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revision 1.11, Wed Nov 29 20:28:52 2006 UTC revision 1.38, Sat Oct 18 09:52:21 2008 UTC
# Line 8  Line 8 
8      use strict;      use strict;
9      use Tracer;      use Tracer;
10      use ERDBLoad;      use ERDBLoad;
11        use Stats;
12        use Time::HiRes qw(time);
13        use FIGRules;
14    
15  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
16    
# Line 27  Line 30 
30  The actual attribute values are stored as a relationship between the attribute  The actual attribute values are stored as a relationship between the attribute
31  keys and the objects. There can be multiple values for a single key/object pair.  keys and the objects. There can be multiple values for a single key/object pair.
32    
33    =head3 Object IDs
34    
35    The object ID is normally represented as
36    
37        I<type>:I<id>
38    
39    where I<type> is the object type (C<Role>, C<Coupling>, etc.) and I<id> is
40    the actual object ID. Note that the object type must consist of only upper- and
41    lower-case letters! Thus, C<GenomeGroup> is a valid object type, but
42    C<genome_group> is not. Given that restriction, the object ID
43    
44        Family:aclame|cluster10
45    
46    would represent the FIG family C<aclame|cluster10>. For historical reasons,
47    there are three exceptions: subsystems, genomes, and features do not need
48    a type. So, for PEG 3361 of Streptomyces coelicolor A3(2), you simply code
49    
50        fig|100226.1.peg.3361
51    
52    The methods L</ParseID> and L</FormID> can be used to make this all seem
53    more consistent. Given any object ID string, L</ParseID> will convert it to an
54    object type and ID, and given any object type and ID, L</FormID> will
55    convert it to an object ID string. The attribute database is pretty
56    freewheeling about what it will allow for an ID; however, for best
57    results, the type should match an entity type from a Sprout genetics
58    database. If this rule is followed, then the database object
59    corresponding to an ID in the attribute database could be retrieved using
60    L</GetTargetObject> method.
61    
62        my $object = CustomAttributes::GetTargetObject($sprout, $idValue);
63    
64    =head3 Retrieval and Logging
65    
66  The full suite of ERDB retrieval capabilities is provided. In addition,  The full suite of ERDB retrieval capabilities is provided. In addition,
67  custom methods are provided specific to this application. To get all  custom methods are provided specific to this application. To get all
68  the values of the attribute C<essential> in a specified B<Feature>, you  the values of the attribute C<essential> in a specified B<Feature>, you
# Line 36  Line 72 
72    
73  where I<$fid> contains the ID of the desired feature.  where I<$fid> contains the ID of the desired feature.
74    
75  New attribute keys must be defined before they can be used. A web interface  Keys can be split into two pieces using the splitter value defined in the
76  is provided for this purpose.  constructor (the default is C<::>). The first piece of the key is called
77    the I<real key>. This portion of the key must be defined using the
78    web interface (C<Attributes.cgi>). The second portion of the key is called
79    the I<sub key>, and can take any value.
80    
81    Major attribute activity is recorded in a log (C<attributes.log>) in the
82    C<$FIG_Config::var> directory. The log reports the user name, time, and
83    the details of the operation. The user name will almost always be unknown,
84    the exception being when it is specified in this object's constructor
85    (see L</new>).
86    
87  =head2 FIG_Config Parameters  =head2 FIG_Config Parameters
88    
# Line 81  Line 126 
126  functions as data to the attribute management process, so if the data is  functions as data to the attribute management process, so if the data is
127  moved, this file must go with it.  moved, this file must go with it.
128    
129    =item attr_default_table
130    
131    Name of the default relationship for attribute values. If not present,
132    C<HasValueFor> is used.
133    
134  =back  =back
135    
136  =head2 Public Methods  =head2 Public Methods
137    
138  =head3 new  =head3 new
139    
140  C<< my $attrDB = CustomAttributes->new($splitter); >>      my $attrDB = CustomAttributes->new(%options);
141    
142  Construct a new CustomAttributes object.  Construct a new CustomAttributes object. The following options are
143    supported.
144    
145  =over 4  =over 4
146    
147  =item splitter  =item splitter
148    
149  Value to be used to split attribute values into sections in the  Value to be used to split attribute values into sections in the
150  L</Fig Replacement Methods>. The default is a double colon C<::>.  L</Fig Replacement Methods>. The default is a double colon C<::>,
151  If you do not use the replacement methods, you do not need to  and should only be overridden in extreme circumstances.
152  worry about this parameter.  
153    =item user
154    
155    Name of the current user. This will appear in the attribute log.
156    
157  =back  =back
158    
# Line 106  Line 160 
160    
161  sub new {  sub new {
162      # Get the parameters.      # Get the parameters.
163      my ($class, $splitter) = @_;      my ($class, %options) = @_;
164        # Get the name ofthe default table.
165      # Connect to the database.      # Connect to the database.
166      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,      my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
167                              $FIG_Config::attrUser, $FIG_Config::attrPass,                              $FIG_Config::attrUser, $FIG_Config::attrPass,
# Line 116  Line 171 
171      my $xmlFileName = $FIG_Config::attrDBD;      my $xmlFileName = $FIG_Config::attrDBD;
172      my $retVal = ERDB::new($class, $dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
173      # Store the splitter value.      # Store the splitter value.
174      $retVal->{splitter} = (defined($splitter) ? $splitter : '::');      $retVal->{splitter} = $options{splitter} || '::';
175        # Store the user name.
176        $retVal->{user} = $options{user} || '<unknown>';
177        Trace("User $retVal->{user} selected for attribute object.") if T(3);
178        # Compute the default value table name. If it's not overridden, the
179        # default is HasValueFor.
180        $retVal->{defaultRel} = $FIG_Config::attr_default_table || 'HasValueFor';
181      # Return the result.      # Return the result.
182      return $retVal;      return $retVal;
183  }  }
184    
185  =head3 StoreAttributeKey  =head3 StoreAttributeKey
186    
187  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>      $attrDB->StoreAttributeKey($attributeName, $notes, \@groups, $table);
188    
189  Create or update an attribute for the database.  Create or update an attribute for the database.
190    
# Line 131  Line 192 
192    
193  =item attributeName  =item attributeName
194    
195  Name of the attribute. It must be a valid ERDB field name, consisting entirely of  Name of the attribute (the real key). If it does not exist already, it will be created.
 letters, digits, and hyphens, with a letter at the beginning. If it does not  
 exist already, it will be created.  
   
 =item type  
   
 Data type of the attribute. This must be a valid ERDB data type name.  
196    
197  =item notes  =item notes
198    
# Line 148  Line 203 
203  Reference to a list of the groups to which the attribute should be associated.  Reference to a list of the groups to which the attribute should be associated.
204  This will replace any groups to which the attribute is currently attached.  This will replace any groups to which the attribute is currently attached.
205    
206    =item table
207    
208    The name of the relationship in which the attribute's values are to be stored.
209    If empty or undefined, the default relationship (usually C<HasValueFor>) will be
210    assumed.
211    
212  =back  =back
213    
214  =cut  =cut
215    
216  sub StoreAttributeKey {  sub StoreAttributeKey {
217      # Get the parameters.      # Get the parameters.
218      my ($self, $attributeName, $type, $notes, $groups) = @_;      my ($self, $attributeName, $notes, $groups, $table) = @_;
219      # Declare the return variable.      # Declare the return variable.
220      my $retVal;      my $retVal;
221        # Default the table name.
222        if (! $table) {
223            $table = $self->{defaultRel};
224        }
225      # Get the data type hash.      # Get the data type hash.
226      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
227      # Validate the initial input values.      # Validate the initial input values.
228      if (! ERDB::ValidateFieldName($attributeName)) {      if ($attributeName =~ /$self->{splitter}/) {
229          Confess("Invalid attribute name \"$attributeName\" specified.");          Confess("Invalid attribute name \"$attributeName\" specified.");
230      } elsif (! $notes || length($notes) < 25) {      } elsif (! $notes) {
231          Confess("Missing or incomplete description for $attributeName.");          Confess("Missing description for $attributeName.");
232      } elsif (! exists $types{$type}) {      } elsif (! grep { $_ eq $table } $self->GetConnectingRelationships('AttributeKey')) {
233          Confess("Invalid data type \"$type\" for $attributeName.");          Confess("Invalid relationship name \"$table\" specified as a custom attribute table.");
234      } else {      } else {
235            # Create a variable to hold the action to be displayed for the log (Add or Update).
236            my $action;
237          # Okay, we're ready to begin. See if this key exists.          # Okay, we're ready to begin. See if this key exists.
238          my $attribute = $self->GetEntity('AttributeKey', $attributeName);          my $attribute = $self->GetEntity('AttributeKey', $attributeName);
239          if (defined($attribute)) {          if (defined($attribute)) {
240              # It does, so we do an update.              # It does, so we do an update.
241                $action = "Update Key";
242              $self->UpdateEntity('AttributeKey', $attributeName,              $self->UpdateEntity('AttributeKey', $attributeName,
243                                  { description => $notes, 'data-type' => $type });                                  { description => $notes,
244                                      'relationship-name' => $table});
245              # Detach the key from its current groups.              # Detach the key from its current groups.
246              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);              $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
247          } else {          } else {
248              # It doesn't, so we do an insert.              # It doesn't, so we do an insert.
249                $action = "Insert Key";
250              $self->InsertObject('AttributeKey', { id => $attributeName,              $self->InsertObject('AttributeKey', { id => $attributeName,
251                                  description => $notes, 'data-type' => $type });                                  description => $notes,
252                                    'relationship-name' => $table});
253          }          }
254          # Attach the key to the specified groups. (We presume the groups already          # Attach the key to the specified groups. (We presume the groups already
255          # exist.)          # exist.)
# Line 186  Line 257 
257              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,              $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
258                                                 'to-link'   => $group });                                                 'to-link'   => $group });
259          }          }
260            # Log the operation.
261            $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
262      }      }
263  }  }
264    
 =head3 LoadAttributeKey  
   
 C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>  
   
 Load the specified attribute from the specified file. The file should be a  
 tab-delimited file with internal tab and new-line characters escaped. This is  
 the typical TBL-style file used by most FIG applications. One of the columns  
 in the input file must contain the appropriate object id value and the other the  
 corresponding attribute value.  
   
 =over 4  
   
 =item keyName  
   
 Key of the attribute to load.  
   
 =item fh  
   
 Open file handle for the input file.  
   
 =item idCol  
   
 Index (0-based) of the column containing the ID field. The ID field should  
 contain the ID of an instance of the named entity.  
   
 =item dataCol  
   
 Index (0-based) of the column containing the data value field.  
   
 =item options  
   
 Hash specifying the options for this load.  
   
 =item RETURN  
   
 Returns a statistics object for the load process.  
   
 =back  
   
 The available options are as follows.  
   
 =over 4  
   
 =item erase  
   
 If TRUE, the key's values will all be erased before loading. (Doing so  
 makes for a faster load.)  
   
 =back  
   
 =cut  
   
 sub LoadAttributeKey {  
     # Get the parameters.  
     my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;  
     # Create the return variable.  
     my $retVal = Stats->new("lineIn", "shortLine", "newObject");  
     # Compute the minimum number of fields required in each input line.  
     my $minCols = ($idCol < $dataCol ? $idCol : $idCol) + 1;  
     # Insure the attribute key exists.  
     my $found = $self->GetEntity('AttributeKey', $keyName);  
     if (! defined $found) {  
         Confess("Attribute key \"$keyName\" not found in database.");  
     } else {  
         # Erase the key's current values.  
         $self->EraseAttribute($keyName);  
         # Save a list of the object IDs we need to add.  
         my %objectIDs = ();  
         # Loop through the input file.  
         while (! eof $fh) {  
             # Get the next line of the file.  
             my @fields = Tracer::GetLine($fh);  
             $retVal->Add(lineIn => 1);  
             # Now we need to validate the line.  
             if (scalar(@fields) < $minCols) {  
                 $retVal->Add(shortLine => 1);  
             } else {  
                 # It's valid, so get the ID and value.  
                 my ($id, $value) = ($fields[$idCol], $fields[$dataCol]);  
                 # Denote we're using this input line.  
                 $retVal->Add(lineUsed => 1);  
                 # Now the fun begins. Find out if we need to create a target object record for this object ID.  
                 if (! exists $objectIDs{$id}) {  
                     my $found = $self->Exists('TargetObject', $id);  
                     if (! $found) {  
                         $self->InsertObject('TargetObject', { id => $id });  
                     }  
                     $objectIDs{$id} = 1;  
                     $retVal->Add(newObject => 1);  
                 }  
                 # Now we insert the attribute.  
                 $self->InsertObject('HasValueFor', { from => $keyName, to => $id, value => $value });  
                 $retVal->Add(newValue => 1);  
             }  
         }  
     }  
     # Return the statistics.  
     return $retVal;  
 }  
   
265    
266  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
267    
268  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>      my $stats = $attrDB->DeleteAttributeKey($attributeName);
269    
270  Delete an attribute from the custom attributes database.  Delete an attribute from the custom attributes database.
271    
# Line 315  Line 288 
288      my ($self, $attributeName) = @_;      my ($self, $attributeName) = @_;
289      # Delete the attribute key.      # Delete the attribute key.
290      my $retVal = $self->Delete('AttributeKey', $attributeName);      my $retVal = $self->Delete('AttributeKey', $attributeName);
291        # Log this operation.
292        $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
293      # Return the result.      # Return the result.
294      return $retVal;      return $retVal;
295    
# Line 322  Line 297 
297    
298  =head3 NewName  =head3 NewName
299    
300  C<< my $text = CustomAttributes::NewName(); >>      my $text = CustomAttributes::NewName();
301    
302  Return the string used to indicate the user wants to add a new attribute.  Return the string used to indicate the user wants to add a new attribute.
303    
# Line 332  Line 307 
307      return "(new)";      return "(new)";
308  }  }
309    
 =head3 ControlForm  
   
 C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>  
   
 Return a form that can be used to control the creation and modification of  
 attributes. Only a subset of the attribute keys will be displayed, as  
 determined by the incoming list.  
   
 =over 4  
   
 =item cgi  
   
 CGI query object used to create HTML.  
   
 =item name  
   
 Name to give to the form. This should be unique for the web page.  
   
 =item keys  
   
 Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the  
 attribute's data type, its description, and a list of the groups in which it participates.  
   
 =item RETURN  
   
 Returns the HTML for a form that can be used to  submit instructions to the C<Attributes.cgi> script  
 for loading, creating, displaying, changing, or deleting an attribute. Note that only the form  
 controls are generated. The form tags are left to the caller.  
   
 =back  
   
 =cut  
   
 sub ControlForm {  
     # Get the parameters.  
     my ($self, $cgi, $name, $keys) = @_;  
     # Declare the return list.  
     my @retVal = ();  
     # We'll put the controls in a table. Nothing else ever seems to look nice.  
     push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });  
     # The first row is for selecting the field name.  
     push @retVal, $cgi->Tr($cgi->th("Select a Field"),  
                            $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,  
                                                      new => 1,  
                                                      notes => "document.$name.notes.value",  
                                                      type => "document.$name.dataType.value",  
                                                      groups => "document.$name.groups")));  
     # Now we set up a dropdown for the data types. The values will be the  
     # data type names, and the labels will be the descriptions.  
     my %types = ERDB::GetDataTypes();  
     my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;  
     my $typeMenu = $cgi->popup_menu(-name   => 'dataType',  
                                     -values => [sort keys %types],  
                                     -labels => \%labelMap,  
                                     -default => 'string');  
     # Allow the user to specify a new field name. This is required if the  
     # user has selected the "(new)" marker. We put a little scriptlet in here that  
     # selects the (new) marker when the user enters the field.  
     push @retVal, "<script language=\"javaScript\">";  
     my $fieldField = "document.$name.fieldName";  
     my $newName = "\"" . NewName() . "\"";  
     push @retVal, $cgi->Tr($cgi->th("New Field Name"),  
                            $cgi->td($cgi->textfield(-name => 'newName',  
                                                     -size => 30,  
                                                     -value => "",  
                                                     -onFocus => "setIfEmpty($fieldField, $newName);")),  
                                     );  
     push @retVal, $cgi->Tr($cgi->th("Data type"),  
                            $cgi->td($typeMenu));  
     # The next row is for the notes.  
     push @retVal, $cgi->Tr($cgi->th("Description"),  
                            $cgi->td($cgi->textarea(-name => 'notes',  
                                                    -rows => 6,  
                                                    -columns => 80))  
                           );  
     # Now we have the groups, which are implemented as a checkbox group.  
     my @groups = $self->GetGroups();  
     push @retVal, $cgi->Tr($cgi->th("Groups"),  
                            $cgi->td($cgi->checkbox_group(-name=>'groups',  
                                     -values=> \@groups))  
                           );  
     # If the user wants to upload new values for the field, then we have  
     # an upload file name and column indicators.  
     push @retVal, $cgi->Tr($cgi->th("Upload Values"),  
                            $cgi->td($cgi->filefield(-name => 'newValueFile',  
                                                     -size => 20) .  
                                     " Key&nbsp;" .  
                                     $cgi->textfield(-name => 'keyCol',  
                                                     -size => 3,  
                                                     -default => 0) .  
                                     " Value&nbsp;" .  
                                     $cgi->textfield(-name => 'valueCol',  
                                                     -size => 3,  
                                                     -default => 1)  
                                    ),  
                           );  
     # Now the three buttons: STORE, SHOW, and DELETE.  
     push @retVal, $cgi->Tr($cgi->th("&nbsp;"),  
                            $cgi->td({align => 'center'},  
                                     $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .  
                                     $cgi->submit(-name => 'Store',  -value => 'STORE') . " " .  
                                     $cgi->submit(-name => 'Show',   -value => 'SHOW')  
                                    )  
                           );  
     # Close the table and the form.  
     push @retVal, $cgi->end_table();  
     # Return the assembled HTML.  
     return join("\n", @retVal, "");  
 }  
   
310  =head3 LoadAttributesFrom  =head3 LoadAttributesFrom
311    
312  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
313    
314  Load attributes from the specified tab-delimited file. Each line of the file must  Load attributes from the specified tab-delimited file. Each line of the file must
315  contain an object ID in the first column, an attribute key name in the second  contain an object ID in the first column, an attribute key name in the second
316  column, and attribute values in the remaining columns. The attribute values will  column, and attribute values in the remaining columns. The attribute values must
317  be assembled into a single value using the splitter code.  be assembled into a single value using the splitter code. In addition, the key names may
318    contain a splitter. If this is the case, the portion of the key after the splitter is
319    treated as a subkey.
320    
321  =over 4  =over 4
322    
323  =item fileName  =item fileName
324    
325  Name of the file from which to load the attributes.  Name of the file from which to load the attributes, or an open handle for the file.
326    (This last enables the method to be used in conjunction with the CGI form upload
327    control.)
328    
329  =item options  =item options
330    
# Line 471  Line 340 
340    
341  =over 4  =over 4
342    
343    =item mode
344    
345    Loading mode. Legal values are C<low_priority> (which reduces the task priority
346    of the load) and C<concurrent> (which reduces the locking cost of the load). The
347    default is a normal load.
348    
349  =item append  =item append
350    
351  If TRUE, then the attributes will be appended to existing data; otherwise, the  If TRUE, then the attributes will be appended to existing data; otherwise, the
352  first time a key name is encountered, it will be erased.  first time a key name is encountered, it will be erased.
353    
354    =item archive
355    
356    If specified, the name of a file into which the incoming data should be saved.
357    If I<resume> is also specified, only the lines actually loaded will be put
358    into this file.
359    
360    =item objectType
361    
362    If specified, the specified object type will be prefixed to each object ID.
363    
364    =item resume
365    
366    If specified, key-value pairs already in the database will not be reinserted.
367    Specify a number to start checking after the specified number of lines and
368    then admit everything after the first line not yet loaded. Specify C<careful>
369    to check every single line. Specify C<none> to ignore this option. The default
370    is C<none>. So, if you believe that a previous load failed somewhere after 50000
371    lines, a resume value of C<50000> would skip 50000 lines in the file, then
372    check each line after that until it finds one not already in the database. The
373    first such line found and all lines after that will be loaded. On the other
374    hand, if you have a file of 100000 records, and some have been loaded and some
375    not, you would use the word C<careful>, so that every line would be checked before
376    it is inserted. A resume of C<0> will start checking the first line of the
377    input file and then begin loading once it finds a line not in the database.
378    
379    =item chunkSize
380    
381    Number of lines to load in each burst. The default is 10,000.
382    
383  =back  =back
384    
385  =cut  =cut
# Line 484  Line 388 
388      # Get the parameters.      # Get the parameters.
389      my ($self, $fileName, %options) = @_;      my ($self, $fileName, %options) = @_;
390      # Declare the return variable.      # Declare the return variable.
391      my $retVal = Stats->new('keys', 'values');      my $retVal = Stats->new('keys', 'values', 'linesOut');
392        # Initialize the timers.
393        my ($eraseTime, $archiveTime, $checkTime) = (0, 0, 0);
394      # Check for append mode.      # Check for append mode.
395      my $append = ($options{append} ? 1 : 0);      my $append = ($options{append} ? 1 : 0);
396        # Check for resume mode.
397        my $resume = (defined($options{resume}) ? $options{resume} : 'none');
398      # Create a hash of key names found.      # Create a hash of key names found.
399      my %keyHash = ();      my %keyHash = ();
400      # Open the file for input.      # Create a hash of table names to files. Most attributes go into the HasValueFor
401      my $fh = Open(undef, "<$fileName");      # table, but some are put into other tables. Each table name will be mapped
402        # to a sub-hash with keys "fileName" (output file for the table) and "count"
403        # (number of lines in the file).
404        my %tableHash = ();
405        # Compute the chunk size.
406        my $chunkSize = ($options{chunkSize} ? $options{chunkSize} : 10000);
407        # Open the file for input. Note we must anticipate the possibility of an
408        # open filehandle being passed in. This occurs when the user is submitting
409        # the load file over the web.
410        my $fh;
411        if (ref $fileName) {
412            Trace("Using file opened by caller.") if T(3);
413            $fh = $fileName;
414        } else {
415            Trace("Attributes will be loaded from $fileName.") if T(3);
416            $fh = Open(undef, "<$fileName");
417        }
418        # Trace the mode.
419        if (T(3)) {
420            if ($options{mode}) {
421                Trace("Mode is $options{mode}.")
422            } else {
423                Trace("No mode specified.")
424            }
425        }
426        # Now check to see if we need to archive.
427        my $ah;
428        if (exists $options{archive}) {
429            my $ah = Open(undef, ">$options{archive}");
430            Trace("Load file will be archived to $options{archive}.") if T(3);
431        }
432        # Insure we recover from errors.
433        eval {
434            # If we have a resume number, process it here.
435            if ($resume =~ /\d+/) {
436                Trace("Skipping $resume lines.") if T(2);
437                my $startTime = time();
438                # Skip the specified number of lines.
439                for (my $skipped = 0; ! eof($fh) && $skipped < $resume; $skipped++) {
440                    my $line = <$fh>;
441                    $retVal->Add(skipped => 1);
442                }
443                $checkTime += time() - $startTime;
444            }
445      # Loop through the file.      # Loop through the file.
446            Trace("Starting load.") if T(2);
447      while (! eof $fh) {      while (! eof $fh) {
448                # Read the current line.
449          my ($id, $key, @values) = Tracer::GetLine($fh);          my ($id, $key, @values) = Tracer::GetLine($fh);
450          $retVal->Add(linesIn => 1);          $retVal->Add(linesIn => 1);
451          # Do some validation.          # Do some validation.
452          if (! defined($id)) {              if (! $id) {
453              # We ignore blank lines.              # We ignore blank lines.
454              $retVal->Add(blankLines => 1);              $retVal->Add(blankLines => 1);
455                } elsif (substr($id, 0, 1) eq '#') {
456                    # A line beginning with a pound sign is a comment.
457                    $retVal->Add(comments => 1);
458          } elsif (! defined($key)) {          } elsif (! defined($key)) {
459              # An ID without a key is a serious error.              # An ID without a key is a serious error.
460              my $lines = $retVal->Ask('linesIn');              my $lines = $retVal->Ask('linesIn');
461              Confess("Line $lines in $fileName has no attribute key.");              Confess("Line $lines in $fileName has no attribute key.");
462                } elsif (! @values) {
463                    # A line with no values is not allowed.
464                    my $lines = $retVal->Ask('linesIn');
465                    Trace("Line $lines for key $key has no attribute values.") if T(1);
466                    $retVal->Add(skipped => 1);
467          } else {          } else {
468                    # Check to see if we need to fix up the object ID.
469                    if ($options{objectType}) {
470                        $id = "$options{objectType}:$id";
471                    }
472                    # The key contains a real part and an optional sub-part. We need the real part.
473                    my ($realKey, $subKey) = $self->SplitKey($key);
474              # Now we need to check for a new key.              # Now we need to check for a new key.
475              if (! exists $keyHash{$key}) {                  if (! exists $keyHash{$realKey}) {
476                  # This is a new key. Verify that it exists.                      my $keyObject = $self->GetEntity(AttributeKey => $realKey);
477                  if (! $self->Exists('AttributeKey', $key)) {                      if (! defined($keyObject)) {
478                            # Here the specified key does not exist, which is an error.
479                      my $line = $retVal->Ask('linesIn');                      my $line = $retVal->Ask('linesIn');
480                      Confess("Attribute \"$key\" on line $line of $fileName not found in database.");                          Confess("Attribute \"$realKey\" on line $line of $fileName not found in database.");
481                  } else {                  } else {
482                      # Make sure we know this is no longer a new key.                          # Make sure we know this is no longer a new key. We do this by putting
483                      $keyHash{$key} = 1;                          # its table name in the key hash.
484                            $keyHash{$realKey} = $keyObject->PrimaryValue('AttributeKey(relationship-name)');
485                      $retVal->Add(keys => 1);                      $retVal->Add(keys => 1);
486                      # If this is NOT append mode, erase the key.                          # If this is NOT append mode, erase the key. This does not delete the key
487                            # itself; it just clears out all the values.
488                      if (! $append) {                      if (! $append) {
489                          $self->EraseAttribute($key);                              my $startTime = time();
490                      }                              $self->EraseAttribute($realKey);
491                                $eraseTime += time() - $startTime;
492                                Trace("Attribute $realKey erased.") if T(3);
493                            }
494                        }
495                        Trace("Key $realKey found.") if T(3);
496                    }
497                    # If we're in resume mode, check to see if this insert is redundant.
498                    my $ok = 1;
499                    if ($resume ne 'none') {
500                        my $startTime = time();
501                        my $count = $self->GetAttributes($id, $key, @values);
502                        if ($count) {
503                            # Here the record is found, so we skip it.
504                            $ok = 0;
505                            $retVal->Add(skipped => 1);
506                        } else {
507                            # Here the record is not found. If we're in non-careful mode, we
508                            # stop resume checking at this point.
509                            if ($resume ne 'careful') {
510                                $resume = 'none';
511                            }
512                        }
513                        $checkTime += time() - $startTime;
514                    }
515                    if ($ok) {
516                        # We're in business. First, archive this row.
517                        if (defined $ah) {
518                            my $startTime = time();
519                            Tracer::PutLine($ah, [$id, $key, @values]);
520                            $archiveTime += time() - $startTime;
521                        }
522                        # We need to format the attribute data so it will work
523                        # as if it were a load file. This means we join the
524                        # values.
525                        my $valueString = join('::', @values);
526                        # Now we need to get access to the key's load file. Check for it in the
527                        # table hash.
528                        my $keyTable = $keyHash{$realKey};
529                        if (! exists $tableHash{$keyTable}) {
530                            # This is a new table, so we need to set it up. First, we get
531                            # a temporary file for it.
532                            my $tempFileName = FIGRules::GetTempFileName(sessionID => $$ . $keyTable,
533                                                                         extension => 'dtx');
534                            my $oh = Open(undef, ">$tempFileName");
535                            # Now we create its descriptor in the table hash.
536                            $tableHash{$keyTable} = {fileName => $tempFileName, handle => $oh, count => 0};
537                        }
538                        # Everything is all set up, so we put the value in the temporary file and
539                        # count it.
540                        my $tableData = $tableHash{$keyTable};
541                        my $startTime = time();
542                        Tracer::PutLine($tableData->{handle}, [$realKey, $id, $subKey, $valueString]);
543                        $archiveTime += time() - $startTime;
544                        $retVal->Add(linesOut => 1);
545                        $tableData->{count}++;
546                        # See if it's time to load a chunk.
547                        if ($tableData->{count} >= $chunkSize) {
548                            # We've filled a chunk, so it's time.
549                            close $tableData->{handle};
550                            $self->_LoadAttributeTable($keyTable, $tableData->{fileName}, $retVal);
551                            # Reset for the next chunk.
552                            $tableData->{count} = 0;
553                            $tableData->{handle} = Open(undef, ">$tableData->{fileName}");
554                  }                  }
555                  Trace("Key $key found.") if T(3);                  } else {
556                        # Here we skipped because of resume mode.
557                        $retVal->Add(resumeSkip => 1);
558              }              }
559              # Now we know the key is valid. Add this value.                  Trace($retVal->Ask('values') . " values processed.") if $retVal->Check(values => 1000) && T(3);
             $self->AddAttribute($id, $key, @values);  
             my $progress = $retVal->Add(values => 1);  
             Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);  
   
560          }          }
561      }      }
562            # Now we close the archive file. Note we undefine the handle so the error methods know
563            # not to worry.
564            if (defined $ah) {
565                close $ah;
566                undef $ah;
567            }
568            # Now we load the residual from the temporary files (if any). This time we'll do an
569            # analyze as well.
570            for my $tableName (keys %tableHash) {
571                # Get the data for this table.
572                my $tableData = $tableHash{$tableName};
573                # Close the handle. ERDB will re-open it for input later.
574                close $tableData->{handle};
575                # Check to see if there's anything left to load.
576                if ($tableData->{count} > 0) {
577                    # Yes, load the data.
578                    $self->_LoadAttributeTable($tableName, $tableData->{fileName}, $retVal);
579                }
580                # Regardless of whether additional loading was required, we need to
581                # analyze the table for performance.
582                my $startTime = time();
583                $self->Analyze($tableName);
584                $retVal->Add(analyzeTime => time() - $startTime);
585            }
586            Trace("Attribute load successful.") if T(2);
587        };
588        # Check for an error.
589        if ($@) {
590            # Here we have an error. Display the error message.
591            my $message = $@;
592            Trace("Error during attribute load: $message") if T(0);
593            $retVal->AddMessage($message);
594            # Close the archive file if it's open. The archive file can sometimes provide
595            # clues as to what happened.
596            if (defined $ah) {
597                close $ah;
598            }
599        }
600        # Store the timers.
601        $retVal->Add(eraseTime   => $eraseTime);
602        $retVal->Add(archiveTime => $archiveTime);
603        $retVal->Add(checkTime   => $checkTime);
604      # Return the result.      # Return the result.
605      return $retVal;      return $retVal;
606  }  }
607    
608  =head3 BackupAllAttributes  =head3 BackupKeys
609    
610  C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>      my $stats = $attrDB->BackupKeys($fileName, %options);
611    
612  Backup all of the attributes to a file. The attributes will be stored in a  Backup the attribute key information from the attribute database.
 tab-delimited file suitable for reloading via L</LoadAttributesFrom>.  
613    
614  =over 4  =over 4
615    
616  =item fileName  =item fileName
617    
618  Name of the file to which the attribute data should be backed up.  Name of the output file.
619    
620  =item options  =item options
621    
622  Hash of options for the backup.  Options for modifying the backup process.
623    
624  =item RETURN  =item RETURN
625    
626  Returns a statistics object describing the backup.  Returns a statistics object for the backup.
627    
628  =back  =back
629    
630  Currently there are no options defined.  Currently there are no options. The backup is straight to a text file in
631    tab-delimited format. Each key is backup up to two lines. The first line
632    is all of the data from the B<AttributeKey> table. The second is a
633    tab-delimited list of all the groups.
634    
635  =cut  =cut
636    
637  sub BackupAllAttributes {  sub BackupKeys {
638      # Get the parameters.      # Get the parameters.
639      my ($self, $fileName, %options) = @_;      my ($self, $fileName, %options) = @_;
640      # Declare the return variable.      # Declare the return variable.
641      my $retVal = Stats->new();      my $retVal = Stats->new();
642      # Get a list of the keys.      # Open the output file.
643      my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');      my $fh = Open(undef, ">$fileName");
644      Trace(scalar(@keys) . " keys found during backup.") if T(2);      # Set up to read the keys.
645      # Open the file for output.      my $keyQuery = $self->Get(['AttributeKey'], "", []);
     my $fh = Open(undef, $fileName);  
646      # Loop through the keys.      # Loop through the keys.
647      for my $key (@keys) {      while (my $keyData = $keyQuery->Fetch()) {
648          Trace("Backing up attribute $key.") if T(3);          $retVal->Add(key => 1);
649          $retVal->Add(keys => 1);          # Get the fields.
650          # Loop through this key's values.          my ($id, $type, $tableName, $description) =
651          my $query = $self->Get(['HasValueFor'], "HasValueFor(to-link) = ?", [$key]);              $keyData->Values(['AttributeKey(id)', 'AttributeKey(relationship-name)',
652          my $valuesFound = 0;                                'AttributeKey(description)']);
653          while (my $line = $query->Fetch()) {          # Escape any tabs or new-lines in the description.
654              $valuesFound++;          my $escapedDescription = Tracer::Escape($description);
655              # Get this row's data.          # Write the key data to the output.
656              my @row = $line->Values(['HasValueFor(from-link)', 'HasValueFor(to-link)',          Tracer::PutLine($fh, [$id, $type, $tableName, $escapedDescription]);
657                                       'HasValueFor(value)']);          # Get the key's groups.
658              # Write it to the file.          my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
659              Tracer::PutLine($fh, \@row);                                      'IsInGroup(to-link)');
660          }          $retVal->Add(memberships => scalar(@groups));
661          Trace("$valuesFound values backed up for key $key.") if T(3);          # Write them to the output. Note we put a marker at the beginning to insure the line
662          $retVal->Add(values => $valuesFound);          # is nonempty.
663            Tracer::PutLine($fh, ['#GROUPS', @groups]);
664      }      }
665        # Log the operation.
666        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
667      # Return the result.      # Return the result.
668      return $retVal;      return $retVal;
669  }  }
670    
671  =head3 FieldMenu  =head3 RestoreKeys
672    
673  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>      my $stats = $attrDB->RestoreKeys($fileName, %options);
674    
675  Return the HTML for a menu to select an attribute field. The menu will  Restore the attribute keys and groups from a backup file.
 be a standard SELECT/OPTION thing which is called "popup menu" in the  
 CGI package, but actually looks like a list. The list will contain  
 one selectable row per field.  
676    
677  =over 4  =over 4
678    
679  =item cgi  =item fileName
   
 CGI query object used to generate HTML.  
680    
681  =item height  Name of the file containing the backed-up keys. Each key has a pair of lines,
682    one containing the key data and one listing its groups.
683    
684  Number of lines to display in the list.  =back
685    
686  =item name  =cut
687    
688  Name to give to the menu. This is the name under which the value will  sub RestoreKeys {
689  appear when the form is submitted.      # Get the parameters.
690        my ($self, $fileName, %options) = @_;
691        # Declare the return variable.
692        my $retVal = Stats->new();
693        # Set up a hash to hold the group IDs.
694        my %groups = ();
695        # Open the file.
696        my $fh = Open(undef, "<$fileName");
697        # Loop until we're done.
698        while (! eof $fh) {
699            # Get a key record.
700            my ($id, $tableName, $description) = Tracer::GetLine($fh);
701            if ($id eq '#GROUPS') {
702                Confess("Group record found when key record expected.");
703            } elsif (! defined($description)) {
704                Confess("Invalid format found for key record.");
705            } else {
706                $retVal->Add("keyIn" => 1);
707                # Add this key to the database.
708                $self->InsertObject('AttributeKey', { id => $id,
709                                                      description => Tracer::UnEscape($description),
710                                                      'relationship-name' => $tableName});
711                Trace("Attribute $id stored.") if T(3);
712                # Get the group line.
713                my ($marker, @groups) = Tracer::GetLine($fh);
714                if (! defined($marker)) {
715                    Confess("End of file found where group record expected.");
716                } elsif ($marker ne '#GROUPS') {
717                    Confess("Group record not found after key record.");
718                } else {
719                    $retVal->Add(memberships => scalar(@groups));
720                    # Connect the groups.
721                    for my $group (@groups) {
722                        # Find out if this is a new group.
723                        if (! $groups{$group}) {
724                            $retVal->Add(newGroup => 1);
725                            # Add the group.
726                            $self->InsertObject('AttributeGroup', { id => $group });
727                            Trace("Group $group created.") if T(3);
728                            # Make sure we know it's not new.
729                            $groups{$group} = 1;
730                        }
731                        # Connect the group to our key.
732                        $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
733                    }
734                    Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
735                }
736            }
737        }
738        # Log the operation.
739        $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
740        # Return the result.
741        return $retVal;
742    }
743    
744  =item keys  =head3 ArchiveFileName
745    
746  Reference to a hash mapping each attribute key name to a list reference,      my $fileName = $ca->ArchiveFileName();
 the list itself consisting of the attribute data type, its description,  
 and a list of its groups.  
747    
748  =item options  Compute a file name for archiving attribute input data. The file will be in the attribute log directory
749    
750  Hash containing options that modify the generation of the menu.  =cut
751    
752  =item RETURN  sub ArchiveFileName {
753        # Get the parameters.
754        my ($self) = @_;
755        # Declare the return variable.
756        my $retVal;
757        # We start by turning the timestamp into something usable as a file name.
758        my $now = Tracer::Now();
759        $now =~ tr/ :\//___/;
760        # Next we get the directory name.
761        my $dir = "$FIG_Config::var/attributes";
762        if (! -e $dir) {
763            Trace("Creating attribute file directory $dir.") if T(1);
764            mkdir $dir;
765        }
766        # Put it together with the field name and the time stamp.
767        $retVal = "$dir/upload.$now";
768        # Modify the file name to insure it's unique.
769        my $seq = 0;
770        while (-e "$retVal.$seq.tbl") { $seq++ }
771        # Use the computed sequence number to get the correct file name.
772        $retVal .= ".$seq.tbl";
773        # Return the result.
774        return $retVal;
775    }
776    
777  Returns the HTML to create a form field that can be used to select an  =head3 BackupAllAttributes
 attribute from the custom attributes system.  
778    
779  =back      my $stats = $attrDB->BackupAllAttributes($fileName, %options);
780    
781  The permissible options are as follows.  Backup all of the attributes to a file. The attributes will be stored in a
782    tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
783    
784  =over 4  =over 4
785    
786  =item new  =item fileName
   
 If TRUE, then extra rows will be provided to allow the user to select  
 a new attribute. In other words, the user can select an existing  
 attribute, or can choose a C<(new)> marker to indicate a field to  
 be created in the parent entity.  
   
 =item notes  
787    
788  If specified, the name of a variable for displaying the notes attached  Name of the file to which the attribute data should be backed up.
 to the field. This must be in Javascript form ready for assignment.  
 So, for example, if you have a variable called C<notes> that  
 represents a paragraph element, you should code C<notes.innerHTML>.  
 If it actually represents a form field you should code C<notes.value>.  
 If an C<innerHTML> coding is used, the text will be HTML-escaped before  
 it is copied in. Specifying this parameter generates Javascript for  
 displaying the field description when a field is selected.  
789    
790  =item type  =item options
791    
792  If specified, the name of a variable for displaying the field's  Hash of options for the backup.
 data type. Data types are a much more controlled vocabulary than  
 notes, so there is no worry about HTML translation. Instead, the  
 raw value is put into the specified variable. Otherwise, the same  
 rules apply to this value that apply to I<$noteControl>.  
793    
794  =item groups  =item RETURN
795    
796  If specified, the name of a multiple-selection list control (also called  Returns a statistics object describing the backup.
 a popup menu) which shall be used to display the selected groups.  
797    
798  =back  =back
799    
800    Currently there are no options defined.
801    
802  =cut  =cut
803    
804  sub FieldMenu {  sub BackupAllAttributes {
805      # Get the parameters.      # Get the parameters.
806      my ($self, $cgi, $height, $name, $keys, %options) = @_;      my ($self, $fileName, %options) = @_;
807      # Reformat the list of keys.      # Declare the return variable.
808      my %keys = %{$keys};      my $retVal = Stats->new();
809      # Add the (new) key, if needed.      # Get a list of the keys.
810      if ($options{new}) {      my %keys = map { $_->[0] => $_->[1] } $self->GetAll(['AttributeKey'],
811          $keys{NewName()} = ["string", ""];                                                          "", [], ['AttributeKey(id)',
812      }                                                                    'AttributeKey(relationship-name)']);
813      # Get a sorted list of key.      Trace(scalar(keys %keys) . " keys found during backup.") if T(2);
814      my @keys = sort keys %keys;      # Open the file for output.
815      # We need to create the name for the onChange function. This function      my $fh = Open(undef, ">$fileName");
     # may not do anything, but we need to know the name to generate the HTML  
     # for the menu.  
     my $changeName = "${name}_setNotes";  
     my $retVal = $cgi->popup_menu({name => $name,  
                                    size => $height,  
                                    onChange => "$changeName(this.value)",  
                                    values => \@keys,  
                                   });  
     # Create the change function.  
     $retVal .= "\n<script language=\"javascript\">\n";  
     $retVal .= "    function $changeName(fieldValue) {\n";  
     # The function only has a body if we have a control to store data about the  
     # attribute.  
     if ($options{notes} || $options{type} || $options{groups}) {  
         # Check to see if we're storing HTML or text into the note control.  
         my $noteControl = $options{notes};  
         my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);  
         # We use a CASE statement based on the newly-selected field value. The  
         # field description will be stored in the JavaScript variable "myText"  
         # and the data type in "myType". Note the default data type is a normal  
         # string, but the default notes is an empty string.  
         $retVal .= "        var myText = \"\";\n";  
         $retVal .= "        var myType = \"string\";\n";  
         $retVal .= "        switch (fieldValue) {\n";  
816          # Loop through the keys.          # Loop through the keys.
817          for my $key (@keys) {      for my $key (sort keys %keys) {
818              # Generate this case.          Trace("Backing up attribute $key.") if T(3);
819              $retVal .= "        case \"$key\" :\n";          $retVal->Add(keys => 1);
820              # Here we either want to update the note display, the          # Get the key's relevant relationship name.
821              # type display, the group list, or a combination of them.          my $relName = $keys{$key};
822              my ($type, $notes, @groups) = @{$keys{$key}};          # Loop through this key's values.
823              if ($noteControl) {          my $query = $self->Get([$relName], "$relName(from-link) = ?", [$key]);
824                  # Insure it's in the proper form.          my $valuesFound = 0;
825                  if ($htmlMode) {          while (my $line = $query->Fetch()) {
826                      $notes = ERDB::HTMLNote($notes);              $valuesFound++;
827                  }              # Get this row's data.
828                  # Escape it for use as a string literal.              my ($id, $key, $subKey, $value) = $line->Values(["$relName(to-link)",
829                  $notes =~ s/\n/\\n/g;                                                               "$relName(from-link)",
830                  $notes =~ s/"/\\"/g;                                                               "$relName(subkey)",
831                  $retVal .= "           myText = \"$notes\";\n";                                                               "$relName(value)"]);
832              }              # Check for a subkey.
833              if ($options{type}) {              if ($subKey ne '') {
834                  # Here we want the type updated.                  $key = "$key$self->{splitter}$subKey";
835                  $retVal .= "           myType = \"$type\";\n";              }
836              }              # Write it to the file.
837              if ($options{groups}) {              Tracer::PutLine($fh, [$id, $key, Escape($value)]);
838                  # Here we want the groups shown. Get a list of this attribute's groups.          }
839                  # We'll search through this list for each group to see if it belongs with          Trace("$valuesFound values backed up for key $key.") if T(3);
840                  # our attribute.          $retVal->Add(values => $valuesFound);
841                  my $groupLiteral = "=" . join("=", @groups) . "=";      }
842                  # Now we need some variables containing useful code for the javascript. It's      # Log the operation.
843                  # worth knowing we go through a bit of pain to insure $groupField[i] isn't      $self->LogOperation("Backup Data", $fileName, $retVal->Display());
                 # parsed as an array element.  
                 my $groupField = $options{groups};  
                 my $currentField = $groupField . "[i]";  
                 # Do the javascript.  
                 $retVal .= "           var groupList = \"$groupLiteral\";\n";  
                 $retVal .= "           for (var i = 0; i < $groupField.length; i++) {\n";  
                 $retVal .= "              var srchString = \"=\" + $currentField.value + \"=\";\n";  
                 $retVal .= "              var srchLoc = groupList.indexOf(srchString);\n";  
                 $retVal .= "              $currentField.checked = (srchLoc >= 0);\n";  
                 $retVal .= "           }\n";  
             }  
             # Close this case.  
             $retVal .= "           break;\n";  
         }  
         # Close the CASE statement and make the appropriate assignments.  
         $retVal .= "        }\n";  
         if ($noteControl) {  
             $retVal .= "        $noteControl = myText;\n";  
         }  
         if ($options{type}) {  
             $retVal .= "        $options{type} = myType;\n";  
         }  
     }  
     # Terminate the change function.  
     $retVal .= "    }\n";  
     $retVal .= "</script>\n";  
844      # Return the result.      # Return the result.
845      return $retVal;      return $retVal;
846  }  }
847    
848    
849  =head3 GetGroups  =head3 GetGroups
850    
851  C<< my @groups = $attrDB->GetGroups(); >>      my @groups = $attrDB->GetGroups();
852    
853  Return a list of the available groups.  Return a list of the available groups.
854    
# Line 784  Line 865 
865    
866  =head3 GetAttributeData  =head3 GetAttributeData
867    
868  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>      my %keys = $attrDB->GetAttributeData($type, @list);
869    
870  Return attribute data for the selected attributes. The attribute  Return attribute data for the selected attributes. The attribute
871  data is a hash mapping each attribute key name to a n-tuple containing the  data is a hash mapping each attribute key name to a n-tuple containing the
872  data type, the description, and the groups. This is the same format expected in  data type, the description, the table name, and the groups.
 the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.  
873    
874  =over 4  =over 4
875    
# Line 804  Line 884 
884    
885  =item RETURN  =item RETURN
886    
887  Returns a hash mapping each attribute key name to its data type, description, and  Returns a hash mapping each attribute key name to its description,
888  parent groups.  table name, and parent groups.
889    
890  =back  =back
891    
# Line 837  Line 917 
917          }          }
918          while (my $row = $query->Fetch()) {          while (my $row = $query->Fetch()) {
919              # Get this attribute's data.              # Get this attribute's data.
920              my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',              my ($key, $relName, $notes) = $row->Values(['AttributeKey(id)',
921                                                         'AttributeKey(relationship-name)',
922                                                       'AttributeKey(description)']);                                                       'AttributeKey(description)']);
923              # If it's new, get its groups and add it to the return hash.              # If it's new, get its groups and add it to the return hash.
924              if (! exists $retVal{$key}) {              if (! exists $retVal{$key}) {
925                  my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",                  my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
926                                              [$key], 'IsInGroup(to-link)');                                              [$key], 'IsInGroup(to-link)');
927                  $retVal{$key} = [$type, $notes, @groups];                  $retVal{$key} = [$relName, $notes, @groups];
928              }              }
929          }          }
930      }      }
# Line 851  Line 932 
932      return %retVal;      return %retVal;
933  }  }
934    
935    =head3 LogOperation
936    
937        $ca->LogOperation($action, $target, $description);
938    
939    Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
940    
941    =over 4
942    
943    =item action
944    
945    Action being logged (e.g. C<Delete Group> or C<Load Key>).
946    
947    =item target
948    
949    ID of the key or group affected.
950    
951    =item description
952    
953    Short description of the action.
954    
955    =back
956    
957    =cut
958    
959    sub LogOperation {
960        # Get the parameters.
961        my ($self, $action, $target, $description) = @_;
962        # Get the user ID.
963        my $user = $self->{user};
964        # Get a timestamp.
965        my $timeString = Tracer::Now();
966        # Open the log file for appending.
967        my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
968        # Write the data to it.
969        Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
970        # Close the log file.
971        close $oh;
972    }
973    
974  =head2 FIG Method Replacements  =head2 FIG Method Replacements
975    
976  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.
# Line 862  Line 982 
982  The idea is that these methods represent attribute manipulation allowed by all users, while  The idea is that these methods represent attribute manipulation allowed by all users, while
983  the others are only for privileged users with access to the attribute server.  the others are only for privileged users with access to the attribute server.
984    
985  In the previous implementation, an attribute had a value and a URL. In the new implementation,  In the previous implementation, an attribute had a value and a URL. In this implementation,
986  there is only a value. In this implementation, each attribute has only a value. These  each attribute has only a value. These methods will treat the value as a list with the individual
987  methods will treat the value as a list with the individual elements separated by the  elements separated by the value of the splitter parameter on the constructor (L</new>). The default
988  value of the splitter parameter on the constructor (L</new>). The default is double  is double colons C<::>.
 colons C<::>.  
989    
990  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
991  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
# Line 879  Line 998 
998    
999  =head3 GetAttributes  =head3 GetAttributes
1000    
1001  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>      my @attributeList = $attrDB->GetAttributes($objectID, $key, @values);
1002    
1003  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1004  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
# Line 918  Line 1037 
1037  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.
1038    
1039  Value matching in this system works very poorly, because of the way multiple values are  Value matching in this system works very poorly, because of the way multiple values are
1040  stored. For the object ID and key name, we create queries that filter for the desired  stored. For the object ID, key name, and first value, we create queries that filter for the
1041  results. For the values, we do a comparison after the attributes are retrieved from the  desired results. On any filtering by value, we must do a comparison after the attributes are
1042  database. As a result, queries in which filter only on value end up reading the entire  retrieved from the database, since the database has no notion of the multiple values, which
1043  attribute table to find the desired results.  are stored in a single string. As a result, queries in which filter only on value end up
1044    reading a lot more than they need to.
1045    
1046  =over 4  =over 4
1047    
# Line 945  Line 1065 
1065  or an empty string is specified, all values in that section will match. A  or an empty string is specified, all values in that section will match. A
1066  generic match can be requested by placing a percent sign (C<%>) at the end.  generic match can be requested by placing a percent sign (C<%>) at the end.
1067  In that case, all values that match up to and not including the percent sign  In that case, all values that match up to and not including the percent sign
1068  will match.  will match. You may also specify a regular expression enclosed
1069    in slashes. All values that match the regular expression will be returned. For
1070    performance reasons, only values have this extra capability.
1071    
1072  =item RETURN  =item RETURN
1073    
# Line 961  Line 1083 
1083  sub GetAttributes {  sub GetAttributes {
1084      # Get the parameters.      # Get the parameters.
1085      my ($self, $objectID, $key, @values) = @_;      my ($self, $objectID, $key, @values) = @_;
1086      # We will create one big honking query. The following hash will build the filter      # Declare the return variable.
1087      # clause and a parameter list.      my @retVal = ();
1088      my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);      # Insure we have at least some sort of filtering going on.
1089        if (! grep { defined $_ } $objectID, $key, @values) {
1090            Confess("No filters specified in GetAttributes call.");
1091        } else {
1092            # This hash will map value-table fields to patterns. We use it to build the
1093            # SQL statement.
1094            my %data;
1095            # Add the object ID to the key information.
1096            $data{'to-link'} = $objectID;
1097            # The first value represents a problem, because we can search it using SQL, but not
1098            # in the normal way. If the user specifies a generic search or exact match for
1099            # every alternative value (remember, the values may be specified as a list),
1100            # then we can create SQL filtering for it. If any of the values are specified
1101            # as a regular expression, however, that's more complicated, because
1102            # we need to read every value to verify a match.
1103            if (@values > 0) {
1104                # Get the first value and put its alternatives in an array.
1105                my $valueParm = $values[0];
1106                my @valueList;
1107                if (ref $valueParm eq 'ARRAY') {
1108                    @valueList = @{$valueParm};
1109                } else {
1110                    @valueList = ($valueParm);
1111                }
1112                # Okay, now we have all the possible criteria for the first value in the list
1113                # @valueList. We'll copy the values to a new array in which they have been
1114                # converted to generic requests. If we find a regular-expression match
1115                # anywhere in the list, we toss the whole thing.
1116                my @valuePatterns = ();
1117                my $okValues = 1;
1118                for my $valuePattern (@valueList) {
1119                    # Check the pattern type.
1120                    if (substr($valuePattern, 0, 1) eq '/') {
1121                        # Regular expressions invalidate the entire process.
1122                        $okValues = 0;
1123                    } elsif (substr($valuePattern, -1, 1) eq '%') {
1124                        # A Generic pattern is passed in unmodified.
1125                        push @valuePatterns, $valuePattern;
1126                    } else {
1127                        # An exact match is converted to generic.
1128                        push @valuePatterns, "$valuePattern%";
1129                    }
1130                }
1131                # If everything works, add the value data to the filtering hash.
1132                if ($okValues) {
1133                    $data{value} = \@valuePatterns;
1134                }
1135            }
1136            # Now comes the really tricky part, which is key handling. The key is
1137            # actually split in two parts: the real key and a sub-key. The real key
1138            # determines which value table contains the relevant values. The information
1139            # we need is kept in here.
1140            my %tables = map { $_ => [] } $self->_GetAllTables();
1141            # See if we have any key filtering to worry about.
1142            if ($key) {
1143                # Here we have either a single key or a list. We convert both cases to a list.
1144                my $keyList = (ref $key ne 'ARRAY' ? [$key] : $key);
1145                # Get easy access to the key/table hash.
1146                my $keyTableHash = $self->_KeyTable();
1147                # Loop through the keys, discovering tables.
1148                for my $keyChoice (@$keyList) {
1149                    # Now we have to start thinking about the real key and the subkeys.
1150                    my ($realKey, $subKey) = $self->_SplitKeyPattern($keyChoice);
1151                    # Find the matches for the real key in the key hash. For each of
1152                    # these, we memorize the table name in the hash below.
1153                    my %tableNames = ();
1154                    for my $keyInTable (keys %{$keyTableHash}) {
1155                        if ($self->_CheckSQLPattern($realKey, $keyInTable)) {
1156                            $tableNames{$keyTableHash->{$key}} = 1;
1157                        }
1158                    }
1159                    # If the key is generic, or didn't match anything, add
1160                    # the default table to the mix.
1161                    if (keys %tableNames == 0 || $keyChoice =~ /%/) {
1162                        $tableNames{$self->{defaultRel}} = 1;
1163                    }
1164                    # Now we add this key combination to the key list for each relevant table.
1165                    for my $tableName (keys %tableNames) {
1166                        push @{$tables{$tableName}}, [$realKey, $subKey];
1167                    }
1168                }
1169            }
1170            # Now we loop through the tables of interest, performing queries.
1171            # Loop through the tables.
1172            for my $table (keys %tables) {
1173                # Get the key pairs for this table.
1174                my $pairs = $tables{$table};
1175                # Does this table have data? It does if there is no key specified or
1176                # it has at least one key pair.
1177                my $pairCount = scalar @{$pairs};
1178                Trace("Pair count for table $table is $pairCount.") if T(3);
1179                if ($pairCount || ! $key) {
1180                    # Create some lists to contain the filter fragments and parameter values.
1181      my @filter = ();      my @filter = ();
1182      my @parms = ();      my @parms = ();
1183      # This next loop goes through the different fields that can be specified in the      # This next loop goes through the different fields that can be specified in the
1184      # parameter list and generates filters for each.                  # parameter list and generates filters for each. The %data hash that we built above
1185                    # contains most of the necessary information to do this. When we're done, we'll
1186                    # paste on stuff for the key pairs.
1187      for my $field (keys %data) {      for my $field (keys %data) {
1188          # Accumulate filter information for this field. We will OR together all the          # Accumulate filter information for this field. We will OR together all the
1189          # elements accumulated to create the final result.          # elements accumulated to create the final result.
1190          my @fieldFilter = ();          my @fieldFilter = ();
1191          # Get the specified data from the caller.                      # Get the specified filter for this field.
1192          my $fieldPattern = $data{$field};          my $fieldPattern = $data{$field};
1193          # Only proceed if the pattern is one that won't match everything.          # Only proceed if the pattern is one that won't match everything.
1194          if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {          if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
# Line 989  Line 1205 
1205              if (@patterns) {              if (@patterns) {
1206                  # Loop through the individual patterns.                  # Loop through the individual patterns.
1207                  for my $pattern (@patterns) {                  for my $pattern (@patterns) {
1208                      # Check for a generic request.                                  my ($clause, $value) = _WherePart($table, $field, $pattern);
1209                      if (substr($pattern, -1, 1) ne '%') {                                  push @fieldFilter, $clause;
1210                          # Here we have a normal request.                                  push @parms, $value;
                         push @fieldFilter, "$field = ?";  
                         push @parms, $pattern;  
                     } else {  
                         # Here we have a generate request, so we will use the LIKE operator to  
                         # filter the field to this value pattern.  
                         push @fieldFilter, "$field LIKE ?";  
                         # We must convert the pattern value to an SQL match pattern. First  
                         # we get a copy of it.  
                         my $actualPattern = $pattern;  
                         # Now we escape the underscores. Underscores are an SQL wild card  
                         # character, but they are used frequently in key names and object IDs.  
                         $actualPattern =~ s/_/\\_/g;  
                         # Add the escaped pattern to the bound parameter list.  
                         push @parms, $actualPattern;  
                     }  
1211                  }                  }
1212                  # Form the filter for this field.                  # Form the filter for this field.
1213                  my $fieldFilterString = join(" OR ", @fieldFilter);                  my $fieldFilterString = join(" OR ", @fieldFilter);
# Line 1014  Line 1215 
1215              }              }
1216          }          }
1217      }      }
1218      # Now @filter contains one or more filter strings and @parms contains the parameter                  # The final filter is for the key pairs. Only proceed if we have some.
1219      # values to bind to them.                  if ($pairCount) {
1220      my $actualFilter = join(" AND ", @filter);                      # We'll accumulate pair filter clauses in here.
1221      # Declare the return variable.                      my @pairFilters = ();
1222      my @retVal = ();                      # Loop through the key pairs.
1223      # Get the number of value sections we have to match.                      for my $pair (@$pairs) {
1224      my $sectionCount = scalar(@values);                          my ($realKey, $subKey) = @{$pair};
1225      # Now we're ready to make our query.                          my ($realClause, $realValue) = _WherePart($table, 'from-link', $realKey);
1226      my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);                          if (! $subKey) {
1227      # Loop through the assignments found.                              # Here the subkey is wild, so only the real key matters.
1228      while (my $row = $query->Fetch()) {                              push @pairFilters, $realClause;
1229          # Get the current row's data.                              push @parms, $realValue;
         my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',  
                                                       'HasValueFor(value)']);  
         # Break the value into sections.  
         my @sections = split($self->{splitter}, $valueString);  
         # Match each section against the incoming values. We'll assume we're  
         # okay unless we learn otherwise.  
         my $matching = 1;  
         for (my $i = 0; $i < $sectionCount && $matching; $i++) {  
             # We need to check to see if this section is generic.  
             if (substr($values[$i], -1, 1) eq '%') {  
                 my $matchLen = length($values[$i] - 1);  
                 $matching = substr($sections[$i], 0, $matchLen) eq  
                             substr($values[$i], 0, $matchLen);  
1230              } else {              } else {
1231                  $matching = ($sections[$i] eq $values[$i]);                              # Here we have to select on both keys.
1232                                my ($subClause, $subValue) = _WherePart($table, 'subkey', $subKey);
1233                                push @pairFilters, "($realClause AND $subClause)";
1234                                push @parms, $realValue, $subValue;
1235              }              }
1236          }          }
1237          # If we match, output this row to the return list.                      # Join the pair filters together to make a giant key filter.
1238          if ($matching) {                      my $pairFilter = "(" . join(" OR ", @pairFilters) . ")";
1239              push @retVal, [$id, $key, @sections];                      push @filter, $pairFilter;
1240                    }
1241                    # At this point, @filter contains one or more filter strings and @parms
1242                    # contains the parameter values to bind to them.
1243                    my $actualFilter = join(" AND ", @filter);
1244                    # Now we're ready to make our query.
1245                    my $query = $self->Get([$table], $actualFilter, \@parms);
1246                    # Format the results.
1247                    push @retVal, $self->_QueryResults($query, $table, @values);
1248          }          }
1249      }      }
1250      # Return the rows found.      }
1251        # The above loop ran the query for each necessary value table and merged the
1252        # results into @retVal. Now we return the rows found.
1253      return @retVal;      return @retVal;
1254  }  }
1255    
1256  =head3 AddAttribute  =head3 AddAttribute
1257    
1258  C<< $attrDB->AddAttribute($objectID, $key, @values); >>      $attrDB->AddAttribute($objectID, $key, @values);
1259    
1260  Add an attribute key/value pair to an object. This method cannot add a new key, merely  Add an attribute key/value pair to an object. This method cannot add a new key, merely
1261  add a value to an existing key. Use L</StoreAttributeKey> to create a new key.  add a value to an existing key. Use L</StoreAttributeKey> to create a new key.
# Line 1093  Line 1294 
1294          # Okay, now we have some reason to believe we can do this. Form the values          # Okay, now we have some reason to believe we can do this. Form the values
1295          # into a scalar.          # into a scalar.
1296          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1297            # Split up the key.
1298            my ($realKey, $subKey) = $self->SplitKey($key);
1299            # Find the table containing the key.
1300            my $table = $self->_KeyTable($realKey);
1301          # Connect the object to the key.          # Connect the object to the key.
1302          $self->InsertObject('HasValueFor', { 'from-link' => $key,          $self->InsertObject($table, { 'from-link' => $realKey,
1303                                               'to-link'   => $objectID,                                               'to-link'   => $objectID,
1304                                                 'subkey'    => $subKey,
1305                                               'value'     => $valueString,                                               'value'     => $valueString,
1306                                         });                                         });
1307      }      }
# Line 1105  Line 1311 
1311    
1312  =head3 DeleteAttribute  =head3 DeleteAttribute
1313    
1314  C<< $attrDB->DeleteAttribute($objectID, $key, @values); >>      $attrDB->DeleteAttribute($objectID, $key, @values);
1315    
1316  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1317    
# Line 1136  Line 1342 
1342          Confess("No object ID specified for DeleteAttribute call.");          Confess("No object ID specified for DeleteAttribute call.");
1343      } elsif (! defined($key)) {      } elsif (! defined($key)) {
1344          Confess("No attribute key specified for DeleteAttribute call.");          Confess("No attribute key specified for DeleteAttribute call.");
1345      } elsif (scalar(@values) == 0) {      } else {
1346          # Here we erase the entire key.          # Split the key into the real key and the subkey.
1347          $self->EraseAttribute($key);          my ($realKey, $subKey) = $self->SplitKey($key);
1348            # Find the table containing the key's values.
1349            my $table = $self->_KeyTable($realKey);
1350            if ($subKey eq '' && scalar(@values) == 0) {
1351                # Here we erase the entire key for this object.
1352                $self->DeleteRow('HasValueFor', $key, $objectID);
1353      } else {      } else {
1354          # Here we erase the matching values.          # Here we erase the matching values.
1355          my $valueString = join($self->{splitter}, @values);          my $valueString = join($self->{splitter}, @values);
1356          $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });              $self->DeleteRow('HasValueFor', $realKey, $objectID,
1357                                 { subkey => $subKey, value => $valueString });
1358            }
1359      }      }
1360      # Return a one. This is for backward compatability.      # Return a one. This is for backward compatability.
1361      return 1;      return 1;
1362  }  }
1363    
1364  =head3 ChangeAttribute  =head3 DeleteMatchingAttributes
1365    
1366  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>      my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values);
1367    
1368  Change the value of an attribute key/value pair for an object.  Delete all attributes that match the specified criteria. This is equivalent to
1369    calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1370    row found.
1371    
1372  =over 4  =over 4
1373    
1374  =item objectID  =item objectID
1375    
1376  ID of the genome or feature to which the attribute is to be changed. In general, an ID that  ID of object whose attributes are to be deleted. If the attributes for multiple
1377  starts with C<fig|> is treated as a feature ID, and an ID that is all digits and periods  objects are to be deleted, this parameter can be specified as a list reference. If
1378  is treated as a genome ID. For IDs of other types, this parameter should be a reference  attributes are to be deleted for all objects, specify C<undef> or an empty string.
1379  to a 2-tuple consisting of the entity type name followed by the object ID.  Finally, you can delete attributes for a range of object IDs by putting a percent
1380    sign (C<%>) at the end.
1381    
1382    =item key
1383    
1384    Attribute key name. A value of C<undef> or an empty string will match all
1385    attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1386    specified as a list reference. Finally, you can delete attributes for a range of
1387    keys by putting a percent sign (C<%>) at the end.
1388    
1389    =item values
1390    
1391    List of the desired attribute values, section by section. If C<undef>
1392    or an empty string is specified, all values in that section will match. A
1393    generic match can be requested by placing a percent sign (C<%>) at the end.
1394    In that case, all values that match up to and not including the percent sign
1395    will match. You may also specify a regular expression enclosed
1396    in slashes. All values that match the regular expression will be deleted. For
1397    performance reasons, only values have this extra capability.
1398    
1399    =item RETURN
1400    
1401    Returns a list of tuples for the attributes that were deleted, in the
1402    same form as L</GetAttributes>.
1403    
1404    =back
1405    
1406    =cut
1407    
1408    sub DeleteMatchingAttributes {
1409        # Get the parameters.
1410        my ($self, $objectID, $key, @values) = @_;
1411        # Get the matching attributes.
1412        my @retVal = $self->GetAttributes($objectID, $key, @values);
1413        # Loop through the attributes, deleting them.
1414        for my $tuple (@retVal) {
1415            $self->DeleteAttribute(@{$tuple});
1416        }
1417        # Log this operation.
1418        my $count = @retVal;
1419        $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1420        # Return the deleted attributes.
1421        return @retVal;
1422    }
1423    
1424    =head3 ChangeAttribute
1425    
1426        $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues);
1427    
1428    Change the value of an attribute key/value pair for an object.
1429    
1430    =over 4
1431    
1432    =item objectID
1433    
1434    ID of the genome or feature to which the attribute is to be changed. In general, an ID that
1435    starts with C<fig|> is treated as a feature ID, and an ID that is all digits and periods
1436    is treated as a genome ID. For IDs of other types, this parameter should be a reference
1437    to a 2-tuple consisting of the entity type name followed by the object ID.
1438    
1439  =item key  =item key
1440    
# Line 1202  Line 1475 
1475    
1476  =head3 EraseAttribute  =head3 EraseAttribute
1477    
1478  C<< $attrDB->EraseAttribute($key); >>      $attrDB->EraseAttribute($key);
1479    
1480  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
1481  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
# Line 1211  Line 1484 
1484    
1485  =item key  =item key
1486    
1487  Key to erase.  Key to erase. This must be a real key; that is, it cannot have a subkey
1488    component.
1489    
1490  =back  =back
1491    
# Line 1220  Line 1494 
1494  sub EraseAttribute {  sub EraseAttribute {
1495      # Get the parameters.      # Get the parameters.
1496      my ($self, $key) = @_;      my ($self, $key) = @_;
1497      # Delete everything connected to the key. The "keepRoot" option keeps the key in the      # Find the table containing the key.
1498      # datanase while deleting everything attached to it.      my $table = $self->_KeyTable($key);
1499      $self->Delete('AttributeKey', $key, keepRoot => 1);      # Is it the default table?
1500        if ($table eq $self->{defaultRel}) {
1501            # Yes, so the key is mixed in with other keys.
1502            # Delete everything connected to it.
1503            $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1504        } else {
1505            # No. Drop and re-create the table.
1506            $self->TruncateTable($table);
1507        }
1508        # Log the operation.
1509        $self->LogOperation("Erase Data", $key);
1510      # Return a 1, for backward compatability.      # Return a 1, for backward compatability.
1511      return 1;      return 1;
1512  }  }
1513    
1514  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1515    
1516  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>      my @keyList = $attrDB->GetAttributeKeys($groupName);
1517    
1518  Return a list of the attribute keys for a particular group.  Return a list of the attribute keys for a particular group.
1519    
# Line 1257  Line 1541 
1541      return sort @groups;      return sort @groups;
1542  }  }
1543    
1544    =head3 QueryAttributes
1545    
1546        my @attributeData = $ca->QueryAttributes($filter, $filterParms);
1547    
1548    Return the attribute data based on an SQL filter clause. In the filter clause,
1549    the name C<$object> should be used for the object ID, C<$key> should be used for
1550    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1551    
1552    =over 4
1553    
1554    =item filter
1555    
1556    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1557    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1558    and C<$value> for the value field. This abstraction enables us to hide the details of
1559    the database construction from the user.
1560    
1561    =item filterParms
1562    
1563    Parameters for the filter clause.
1564    
1565    =item RETURN
1566    
1567    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1568    one or more attribute values.
1569    
1570    =back
1571    
1572    =cut
1573    
1574    # This hash is used to drive the substitution process.
1575    my %AttributeParms = (object => 'to-link',
1576                          key    => 'from-link',
1577                          subkey => 'subkey',
1578                          value  => 'value');
1579    
1580    sub QueryAttributes {
1581        # Get the parameters.
1582        my ($self, $filter, $filterParms) = @_;
1583        # Declare the return variable.
1584        my @retVal = ();
1585        # Make sue we have filter parameters.
1586        my $realParms = (defined($filterParms) ? $filterParms : []);
1587        # Loop through all the value tables.
1588        for my $table ($self->_GetAllTables()) {
1589            # Create the query for this table by converting the filter.
1590            my $realFilter = $filter;
1591            for my $name (keys %AttributeParms) {
1592                $realFilter =~ s/\$$name/$table($AttributeParms{$name})/g;
1593            }
1594            my $query = $self->Get([$table], $realFilter, $realParms);
1595            # Loop through the results, forming the output attribute tuples.
1596            while (my $result = $query->Fetch()) {
1597                # Get the four values from this query result row.
1598                my ($objectID, $key, $subkey, $value) = $result->Values(["$table($AttributeParms{object})",
1599                                                                        "$table($AttributeParms{key})",
1600                                                                        "$table($AttributeParms{subkey})",
1601                                                                        "$table($AttributeParms{value})"]);
1602                # Combine the key and the subkey.
1603                my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1604                # Split the value.
1605                my @values = split $self->{splitter}, $value;
1606                # Output the result.
1607                push @retVal, [$objectID, $realKey, @values];
1608            }
1609        }
1610        # Return the result.
1611        return @retVal;
1612    }
1613    
1614    =head2 Key and ID Manipulation Methods
1615    
1616    =head3 ParseID
1617    
1618        my ($type, $id) = CustomAttributes::ParseID($idValue);
1619    
1620    Determine the type and object ID corresponding to an ID value from the attribute database.
1621    Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
1622    however, Genomes, Features, and Subsystems are not stored with a type name, so we need to
1623    deduce the type from the ID value structure.
1624    
1625    The theory here is that you can plug the ID and type directly into a Sprout database method, as
1626    follows
1627    
1628        my ($type, $id) = CustomAttributes::ParseID($attrList[$num]->[0]);
1629        my $target = $sprout->GetEntity($type, $id);
1630    
1631    =over 4
1632    
1633    =item idValue
1634    
1635    ID value taken from the attribute database.
1636    
1637    =item RETURN
1638    
1639    Returns a two-element list. The first element is the type of object indicated by the ID value,
1640    and the second element is the actual object ID.
1641    
1642    =back
1643    
1644    =cut
1645    
1646    sub ParseID {
1647        # Get the parameters.
1648        my ($idValue) = @_;
1649        # Declare the return variables.
1650        my ($type, $id);
1651        # Parse the incoming ID. We first check for the presence of an entity name. Entity names
1652        # can only contain letters, which helps to insure typed object IDs don't collide with
1653        # subsystem names (which are untyped).
1654        if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1655            # Here we have a typed ID.
1656            ($type, $id) = ($1, $2);
1657            # Fix the case sensitivity on PDB IDs.
1658            if ($type eq 'PDB') { $id = lc $id; }
1659        } elsif ($idValue =~ /fig\|/) {
1660            # Here we have a feature ID.
1661            ($type, $id) = (Feature => $idValue);
1662        } elsif ($idValue =~ /\d+\.\d+/) {
1663            # Here we have a genome ID.
1664            ($type, $id) = (Genome => $idValue);
1665        } else {
1666            # The default is a subsystem ID.
1667            ($type, $id) = (Subsystem => $idValue);
1668        }
1669        # Return the results.
1670        return ($type, $id);
1671    }
1672    
1673    =head3 FormID
1674    
1675        my $idValue = CustomAttributes::FormID($type, $id);
1676    
1677    Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1678    genomes, and features are stored in the database without type information, but all other object IDs
1679    must be prefixed with the object type.
1680    
1681    =over 4
1682    
1683    =item type
1684    
1685    Relevant object type.
1686    
1687    =item id
1688    
1689    ID of the object in question.
1690    
1691    =item RETURN
1692    
1693    Returns a string that will be recognized as an object ID in the attribute database.
1694    
1695    =back
1696    
1697    =cut
1698    
1699    sub FormID {
1700        # Get the parameters.
1701        my ($type, $id) = @_;
1702        # Declare the return variable.
1703        my $retVal;
1704        # Compute the ID string from the type.
1705        if (grep { $type eq $_ } qw(Feature Genome Subsystem)) {
1706            $retVal = $id;
1707        } else {
1708            $retVal = "$type:$id";
1709        }
1710        # Return the result.
1711        return $retVal;
1712    }
1713    
1714    =head3 GetTargetObject
1715    
1716        my $object = CustomAttributes::GetTargetObject($erdb, $idValue);
1717    
1718    Return the database object corresponding to the specified attribute object ID. The
1719    object type associated with the ID value must correspond to an entity name in the
1720    specified database.
1721    
1722    =over 4
1723    
1724    =item erdb
1725    
1726    B<ERDB> object for accessing the target database.
1727    
1728    =item idValue
1729    
1730    ID value retrieved from the attribute database.
1731    
1732    =item RETURN
1733    
1734    Returns a B<ERDBObject> for the attribute value's target object.
1735    
1736    =back
1737    
1738    =cut
1739    
1740    sub GetTargetObject {
1741        # Get the parameters.
1742        my ($erdb, $idValue) = @_;
1743        # Declare the return variable.
1744        my $retVal;
1745        # Get the type and ID for the target object.
1746        my ($type, $id) = ParseID($idValue);
1747        # Plug them into the GetEntity method.
1748        $retVal = $erdb->GetEntity($type, $id);
1749        # Return the resulting object.
1750        return $retVal;
1751    }
1752    
1753    =head3 SplitKey
1754    
1755        my ($realKey, $subKey) = $ca->SplitKey($key);
1756    
1757    Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1758    The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
1759    then the sub key is presumed to be an empty string.
1760    
1761    =over 4
1762    
1763    =item key
1764    
1765    Incoming key to be split.
1766    
1767    =item RETURN
1768    
1769    Returns a two-element list, the first element of which is the real key and the second element of
1770    which is the sub key.
1771    
1772    =back
1773    
1774    =cut
1775    
1776    sub SplitKey {
1777        # Get the parameters.
1778        my ($self, $key) = @_;
1779        # Do the split.
1780        my ($realKey, $subKey) = split($self->{splitter}, $key, 2);
1781        # Insure the subkey has a value.
1782        if (! defined $subKey) {
1783            $subKey = '';
1784        }
1785        # Return the results.
1786        return ($realKey, $subKey);
1787    }
1788    
1789    
1790    =head3 JoinKey
1791    
1792        my $key = $ca->JoinKey($realKey, $subKey);
1793    
1794    Join a real key and a subkey together to make an external key. The external key is the attribute key
1795    used by the caller. The real key and the subkey are how the keys are represented in the database. The
1796    real key is the key to the B<AttributeKey> entity. The subkey is an attribute of the B<HasValueFor>
1797    relationship.
1798    
1799    =over 4
1800    
1801    =item realKey
1802    
1803    The real attribute key.
1804    
1805    =item subKey
1806    
1807    The subordinate portion of the attribute key.
1808    
1809    =item RETURN
1810    
1811    Returns a single string representing both keys.
1812    
1813    =back
1814    
1815    =cut
1816    
1817    sub JoinKey {
1818        # Get the parameters.
1819        my ($self, $realKey, $subKey) = @_;
1820        # Declare the return variable.
1821        my $retVal;
1822        # Check for a subkey.
1823        if ($subKey eq '') {
1824            # No subkey, so the real key is the key.
1825            $retVal = $realKey;
1826        } else {
1827            # Subkey found, so the two pieces must be joined by a splitter.
1828            $retVal = "$realKey$self->{splitter}$subKey";
1829        }
1830        # Return the result.
1831        return $retVal;
1832    }
1833    
1834    
1835    =head3 AttributeTable
1836    
1837        my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList);
1838    
1839    Format the attribute data into an HTML table.
1840    
1841    =over 4
1842    
1843    =item cgi
1844    
1845    CGI query object used to generate the HTML
1846    
1847    =item attrList
1848    
1849    List of attribute results, in the format returned by the L</GetAttributes> or
1850    L</QueryAttributes> methods.
1851    
1852    =item RETURN
1853    
1854    Returns an HTML table displaying the attribute keys and values.
1855    
1856    =back
1857    
1858    =cut
1859    
1860    sub AttributeTable {
1861        # Get the parameters.
1862        my ($cgi, @attrList) = @_;
1863        # Accumulate the table rows.
1864        my @html = ();
1865        for my $attrData (@attrList) {
1866            # Format the object ID and key.
1867            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
1868            # Now we format the values. These remain unchanged unless one of them is a URL.
1869            my $lastValue = scalar(@{$attrData}) - 1;
1870            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
1871            # Assemble the values into a table row.
1872            push @html, $cgi->Tr($cgi->td(\@columns));
1873        }
1874        # Format the table in the return variable.
1875        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
1876        # Return it.
1877        return $retVal;
1878    }
1879    
1880    
1881    =head2 Internal Utility Methods
1882    
1883    =head3 _KeyTable
1884    
1885        my $tableName = $ca->_KeyTable($keyName);
1886    
1887    Return the name of the table that contains the attribute values for the
1888    specified key.
1889    
1890    Most attribute values are stored in the default table (usually C<HasValueFor>).
1891    Some, however, are placed in private tables by themselves for performance reasons.
1892    
1893    =over 4
1894    
1895    =item keyName (optional)
1896    
1897    Name of the attribute key whose table name is desired. If not specified, the
1898    entire key/table hash is returned.
1899    
1900    =item RETURN
1901    
1902    Returns the name of the table containing the specified attribute key's values,
1903    or a reference to a hash that maps key names to table names.
1904    
1905    =back
1906    
1907    =cut
1908    
1909    sub _KeyTable {
1910        # Get the parameters.
1911        my ($self, $keyName) = @_;
1912        # Declare the return variable.
1913        my $retVal;
1914        # Insure the key table hash is present.
1915        if (! exists $self->{keyTables}) {
1916            $self->{keyTables} = { map { $_->[0] => $_->[1] } $self->GetAll(['AttributeKey'],
1917                                                    "AttributeKey(relationship-name) <> ?",
1918                                                    [$self->{defaultRel}],
1919                                                    ['AttributeKey(id)', 'AttributeKey(relationship-name)']) };
1920        }
1921        # Get the key hash.
1922        my $keyHash = $self->{keyTables};
1923        # Does the user want a specific table or the whole thing?
1924        if ($keyName) {
1925            # Here we want a specific table. Is this key in the hash?
1926            if (exists $keyHash->{$keyName}) {
1927                # It's there, so return the specified table.
1928                $retVal = $keyHash->{$keyName};
1929            } else {
1930                # No, return the default table name.
1931                $retVal = $self->{defaultRel};
1932            }
1933        } else {
1934            # Here we want the whole hash.
1935            $retVal = $keyHash;
1936        }
1937        # Return the result.
1938        return $retVal;
1939    }
1940    
1941    
1942    =head3 _QueryResults
1943    
1944        my @attributeList = $attrDB->_QueryResults($query, $table, @values);
1945    
1946    Match the results of a query against value criteria and return
1947    the results. This is an internal method that splits the values coming back
1948    and matches the sections against the specified section patterns. It serves
1949    as the back end to L</GetAttributes> and L</FindAttributes>.
1950    
1951    =over 4
1952    
1953    =item query
1954    
1955    A query object that will return the desired records.
1956    
1957    =item table
1958    
1959    Name of the value table for the query.
1960    
1961    =item values
1962    
1963    List of the desired attribute values, section by section. If C<undef>
1964    or an empty string is specified, all values in that section will match. A
1965    generic match can be requested by placing a percent sign (C<%>) at the end.
1966    In that case, all values that match up to and not including the percent sign
1967    will match. You may also specify a regular expression enclosed
1968    in slashes. All values that match the regular expression will be returned. For
1969    performance reasons, only values have this extra capability.
1970    
1971    =item RETURN
1972    
1973    Returns a list of tuples. The first element in the tuple is an object ID, the
1974    second is an attribute key, and the remaining elements are the sections of
1975    the attribute value. All of the tuples will match the criteria set forth in
1976    the parameter list.
1977    
1978    =back
1979    
1980    =cut
1981    
1982    sub _QueryResults {
1983        # Get the parameters.
1984        my ($self, $query, $table, @values) = @_;
1985        # Declare the return value.
1986        my @retVal = ();
1987        # We use this hash to check for duplicates.
1988        my %dupHash = ();
1989        # Get the number of value sections we have to match.
1990        my $sectionCount = scalar(@values);
1991        # Loop through the assignments found.
1992        while (my $row = $query->Fetch()) {
1993            # Get the current row's data.
1994            my ($id, $realKey, $subKey, $valueString) = $row->Values(["$table(to-link)",
1995                                                                      "$table(from-link)",
1996                                                                      "$table(subkey)",
1997                                                                      "$table(value)"
1998                                                                    ]);
1999            # Form the key from the real key and the sub key.
2000            my $key = $self->JoinKey($realKey, $subKey);
2001            # Break the value into sections.
2002            my @sections = split($self->{splitter}, $valueString);
2003            # Match each section against the incoming values. We'll assume we're
2004            # okay unless we learn otherwise.
2005            my $matching = 1;
2006            for (my $i = 0; $i < $sectionCount && $matching; $i++) {
2007                # We need to check to see if this section is generic.
2008                my $value = $values[$i];
2009                Trace("Current value pattern is \"$value\".") if T(4);
2010                if ($value =~ m#^/(.+)/[a-z]*$#) {
2011                    Trace("Regular expression detected.") if T(4);
2012                    # Here we have a regular expression match.
2013                    my $section = $sections[$i];
2014                    $matching = eval("\$section =~ $value");
2015                } else {
2016                    # Here we have a normal match.
2017                    Trace("SQL match used.") if T(4);
2018                    $matching = _CheckSQLPattern($values[$i], $sections[$i]);
2019                }
2020            }
2021            # If we match, consider writing this row to the return list.
2022            if ($matching) {
2023                # Check for a duplicate.
2024                my $wholeThing = join($self->{splitter}, $id, $key, $valueString);
2025                if (! $dupHash{$wholeThing}) {
2026                    # It's okay, we're not a duplicate. Insure we don't duplicate this result.
2027                    $dupHash{$wholeThing} = 1;
2028                    push @retVal, [$id, $key, @sections];
2029                }
2030            }
2031        }
2032        # Return the rows found.
2033        return @retVal;
2034    }
2035    
2036    
2037    =head3 _LoadAttributeTable
2038    
2039        $attr->_LoadAttributeTable($tableName, $fileName, $stats, $mode);
2040    
2041    Load a file's data into an attribute table. This is an internal method
2042    provided for the convenience of L</LoadAttributesFrom>. It loads the
2043    specified file into the specified table and updates the statistics
2044    object.
2045    
2046    =over 4
2047    
2048    =item tableName
2049    
2050    Name of the table being loaded. This is usually C<HasValueFor>, but may
2051    be a different table for some specific attribute keys.
2052    
2053    =item fileName
2054    
2055    Name of the file containing a chunk of attribute data to load.
2056    
2057    =item stats
2058    
2059    Statistics object into which counts and times should be placed.
2060    
2061    =item mode
2062    
2063    Load mode for the file, usually C<low_priority>, C<concurrent>, or
2064    an empty string. The mode is used by some applications to control access
2065    to the table while it's being loaded. The default (empty string) is to lock the
2066    table until all the data's in place.
2067    
2068    =back
2069    
2070    =cut
2071    
2072    sub _LoadAttributeTable {
2073        # Get the parameters.
2074        my ($self, $tableName, $fileName, $stats, $mode) = @_;
2075        # Load the table from the file. Note that we don't do an analyze.
2076        # The analyze is done only after everything is complete.
2077        my $startTime = time();
2078        Trace("Loading attributes from $fileName: " . (-s $fileName) .
2079              " characters.") if T(3);
2080        my $loadStats = $self->LoadTable($fileName, $tableName,
2081                                         mode => $mode, partial => 1);
2082        # Record the load time.
2083        $stats->Add(insertTime => time() - $startTime);
2084        # Roll up the other statistics.
2085        $stats->Accumulate($loadStats);
2086    }
2087    
2088    
2089    =head3 _GetAllTables
2090    
2091        my @tables = $ca->_GetAllTables();
2092    
2093    Return a list of the names of all the tables used to store attribute
2094    values.
2095    
2096    =cut
2097    
2098    sub _GetAllTables {
2099        # Get the parameters.
2100        my ($self) = @_;
2101        # Start with the default table.
2102        my @retVal = $self->{defaultRel};
2103        # Add the tables named in the key hash. These tables are automatically
2104        # NOT the default, and each can only occur once, because alternate tables
2105        # are allocated on a per-key basis.
2106        my $keyHash = $self->_KeyTable();
2107        push @retVal, values %$keyHash;
2108        # Return the result.
2109        return @retVal;
2110    }
2111    
2112    
2113    =head3 _SplitKeyPattern
2114    
2115        my ($realKey, $subKey) = $ca->_SplitKeyPattern($keyChoice);
2116    
2117    Split a key pattern into the main part (the I<real key>) and a sub-part
2118    (the I<sub key>). This method differs from L</SplitKey> in that it treats
2119    the key as an SQL pattern instead of a raw string. Also, if there is no
2120    incoming sub-part, the sub-key will be undefined instead of an empty
2121    string.
2122    
2123    =over 4
2124    
2125    =item keyChoice
2126    
2127    SQL key pattern to be examined. This can either be a literal, an SQL pattern,
2128    a literal with an internal splitter code (usually C<::>) or an SQL pattern with
2129    an internal splitter. Note that the only SQL pattern we support is a percent
2130    sign (C<%>) at the end. This is the way we've declared things in the documentation,
2131    so users who try anything else will have problems.
2132    
2133    =item RETURN
2134    
2135    Returns a two-element list. The first element is the SQL pattern for the
2136    real key and the second is the SQL pattern for the sub-key. If the value
2137    for either one does not matter (e.g., the user wants a real key value of
2138    C<iedb> and doesn't care about the sub-key value), it will be undefined.
2139    
2140    =back
2141    
2142    =cut
2143    
2144    sub _SplitKeyPattern {
2145        # Get the parameters.
2146        my ($self, $keyChoice) = @_;
2147        # Declare the return variables.
2148        my ($realKey, $subKey);
2149        # Look for a splitter in the input.
2150        if ($keyChoice =~ /^(.*?)$self->{splitter}(.*)/) {
2151            # We found one. This means we can treat both sides of the
2152            # splitter as known patterns.
2153            ($realKey, $subKey) = ($1, $2);
2154        } elsif ($keyChoice =~ /%$/) {
2155            # Here we have a generic pattern for the whole key. The pattern
2156            # is treated as the correct pattern for the real key, but the
2157            # sub-key is considered to be wild.
2158            $realKey = $keyChoice;
2159        } else {
2160            # Here we have a literal pattern for the whole key. The pattern
2161            # is treated as the correct pattern for the real key, and the
2162            # sub-key is required to be blank.
2163            $realKey = $keyChoice;
2164            $subKey = '';
2165        }
2166        # Return the results.
2167        return ($realKey, $subKey);
2168    }
2169    
2170    
2171    =head3 _WherePart
2172    
2173        my ($sqlClause, $escapedValue) = _WherePart($tableName, $fieldName, $sqlPattern);
2174    
2175    Return the SQL clause and value for checking a field against the
2176    specified SQL pattern value. If the pattern is generic (ends in a C<%>),
2177    then a C<LIKE> expression is returned. Otherwise, an equality expression
2178    is returned. We take in information describing the field being checked,
2179    and the pattern we're checking against it. The output is a WHERE clause
2180    fragment for the comparison and a value to be used as a bound parameter
2181    value for the clause.
2182    
2183    =over 4
2184    
2185    =item tableName
2186    
2187    Name of the table containing the field we want checked by the clause.
2188    
2189    =item fieldName
2190    
2191    Name of the field to check in that table.
2192    
2193    =item sqlPattern
2194    
2195    Pattern to be compared against the field. If the last character is a percent sign
2196    (C<%>), it will be treated as a generic SQL pattern; otherwise, it will be treated
2197    as a literal.
2198    
2199    =item RETURN
2200    
2201    Returns a two-element list. The first element will be an SQL comparison expression
2202    and the second will be the value to be used as a bound parameter for the expression
2203    in order to
2204    
2205    =back
2206    
2207    =cut
2208    
2209    sub _WherePart {
2210        # Get the parameters.
2211        my ($tableName, $fieldName, $sqlPattern) = @_;
2212        # Declare the return variables.
2213        my ($sqlClause, $escapedValue);
2214        # Copy the pattern into the return area.
2215        $escapedValue = $sqlPattern;
2216        # Check the pattern. Is it generic or exact?
2217        if ($sqlPattern =~ /(.+)%$/) {
2218            # Yes, it is. We need a LIKE clause and we must escape the underscores
2219            # and percents in the pattern (except for the last one, of course).
2220            $escapedValue = $1;
2221            $escapedValue =~ s/(%|_)/\\$1/g;
2222            $escapedValue .= "%";
2223            $sqlClause = "$tableName($fieldName) LIKE ?";
2224        } else {
2225            # No, it isn't. We use an equality clause.
2226            $sqlClause = "$tableName($fieldName) = ?";
2227        }
2228        # Return the results.
2229        return ($sqlClause, $escapedValue);
2230    }
2231    
2232    
2233    =head3 _CheckSQLPattern
2234    
2235        my $flag = _CheckSQLPattern($pattern, $value);
2236    
2237    Return TRUE if the specified SQL pattern matches the specified value,
2238    else FALSE. The pattern is not a true full-blown SQL LIKE pattern: the
2239    only wild-carding allowed is a percent sign (C<%>) at the end.
2240    
2241    =over 4
2242    
2243    =item pattern
2244    
2245    SQL pattern to match against a value.
2246    
2247    =item value
2248    
2249    Value to match against an SQL pattern.
2250    
2251    =item RETURN
2252    
2253    Returns TRUE if the pattern matches the value, else FALSE.
2254    
2255    =back
2256    
2257    =cut
2258    
2259    sub _CheckSQLPattern {
2260        # Get the parameters.
2261        my ($pattern, $value) = @_;
2262        # Declare the return variable.
2263        my $retVal;
2264        # Check for a generic pattern.
2265        if ($pattern =~ /(.*)%$/) {
2266            # Here we have one. Do a substring match.
2267            $retVal = (substr($value, 0, length $1) eq $1);
2268        } else {
2269            # Here it's an exact match.
2270            $retVal = ($pattern eq $value);
2271        }
2272        # Return the result.
2273        return $retVal;
2274    }
2275    
2276  1;  1;

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