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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.32, Sat Jan 28 08:58:53 2006 UTC
# Line 2  Line 2 
2    
3          use strict;          use strict;
4          use Tracer;          use Tracer;
5          use DBKernel;      use DBrtns;
6          use Data::Dumper;          use Data::Dumper;
7          use XML::Simple;          use XML::Simple;
8          use DBQuery;          use DBQuery;
9          use DBObject;          use DBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use FIG;
13    
14  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
15    
# Line 32  Line 33 
33  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
34  The B<FEATURE> entity also contains an optional virulence number. This is implemented  The B<FEATURE> entity also contains an optional virulence number. This is implemented
35  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
36  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in the  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
37  C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence number.  the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
38  If the virulence of I<ABC> is not known, there will not be any rows for it in C<FeatureVirulence>.  number. If the virulence of I<ABC> is not known, there will not be any rows for it in
39    C<FeatureVirulence>.
40    
41  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
42  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
# Line 69  Line 71 
71  is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet
72  fully implemented.  fully implemented.
73    
74    =head2 XML Database Description
75    
76    =head3 Data Types
77    
78    The ERDB system supports the following data types. Note that there are numerous string
79    types depending on the maximum length. Some database packages limit the total number of
80    characters you have in an index key; to insure the database works in all environments,
81    the type of string should be the shortest one possible that supports all the known values.
82    
83    =over 4
84    
85    =item char
86    
87    single ASCII character
88    
89    =item int
90    
91    32-bit signed integer
92    
93    =item date
94    
95    64-bit unsigned integer, representing a PERL date/time value
96    
97    =item text
98    
99    long string; Text fields cannot be used in indexes or sorting and do not support the
100    normal syntax of filter clauses, but can be up to a billion character in length
101    
102    =item float
103    
104    double-precision floating-point number
105    
106    =item boolean
107    
108    single-bit numeric value; The value is stored as a 16-bit signed integer (for
109    compatability with certain database packages), but the only values supported are
110    0 and 1.
111    
112    =item key-string
113    
114    variable-length string, maximum 40 characters
115    
116    =item name-string
117    
118    variable-length string, maximum 80 characters
119    
120    =item medium-string
121    
122    variable-length string, maximum 160 characters
123    
124    =item string
125    
126    variable-length string, maximum 255 characters
127    
128    =back
129    
130    =head3 Global Tags
131    
132    The entire database definition must be inside a B<Database> tag. The display name of
133    the database is given by the text associated with the B<Title> tag. The display name
134    is only used in the automated documentation. It has no other effect. The entities and
135    relationships are listed inside the B<Entities> and B<Relationships> tags,
136    respectively. None of these tags have attributes.
137    
138        <Database>
139            <Title>... display title here...</Title>
140            <Entities>
141                ... entity definitions here ...
142            </Entities>
143            <Relationships>
144                ... relationship definitions here...
145            </Relationships>
146        </Database>
147    
148    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
149    The text inside the B<Notes> tag contains comments that will appear when the database
150    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
151    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
152    
153    =head3 Fields
154    
155    Both entities and relationships have fields described by B<Field> tags. A B<Field>
156    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
157    object mus be inside B<Fields> tags.
158    
159        <Entity ... >
160            <Fields>
161                ... Field tags ...
162            </Fields>
163        </Entity>
164    
165    The attributes for the B<Field> tag are as follows.
166    
167    =over 4
168    
169    =item name
170    
171    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
172    and the first character should be a letter. Most underlying databases are case-insensitive
173    with the respect to field names, so a best practice is to use lower-case letters only.
174    
175    =item type
176    
177    Data type of the field. The legal data types are given above.
178    
179    =item relation
180    
181    Name of the relation containing the field. This should only be specified for entity
182    fields. The ERDB system does not support optional fields or multi-occurring fields
183    in the primary relation of an entity. Instead, they are put into secondary relations.
184    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
185    grouping used to select a subset of the genomes. A given genome may not be in any
186    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
187    value. The relation name specified must be a valid table name. By convention, it is
188    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
189    entity, the fields without a relation attribute are said to belong to the
190    I<primary relation>. This relation has the same name as the entity itself.
191    
192    =back
193    
194    =head3 Indexes
195    
196    An entity can have multiple alternate indexes associated with it. The fields must
197    be from the primary relation. The alternate indexes assist in ordering results
198    from a query. A relationship can have up to two indexes-- a I<to-index> and a
199    I<from-index>. These order the results when crossing the relationship. For
200    example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
201    from-index would order the contigs of a ganome, and the to-index would order
202    the genomes of a contig. A relationship's index must specify only fields in
203    the relationship.
204    
205    The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
206    of a relationship is specified using the B<FromIndex> tag; the to-index is specified
207    using the B<ToIndex> tag.
208    
209    Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
210    tag containing the B<IndexField> tags. These specify, in order, the fields used in
211    the index. The attributes of an B<IndexField> tag are as follows.
212    
213    =over 4
214    
215    =item name
216    
217    Name of the field.
218    
219    =item order
220    
221    Sort order of the field-- C<ascending> or C<descending>.
222    
223    =back
224    
225    The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
226    
227    =head3 Object and Field Names
228    
229    By convention entity and relationship names use capital casing (e.g. C<Genome> or
230    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
231    with respect to relation names, converting them internally to all-upper case or
232    all-lower case.
233    
234    If syntax or parsing errors occur when you try to load or use an ERDB database, the
235    most likely reason is that one of your objects has an SQL reserved word as its name.
236    The list of SQL reserved words keeps increasing; however, most are unlikely to show
237    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
238    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
239    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
240    
241    Every entity has a field called C<id> that acts as its primary key. Every relationship
242    has fields called C<from-link> and C<to-link> that contain copies of the relevant
243    entity IDs. These are essentially ERDB's reserved words, and should not be used
244    for user-defined field names.
245    
246    =head3 Entities
247    
248    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
249    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
250    containing one or more fields. The attributes of the B<Entity> tag are as follows.
251    
252    =over 4
253    
254    =item name
255    
256    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
257    or C<GroupBlock>) and should be a noun or noun phrase.
258    
259    =item keyType
260    
261    Data type of the primary key. The primary key is always named C<id>.
262    
263    =back
264    
265    =head3 Relationships
266    
267    A relationship is described by the C<Relationship> tag. Within a relationship,
268    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
269    fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
270    the to-index.
271    
272    The C<Relationship> tag has the following attributes.
273    
274    =over 4
275    
276    =item name
277    
278    Name of the relationship. The relationship name, by convention, uses capital casing
279    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
280    phrase, designed to fit between the from-entity and the to-entity (e.g.
281    Block C<ContainsRegionIn> Genome).
282    
283    =item from
284    
285    Name of the entity from which the relationship starts.
286    
287    =item to
288    
289    Name of the entity to which the relationship proceeds.
290    
291    =item arity
292    
293    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
294    
295    =back
296    
297  =cut  =cut
298    
299  # GLOBALS  # GLOBALS
# Line 76  Line 301 
301  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
302  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
303  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation
304   #string is specified in the field definition.  # string is specified in the field definition. "avgLen" is the average byte length for estimating
305  my %TypeTable = ( char =>        { sqlType => 'CHAR(1)',                        maxLen => 1,                    dataGen => "StringGen('A')" },  # record sizes.
306                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },
307                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },
308                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },
309                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },
310                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
311                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },
312                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },
313                               'key-string' =>                               'key-string' =>
314                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },
315                                   'name-string' =>                                   'name-string' =>
316                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },
317                                   'medium-string' =>                                   'medium-string' =>
318                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },
319                                  );                                  );
320    
321  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 145  Line 371 
371    
372  =head3 ShowMetaData  =head3 ShowMetaData
373    
374  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
375    
376  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
377  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 282  Line 508 
508                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
509                  $joinKey =~ m!^([^/]+)/(.+)$!;                  $joinKey =~ m!^([^/]+)/(.+)$!;
510                  my ($sourceRelation, $targetRelation) = ($1, $2);                  my ($sourceRelation, $targetRelation) = ($1, $2);
511                  Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
512                  my $source = $self->ComputeObjectSentence($sourceRelation);                  my $source = $self->ComputeObjectSentence($sourceRelation);
513                  my $target = $self->ComputeObjectSentence($targetRelation);                  my $target = $self->ComputeObjectSentence($targetRelation);
514                  my $clause = $joinTable->{$joinKey};                  my $clause = $joinTable->{$joinKey};
# Line 300  Line 526 
526    
527  =head3 DumpMetaData  =head3 DumpMetaData
528    
529  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
530    
531  Return a dump of the metadata structure.  Return a dump of the metadata structure.
532    
# Line 315  Line 541 
541    
542  =head3 CreateTables  =head3 CreateTables
543    
544  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
545    
546  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
547  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 327  Line 553 
553  sub CreateTables {  sub CreateTables {
554          # Get the parameters.          # Get the parameters.
555          my ($self) = @_;          my ($self) = @_;
556          my $metadata = $self->{_metaData};      # Get the relation names.
557          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
558          # Loop through the entities.      # Loop through the relations.
559          my $entityHash = $metadata->{Entities};      for my $relationName (@relNames) {
         for my $entityName (keys %{$entityHash}) {  
                 my $entityData = $entityHash->{$entityName};  
                 # Tell the user what we're doing.  
                 Trace("Creating relations for entity $entityName.") if T(1);  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entityData->{Relations}}) {  
560                          # Create a table for this relation.                          # Create a table for this relation.
561                          $self->CreateTable($relationName);                          $self->CreateTable($relationName);
562                          Trace("Relation $relationName created.") if T(1);          Trace("Relation $relationName created.") if T(2);
                 }  
         }  
         # Loop through the relationships.  
         my $relationshipTable = $metadata->{Relationships};  
         for my $relationshipName (keys %{$metadata->{Relationships}}) {  
                 # Create a table for this relationship.  
                 Trace("Creating relationship $relationshipName.") if T(1);  
                 $self->CreateTable($relationshipName);  
563          }          }
564  }  }
565    
566  =head3 CreateTable  =head3 CreateTable
567    
568  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
569    
570  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
571    
# Line 363  Line 575 
575    
576  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
577    
578  =item $indexFlag  =item indexFlag
579    
580  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
581  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
582    
583    =item estimatedRows (optional)
584    
585    If specified, the estimated maximum number of rows for the relation. This
586    information allows the creation of tables using storage engines that are
587    faster but require size estimates, such as MyISAM.
588    
589  =back  =back
590    
591  =cut  =cut
592    
593  sub CreateTable {  sub CreateTable {
594          # Get the parameters.          # Get the parameters.
595          my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
596          # Get the database handle.          # Get the database handle.
597          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
598          # Get the relation data and determine whether or not the relation is primary.          # Get the relation data and determine whether or not the relation is primary.
# Line 398  Line 616 
616          # Insure the table is not already there.          # Insure the table is not already there.
617          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
618          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
619        # If there are estimated rows, create an estimate so we can take advantage of
620        # faster DB technologies.
621        my $estimation = undef;
622        if ($estimatedRows) {
623            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
624        }
625          # Create the table.          # Create the table.
626          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
627          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
628          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
629          # If we want to build the indexes, we do it here.          # If we want to build the indexes, we do it here.
630          if ($indexFlag) {          if ($indexFlag) {
# Line 408  Line 632 
632          }          }
633  }  }
634    
635    =head3 VerifyFields
636    
637    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
638    
639    Run through the list of proposed field values, insuring that all the character fields are
640    below the maximum length. If any fields are too long, they will be truncated in place.
641    
642    =over 4
643    
644    =item relName
645    
646    Name of the relation for which the specified fields are destined.
647    
648    =item fieldList
649    
650    Reference to a list, in order, of the fields to be put into the relation.
651    
652    =item RETURN
653    
654    Returns the number of fields truncated.
655    
656    =back
657    
658    =cut
659    
660    sub VerifyFields {
661        # Get the parameters.
662        my ($self, $relName, $fieldList) = @_;
663        # Initialize the return value.
664        my $retVal = 0;
665        # Get the relation definition.
666        my $relData = $self->_FindRelation($relName);
667        # Get the list of field descriptors.
668        my $fieldTypes = $relData->{Fields};
669        my $fieldCount = scalar @{$fieldTypes};
670        # Loop through the two lists.
671        for (my $i = 0; $i < $fieldCount; $i++) {
672            # Get the type of the current field.
673            my $fieldType = $fieldTypes->[$i]->{type};
674            # If it's a character field, verify the length.
675            if ($fieldType =~ /string/) {
676                my $maxLen = $TypeTable{$fieldType}->{maxLen};
677                my $oldString = $fieldList->[$i];
678                if (length($oldString) > $maxLen) {
679                    # Here it's too big, so we truncate it.
680                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
681                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
682                    $retVal++;
683                }
684            }
685        }
686        # Return the truncation count.
687        return $retVal;
688    }
689    
690  =head3 CreateIndex  =head3 CreateIndex
691    
692  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
693    
694  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
695  is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
696  the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  If that is the case, then L</CreateTable> should be called with the index flag set to
697  method used after the load to create the indexes for the table.  FALSE, and this method used after the load to create the indexes for the table.
698    
699  =cut  =cut
700    
# Line 436  Line 715 
715                  # Get the index's uniqueness flag.                  # Get the index's uniqueness flag.
716                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
717                  # Create the index.                  # Create the index.
718                  $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
719                                        flds => $flds, unique => $unique);
720            if ($rv) {
721                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);
722            } else {
723                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
724            }
725          }          }
726  }  }
727    
728  =head3 LoadTables  =head3 LoadTables
729    
730  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
731    
732  This method will load the database tables from a directory. The tables must already have been created  This method will load the database tables from a directory. The tables must already have been created
733  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
# Line 486  Line 770 
770          $directoryName =~ s!/\\$!!;          $directoryName =~ s!/\\$!!;
771          # Declare the return variable.          # Declare the return variable.
772          my $retVal = Stats->new();          my $retVal = Stats->new();
773          # Get the metadata structure.      # Get the relation names.
774          my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
775          # Loop through the entities.      for my $relationName (@relNames) {
         for my $entity (values %{$metaData->{Entities}}) {  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entity->{Relations}}) {  
776                          # Try to load this relation.                          # Try to load this relation.
777                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
778                          # Accumulate the statistics.                          # Accumulate the statistics.
779                          $retVal->Accumulate($result);                          $retVal->Accumulate($result);
780                  }                  }
         }  
         # Loop through the relationships.  
         for my $relationshipName (keys %{$metaData->{Relationships}}) {  
                 # Try to load this relationship's relation.  
                 my $result = $self->_LoadRelation($directoryName, $relationshipName, $rebuild);  
                 # Accumulate the statistics.  
                 $retVal->Accumulate($result);  
         }  
781          # Add the duration of the load to the statistical object.          # Add the duration of the load to the statistical object.
782          $retVal->Add('duration', gettimeofday - $startTime);          $retVal->Add('duration', gettimeofday - $startTime);
783          # Return the accumulated statistics.          # Return the accumulated statistics.
784          return $retVal;          return $retVal;
785  }  }
786    
787    
788  =head3 GetTableNames  =head3 GetTableNames
789    
790  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
791    
792  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
793    
# Line 530  Line 804 
804    
805  =head3 GetEntityTypes  =head3 GetEntityTypes
806    
807  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
808    
809  Return a list of the entity type names.  Return a list of the entity type names.
810    
# Line 545  Line 819 
819          return sort keys %{$entityList};          return sort keys %{$entityList};
820  }  }
821    
822    =head3 IsEntity
823    
824    C<< my $flag = $erdb->IsEntity($entityName); >>
825    
826    Return TRUE if the parameter is an entity name, else FALSE.
827    
828    =over 4
829    
830    =item entityName
831    
832    Object name to be tested.
833    
834    =item RETURN
835    
836    Returns TRUE if the specified string is an entity name, else FALSE.
837    
838    =back
839    
840    =cut
841    
842    sub IsEntity {
843        # Get the parameters.
844        my ($self, $entityName) = @_;
845        # Test to see if it's an entity.
846        return exists $self->{_metaData}->{Entities}->{$entityName};
847    }
848    
849  =head3 Get  =head3 Get
850    
851  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
852    
853  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
854  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 555  Line 856 
856  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
857  $genus.  $genus.
858    
859  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>
860    
861  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
862  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
863    
864  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
865    
866  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
867  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 572  Line 873 
873  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
874  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
875    
876  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>
877    
878  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
879  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
# Line 605  Line 906 
906    
907  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
908    
909    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
910    be processed. The idea is to make it less likely to find the verb by accident.
911    
912  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
913  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
914  relation.  relation.
# Line 713  Line 1017 
1017                                  $lastObject = $thisObject;                                  $lastObject = $thisObject;
1018                          }                          }
1019                  }                  }
1020                  # Now we need to handle the whole ORDER BY thing. We'll put the order by clause          # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
1021                  # in the following variable.          # here is we want the filter clause to be empty if there's no WHERE filter.
1022            # We'll put the ORDER BY / LIMIT clauses in the following variable.
1023                  my $orderClause = "";                  my $orderClause = "";
1024                  # Locate the ORDER BY verb (if any).          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
1025                  if ($filterString =~ m/^(.*)ORDER BY/g) {          # operator so that we find the first occurrence of either verb.
1026                          # Here we have an ORDER BY verb. Split it off of the filter string.          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
1027                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
1028                          my $pos = pos $filterString;                          my $pos = pos $filterString;
1029                          $orderClause = substr($filterString, $pos);              $orderClause = $2 . substr($filterString, $pos);
1030                          $filterString = $1;                          $filterString = $1;
1031                  }                  }
1032                  # Add the filter and the join clauses (if any) to the SELECT command.                  # Add the filter and the join clauses (if any) to the SELECT command.
# Line 730  Line 1036 
1036                  if (@joinWhere) {                  if (@joinWhere) {
1037                          $command .= " WHERE " . join(' AND ', @joinWhere);                          $command .= " WHERE " . join(' AND ', @joinWhere);
1038                  }                  }
1039                  # Add the sort clause (if any) to the SELECT command.          # Add the sort or limit clause (if any) to the SELECT command.
1040                  if ($orderClause) {                  if ($orderClause) {
1041                          $command .= " ORDER BY $orderClause";              $command .= " $orderClause";
1042                  }                  }
1043          }          }
1044          Trace("SQL query: $command") if T(2);      Trace("SQL query: $command") if T(SQL => 4);
1045          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));
1046          my $sth = $dbh->prepare_command($command);          my $sth = $dbh->prepare_command($command);
1047          # Execute it with the parameters bound in.          # Execute it with the parameters bound in.
1048          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());
# Line 745  Line 1051 
1051          return $retVal;          return $retVal;
1052  }  }
1053    
1054    =head3 Delete
1055    
1056    C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1057    
1058    Delete an entity instance from the database. The instance is deleted along with all entity and
1059    relationship instances dependent on it. The idea of dependence here is recursive. An object is
1060    always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1061    relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1062    dependent relationship.
1063    
1064    =over 4
1065    
1066    =item entityName
1067    
1068    Name of the entity type for the instance being deleted.
1069    
1070    =item objectID
1071    
1072    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1073    then it is presumed to by a LIKE pattern.
1074    
1075    =item testFlag
1076    
1077    If TRUE, the delete statements will be traced without being executed.
1078    
1079    =item RETURN
1080    
1081    Returns a statistics object indicating how many records of each particular table were
1082    deleted.
1083    
1084    =back
1085    
1086    =cut
1087    #: Return Type $%;
1088    sub Delete {
1089        # Get the parameters.
1090        my ($self, $entityName, $objectID, $testFlag) = @_;
1091        # Declare the return variable.
1092        my $retVal = Stats->new();
1093        # Get the DBKernel object.
1094        my $db = $self->{_dbh};
1095        # We're going to generate all the paths branching out from the starting entity. One of
1096        # the things we have to be careful about is preventing loops. We'll use a hash to
1097        # determine if we've hit a loop.
1098        my %alreadyFound = ();
1099        # This next list will serve as our result stack. We start by pushing object lists onto
1100        # the stack, and then popping them off to do the deletes. This means the deletes will
1101        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1102        # sure we don't delete records that might be needed to forge relationships back to the
1103        # original item.
1104        my @pathList = ();
1105        # This final hash is used to remember what work still needs to be done. We push paths
1106        # onto the list, then pop them off to extend the paths. We prime it with the starting
1107        # point. Note that we will work hard to insure that the last item on a path in the
1108        # TODO list is always an entity.
1109        my @todoList = ([$entityName]);
1110        while (@todoList) {
1111            # Get the current path.
1112            my $current = pop @todoList;
1113            # Copy it into a list.
1114            my @stackedPath = @{$current};
1115            # Pull off the last item on the path. It will always be an entity.
1116            my $entityName = pop @stackedPath;
1117            # Add it to the alreadyFound list.
1118            $alreadyFound{$entityName} = 1;
1119            # Get the entity data.
1120            my $entityData = $self->_GetStructure($entityName);
1121            # The first task is to loop through the entity's relation. A DELETE command will
1122            # be needed for each of them.
1123            my $relations = $entityData->{Relations};
1124            for my $relation (keys %{$relations}) {
1125                my @augmentedList = (@stackedPath, $relation);
1126                push @pathList, \@augmentedList;
1127            }
1128            # Now we need to look for relationships connected to this entity.
1129            my $relationshipList = $self->{_metaData}->{Relationships};
1130            for my $relationshipName (keys %{$relationshipList}) {
1131                my $relationship = $relationshipList->{$relationshipName};
1132                # Check the FROM field. We're only interested if it's us.
1133                if ($relationship->{from} eq $entityName) {
1134                    # Add the path to this relationship.
1135                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1136                    push @pathList, \@augmentedList;
1137                    # Check the arity. If it's MM we're done. If it's 1M
1138                    # and the target hasn't been seen yet, we want to
1139                    # stack the entity for future processing.
1140                    if ($relationship->{arity} eq '1M') {
1141                        my $toEntity = $relationship->{to};
1142                        if (! exists $alreadyFound{$toEntity}) {
1143                            # Here we have a new entity that's dependent on
1144                            # the current entity, so we need to stack it.
1145                            my @stackList = (@augmentedList, $toEntity);
1146                            push @pathList, \@stackList;
1147                        }
1148                    }
1149                }
1150                # Now check the TO field. In this case only the relationship needs
1151                # deletion.
1152                if ($relationship->{to} eq $entityName) {
1153                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1154                    push @pathList, \@augmentedList;
1155                }
1156            }
1157        }
1158        # Create the first qualifier for the WHERE clause. This selects the
1159        # keys of the primary entity records to be deleted. When we're deleting
1160        # from a dependent table, we construct a join page from the first qualifier
1161        # to the table containing the dependent records to delete.
1162        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1163        # Now it's time to do the deletes. We simply pop the paths off the stack.
1164        while (my $path = pop @pathList) {
1165            # Get the table whose rows are to be deleted.
1166            my @pathTables = @{$path};
1167            # Start the DELETE statement.
1168            my $target = $pathTables[$#pathTables];
1169            my $stmt = "DELETE FROM $target";
1170            # If there's more than just the one table, we need a USING clause.
1171            if (@pathTables > 1) {
1172                $stmt .= " USING " . join(", ", @pathTables[0 .. ($#pathTables - 1)]);
1173            }
1174            # Now start the WHERE. The first thing is the ID field from the starting table. That
1175            # starting table will either be the entity relation or one of the entity's
1176            # sub-relations.
1177            $stmt .= " WHERE $pathTables[0].id $qualifier";
1178            # Now we run through the remaining entities in the path, connecting them up.
1179            for (my $i = 1; $i <= $#pathTables; $i += 2) {
1180                # Connect the current relationship to the preceding entity.
1181                my ($entity, $rel) = @pathTables[$i-1,$i];
1182                # The style of connection depends on the direction of the relationship.
1183                # We compute the direction by checking whether the preceding entity is
1184                # the FROM or TO entity.
1185                my $relationship = $self->_GetStructure($rel);
1186                if ($relationship->{to} eq $entity) {
1187                    # Here we're the TO. A TO link is always the end of a chain, so
1188                    # we just tack it on at the end.
1189                    $stmt .= " AND $entity.id = $rel.to_link";
1190                } else {
1191                    # Here we're the FROM. In that case, we'll need to check for a
1192                    # next entity.
1193                    $stmt .= " AND $entity.id = $rel.from_link";
1194                    if ($i + 1 <= $#pathTables) {
1195                        # Here there's a next entity, so connect that to the relationship's
1196                        # to-link.
1197                        my $entity2 = $pathTables[$i+1];
1198                        $stmt .= " AND $rel.to_link = $entity2.id";
1199                    }
1200                }
1201            }
1202            # Now we have our desired DELETE statement.
1203            if ($testFlag) {
1204                # Here the user wants to trace without executing.
1205                Trace($stmt) if T(0);
1206            } else {
1207                # Here we can delete. Note that the SQL method dies with a confessing
1208                # if an error occurs, so we just go ahead and do it.
1209                Trace("Executing delete: $stmt") if T(3);
1210                my $rv = $db->SQL($stmt, 0, [$objectID]);
1211                # Accumulate the statistics for this delete. The only rows deleted
1212                # are from the target table, so we use its name to record the
1213                # statistic.
1214                $retVal->Add($target, $rv);
1215            }
1216        }
1217        # Return the result.
1218        return $retVal;
1219    }
1220    
1221  =head3 GetList  =head3 GetList
1222    
1223  C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
1224    
1225  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
1226  specified filter clause.  specified filter clause.
1227    
1228  This method is essentially the same as L</Get> except it returns a list of objects rather  This method is essentially the same as L</Get> except it returns a list of objects rather
1229  that a query object that can be used to get the results one record at a time.  than a query object that can be used to get the results one record at a time.
   
 =over 4  
1230    
1231  =over 4  =over 4
1232    
# Line 812  Line 1283 
1283    
1284  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1285    
1286  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1287    
1288  Check an object name, and if it is a relationship convert it to a relationship sentence.  Check an object name, and if it is a relationship convert it to a relationship sentence.
1289    
# Line 847  Line 1318 
1318    
1319  =head3 DumpRelations  =head3 DumpRelations
1320    
1321  C<< $database->DumpRelations($outputDirectory); >>  C<< $erdb->DumpRelations($outputDirectory); >>
1322    
1323  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
1324  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 889  Line 1360 
1360    
1361  =head3 InsertObject  =head3 InsertObject
1362    
1363  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1364    
1365  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
1366  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 898  Line 1369 
1369  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
1370  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
1371    
1372  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
1373    
1374  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
1375  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
1376    
1377  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1378    
1379  =over 4  =over 4
1380    
# Line 1028  Line 1499 
1499    
1500  =head3 LoadTable  =head3 LoadTable
1501    
1502  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
1503    
1504  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  Load data from a tab-delimited file into a specified table, optionally re-creating the table
1505    first.
1506    
1507  =over 4  =over 4
1508    
# Line 1048  Line 1520 
1520    
1521  =item RETURN  =item RETURN
1522    
1523  Returns a statistical object containing the number of records read and a list of the error messages.  Returns a statistical object containing a list of the error messages.
1524    
1525  =back  =back
1526    
# Line 1059  Line 1531 
1531          # Create the statistical return object.          # Create the statistical return object.
1532          my $retVal = _GetLoadStats();          my $retVal = _GetLoadStats();
1533          # Trace the fact of the load.          # Trace the fact of the load.
1534          Trace("Loading table $relationName from $fileName") if T(1);      Trace("Loading table $relationName from $fileName") if T(2);
1535          # Get the database handle.          # Get the database handle.
1536          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
1537        # Get the input file size.
1538        my $fileSize = -s $fileName;
1539          # Get the relation data.          # Get the relation data.
1540          my $relation = $self->_FindRelation($relationName);          my $relation = $self->_FindRelation($relationName);
1541          # Check the truncation flag.          # Check the truncation flag.
1542          if ($truncateFlag) {          if ($truncateFlag) {
1543                  Trace("Creating table $relationName") if T(1);          Trace("Creating table $relationName") if T(2);
1544            # Compute the row count estimate. We take the size of the load file,
1545            # divide it by the estimated row size, and then multiply by 1.5 to
1546            # leave extra room. We postulate a minimum row count of 1000 to
1547            # prevent problems with incoming empty load files.
1548            my $rowSize = $self->EstimateRowSize($relationName);
1549            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
1550                  # Re-create the table without its index.                  # Re-create the table without its index.
1551                  $self->CreateTable($relationName, 0);          $self->CreateTable($relationName, 0, $estimate);
1552            # If this is a pre-index DBMS, create the index here.
1553            if ($dbh->{_preIndex}) {
1554                eval {
1555                    $self->CreateIndex($relationName);
1556                };
1557                if ($@) {
1558                    $retVal->AddMessage($@);
1559                }
1560            }
1561          }          }
         # Determine whether or not this is a primary relation. Primary relations have an extra  
         # field indicating whether or not a given object is new or was loaded from the flat files.  
         my $primary = $self->_IsPrimary($relationName);  
         # Get the number of fields in this relation.  
         my @fieldList = @{$relation->{Fields}};  
         my $fieldCount = @fieldList;  
         # Record the number of expected fields.  
         my $expectedFields = $fieldCount + ($primary ? 1 : 0);  
         # Start a database transaction.  
         $dbh->begin_tran;  
         # Open the relation file. We need to create a cleaned-up copy before loading.  
         open TABLEIN, '<', $fileName;  
         my $tempName = "$fileName.tbl";  
         open TABLEOUT, '>', $tempName;  
         # Loop through the file.  
         while (<TABLEIN>) {  
                 # Chop off the new-line character.  
                 my $record = $_;  
                 chomp $record;  
         # Only proceed if the record is non-blank.  
         if ($record) {  
             # Escape all the backslashes found in the line.  
             $record =~ s/\\/\\\\/g;  
             # Eliminate any trailing tabs.  
             chop $record while substr($record, -1) eq "\t";  
             # If this is a primary relation, add a 0 for the new-record flag (indicating that  
             # this record is not new, but part of the original load).  
             if ($primary) {  
                 $record .= "\t0";  
             }  
             # Write the record.  
             print TABLEOUT "$record\n";  
             # Count the record read.  
             my $count = $retVal->Add('records');  
             my $len = length $record;  
             Trace("Record $count written with $len characters.") if T(4);  
         }  
         }  
         # Close the files.  
         close TABLEIN;  
         close TABLEOUT;  
     Trace("Temporary file $tempName created.") if T(4);  
1562      # Load the table.      # Load the table.
1563          my $rv;          my $rv;
1564          eval {          eval {
1565                  $rv = $dbh->load_table(file => $tempName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
1566          };          };
1567          if (!defined $rv) {          if (!defined $rv) {
1568          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
1569          $retVal->AddMessage("Table load failed for $relationName using $tempName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName.");
1570                  Trace("Table load failed for $relationName.") if T(1);                  Trace("Table load failed for $relationName.") if T(1);
1571          } else {          } else {
1572                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we successfully loaded the table.
1573                  Trace("$retVal->{records} records read for $relationName.") if T(1);          $retVal->Add("tables");
1574            my $size = -s $fileName;
1575            Trace("$size bytes loaded into $relationName.") if T(2);
1576                  # If we're rebuilding, we need to create the table indexes.                  # If we're rebuilding, we need to create the table indexes.
1577                  if ($truncateFlag) {          if ($truncateFlag && ! $dbh->{_preIndex}) {
1578                          eval {                          eval {
1579                                  $self->CreateIndex($relationName);                                  $self->CreateIndex($relationName);
1580                          };                          };
# Line 1134  Line 1583 
1583                          }                          }
1584                  }                  }
1585          }          }
1586          # Commit the database changes.      # Analyze the table to improve performance.
1587          $dbh->commit_tran;      $dbh->vacuum_it($relationName);
         # Delete the temporary file.  
         unlink $tempName;  
1588          # Return the statistics.          # Return the statistics.
1589          return $retVal;          return $retVal;
1590  }  }
1591    
1592  =head3 GenerateEntity  =head3 GenerateEntity
1593    
1594  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
1595    
1596  Generate the data for a new entity instance. This method creates a field hash suitable for  Generate the data for a new entity instance. This method creates a field hash suitable for
1597  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest
# Line 1202  Line 1649 
1649    
1650  =head3 GetEntity  =head3 GetEntity
1651    
1652  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
1653    
1654  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
1655    
# Line 1238  Line 1685 
1685    
1686  =head3 GetEntityValues  =head3 GetEntityValues
1687    
1688  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1689    
1690  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance.
1691    
# Line 1279  Line 1726 
1726          return @retVal;          return @retVal;
1727  }  }
1728    
1729    =head3 GetAll
1730    
1731    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
1732    
1733    Return a list of values taken from the objects returned by a query. The first three
1734    parameters correspond to the parameters of the L</Get> method. The final parameter is
1735    a list of the fields desired from each record found by the query. The field name
1736    syntax is the standard syntax used for fields in the B<ERDB> system--
1737    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
1738    or relationship and I<fieldName> is the name of the field.
1739    
1740    The list returned will be a list of lists. Each element of the list will contain
1741    the values returned for the fields specified in the fourth parameter. If one of the
1742    fields specified returns multiple values, they are flattened in with the rest. For
1743    example, the following call will return a list of the features in a particular
1744    spreadsheet cell, and each feature will be represented by a list containing the
1745    feature ID followed by all of its aliases.
1746    
1747    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
1748    
1749    =over 4
1750    
1751    =item objectNames
1752    
1753    List containing the names of the entity and relationship objects to be retrieved.
1754    
1755    =item filterClause
1756    
1757    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1758    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1759    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1760    parameter list as additional parameters. The fields in a filter clause can come from primary
1761    entity relations, relationship relations, or secondary entity relations; however, all of the
1762    entities and relationships involved must be included in the list of object names.
1763    
1764    =item parameterList
1765    
1766    List of the parameters to be substituted in for the parameters marks in the filter clause.
1767    
1768    =item fields
1769    
1770    List of the fields to be returned in each element of the list returned.
1771    
1772    =item count
1773    
1774    Maximum number of records to return. If omitted or 0, all available records will be returned.
1775    
1776    =item RETURN
1777    
1778    Returns a list of list references. Each element of the return list contains the values for the
1779    fields specified in the B<fields> parameter.
1780    
1781    =back
1782    
1783    =cut
1784    #: Return Type @@;
1785    sub GetAll {
1786        # Get the parameters.
1787        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
1788        # Translate the parameters from a list reference to a list. If the parameter
1789        # list is a scalar we convert it into a singleton list.
1790        my @parmList = ();
1791        if (ref $parameterList eq "ARRAY") {
1792            @parmList = @{$parameterList};
1793        } else {
1794            push @parmList, $parameterList;
1795        }
1796        # Insure the counter has a value.
1797        if (!defined $count) {
1798            $count = 0;
1799        }
1800        # Add the row limit to the filter clause.
1801        if ($count > 0) {
1802            $filterClause .= " LIMIT $count";
1803        }
1804        # Create the query.
1805        my $query = $self->Get($objectNames, $filterClause, @parmList);
1806        # Set up a counter of the number of records read.
1807        my $fetched = 0;
1808        # Loop through the records returned, extracting the fields. Note that if the
1809        # counter is non-zero, we stop when the number of records read hits the count.
1810        my @retVal = ();
1811        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
1812            my @rowData = $row->Values($fields);
1813            push @retVal, \@rowData;
1814            $fetched++;
1815        }
1816        # Return the resulting list.
1817        return @retVal;
1818    }
1819    
1820    =head3 EstimateRowSize
1821    
1822    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
1823    
1824    Estimate the row size of the specified relation. The estimated row size is computed by adding
1825    up the average length for each data type.
1826    
1827    =over 4
1828    
1829    =item relName
1830    
1831    Name of the relation whose estimated row size is desired.
1832    
1833    =item RETURN
1834    
1835    Returns an estimate of the row size for the specified relation.
1836    
1837    =back
1838    
1839    =cut
1840    #: Return Type $;
1841    sub EstimateRowSize {
1842        # Get the parameters.
1843        my ($self, $relName) = @_;
1844        # Declare the return variable.
1845        my $retVal = 0;
1846        # Find the relation descriptor.
1847        my $relation = $self->_FindRelation($relName);
1848        # Get the list of fields.
1849        for my $fieldData (@{$relation->{Fields}}) {
1850            # Get the field type and add its length.
1851            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
1852            $retVal += $fieldLen;
1853        }
1854        # Return the result.
1855        return $retVal;
1856    }
1857    
1858  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1859    
1860  =head3 GetLoadStats  =head3 GetLoadStats
# Line 1290  Line 1866 
1866  =cut  =cut
1867    
1868  sub _GetLoadStats {  sub _GetLoadStats {
1869          return Stats->new('records');      return Stats->new();
1870  }  }
1871    
1872  =head3 GenerateFields  =head3 GenerateFields
# Line 1654  Line 2230 
2230  sub _LoadMetaData {  sub _LoadMetaData {
2231          # Get the parameters.          # Get the parameters.
2232          my ($filename) = @_;          my ($filename) = @_;
2233        Trace("Reading Sprout DBD from $filename.") if T(2);
2234          # Slurp the XML file into a variable. Extensive use of options is used to insure we          # Slurp the XML file into a variable. Extensive use of options is used to insure we
2235          # get the exact structure we want.          # get the exact structure we want.
2236          my $metadata = XML::Simple::XMLin($filename,          my $metadata = XML::Simple::XMLin($filename,
# Line 1681  Line 2258 
2258          for my $entityName (keys %{$entityList}) {          for my $entityName (keys %{$entityList}) {
2259                  my $entityStructure = $entityList->{$entityName};                  my $entityStructure = $entityList->{$entityName};
2260                  #                  #
2261                  # The first step is to run creating all the entity's default values. For C<Field> elements,          # The first step is to create all the entity's default values. For C<Field> elements,
2262                  # the relation name must be added where it is not specified. For relationships,                  # the relation name must be added where it is not specified. For relationships,
2263                  # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>                  # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
2264                  # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute                  # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
# Line 1860  Line 2437 
2437                  my @fromList = ();                  my @fromList = ();
2438                  my @toList = ();                  my @toList = ();
2439                  my @bothList = ();                  my @bothList = ();
2440                  Trace("Join table build for $entityName.") if T(3);          Trace("Join table build for $entityName.") if T(metadata => 4);
2441                  for my $relationshipName (keys %{$relationshipList}) {                  for my $relationshipName (keys %{$relationshipList}) {
2442                          my $relationship = $relationshipList->{$relationshipName};                          my $relationship = $relationshipList->{$relationshipName};
2443                          # Determine if this relationship has our entity in one of its link fields.                          # Determine if this relationship has our entity in one of its link fields.
2444                          my $fromEntity = $relationship->{from};                          my $fromEntity = $relationship->{from};
2445                          my $toEntity = $relationship->{to};                          my $toEntity = $relationship->{to};
2446                          Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(3);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);
2447                          if ($fromEntity eq $entityName) {                          if ($fromEntity eq $entityName) {
2448                                  if ($toEntity eq $entityName) {                                  if ($toEntity eq $entityName) {
2449                                          # Here the relationship is recursive.                                          # Here the relationship is recursive.
2450                                          push @bothList, $relationshipName;                                          push @bothList, $relationshipName;
2451                                          Trace("Relationship $relationshipName put in both-list.") if T(3);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
2452                                  } else {                                  } else {
2453                                          # Here the relationship comes from the entity.                                          # Here the relationship comes from the entity.
2454                                          push @fromList, $relationshipName;                                          push @fromList, $relationshipName;
2455                                          Trace("Relationship $relationshipName put in from-list.") if T(3);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
2456                                  }                                  }
2457                          } elsif ($toEntity eq $entityName) {                          } elsif ($toEntity eq $entityName) {
2458                                  # Here the relationship goes to the entity.                                  # Here the relationship goes to the entity.
2459                                  push @toList, $relationshipName;                                  push @toList, $relationshipName;
2460                                  Trace("Relationship $relationshipName put in to-list.") if T(3);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
2461                          }                          }
2462                  }                  }
2463                  # Create the nonrecursive joins. Note that we build two hashes for running                  # Create the nonrecursive joins. Note that we build two hashes for running
# Line 1896  Line 2473 
2473                                  # Create joins between the entity and this relationship.                                  # Create joins between the entity and this relationship.
2474                                  my $linkField = "$relationshipName.${linkType}_link";                                  my $linkField = "$relationshipName.${linkType}_link";
2475                                  my $joinClause = "$entityName.id = $linkField";                                  my $joinClause = "$entityName.id = $linkField";
2476                                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(4);                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
2477                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
2478                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
2479                                  # Create joins between this relationship and the other relationships.                                  # Create joins between this relationship and the other relationships.
# Line 1917  Line 2494 
2494                                                          # relationship and itself are prohibited.                                                          # relationship and itself are prohibited.
2495                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";
2496                                                          $joinTable{$joinKey} = $relJoinClause;                                                          $joinTable{$joinKey} = $relJoinClause;
2497                                                          Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
2498                                                  }                                                  }
2499                                          }                                          }
2500                                  }                                  }
# Line 1926  Line 2503 
2503                                  # relationship can only be ambiguous with another recursive relationship,                                  # relationship can only be ambiguous with another recursive relationship,
2504                                  # and the incoming relationship from the outer loop is never recursive.                                  # and the incoming relationship from the outer loop is never recursive.
2505                                  for my $otherName (@bothList) {                                  for my $otherName (@bothList) {
2506                                          Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(3);                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
2507                                          # Join from the left.                                          # Join from the left.
2508                                          $joinTable{"$relationshipName/$otherName"} =                                          $joinTable{"$relationshipName/$otherName"} =
2509                                                  "$linkField = $otherName.from_link";                                                  "$linkField = $otherName.from_link";
# Line 1941  Line 2518 
2518                  # rise to situations where we can't create the path we want; however, it is always                  # rise to situations where we can't create the path we want; however, it is always
2519                  # possible to get the same effect using multiple queries.                  # possible to get the same effect using multiple queries.
2520                  for my $relationshipName (@bothList) {                  for my $relationshipName (@bothList) {
2521                          Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(3);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
2522                          # Join to the entity from each direction.                          # Join to the entity from each direction.
2523                          $joinTable{"$entityName/$relationshipName"} =                          $joinTable{"$entityName/$relationshipName"} =
2524                                  "$entityName.id = $relationshipName.from_link";                                  "$entityName.id = $relationshipName.from_link";
# Line 1992  Line 2569 
2569          # index descriptor does not exist, it will be created automatically so we can add          # index descriptor does not exist, it will be created automatically so we can add
2570          # the field to it.          # the field to it.
2571          unshift @{$newIndex->{IndexFields}}, $firstField;          unshift @{$newIndex->{IndexFields}}, $firstField;
2572        # If this is a one-to-many relationship, the "To" index is unique.
2573        if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
2574            $newIndex->{Unique} = 'true';
2575        }
2576          # Add the index to the relation.          # Add the index to the relation.
2577          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
2578  }  }
# Line 2083  Line 2664 
2664                  # Here we have a field list. Loop through its fields.                  # Here we have a field list. Loop through its fields.
2665                  my $fieldStructures = $structure->{Fields};                  my $fieldStructures = $structure->{Fields};
2666                  for my $fieldName (keys %{$fieldStructures}) {                  for my $fieldName (keys %{$fieldStructures}) {
2667                Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
2668                          my $fieldData = $fieldStructures->{$fieldName};                          my $fieldData = $fieldStructures->{$fieldName};
2669                          # Get the field type.                          # Get the field type.
2670                          my $type = $fieldData->{type};                          my $type = $fieldData->{type};

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