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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.18, Sun Aug 14 23:32:08 2005 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;
# Line 32  Line 32 
32  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>).
33  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
34  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
35  (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
36  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
37  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
38    C<FeatureVirulence>.
39    
40  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
41  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 70 
70  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
71  fully implemented.  fully implemented.
72    
73    =head2 XML Database Description
74    
75    =head3 Data Types
76    
77    The ERDB system supports the following data types. Note that there are numerous string
78    types depending on the maximum length. Some database packages limit the total number of
79    characters you have in an index key; to insure the database works in all environments,
80    the type of string should be the shortest one possible that supports all the known values.
81    
82    =over 4
83    
84    =item char
85    
86    single ASCII character
87    
88    =item int
89    
90    32-bit signed integer
91    
92    =item date
93    
94    64-bit unsigned integer, representing a PERL date/time value
95    
96    =item text
97    
98    long string; Text fields cannot be used in indexes or sorting and do not support the
99    normal syntax of filter clauses, but can be up to a billion character in length
100    
101    =item float
102    
103    double-precision floating-point number
104    
105    =item boolean
106    
107    single-bit numeric value; The value is stored as a 16-bit signed integer (for
108    compatability with certain database packages), but the only values supported are
109    0 and 1.
110    
111    =item key-string
112    
113    variable-length string, maximum 40 characters
114    
115    =item name-string
116    
117    variable-length string, maximum 80 characters
118    
119    =item medium-string
120    
121    variable-length string, maximum 160 characters
122    
123    =item string
124    
125    variable-length string, maximum 255 characters
126    
127    =back
128    
129    =head3 Global Tags
130    
131    The entire database definition must be inside a B<Database> tag. The display name of
132    the database is given by the text associated with the B<Title> tag. The display name
133    is only used in the automated documentation. It has no other effect. The entities and
134    relationships are listed inside the B<Entities> and B<Relationships> tags,
135    respectively. None of these tags have attributes.
136    
137        <Database>
138            <Title>... display title here...</Title>
139            <Entities>
140                ... entity definitions here ...
141            </Entities>
142            <Relationships>
143                ... relationship definitions here...
144            </Relationships>
145        </Database>
146    
147    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
148    The text inside the B<Notes> tag contains comments that will appear when the database
149    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
150    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
151    
152    =head3 Fields
153    
154    Both entities and relationships have fields described by B<Field> tags. A B<Field>
155    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
156    object mus be inside B<Fields> tags.
157    
158        <Entity ... >
159            <Fields>
160                ... Field tags ...
161            </Fields>
162        </Entity>
163    
164    The attributes for the B<Field> tag are as follows.
165    
166    =over 4
167    
168    =item name
169    
170    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
171    and the first character should be a letter. Most underlying databases are case-insensitive
172    with the respect to field names, so a best practice is to use lower-case letters only.
173    
174    =item type
175    
176    Data type of the field. The legal data types are given above.
177    
178    =item relation
179    
180    Name of the relation containing the field. This should only be specified for entity
181    fields. The ERDB system does not support optional fields or multi-occurring fields
182    in the primary relation of an entity. Instead, they are put into secondary relations.
183    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
184    grouping used to select a subset of the genomes. A given genome may not be in any
185    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
186    value. The relation name specified must be a valid table name. By convention, it is
187    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
188    entity, the fields without a relation attribute are said to belong to the
189    I<primary relation>. This relation has the same name as the entity itself.
190    
191    =back
192    
193    =head3 Indexes
194    
195    An entity can have multiple alternate indexes associated with it. The fields must
196    be from the primary relation. The alternate indexes assist in ordering results
197    from a query. A relationship can have up to two indexes-- a I<to-index> and a
198    I<from-index>. These order the results when crossing the relationship. For
199    example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
200    from-index would order the contigs of a ganome, and the to-index would order
201    the genomes of a contig. A relationship's index must specify only fields in
202    the relationship.
203    
204    The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
205    of a relationship is specified using the B<FromIndex> tag; the to-index is specified
206    using the B<ToIndex> tag.
207    
208    Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
209    tag containing the B<IndexField> tags. These specify, in order, the fields used in
210    the index. The attributes of an B<IndexField> tag are as follows.
211    
212    =over 4
213    
214    =item name
215    
216    Name of the field.
217    
218    =item order
219    
220    Sort order of the field-- C<ascending> or C<descending>.
221    
222    =back
223    
224    The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
225    
226    =head3 Object and Field Names
227    
228    By convention entity and relationship names use capital casing (e.g. C<Genome> or
229    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
230    with respect to relation names, converting them internally to all-upper case or
231    all-lower case.
232    
233    If syntax or parsing errors occur when you try to load or use an ERDB database, the
234    most likely reason is that one of your objects has an SQL reserved word as its name.
235    The list of SQL reserved words keeps increasing; however, most are unlikely to show
236    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
237    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
238    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
239    
240    Every entity has a field called C<id> that acts as its primary key. Every relationship
241    has fields called C<from-link> and C<to-link> that contain copies of the relevant
242    entity IDs. These are essentially ERDB's reserved words, and should not be used
243    for user-defined field names.
244    
245    =head3 Entities
246    
247    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
248    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
249    containing one or more fields. The attributes of the B<Entity> tag are as follows.
250    
251    =over 4
252    
253    =item name
254    
255    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
256    or C<GroupBlock>) and should be a noun or noun phrase.
257    
258    =item keyType
259    
260    Data type of the primary key. The primary key is always named C<id>.
261    
262    =back
263    
264    =head3 Relationships
265    
266    A relationship is described by the C<Relationship> tag. Within a relationship,
267    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
268    fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
269    the to-index.
270    
271    The C<Relationship> tag has the following attributes.
272    
273    =over 4
274    
275    =item name
276    
277    Name of the relationship. The relationship name, by convention, uses capital casing
278    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
279    phrase, designed to fit between the from-entity and the to-entity (e.g.
280    Block C<ContainsRegionIn> Genome).
281    
282    =item from
283    
284    Name of the entity from which the relationship starts.
285    
286    =item to
287    
288    Name of the entity to which the relationship proceeds.
289    
290    =item arity
291    
292    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
293    
294    =back
295    
296  =cut  =cut
297    
298  # GLOBALS  # GLOBALS
# Line 76  Line 300 
300  # 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.
301  # "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
302  # 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
303   #string is specified in the field definition.  # string is specified in the field definition. "avgLen" is the average byte length for estimating
304  my %TypeTable = ( char =>        { sqlType => 'CHAR(1)',                        maxLen => 1,                    dataGen => "StringGen('A')" },  # record sizes.
305                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },
306                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },
307                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },
308                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },
309                                    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))" },
310                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },
311                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   2, dataGen => "IntGen(0, 1)" },
312                               'key-string' =>                               'key-string' =>
313                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },
314                                   'name-string' =>                                   'name-string' =>
315                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },
316                                   'medium-string' =>                                   'medium-string' =>
317                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },
318                                  );                                  );
319    
320  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 145  Line 370 
370    
371  =head3 ShowMetaData  =head3 ShowMetaData
372    
373  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
374    
375  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
376  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 300  Line 525 
525    
526  =head3 DumpMetaData  =head3 DumpMetaData
527    
528  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
529    
530  Return a dump of the metadata structure.  Return a dump of the metadata structure.
531    
# Line 315  Line 540 
540    
541  =head3 CreateTables  =head3 CreateTables
542    
543  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
544    
545  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
546  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 353  Line 578 
578    
579  =head3 CreateTable  =head3 CreateTable
580    
581  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
582    
583  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
584    
# Line 363  Line 588 
588    
589  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
590    
591  =item $indexFlag  =item indexFlag
592    
593  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
594  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
595    
596    =item estimatedRows (optional)
597    
598    If specified, the estimated maximum number of rows for the relation. This
599    information allows the creation of tables using storage engines that are
600    faster but require size estimates, such as MyISAM.
601    
602  =back  =back
603    
604  =cut  =cut
605    
606  sub CreateTable {  sub CreateTable {
607          # Get the parameters.          # Get the parameters.
608          my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
609          # Get the database handle.          # Get the database handle.
610          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
611          # 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 629 
629          # Insure the table is not already there.          # Insure the table is not already there.
630          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
631          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
632        # If there are estimated rows, create an estimate so we can take advantage of
633        # faster DB technologies.
634        my $estimation = undef;
635        if ($estimatedRows) {
636            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
637        }
638          # Create the table.          # Create the table.
639          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
640          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
641          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
642          # If we want to build the indexes, we do it here.          # If we want to build the indexes, we do it here.
643          if ($indexFlag) {          if ($indexFlag) {
# Line 410  Line 647 
647    
648  =head3 CreateIndex  =head3 CreateIndex
649    
650  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
651    
652  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
653  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.
654  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
655  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.
656    
657  =cut  =cut
658    
# Line 443  Line 680 
680    
681  =head3 LoadTables  =head3 LoadTables
682    
683  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
684    
685  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
686  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 513  Line 750 
750    
751  =head3 GetTableNames  =head3 GetTableNames
752    
753  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
754    
755  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
756    
# Line 530  Line 767 
767    
768  =head3 GetEntityTypes  =head3 GetEntityTypes
769    
770  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
771    
772  Return a list of the entity type names.  Return a list of the entity type names.
773    
# Line 547  Line 784 
784    
785  =head3 Get  =head3 Get
786    
787  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
788    
789  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.
790  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 792 
792  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
793  $genus.  $genus.
794    
795  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>
796    
797  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
798  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
799    
800  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
801    
802  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
803  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 572  Line 809 
809  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
810  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,
811    
812  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>
813    
814  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
815  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 972 
972                          $command .= " ORDER BY $orderClause";                          $command .= " ORDER BY $orderClause";
973                  }                  }
974          }          }
975          Trace("SQL query: $command") if T(2);      Trace("SQL query: $command") if T(3);
976          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(4) && (@params > 0));
977          my $sth = $dbh->prepare_command($command);          my $sth = $dbh->prepare_command($command);
978          # Execute it with the parameters bound in.          # Execute it with the parameters bound in.
979          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());
# Line 747  Line 984 
984    
985  =head3 GetList  =head3 GetList
986    
987  C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
988    
989  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
990  specified filter clause.  specified filter clause.
991    
992  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
993  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  
994    
995  =over 4  =over 4
996    
# Line 812  Line 1047 
1047    
1048  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1049    
1050  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1051    
1052  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.
1053    
# Line 847  Line 1082 
1082    
1083  =head3 DumpRelations  =head3 DumpRelations
1084    
1085  C<< $database->DumpRelations($outputDirectory); >>  C<< $erdb->DumpRelations($outputDirectory); >>
1086    
1087  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.
1088  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 1124 
1124    
1125  =head3 InsertObject  =head3 InsertObject
1126    
1127  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1128    
1129  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
1130  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 1133 
1133  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
1134  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
1135    
1136  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']}); >>
1137    
1138  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
1139  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>.
1140    
1141  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'}); >>
1142    
1143  =over 4  =over 4
1144    
# Line 1028  Line 1263 
1263    
1264  =head3 LoadTable  =head3 LoadTable
1265    
1266  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
1267    
1268  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
1269    first.
1270    
1271  =over 4  =over 4
1272    
# Line 1048  Line 1284 
1284    
1285  =item RETURN  =item RETURN
1286    
1287  Returns a statistical object containing the number of records read and a list of the error messages.  Returns a statistical object containing the number of records read and a list of
1288    the error messages.
1289    
1290  =back  =back
1291    
# Line 1059  Line 1296 
1296          # Create the statistical return object.          # Create the statistical return object.
1297          my $retVal = _GetLoadStats();          my $retVal = _GetLoadStats();
1298          # Trace the fact of the load.          # Trace the fact of the load.
1299          Trace("Loading table $relationName from $fileName") if T(1);      Trace("Loading table $relationName from $fileName") if T(2);
1300          # Get the database handle.          # Get the database handle.
1301          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
1302          # Get the relation data.          # Get the relation data.
1303          my $relation = $self->_FindRelation($relationName);          my $relation = $self->_FindRelation($relationName);
1304          # Check the truncation flag.          # Check the truncation flag.
1305          if ($truncateFlag) {          if ($truncateFlag) {
1306                  Trace("Creating table $relationName") if T(1);          Trace("Creating table $relationName") if T(2);
1307                  # Re-create the table without its index.                  # Re-create the table without its index.
1308                  $self->CreateTable($relationName, 0);                  $self->CreateTable($relationName, 0);
1309            # If this is a pre-index DBMS, create the index here.
1310            if ($dbh->{_preIndex}) {
1311                eval {
1312                    $self->CreateIndex($relationName);
1313                };
1314                if ($@) {
1315                    $retVal->AddMessage($@);
1316                }
1317            }
1318          }          }
1319          # Determine whether or not this is a primary relation. Primary relations have an extra          # Determine whether or not this is a primary relation. Primary relations have an extra
1320          # field indicating whether or not a given object is new or was loaded from the flat files.          # field indicating whether or not a given object is new or was loaded from the flat files.
# Line 1076  Line 1322 
1322          # Get the number of fields in this relation.          # Get the number of fields in this relation.
1323          my @fieldList = @{$relation->{Fields}};          my @fieldList = @{$relation->{Fields}};
1324          my $fieldCount = @fieldList;          my $fieldCount = @fieldList;
         # Record the number of expected fields.  
         my $expectedFields = $fieldCount + ($primary ? 1 : 0);  
1325          # Start a database transaction.          # Start a database transaction.
1326          $dbh->begin_tran;          $dbh->begin_tran;
1327          # Open the relation file. We need to create a cleaned-up copy before loading.          # Open the relation file. We need to create a cleaned-up copy before loading.
1328          open TABLEIN, '<', $fileName;          open TABLEIN, '<', $fileName;
1329          my $tempName = "$fileName.tbl";          my $tempName = "$fileName.tbl";
1330          open TABLEOUT, '>', $tempName;          open TABLEOUT, '>', $tempName;
1331        my $inputCount = 0;
1332          # Loop through the file.          # Loop through the file.
1333          while (<TABLEIN>) {          while (<TABLEIN>) {
1334            $inputCount++;
1335                  # Chop off the new-line character.                  # Chop off the new-line character.
1336                  my $record = $_;          my $record = Tracer::Strip($_);
                 chomp $record;  
1337          # Only proceed if the record is non-blank.          # Only proceed if the record is non-blank.
1338          if ($record) {          if ($record) {
1339              # Escape all the backslashes found in the line.              # Escape all the backslashes found in the line.
1340              $record =~ s/\\/\\\\/g;              $record =~ s/\\/\\\\/g;
1341              # Eliminate any trailing tabs.              # Insure the number of fields is correct.
1342              chop $record while substr($record, -1) eq "\t";              my @fields = split /\t/, $record;
1343                while (@fields > $fieldCount) {
1344                    my $extraField = $fields[$#fields];
1345                    delete $fields[$#fields];
1346                    if ($extraField) {
1347                        Trace("Nonblank extra field value \"$extraField\" deleted from record $inputCount of $fileName.") if T(1);
1348                    }
1349                }
1350                while (@fields < $fieldCount) {
1351                    push @fields, "";
1352                }
1353              # If this is a primary relation, add a 0 for the new-record flag (indicating that              # If this is a primary relation, add a 0 for the new-record flag (indicating that
1354              # this record is not new, but part of the original load).              # this record is not new, but part of the original load).
1355              if ($primary) {              if ($primary) {
1356                  $record .= "\t0";                  push @fields, "0";
1357              }              }
1358              # Write the record.              # Write the record.
1359                $record = join "\t", @fields;
1360              print TABLEOUT "$record\n";              print TABLEOUT "$record\n";
1361              # Count the record read.              # Count the record written.
1362              my $count = $retVal->Add('records');              my $count = $retVal->Add('records');
1363              my $len = length $record;              my $len = length $record;
1364              Trace("Record $count written with $len characters.") if T(4);              Trace("Record $count written with $len characters.") if T(4);
1365            } else {
1366                # Here we have a blank record.
1367                $retVal->Add('skipped');
1368          }          }
1369          }          }
1370          # Close the files.          # Close the files.
1371          close TABLEIN;          close TABLEIN;
1372          close TABLEOUT;          close TABLEOUT;
1373      Trace("Temporary file $tempName created.") if T(4);      Trace("Temporary file $tempName created.") if T(2);
1374      # Load the table.      # Load the table.
1375          my $rv;          my $rv;
1376          eval {          eval {
# Line 1123  Line 1382 
1382                  Trace("Table load failed for $relationName.") if T(1);                  Trace("Table load failed for $relationName.") if T(1);
1383          } else {          } else {
1384                  # Here we successfully loaded the table. Trace the number of records loaded.                  # Here we successfully loaded the table. Trace the number of records loaded.
1385                  Trace("$retVal->{records} records read for $relationName.") if T(1);          Trace("$retVal->{records} records read for $relationName.") if T(2);
1386                  # If we're rebuilding, we need to create the table indexes.                  # If we're rebuilding, we need to create the table indexes.
1387                  if ($truncateFlag) {          if ($truncateFlag && ! $dbh->{_preIndex}) {
1388                          eval {                          eval {
1389                                  $self->CreateIndex($relationName);                                  $self->CreateIndex($relationName);
1390                          };                          };
# Line 1133  Line 1392 
1392                                  $retVal->AddMessage($@);                                  $retVal->AddMessage($@);
1393                          }                          }
1394                  }                  }
1395            # Analyze the table to help optimize tables.
1396          }          }
1397          # Commit the database changes.          # Commit the database changes.
1398          $dbh->commit_tran;          $dbh->commit_tran;
1399        $dbh->vacuum_it($relationName);
1400          # Delete the temporary file.          # Delete the temporary file.
1401          unlink $tempName;          unlink $tempName;
1402          # Return the statistics.          # Return the statistics.
# Line 1144  Line 1405 
1405    
1406  =head3 GenerateEntity  =head3 GenerateEntity
1407    
1408  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
1409    
1410  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
1411  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 1463 
1463    
1464  =head3 GetEntity  =head3 GetEntity
1465    
1466  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
1467    
1468  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
1469    
# Line 1238  Line 1499 
1499    
1500  =head3 GetEntityValues  =head3 GetEntityValues
1501    
1502  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1503    
1504  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance.
1505    
# Line 1279  Line 1540 
1540          return @retVal;          return @retVal;
1541  }  }
1542    
1543    =head3 GetAll
1544    
1545    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
1546    
1547    Return a list of values taken from the objects returned by a query. The first three
1548    parameters correspond to the parameters of the L</Get> method. The final parameter is
1549    a list of the fields desired from each record found by the query. The field name
1550    syntax is the standard syntax used for fields in the B<ERDB> system--
1551    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
1552    or relationship and I<fieldName> is the name of the field.
1553    
1554    The list returned will be a list of lists. Each element of the list will contain
1555    the values returned for the fields specified in the fourth parameter. If one of the
1556    fields specified returns multiple values, they are flattened in with the rest. For
1557    example, the following call will return a list of the features in a particular
1558    spreadsheet cell, and each feature will be represented by a list containing the
1559    feature ID followed by all of its aliases.
1560    
1561    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
1562    
1563    =over 4
1564    
1565    =item objectNames
1566    
1567    List containing the names of the entity and relationship objects to be retrieved.
1568    
1569    =item filterClause
1570    
1571    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1572    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1573    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1574    parameter list as additional parameters. The fields in a filter clause can come from primary
1575    entity relations, relationship relations, or secondary entity relations; however, all of the
1576    entities and relationships involved must be included in the list of object names.
1577    
1578    =item parameterList
1579    
1580    List of the parameters to be substituted in for the parameters marks in the filter clause.
1581    
1582    =item fields
1583    
1584    List of the fields to be returned in each element of the list returned.
1585    
1586    =item count
1587    
1588    Maximum number of records to return. If omitted or 0, all available records will be returned.
1589    
1590    =item RETURN
1591    
1592    Returns a list of list references. Each element of the return list contains the values for the
1593    fields specified in the B<fields> parameter.
1594    
1595    =back
1596    
1597    =cut
1598    #: Return Type @@;
1599    sub GetAll {
1600        # Get the parameters.
1601        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
1602        # Translate the parameters from a list reference to a list. If the parameter
1603        # list is a scalar we convert it into a singleton list.
1604        my @parmList = ();
1605        if (ref $parameterList eq "ARRAY") {
1606            @parmList = @{$parameterList};
1607        } else {
1608            push @parmList, $parameterList;
1609        }
1610        # Create the query.
1611        my $query = $self->Get($objectNames, $filterClause, @parmList);
1612        # Set up a counter of the number of records read.
1613        my $fetched = 0;
1614        # Insure the counter has a value.
1615        if (!defined $count) {
1616            $count = 0;
1617        }
1618        # Loop through the records returned, extracting the fields. Note that if the
1619        # counter is non-zero, we stop when the number of records read hits the count.
1620        my @retVal = ();
1621        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
1622            my @rowData = $row->Values($fields);
1623            push @retVal, \@rowData;
1624            $fetched++;
1625        }
1626        # Return the resulting list.
1627        return @retVal;
1628    }
1629    
1630    =head3 EstimateRowSize
1631    
1632    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
1633    
1634    Estimate the row size of the specified relation. The estimated row size is computed by adding
1635    up the average length for each data type.
1636    
1637    =over 4
1638    
1639    =item relName
1640    
1641    Name of the relation whose estimated row size is desired.
1642    
1643    =item RETURN
1644    
1645    Returns an estimate of the row size for the specified relation.
1646    
1647    =back
1648    
1649    =cut
1650    #: Return Type $;
1651    sub EstimateRowSize {
1652        # Get the parameters.
1653        my ($self, $relName) = @_;
1654        # Declare the return variable.
1655        my $retVal = 0;
1656        # Find the relation descriptor.
1657        my $relation = $self->_FindRelation($relName);
1658        # Get the list of fields.
1659        for my $fieldData (@{$relation->{Fields}}) {
1660            # Get the field type and add its length.
1661            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
1662            $retVal += $fieldLen;
1663        }
1664        # Return the result.
1665        return $retVal;
1666    }
1667    
1668  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1669    
1670  =head3 GetLoadStats  =head3 GetLoadStats
# Line 1654  Line 2040 
2040  sub _LoadMetaData {  sub _LoadMetaData {
2041          # Get the parameters.          # Get the parameters.
2042          my ($filename) = @_;          my ($filename) = @_;
2043        Trace("Reading Sprout DBD from $filename.") if T(2);
2044          # 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
2045          # get the exact structure we want.          # get the exact structure we want.
2046          my $metadata = XML::Simple::XMLin($filename,          my $metadata = XML::Simple::XMLin($filename,
# Line 1681  Line 2068 
2068          for my $entityName (keys %{$entityList}) {          for my $entityName (keys %{$entityList}) {
2069                  my $entityStructure = $entityList->{$entityName};                  my $entityStructure = $entityList->{$entityName};
2070                  #                  #
2071                  # 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,
2072                  # 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,
2073                  # 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>
2074                  # 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 2247 
2247                  my @fromList = ();                  my @fromList = ();
2248                  my @toList = ();                  my @toList = ();
2249                  my @bothList = ();                  my @bothList = ();
2250                  Trace("Join table build for $entityName.") if T(3);          Trace("Join table build for $entityName.") if T(4);
2251                  for my $relationshipName (keys %{$relationshipList}) {                  for my $relationshipName (keys %{$relationshipList}) {
2252                          my $relationship = $relationshipList->{$relationshipName};                          my $relationship = $relationshipList->{$relationshipName};
2253                          # 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.
2254                          my $fromEntity = $relationship->{from};                          my $fromEntity = $relationship->{from};
2255                          my $toEntity = $relationship->{to};                          my $toEntity = $relationship->{to};
2256                          Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(3);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);
2257                          if ($fromEntity eq $entityName) {                          if ($fromEntity eq $entityName) {
2258                                  if ($toEntity eq $entityName) {                                  if ($toEntity eq $entityName) {
2259                                          # Here the relationship is recursive.                                          # Here the relationship is recursive.
2260                                          push @bothList, $relationshipName;                                          push @bothList, $relationshipName;
2261                                          Trace("Relationship $relationshipName put in both-list.") if T(3);                      Trace("Relationship $relationshipName put in both-list.") if T(4);
2262                                  } else {                                  } else {
2263                                          # Here the relationship comes from the entity.                                          # Here the relationship comes from the entity.
2264                                          push @fromList, $relationshipName;                                          push @fromList, $relationshipName;
2265                                          Trace("Relationship $relationshipName put in from-list.") if T(3);                      Trace("Relationship $relationshipName put in from-list.") if T(4);
2266                                  }                                  }
2267                          } elsif ($toEntity eq $entityName) {                          } elsif ($toEntity eq $entityName) {
2268                                  # Here the relationship goes to the entity.                                  # Here the relationship goes to the entity.
2269                                  push @toList, $relationshipName;                                  push @toList, $relationshipName;
2270                                  Trace("Relationship $relationshipName put in to-list.") if T(3);                  Trace("Relationship $relationshipName put in to-list.") if T(4);
2271                          }                          }
2272                  }                  }
2273                  # 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 1926  Line 2313 
2313                                  # relationship can only be ambiguous with another recursive relationship,                                  # relationship can only be ambiguous with another recursive relationship,
2314                                  # and the incoming relationship from the outer loop is never recursive.                                  # and the incoming relationship from the outer loop is never recursive.
2315                                  for my $otherName (@bothList) {                                  for my $otherName (@bothList) {
2316                                          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(4);
2317                                          # Join from the left.                                          # Join from the left.
2318                                          $joinTable{"$relationshipName/$otherName"} =                                          $joinTable{"$relationshipName/$otherName"} =
2319                                                  "$linkField = $otherName.from_link";                                                  "$linkField = $otherName.from_link";
# Line 1941  Line 2328 
2328                  # 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
2329                  # possible to get the same effect using multiple queries.                  # possible to get the same effect using multiple queries.
2330                  for my $relationshipName (@bothList) {                  for my $relationshipName (@bothList) {
2331                          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(4);
2332                          # Join to the entity from each direction.                          # Join to the entity from each direction.
2333                          $joinTable{"$entityName/$relationshipName"} =                          $joinTable{"$entityName/$relationshipName"} =
2334                                  "$entityName.id = $relationshipName.from_link";                                  "$entityName.id = $relationshipName.from_link";
# Line 1992  Line 2379 
2379          # index descriptor does not exist, it will be created automatically so we can add          # index descriptor does not exist, it will be created automatically so we can add
2380          # the field to it.          # the field to it.
2381          unshift @{$newIndex->{IndexFields}}, $firstField;          unshift @{$newIndex->{IndexFields}}, $firstField;
2382        # If this is a one-to-many relationship, the "To" index is unique.
2383        if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
2384            $newIndex->{Unique} = 'true';
2385        }
2386          # Add the index to the relation.          # Add the index to the relation.
2387          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
2388  }  }
# Line 2083  Line 2474 
2474                  # Here we have a field list. Loop through its fields.                  # Here we have a field list. Loop through its fields.
2475                  my $fieldStructures = $structure->{Fields};                  my $fieldStructures = $structure->{Fields};
2476                  for my $fieldName (keys %{$fieldStructures}) {                  for my $fieldName (keys %{$fieldStructures}) {
2477                Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
2478                          my $fieldData = $fieldStructures->{$fieldName};                          my $fieldData = $fieldStructures->{$fieldName};
2479                          # Get the field type.                          # Get the field type.
2480                          my $type = $fieldData->{type};                          my $type = $fieldData->{type};
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