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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.29, Fri Jan 6 20:34:19 2006 UTC
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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 =>   2, 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 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 410  Line 634 
634    
635  =head3 CreateIndex  =head3 CreateIndex
636    
637  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
638    
639  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
640  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.
641  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
642  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.
643    
644  =cut  =cut
645    
# Line 436  Line 660 
660                  # Get the index's uniqueness flag.                  # Get the index's uniqueness flag.
661                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
662                  # Create the index.                  # Create the index.
663                  $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
664                                        flds => $flds, unique => $unique);
665            if ($rv) {
666                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);
667            } else {
668                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
669            }
670          }          }
671  }  }
672    
673  =head3 LoadTables  =head3 LoadTables
674    
675  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
676    
677  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
678  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 715 
715          $directoryName =~ s!/\\$!!;          $directoryName =~ s!/\\$!!;
716          # Declare the return variable.          # Declare the return variable.
717          my $retVal = Stats->new();          my $retVal = Stats->new();
718          # Get the metadata structure.      # Get the relation names.
719          my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
720          # 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}}) {  
721                          # Try to load this relation.                          # Try to load this relation.
722                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
723                          # Accumulate the statistics.                          # Accumulate the statistics.
724                          $retVal->Accumulate($result);                          $retVal->Accumulate($result);
725                  }                  }
         }  
         # 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);  
         }  
726          # Add the duration of the load to the statistical object.          # Add the duration of the load to the statistical object.
727          $retVal->Add('duration', gettimeofday - $startTime);          $retVal->Add('duration', gettimeofday - $startTime);
728          # Return the accumulated statistics.          # Return the accumulated statistics.
729          return $retVal;          return $retVal;
730  }  }
731    
732    
733  =head3 GetTableNames  =head3 GetTableNames
734    
735  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
736    
737  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
738    
# Line 530  Line 749 
749    
750  =head3 GetEntityTypes  =head3 GetEntityTypes
751    
752  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
753    
754  Return a list of the entity type names.  Return a list of the entity type names.
755    
# Line 545  Line 764 
764          return sort keys %{$entityList};          return sort keys %{$entityList};
765  }  }
766    
767    =head3 IsEntity
768    
769    C<< my $flag = $erdb->IsEntity($entityName); >>
770    
771    Return TRUE if the parameter is an entity name, else FALSE.
772    
773    =over 4
774    
775    =item entityName
776    
777    Object name to be tested.
778    
779    =item RETURN
780    
781    Returns TRUE if the specified string is an entity name, else FALSE.
782    
783    =back
784    
785    =cut
786    
787    sub IsEntity {
788        # Get the parameters.
789        my ($self, $entityName) = @_;
790        # Test to see if it's an entity.
791        return exists $self->{_metaData}->{Entities}->{$entityName};
792    }
793    
794  =head3 Get  =head3 Get
795    
796  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
797    
798  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.
799  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 801 
801  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
802  $genus.  $genus.
803    
804  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>
805    
806  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
807  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
808    
809  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
810    
811  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
812  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 572  Line 818 
818  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
819  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,
820    
821  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>
822    
823  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
824  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 735  Line 981 
981                          $command .= " ORDER BY $orderClause";                          $command .= " ORDER BY $orderClause";
982                  }                  }
983          }          }
984          Trace("SQL query: $command") if T(2);      Trace("SQL query: $command") if T(SQL => 4);
985          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));
986          my $sth = $dbh->prepare_command($command);          my $sth = $dbh->prepare_command($command);
987          # Execute it with the parameters bound in.          # Execute it with the parameters bound in.
988          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());
# Line 747  Line 993 
993    
994  =head3 GetList  =head3 GetList
995    
996  C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
997    
998  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
999  specified filter clause.  specified filter clause.
1000    
1001  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
1002  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  
1003    
1004  =over 4  =over 4
1005    
# Line 812  Line 1056 
1056    
1057  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1058    
1059  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1060    
1061  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.
1062    
# Line 847  Line 1091 
1091    
1092  =head3 DumpRelations  =head3 DumpRelations
1093    
1094  C<< $database->DumpRelations($outputDirectory); >>  C<< $erdb->DumpRelations($outputDirectory); >>
1095    
1096  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.
1097  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 1133 
1133    
1134  =head3 InsertObject  =head3 InsertObject
1135    
1136  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1137    
1138  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
1139  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 1142 
1142  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
1143  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
1144    
1145  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']}); >>
1146    
1147  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
1148  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>.
1149    
1150  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'}); >>
1151    
1152  =over 4  =over 4
1153    
# Line 1028  Line 1272 
1272    
1273  =head3 LoadTable  =head3 LoadTable
1274    
1275  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
1276    
1277  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
1278    first.
1279    
1280  =over 4  =over 4
1281    
# Line 1048  Line 1293 
1293    
1294  =item RETURN  =item RETURN
1295    
1296  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.
1297    
1298  =back  =back
1299    
# Line 1059  Line 1304 
1304          # Create the statistical return object.          # Create the statistical return object.
1305          my $retVal = _GetLoadStats();          my $retVal = _GetLoadStats();
1306          # Trace the fact of the load.          # Trace the fact of the load.
1307          Trace("Loading table $relationName from $fileName") if T(1);      Trace("Loading table $relationName from $fileName") if T(2);
1308          # Get the database handle.          # Get the database handle.
1309          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
1310        # Get the input file size.
1311        my $fileSize = -s $fileName;
1312          # Get the relation data.          # Get the relation data.
1313          my $relation = $self->_FindRelation($relationName);          my $relation = $self->_FindRelation($relationName);
1314          # Check the truncation flag.          # Check the truncation flag.
1315          if ($truncateFlag) {          if ($truncateFlag) {
1316                  Trace("Creating table $relationName") if T(1);          Trace("Creating table $relationName") if T(2);
1317            # Compute the row count estimate. We take the size of the load file,
1318            # divide it by the estimated row size, and then multiply by 1.5 to
1319            # leave extra room. We postulate a minimum row count of 1000 to
1320            # prevent problems with incoming empty load files.
1321            my $rowSize = $self->EstimateRowSize($relationName);
1322            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
1323                  # Re-create the table without its index.                  # Re-create the table without its index.
1324                  $self->CreateTable($relationName, 0);          $self->CreateTable($relationName, 0, $estimate);
1325            # If this is a pre-index DBMS, create the index here.
1326            if ($dbh->{_preIndex}) {
1327                eval {
1328                    $self->CreateIndex($relationName);
1329                };
1330                if ($@) {
1331                    $retVal->AddMessage($@);
1332                }
1333            }
1334          }          }
         # 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);  
1335      # Load the table.      # Load the table.
1336          my $rv;          my $rv;
1337          eval {          eval {
1338                  $rv = $dbh->load_table(file => $tempName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
1339          };          };
1340          if (!defined $rv) {          if (!defined $rv) {
1341          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
1342          $retVal->AddMessage("Table load failed for $relationName using $tempName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName.");
1343                  Trace("Table load failed for $relationName.") if T(1);                  Trace("Table load failed for $relationName.") if T(1);
1344          } else {          } else {
1345                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we successfully loaded the table.
1346                  Trace("$retVal->{records} records read for $relationName.") if T(1);          $retVal->Add("tables");
1347            my $size = -s $fileName;
1348            Trace("$size bytes loaded into $relationName.") if T(2);
1349                  # If we're rebuilding, we need to create the table indexes.                  # If we're rebuilding, we need to create the table indexes.
1350                  if ($truncateFlag) {          if ($truncateFlag && ! $dbh->{_preIndex}) {
1351                          eval {                          eval {
1352                                  $self->CreateIndex($relationName);                                  $self->CreateIndex($relationName);
1353                          };                          };
# Line 1134  Line 1356 
1356                          }                          }
1357                  }                  }
1358          }          }
1359          # Commit the database changes.      # Analyze the table to improve performance.
1360          $dbh->commit_tran;      $dbh->vacuum_it($relationName);
         # Delete the temporary file.  
         unlink $tempName;  
1361          # Return the statistics.          # Return the statistics.
1362          return $retVal;          return $retVal;
1363  }  }
1364    
1365  =head3 GenerateEntity  =head3 GenerateEntity
1366    
1367  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
1368    
1369  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
1370  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 1422 
1422    
1423  =head3 GetEntity  =head3 GetEntity
1424    
1425  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
1426    
1427  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
1428    
# Line 1238  Line 1458 
1458    
1459  =head3 GetEntityValues  =head3 GetEntityValues
1460    
1461  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1462    
1463  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance.
1464    
# Line 1279  Line 1499 
1499          return @retVal;          return @retVal;
1500  }  }
1501    
1502    =head3 GetAll
1503    
1504    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
1505    
1506    Return a list of values taken from the objects returned by a query. The first three
1507    parameters correspond to the parameters of the L</Get> method. The final parameter is
1508    a list of the fields desired from each record found by the query. The field name
1509    syntax is the standard syntax used for fields in the B<ERDB> system--
1510    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
1511    or relationship and I<fieldName> is the name of the field.
1512    
1513    The list returned will be a list of lists. Each element of the list will contain
1514    the values returned for the fields specified in the fourth parameter. If one of the
1515    fields specified returns multiple values, they are flattened in with the rest. For
1516    example, the following call will return a list of the features in a particular
1517    spreadsheet cell, and each feature will be represented by a list containing the
1518    feature ID followed by all of its aliases.
1519    
1520    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
1521    
1522    =over 4
1523    
1524    =item objectNames
1525    
1526    List containing the names of the entity and relationship objects to be retrieved.
1527    
1528    =item filterClause
1529    
1530    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1531    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1532    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1533    parameter list as additional parameters. The fields in a filter clause can come from primary
1534    entity relations, relationship relations, or secondary entity relations; however, all of the
1535    entities and relationships involved must be included in the list of object names.
1536    
1537    =item parameterList
1538    
1539    List of the parameters to be substituted in for the parameters marks in the filter clause.
1540    
1541    =item fields
1542    
1543    List of the fields to be returned in each element of the list returned.
1544    
1545    =item count
1546    
1547    Maximum number of records to return. If omitted or 0, all available records will be returned.
1548    
1549    =item RETURN
1550    
1551    Returns a list of list references. Each element of the return list contains the values for the
1552    fields specified in the B<fields> parameter.
1553    
1554    =back
1555    
1556    =cut
1557    #: Return Type @@;
1558    sub GetAll {
1559        # Get the parameters.
1560        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
1561        # Translate the parameters from a list reference to a list. If the parameter
1562        # list is a scalar we convert it into a singleton list.
1563        my @parmList = ();
1564        if (ref $parameterList eq "ARRAY") {
1565            @parmList = @{$parameterList};
1566        } else {
1567            push @parmList, $parameterList;
1568        }
1569        # Create the query.
1570        my $query = $self->Get($objectNames, $filterClause, @parmList);
1571        # Set up a counter of the number of records read.
1572        my $fetched = 0;
1573        # Insure the counter has a value.
1574        if (!defined $count) {
1575            $count = 0;
1576        }
1577        # Loop through the records returned, extracting the fields. Note that if the
1578        # counter is non-zero, we stop when the number of records read hits the count.
1579        my @retVal = ();
1580        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
1581            my @rowData = $row->Values($fields);
1582            push @retVal, \@rowData;
1583            $fetched++;
1584        }
1585        # Return the resulting list.
1586        return @retVal;
1587    }
1588    
1589    =head3 EstimateRowSize
1590    
1591    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
1592    
1593    Estimate the row size of the specified relation. The estimated row size is computed by adding
1594    up the average length for each data type.
1595    
1596    =over 4
1597    
1598    =item relName
1599    
1600    Name of the relation whose estimated row size is desired.
1601    
1602    =item RETURN
1603    
1604    Returns an estimate of the row size for the specified relation.
1605    
1606    =back
1607    
1608    =cut
1609    #: Return Type $;
1610    sub EstimateRowSize {
1611        # Get the parameters.
1612        my ($self, $relName) = @_;
1613        # Declare the return variable.
1614        my $retVal = 0;
1615        # Find the relation descriptor.
1616        my $relation = $self->_FindRelation($relName);
1617        # Get the list of fields.
1618        for my $fieldData (@{$relation->{Fields}}) {
1619            # Get the field type and add its length.
1620            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
1621            $retVal += $fieldLen;
1622        }
1623        # Return the result.
1624        return $retVal;
1625    }
1626    
1627  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1628    
1629  =head3 GetLoadStats  =head3 GetLoadStats
# Line 1290  Line 1635 
1635  =cut  =cut
1636    
1637  sub _GetLoadStats {  sub _GetLoadStats {
1638          return Stats->new('records');      return Stats->new();
1639  }  }
1640    
1641  =head3 GenerateFields  =head3 GenerateFields
# Line 1654  Line 1999 
1999  sub _LoadMetaData {  sub _LoadMetaData {
2000          # Get the parameters.          # Get the parameters.
2001          my ($filename) = @_;          my ($filename) = @_;
2002        Trace("Reading Sprout DBD from $filename.") if T(2);
2003          # 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
2004          # get the exact structure we want.          # get the exact structure we want.
2005          my $metadata = XML::Simple::XMLin($filename,          my $metadata = XML::Simple::XMLin($filename,
# Line 1681  Line 2027 
2027          for my $entityName (keys %{$entityList}) {          for my $entityName (keys %{$entityList}) {
2028                  my $entityStructure = $entityList->{$entityName};                  my $entityStructure = $entityList->{$entityName};
2029                  #                  #
2030                  # 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,
2031                  # 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,
2032                  # 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>
2033                  # 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 2206 
2206                  my @fromList = ();                  my @fromList = ();
2207                  my @toList = ();                  my @toList = ();
2208                  my @bothList = ();                  my @bothList = ();
2209                  Trace("Join table build for $entityName.") if T(3);          Trace("Join table build for $entityName.") if T(metadata => 4);
2210                  for my $relationshipName (keys %{$relationshipList}) {                  for my $relationshipName (keys %{$relationshipList}) {
2211                          my $relationship = $relationshipList->{$relationshipName};                          my $relationship = $relationshipList->{$relationshipName};
2212                          # 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.
2213                          my $fromEntity = $relationship->{from};                          my $fromEntity = $relationship->{from};
2214                          my $toEntity = $relationship->{to};                          my $toEntity = $relationship->{to};
2215                          Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(3);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);
2216                          if ($fromEntity eq $entityName) {                          if ($fromEntity eq $entityName) {
2217                                  if ($toEntity eq $entityName) {                                  if ($toEntity eq $entityName) {
2218                                          # Here the relationship is recursive.                                          # Here the relationship is recursive.
2219                                          push @bothList, $relationshipName;                                          push @bothList, $relationshipName;
2220                                          Trace("Relationship $relationshipName put in both-list.") if T(3);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
2221                                  } else {                                  } else {
2222                                          # Here the relationship comes from the entity.                                          # Here the relationship comes from the entity.
2223                                          push @fromList, $relationshipName;                                          push @fromList, $relationshipName;
2224                                          Trace("Relationship $relationshipName put in from-list.") if T(3);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
2225                                  }                                  }
2226                          } elsif ($toEntity eq $entityName) {                          } elsif ($toEntity eq $entityName) {
2227                                  # Here the relationship goes to the entity.                                  # Here the relationship goes to the entity.
2228                                  push @toList, $relationshipName;                                  push @toList, $relationshipName;
2229                                  Trace("Relationship $relationshipName put in to-list.") if T(3);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
2230                          }                          }
2231                  }                  }
2232                  # 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 2242 
2242                                  # Create joins between the entity and this relationship.                                  # Create joins between the entity and this relationship.
2243                                  my $linkField = "$relationshipName.${linkType}_link";                                  my $linkField = "$relationshipName.${linkType}_link";
2244                                  my $joinClause = "$entityName.id = $linkField";                                  my $joinClause = "$entityName.id = $linkField";
2245                                  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);
2246                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
2247                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
2248                                  # Create joins between this relationship and the other relationships.                                  # Create joins between this relationship and the other relationships.
# Line 1917  Line 2263 
2263                                                          # relationship and itself are prohibited.                                                          # relationship and itself are prohibited.
2264                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";
2265                                                          $joinTable{$joinKey} = $relJoinClause;                                                          $joinTable{$joinKey} = $relJoinClause;
2266                                                          Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
2267                                                  }                                                  }
2268                                          }                                          }
2269                                  }                                  }
# Line 1926  Line 2272 
2272                                  # relationship can only be ambiguous with another recursive relationship,                                  # relationship can only be ambiguous with another recursive relationship,
2273                                  # and the incoming relationship from the outer loop is never recursive.                                  # and the incoming relationship from the outer loop is never recursive.
2274                                  for my $otherName (@bothList) {                                  for my $otherName (@bothList) {
2275                                          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);
2276                                          # Join from the left.                                          # Join from the left.
2277                                          $joinTable{"$relationshipName/$otherName"} =                                          $joinTable{"$relationshipName/$otherName"} =
2278                                                  "$linkField = $otherName.from_link";                                                  "$linkField = $otherName.from_link";
# Line 1941  Line 2287 
2287                  # 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
2288                  # possible to get the same effect using multiple queries.                  # possible to get the same effect using multiple queries.
2289                  for my $relationshipName (@bothList) {                  for my $relationshipName (@bothList) {
2290                          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);
2291                          # Join to the entity from each direction.                          # Join to the entity from each direction.
2292                          $joinTable{"$entityName/$relationshipName"} =                          $joinTable{"$entityName/$relationshipName"} =
2293                                  "$entityName.id = $relationshipName.from_link";                                  "$entityName.id = $relationshipName.from_link";
# Line 1992  Line 2338 
2338          # index descriptor does not exist, it will be created automatically so we can add          # index descriptor does not exist, it will be created automatically so we can add
2339          # the field to it.          # the field to it.
2340          unshift @{$newIndex->{IndexFields}}, $firstField;          unshift @{$newIndex->{IndexFields}}, $firstField;
2341        # If this is a one-to-many relationship, the "To" index is unique.
2342        if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
2343            $newIndex->{Unique} = 'true';
2344        }
2345          # Add the index to the relation.          # Add the index to the relation.
2346          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
2347  }  }
# Line 2083  Line 2433 
2433                  # Here we have a field list. Loop through its fields.                  # Here we have a field list. Loop through its fields.
2434                  my $fieldStructures = $structure->{Fields};                  my $fieldStructures = $structure->{Fields};
2435                  for my $fieldName (keys %{$fieldStructures}) {                  for my $fieldName (keys %{$fieldStructures}) {
2436                Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
2437                          my $fieldData = $fieldStructures->{$fieldName};                          my $fieldData = $fieldStructures->{$fieldName};
2438                          # Get the field type.                          # Get the field type.
2439                          my $type = $fieldData->{type};                          my $type = $fieldData->{type};

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