[Bio] / Sprout / CustomAttributes.pm Repository:
ViewVC logotype

Diff of /Sprout/CustomAttributes.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.9, Thu Nov 16 22:09:33 2006 UTC revision 1.15, Tue Jan 9 01:49:08 2007 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);  
         }  
     }  
     return $retVal;  
 }  
   
 =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);  
189          }          }
190      }      }
     # 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.  
   
 =item fieldName  
206    
207  Name of the actual attribute.  Key of the attribute to load.
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        if (! defined $found) {
255            Confess("Attribute key \"$keyName\" not found in database.");
256      } else {      } else {
257          # Get the field structure for the named entity.          # Erase the key's current values.
258          my $fieldHash = $self->GetFieldTable($entityName);          $self->EraseAttribute($keyName);
259          # Verify that the attribute exists.          # Save a list of the object IDs we need to add.
260          if (! exists $fieldHash->{$fieldName}) {          my %objectIDs = ();
             Confess("Attribute key \"$fieldName\" does not exist in entity $entityName.");  
         } else {  
             # Create a loader for the specified attribute. We need the  
             # relation name first.  
             my $relName = $fieldHash->{$fieldName}->{relation};  
             my $loadAttribute = ERDBLoad->new($self, $relName, $FIG_Config::temp);  
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 we insert the attribute.
275                    $self->InsertObject('HasValueFor', { from => $keyName, to => $id,
276                                                         keywords => $self->_KeywordString($keyName, $value),
277                                                         value => $value });
278                    $retVal->Add(newValue => 1);
279              }              }
             # Finish the load.  
             $retVal = $loadAttribute->FinishAndLoad();  
280          }          }
281      }      }
282      # Return the statistics.      # Return the statistics.
# Line 386  Line 286 
286    
287  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
288    
289  C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
290    
291  Delete an attribute from the custom attributes database.  Delete an attribute from the custom attributes database.
292    
293  =over 4  =over 4
294    
 =item entityName  
   
 Name of the entity possessing the attribute.  
   
295  =item attributeName  =item attributeName
296    
297  Name of the attribute to delete.  Name of the attribute to delete.
298    
299    =item RETURN
300    
301    Returns a statistics object describing the effects of the deletion.
302    
303  =back  =back
304    
305  =cut  =cut
306    
307  sub DeleteAttributeKey {  sub DeleteAttributeKey {
308      # Get the parameters.      # Get the parameters.
309      my ($entityName, $attributeName) = @_;      my ($self, $attributeName) = @_;
310      # Read in the XML for the database defintion. We need to verify that      # Delete the attribute key.
311      # the named entity exists and it has the named attribute.      my $retVal = $self->Delete('AttributeKey', $attributeName);
312      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Return the result.
313      my $entityHash = $metadata->{Entities};      return $retVal;
314      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);  
         }  
315      }      }
316    
317    =head3 NewName
318    
319    C<< my $text = CustomAttributes::NewName(); >>
320    
321    Return the string used to indicate the user wants to add a new attribute.
322    
323    =cut
324    
325    sub NewName {
326        return "(new)";
327  }  }
328    
329  =head3 ControlForm  =head3 ControlForm
330    
331  C<< my $formHtml = $attrDB->ControlForm($cgi, $name); >>  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
332    
333  Return a form that can be used to control the creation and modification of  Return a form that can be used to control the creation and modification of
334  attributes.  attributes. Only a subset of the attribute keys will be displayed, as
335    determined by the incoming list.
336    
337  =over 4  =over 4
338    
# Line 458  Line 344 
344    
345  Name to give to the form. This should be unique for the web page.  Name to give to the form. This should be unique for the web page.
346    
347    =item keys
348    
349    Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
350    attribute's data type, its description, and a list of the groups in which it participates.
351    
352  =item RETURN  =item RETURN
353    
354  Returns the HTML for a form that submits instructions to the C<Attributes.cgi> script  Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script
355  for loading, creating, or deleting an attribute.  for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
356    controls are generated. The form tags are left to the caller.
357    
358  =back  =back
359    
# Line 469  Line 361 
361    
362  sub ControlForm {  sub ControlForm {
363      # Get the parameters.      # Get the parameters.
364      my ($self, $cgi, $name) = @_;      my ($self, $cgi, $name, $keys) = @_;
365      # Declare the return list.      # Declare the return list.
366      my @retVal = ();      my @retVal = ();
     # Start the form. We use multipart to support the upload control.  
     push @retVal, $cgi->start_multipart_form(-name => $name);  
367      # 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.
368      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
369      # The first row is for selecting the field name.      # The first row is for selecting the field name.
370      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      push @retVal, $cgi->Tr($cgi->th("Select a Field"),
371                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
372                                                       "document.$name.notes.value",                                                       new => 1,
373                                                       "document.$name.dataType.value")));                                                       notes => "document.$name.notes.value",
374                                                         type => "document.$name.dataType.value",
375                                                         groups => "document.$name.groups")));
376      # 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
377      # data type names, and the labels will be the descriptions.      # data type names, and the labels will be the descriptions.
378      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
379      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
380      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',
381                                      -values => [sort keys %types],                                      -values => [sort keys %types],
382                                      -labels => \%labelMap);                                      -labels => \%labelMap,
383                                        -default => 'string');
384        # Allow the user to specify a new field name. This is required if the
385        # user has selected the "(new)" marker. We put a little scriptlet in here that
386        # selects the (new) marker when the user enters the field.
387        push @retVal, "<script language=\"javaScript\">";
388        my $fieldField = "document.$name.fieldName";
389        my $newName = "\"" . NewName() . "\"";
390        push @retVal, $cgi->Tr($cgi->th("New Field Name"),
391                               $cgi->td($cgi->textfield(-name => 'newName',
392                                                        -size => 30,
393                                                        -value => "",
394                                                        -onFocus => "setIfEmpty($fieldField, $newName);")),
395                                        );
396      push @retVal, $cgi->Tr($cgi->th("Data type"),      push @retVal, $cgi->Tr($cgi->th("Data type"),
397                             $cgi->td($typeMenu));                             $cgi->td($typeMenu));
398      # The next row is for the notes.      # The next row is for the notes.
# Line 496  Line 401 
401                                                     -rows => 6,                                                     -rows => 6,
402                                                     -columns => 80))                                                     -columns => 80))
403                            );                            );
404      # 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.
405      # user has selected one of the "(new)" markers.      my @groups = $self->GetGroups();
406      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      push @retVal, $cgi->Tr($cgi->th("Groups"),
407                             $cgi->td($cgi->textfield(-name => 'newName',                             $cgi->td($cgi->checkbox_group(-name=>'groups',
408                                                      -size => 30)),                                      -values=> \@groups))
409                                      );                                      );
410      # 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
411      # an upload file name and column indicators.      # an upload file name and column indicators.
# Line 517  Line 422 
422                                                      -default => 1)                                                      -default => 1)
423                                     ),                                     ),
424                            );                            );
425      # Now the three buttons: UPDATE, SHOW, and DELETE.      # Now the three buttons: STORE, SHOW, and DELETE.
426      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
427                             $cgi->td({align => 'center'},                             $cgi->td({align => 'center'},
428                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .
# Line 527  Line 432 
432                            );                            );
433      # Close the table and the form.      # Close the table and the form.
434      push @retVal, $cgi->end_table();      push @retVal, $cgi->end_table();
     push @retVal, $cgi->end_form();  
435      # Return the assembled HTML.      # Return the assembled HTML.
436      return join("\n", @retVal, "");      return join("\n", @retVal, "");
437  }  }
438    
439    =head3 LoadAttributesFrom
440    
441    C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
442    
443    Load attributes from the specified tab-delimited file. Each line of the file must
444    contain an object ID in the first column, an attribute key name in the second
445    column, and attribute values in the remaining columns. The attribute values will
446    be assembled into a single value using the splitter code.
447    
448    =over 4
449    
450    =item fileName
451    
452    Name of the file from which to load the attributes.
453    
454    =item options
455    
456    Hash of options for modifying the load process.
457    
458    =item RETURN
459    
460    Returns a statistics object describing the load.
461    
462    =back
463    
464    Permissible option values are as follows.
465    
466    =over 4
467    
468    =item append
469    
470    If TRUE, then the attributes will be appended to existing data; otherwise, the
471    first time a key name is encountered, it will be erased.
472    
473    =back
474    
475    =cut
476    
477    sub LoadAttributesFrom {
478        # Get the parameters.
479        my ($self, $fileName, %options) = @_;
480        # Declare the return variable.
481        my $retVal = Stats->new('keys', 'values');
482        # Check for append mode.
483        my $append = ($options{append} ? 1 : 0);
484        # Create a hash of key names found.
485        my %keyHash = ();
486        # Open the file for input.
487        my $fh = Open(undef, "<$fileName");
488        # Loop through the file.
489        while (! eof $fh) {
490            my ($id, $key, @values) = Tracer::GetLine($fh);
491            $retVal->Add(linesIn => 1);
492            # Do some validation.
493            if (! defined($id)) {
494                # We ignore blank lines.
495                $retVal->Add(blankLines => 1);
496            } elsif (! defined($key)) {
497                # An ID without a key is a serious error.
498                my $lines = $retVal->Ask('linesIn');
499                Confess("Line $lines in $fileName has no attribute key.");
500            } else {
501                # Now we need to check for a new key.
502                if (! exists $keyHash{$key}) {
503                    # This is a new key. Verify that it exists.
504                    if (! $self->Exists('AttributeKey', $key)) {
505                        my $line = $retVal->Ask('linesIn');
506                        Confess("Attribute \"$key\" on line $line of $fileName not found in database.");
507                    } else {
508                        # Make sure we know this is no longer a new key.
509                        $keyHash{$key} = 1;
510                        $retVal->Add(keys => 1);
511                        # If this is NOT append mode, erase the key.
512                        if (! $append) {
513                            $self->EraseAttribute($key);
514                        }
515                    }
516                    Trace("Key $key found.") if T(3);
517                }
518                # Now we know the key is valid. Add this value.
519                $self->AddAttribute($id, $key, @values);
520                my $progress = $retVal->Add(values => 1);
521                Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
522    
523            }
524        }
525        # Return the result.
526        return $retVal;
527    }
528    
529    =head3 BackupKeys
530    
531    C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
532    
533    Backup the attribute key information from the attribute database.
534    
535    =over 4
536    
537    =item fileName
538    
539    Name of the output file.
540    
541    =item options
542    
543    Options for modifying the backup process.
544    
545    =item RETURN
546    
547    Returns a statistics object for the backup.
548    
549    =back
550    
551    Currently there are no options. The backup is straight to a text file in
552    tab-delimited format. Each key is backup up to two lines. The first line
553    is all of the data from the B<AttributeKey> table. The second is a
554    tab-delimited list of all the groups.
555    
556    =cut
557    
558    sub BackupKeys {
559        # Get the parameters.
560        my ($self, $fileName, %options) = @_;
561        # Declare the return variable.
562        my $retVal = Stats->new();
563        # Open the output file.
564        my $fh = Open(undef, ">$fileName");
565        # Set up to read the keys.
566        my $keyQuery = $self->Get(['AttributeKey'], "", []);
567        # Loop through the keys.
568        while (my $keyData = $keyQuery->Fetch()) {
569            $retVal->Add(key => 1);
570            # Get the fields.
571            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
572                                                              'AttributeKey(description)']);
573            # Escape any tabs or new-lines in the description.
574            my $escapedDescription = Tracer::Escape($description);
575            # Write the key data to the output.
576            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
577            # Get the key's groups.
578            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
579                                        'IsInGroup(to-link)');
580            $retVal->Add(memberships => scalar(@groups));
581            # Write them to the output. Note we put a marker at the beginning to insure the line
582            # is nonempty.
583            Tracer::PutLine($fh, ['#GROUPS', @groups]);
584        }
585        # Return the result.
586        return $retVal;
587    }
588    
589    =head3 RestoreKeys
590    
591    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
592    
593    Restore the attribute keys and groups from a backup file.
594    
595    =over 4
596    
597    =item fileName
598    
599    Name of the file containing the backed-up keys. Each key has a pair of lines,
600    one containing the key data and one listing its groups.
601    
602    =back
603    
604    =cut
605    
606    sub RestoreKeys {
607        # Get the parameters.
608        my ($self, $fileName, %options) = @_;
609        # Declare the return variable.
610        my $retVal = Stats->new();
611        # Set up a hash to hold the group IDs.
612        my %groups = ();
613        # Open the file.
614        my $fh = Open(undef, "<$fileName");
615        # Loop until we're done.
616        while (! eof $fh) {
617            # Get a key record.
618            my ($id, $dataType, $description) = Tracer::GetLine($fh);
619            if ($id eq '#GROUPS') {
620                Confess("Group record found when key record expected.");
621            } elsif (! defined($description)) {
622                Confess("Invalid format found for key record.");
623            } else {
624                $retVal->Add("keyIn" => 1);
625                # Add this key to the database.
626                $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
627                                                      description => Tracer::UnEscape($description) });
628                Trace("Attribute $id stored.") if T(3);
629                # Get the group line.
630                my ($marker, @groups) = Tracer::GetLine($fh);
631                if (! defined($marker)) {
632                    Confess("End of file found where group record expected.");
633                } elsif ($marker ne '#GROUPS') {
634                    Confess("Group record not found after key record.");
635                } else {
636                    $retVal->Add(memberships => scalar(@groups));
637                    # Connect the groups.
638                    for my $group (@groups) {
639                        # Find out if this is a new group.
640                        if (! $groups{$group}) {
641                            $retVal->Add(newGroup => 1);
642                            # Add the group.
643                            $self->InsertObject('AttributeGroup', { id => $group });
644                            Trace("Group $group created.") if T(3);
645                            # Make sure we know it's not new.
646                            $groups{$group} = 1;
647                        }
648                        # Connect the group to our key.
649                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
650                    }
651                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
652                }
653            }
654        }
655        # Return the result.
656        return $retVal;
657    }
658    
659    
660    =head3 BackupAllAttributes
661    
662    C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
663    
664    Backup all of the attributes to a file. The attributes will be stored in a
665    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
666    
667    =over 4
668    
669    =item fileName
670    
671    Name of the file to which the attribute data should be backed up.
672    
673    =item options
674    
675    Hash of options for the backup.
676    
677    =item RETURN
678    
679    Returns a statistics object describing the backup.
680    
681    =back
682    
683    Currently there are no options defined.
684    
685    =cut
686    
687    sub BackupAllAttributes {
688        # Get the parameters.
689        my ($self, $fileName, %options) = @_;
690        # Declare the return variable.
691        my $retVal = Stats->new();
692        # Get a list of the keys.
693        my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
694        Trace(scalar(@keys) . " keys found during backup.") if T(2);
695        # Open the file for output.
696        my $fh = Open(undef, ">$fileName");
697        # Loop through the keys.
698        for my $key (@keys) {
699            Trace("Backing up attribute $key.") if T(3);
700            $retVal->Add(keys => 1);
701            # Loop through this key's values.
702            my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
703            my $valuesFound = 0;
704            while (my $line = $query->Fetch()) {
705                $valuesFound++;
706                # Get this row's data.
707                my @row = $line->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
708                                         'HasValueFor(value)']);
709                # Write it to the file.
710                Tracer::PutLine($fh, \@row);
711            }
712            Trace("$valuesFound values backed up for key $key.") if T(3);
713            $retVal->Add(values => $valuesFound);
714        }
715        # Return the result.
716        return $retVal;
717    }
718    
719  =head3 FieldMenu  =head3 FieldMenu
720    
721  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
722    
723  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
724  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
725  CGI package, but actually looks like a list. The list will contain  CGI package, but actually looks like a list. The list will contain
726  one selectable row per field, grouped by entity.  one selectable row per field.
727    
728  =over 4  =over 4
729    
# Line 556  Line 740 
740  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
741  appear when the form is submitted.  appear when the form is submitted.
742    
743  =item newFlag (optional)  =item keys
744    
745    Reference to a hash mapping each attribute key name to a list reference,
746    the list itself consisting of the attribute data type, its description,
747    and a list of its groups.
748    
749    =item options
750    
751    Hash containing options that modify the generation of the menu.
752    
753    =item RETURN
754    
755    Returns the HTML to create a form field that can be used to select an
756    attribute from the custom attributes system.
757    
758    =back
759    
760    The permissible options are as follows.
761    
762    =over 4
763    
764    =item new
765    
766  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
767  a new attribute. In other words, the user can select an existing  a new attribute. In other words, the user can select an existing
768  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
769  be created in the parent entity.  be created in the parent entity.
770    
771  =item noteControl (optional)  =item notes
772    
773  If specified, the name of a variable for displaying the notes attached  If specified, the name of a variable for displaying the notes attached
774  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 779 
779  it is copied in. Specifying this parameter generates Javascript for  it is copied in. Specifying this parameter generates Javascript for
780  displaying the field description when a field is selected.  displaying the field description when a field is selected.
781    
782  =item typeControl (optional)  =item type
783    
784  If specified, the name of a variable for displaying the field's  If specified, the name of a variable for displaying the field's
785  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 787 
787  raw value is put into the specified variable. Otherwise, the same  raw value is put into the specified variable. Otherwise, the same
788  rules apply to this value that apply to I<$noteControl>.  rules apply to this value that apply to I<$noteControl>.
789    
790  =item RETURN  =item groups
791    
792  Returns the HTML to create a form field that can be used to select an  If specified, the name of a multiple-selection list control (also called
793  attribute from the custom attributes system.  a popup menu) which shall be used to display the selected groups.
794    
795  =back  =back
796    
# Line 593  Line 798 
798    
799  sub FieldMenu {  sub FieldMenu {
800      # Get the parameters.      # Get the parameters.
801      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self, $cgi, $height, $name, $keys, %options) = @_;
802      # These next two hashes make everything happen. "entities"      # Reformat the list of keys.
803      # maps each entity name to the list of values to be put into its      my %keys = %{$keys};
804      # option group. "labels" maps each entity name to a map from values      # Add the (new) key, if needed.
805      # to labels.      if ($options{new}) {
806      my @entityNames = sort ($self->GetEntityTypes());          $keys{NewName()} = ["string", ""];
807      my %entities = map { $_ => [] } @entityNames;      }
808      my %labels = map { $_ => { }} @entityNames;      # Get a sorted list of key.
809      # Loop through the entities, adding the existing attributes.      my @keys = sort keys %keys;
810      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  
811      # 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
812      # for the menu.      # for the menu.
813      my $changeName = "${name}_setNotes";      my $changeName = "${name}_setNotes";
814      my $retVal = $cgi->popup_menu({name => $name,      my $retVal = $cgi->popup_menu({name => $name,
815                                     size => $height,                                     size => $height,
816                                     onChange => "$changeName(this.value)",                                     onChange => "$changeName(this.value)",
817                                     values => [map { $cgi->optgroup(-name => $_,                                     values => \@keys,
818                                                                     -values => $entities{$_},                                    });
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
819      # Create the change function.      # Create the change function.
820      $retVal .= "\n<script language=\"javascript\">\n";      $retVal .= "\n<script language=\"javascript\">\n";
821      $retVal .= "    function $changeName(fieldValue) {\n";      $retVal .= "    function $changeName(fieldValue) {\n";
822      # The function only has a body if we have a notes control to store the description.      # The function only has a body if we have a control to store data about the
823      if ($noteControl || $typeControl) {      # attribute.
824        if ($options{notes} || $options{type} || $options{groups}) {
825          # 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.
826            my $noteControl = $options{notes};
827          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
828          # 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
829          # field description will be stored in the JavaScript variable "myText"          # field description will be stored in the JavaScript variable "myText"
# Line 652  Line 832 
832          $retVal .= "        var myText = \"\";\n";          $retVal .= "        var myText = \"\";\n";
833          $retVal .= "        var myType = \"string\";\n";          $retVal .= "        var myType = \"string\";\n";
834          $retVal .= "        switch (fieldValue) {\n";          $retVal .= "        switch (fieldValue) {\n";
835          # Loop through the entities.          # Loop through the keys.
836          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};  
837                      # Generate this case.                      # Generate this case.
838                      $retVal .= "        case \"$value\" :\n";              $retVal .= "        case \"$key\" :\n";
839                      # Here we either want to update the note display, the                      # Here we either want to update the note display, the
840                      # type display, or both.              # type display, the group list, or a combination of them.
841                my ($type, $notes, @groups) = @{$keys{$key}};
842                      if ($noteControl) {                      if ($noteControl) {
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
843                          # Insure it's in the proper form.                          # Insure it's in the proper form.
844                          if ($htmlMode) {                          if ($htmlMode) {
845                              $notes = ERDB::HTMLNote($notes);                              $notes = ERDB::HTMLNote($notes);
# Line 679  Line 849 
849                          $notes =~ s/"/\\"/g;                          $notes =~ s/"/\\"/g;
850                          $retVal .= "           myText = \"$notes\";\n";                          $retVal .= "           myText = \"$notes\";\n";
851                      }                      }
852                      if ($typeControl) {              if ($options{type}) {
853                          # Here we want the type updated.                          # Here we want the type updated.
                         my $type = $element->{type};  
854                          $retVal .= "           myType = \"$type\";\n";                          $retVal .= "           myType = \"$type\";\n";
855                      }                      }
856                if ($options{groups}) {
857                    # Here we want the groups shown. Get a list of this attribute's groups.
858                    # We'll search through this list for each group to see if it belongs with
859                    # our attribute.
860                    my $groupLiteral = "=" . join("=", @groups) . "=";
861                    # Now we need some variables containing useful code for the javascript. It's
862                    # worth knowing we go through a bit of pain to insure $groupField[i] isn't
863                    # parsed as an array element.
864                    my $groupField = $options{groups};
865                    my $currentField = $groupField . "[i]";
866                    # Do the javascript.
867                    $retVal .= "           var groupList = \"$groupLiteral\";\n";
868                    $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";
869                    $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";
870                    $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";
871                    $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";
872                    $retVal .= "           }\n";
873                }
874                      # Close this case.                      # Close this case.
875                      $retVal .= "           break;\n";                      $retVal .= "           break;\n";
876                  }                  }
             }  
         }  
877          # Close the CASE statement and make the appropriate assignments.          # Close the CASE statement and make the appropriate assignments.
878          $retVal .= "        }\n";          $retVal .= "        }\n";
879          if ($noteControl) {          if ($noteControl) {
880              $retVal .= "        $noteControl = myText;\n";              $retVal .= "        $noteControl = myText;\n";
881          }          }
882          if ($typeControl) {          if ($options{type}) {
883              $retVal .= "        $typeControl = myType;\n";              $retVal .= "        $options{type} = myType;\n";
884          }          }
885      }      }
886      # Terminate the change function.      # Terminate the change function.
# Line 705  Line 890 
890      return $retVal;      return $retVal;
891  }  }
892    
893  =head3 MatchSqlPattern  =head3 GetGroups
894    
895    C<< my @groups = $attrDB->GetGroups(); >>
896    
897    Return a list of the available groups.
898    
899    =cut
900    
901    sub GetGroups {
902        # Get the parameters.
903        my ($self) = @_;
904        # Get the groups.
905        my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
906        # Return them.
907        return @retVal;
908    }
909    
910    =head3 GetAttributeData
911    
912  C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
913    
914  Determine whether or not a specified value matches an SQL pattern. An SQL  Return attribute data for the selected attributes. The attribute
915  pattern has two wild card characters: C<%> that matches multiple characters,  data is a hash mapping each attribute key name to a n-tuple containing the
916  and C<_> that matches a single character. These can be escaped using a  data type, the description, and the groups. This is the same format expected in
917  backslash (C<\>). We pull this off by converting the SQL pattern to a  the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.
 PERL regular expression. As per SQL rules, the match is case-insensitive.  
918    
919  =over 4  =over 4
920    
921  =item value  =item type
922    
923  Value to be matched against the pattern. Note that an undefined or empty  Type of attribute criterion: C<name> for attributes whose names begin with the
924  value will not match anything.  specified string, or C<group> for attributes in the specified group.
925    
926  =item pattern  =item list
927    
928  SQL pattern against which to match the value. An undefined or empty pattern will  List containing the names of the groups or keys for the desired attributes.
 match everything.  
929    
930  =item RETURN  =item RETURN
931    
932  Returns TRUE if the value and pattern match, else FALSE.  Returns a hash mapping each attribute key name to its data type, description, and
933    parent groups.
934    
935  =back  =back
936    
937  =cut  =cut
938    
939  sub MatchSqlPattern {  sub GetAttributeData {
940      # Get the parameters.      # Get the parameters.
941      my ($value, $pattern) = @_;      my ($self, $type, @list) = @_;
942      # Declare the return variable.      # Set up a hash to store the attribute data.
943      my $retVal;      my %retVal = ();
944      # Insure we have a pattern.      # Loop through the list items.
945      if (! defined($pattern) || $pattern eq "") {      for my $item (@list) {
946          $retVal = 1;          # Set up a query for the desired attributes.
947            my $query;
948            if ($type eq 'name') {
949                # Here we're doing a generic name search. We need to escape it and then tack
950                # on a %.
951                my $parm = $item;
952                $parm =~ s/_/\\_/g;
953                $parm =~ s/%/\\%/g;
954                $parm .= "%";
955                # Ask for matching attributes. (Note that if the user passed in a null string
956                # he'll get everything.)
957                $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
958            } elsif ($type eq 'group') {
959                $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
960      } else {      } else {
961          # Break the pattern into pieces around the wildcard characters. Because we              Confess("Unknown attribute query type \"$type\".");
         # 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);  
962                  }                  }
963            while (my $row = $query->Fetch()) {
964                # Get this attribute's data.
965                my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
966                                                         'AttributeKey(description)']);
967                # If it's new, get its groups and add it to the return hash.
968                if (! exists $retVal{$key}) {
969                    my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
970                                                [$key], 'IsInGroup(to-link)');
971                    $retVal{$key} = [$type, $notes, @groups];
972              }              }
             # Do the match.  
             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);  
973          }          }
974      }      }
975      # Return the result.      # Return the result.
976      return $retVal;      return %retVal;
977  }  }
978    
979  =head3 MigrateAttributes  =head2 Internal Utility Methods
980    
981    =head3 _KeywordString
982    
983    C<< my $keywordString = $ca->_KeywordString($key, $value); >>
984    
985  C<< CustomAttributes::MigrateAttributes($fig); >>  Compute the keyword string for a specified key/value pair. This consists of the
986    key name and value converted to lower case with underscores translated to spaces.
987    
988  Migrate all the attributes data from the specified FIG instance. This is a long, slow  This method is for internal use only. It is called whenever we need to update or
989  method used to convert the old attribute data to the new system. Only attribute  insert a B<HasValueFor> record.
 keys that are not already in the database will be loaded, and only for entity instances  
 current in the database. To get an accurate capture of the attributes in the given  
 instance, you may want to clear the database and the DBD before starting and  
 run L</Refresh> to populate the entities.  
990    
991  =over 4  =over 4
992    
993  =item fig  =item key
994    
995    Name of the relevant attribute key.
996    
997    =item target
998    
999    ID of the target object to which this key/value pair will be associated.
1000    
1001    =item value
1002    
1003    The value to store for this key/object combination.
1004    
1005  A FIG object that can be used to retrieve attributes for migration purposes.  =item RETURN
1006    
1007    Returns the value that should be stored as the keyword string for the specified
1008    key/value pair.
1009    
1010  =back  =back
1011    
1012  =cut  =cut
1013    
1014  sub MigrateAttributes {  sub _KeywordString {
1015      # Get the parameters.      # Get the parameters.
1016      my ($fig) = @_;      my ($self, $key, $value) = @_;
1017      # Get a list of the objects to migrate. This requires connecting. Note we      # Get a copy of the key name and convert underscores to spaces.
1018      # will map each entity type to a file name. The file will contain a list      my $keywordString = $key;
1019      # of the object's IDs so we can get to them when we're not connected to      $keywordString =~ s/_/ /g;
1020      # the database.      # Add the value convert it all to lower case.
1021      my $ca = CustomAttributes->new();      my $retVal = lc "$keywordString $value";
1022      my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();      # Return the result.
1023      # Set up hash of the existing attribute keys for each entity type.      return $retVal;
     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 $entityType.") if T(2);  
     }  
     # All keys for all entity types are now loaded.  
     Trace("Migration complete.") if T(2);  
1024  }  }
1025    
1026  =head3 ComputeObjectTypeFromID  =head3 _QueryResults
1027    
1028  C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>  C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1029    
1030  This method will compute the entity type corresponding to a specified object ID.  Match the results of a B<HasValueFor> query against value criteria and return
1031  If the object ID begins with C<fig|>, it is presumed to be a feature ID. If it  the results. This is an internal method that splits the values coming back
1032  is all digits with a single period, it is presumed to by a genome ID. Otherwise,  and matches the sections against the specified section patterns. It serves
1033  it must be a list reference. In this last case the first list element will be  as the back end to L</GetAttributes> and L</FindAttributes>.
 taken as the entity type and the second will be taken as the actual ID.  
1034    
1035  =over 4  =over 4
1036    
1037  =item objectID  =item query
1038    
1039  Object ID to examine.  A query object that will return the desired B<HasValueFor> records.
1040    
1041    =item values
1042    
1043    List of the desired attribute values, section by section. If C<undef>
1044    or an empty string is specified, all values in that section will match. A
1045    generic match can be requested by placing a percent sign (C<%>) at the end.
1046    In that case, all values that match up to and not including the percent sign
1047    will match. You may also specify a regular expression enclosed
1048    in slashes. All values that match the regular expression will be returned. For
1049    performance reasons, only values have this extra capability.
1050    
1051  =item RETURN  =item RETURN
1052    
1053  Returns a 2-element list consisting of the entity type followed by the specified ID.  Returns a list of tuples. The first element in the tuple is an object ID, the
1054    second is an attribute key, and the remaining elements are the sections of
1055    the attribute value. All of the tuples will match the criteria set forth in
1056    the parameter list.
1057    
1058  =back  =back
1059    
1060  =cut  =cut
1061    
1062  sub ComputeObjectTypeFromID {  sub _QueryResults {
1063      # Get the parameters.      # Get the parameters.
1064      my ($objectID) = @_;      my ($self, $query, @values) = @_;
1065      # Declare the return variables.      # Declare the return value.
1066      my ($entityName, $id);      my @retVal = ();
1067      # Only proceed if the object ID is defined. If it's not, we'll be returning a      # Get the number of value sections we have to match.
1068      # pair of undefs.      my $sectionCount = scalar(@values);
1069      if ($objectID) {      # Loop through the assignments found.
1070          if (ref $objectID eq 'ARRAY') {      while (my $row = $query->Fetch()) {
1071              # Here we have the new-style list reference. Pull out its pieces.          # Get the current row's data.
1072              ($entityName, $id) = @{$objectID};          my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
1073          } else {                                                        'HasValueFor(value)']);
1074              # Here the ID is the outgoing ID, and we need to look at its structure          # Break the value into sections.
1075              # to determine the entity type.          my @sections = split($self->{splitter}, $valueString);
1076              $id = $objectID;          # Match each section against the incoming values. We'll assume we're
1077              if ($objectID =~ /^\d+\.\d+/) {          # okay unless we learn otherwise.
1078                  # Digits with a single period is a genome.          my $matching = 1;
1079                  $entityName = 'Genome';          for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1080              } elsif ($objectID =~ /^fig\|/) {              # We need to check to see if this section is generic.
1081                  # The "fig|" prefix indicates a feature.              my $value = $values[$i];
1082                  $entityName = 'Feature';              Trace("Current value pattern is \"$value\".") if T(4);
1083                if (substr($value, -1, 1) eq '%') {
1084                    Trace("Generic match used.") if T(4);
1085                    # Here we have a generic match.
1086                    my $matchLen = length($values[$i] - 1);
1087                    $matching = substr($sections[$i], 0, $matchLen) eq
1088                                substr($values[$i], 0, $matchLen);
1089                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1090                    Trace("Regular expression detected.") if T(4);
1091                    # Here we have a regular expression match.
1092                    my $section = $sections[$i];
1093                    $matching = eval("\$section =~ $value");
1094              } else {              } else {
1095                  # Anything else is illegal!                  # Here we have a strict match.
1096                  Confess("Invalid attribute ID specification \"$objectID\".");                  Trace("Strict match used.") if T(4);
1097                    $matching = ($sections[$i] eq $values[$i]);
1098              }              }
1099          }          }
1100            # If we match, output this row to the return list.
1101            if ($matching) {
1102                push @retVal, [$id, $key, @sections];
1103      }      }
1104      # Return the result.      }
1105      return ($entityName, $id);      # Return the rows found.
1106        return @retVal;
1107  }  }
1108    
1109  =head2 FIG Method Replacements  =head2 FIG Method Replacements
1110    
1111  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.
1112  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
1113  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
1114  capabilities were used in the old system.  capabilities were used in the old system.
1115    
# Line 999  Line 1123 
1123  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
1124  colons C<::>.  colons C<::>.
1125    
1126  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
1127  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
1128  splitter value would be stored as  splitter value would be stored as
1129    
# Line 1010  Line 1134 
1134    
1135  =head3 GetAttributes  =head3 GetAttributes
1136    
1137  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1138    
1139  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1140  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
1141  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
1142  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1143  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.  
1144    
1145  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
1146  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
1147  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1148    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1149    of the parameters. So, for example,
1150    
1151      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1152    
1153  would return something like  would return something like
1154    
# Line 1033  Line 1157 
1157      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1158      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1159    
1160  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1161  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1162  matches any sequence of characters, and C<_>, which matches any single character.  
1163  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1164  underscore.)  
1165    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1166    features.
1167    
1168  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1169  values, so even  values, so even
1170    
1171      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1172    
1173  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.
1174    
1175  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
1176  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
1177  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
1178  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
1179  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.  
1180    
1181  =over 4  =over 4
1182    
1183  =item objectID  =item objectID
1184    
1185  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
1186  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
1187  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
1188  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.  
1189    
1190  =item key  =item key
1191    
1192  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
1193  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
1194  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
1195  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.  
1196    
1197  =item valuePatterns  =item values
1198    
1199  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1200  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
1201    generic match can be requested by placing a percent sign (C<%>) at the end.
1202    In that case, all values that match up to and not including the percent sign
1203    will match. You may also specify a regular expression enclosed
1204    in slashes. All values that match the regular expression will be returned. For
1205    performance reasons, only values have this extra capability.
1206    
1207  =item RETURN  =item RETURN
1208    
# Line 1107  Line 1217 
1217    
1218  sub GetAttributes {  sub GetAttributes {
1219      # Get the parameters.      # Get the parameters.
1220      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1221      # Declare the return variable.      # We will create one big honking query. The following hash will build the filter
1222      my @retVal = ();      # clause and a parameter list.
1223      # Determine the entity types for our search.      my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);
1224      my @objects = ();      my @filter = ();
1225      my ($actualObjectID, $computedType);      my @parms = ();
1226      if (! $objectID) {      # This next loop goes through the different fields that can be specified in the
1227          push @objects, $self->GetEntityTypes();      # parameter list and generates filters for each.
1228        for my $field (keys %data) {
1229            # Accumulate filter information for this field. We will OR together all the
1230            # elements accumulated to create the final result.
1231            my @fieldFilter = ();
1232            # Get the specified data from the caller.
1233            my $fieldPattern = $data{$field};
1234            # Only proceed if the pattern is one that won't match everything.
1235            if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1236                # Convert the pattern to an array.
1237                my @patterns = ();
1238                if (ref $fieldPattern eq 'ARRAY') {
1239                    push @patterns, @{$fieldPattern};
1240      } else {      } else {
1241          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);                  push @patterns, $fieldPattern;
         push @objects, $computedType;  
1242      }      }
1243      # Loop through the entity types.              # Only proceed if the array is nonempty. The loop will work fine if the
1244      for my $entityType (@objects) {              # array is empty, but when we build the filter string at the end we'll
1245          # Now we need to find all the matching keys. The keys are actually stored in              # get "()" in the filter list, which will result in an SQL syntax error.
1246          # our database object, so this process is fast. Note that our              if (@patterns) {
1247          # MatchSqlPattern method                  # Loop through the individual patterns.
1248          my %secondaries = $self->GetSecondaryFields($entityType);                  for my $pattern (@patterns) {
1249          my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;                      # Check for a generic request.
1250          # Now we figure out whether or not we need to filter by object. We will always                      if (substr($pattern, -1, 1) ne '%') {
1251          # filter by key to a limited extent, so if we're filtering by object we need an                          # Here we have a normal request.
1252          # AND to join the object ID filter with the key filter.                          push @fieldFilter, "$field = ?";
1253          my $filter = "";                          push @parms, $pattern;
1254          my @params = ();                      } else {
1255          if (defined($actualObjectID)) {                          # Here we have a generate request, so we will use the LIKE operator to
1256              # Here the caller wants to filter on object ID. Check for a pattern.                          # filter the field to this value pattern.
1257              my $comparator = ($actualObjectID =~ /%/ ? "LIKE" : "=");                          push @fieldFilter, "$field LIKE ?";
1258              # Update the filter and the parameter list.                          # We must convert the pattern value to an SQL match pattern. First
1259              $filter = "$entityType(id) $comparator ? AND ";                          # we get a copy of it.
1260              push @params, $actualObjectID;                          my $actualPattern = $pattern;
1261          }                          # Now we escape the underscores. Underscores are an SQL wild card
1262          # It's time to begin making queries. We process one attribute key at a time, because                          # character, but they are used frequently in key names and object IDs.
1263          # each attribute is actually a different field in the database. We know here that                          $actualPattern =~ s/_/\\_/g;
1264          # all the keys we've collected are for the correct entity because we got them from                          # Add the escaped pattern to the bound parameter list.
1265          # the DBD. That's a good thing, because an invalid key name will cause an SQL error.                          push @parms, $actualPattern;
1266          for my $key (@fieldList) {                      }
1267              # Get all of the attribute values for this key.                  }
1268              my @dataRows = $self->GetAll([$entityType], "$filter$entityType($key) IS NOT NULL",                  # Form the filter for this field.
1269                                           \@params, ["$entityType(id)", "$entityType($key)"]);                  my $fieldFilterString = join(" OR ", @fieldFilter);
1270              # Process each value separately. We need to verify the values and reformat the                  push @filter, "($fieldFilterString)";
             # 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.  
1271              }              }
             # Here we've processed all the rows returned by GetAll. In general, there will  
             # be one row per object ID.  
1272          }          }
         # Here we've processed all the matching attribute keys.  
1273      }      }
1274      # Here we've processed all the entity types. That means @retVal has all the matching      # Now @filter contains one or more filter strings and @parms contains the parameter
1275      # results.      # values to bind to them.
1276        my $actualFilter = join(" AND ", @filter);
1277        # Now we're ready to make our query.
1278        my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1279        # Format the results.
1280        my @retVal = $self->_QueryResults($query, @values);
1281        # Return the rows found.
1282        return @retVal;
1283    }
1284    
1285    =head3 FindAttributes
1286    
1287    C<< my @attributeList = $attrDB->FindAttributes($searchString); >>
1288    
1289    Search for attributes relevant to a specified keyword. This method performs
1290    a full-text search for attribute data. It returns the same information as
1291    L</GetAttributes>, except instead of filtering on specific keys or objects we do
1292    a text search of the entire <strong>HasValueFor</strong> table.
1293    
1294    =over 4
1295    
1296    =item searchString
1297    
1298    Search string to use. The syntax is the same as it is for any ERDB keyword
1299    search.
1300    
1301    =item RETURN
1302    
1303    Returns a list of tuples. The first element in the tuple is an object ID, the
1304    second is an attribute key, and the remaining elements are the sections of
1305    the attribute value. All of the tuples will match the criteria expressed in
1306    the search string.
1307    
1308    =back
1309    
1310    =cut
1311    
1312    sub FindAttributes {
1313        # Get the parameters.
1314        my ($self, $searchString) = @_;
1315        # Search the database.
1316        my $query = $self->Search($searchString, 0, ['HasValueFor'], "", []);
1317        # Build the results from the query.
1318        my @retVal = $self->_QueryResults($query);
1319        # Return the result.
1320      return @retVal;      return @retVal;
1321  }  }
1322    
# Line 1195  Line 1331 
1331    
1332  =item objectID  =item objectID
1333    
1334  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.  
1335    
1336  =item key  =item key
1337    
1338  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1339    
1340  =item values  =item values
1341    
# Line 1225  Line 1358 
1358      } elsif (! @values) {      } elsif (! @values) {
1359          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1360      } else {      } else {
1361          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1362          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1363          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1364          # Insert the value.          # Connect the object to the key.
1365          $self->InsertValue($id, "$entityName($key)", $valueString);          $self->InsertObject('HasValueFor', { 'from-link' => $key,
1366                                                 'to-link'   => $objectID,
1367                                                 'keywords' => $self->_KeywordString($key, $valueString),
1368                                                 'value'     => $valueString,
1369                                           });
1370      }      }
1371      # Return a one. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1372      return 1;      return 1;
1373  }  }
1374    
# Line 1243  Line 1378 
1378    
1379  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1380    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1381  =over 4  =over 4
1382    
1383  =item objectID  =item objectID
1384    
1385  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.  
1386    
1387  =item key  =item key
1388    
1389  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1390    
1391  =item values  =item values
1392    
1393  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
1394    will be deleted. Otherwise, only a matching value will be deleted.
1395    
1396  =back  =back
1397    
# Line 1275  Line 1405 
1405          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1406      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1407          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1408      } elsif (! @values) {      } elsif (scalar(@values) == 0) {
1409          Confess("No values specified in DeleteAttribute call for key $key.");          # Here we erase the entire key.
1410            $self->EraseAttribute($key);
1411      } else {      } else {
1412          # Now compute the object type and ID.          # Here we erase the matching values.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1413          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1414          # Delete the value.          $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });
         $self->DeleteValue($entityName, $id, $key, $valueString);  
1415      }      }
1416      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1417      return 1;      return 1;
# Line 1333  Line 1461 
1461      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1462          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1463      } else {      } else {
1464          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1465          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1466          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1467      }      }
# Line 1343  Line 1471 
1471    
1472  =head3 EraseAttribute  =head3 EraseAttribute
1473    
1474  C<< $attrDB->EraseAttribute($entityName, $key); >>  C<< $attrDB->EraseAttribute($key); >>
1475    
1476  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
1477  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
1478    
1479  =over 4  =over 4
1480    
 =item entityName  
   
 Name of the entity to which the key belongs. If undefined, all entities will be  
 examined for the desired key.  
   
1481  =item key  =item key
1482    
1483  Key to erase.  Key to erase.
# Line 1365  Line 1488 
1488    
1489  sub EraseAttribute {  sub EraseAttribute {
1490      # Get the parameters.      # Get the parameters.
1491      my ($self, $entityName, $key) = @_;      my ($self, $key) = @_;
1492      # Determine the relevant entity types.      # Delete everything connected to the key. The "keepRoot" option keeps the key in the
1493      my @objects = ();      # datanase while deleting everything attached to it.
1494      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);  
         }  
     }  
1495      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1496      return 1;      return 1;
1497  }  }
1498    
1499  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1500    
1501  C<< my @keyList = $attrDB->GetAttributeKeys($entityName); >>  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1502    
1503  Return a list of the attribute keys for a particular entity type.  Return a list of the attribute keys for a particular group.
1504    
1505  =over 4  =over 4
1506    
1507  =item entityName  =item groupName
1508    
1509  Name of the entity whose keys are desired.  Name of the group whose keys are desired.
1510    
1511  =item RETURN  =item RETURN
1512    
1513  Returns a list of the attribute keys for the specified entity.  Returns a list of the attribute keys for the specified group.
1514    
1515  =back  =back
1516    
# Line 1408  Line 1518 
1518    
1519  sub GetAttributeKeys {  sub GetAttributeKeys {
1520      # Get the parameters.      # Get the parameters.
1521      my ($self, $entityName) = @_;      my ($self, $groupName) = @_;
1522      # Get the entity's secondary fields.      # Get the attributes for the specified group.
1523      my %keyList = $self->GetSecondaryFields($entityName);      my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1524                                    'IsInGroup(from-link)');
1525      # Return the keys.      # Return the keys.
1526      return sort keys %keyList;      return sort @groups;
1527  }  }
1528    
1529  1;  1;

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.15

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3