[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 1.18, Tue Feb 6 16:28:40 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<$fid> contains the ID of the desired feature.
39    
40  where I<$fid> contains the ID of the desired feature. Each attribute has  New attribute keys must be defined before they can be used. A web interface
41  an alternate index to allow searching for attributes by value.  is provided for this purpose.
42    
43  New attributes are introduced by updating the database definition at  Major attribute activity is recorded in a log (C<attributes.log>) in the
44  run-time. Attribute values are stored by uploading data from files.  C<$FIG_Config::var> directory. The log reports the user name, time, and
45  A web interface is provided for both these activities.  the details of the operation. The user name will almost always be unknown,
46    except when it is specified in this object's constructor (see L</new>).
47    
48  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
49    
# Line 76  Line 89 
89    
90  =back  =back
91    
 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.  
   
92  =head2 Public Methods  =head2 Public Methods
93    
94  =head3 new  =head3 new
95    
96  C<< my $attrDB = CustomAttributes->new($splitter); >>  C<< my $attrDB = CustomAttributes->new(%options); >>
97    
98  Construct a new CustomAttributes object. This object cannot be used to add or  Construct a new CustomAttributes object. The following options are
99  delete keys because that requires modifying the database design. To do that,  supported.
 you need to use the static L</StoreAttributeKey> or L</DeleteAttributeKey>  
 methods.  
100    
101  =over 4  =over 4
102    
103  =item splitter  =item splitter
104    
105  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
106  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
107  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
108  worry about this parameter.  
109    =item user
110    
111    Name of the current user. This will appear in the attribute log.
112    
113  =back  =back
114    
# Line 142  Line 116 
116    
117  sub new {  sub new {
118      # Get the parameters.      # Get the parameters.
119      my ($class, $splitter) = @_;      my ($class, %options) = @_;
120      # Connect to the database.      # Connect to the database.
121      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
122                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 152  Line 126 
126      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
127      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
128      # Store the splitter value.      # Store the splitter value.
129      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
130        # Store the user name.
131        $retVal->{user} = $options{user} || '<unknown>';
132        Trace("User $retVal->{user} selected for attribute object.") if T(3);
133      # Return the result.      # Return the result.
134      return $retVal;      return $retVal;
135  }  }
136    
137  =head3 StoreAttributeKey  =head3 StoreAttributeKey
138    
139  C<< my $attrDB = CustomAttributes::StoreAttributeKey($entityName, $attributeName, $type, $notes); >>  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>
140    
141  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.  
142    
143  =over 4  =over 4
144    
 =item entityName  
   
 Name of the entity containing the attribute. The entity must exist.  
   
145  =item attributeName  =item attributeName
146    
147  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 156 
156    
157  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.
158    
159  =item RETURN  =item groups
160    
161  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.
162  error will be thrown.  This will replace any groups to which the attribute is currently attached.
163    
164  =back  =back
165    
# Line 196  Line 167 
167    
168  sub StoreAttributeKey {  sub StoreAttributeKey {
169      # Get the parameters.      # Get the parameters.
170      my ($entityName, $attributeName, $type, $notes) = @_;      my ($self, $attributeName, $type, $notes, $groups) = @_;
171      # Declare the return variable.      # Declare the return variable.
172      my $retVal;      my $retVal;
173      # Get the data type hash.      # Get the data type hash.
# Line 208  Line 179 
179          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing or incomplete description for $attributeName.");
180      } elsif (! exists $types{$type}) {      } elsif (! exists $types{$type}) {
181          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.");  
182      } else {      } else {
183          # Okay, we're ready to begin. Get the entity hash and the field hash.          # Create a variable to hold the action to be displayed for the log (Add or Update).
184          my $entityData = $entityHash->{$entityName};          my $action;
185          my $fieldHash = ERDB::GetEntityFieldHash($metadata, $entityName);          # Okay, we're ready to begin. See if this key exists.
186          # Compare the old attribute data to the new data.          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
187          my $bigChange = 1;          if (defined($attribute)) {
188          if (exists $fieldHash->{$attributeName} && $fieldHash->{$attributeName}->{type} eq $type) {              # It does, so we do an update.
189              $bigChange = 0;              $action = "Update Key";
190          }              $self->UpdateEntity('AttributeKey', $attributeName,
191          # Compute the attribute's relation name.                                  { description => $notes, 'data-type' => $type });
192          my $relName = join("", $entityName, map { ucfirst $_ } split(/-|_/, $attributeName));              # Detach the key from its current groups.
193          # Store the attribute's field data. Note the use of the "content" hash for              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
194          # the notes. This is how the XML writer knows Notes is a text tag instead of          } else {
195          # an attribute.              # It doesn't, so we do an insert.
196          $fieldHash->{$attributeName} = { type => $type, relation => $relName,              $action = "Insert Key";
197                                           Notes => { content => $notes } };              $self->InsertObject('AttributeKey', { id => $attributeName,
198          # Insure we have an index for this attribute.                                  description => $notes, 'data-type' => $type });
199          my $index = ERDB::FindIndexForEntity($metadata, $entityName, $attributeName);          }
200          if (! defined($index)) {          # Attach the key to the specified groups. (We presume the groups already
201              push @{$entityData->{Indexes}}, { IndexFields => [ { name => $attributeName, order => 'ascending' } ],          # exist.)
202                                                Notes       => "Alternate index provided for access by $attributeName." };          for my $group (@{$groups}) {
203          }              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
204          # Write the XML back out.                                                 'to-link'   => $group });
         ERDB::WriteMetaXML($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);  
205          }          }
206            # Log the operation.
207            $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
208      }      }
     # 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);  
209  }  }
210    
211  =head3 LoadAttributeKey  =head3 LoadAttributeKey
212    
213  C<< my $stats = $attrDB->LoadAttributeKey($entityName, $fieldName, $fh, $keyCol, $dataCol); >>  C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>
214    
215  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
216  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
217  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
218  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
219  corresponding attribute value.  corresponding attribute value.
220    
221  =over 4  =over 4
222    
223  =item entityName  =item keyName
   
 Name of the entity containing the attribute.  
   
 =item fieldName  
224    
225  Name of the actual attribute.  Key of the attribute to load.
226    
227  =item fh  =item fh
228    
229  Open file handle for the input file.  Open file handle for the input file.
230    
231  =item keyCol  =item idCol
232    
233  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
234  contain the ID of an instance of the named entity.  contain the ID of an instance of the named entity.
235    
236  =item dataCol  =item dataCol
237    
238  Index (0-based) of the column containing the data value field.  Index (0-based) of the column containing the data value field.
239    
240    =item options
241    
242    Hash specifying the options for this load.
243    
244  =item RETURN  =item RETURN
245    
246  Returns a statistics object for the load process.  Returns a statistics object for the load process.
247    
248  =back  =back
249    
250    The available options are as follows.
251    
252    =over 4
253    
254    =item erase
255    
256    If TRUE, the key's values will all be erased before loading. (Doing so
257    makes for a faster load.)
258    
259    =back
260    
261  =cut  =cut
262    
263  sub LoadAttributeKey {  sub LoadAttributeKey {
264      # Get the parameters.      # Get the parameters.
265      my ($self, $entityName, $fieldName, $fh, $keyCol, $dataCol) = @_;      my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;
266      # Create the return variable.      # Create the return variable.
267      my $retVal;      my $retVal = Stats->new("lineIn", "shortLine");
268      # Insure the entity exists.      # Compute the minimum number of fields required in each input line. The user specifies two
269      my $found = grep { $_ eq $entityName } $self->GetEntityTypes();      # columns, and we need to make sure both columns are in every record.
270      if (! $found) {      my $minCols = ($idCol < $dataCol ? $idCol : $idCol) + 1;
271          Confess("Entity \"$entityName\" not found in database.");      # Insure the attribute key exists.
272        my $found = $self->GetEntity('AttributeKey', $keyName);
273        if (! defined $found) {
274            Confess("Attribute key \"$keyName\" not found in database.");
275      } else {      } else {
276          # Get the field structure for the named entity.          # Erase the key's current values.
277          my $fieldHash = $self->GetFieldTable($entityName);          $self->EraseAttribute($keyName);
278          # Verify that the attribute exists.          # Save a list of the object IDs we need to add.
279          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);  
280              # Loop through the input file.              # Loop through the input file.
281              while (! eof $fh) {              while (! eof $fh) {
282                  # Get the next line of the file.                  # Get the next line of the file.
283                  my @fields = Tracer::GetLine($fh);                  my @fields = Tracer::GetLine($fh);
284                  $loadAttribute->Add("lineIn");              $retVal->Add(lineIn => 1);
285                  # Now we need to validate the line.                  # Now we need to validate the line.
286                  if ($#fields < $dataCol) {              if (scalar(@fields) < $minCols) {
287                      $loadAttribute->Add("shortLine");                  $retVal->Add(shortLine => 1);
                 } elsif (! $self->Exists($entityName, $fields[$keyCol])) {  
                     $loadAttribute->Add("badKey");  
288                  } else {                  } else {
289                      # It's valid,so send it to the loader.                  # It's valid, so get the ID and value.
290                      $loadAttribute->Put($fields[$keyCol], $fields[$dataCol]);                  my ($id, $value) = ($fields[$idCol], $fields[$dataCol]);
291                      $loadAttribute->Add("lineUsed");                  # Denote we're using this input line.
292                  }                  $retVal->Add(lineUsed => 1);
293                    # Now we insert the attribute.
294                    $self->InsertObject('HasValueFor', { from => $keyName, to => $id,
295                                                         value => $value });
296                    $retVal->Add(newValue => 1);
297              }              }
             # Finish the load.  
             $retVal = $loadAttribute->FinishAndLoad();  
298          }          }
299            # Log this operation.
300            $self->LogOperation("Load Key", $keyName, $retVal->Display());
301      }      }
302      # Return the statistics.      # Return the statistics.
303      return $retVal;      return $retVal;
# Line 386  Line 306 
306    
307  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
308    
309  C<< CustomAttributes::DeleteAttributeKey($entityName, $attributeName); >>  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
310    
311  Delete an attribute from the custom attributes database.  Delete an attribute from the custom attributes database.
312    
313  =over 4  =over 4
314    
 =item entityName  
   
 Name of the entity possessing the attribute.  
   
315  =item attributeName  =item attributeName
316    
317  Name of the attribute to delete.  Name of the attribute to delete.
318    
319    =item RETURN
320    
321    Returns a statistics object describing the effects of the deletion.
322    
323  =back  =back
324    
325  =cut  =cut
326    
327  sub DeleteAttributeKey {  sub DeleteAttributeKey {
328      # Get the parameters.      # Get the parameters.
329      my ($entityName, $attributeName) = @_;      my ($self, $attributeName) = @_;
330      # Read in the XML for the database defintion. We need to verify that      # Delete the attribute key.
331      # the named entity exists and it has the named attribute.      my $retVal = $self->Delete('AttributeKey', $attributeName);
332      my $metadata = ERDB::ReadMetaXML($FIG_Config::attrDBD);      # Log this operation.
333      my $entityHash = $metadata->{Entities};      $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
334      if (! exists $entityHash->{$entityName}) {      # Return the result.
335          Confess("Entity \"$entityName\" not found.");      return $retVal;
336      } 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);  
         }  
337      }      }
338    
339    =head3 NewName
340    
341    C<< my $text = CustomAttributes::NewName(); >>
342    
343    Return the string used to indicate the user wants to add a new attribute.
344    
345    =cut
346    
347    sub NewName {
348        return "(new)";
349  }  }
350    
351  =head3 ControlForm  =head3 ControlForm
352    
353  C<< my $formHtml = $attrDB->ControlForm($cgi, $name); >>  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
354    
355  Return a form that can be used to control the creation and modification of  Return a form that can be used to control the creation and modification of
356  attributes.  attributes. Only a subset of the attribute keys will be displayed, as
357    determined by the incoming list.
358    
359  =over 4  =over 4
360    
# Line 458  Line 366 
366    
367  Name to give to the form. This should be unique for the web page.  Name to give to the form. This should be unique for the web page.
368    
369    =item keys
370    
371    Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
372    attribute's data type, its description, and a list of the groups in which it participates.
373    
374  =item RETURN  =item RETURN
375    
376  Returns the HTML for a form that submits instructions to the C<Attributes.cgi> script  Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script
377  for loading, creating, or deleting an attribute.  for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
378    controls are generated. The form tags are left to the caller.
379    
380  =back  =back
381    
# Line 469  Line 383 
383    
384  sub ControlForm {  sub ControlForm {
385      # Get the parameters.      # Get the parameters.
386      my ($self, $cgi, $name) = @_;      my ($self, $cgi, $name, $keys) = @_;
387      # Declare the return list.      # Declare the return list.
388      my @retVal = ();      my @retVal = ();
     # Start the form. We use multipart to support the upload control.  
     push @retVal, $cgi->start_multipart_form(-name => $name);  
389      # 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.
390      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });      push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
391      # The first row is for selecting the field name.      # The first row is for selecting the field name.
392      push @retVal, $cgi->Tr($cgi->th("Select a Field"),      push @retVal, $cgi->Tr($cgi->th("Select a Field"),
393                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', 1,                             $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
394                                                       "document.$name.notes.value",                                                       new => 1,
395                                                       "document.$name.dataType.value")));                                                       notes => "document.$name.notes.value",
396                                                         type => "document.$name.dataType.value",
397                                                         groups => "document.$name.groups")));
398      # 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
399      # data type names, and the labels will be the descriptions.      # data type names, and the labels will be the descriptions.
400      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
401      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;      my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
402      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',      my $typeMenu = $cgi->popup_menu(-name   => 'dataType',
403                                      -values => [sort keys %types],                                      -values => [sort keys %types],
404                                      -labels => \%labelMap);                                      -labels => \%labelMap,
405                                        -default => 'string');
406        # Allow the user to specify a new field name. This is required if the
407        # user has selected the "(new)" marker. We put a little scriptlet in here that
408        # selects the (new) marker when the user enters the field.
409        push @retVal, "<script language=\"javaScript\">";
410        my $fieldField = "document.$name.fieldName";
411        my $newName = "\"" . NewName() . "\"";
412        push @retVal, $cgi->Tr($cgi->th("New Field Name"),
413                               $cgi->td($cgi->textfield(-name => 'newName',
414                                                        -size => 30,
415                                                        -value => "",
416                                                        -onFocus => "setIfEmpty($fieldField, $newName);")),
417                                        );
418      push @retVal, $cgi->Tr($cgi->th("Data type"),      push @retVal, $cgi->Tr($cgi->th("Data type"),
419                             $cgi->td($typeMenu));                             $cgi->td($typeMenu));
420      # The next row is for the notes.      # The next row is for the notes.
# Line 496  Line 423 
423                                                     -rows => 6,                                                     -rows => 6,
424                                                     -columns => 80))                                                     -columns => 80))
425                            );                            );
426      # 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.
427      # user has selected one of the "(new)" markers.      my @groups = $self->GetGroups();
428      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      push @retVal, $cgi->Tr($cgi->th("Groups"),
429                             $cgi->td($cgi->textfield(-name => 'newName',                             $cgi->td($cgi->checkbox_group(-name=>'groups',
430                                                      -size => 30)),                                      -values=> \@groups))
431                                      );                                      );
432      # 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
433      # an upload file name and column indicators.      # an upload file name and column indicators.
# Line 517  Line 444 
444                                                      -default => 1)                                                      -default => 1)
445                                     ),                                     ),
446                            );                            );
447      # Now the three buttons: UPDATE, SHOW, and DELETE.      # Now the three buttons: STORE, SHOW, and DELETE.
448      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),      push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
449                             $cgi->td({align => 'center'},                             $cgi->td({align => 'center'},
450                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .                                      $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .
# Line 527  Line 454 
454                            );                            );
455      # Close the table and the form.      # Close the table and the form.
456      push @retVal, $cgi->end_table();      push @retVal, $cgi->end_table();
     push @retVal, $cgi->end_form();  
457      # Return the assembled HTML.      # Return the assembled HTML.
458      return join("\n", @retVal, "");      return join("\n", @retVal, "");
459  }  }
460    
461    =head3 LoadAttributesFrom
462    
463    C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
464    
465    Load attributes from the specified tab-delimited file. Each line of the file must
466    contain an object ID in the first column, an attribute key name in the second
467    column, and attribute values in the remaining columns. The attribute values will
468    be assembled into a single value using the splitter code.
469    
470    =over 4
471    
472    =item fileName
473    
474    Name of the file from which to load the attributes.
475    
476    =item options
477    
478    Hash of options for modifying the load process.
479    
480    =item RETURN
481    
482    Returns a statistics object describing the load.
483    
484    =back
485    
486    Permissible option values are as follows.
487    
488    =over 4
489    
490    =item append
491    
492    If TRUE, then the attributes will be appended to existing data; otherwise, the
493    first time a key name is encountered, it will be erased.
494    
495    =back
496    
497    =cut
498    
499    sub LoadAttributesFrom {
500        # Get the parameters.
501        my ($self, $fileName, %options) = @_;
502        # Declare the return variable.
503        my $retVal = Stats->new('keys', 'values');
504        # Check for append mode.
505        my $append = ($options{append} ? 1 : 0);
506        # Create a hash of key names found.
507        my %keyHash = ();
508        # Open the file for input.
509        my $fh = Open(undef, "<$fileName");
510        # Loop through the file.
511        while (! eof $fh) {
512            my ($id, $key, @values) = Tracer::GetLine($fh);
513            $retVal->Add(linesIn => 1);
514            # Do some validation.
515            if (! defined($id)) {
516                # We ignore blank lines.
517                $retVal->Add(blankLines => 1);
518            } elsif (! defined($key)) {
519                # An ID without a key is a serious error.
520                my $lines = $retVal->Ask('linesIn');
521                Confess("Line $lines in $fileName has no attribute key.");
522            } else {
523                # Now we need to check for a new key.
524                if (! exists $keyHash{$key}) {
525                    # This is a new key. Verify that it exists.
526                    if (! $self->Exists('AttributeKey', $key)) {
527                        my $line = $retVal->Ask('linesIn');
528                        Confess("Attribute \"$key\" on line $line of $fileName not found in database.");
529                    } else {
530                        # Make sure we know this is no longer a new key.
531                        $keyHash{$key} = 1;
532                        $retVal->Add(keys => 1);
533                        # If this is NOT append mode, erase the key.
534                        if (! $append) {
535                            $self->EraseAttribute($key);
536                        }
537                    }
538                    Trace("Key $key found.") if T(3);
539                }
540                # Now we know the key is valid. Add this value.
541                $self->AddAttribute($id, $key, @values);
542                my $progress = $retVal->Add(values => 1);
543                Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
544    
545            }
546        }
547        # Return the result.
548        return $retVal;
549    }
550    
551    =head3 BackupKeys
552    
553    C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
554    
555    Backup the attribute key information from the attribute database.
556    
557    =over 4
558    
559    =item fileName
560    
561    Name of the output file.
562    
563    =item options
564    
565    Options for modifying the backup process.
566    
567    =item RETURN
568    
569    Returns a statistics object for the backup.
570    
571    =back
572    
573    Currently there are no options. The backup is straight to a text file in
574    tab-delimited format. Each key is backup up to two lines. The first line
575    is all of the data from the B<AttributeKey> table. The second is a
576    tab-delimited list of all the groups.
577    
578    =cut
579    
580    sub BackupKeys {
581        # Get the parameters.
582        my ($self, $fileName, %options) = @_;
583        # Declare the return variable.
584        my $retVal = Stats->new();
585        # Open the output file.
586        my $fh = Open(undef, ">$fileName");
587        # Set up to read the keys.
588        my $keyQuery = $self->Get(['AttributeKey'], "", []);
589        # Loop through the keys.
590        while (my $keyData = $keyQuery->Fetch()) {
591            $retVal->Add(key => 1);
592            # Get the fields.
593            my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
594                                                              'AttributeKey(description)']);
595            # Escape any tabs or new-lines in the description.
596            my $escapedDescription = Tracer::Escape($description);
597            # Write the key data to the output.
598            Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
599            # Get the key's groups.
600            my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
601                                        'IsInGroup(to-link)');
602            $retVal->Add(memberships => scalar(@groups));
603            # Write them to the output. Note we put a marker at the beginning to insure the line
604            # is nonempty.
605            Tracer::PutLine($fh, ['#GROUPS', @groups]);
606        }
607        # Log the operation.
608        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
609        # Return the result.
610        return $retVal;
611    }
612    
613    =head3 RestoreKeys
614    
615    C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
616    
617    Restore the attribute keys and groups from a backup file.
618    
619    =over 4
620    
621    =item fileName
622    
623    Name of the file containing the backed-up keys. Each key has a pair of lines,
624    one containing the key data and one listing its groups.
625    
626    =back
627    
628    =cut
629    
630    sub RestoreKeys {
631        # Get the parameters.
632        my ($self, $fileName, %options) = @_;
633        # Declare the return variable.
634        my $retVal = Stats->new();
635        # Set up a hash to hold the group IDs.
636        my %groups = ();
637        # Open the file.
638        my $fh = Open(undef, "<$fileName");
639        # Loop until we're done.
640        while (! eof $fh) {
641            # Get a key record.
642            my ($id, $dataType, $description) = Tracer::GetLine($fh);
643            if ($id eq '#GROUPS') {
644                Confess("Group record found when key record expected.");
645            } elsif (! defined($description)) {
646                Confess("Invalid format found for key record.");
647            } else {
648                $retVal->Add("keyIn" => 1);
649                # Add this key to the database.
650                $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
651                                                      description => Tracer::UnEscape($description) });
652                Trace("Attribute $id stored.") if T(3);
653                # Get the group line.
654                my ($marker, @groups) = Tracer::GetLine($fh);
655                if (! defined($marker)) {
656                    Confess("End of file found where group record expected.");
657                } elsif ($marker ne '#GROUPS') {
658                    Confess("Group record not found after key record.");
659                } else {
660                    $retVal->Add(memberships => scalar(@groups));
661                    # Connect the groups.
662                    for my $group (@groups) {
663                        # Find out if this is a new group.
664                        if (! $groups{$group}) {
665                            $retVal->Add(newGroup => 1);
666                            # Add the group.
667                            $self->InsertObject('AttributeGroup', { id => $group });
668                            Trace("Group $group created.") if T(3);
669                            # Make sure we know it's not new.
670                            $groups{$group} = 1;
671                        }
672                        # Connect the group to our key.
673                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
674                    }
675                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
676                }
677            }
678        }
679        # Log the operation.
680        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
681        # Return the result.
682        return $retVal;
683    }
684    
685    
686    =head3 BackupAllAttributes
687    
688    C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
689    
690    Backup all of the attributes to a file. The attributes will be stored in a
691    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
692    
693    =over 4
694    
695    =item fileName
696    
697    Name of the file to which the attribute data should be backed up.
698    
699    =item options
700    
701    Hash of options for the backup.
702    
703    =item RETURN
704    
705    Returns a statistics object describing the backup.
706    
707    =back
708    
709    Currently there are no options defined.
710    
711    =cut
712    
713    sub BackupAllAttributes {
714        # Get the parameters.
715        my ($self, $fileName, %options) = @_;
716        # Declare the return variable.
717        my $retVal = Stats->new();
718        # Get a list of the keys.
719        my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
720        Trace(scalar(@keys) . " keys found during backup.") if T(2);
721        # Open the file for output.
722        my $fh = Open(undef, ">$fileName");
723        # Loop through the keys.
724        for my $key (@keys) {
725            Trace("Backing up attribute $key.") if T(3);
726            $retVal->Add(keys => 1);
727            # Loop through this key's values.
728            my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
729            my $valuesFound = 0;
730            while (my $line = $query->Fetch()) {
731                $valuesFound++;
732                # Get this row's data.
733                my @row = $line->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
734                                         'HasValueFor(value)']);
735                # Write it to the file.
736                Tracer::PutLine($fh, \@row);
737            }
738            Trace("$valuesFound values backed up for key $key.") if T(3);
739            $retVal->Add(values => $valuesFound);
740        }
741        # Log the operation.
742        $self->LogOperation("Backup Data", $fileName, $retVal->Display());
743        # Return the result.
744        return $retVal;
745    }
746    
747  =head3 FieldMenu  =head3 FieldMenu
748    
749  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $newFlag, $noteControl, $typeControl); >>  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
750    
751  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
752  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
753  CGI package, but actually looks like a list. The list will contain  CGI package, but actually looks like a list. The list will contain
754  one selectable row per field, grouped by entity.  one selectable row per field.
755    
756  =over 4  =over 4
757    
# Line 556  Line 768 
768  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
769  appear when the form is submitted.  appear when the form is submitted.
770    
771  =item newFlag (optional)  =item keys
772    
773    Reference to a hash mapping each attribute key name to a list reference,
774    the list itself consisting of the attribute data type, its description,
775    and a list of its groups.
776    
777    =item options
778    
779    Hash containing options that modify the generation of the menu.
780    
781    =item RETURN
782    
783    Returns the HTML to create a form field that can be used to select an
784    attribute from the custom attributes system.
785    
786    =back
787    
788    The permissible options are as follows.
789    
790    =over 4
791    
792    =item new
793    
794  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
795  a new attribute. In other words, the user can select an existing  a new attribute. In other words, the user can select an existing
796  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
797  be created in the parent entity.  be created in the parent entity.
798    
799  =item noteControl (optional)  =item notes
800    
801  If specified, the name of a variable for displaying the notes attached  If specified, the name of a variable for displaying the notes attached
802  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 807 
807  it is copied in. Specifying this parameter generates Javascript for  it is copied in. Specifying this parameter generates Javascript for
808  displaying the field description when a field is selected.  displaying the field description when a field is selected.
809    
810  =item typeControl (optional)  =item type
811    
812  If specified, the name of a variable for displaying the field's  If specified, the name of a variable for displaying the field's
813  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 815 
815  raw value is put into the specified variable. Otherwise, the same  raw value is put into the specified variable. Otherwise, the same
816  rules apply to this value that apply to I<$noteControl>.  rules apply to this value that apply to I<$noteControl>.
817    
818  =item RETURN  =item groups
819    
820  Returns the HTML to create a form field that can be used to select an  If specified, the name of a multiple-selection list control (also called
821  attribute from the custom attributes system.  a popup menu) which shall be used to display the selected groups.
822    
823  =back  =back
824    
# Line 593  Line 826 
826    
827  sub FieldMenu {  sub FieldMenu {
828      # Get the parameters.      # Get the parameters.
829      my ($self, $cgi, $height, $name, $newFlag, $noteControl, $typeControl) = @_;      my ($self, $cgi, $height, $name, $keys, %options) = @_;
830      # These next two hashes make everything happen. "entities"      # Reformat the list of keys.
831      # maps each entity name to the list of values to be put into its      my %keys = %{$keys};
832      # option group. "labels" maps each entity name to a map from values      # Add the (new) key, if needed.
833      # to labels.      if ($options{new}) {
834      my @entityNames = sort ($self->GetEntityTypes());          $keys{NewName()} = ["string", ""];
835      my %entities = map { $_ => [] } @entityNames;      }
836      my %labels = map { $_ => { }} @entityNames;      # Get a sorted list of key.
837      # Loop through the entities, adding the existing attributes.      my @keys = sort keys %keys;
838      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  
839      # 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
840      # for the menu.      # for the menu.
841      my $changeName = "${name}_setNotes";      my $changeName = "${name}_setNotes";
842      my $retVal = $cgi->popup_menu({name => $name,      my $retVal = $cgi->popup_menu({name => $name,
843                                     size => $height,                                     size => $height,
844                                     onChange => "$changeName(this.value)",                                     onChange => "$changeName(this.value)",
845                                     values => [map { $cgi->optgroup(-name => $_,                                     values => \@keys,
846                                                                     -values => $entities{$_},                                    });
                                                                    -labels => $labels{$_})  
                                                   } @entityNames]}  
                                  );  
847      # Create the change function.      # Create the change function.
848      $retVal .= "\n<script language=\"javascript\">\n";      $retVal .= "\n<script language=\"javascript\">\n";
849      $retVal .= "    function $changeName(fieldValue) {\n";      $retVal .= "    function $changeName(fieldValue) {\n";
850      # The function only has a body if we have a notes control to store the description.      # The function only has a body if we have a control to store data about the
851      if ($noteControl || $typeControl) {      # attribute.
852        if ($options{notes} || $options{type} || $options{groups}) {
853          # 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.
854            my $noteControl = $options{notes};
855          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);          my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
856          # 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
857          # field description will be stored in the JavaScript variable "myText"          # field description will be stored in the JavaScript variable "myText"
# Line 652  Line 860 
860          $retVal .= "        var myText = \"\";\n";          $retVal .= "        var myText = \"\";\n";
861          $retVal .= "        var myType = \"string\";\n";          $retVal .= "        var myType = \"string\";\n";
862          $retVal .= "        switch (fieldValue) {\n";          $retVal .= "        switch (fieldValue) {\n";
863          # Loop through the entities.          # Loop through the keys.
864          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};  
865                      # Generate this case.                      # Generate this case.
866                      $retVal .= "        case \"$value\" :\n";              $retVal .= "        case \"$key\" :\n";
867                      # Here we either want to update the note display, the                      # Here we either want to update the note display, the
868                      # type display, or both.              # type display, the group list, or a combination of them.
869                my ($type, $notes, @groups) = @{$keys{$key}};
870                      if ($noteControl) {                      if ($noteControl) {
                         # Here we want the notes updated.  
                         my $notes = $element->{Notes}->{content};  
871                          # Insure it's in the proper form.                          # Insure it's in the proper form.
872                          if ($htmlMode) {                          if ($htmlMode) {
873                              $notes = ERDB::HTMLNote($notes);                              $notes = ERDB::HTMLNote($notes);
# Line 679  Line 877 
877                          $notes =~ s/"/\\"/g;                          $notes =~ s/"/\\"/g;
878                          $retVal .= "           myText = \"$notes\";\n";                          $retVal .= "           myText = \"$notes\";\n";
879                      }                      }
880                      if ($typeControl) {              if ($options{type}) {
881                          # Here we want the type updated.                          # Here we want the type updated.
                         my $type = $element->{type};  
882                          $retVal .= "           myType = \"$type\";\n";                          $retVal .= "           myType = \"$type\";\n";
883                      }                      }
884                if ($options{groups}) {
885                    # Here we want the groups shown. Get a list of this attribute's groups.
886                    # We'll search through this list for each group to see if it belongs with
887                    # our attribute.
888                    my $groupLiteral = "=" . join("=", @groups) . "=";
889                    # Now we need some variables containing useful code for the javascript. It's
890                    # worth knowing we go through a bit of pain to insure $groupField[i] isn't
891                    # parsed as an array element.
892                    my $groupField = $options{groups};
893                    my $currentField = $groupField . "[i]";
894                    # Do the javascript.
895                    $retVal .= "           var groupList = \"$groupLiteral\";\n";
896                    $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";
897                    $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";
898                    $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";
899                    $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";
900                    $retVal .= "           }\n";
901                }
902                      # Close this case.                      # Close this case.
903                      $retVal .= "           break;\n";                      $retVal .= "           break;\n";
904                  }                  }
             }  
         }  
905          # Close the CASE statement and make the appropriate assignments.          # Close the CASE statement and make the appropriate assignments.
906          $retVal .= "        }\n";          $retVal .= "        }\n";
907          if ($noteControl) {          if ($noteControl) {
908              $retVal .= "        $noteControl = myText;\n";              $retVal .= "        $noteControl = myText;\n";
909          }          }
910          if ($typeControl) {          if ($options{type}) {
911              $retVal .= "        $typeControl = myType;\n";              $retVal .= "        $options{type} = myType;\n";
912          }          }
913      }      }
914      # Terminate the change function.      # Terminate the change function.
# Line 705  Line 918 
918      return $retVal;      return $retVal;
919  }  }
920    
921  =head3 MatchSqlPattern  =head3 GetGroups
922    
923    C<< my @groups = $attrDB->GetGroups(); >>
924    
925    Return a list of the available groups.
926    
927    =cut
928    
929    sub GetGroups {
930        # Get the parameters.
931        my ($self) = @_;
932        # Get the groups.
933        my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
934        # Return them.
935        return @retVal;
936    }
937    
938    =head3 GetAttributeData
939    
940  C<< my $matched = CustomAttributes::MatchSqlPattern($value, $pattern); >>  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
941    
942  Determine whether or not a specified value matches an SQL pattern. An SQL  Return attribute data for the selected attributes. The attribute
943  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
944  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
945  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.  
946    
947  =over 4  =over 4
948    
949  =item value  =item type
950    
951  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
952  value will not match anything.  specified string, or C<group> for attributes in the specified group.
953    
954  =item pattern  =item list
955    
956  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.  
957    
958  =item RETURN  =item RETURN
959    
960  Returns TRUE if the value and pattern match, else FALSE.  Returns a hash mapping each attribute key name to its data type, description, and
961    parent groups.
962    
963  =back  =back
964    
965  =cut  =cut
966    
967  sub MatchSqlPattern {  sub GetAttributeData {
968      # Get the parameters.      # Get the parameters.
969      my ($value, $pattern) = @_;      my ($self, $type, @list) = @_;
970      # Declare the return variable.      # Set up a hash to store the attribute data.
971      my $retVal;      my %retVal = ();
972      # Insure we have a pattern.      # Loop through the list items.
973      if (! defined($pattern) || $pattern eq "") {      for my $item (@list) {
974          $retVal = 1;          # Set up a query for the desired attributes.
975            my $query;
976            if ($type eq 'name') {
977                # Here we're doing a generic name search. We need to escape it and then tack
978                # on a %.
979                my $parm = $item;
980                $parm =~ s/_/\\_/g;
981                $parm =~ s/%/\\%/g;
982                $parm .= "%";
983                # Ask for matching attributes. (Note that if the user passed in a null string
984                # he'll get everything.)
985                $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
986            } elsif ($type eq 'group') {
987                $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
988      } else {      } else {
989          # 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);  
990                  }                  }
991            while (my $row = $query->Fetch()) {
992                # Get this attribute's data.
993                my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
994                                                         'AttributeKey(description)']);
995                # If it's new, get its groups and add it to the return hash.
996                if (! exists $retVal{$key}) {
997                    my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
998                                                [$key], 'IsInGroup(to-link)');
999                    $retVal{$key} = [$type, $notes, @groups];
1000              }              }
             # Do the match.  
             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);  
1001          }          }
1002      }      }
1003      # Return the result.      # Return the result.
1004      return $retVal;      return %retVal;
1005  }  }
1006    
1007  =head3 MigrateAttributes  =head3 LogOperation
1008    
1009  C<< CustomAttributes::MigrateAttributes($fig); >>  C<< $ca->LogOperation($action, $target, $description); >>
1010    
1011  Migrate all the attributes data from the specified FIG instance. This is a long, slow  Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
 method used to convert the old attribute data to the new system. Only attribute  
 keys that are not already in the database will be loaded, and only for entity instances  
 current in the database. To get an accurate capture of the attributes in the given  
 instance, you may want to clear the database and the DBD before starting and  
 run L</Refresh> to populate the entities.  
1012    
1013  =over 4  =over 4
1014    
1015  =item fig  =item action
1016    
1017    Action being logged (e.g. C<Delete Group> or C<Load Key>).
1018    
1019    =item target
1020    
1021  A FIG object that can be used to retrieve attributes for migration purposes.  ID of the key or group affected.
1022    
1023    =item description
1024    
1025    Short description of the action.
1026    
1027  =back  =back
1028    
1029  =cut  =cut
1030    
1031  sub MigrateAttributes {  sub LogOperation {
1032      # Get the parameters.      # Get the parameters.
1033      my ($fig) = @_;      my ($self, $action, $target, $description) = @_;
1034      # Get a list of the objects to migrate. This requires connecting. Note we      # Get the user ID.
1035      # will map each entity type to a file name. The file will contain a list      my $user = $self->{user};
1036      # of the object's IDs so we can get to them when we're not connected to      # Get a timestamp.
1037      # the database.      my $timeString = Tracer::Now();
1038      my $ca = CustomAttributes->new();      # Open the log file for appending.
1039      my %objects = map { $_ => "$FIG_Config::temp/$_.keys.tbl" } $ca->GetEntityTypes();      my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
1040      # Set up hash of the existing attribute keys for each entity type.      # Write the data to it.
1041      my %oldKeys = ();      Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
1042      # Finally, we have a hash that counts the IDs for each entity type.      # Close the log file.
1043      my %idCounts = map { $_ => 0 } keys %objects;      close $oh;
1044      # Loop through the list, creating key files to read back in.  }
1045      for my $entityType (keys %objects) {  
1046          Trace("Retrieving keys for $entityType.") if T(2);  =head2 Internal Utility Methods
1047          # Create the key file.  
1048          my $idFile = Open(undef, ">$objects{$entityType}");  =head3 _KeywordString
1049          # Loop through the keys.  
1050          my @ids = $ca->GetFlat([$entityType], "", [], "$entityType(id)");  C<< my $keywordString = $ca->_KeywordString($key, $value); >>
1051          for my $id (@ids) {  
1052              print $idFile "$id\n";  Compute the keyword string for a specified key/value pair. This consists of the
1053          }  key name and value converted to lower case with underscores translated to spaces.
1054          close $idFile;  
1055          # In addition to the key file, we must get a list of attributes already  This method is for internal use only. It is called whenever we need to update or
1056          # in the database. This avoids a circularity problem that might occur if the $fig  insert a B<HasValueFor> record.
1057          # object is retrieving from the custom attributes database already.  
1058          my %fields = $ca->GetSecondaryFields($entityType);  =over 4
1059          $oldKeys{$entityType} = \%fields;  
1060          # Finally, we have the ID count.  =item key
1061          $idCounts{$entityType} = scalar @ids;  
1062      }  Name of the relevant attribute key.
1063      # Release the custom attributes database so we can add attributes.  
1064      undef $ca;  =item target
1065      # Loop through the objects.  
1066      for my $entityType (keys %objects) {  ID of the target object to which this key/value pair will be associated.
1067          # Get a hash of all the attributes already in this database. These are  
1068          # left untouched.  =item value
1069          my $myOldKeys = $oldKeys{$entityType};  
1070          # Create a hash to control the load file names for each attribute key we find.  The value to store for this key/object combination.
1071          my %keyHash = ();  
1072          # Set up some counters so we can trace our progress.  =item RETURN
1073          my ($totalIDs, $processedIDs, $keyCount, $valueCount) = ($idCounts{$entityType}, 0, 0, 0);  
1074          # Open this object's ID file.  Returns the value that should be stored as the keyword string for the specified
1075          Trace("Migrating data for $entityType. $totalIDs found.") if T(3);  key/value pair.
1076          my $keysIn = Open(undef, "<$objects{$entityType}");  
1077          while (my $id = <$keysIn>) {  =back
1078              # Remove the EOL characters.  
1079              chomp $id;  =cut
1080              # Get this object's attributes.  
1081              my @allData = $fig->get_attributes($id);  sub _KeywordString {
1082              Trace(scalar(@allData) . " attribute values found for $entityType($id).") if T(4);      # Get the parameters.
1083              # Loop through the attribute values one at a time.      my ($self, $key, $value) = @_;
1084              for my $dataTuple (@allData) {      # Get a copy of the key name and convert underscores to spaces.
1085                  # Get the key, value, and URL. We ignore the first element because that's the      my $keywordString = $key;
1086                  # object ID, and we already know the object ID.      $keywordString =~ s/_/ /g;
1087                  my (undef, $key, $value, $url) = @{$dataTuple};      # Add the value convert it all to lower case.
1088                  # Remove the buggy "1" for $url.      my $retVal = lc "$keywordString $value";
1089                  if ($url eq "1") {      # Return the result.
1090                      $url = undef;      return $retVal;
                 }  
                 # Only proceed if this is not an old key.  
                 if (! $myOldKeys->{$key}) {  
                     # See if we've run into this key before.  
                     if (! exists $keyHash{$key}) {  
                         # Here we need to create the attribute key in the database.  
                         StoreAttributeKey($entityType, $key, 'text',  
                                           "Key migrated automatically from the FIG system. " .  
                                           "Please replace these notes as soon as possible " .  
                                           "with useful text."  
                                          );  
                         # Compute the attribute's load file name and open it for output.  
                         my $fileName = "$FIG_Config::temp/$entityType.$key.load.tbl";  
                         my $fh = Open(undef, ">$fileName");  
                         # Store the file name and handle.  
                         $keyHash{$key} = {h => $fh, name => $fileName};  
                         # Count this key.  
                         $keyCount++;  
                     }  
                     # Smash the value and the URL together.  
                     if (defined($url) && length($url) > 0) {  
                         $value .= "::$url";  
                     }  
                     # Write the attribute value to the load file.  
                     Tracer::PutLine($keyHash{$key}->{h}, [$id, $value]);  
                     $valueCount++;  
                 }  
             }  
             # Now we've finished all the attributes for this object. Count and trace it.  
             $processedIDs++;  
             if ($processedIDs % 500 == 0) {  
                 Trace("$processedIDs of $totalIDs ${entityType}s processed.") if T(3);  
                 Trace("$entityType has $keyCount keys and $valueCount values so far.") if T(3);  
             }  
         }  
         # Now we've finished all the attributes for all objects of this type.  
         Trace("$processedIDs ${entityType}s processed, with $keyCount keys and $valueCount values.") if T(2);  
         # Loop through the files, loading the keys into the database.  
         Trace("Connecting to database.") if T(2);  
         my $objectCA = CustomAttributes->new();  
         Trace("Loading key files.") if T(2);  
         for my $key (sort keys %keyHash) {  
             # Close the key's load file.  
             close $keyHash{$key}->{h};  
             # Reopen it for input.  
             my $fileName = $keyHash{$key}->{name};  
             my $fh = Open(undef, "<$fileName");  
             Trace("Loading $key from $fileName.") if T(3);  
             my $stats = $objectCA->LoadAttributeKey($entityType, $key, $fh, 0, 1);  
             Trace("Statistics for $key of $entityType:\n" . $stats->Show()) if T(3);  
         }  
         # All the keys for this entity type are now loaded.  
         Trace("Key files loaded for $entityType.") if T(2);  
     }  
     # All keys for all entity types are now loaded.  
     Trace("Migration complete.") if T(2);  
1091  }  }
1092    
1093  =head3 ComputeObjectTypeFromID  =head3 _QueryResults
1094    
1095  C<< my ($entityName, $id) = CustomAttributes::ComputeObjectTypeFromID($objectID); >>  C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1096    
1097  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
1098  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
1099  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
1100  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.  
1101    
1102  =over 4  =over 4
1103    
1104  =item objectID  =item query
1105    
1106  Object ID to examine.  A query object that will return the desired B<HasValueFor> records.
1107    
1108    =item values
1109    
1110    List of the desired attribute values, section by section. If C<undef>
1111    or an empty string is specified, all values in that section will match. A
1112    generic match can be requested by placing a percent sign (C<%>) at the end.
1113    In that case, all values that match up to and not including the percent sign
1114    will match. You may also specify a regular expression enclosed
1115    in slashes. All values that match the regular expression will be returned. For
1116    performance reasons, only values have this extra capability.
1117    
1118  =item RETURN  =item RETURN
1119    
1120  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
1121    second is an attribute key, and the remaining elements are the sections of
1122    the attribute value. All of the tuples will match the criteria set forth in
1123    the parameter list.
1124    
1125  =back  =back
1126    
1127  =cut  =cut
1128    
1129  sub ComputeObjectTypeFromID {  sub _QueryResults {
1130      # Get the parameters.      # Get the parameters.
1131      my ($objectID) = @_;      my ($self, $query, @values) = @_;
1132      # Declare the return variables.      # Declare the return value.
1133      my ($entityName, $id);      my @retVal = ();
1134      # 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.
1135      # pair of undefs.      my $sectionCount = scalar(@values);
1136      if ($objectID) {      # Loop through the assignments found.
1137          if (ref $objectID eq 'ARRAY') {      while (my $row = $query->Fetch()) {
1138              # Here we have the new-style list reference. Pull out its pieces.          # Get the current row's data.
1139              ($entityName, $id) = @{$objectID};          my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
1140          } else {                                                        'HasValueFor(value)']);
1141              # Here the ID is the outgoing ID, and we need to look at its structure          # Break the value into sections.
1142              # to determine the entity type.          my @sections = split($self->{splitter}, $valueString);
1143              $id = $objectID;          # Match each section against the incoming values. We'll assume we're
1144              if ($objectID =~ /^\d+\.\d+/) {          # okay unless we learn otherwise.
1145                  # Digits with a single period is a genome.          my $matching = 1;
1146                  $entityName = 'Genome';          for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1147              } elsif ($objectID =~ /^fig\|/) {              # We need to check to see if this section is generic.
1148                  # The "fig|" prefix indicates a feature.              my $value = $values[$i];
1149                  $entityName = 'Feature';              Trace("Current value pattern is \"$value\".") if T(4);
1150                if (substr($value, -1, 1) eq '%') {
1151                    Trace("Generic match used.") if T(4);
1152                    # Here we have a generic match.
1153                    my $matchLen = length($values[$i] - 1);
1154                    $matching = substr($sections[$i], 0, $matchLen) eq
1155                                substr($values[$i], 0, $matchLen);
1156                } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1157                    Trace("Regular expression detected.") if T(4);
1158                    # Here we have a regular expression match.
1159                    my $section = $sections[$i];
1160                    $matching = eval("\$section =~ $value");
1161              } else {              } else {
1162                  # Anything else is illegal!                  # Here we have a strict match.
1163                  Confess("Invalid attribute ID specification \"$objectID\".");                  Trace("Strict match used.") if T(4);
1164                    $matching = ($sections[$i] eq $values[$i]);
1165              }              }
1166          }          }
1167            # If we match, output this row to the return list.
1168            if ($matching) {
1169                push @retVal, [$id, $key, @sections];
1170      }      }
1171      # Return the result.      }
1172      return ($entityName, $id);      # Return the rows found.
1173        return @retVal;
1174  }  }
1175    
1176  =head2 FIG Method Replacements  =head2 FIG Method Replacements
1177    
1178  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.
1179  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
1180  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
1181  capabilities were used in the old system.  capabilities were used in the old system.
1182    
# Line 999  Line 1190 
1190  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
1191  colons C<::>.  colons C<::>.
1192    
1193  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
1194  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
1195  splitter value would be stored as  splitter value would be stored as
1196    
# Line 1010  Line 1201 
1201    
1202  =head3 GetAttributes  =head3 GetAttributes
1203    
1204  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @valuePatterns); >>  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1205    
1206  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1207  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
1208  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
1209  these methods. If you are using the static method calls instead of the  these methods. If a value has multiple sections, each section
1210  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.  
1211    
1212  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
1213  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
1214  method therefore correspond structurally to the values expected in each tuple.  method therefore correspond structurally to the values expected in each tuple. In
1215    addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1216    of the parameters. So, for example,
1217    
1218      my @attributeList = GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);      my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1219    
1220  would return something like  would return something like
1221    
# Line 1033  Line 1224 
1224      ['fig}100226.1.peg.1004', 'structure2', 1, 2]      ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1225      ['fig}100226.1.peg.1004', 'structureA', 1, 2]      ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1226    
1227  Use of C<undef> in any position acts as a wild card (all values). In addition,  Use of C<undef> in any position acts as a wild card (all values). You can also specify
1228  the I<$key> and I<@valuePatterns> parameters can contain SQL pattern characters: C<%>, which  a list reference in the ID column. Thus,
1229  matches any sequence of characters, and C<_>, which matches any single character.  
1230  (You can use an escape sequence C<\%> or C<\_> to match an actual percent sign or      my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1231  underscore.)  
1232    would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1233    features.
1234    
1235  In addition to values in multiple sections, a single attribute key can have multiple  In addition to values in multiple sections, a single attribute key can have multiple
1236  values, so even  values, so even
1237    
1238      my @attributeList = GetAttributes($peg, 'virulent');      my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1239    
1240  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.
1241    
1242  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
1243  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
1244  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
1245  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
1246  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.  
1247    
1248  =over 4  =over 4
1249    
1250  =item objectID  =item objectID
1251    
1252  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
1253  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
1254  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
1255  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.  
1256    
1257  =item key  =item key
1258    
1259  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
1260  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
1261  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
1262  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.  
1263    
1264  =item valuePatterns  =item values
1265    
1266  List of the desired attribute values, section by section. If C<undef>  List of the desired attribute values, section by section. If C<undef>
1267  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
1268    generic match can be requested by placing a percent sign (C<%>) at the end.
1269    In that case, all values that match up to and not including the percent sign
1270    will match. You may also specify a regular expression enclosed
1271    in slashes. All values that match the regular expression will be returned. For
1272    performance reasons, only values have this extra capability.
1273    
1274  =item RETURN  =item RETURN
1275    
# Line 1107  Line 1284 
1284    
1285  sub GetAttributes {  sub GetAttributes {
1286      # Get the parameters.      # Get the parameters.
1287      my ($self, $objectID, $key, @valuePatterns) = @_;      my ($self, $objectID, $key, @values) = @_;
1288      # Declare the return variable.      # We will create one big honking query. The following hash will build the filter
1289      my @retVal = ();      # clause and a parameter list.
1290      # Determine the entity types for our search.      my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);
1291      my @objects = ();      my @filter = ();
1292      my ($actualObjectID, $computedType);      my @parms = ();
1293      if (! $objectID) {      # This next loop goes through the different fields that can be specified in the
1294          push @objects, $self->GetEntityTypes();      # parameter list and generates filters for each.
1295        for my $field (keys %data) {
1296            # Accumulate filter information for this field. We will OR together all the
1297            # elements accumulated to create the final result.
1298            my @fieldFilter = ();
1299            # Get the specified data from the caller.
1300            my $fieldPattern = $data{$field};
1301            # Only proceed if the pattern is one that won't match everything.
1302            if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1303                # Convert the pattern to an array.
1304                my @patterns = ();
1305                if (ref $fieldPattern eq 'ARRAY') {
1306                    push @patterns, @{$fieldPattern};
1307      } else {      } else {
1308          ($computedType, $actualObjectID) = ComputeObjectTypeFromID($objectID);                  push @patterns, $fieldPattern;
         push @objects, $computedType;  
1309      }      }
1310      # Loop through the entity types.              # Only proceed if the array is nonempty. The loop will work fine if the
1311      for my $entityType (@objects) {              # array is empty, but when we build the filter string at the end we'll
1312          # 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.
1313          # our database object, so this process is fast. Note that our              if (@patterns) {
1314          # MatchSqlPattern method                  # Loop through the individual patterns.
1315          my %secondaries = $self->GetSecondaryFields($entityType);                  for my $pattern (@patterns) {
1316          my @fieldList = grep { MatchSqlPattern($_, $key) } keys %secondaries;                      # Check for a generic request.
1317          # Now we figure out whether or not we need to filter by object. We will always                      if (substr($pattern, -1, 1) ne '%') {
1318          # filter by key to a limited extent, so if we're filtering by object we need an                          # Here we have a normal request.
1319          # AND to join the object ID filter with the key filter.                          push @fieldFilter, "$field = ?";
1320          my $filter = "";                          push @parms, $pattern;
1321          my @params = ();                      } else {
1322          if (defined($actualObjectID)) {                          # Here we have a generate request, so we will use the LIKE operator to
1323              # Here the caller wants to filter on object ID. Check for a pattern.                          # filter the field to this value pattern.
1324              my $comparator = ($actualObjectID =~ /%/ ? "LIKE" : "=");                          push @fieldFilter, "$field LIKE ?";
1325              # Update the filter and the parameter list.                          # We must convert the pattern value to an SQL match pattern. First
1326              $filter = "$entityType(id) $comparator ? AND ";                          # we get a copy of it.
1327              push @params, $actualObjectID;                          my $actualPattern = $pattern;
1328          }                          # Now we escape the underscores. Underscores are an SQL wild card
1329          # 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.
1330          # each attribute is actually a different field in the database. We know here that                          $actualPattern =~ s/_/\\_/g;
1331          # 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.
1332          # the DBD. That's a good thing, because an invalid key name will cause an SQL error.                          push @parms, $actualPattern;
1333          for my $key (@fieldList) {                      }
1334              # Get all of the attribute values for this key.                  }
1335              my @dataRows = $self->GetAll([$entityType], "$filter$entityType($key) IS NOT NULL",                  # Form the filter for this field.
1336                                           \@params, ["$entityType(id)", "$entityType($key)"]);                  my $fieldFilterString = join(" OR ", @fieldFilter);
1337              # Process each value separately. We need to verify the values and reformat the                  push @filter, "($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.  
1338              }              }
             # Here we've processed all the rows returned by GetAll. In general, there will  
             # be one row per object ID.  
1339          }          }
         # Here we've processed all the matching attribute keys.  
1340      }      }
1341      # 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
1342      # results.      # values to bind to them.
1343        my $actualFilter = join(" AND ", @filter);
1344        # Now we're ready to make our query.
1345        my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1346        # Format the results.
1347        my @retVal = $self->_QueryResults($query, @values);
1348        # Return the rows found.
1349      return @retVal;      return @retVal;
1350  }  }
1351    
# Line 1195  Line 1360 
1360    
1361  =item objectID  =item objectID
1362    
1363  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.  
1364    
1365  =item key  =item key
1366    
1367  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1368    
1369  =item values  =item values
1370    
# Line 1225  Line 1387 
1387      } elsif (! @values) {      } elsif (! @values) {
1388          Confess("No values specified in AddAttribute call for key $key.");          Confess("No values specified in AddAttribute call for key $key.");
1389      } else {      } else {
1390          # Okay, now we have some reason to believe we can do this. Start by          # Okay, now we have some reason to believe we can do this. Form the values
1391          # computing the object type and ID.          # into a scalar.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1392          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1393          # Insert the value.          # Connect the object to the key.
1394          $self->InsertValue($id, "$entityName($key)", $valueString);          $self->InsertObject('HasValueFor', { 'from-link' => $key,
1395                                                 'to-link'   => $objectID,
1396                                                 'value'     => $valueString,
1397                                           });
1398      }      }
1399      # Return a one. We do this for backward compatability.      # Return a one, indicating success. We do this for backward compatability.
1400      return 1;      return 1;
1401  }  }
1402    
# Line 1243  Line 1406 
1406    
1407  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1408    
 The first form will connect to the database and release it. The second form  
 uses the database connection contained in the object.  
   
1409  =over 4  =over 4
1410    
1411  =item objectID  =item objectID
1412    
1413  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.  
1414    
1415  =item key  =item key
1416    
1417  Attribute key name. This corresponds to the name of a field in the database.  Attribute key name.
1418    
1419  =item values  =item values
1420    
1421  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
1422    will be deleted. Otherwise, only a matching value will be deleted.
1423    
1424  =back  =back
1425    
# Line 1275  Line 1433 
1433          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1434      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1435          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1436      } elsif (! @values) {      } elsif (scalar(@values) == 0) {
1437          Confess("No values specified in DeleteAttribute call for key $key.");          # Here we erase the entire key for this object.
1438            $self->DeleteRow('HasValueFor', $key, $objectID);
1439      } else {      } else {
1440          # Now compute the object type and ID.          # Here we erase the matching values.
         my ($entityName, $id) = ComputeObjectTypeFromID($objectID);  
         # Form the values into a scalar.  
1441          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1442          # Delete the value.          $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });
         $self->DeleteValue($entityName, $id, $key, $valueString);  
1443      }      }
1444      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1445      return 1;      return 1;
1446  }  }
1447    
1448    =head3 DeleteMatchingAttributes
1449    
1450    C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>
1451    
1452    Delete all attributes that match the specified criteria. This is equivalent to
1453    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1454    row found.
1455    
1456    =over 4
1457    
1458    =item objectID
1459    
1460    ID of object whose attributes are to be deleted. If the attributes for multiple
1461    objects are to be deleted, this parameter can be specified as a list reference. If
1462    attributes are to be deleted for all objects, specify C<undef> or an empty string.
1463    Finally, you can delete attributes for a range of object IDs by putting a percent
1464    sign (C<%>) at the end.
1465    
1466    =item key
1467    
1468    Attribute key name. A value of C<undef> or an empty string will match all
1469    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1470    specified as a list reference. Finally, you can delete attributes for a range of
1471    keys by putting a percent sign (C<%>) at the end.
1472    
1473    =item values
1474    
1475    List of the desired attribute values, section by section. If C<undef>
1476    or an empty string is specified, all values in that section will match. A
1477    generic match can be requested by placing a percent sign (C<%>) at the end.
1478    In that case, all values that match up to and not including the percent sign
1479    will match. You may also specify a regular expression enclosed
1480    in slashes. All values that match the regular expression will be deleted. For
1481    performance reasons, only values have this extra capability.
1482    
1483    =item RETURN
1484    
1485    Returns a list of tuples for the attributes that were deleted, in the
1486    same form as L</GetAttributes>.
1487    
1488    =back
1489    
1490    =cut
1491    
1492    sub DeleteMatchingAttributes {
1493        # Get the parameters.
1494        my ($self, $objectID, $key, @values) = @_;
1495        # Get the matching attributes.
1496        my @retVal = $self->GetAttributes($objectID, $key, @values);
1497        # Loop through the attributes, deleting them.
1498        for my $tuple (@retVal) {
1499            $self->DeleteAttribute(@{$tuple});
1500        }
1501        # Log this operation.
1502        my $count = @retVal;
1503        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1504        # Return the deleted attributes.
1505        return @retVal;
1506    }
1507    
1508  =head3 ChangeAttribute  =head3 ChangeAttribute
1509    
1510  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>
# Line 1333  Line 1549 
1549      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {      } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1550          Confess("No new values specified in ChangeAttribute call for key $key.");          Confess("No new values specified in ChangeAttribute call for key $key.");
1551      } else {      } else {
1552          # Okay, now we do the change as a delete/add.          # We do the change as a delete/add.
1553          $self->DeleteAttribute($objectID, $key, @{$oldValues});          $self->DeleteAttribute($objectID, $key, @{$oldValues});
1554          $self->AddAttribute($objectID, $key, @{$newValues});          $self->AddAttribute($objectID, $key, @{$newValues});
1555      }      }
# Line 1343  Line 1559 
1559    
1560  =head3 EraseAttribute  =head3 EraseAttribute
1561    
1562  C<< $attrDB->EraseAttribute($entityName, $key); >>  C<< $attrDB->EraseAttribute($key); >>
1563    
1564  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
1565  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
1566    
1567  =over 4  =over 4
1568    
 =item entityName  
   
 Name of the entity to which the key belongs. If undefined, all entities will be  
 examined for the desired key.  
   
1569  =item key  =item key
1570    
1571  Key to erase.  Key to erase.
# Line 1365  Line 1576 
1576    
1577  sub EraseAttribute {  sub EraseAttribute {
1578      # Get the parameters.      # Get the parameters.
1579      my ($self, $entityName, $key) = @_;      my ($self, $key) = @_;
1580      # Determine the relevant entity types.      # Delete everything connected to the key.
1581      my @objects = ();      $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1582      if (! $entityName) {      # Log the operation.
1583          push @objects, $self->GetEntityTypes();      $self->LogOperation("Erase Data", $key);
     } else {  
         push @objects, $entityName;  
     }  
     # Loop through the entity types.  
     for my $entityType (@objects) {  
         # Now check for this key in this entity.  
         my %secondaries = $self->GetSecondaryFields($entityType);  
         if (exists $secondaries{$key}) {  
             # We found it, so delete all the values of the key.  
             $self->DeleteValue($entityType, undef, $key);  
         }  
     }  
1584      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1585      return 1;      return 1;
1586  }  }
1587    
1588  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1589    
1590  C<< my @keyList = $attrDB->GetAttributeKeys($entityName); >>  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1591    
1592  Return a list of the attribute keys for a particular entity type.  Return a list of the attribute keys for a particular group.
1593    
1594  =over 4  =over 4
1595    
1596  =item entityName  =item groupName
1597    
1598  Name of the entity whose keys are desired.  Name of the group whose keys are desired.
1599    
1600  =item RETURN  =item RETURN
1601    
1602  Returns a list of the attribute keys for the specified entity.  Returns a list of the attribute keys for the specified group.
1603    
1604  =back  =back
1605    
# Line 1408  Line 1607 
1607    
1608  sub GetAttributeKeys {  sub GetAttributeKeys {
1609      # Get the parameters.      # Get the parameters.
1610      my ($self, $entityName) = @_;      my ($self, $groupName) = @_;
1611      # Get the entity's secondary fields.      # Get the attributes for the specified group.
1612      my %keyList = $self->GetSecondaryFields($entityName);      my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1613                                    'IsInGroup(from-link)');
1614      # Return the keys.      # Return the keys.
1615      return sort keys %keyList;      return sort @groups;
1616  }  }
1617    
1618  1;  1;

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.18

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3