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revision 1.30, Fri Oct 5 01:40:58 2007 UTC revision 1.31, Thu Dec 6 14:58:03 2007 UTC
# Line 131  Line 131 
131    
132  =head3 new  =head3 new
133    
134  C<< my $attrDB = CustomAttributes->new(%options); >>      my $attrDB = CustomAttributes->new(%options);
135    
136  Construct a new CustomAttributes object. The following options are  Construct a new CustomAttributes object. The following options are
137  supported.  supported.
# Line 174  Line 174 
174    
175  =head3 StoreAttributeKey  =head3 StoreAttributeKey
176    
177  C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>      $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups);
178    
179  Create or update an attribute for the database.  Create or update an attribute for the database.
180    
# Line 247  Line 247 
247    
248  =head3 DeleteAttributeKey  =head3 DeleteAttributeKey
249    
250  C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>      my $stats = $attrDB->DeleteAttributeKey($attributeName);
251    
252  Delete an attribute from the custom attributes database.  Delete an attribute from the custom attributes database.
253    
# Line 279  Line 279 
279    
280  =head3 NewName  =head3 NewName
281    
282  C<< my $text = CustomAttributes::NewName(); >>      my $text = CustomAttributes::NewName();
283    
284  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.
285    
# Line 291  Line 291 
291    
292  =head3 ControlForm  =head3 ControlForm
293    
294  C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>      my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys);
295    
296  Return a form that can be used to control the creation and modification of  Return a form that can be used to control the creation and modification of
297  attributes. Only a subset of the attribute keys will be displayed, as  attributes. Only a subset of the attribute keys will be displayed, as
# Line 385  Line 385 
385    
386  =head3 LoadAttributesFrom  =head3 LoadAttributesFrom
387    
388  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>      my $stats = $attrDB->LoadAttributesFrom($fileName, %options);
389  s  s
390  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
391  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
# Line 568  Line 568 
568    
569  =head3 BackupKeys  =head3 BackupKeys
570    
571  C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>      my $stats = $attrDB->BackupKeys($fileName, %options);
572    
573  Backup the attribute key information from the attribute database.  Backup the attribute key information from the attribute database.
574    
# Line 630  Line 630 
630    
631  =head3 RestoreKeys  =head3 RestoreKeys
632    
633  C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>      my $stats = $attrDB->RestoreKeys($fileName, %options);
634    
635  Restore the attribute keys and groups from a backup file.  Restore the attribute keys and groups from a backup file.
636    
# Line 702  Line 702 
702    
703  =head3 ArchiveFileName  =head3 ArchiveFileName
704    
705  C<< my $fileName = $ca->ArchiveFileName(); >>      my $fileName = $ca->ArchiveFileName();
706    
707  Compute a file name for archiving attribute input data. The file will be in the attribute log directory  Compute a file name for archiving attribute input data. The file will be in the attribute log directory
708    
# Line 735  Line 735 
735    
736  =head3 BackupAllAttributes  =head3 BackupAllAttributes
737    
738  C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>      my $stats = $attrDB->BackupAllAttributes($fileName, %options);
739    
740  Backup all of the attributes to a file. The attributes will be stored in a  Backup all of the attributes to a file. The attributes will be stored in a
741  tab-delimited file suitable for reloading via L</LoadAttributesFrom>.  tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
# Line 802  Line 802 
802    
803  =head3 FieldMenu  =head3 FieldMenu
804    
805  C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>      my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options);
806    
807  Return the HTML for a menu to select an attribute field. The menu will  Return the HTML for a menu to select an attribute field. The menu will
808  be a standard SELECT/OPTION thing which is called "popup menu" in the  be a standard SELECT/OPTION thing which is called "popup menu" in the
# Line 976  Line 976 
976    
977  =head3 GetGroups  =head3 GetGroups
978    
979  C<< my @groups = $attrDB->GetGroups(); >>      my @groups = $attrDB->GetGroups();
980    
981  Return a list of the available groups.  Return a list of the available groups.
982    
# Line 993  Line 993 
993    
994  =head3 GetAttributeData  =head3 GetAttributeData
995    
996  C<< my %keys = $attrDB->GetAttributeData($type, @list); >>      my %keys = $attrDB->GetAttributeData($type, @list);
997    
998  Return attribute data for the selected attributes. The attribute  Return attribute data for the selected attributes. The attribute
999  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
# Line 1062  Line 1062 
1062    
1063  =head3 LogOperation  =head3 LogOperation
1064    
1065  C<< $ca->LogOperation($action, $target, $description); >>      $ca->LogOperation($action, $target, $description);
1066    
1067  Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).  Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
1068    
# Line 1103  Line 1103 
1103    
1104  =head3 _KeywordString  =head3 _KeywordString
1105    
1106  C<< my $keywordString = $ca->_KeywordString($key, $value); >>      my $keywordString = $ca->_KeywordString($key, $value);
1107    
1108  Compute the keyword string for a specified key/value pair. This consists of the  Compute the keyword string for a specified key/value pair. This consists of the
1109  key name and value converted to lower case with underscores translated to spaces.  key name and value converted to lower case with underscores translated to spaces.
# Line 1148  Line 1148 
1148    
1149  =head3 _QueryResults  =head3 _QueryResults
1150    
1151  C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>      my @attributeList = $attrDB->_QueryResults($query, @values);
1152    
1153  Match the results of a B<HasValueFor> query against value criteria and return  Match the results of a B<HasValueFor> query against value criteria and return
1154  the results. This is an internal method that splits the values coming back  the results. This is an internal method that splits the values coming back
# Line 1261  Line 1261 
1261    
1262  =head3 GetAttributes  =head3 GetAttributes
1263    
1264  C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>      my @attributeList = $attrDB->GetAttributes($objectID, $key, @values);
1265    
1266  In the database, attribute values are sectioned into pieces using a splitter  In the database, attribute values are sectioned into pieces using a splitter
1267  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 1480  Line 1480 
1480    
1481  =head3 AddAttribute  =head3 AddAttribute
1482    
1483  C<< $attrDB->AddAttribute($objectID, $key, @values); >>      $attrDB->AddAttribute($objectID, $key, @values);
1484    
1485  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
1486  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 1534  Line 1534 
1534    
1535  =head3 DeleteAttribute  =head3 DeleteAttribute
1536    
1537  C<< $attrDB->DeleteAttribute($objectID, $key, @values); >>      $attrDB->DeleteAttribute($objectID, $key, @values);
1538    
1539  Delete the specified attribute key/value combination from the database.  Delete the specified attribute key/value combination from the database.
1540    
# Line 1584  Line 1584 
1584    
1585  =head3 DeleteMatchingAttributes  =head3 DeleteMatchingAttributes
1586    
1587  C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>      my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values);
1588    
1589  Delete all attributes that match the specified criteria. This is equivalent to  Delete all attributes that match the specified criteria. This is equivalent to
1590  calling L</GetAttributes> and then invoking L</DeleteAttribute> for each  calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
# Line 1644  Line 1644 
1644    
1645  =head3 ChangeAttribute  =head3 ChangeAttribute
1646    
1647  C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>      $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues);
1648    
1649  Change the value of an attribute key/value pair for an object.  Change the value of an attribute key/value pair for an object.
1650    
# Line 1696  Line 1696 
1696    
1697  =head3 EraseAttribute  =head3 EraseAttribute
1698    
1699  C<< $attrDB->EraseAttribute($key); >>      $attrDB->EraseAttribute($key);
1700    
1701  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
1702  key from the database; it merely removes all the values.  key from the database; it merely removes all the values.
# Line 1725  Line 1725 
1725    
1726  =head3 GetAttributeKeys  =head3 GetAttributeKeys
1727    
1728  C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>      my @keyList = $attrDB->GetAttributeKeys($groupName);
1729    
1730  Return a list of the attribute keys for a particular group.  Return a list of the attribute keys for a particular group.
1731    
# Line 1755  Line 1755 
1755    
1756  =head3 QueryAttributes  =head3 QueryAttributes
1757    
1758  C<< my @attributeData = $ca->QueryAttributes($filter, $filterParms); >>      my @attributeData = $ca->QueryAttributes($filter, $filterParms);
1759    
1760  Return the attribute data based on an SQL filter clause. In the filter clause,  Return the attribute data based on an SQL filter clause. In the filter clause,
1761  the name C<$object> should be used for the object ID, C<$key> should be used for  the name C<$object> should be used for the object ID, C<$key> should be used for
# Line 1824  Line 1824 
1824    
1825  =head3 ParseID  =head3 ParseID
1826    
1827  C<< my ($type, $id) = CustomAttributes::ParseID($idValue); >>      my ($type, $id) = CustomAttributes::ParseID($idValue);
1828    
1829  Determine the type and object ID corresponding to an ID value from the attribute database.  Determine the type and object ID corresponding to an ID value from the attribute database.
1830  Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);  Most ID values consist of a type name and an ID, separated by a colon (e.g. C<Family:aclame|cluster10>);
# Line 1881  Line 1881 
1881    
1882  =head3 FormID  =head3 FormID
1883    
1884  C<< my $idValue = CustomAttributes::FormID($type, $id); >>      my $idValue = CustomAttributes::FormID($type, $id);
1885    
1886  Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,  Convert an object type and ID pair into an object ID string for the attribute system. Subsystems,
1887  genomes, and features are stored in the database without type information, but all other object IDs  genomes, and features are stored in the database without type information, but all other object IDs
# Line 1922  Line 1922 
1922    
1923  =head3 GetTargetObject  =head3 GetTargetObject
1924    
1925  C<< my $object = CustomAttributes::GetTargetObject($erdb, $idValue); >>      my $object = CustomAttributes::GetTargetObject($erdb, $idValue);
1926    
1927  Return the database object corresponding to the specified attribute object ID. The  Return the database object corresponding to the specified attribute object ID. The
1928  object type associated with the ID value must correspond to an entity name in the  object type associated with the ID value must correspond to an entity name in the
# Line 1961  Line 1961 
1961    
1962  =head3 SplitKey  =head3 SplitKey
1963    
1964  C<< my ($realKey, $subKey) = $ca->SplitKey($key); >>      my ($realKey, $subKey) = $ca->SplitKey($key);
1965    
1966  Split an external key (that is, one passed in by a caller) into the real key and the sub key.  Split an external key (that is, one passed in by a caller) into the real key and the sub key.
1967  The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,  The real and sub keys are separated by a splitter value (usually C<::>). If there is no splitter,
# Line 1997  Line 1997 
1997    
1998  =head3 JoinKey  =head3 JoinKey
1999    
2000  C<< my $key = $ca->JoinKey($realKey, $subKey); >>      my $key = $ca->JoinKey($realKey, $subKey);
2001    
2002  Join a real key and a subkey together to make an external key. The external key is the attribute key  Join a real key and a subkey together to make an external key. The external key is the attribute key
2003  used by the caller. The real key and the subkey are how the keys are represented in the database. The  used by the caller. The real key and the subkey are how the keys are represented in the database. The
# Line 2042  Line 2042 
2042    
2043  =head3 AttributeTable  =head3 AttributeTable
2044    
2045  C<< my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList); >>      my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList);
2046    
2047  Format the attribute data into an HTML table.  Format the attribute data into an HTML table.
2048    
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