statistics object describing the effects of the deletion.
309    
310  =back  =back
311    
312  =cut  =cut
313    
314  sub DeleteAttributeKey {  sub DeleteAttributeKey {
315      # Get the parameters.      # Get the parameters.
316      my ($entityName, $attributeName) = @_;      my ($self, $attributeName) = @_;
317      # Read in the XML for the database defintion. We need to verify that      # Delete the attribute key.
318      # the named entity exists and it has the named attribute.      my $retVal = $self->Delete('AttributeKey', $attributeName);
319      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Return the result.
320      my $entityHash = $metadata->{Entities};      return $retVal;
321      if (! exists $entityHash->{$entityName}) {  
         Confess("Entity \"$entityName\" not found.");  
     } else {  
         # Get the field hash.  
         my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);  
         if (! exists $fieldHash->{$attributeName}) {  
             Confess("Attribute key \"$attributeName\" not found in entity $entityName.");  
         } else {  
             # Get the attribute's relation name.  
             my $relName = $fieldHash->{$attributeName}->{relation};  
             # Check for an index.  
             my $indexIdx = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);  
             if (defined($indexIdx)) {  
                 Trace("Index for $attributeName found at position $indexIdx for $entityName.") if T(3);  
                 delete $entityHash->{$entityName}->{Indexes}->[$indexIdx];  
             }  
             # Delete the attribute from the field hash.  
             Trace("Deleting attribute $attributeName from $entityName.") if T(3);  
             delete $fieldHash->{$attributeName};  
             # Write the XML back out.  
             ERDB::WriteMetaXML($metadata, $FIG_Config::attrDBD);  
             # Insure the relation does not exist in the database. This requires connecting  
             # since we may have to do a table drop.  
             my $attrDB = CustomAttributes->new();  
             Trace("Dropping table $relName.") if T(3);  
             $attrDB->DropRelation($relName);  
         }  
322      }      }
323    
324    =head3 NewName
325    
326    C<< my $text = CustomAttributes::NewName(); >>
327    
328    Return the string used to indicate the user wants to add a new attribute.
329    
330    =cut
331    
332    sub NewName {
333        return "(new)";
334  }  }
335    
336  =head3 ControlForm  =head3 ControlForm
337    
338  C<< my $formHtml = $attrDB->ControlForm($cgi, $name); >>  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
339    
340  Return a form that can be used to control the creation and modification of  Return a form that can be used to control the creation and modification of
341  attributes.  attributes. Only a subset of the attribute keys will be displayed, as
342    determined by the incoming list.
343    
344  =over 4  =over 4
345    
# Line 458  Line 351 
351    
352  Name to give to the form. This should be unique for the web page.  Name to give to the form. This should be unique for the web page.
353    
354    =item keys
355    
356    Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
357    attribute's data type, its description, and a list of the groups in which it participates.
358    
359  =item RETURN  =item RETURN
360    
361  Returns the HTML for a form that submits instructions to the C<Attributes.cgi> script  Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script
362  for loading, creating, or deleting an attribute.  for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
363    controls are generated. The form tags are left to the caller.
364    
365  =back  =back
366    
# Line 469  Line 368 
368    
369  sub ControlForm {  sub ControlForm {
370      # Get the parameters.      # Get the parameters.
371      my ($self, $cgi, $name) = @_;      my ($self, $cgi, $name, $keys) = @_;
372      # Declare the return list.      # Declare the return list.
373      my @retVal = ();      my @retVal = ();
     # Start the form. We use multipart to support the upload control.  
     push @retVal, $cgi->start_multipart_form(-name => $name);  
374      # We'll put the controls in a table. Nothing else ever seems to look nice.      # We'll put the controls in a table. Nothing else ever seems to look nice.
375      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
376      # The first row is for selecting the field name.      # The first row is for selecting the field name.
377      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      push @retVal, $cgi->Tr($cgi->th("Select a Field"),
378                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
379                                                       "document.$name.notes.value",                                                       new => 1,
380                                                       "document.$name.dataType.value")));                                                       notes => "document.$name.notes.value",
381                                                         type => "document.$name.dataType.value",
382                                                         groups => "document.$name.groups")));
383      # Now we set up a dropdown for the data types. The values will be the      # Now we set up a dropdown for the data types. The values will be the
384      # data type names, and the labels will be the descriptions.      # data type names, and the labels will be the descriptions.
385      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
386      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
387      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',
388                                      -values => [sort keys %types],                                      -values => [sort keys %types],
389                                      -labels => \%labelMap);                                      -labels => \%labelMap,
390                                        -default => 'string');
391        # Allow the user to specify a new field name. This is required if the
392        # user has selected the "(new)" marker. We put a little scriptlet in here that
393        # selects the (new) marker when the user enters the field.
394        push @retVal, "<script language=\"javaScript\">";
395        my $fieldField = "document.$name.fieldName";
396        my $newName = "\"" . NewName() . "\"";
397        push @retVal, $cgi->Tr($cgi->th("New Field Name"),
398                               $cgi->td($cgi->textfield(-name => 'newName',
399                                                        -size => 30,
400                                                        -value => "",
401                                                        -onFocus => "setIfEmpty($fieldField, $newName);")),
402                                        );
403      push @retVal, $cgi->Tr($cgi->th("Data type"),      push @retVal, $cgi->Tr($cgi->th("Data type"),
404                             $cgi->td($typeMenu));                             $cgi->td($typeMenu));
405      # The next row is for the notes.      # The next row is for the notes.
# Line 496  Line 408 
408                                                     -rows => 6,                                                     -rows => 6,
409                                                     -columns => 80))                                                     -columns => 80))
410                            );                            );
411      # Allow the user to specify a new field name. This is required if the      # Now we have the groups, which are implemented as a checkbox group.
412      # user has selected one of the "(new)" markers.      my @groups = $self->GetGroups();
413      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      push @retVal, $cgi->Tr($cgi->th("Groups"),
414                             $cgi->td($cgi->textfield(-name => 'newName',                             $cgi->td($cgi->checkbox_group(-name=>'groups',
415                                                      -size => 30)),                                      -values=> \@groups))
416                                      );                                      );
417      # If the user wants to upload new values for the field, then we have      # If the user wants to upload new values for the field, then we have
418      # an upload file name and column indicators.      # an upload file name and column indicators.
# Line 517  Line 429 
429                                                      -default => 1)                                                      -default => 1)
430                                     ),                                     ),
431                            );                            );
432      # Now the three buttons: UPDATE, SHOW, and DELETE.      # Now the three buttons: STORE, SHOW, and DELETE.
433      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
434                             $cgi->td({align => 'center'},                             $cgi->td({align => 'center'},
435                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .
# Line 527  Line 439 
439                            );                            );
440      # Close the table and the form.      # Close the table and the form.
441      push @retVal, $cgi->end_table();      push @retVal, $cgi->end_table();
     push @retVal, $cgi->end_form();  
442      # Return the assembled HTML.      # Return the assembled HTML.
443      return join("\n", @retVal, "");      return join("\n", @retVal, "");
444  }  }
445    
446    =head3 LoadAttributesFrom
447    
448    C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
449    
450    Load attributes from the specified tab-delimited file. Each line of the file must
451    contain an object ID in the first column, an attribute key name in the second
452    column, and attribute values in the remaining columns. The attribute values will
453    be assembled into a single value using the splitter code.
454    
455    =over 4
456    
457    =item fileName
458    
459    Name of the file from which to load the attributes.
460    
461    =item options
462    
463    Hash of options for modifying the load process.
464    
465    =item RETURN
466    
467    Returns a statistics object describing the load.
468    
469    =back
470    
471    Permissible option values are as follows.
472    
473    =over 4
474    
475    =item append
476    
477    If TRUE, then the attributes will be appended to existing data; otherwise, the
478    first time a key name is encountered, it will be erased.
479    
480    =back
481    
482    =cut
483    
484    sub LoadAttributesFrom {
485        # Get the parameters.
486        my ($self, $fileName, %options) = @_;
487        # Declare the return variable.
488        my $retVal = Stats->new('keys', 'values');
489        # Check for append mode.
490        my $append = ($options{append} ? 1 : 0);
491        # Create a hash of key names found.
492        my %keyHash = ();
493        # Open the file for input.
494        my $fh = Open(undef, "<$fileName");
495        # Loop through the file.
496        while (! eof $fh) {
497            my ($id, $key, @values) = Tracer::GetLine($fh);
498            $retVal->Add(linesIn => 1);
499            # Do some validation.
500            if (! defined($id)) {
501                # We ignore blank lines.
502                $retVal->Add(blankLines => 1);
503            } elsif (! defined($key)) {
504                # An ID without a key is a serious error.
505                my $lines = $retVal->Ask('linesIn');
506                Confess("Line $lines in $fileName has no attribute key.");
507            } else {
508                # Now we need to check for a new key.
509                if (! exists $keyHash{$key}) {
510                    # This is a new key. Verify that it exists.
511                    if (! $self->Exists('AttributeKey', $key)) {
512                        my $line = $retVal->Ask('linesIn');
513                        Confess("Attribute \"$key\" on line $line of $fileName not found in database.");
514                    } else {
515                        # Make sure we know this is no longer a new key.
516                        $keyHash{$key} = 1;
517                        $retVal->Add(keys => 1);
518                        # If this is NOT append mode, erase the key.
519                        if (! $append) {
520                            $self->EraseAttribute($key);
521                        }
522                    }
523                    Trace("Key $key found.") if T(3);
524                }
525                # Now we know the key is valid. Add this value.
526                $self->AddAttribute($id, $key, @values);
527                my $progress = $retVal->Add(values => 1);
528                Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
529    
530            }
531        }
532        # Return the result.
533        return $retVal;
534    }
535    
536    =head3 BackupKeys
537    
538    C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
539    
540    Backup the attribute key information from the attribute database.
541    
542    =over 4
543    
544    =item fileName
545    
546    Name of the output file.
547    
548    =item options
549    
550    Options for modifying the backup process.
551    
552    =item RETURN
553    
554    Returns a statistics object for the backup.
555    
556    =back
557    
558    Currently there are no options. The backup is straight to a text file in
559    tab-delimited format. Each key is backup up to two lines. The first line
560    is all of the data from the B<AttributeKey> table. The second is a
561    tab-delimited list of all the groups.
562    
563    =cut
564    
565    sub BackupKeys {
566        # Get the parameters.
567        my ($self, $fileName, %options) = @_;
568        # Declare the return variable.
569        my $retVal = Stats->new();
570        # Open the output file.
571        my $fh = Open(undef, ">$fileName");
572        # Set up to read the keys.
573        my $keyQuery = $self->Get(['AttributeKey'], "", []);
574        # Loop through the keys.
575        while (my $keyData = $keyQuery->Fetch()) {
576            $retVal->Add(key => 1);
577            # Get the fields.
578            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
579                                                              'AttributeKey(description)']);
580            # Escape any tabs or new-lines in the description.
581            my $escapedDescription = Tracer::Escape($description);
582            # Write the key data to the output.
583            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
584            # Get the key's groups.
585            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
586                                        'IsInGroup(to-link)');
587            $retVal->Add(memberships => scalar(@groups));
588            # Write them to the output. Note we put a marker at the beginning to insure the line
589            # is nonempty.
590            Tracer::PutLine($fh, ['#GROUPS', @groups]);
591        }
592        # Return the result.
593        return $retVal;
594    }
595    
596    =head3 RestoreKeys
597    
598    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
599    
600    Restore the attribute keys and groups from a backup file.
601    
602    =over 4
603    
604    =item fileName
605    
606    Name of the file containing the backed-up keys. Each key has a pair of lines,
607    one containing the key data and one listing its groups.
608    
609    =back
610    
611    =cut
612    
613    sub RestoreKeys {
614        # Get the parameters.
615        my ($self, $fileName, %options) = @_;
616        # Declare the return variable.
617        my $retVal = Stats->new();
618        # Set up a hash to hold the group IDs.
619        my %groups = ();
620        # Open the file.
621        my $fh = Open(undef, "<$fileName");
622        # Loop until we're done.
623        while (! eof $fh) {
624            # Get a key record.
625            my ($id, $dataType, $description) = Tracer::GetLine($fh);
626            if ($id eq '#GROUPS') {
627                Confess("Group record found when key record expected.");
628            } elsif (! defined($description)) {
629                Confess("Invalid format found for key record.");
630            } else {
631                $retVal->Add("keyIn" => 1);
632                # Add this key to the database.
633                $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
634                                                      description => Tracer::UnEscape($description) });
635                Trace("Attribute $id stored.") if T(3);
636                # Get the group line.
637                my ($marker, @groups) = Tracer::GetLine($fh);
638                if (! defined($marker)) {
639                    Confess("End of file found where group record expected.");
640                } elsif ($marker ne '#GROUPS') {
641                    Confess("Group record not found after key record.");
642                } else {
643                    $retVal->Add(memberships => scalar(@groups));
644                    # Connect the groups.
645                    for my $group (@groups) {
646                        # Find out if this is a new group.
647                        if (! $groups{$group}) {
648                            $retVal->Add(newGroup => 1);
649                            # Add the group.
650                            $self->InsertObject('AttributeGroup', { id => $group });
651                            Trace("Group $group created.") if T(3);
652                            # Make sure we know it's not new.
653                            $groups{$group} = 1;
654                        }
655                        # Connect the group to our key.
656                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
657                    }
658                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
659                }
660            }
661        }
662        # Return the result.
663        return $retVal;
664    }
665    
666    
667    =head3 BackupAllAttributes
668    
669    C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
670    
671    Backup all of the attributes to a file. The attributes will be stored in a
672    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
673    
674    =over 4
675    
676    =item fileName
677    
678    Name of the file to which the attribute data should be backed up.
679    
680    =item options
681    
682    Hash of options for the backup.
683    
684    =item RETURN
685    
686    Returns a statistics object describing the backup.
687    
688    =back
689    
690    Currently there are no options defined.
691    
692    =cut
693    
694    sub BackupAllAttributes {
695        # Get the parameters.
696        my ($self, $fileName, %options) = @_;
697        # Declare the return variable.
698        my $retVal = Stats->new();
699        # Get a list of the keys.
700        my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
701        Trace(scalar(@keys) . " keys found during backup.") if T(2);
702        # Open the file for output.
703        my $fh = Open(undef, ">$fileName");
704        # Loop through the keys.
705        for my $key (@keys) {
706            Trace("Backing up attribute $key.") if T(3);
707            $retVal->Add(keys => 1);
708            # Loop through this key's values.
709            my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
710            my $valuesFound = 0;
711            while (my $line = $query->Fetch()) {
712                $valuesFound++;
713                # Get this row's data.
714                my @row = $line->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
715                                         'HasValueFor(value)']);
716                # Write it to the file.
717                Tracer::PutLine($fh, \@row);
718            }
719            Trace("$valuesFound values backed up for key $key.") if T(3);
720            $retVal->Add(values => $valuesFound);
721        }
722        # Return the result.
723        return $retVal;
724    }
725    
726  =head3 FieldMenu  =head3 FieldMenu
727    
728  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
729    
730  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
731  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
732  CGI package, but actually looks like a list. The list will contain  CGI package, but actually looks like a list. The list will contain
733  one selectable row per field, grouped by entity.  one selectable row per field.
734    
735  =over 4  =over 4
736    
# Line 556  Line 747 
747  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
748  appear when the form is submitted.  appear when the form is submitted.
749    
750  =item newFlag (optional)  =item keys
751    
752    Reference to a hash mapping each attribute key name to a list reference,
753    the list itself consisting of the attribute data type, its description,
754    and a list of its groups.
755    
756    =item options
757    
758    Hash containing options that modify the generation of the menu.
759    
760    =item RETURN
761    
762    Returns the HTML to create a form field that can be used to select an
763    attribute from the custom attributes system.
764    
765    =back
766    
767    The permissible options are as follows.
768    
769    =over 4
770    
771    =item new
772    
773  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
774  a new attribute. In other words, the user can select an existing  a new attribute. In other words, the user can select an existing
775  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
776  be created in the parent entity.  be created in the parent entity.
777    
778  =item noteControl (optional)  =item notes
779    
780  If specified, the name of a variable for displaying the notes attached  If specified, the name of a variable for displaying the notes attached
781  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 786 
786  it is copied in. Specifying this parameter generates Javascript for  it is copied in. Specifying this parameter generates Javascript for
787  displaying the field description when a field is selected.  displaying the field description when a field is selected.
788    
789  =item typeControl (optional)  =item type
790    
791  If specified, the name of a variable for displaying the field's  If specified, the name of a variable for displaying the field's
792  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 794 
794  raw value is put into the specified variable. Otherwise, the same  raw value is put into the specified variable. Otherwise, the same
795  rules apply to this value that apply to I<$noteControl>.  rules apply to this value that apply to I<$noteControl>.
796    
797  =item RETURN  =item groups
798    
799  Returns the HTML to create a form field that can be used to select an  If specified, the name of a multiple-selection list control (also called
800  attribute from the custom attributes system.  a popup menu) which shall be used to display the selected groups.
801    
802  =back  =back
803    
# Line 593  Line 805 
805    
806  sub FieldMenu {  sub FieldMenu {
807      # Get the parameters.      # Get the parameters.
808      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self, $cgi, $height, $name, $keys, %options) = @_;
809      # These next two hashes make everything happen. "entities"      # Reformat the list of keys.
810      # maps each entity name to the list of values to be put into its      my %keys = %{$keys};
811      # option group. "labels" maps each entity name to a map from values      # Add the (new) key, if needed.
812      # to labels.      if ($options{new}) {
813      my @entityNames = sort ($self->GetEntityTypes());          $keys{NewName()} = ["string", ""];
814      my %entities = map { $_ => [] } @entityNames;      }
815      my %labels = map { $_ => { }} @entityNames;      # Get a sorted list of key.
816      # Loop through the entities, adding the existing attributes.      my @keys = sort keys %keys;
817      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  
818      # 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
819      # for the menu.      # for the menu.
820      my $changeName = "${name}_setNotes";      my $changeName = "${name}_setNotes";
821      my $retVal = $cgi->popup_menu({name => $name,      my $retVal = $cgi->popup_menu({name => $name,
822                                     size => $height,                                     size => $height,
823                                     onChange => "$changeName(this.value)",                                     onChange => "$changeName(this.value)",
824                                     values => [map { $cgi->optgroup(-name => $_,                                     values => \@keys,
825                                                                     -values => $entities{$_},                                    });
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
826      # Create the change function.      # Create the change function.
827      $retVal .= "\n<script language=\"javascript\">\n";      $retVal .= "\n<script language=\"javascript\">\n";
828      $retVal .= "    function $changeName(fieldValue) {\n";      $retVal .= "    function $changeName(fieldValue) {\n";
829      # The function only has a body if we have a notes control to store the description.      # The function only has a body if we have a control to store data about the
830      if ($noteControl || $typeControl) {      # attribute.
831        if ($options{notes} || $options{type} || $options{groups}) {
832          # 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.
833            my $noteControl = $options{notes};
834          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
835          # 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
836          # field description will be stored in the JavaScript variable "myText"          # field description will be stored in the JavaScript variable "myText"
# Line 652  Line 839 
839          $retVal .= "        var myText = \"\";\n";          $retVal .= "        var myText = \"\";\n";
840          $retVal .= "        var myType = \"string\";\n";          $retVal .= "        var myType = \"string\";\n";
841          $retVal .= "        switch (fieldValue) {\n";          $retVal .= "        switch (fieldValue) {\n";
842          # Loop through the entities.          # Loop through the keys.
843          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};  
844                      # Generate this case.                      # Generate this case.
845                      $retVal .= "        case \"$value\" :\n";              $retVal .= "        case \"$key\" :\n";
846                      # Here we either want to update the note display, the                      # Here we either want to update the note display, the
847                      # type display, or both.              # type display, the group list, or a combination of them.
848                my ($type, $notes, @groups) = @{$keys{$key}};
849                      if ($noteControl) {                      if ($noteControl) {
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
850                          # Insure it's in the proper form.                          # Insure it's in the proper form.
851                          if ($htmlMode) {                          if ($htmlMode) {
852                              $notes = ERDB::HTMLNote($notes);                              $notes = ERDB::HTMLNote($notes);
# Line 679  Line 856 
856                          $notes =~ s/"/\\"/g;                          $notes =~ s/"/\\"/g;
857                          $retVal .= "           myText = \"$notes\";\n";                          $retVal .= "           myText = \"$notes\";\n";
858                      }                      }
859                      if ($typeControl) {              if ($options{type}) {
860                          # Here we want the type updated.                          # Here we want the type updated.
                         my $type = $element->{type};  
861                          $retVal .= "           myType = \"$type\";\n";                          $retVal .= "           myType = \"$type\";\n";
862                      }                      }
863                if ($options{groups}) {
864                    # Here we want the groups shown. Get a list of this attribute's groups.
865                    # We'll search through this list for each group to see if it belongs with
866                    # our attribute.
867                    my $groupLiteral = "=" . join("=", @groups) . "=";
868                    # Now we need some variables containing useful code for the javascript. It's
869                    # worth knowing we go through a bit of pain to insure $groupField[i] isn't
870                    # parsed as an array element.
871                    my $groupField = $options{groups};
872                    my $currentField = $groupField . "[i]";
873                    # Do the javascript.
874                    $retVal .= "           var groupList = \"$groupLiteral\";\n";
875                    $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";
876                    $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";
877                    $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";
878                    $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";
879                    $retVal .= "           }\n";
880                }
881                      # Close this case.                      # Close this case.
882                      $retVal .= "           break;\n";                      $retVal .= "           break;\n";
883                  }                  }
             }  
         }  
884          # Close the CASE statement and make the appropriate assignments.          # Close the CASE statement and make the appropriate assignments.
885          $retVal .= "        }\n";          $retVal .= "        }\n";
886          if ($noteControl) {          if ($noteControl) {
887              $retVal .= "        $noteControl = myText;\n";              $retVal .= "        $noteControl = myText;\n";
888          }          }
889          if ($typeControl) {          if ($options{type}) {
890              $retVal .= "        $typeControl = myType;\n";              $retVal .= "        $options{type} = myType;\n";
891          }          }
892      }      }
893      # Terminate the change function.      # Terminate the change function.
# Line 705  Line 897 
897      return $retVal;      return $retVal;
898  }  }
899    
900  =head3 MatchSqlPattern  =head3 GetGroups
   
 C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>  
901    
902  Determine whether or not a specified value matches an SQL pattern. An SQL  C<< my @groups = $attrDB->GetGroups(); >>
 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.  
   
 =over 4  
903    
904  =item value  Return a list of the available groups.
   
 Value to be matched against the pattern. Note that an undefined or empty  
 value will not match anything.  
   
 =item pattern  
   
 SQL pattern against which to match the value. An undefined or empty pattern will  
 match everything.  
   
 =item RETURN  
   
 Returns TRUE if the value and pattern match, else FALSE.  
   
 =back  
905    
906  =cut  =cut
907    
908  sub MatchSqlPattern {  sub GetGroups {
909      # Get the parameters.      # Get the parameters.
910      my ($value, $pattern) = @_;      my ($self) = @_;
911      # Declare the return variable.      # Get the groups.
912      my $retVal;      my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
913      # Insure we have a pattern.      # Return them.
914      if (! defined($pattern) || $pattern eq "") {      return @retVal;
         $retVal = 1;  
     } else {  
         # Break the pattern into pieces around the wildcard characters. Because we  
         # use parentheses in the split function's delimiter expression, we'll get  
         # list elements for the delimiters as well as the rest of the string.  
         my @pieces = split /([_%]|\\[_%])/, $pattern;  
         # Check some fast special cases.  
         if ($pattern eq '%') {  
             # A null pattern matches everything.  
             $retVal = 1;  
         } elsif (@pieces == 1) {  
             # No wildcards, so we have a literal comparison. Note we're case-insensitive.  
             $retVal = (lc($value) eq lc($pattern));  
         } elsif (@pieces == 2 && $pieces[1] eq '%') {  
             # 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);  
                 } else {  
                     # Here we have raw text.  
                     $realPattern .= quotemeta($piece);  
                 }  
             }  
             # Do the match.  
             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);  
         }  
     }  
     # Return the result.  
     return $retVal;  
915  }  }
916    
917  =head3 MigrateAttributes  =head3 GetAttributeData
918    
919  C<< CustomAttributes::MigrateAttributes($fig); >>  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
920    
921  Migrate all the attributes data from the specified FIG instance. This is a long, slow  Return attribute data for the selected attributes. The attribute
922  method used to convert the old attribute data to the new system. Only attribute  data is a hash mapping each attribute key name to a n-tuple containing the
923  keys that are not already in the database will be loaded, and only for entity instances  data type, the description, and the groups. This is the same format expected in
924  current in the database. To get an accurate capture of the attributes in the given  the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.
 instance, you may want to clear the database and the DBD before starting and  
 run L</Refresh> to populate the entities.  
925    
926  =over 4  =over 4
927    
928  =item fig  =item type
   
 A FIG object that can be used to retrieve attributes for migration purposes.  
   
 =back  
   
 =cut  
   
 sub MigrateAttributes {  
     # Get the parameters.  
     my ($fig) = @_;  
     # Get a list of the objects to migrate. This requires connecting. Note we  
     # will map each entity type to a file name. The file will contain a list  
     # of the object's IDs so we can get to them when we're not connected to  
     # the database.  
     my $ca = CustomAttributes->new();  
     my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();  
     # Set up hash of the existing attribute keys for each entity type.  
     my %oldKeys = ();  
     # Finally, we have a hash that counts the IDs for each entity type.  
     my %idCounts = map { $_ => 0 } keys %objects;  
     # Loop through the list, creating key files to read back in.  
     for my $entityType (keys %objects) {  
         Trace("Retrieving keys for $entityType.") if T(2);  
         # Create the key file.  
         my $idFile = Open(undef, ">$objects{$entityType}");  
         # Loop through the keys.  
         my @ids = $ca->GetFlat([$entityType], "", [], "$entityType(id)");  
         for my $id (@ids) {  
             print $idFile "$id\n";  
         }  
         close $idFile;  
         # In addition to the key file, we must get a list of attributes already  
         # in the database. This avoids a circularity problem that might occur if the $fig  
         # object is retrieving from the custom attributes database already.  
         my %fields = $ca->GetSecondaryFields($entityType);  
         $oldKeys{$entityType} = \%fields;  
         # Finally, we have the ID count.  
         $idCounts{$entityType} = scalar @ids;  
     }  
     # Release the custom attributes database so we can add attributes.  
     undef $ca;  
     # Loop through the objects.  
     for my $entityType (keys %objects) {  
         # Get a hash of all the attributes already in this database. These are  
         # left untouched.  
         my $myOldKeys = $oldKeys{$entityType};  
         # Create a hash to control the load file names for each attribute key we find.  
         my %keyHash = ();  
         # Set up some counters so we can trace our progress.  
         my ($totalIDs, $processedIDs, $keyCount, $valueCount) = ($idCounts{$entityType}, 0, 0, 0);  
         # Open this object's ID file.  
         Trace("Migrating data for $entityType. $totalIDs found.") if T(3);  
         my $keysIn = Open(undef, "<$objects{$entityType}");  
         while (my $id = <$keysIn>) {  
             # Remove the EOL characters.  
             chomp $id;  
             # Get this object's attributes.  
             my @allData = $fig->get_attributes($id);  
             Trace(scalar(@allData) . " attribute values found for $entityType($id).") if T(4);  
             # Loop through the attribute values one at a time.  
             for my $dataTuple (@allData) {  
                 # Get the key, value, and URL. We ignore the first element because that's the  
                 # object ID, and we already know the object ID.  
                 my (undef, $key, $value, $url) = @{$dataTuple};  
                 # Remove the buggy "1" for $url.  
                 if ($url eq "1") {  
                     $url = undef;  
                 }  
                 # 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);  
 }  
   
 =head3 ComputeObjectTypeFromID  
   
 C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>  
   
 This method will compute the entity type corresponding to a specified object ID.  
 If the object ID begins with C<fig|>, it is presumed to be a feature ID. If it  
 is all digits with a single period, it is presumed to by a genome ID. Otherwise,  
 it must be a list reference. In this last case the first list element will be  
 taken as the entity type and the second will be taken as the actual ID.  
929    
930  =over 4  Type of attribute criterion: C<name> for attributes whose names begin with the
931    specified string, or C<group> for attributes in the specified group.
932    
933  =item objectID  =item list
934    
935  Object ID to examine.  List containing the names of the groups or keys for the desired attributes.
936    
937  =item RETURN  =item RETURN
938    
939  Returns a 2-element list consisting of the entity type followed by the specified ID.  Returns a hash mapping each attribute key name to its data type, description, and
940    parent groups.
941    
942  =back  =back
943    
944  =cut  =cut
945    
946  sub ComputeObjectTypeFromID {  sub GetAttributeData {
947      # Get the parameters.      # Get the parameters.
948      my ($objectID) = @_;      my ($self, $type, @list) = @_;
949      # Declare the return variables.      # Set up a hash to store the attribute data.
950      my ($entityName, $id);      my %retVal = ();
951      # Only proceed if the object ID is defined. If it's not, we'll be returning a      # Loop through the list items.
952      # pair of undefs.      for my $item (@list) {
953      if ($objectID) {          # Set up a query for the desired attributes.
954          if (ref $objectID eq 'ARRAY') {          my $query;
955              # Here we have the new-style list reference. Pull out its pieces.          if ($type eq 'name') {
956              ($entityName, $id) = @{$objectID};              # Here we're doing a generic name search. We need to escape it and then tack
957          } else {              # on a %.
958              # Here the ID is the outgoing ID, and we need to look at its structure              my $parm = $item;
959              # to determine the entity type.              $parm =~ s/_/\\_/g;
960              $id = $objectID;              $parm =~ s/%/\\%/g;
961              if ($objectID =~ /^\d+\.\d+/) {              $parm .= "%";
962                  # Digits with a single period is a genome.              # Ask for matching attributes. (Note that if the user passed in a null string
963                  $entityName = 'Genome';              # he'll get everything.)
964              } elsif ($objectID =~ /^fig\|/) {              $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
965                  # The "fig|" prefix indicates a feature.          } elsif ($type eq 'group') {
966                  $entityName = 'Feature';              $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
967              } else {              } else {
968                  # Anything else is illegal!              Confess("Unknown attribute query type \"$type\".");
969                  Confess("Invalid attribute ID specification \"$objectID\".");          }
970            while (my $row = $query->Fetch()) {
971                # Get this attribute's data.
972                my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
973                                                         'AttributeKey(description)']);
974                # If it's new, get its groups and add it to the return hash.
975                if (! exists $retVal{$key}) {
976                    my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
977                                                [$key], 'IsInGroup(to-link)');
978                    $retVal{$key} = [$type, $notes, @groups];
979              }              }
980          }          }
981      }      }
982      # Return the result.      # Return the result.
983      return ($entityName, $id);      return %retVal;
984  }  }
985    
986  =head2 FIG Method Replacements  =head2 FIG Method Replacements
987    
988  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.
989  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
990  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
991  capabilities were used in the old system.  capabilities were used in the old system.
992    
# Line 999  Line 1000 
1000  value of the splitter parameter on the constructor (L</new>). The default is double  value of the splitter parameter on the constructor (L</new>). The default is double
1001  colons C<::>.  colons C<::>.
1002    
1003  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
1004  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
1005  splitter value would be stored as  splitter value would be stored as
1006    
# Line 1010  Line 1011 
1011    
1012  =head3 GetAttributes  =head3 GetAttributes
1013    
1014  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1015    
1016  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1017  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
1018  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
1019  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1020  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.  
1021    
1022  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
1023  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
1024  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1025    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1026    of the parameters. So, for example,
1027    
1028      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1029    
1030  would return something like  would return something like
1031    
# Line 1033  Line 1034 
1034      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1035      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1036    
1037  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1038  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1039  matches any sequence of characters, and C<_>, which matches any single character.  
1040  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1041  underscore.)  
1042    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1043    features.
1044    
1045  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1046  values, so even  values, so even
1047    
1048      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1049    
1050  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.
1051    
1052  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
1053  determine the entity type. In that case the only two types allowed are C<Genome> and  stored. For the object ID and key name, we create queries that filter for the desired
1054  C<Feature>. An alternative method is to use a list reference, with the list consisting  results. For the values, we do a comparison after the attributes are retrieved from the
1055  of an entity type name and the actual ID. Thus, the above example could equivalently  database. As a result, queries in which filter only on value end up reading the entire
1056  be written as  attribute table to find the desired results.
   
     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.  
1057    
1058  =over 4  =over 4
1059    
1060  =item objectID  =item objectID
1061    
1062  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
1063  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
1064  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
1065  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.  
1066    
1067  =item key  =item key
1068    
1069  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
1070  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
1071  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
1072  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.  
1073    
1074  =item valuePatterns  =item values
1075    
1076  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1077  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
1078    generic match can be requested by placing a percent sign (C<%>) at the end.
1079    In that case, all values that match up to and not including the percent sign
1080    will match. You may also specify a regular expression enclosed
1081    in slashes. All values that match the regular expression will be returned. For
1082    performance reasons, only values have this extra capability.
1083    
1084  =item RETURN  =item RETURN
1085    
# Line 1107  Line 1094 
1094    
1095  sub GetAttributes {  sub GetAttributes {
1096      # Get the parameters.      # Get the parameters.
1097      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1098        # We will create one big honking query. The following hash will build the filter
1099        # clause and a parameter list.
1100        my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);
1101        my @filter = ();
1102        my @parms = ();
1103        # This next loop goes through the different fields that can be specified in the
1104        # parameter list and generates filters for each.
1105        for my $field (keys %data) {
1106            # Accumulate filter information for this field. We will OR together all the
1107            # elements accumulated to create the final result.
1108            my @fieldFilter = ();
1109            # Get the specified data from the caller.
1110            my $fieldPattern = $data{$field};
1111            # Only proceed if the pattern is one that won't match everything.
1112            if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1113                # Convert the pattern to an array.
1114                my @patterns = ();
1115                if (ref $fieldPattern eq 'ARRAY') {
1116                    push @patterns, @{$fieldPattern};
1117                } else {
1118                    push @patterns, $fieldPattern;
1119                }
1120                # Only proceed if the array is nonempty. The loop will work fine if the
1121                # array is empty, but when we build the filter string at the end we'll
1122                # get "()" in the filter list, which will result in an SQL syntax error.
1123                if (@patterns) {
1124                    # Loop through the individual patterns.
1125                    for my $pattern (@patterns) {
1126                        # Check for a generic request.
1127                        if (substr($pattern, -1, 1) ne '%') {
1128                            # Here we have a normal request.
1129                            push @fieldFilter, "$field = ?";
1130                            push @parms, $pattern;
1131                        } else {
1132                            # Here we have a generate request, so we will use the LIKE operator to
1133                            # filter the field to this value pattern.
1134                            push @fieldFilter, "$field LIKE ?";
1135                            # We must convert the pattern value to an SQL match pattern. First
1136                            # we get a copy of it.
1137                            my $actualPattern = $pattern;
1138                            # Now we escape the underscores. Underscores are an SQL wild card
1139                            # character, but they are used frequently in key names and object IDs.
1140                            $actualPattern =~ s/_/\\_/g;
1141                            # Add the escaped pattern to the bound parameter list.
1142                            push @parms, $actualPattern;
1143                        }
1144                    }
1145                    # Form the filter for this field.
1146                    my $fieldFilterString = join(" OR ", @fieldFilter);
1147                    push @filter, "($fieldFilterString)";
1148                }
1149            }
1150        }
1151        # Now @filter contains one or more filter strings and @parms contains the parameter
1152        # values to bind to them.
1153        my $actualFilter = join(" AND ", @filter);
1154      # Declare the return variable.      # Declare the return variable.
1155      my @retVal = ();      my @retVal = ();
1156      # Determine the entity types for our search.      # Get the number of value sections we have to match.
1157      my @objects = ();      my $sectionCount = scalar(@values);
1158      my ($actualObjectID, $computedType);      # Now we're ready to make our query.
1159      if (! $objectID) {      my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1160          push @objects, $self->GetEntityTypes();      # Loop through the assignments found.
1161        while (my $row = $query->Fetch()) {
1162            # Get the current row's data.
1163            my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
1164                                                          'HasValueFor(value)']);
1165            # Break the value into sections.
1166            my @sections = split($self->{splitter}, $valueString);
1167            # Match each section against the incoming values. We'll assume we're
1168            # okay unless we learn otherwise.
1169            my $matching = 1;
1170            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1171                # We need to check to see if this section is generic.
1172                my $value = $values[$i];
1173                Trace("Current value pattern is \"$value\".") if T(4);
1174                if (substr($value, -1, 1) eq '%') {
1175                    Trace("Generic match used.") if T(4);
1176                    # Here we have a generic match.
1177                    my $matchLen = length($values[$i] - 1);
1178                    $matching = substr($sections[$i], 0, $matchLen) eq
1179                                substr($values[$i], 0, $matchLen);
1180                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1181                    Trace("Regular expression detected.") if T(4);
1182                    # Here we have a regular expression match.
1183                    my $section = $sections[$i];
1184                    $matching = eval("\$section =~ $value");
1185      } else {      } else {
1186          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);                  # Here we have a strict match.
1187          push @objects, $computedType;                  Trace("Strict match used.") if T(4);
1188                    $matching = ($sections[$i] eq $values[$i]);
1189      }      }
     # Loop through the entity types.  
     for my $entityType (@objects) {  
         # Now we need to find all the matching keys. The keys are actually stored in  
         # our database object, so this process is fast. Note that our  
         # MatchSqlPattern method  
         my %secondaries = $self->GetSecondaryFields($entityType);  
         my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;  
         # Now we figure out whether or not we need to filter by object. We will always  
         # filter by key to a limited extent, so if we're filtering by object we need an  
         # AND to join the object ID filter with the key filter.  
         my $filter = "";  
         my @params = ();  
         if (defined($actualObjectID)) {  
             # Here the caller wants to filter on object ID. Check for a pattern.  
             my $comparator = ($actualObjectID =~ /%/ ? "LIKE" : "=");  
             # Update the filter and the parameter list.  
             $filter = "$entityType(id) $comparator ? AND ";  
             push @params, $actualObjectID;  
         }  
         # It's time to begin making queries. We process one attribute key at a time, because  
         # each attribute is actually a different field in the database. We know here that  
         # all the keys we've collected are for the correct entity because we got them from  
         # the DBD. That's a good thing, because an invalid key name will cause an SQL error.  
         for my $key (@fieldList) {  
             # Get all of the attribute values for this key.  
             my @dataRows = $self->GetAll([$entityType], "$filter$entityType($key) IS NOT NULL",  
                                          \@params, ["$entityType(id)", "$entityType($key)"]);  
             # Process each value separately. We need to verify the values and reformat the  
             # tuples. Note that GetAll will give us one row per matching object ID,  
             # with the ID first followed by a list of the data values. This is very  
             # different from the structure we'll be returning, which has one row  
             # per value.  
             for my $dataRow (@dataRows) {  
                 # Get the object ID and the list of values.  
                 my ($rowObjectID, @dataValues) = @{$dataRow};  
                 # Loop through the values. There will be one result row per attribute value.  
                 for my $dataValue (@dataValues) {  
                     # Separate this value into sections.  
                     my @sections = split("::", $dataValue);  
                     # Loop through the value patterns, looking for a mismatch. Note that  
                     # since we're working through parallel arrays, we are using an index  
                     # loop. As soon as a match fails we stop checking. This means that  
                     # if the value pattern list is longer than the number of sections,  
                     # we will fail as soon as we run out of sections.  
                     my $match = 1;  
                     for (my $i = 0; $i <= $#valuePatterns && $match; $i++) {  
                         $match = MatchSqlPattern($sections[$i], $valuePatterns[$i]);  
                     }  
                     # If we match, we save this value in the output list.  
                     if ($match) {  
                         push @retVal, [$rowObjectID, $key, @sections];  
                     }  
                 }  
                 # Here we've processed all the attribute values for the current object ID.  
1190              }              }
1191              # Here we've processed all the rows returned by GetAll. In general, there will          # If we match, output this row to the return list.
1192              # be one row per object ID.          if ($matching) {
1193                push @retVal, [$id, $key, @sections];
1194          }          }
         # Here we've processed all the matching attribute keys.  
1195      }      }
1196      # Here we've processed all the entity types. That means @retVal has all the matching      # Return the rows found.
     # results.  
1197      return @retVal;      return @retVal;
1198  }  }
1199    
# Line 1195  Line 1208 
1208    
1209  =item objectID  =item objectID
1210    
1211  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.  
1212    
1213  =item key  =item key
1214    
1215  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1216    
1217  =item values  =item values
1218    
# Line 1225  Line 1235 
1235      } elsif (! @values) {      } elsif (! @values) {
1236          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1237      } else {      } else {
1238          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1239          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1240          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1241          # Insert the value.          # Connect the object to the key.
1242          $self->InsertValue($id, "$entityName($key)", $valueString);          $self->InsertObject('HasValueFor', { 'from-link' => $key,
1243                                                 'to-link'   => $objectID,
1244                                                 'value'     => $valueString,
1245                                           });
1246      }      }
1247      # Return a one. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1248      return 1;      return 1;
1249  }  }
1250    
# Line 1243  Line 1254 
1254    
1255  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1256    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1257  =over 4  =over 4
1258    
1259  =item objectID  =item objectID
1260    
1261  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.  
1262    
1263  =item key  =item key
1264    
1265  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1266    
1267  =item values  =item values
1268    
1269  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
1270    will be deleted. Otherwise, only a matching value will be deleted.
1271    
1272  =back  =back
1273    
# Line 1275  Line 1281 
1281          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1282      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1283          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1284      } elsif (! @values) {      } elsif (scalar(@values) == 0) {
1285          Confess("No values specified in DeleteAttribute call for key $key.");          # Here we erase the entire key.
1286            $self->EraseAttribute($key);
1287      } else {      } else {
1288          # Now compute the object type and ID.          # Here we erase the matching values.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1289          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1290          # Delete the value.          $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });
         $self->DeleteValue($entityName, $id, $key, $valueString);  
1291      }      }
1292      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1293      return 1;      return 1;
# Line 1333  Line 1337 
1337      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1338          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1339      } else {      } else {
1340          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1341          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1342          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1343      }      }
# Line 1343  Line 1347 
1347    
1348  =head3 EraseAttribute  =head3 EraseAttribute
1349    
1350  C<< $attrDB->EraseAttribute($entityName, $key); >>  C<< $attrDB->EraseAttribute($key); >>
1351    
1352  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
1353  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
1354    
1355  =over 4  =over 4
1356    
 =item entityName  
   
 Name of the entity to which the key belongs. If undefined, all entities will be  
 examined for the desired key.  
   
1357  =item key  =item key
1358    
1359  Key to erase.  Key to erase.
# Line 1365  Line 1364 
1364    
1365  sub EraseAttribute {  sub EraseAttribute {
1366      # Get the parameters.      # Get the parameters.
1367      my ($self, $entityName, $key) = @_;      my ($self, $key) = @_;
1368      # Determine the relevant entity types.      # Delete everything connected to the key. The "keepRoot" option keeps the key in the
1369      my @objects = ();      # datanase while deleting everything attached to it.
1370      if (! $entityName) {      $self->Delete('AttributeKey', $key, keepRoot => 1);
         push @objects, $self->GetEntityTypes();  
     } 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);  
         }  
     }  
1371      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1372      return 1;      return 1;
1373  }  }
1374    
1375  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1376    
1377  C<< my @keyList = $attrDB->GetAttributeKeys($entityName); >>  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1378    
1379  Return a list of the attribute keys for a particular entity type.  Return a list of the attribute keys for a particular group.
1380    
1381  =over 4  =over 4
1382    
1383  =item entityName  =item groupName
1384    
1385  Name of the entity whose keys are desired.  Name of the group whose keys are desired.
1386    
1387  =item RETURN  =item RETURN
1388    
1389  Returns a list of the attribute keys for the specified entity.  Returns a list of the attribute keys for the specified group.
1390    
1391  =back  =back
1392    
# Line 1408  Line 1394 
1394    
1395  sub GetAttributeKeys {  sub GetAttributeKeys {
1396      # Get the parameters.      # Get the parameters.
1397      my ($self, $entityName) = @_;      my ($self, $groupName) = @_;
1398      # Get the entity's secondary fields.      # Get the attributes for the specified group.
1399      my %keyList = $self->GetSecondaryFields($entityName);      my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1400                                    'IsInGroup(from-link)');
1401      # Return the keys.      # Return the keys.
1402      return sort keys %keyList;      return sort @groups;
1403  }  }
1404    
1405  1;  1;

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