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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.105, Tue Sep 23 20:43:42 2008 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 ERDBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13        use CGI;
14        use WikiTools;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 32  Line 35 
35  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>).
36  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
37  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
38  (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
39  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
40  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
41    C<FeatureVirulence>.
42    
43  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
44  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 56  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
76  To facilitate testing, the ERDB module supports automatic generation of test data. This process  =head2 XML Database Description
77  is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
78  fully implemented.  =head3 Data Types
79    
80    The ERDB system supports the following data types. Note that there are numerous string
81    types depending on the maximum length. Some database packages limit the total number of
82    characters you have in an index key; to insure the database works in all environments,
83    the type of string should be the shortest one possible that supports all the known values.
84    
85    =over 4
86    
87    =item char
88    
89    single ASCII character
90    
91    =item int
92    
93    32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99    =item date
100    
101    64-bit unsigned integer, representing a PERL date/time value
102    
103    =item text
104    
105    long string; Text fields do not support the normal syntax of filter clauses,
106    but can be up to a billion character in length
107    
108    =item dna
109    
110    long string, used to store DNA and protein sequences
111    
112    =item image
113    
114    long string, used to store encoded image data
115    
116    =item float
117    
118    double-precision floating-point number
119    
120    =item boolean
121    
122    single-bit numeric value; The value is stored as a 16-bit signed integer (for
123    compatability with certain database packages), but the only values supported are
124    0 and 1.
125    
126    =item id-string
127    
128    variable-length string, maximum 25 characters
129    
130    =item key-string
131    
132    variable-length string, maximum 40 characters
133    
134    =item name-string
135    
136    variable-length string, maximum 80 characters
137    
138    =item medium-string
139    
140    variable-length string, maximum 160 characters
141    
142    =item string
143    
144    variable-length string, maximum 255 characters
145    
146    =item hash-string
147    
148    variable-length string, maximum 22 characters
149    
150    =back
151    
152    The hash-string data type has a special meaning. The actual key passed into the loader will
153    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
154    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
155    digest. Therefore, it is presumed the keys will be unique. When the database is actually
156    in use, the hashed keys will be presented rather than the original values. For this reason,
157    they should not be used for entities where the key is meaningful.
158    
159    =head3 Global Tags
160    
161    The entire database definition must be inside a B<Database> tag. The display name of
162    the database is given by the text associated with the B<Title> tag. The display name
163    is only used in the automated documentation. It has no other effect. The entities and
164    relationships are listed inside the B<Entities> and B<Relationships> tags,
165    respectively. None of these tags have attributes.
166    
167        <Database>
168            <Title>... display title here...</Title>
169            <Entities>
170                ... entity definitions here ...
171            </Entities>
172            <Relationships>
173                ... relationship definitions here...
174            </Relationships>
175        </Database>
176    
177    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
178    The text inside the B<Notes> tag contains comments that will appear when the database
179    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
180    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
181    
182    =head3 Fields
183    
184    Both entities and relationships have fields described by B<Field> tags. A B<Field>
185    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
186    object mus be inside B<Fields> tags.
187    
188        <Entity ... >
189            <Fields>
190                ... Field tags ...
191            </Fields>
192        </Entity>
193    
194    The attributes for the B<Field> tag are as follows.
195    
196    =over 4
197    
198    =item name
199    
200    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
201    and the first character should be a letter. Most underlying databases are case-insensitive
202    with the respect to field names, so a best practice is to use lower-case letters only. Finally,
203    the name C<search-relevance> has special meaning for full-text searches and should not be
204    used as a field name.
205    
206    =item type
207    
208    Data type of the field. The legal data types are given above.
209    
210    =item relation
211    
212    Name of the relation containing the field. This should only be specified for entity
213    fields. The ERDB system does not support optional fields or multi-occurring fields
214    in the primary relation of an entity. Instead, they are put into secondary relations.
215    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
216    grouping used to select a subset of the genomes. A given genome may not be in any
217    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
218    value. The relation name specified must be a valid table name. By convention, it is
219    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
220    entity, the fields without a relation attribute are said to belong to the
221    I<primary relation>. This relation has the same name as the entity itself.
222    
223    =item searchable
224    
225    If specified, then the field is a candidate for full-text searching. A single full-text
226    index will be created for each relation with at least one searchable field in it.
227    For best results, this option should only be used for string or text fields.
228    
229    =item special
230    
231    This attribute allows the subclass to assign special meaning for certain fields.
232    The interpretation is up to the subclass itself. Currently, only entity fields
233    can have this attribute.
234    
235    =back
236    
237    =head3 Indexes
238    
239    An entity can have multiple alternate indexes associated with it. The fields in an
240    index must all be from the same relation. The alternate indexes assist in searching
241    on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
242    I<from-index> that order the results when crossing the relationship. For
243    example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
244    from-index would order the contigs of a ganome, and the to-index would order
245    the genomes of a contig. In addition, it can have zero or more alternate
246    indexes. A relationship's index must specify only fields in
247    the relationship.
248    
249    The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
250    The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
251    specified using the B<ToIndex> tag.
252    
253    Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
254    tag containing the B<IndexField> tags. These specify, in order, the fields used in
255    the index. The attributes of an B<IndexField> tag are as follows.
256    
257    =over 4
258    
259    =item name
260    
261    Name of the field.
262    
263    =item order
264    
265    Sort order of the field-- C<ascending> or C<descending>.
266    
267    =back
268    
269    The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
270    have a B<Unique> attribute. If specified, the index will be generated as a unique
271    index.
272    
273    =head3 Object and Field Names
274    
275    By convention entity and relationship names use capital casing (e.g. C<Genome> or
276    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
277    with respect to relation names, converting them internally to all-upper case or
278    all-lower case.
279    
280    If syntax or parsing errors occur when you try to load or use an ERDB database, the
281    most likely reason is that one of your objects has an SQL reserved word as its name.
282    The list of SQL reserved words keeps increasing; however, most are unlikely to show
283    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
284    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
285    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
286    
287    Every entity has a field called C<id> that acts as its primary key. Every relationship
288    has fields called C<from-link> and C<to-link> that contain copies of the relevant
289    entity IDs. These are essentially ERDB's reserved words, and should not be used
290    for user-defined field names.
291    
292    =head3 Entities
293    
294    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
295    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
296    containing one or more fields. The attributes of the B<Entity> tag are as follows.
297    
298    =over 4
299    
300    =item name
301    
302    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
303    or C<GroupBlock>) and should be a noun or noun phrase.
304    
305    =item keyType
306    
307    Data type of the primary key. The primary key is always named C<id>.
308    
309    =back
310    
311    =head3 Relationships
312    
313    A relationship is described by the C<Relationship> tag. Within a relationship,
314    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
315    fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
316    the to-index, and an C<Indexes> tag containing the alternate indexes.
317    
318    The C<Relationship> tag has the following attributes.
319    
320    =over 4
321    
322    =item name
323    
324    Name of the relationship. The relationship name, by convention, uses capital casing
325    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
326    phrase, designed to fit between the from-entity and the to-entity (e.g.
327    Block C<ContainsRegionIn> Genome).
328    
329    =item from
330    
331    Name of the entity from which the relationship starts.
332    
333    =item to
334    
335    Name of the entity to which the relationship proceeds.
336    
337    =item arity
338    
339    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
340    
341    =back
342    
343  =cut  =cut
344    
# Line 75  Line 346 
346    
347  # 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.
348  # "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
349  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "avgLen" is the average byte length for estimating
350   #string is specified in the field definition.  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
351  my %TypeTable = ( char =>        { sqlType => 'CHAR(1)',                        maxLen => 1,                    dataGen => "StringGen('A')" },  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
352                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  # index
353                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
354                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "single ASCII character"},
355                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
356                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
357                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
358                                   indexMod =>   0, notes => "unsigned 32-bit integer"},
359                      image =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 100000, sort => "",
360                                   indexMod => 255, notes => "UUencoded image, suitable for import into GD, should never be indexed"},
361                      dna =>      { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 100000, sort => "",
362                                   indexMod => 255, notes => "DNA or protein sequence, should never be indexed"},
363                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
364                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
365                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
366                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
367                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
368                                   indexMod =>   0, notes => "signed, 64-bit integer"},
369                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
370                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
371                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
372                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
373                     'hash-string' =>
374                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
375                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
376                     'id-string' =>
377                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
378                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
379                               'key-string' =>                               'key-string' =>
380                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
381                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
382                                   'name-string' =>                                   'name-string' =>
383                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
384                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
385                                   'medium-string' =>                                   'medium-string' =>
386                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
387                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
388                     'long-string' =>
389                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
390                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
391                                  );                                  );
392    
393  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 98  Line 396 
396                                     'MM' => 'many-to-many'                                     'MM' => 'many-to-many'
397                                   );                                   );
398    
399  # Table for interpreting string patterns.  # Options for XML input and output.
400    
401    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
402                                      Entities => 'Entity',
403                                      Fields => 'Field',
404                                      Indexes => 'Index',
405                                      IndexFields => 'IndexField',
406                                      Issues => 'Issue',
407                                      Shapes => 'Shape'
408                                    },
409                      KeyAttr =>    { Relationship => 'name',
410                                      Entity => 'name',
411                                      Field => 'name',
412                                      Shape => 'name'
413                                    },
414                      SuppressEmpty => 1,
415                     );
416    
417  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
418                                           '9' => "0123456789",                    ForceArray => [qw(Field Index IndexField Relationship Entity Shape)],
419                                           'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
420                                           'V' => "aeiou",                    NormalizeSpace => 2,
421                                           'K' => "bcdfghjklmnoprstvwxyz"                   );
422    my %XmlOutOpts = (
423                      RootName => 'Database',
424                      XMLDecl => 1,
425                                     );                                     );
426    
427  =head2 Public Methods  =head2 Public Methods
428    
429  =head3 new  =head3 new
430    
431  C<< my $database = ERDB->new($dbh, $metaFileName); >>      my $database = ERDB->new($dbh, $metaFileName);
432    
433  Create a new ERDB object.  Create a new ERDB object.
434    
# Line 131  Line 448 
448    
449  sub new {  sub new {
450          # Get the parameters.          # Get the parameters.
451          my ($class, $dbh, $metaFileName, $options) = @_;      my ($class, $dbh, $metaFileName, %options) = @_;
452          # Load the meta-data.          # Load the meta-data.
453          my $metaData = _LoadMetaData($metaFileName);          my $metaData = _LoadMetaData($metaFileName);
454          # Create the object.          # Create the object.
# Line 145  Line 462 
462    
463  =head3 ShowMetaData  =head3 ShowMetaData
464    
465  C<< $database->ShowMetaData($fileName); >>      $erdb->ShowMetaData($fileName);
466    
467  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
468  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 176  Line 493 
493          # Write the HTML heading stuff.          # Write the HTML heading stuff.
494          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
495          print HTMLOUT "</head>\n<body>\n";          print HTMLOUT "</head>\n<body>\n";
496        # Write the documentation.
497        print HTMLOUT $self->DisplayMetaData();
498        # Close the document.
499        print HTMLOUT "</body>\n</html>\n";
500        # Close the file.
501        close HTMLOUT;
502    }
503    
504    =head3 DisplayMetaData
505    
506        my $html = $erdb->DisplayMetaData();
507    
508    Return an HTML description of the database. This description can be used to help users create
509    the data to be loaded into the relations and form queries. The output is raw includable HTML
510    without any HEAD or BODY tags.
511    
512    =over 4
513    
514    =item filename
515    
516    The name of the output file.
517    
518    =back
519    
520    =cut
521    
522    sub DisplayMetaData {
523        # Get the parameters.
524        my ($self) = @_;
525        # Get the metadata and the title string.
526        my $metadata = $self->{_metaData};
527        # Get the title string.
528        my $title = $metadata->{Title};
529        # Get the entity and relationship lists.
530        my $entityList = $metadata->{Entities};
531        my $relationshipList = $metadata->{Relationships};
532        # Declare the return variable.
533        my $retVal = "";
534        # Open the output file.
535        Trace("Building MetaData table of contents.") if T(4);
536          # Here we do the table of contents. It starts as an unordered list of section names. Each          # Here we do the table of contents. It starts as an unordered list of section names. Each
537          # section contains an ordered list of entity or relationship subsections.          # section contains an ordered list of entity or relationship subsections.
538          print HTMLOUT "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";      $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
539          # Loop through the Entities, displaying a list item for each.          # Loop through the Entities, displaying a list item for each.
540          foreach my $key (sort keys %{$entityList}) {          foreach my $key (sort keys %{$entityList}) {
541                  # Display this item.                  # Display this item.
542                  print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
543          }          }
544          # Close off the entity section and start the relationship section.          # Close off the entity section and start the relationship section.
545          print HTMLOUT "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";      $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
546          # Loop through the Relationships.          # Loop through the Relationships.
547          foreach my $key (sort keys %{$relationshipList}) {          foreach my $key (sort keys %{$relationshipList}) {
548                  # Display this item.                  # Display this item.
549                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
550                  print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
551          }          }
552          # Close off the relationship section and list the join table section.          # Close off the relationship section and list the join table section.
553          print HTMLOUT "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";      $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
554          # Close off the table of contents itself.          # Close off the table of contents itself.
555          print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
556          # Now we start with the actual data. Denote we're starting the entity section.          # Now we start with the actual data. Denote we're starting the entity section.
557          print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
558          # Loop through the entities.          # Loop through the entities.
559          for my $key (sort keys %{$entityList}) {          for my $key (sort keys %{$entityList}) {
560                  Trace("Building MetaData entry for $key entity.") if T(4);                  Trace("Building MetaData entry for $key entity.") if T(4);
561                  # Create the entity header. It contains a bookmark and the entity name.                  # Create the entity header. It contains a bookmark and the entity name.
562                  print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
563                  # Get the entity data.                  # Get the entity data.
564                  my $entityData = $entityList->{$key};                  my $entityData = $entityList->{$key};
565                  # If there's descriptive text, display it.                  # If there's descriptive text, display it.
566                  if (my $notes = $entityData->{Notes}) {                  if (my $notes = $entityData->{Notes}) {
567                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
568                  }                  }
569                  # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
570                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
571            if ($relCount > 0) {
572                # First, we set up the relationship subsection.
573                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
574                  # Loop through the relationships.                  # Loop through the relationships.
575                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
576                          # Get the relationship data.                          # Get the relationship data.
# Line 220  Line 580 
580                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
581                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
582                                  # Display the relationship data.                                  # Display the relationship data.
583                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
584                          }                          }
585                  }                  }
586                  # Close off the relationship list.                  # Close off the relationship list.
587                  print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
588            }
589                  # Get the entity's relations.                  # Get the entity's relations.
590                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
591                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
592                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
593                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
594                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
595                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
596                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
597                  }                  }
598          }          }
599          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
600          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
601          # Loop through the relationships.          # Loop through the relationships.
602          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
603                  Trace("Building MetaData entry for $key relationship.") if T(4);                  Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 244  Line 605 
605                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
606                  # Create the relationship header.                  # Create the relationship header.
607                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
608                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
609                  # Get the entity names.                  # Get the entity names.
610                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
611                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 254  Line 615 
615                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
616                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
617                  if ($arity eq "11") {                  if ($arity eq "11") {
618                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
619                  } else {                  } else {
620                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
621                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
622                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
623                          }                          }
624                  }                  }
625                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
626                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
627                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
628                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
629                  }                  }
630                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
631                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
632                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
633          }          }
634          Trace("Building MetaData join table.") if T(4);          Trace("Building MetaData join table.") if T(4);
635          # Denote we're starting the join table.          # Denote we're starting the join table.
636          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
637          # Create a table header.          # Create a table header.
638          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
639          # Loop through the joins.          # Loop through the joins.
640          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
641          my @joinKeys = keys %{$joinTable};          my @joinKeys = keys %{$joinTable};
# Line 282  Line 643 
643                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
644                  $joinKey =~ m!^([^/]+)/(.+)$!;                  $joinKey =~ m!^([^/]+)/(.+)$!;
645                  my ($sourceRelation, $targetRelation) = ($1, $2);                  my ($sourceRelation, $targetRelation) = ($1, $2);
646                  Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
647                  my $source = $self->ComputeObjectSentence($sourceRelation);                  my $source = $self->ComputeObjectSentence($sourceRelation);
648                  my $target = $self->ComputeObjectSentence($targetRelation);                  my $target = $self->ComputeObjectSentence($targetRelation);
649                  my $clause = $joinTable->{$joinKey};                  my $clause = $joinTable->{$joinKey};
650                  # Display them in a table row.                  # Display them in a table row.
651                  print HTMLOUT "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";          $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
652          }          }
653          # Close the table.          # Close the table.
654          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
655          # Close the document.      Trace("Built MetaData HTML.") if T(3);
656          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
657          # Close the file.      return $retVal;
         close HTMLOUT;  
         Trace("Built MetaData web page.") if T(3);  
658  }  }
659    
660  =head3 DumpMetaData  =head3 DumpMetaData
661    
662  C<< $database->DumpMetaData(); >>      $erdb->DumpMetaData();
663    
664  Return a dump of the metadata structure.  Return a dump of the metadata structure.
665    
# Line 313  Line 672 
672          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
673  }  }
674    
675  =head3 CreateTables  =head3 GenerateWikiData
676    
677  C<< $datanase->CreateTables(); >>      my @wikiLines = $erdb->GenerateWikiData();
678    
679  This method creates the tables for the database from the metadata structure loaded by the  Build a description of the database for the wiki. The database will be
680  constructor. It is expected this function will only be used on rare occasions, when the  organized into a single page, with sections for each entity and relationship.
681  user needs to start with an empty database. Otherwise, the L</LoadTables> method can be  The return value is a list of text lines.
 used by itself with the truncate flag turned on.  
682    
683  =cut  =cut
684    
685  sub CreateTables {  sub GenerateWikiData {
686          # Get the parameters.          # Get the parameters.
687          my ($self) = @_;          my ($self) = @_;
688        # We'll build the wiki text in here.
689        my @retVal = ();
690        # Get the metadata object.
691          my $metadata = $self->{_metaData};          my $metadata = $self->{_metaData};
692          my $dbh = $self->{_dbh};      # Get the title string. This will become the page name.
693          # Loop through the entities.      my $title = $metadata->{Title}->{content};
694          my $entityHash = $metadata->{Entities};      # Get the entity and relationship lists.
695          for my $entityName (keys %{$entityHash}) {      my $entityList = $metadata->{Entities};
696                  my $entityData = $entityHash->{$entityName};      my $relationshipList = $metadata->{Relationships};
697                  # Tell the user what we're doing.      my $shapeList = $metadata->{Shapes};
698                  Trace("Creating relations for entity $entityName.") if T(1);      # Start with the introductory text.
699                  # Loop through the entity's relations.      push @retVal, WikiTools::Heading(2, "Introduction");
700                  for my $relationName (keys %{$entityData->{Relations}}) {      if (my $notes = $metadata->{Notes}) {
701                          # Create a table for this relation.          push @retVal, WikiNote($notes->{content});
702                          $self->CreateTable($relationName);      }
703                          Trace("Relation $relationName created.") if T(1);      # Generate issue list.
704        if (my $issues = $metadata->{Issues}) {
705            push @retVal, WikiTools::Heading(3, 'Issues');
706            push @retVal, WikiTools::List(map { $_->{content} } @{$issues});
707        }
708        # Start the entity section.
709        push @retVal, WikiTools::Heading(2, "Entities");
710        # Loop through the entities. Note that unlike the situation with HTML, we
711        # don't need to generate the table of contents manually, just the data
712        # itself.
713        for my $key (sort keys %$entityList) {
714            # Create a header for this entity.
715            push @retVal, "", WikiTools::Heading(3, $key);
716            # Get the entity data.
717            my $entityData = $entityList->{$key};
718            # Plant the notes here, if there are any.
719            push @retVal, _ObjectNotes($entityData);
720            # Now we list the entity's relationships (if any). First, we build a list
721            # of the relationships relevant to this entity.
722            my @rels = ();
723            for my $rel (sort keys %$relationshipList) {
724                my $relStructure = $relationshipList->{$rel};
725                if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
726                    # Get the relationship sentence.
727                    my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
728                    # Linkify it.
729                    my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
730                    $relSentence =~ s/$rel/$linkedRel/;
731                    push @rels, $relSentence;
732                  }                  }
733          }          }
734          # Loop through the relationships.          # Add the relationships as a Wiki list.
735          my $relationshipTable = $metadata->{Relationships};          push @retVal, WikiTools::List(@rels);
736          for my $relationshipName (keys %{$metadata->{Relationships}}) {          # Get the entity's relations.
737                  # Create a table for this relationship.          my $relationList = $entityData->{Relations};
738                  Trace("Creating relationship $relationshipName.") if T(1);          # Loop through the relations, displaying them.
739                  $self->CreateTable($relationshipName);          for my $relation (sort keys %{$relationList}) {
740                my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
741                push @retVal, $wikiString;
742            }
743        }
744        # Now the entities are documented. Next we do the relationships.
745        push @retVal, WikiTools::Heading(2, "Relationships");
746        for my $key (sort keys %$relationshipList) {
747            my $relationshipData = $relationshipList->{$key};
748            # Create the relationship heading.
749            push @retVal, WikiTools::Heading(3, $key);
750            # Describe the relationship arity. Note there's a bit of trickiness involving recursive
751            # many-to-many relationships. In a normal many-to-many we use two sentences to describe
752            # the arity (one for each direction). This is a bad idea for a recursive relationship,
753            # since both sentences will say the same thing.
754            my $arity = $relationshipData->{arity};
755            my $fromEntity = $relationshipData->{from};
756            my $toEntity = $relationshipData->{to};
757            my @listElements = ();
758            my $boldCode = WikiTools::BoldCode();
759            if ($arity eq "11") {
760                push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
761            } else {
762                push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.";
763                if ($arity eq "MM" && $fromEntity ne $toEntity) {
764                    push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.";
765          }          }
766  }  }
767            push @retVal, WikiTools::List(@listElements);
768            # Plant the notes here, if there are any.
769            push @retVal, _ObjectNotes($relationshipData);
770            # Finally, the relationship table.
771            my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
772            push @retVal, $wikiString;
773        }
774        # Now loop through the miscellaneous shapes.
775        if ($shapeList) {
776            push @retVal, WikiTools::Heading(2, "Miscellaneous");
777            for my $shape (sort keys %$shapeList) {
778                push @retVal, WikiTools::Heading(3, $shape);
779                my $shapeData = $shapeList->{$shape};
780                push @retVal, _ObjectNotes($shapeData);
781            }
782        }
783        # All done. Return the lines.
784        return @retVal;
785    }
786    
 =head3 CreateTable  
787    
788  C<< $database->CreateTable($tableName, $indexFlag); >>  =head3 CreatePPO
789    
790  Create the table for a relation and optionally create its indexes.      ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
791    
792    Create a PPO XML file from an ERDB data definition XML file. At the
793    current time, the PPO XML file can be used to create a database with
794    similar functionality. Eventually, the PPO will be able to use the
795    created XML to access the live ERDB database.
796    
797  =over 4  =over 4
798    
799  =item relationName  =item erdbXMLFile
800    
801  Name of the relation (which will also be the table name).  Name of the XML data definition file for the ERDB database. This
802    file must exist.
803    
804  =item $indexFlag  =item ppoXMLFile
805    
806  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  Output file for the PPO XML definition. If this file exists, it
807  L</CreateIndexes> must be called later to bring the indexes into existence.  will be overwritten.
808    
809  =back  =back
810    
811  =cut  =cut
812    
813  sub CreateTable {  sub CreatePPO {
814          # Get the parameters.          # Get the parameters.
815          my ($self, $relationName, $indexFlag) = @_;      my ($erdbXMLFile, $ppoXMLFile) = @_;
816          # Get the database handle.      # First, we want to slurp in the ERDB XML file in its raw form.
817          my $dbh = $self->{_dbh};      my $xml = ReadMetaXML($erdbXMLFile);
818          # Get the relation data and determine whether or not the relation is primary.      # Create a variable to hold all of the objects in the PPO project.
819          my $relationData = $self->_FindRelation($relationName);      my @objects = ();
820          my $rootFlag = $self->_IsPrimary($relationName);      # Get the relationship hash.
821          # Create a list of the field data.      my $relationships = $xml->{Relationships};
822          my @fieldList;      # Loop through the entities.
823          for my $fieldData (@{$relationData->{Fields}}) {      my $entities = $xml->{Entities};
824                  # Assemble the field name and type.      for my $entityName (keys %{$entities}) {
825                  my $fieldName = _FixName($fieldData->{name});          # Get the entity's data structures.
826                  my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";          my $entityObject = $entities->{$entityName};
827                  # Push the result into the field list.          # We put the object's fields in here, according to their type.
828                  push @fieldList, $fieldString;          my (@object_refs, @scalars, @indexes, @arrays);
829            # Create the ID field for the entity. We get the key type from the
830            # entity object and compute the corresponding SQL type.
831            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
832            push @scalars, { label => 'id', type => $type };
833            # Loop through the entity fields.
834            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
835                # Get the field object.
836                my $fieldObject = $entityObject->{Fields}->{$fieldName};
837                # Convert it to a scalar tag.
838                my $scalar = _CreatePPOField($fieldName, $fieldObject);
839                # If we have a relation, this field is stored in an array.
840                # otherwise, it is a scalar. The array tag has scalars
841                # stored as an XML array. In ERDB, there is only ever one,
842                # but PPO can have more.
843                my $relation = $fieldObject->{relation};
844                if ($relation) {
845                    push @arrays, { scalar => [$scalar] };
846                } else {
847                    push @scalars, $scalar;
848          }          }
         # If this is a root table, add the "new_record" flag. It defaults to 0, so  
         if ($rootFlag) {  
                 push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";  
849          }          }
850          # Convert the field list into a comma-delimited string.          # Loop through the relationships. If this entity is the to-entity
851          my $fieldThing = join(', ', @fieldList);          # on a relationship of 1M arity, then it is implemented as a PPO
852          # Insure the table is not already there.          # object reference.
853          $dbh->drop_table(tbl => $relationName);          for my $relationshipName (keys %{$relationships}) {
854          Trace("Table $relationName dropped.") if T(2);              # Get the relationship data.
855          # Create the table.              my $relationshipData = $relationships->{$relationshipName};
856          Trace("Creating table $relationName: $fieldThing") if T(2);              # If we have a from for this entity and an arity of 1M, we
857          $dbh->create_table(tbl => $relationName, flds => $fieldThing);              # have an object reference.
858          Trace("Relation $relationName created in database.") if T(2);              if ($relationshipData->{to} eq $entityName &&
859          # If we want to build the indexes, we do it here.                  $relationshipData->{arity} eq '1M') {
860          if ($indexFlag) {                  # Build the object reference tag.
861                  $self->CreateIndex($relationName);                  push @object_refs, { label => $relationshipName,
862                                         type => $relationshipData->{from} };
863                }
864            }
865            # Create the indexes.
866            my $indexList = $entityObject->{Indexes};
867            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
868            # Build the object XML tree.
869            my $object = { label => $entityName,
870                           object_ref => \@object_refs,
871                           scalar => \@scalars,
872                           index => \@indexes,
873                           array => \@arrays
874                          };
875            # Push the object onto the objects list.
876            push @objects, $object;
877        }
878        # Loop through the relationships, searching for MMs. The 1Ms were
879        # already handled by the entity search above.
880        for my $relationshipName (keys %{$relationships}) {
881            # Get this relationship's object.
882            my $relationshipObject = $relationships->{$relationshipName};
883            # Only proceed if it's many-to-many.
884            if ($relationshipObject->{arity} eq 'MM') {
885                # Create the tag lists for the relationship object.
886                my (@object_refs, @scalars, @indexes);
887                # The relationship will be created as an object with object
888                # references for its links to the participating entities.
889                my %links = ( from_link => $relationshipObject->{from},
890                              to_link => $relationshipObject->{to} );
891                for my $link (keys %links) {
892                    # Create an object_ref tag for this piece of the
893                    # relationship (from or to).
894                    my $object_ref = { label => $link,
895                                       type => $links{$link} };
896                    push @object_refs, $object_ref;
897                }
898                # Loop through the intersection data fields, creating scalar tags.
899                # There are no fancy array tags in a relationship.
900                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
901                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
902                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
903                }
904                # Finally, the indexes: currently we cannot support the to-index and
905                # from-index in PPO, so we just process the alternate indexes.
906                my $indexList = $relationshipObject->{Indexes};
907                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
908                # Wrap up all the stuff about this relationship.
909                my $object = { label => $relationshipName,
910                               scalar => \@scalars,
911                               object_ref => \@object_refs,
912                               index => \@indexes
913                             };
914                # Push it into the object list.
915                push @objects, $object;
916          }          }
917  }  }
918        # Compute a title.
919        my $title;
920        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
921            # Here we have a standard file name we can use for a title.
922            $title = $2;
923        } else {
924            # Here the file name is non-standard, so we carve up the
925            # database title.
926            $title = $xml->{Title}->{content};
927            $title =~ s/\s\.,//g;
928        }
929        # Wrap up the XML as a project.
930        my $ppoXML = { project => { label => $title,
931                                    object => \@objects }};
932        # Write out the results.
933        my $ppoString = XML::Simple::XMLout($ppoXML,
934                                            AttrIndent => 1,
935                                            KeepRoot => 1);
936        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
937    }
938    
939  =head3 CreateIndex  =head3 FindIndexForEntity
940    
941  C<< $database->CreateIndex($relationName); >>      my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
942    
943  Create the indexes for a relation. If a table is being loaded from a large source file (as  This method locates the entry in an entity's index list that begins with the
944  is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  specified attribute name. If the entity has no index list, one will be
945  the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  created. This method works on raw XML, not a live ERDB object.
 method used after the load to create the indexes for the table.  
946    
947  =cut  =over 4
948    
949  sub CreateIndex {  =item xml
         # Get the parameters.  
         my ($self, $relationName) = @_;  
         # Get the relation's descriptor.  
         my $relationData = $self->_FindRelation($relationName);  
         # Get the database handle.  
         my $dbh = $self->{_dbh};  
         # Now we need to create this relation's indexes. We do this by looping through its index table.  
         my $indexHash = $relationData->{Indexes};  
         for my $indexName (keys %{$indexHash}) {  
                 my $indexData = $indexHash->{$indexName};  
                 # Get the index's field list.  
                 my @fieldList = _FixNames(@{$indexData->{IndexFields}});  
                 my $flds = join(', ', @fieldList);  
                 # Get the index's uniqueness flag.  
                 my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');  
                 # Create the index.  
                 $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);  
                 Trace("Index created: $indexName for $relationName ($flds)") if T(1);  
         }  
 }  
950    
951  =head3 LoadTables  The raw XML structure defining the database.
952    
953  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  =item entityName
954    
955  This method will load the database tables from a directory. The tables must already have been created  The name of the relevant entity.
 in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  
 all of the relations to be loaded must have a file in the directory with the same name as the relation  
 (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each  
 line of the file will be loaded as a row of the target relation table. The field values should be in  
 the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is  
 erased before the new data is loaded in.  
   
 A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and  
 tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must  
 be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.  
   
 =over 4  
   
 =item directoryName  
   
 Name of the directory containing the relation files to be loaded.  
956    
957  =item rebuild  =item attributeName
958    
959  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the  The name of the attribute relevant to the search.
 only way to erase existing data in the tables, since the TRUNCATE command is not supported  
 by all of the DB engines we use.  
960    
961  =item RETURN  =item RETURN
962    
963  Returns a statistical object describing the number of records read and a list of the error messages.  The numerical index in the index list of the index entry for the specified entity and
964    attribute, or C<undef> if no such index exists.
965    
966  =back  =back
967    
968  =cut  =cut
969    
970  sub LoadTables {  sub FindIndexForEntity {
971          # Get the parameters.          # Get the parameters.
972          my ($self, $directoryName, $rebuild) = @_;      my ($xml, $entityName, $attributeName) = @_;
         # Start the timer.  
         my $startTime = gettimeofday;  
         # Clean any trailing slash from the directory name.  
         $directoryName =~ s!/\\$!!;  
973          # Declare the return variable.          # Declare the return variable.
974          my $retVal = Stats->new();      my $retVal;
975          # Get the metadata structure.      # Get the named entity.
976          my $metaData = $self->{_metaData};      my $entityData = $xml->{Entities}->{$entityName};
977          # Loop through the entities.      if (! $entityData) {
978          for my $entity (values %{$metaData->{Entities}}) {          Confess("Entity $entityName not found in DBD structure.");
979                  # Loop through the entity's relations.      } else {
980                  for my $relationName (keys %{$entity->{Relations}}) {          # Insure it has an index list.
981                          # Try to load this relation.          if (! exists $entityData->{Indexes}) {
982                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              $entityData->{Indexes} = [];
983                          # Accumulate the statistics.          } else {
984                          $retVal->Accumulate($result);              # Search for the desired index.
985                my $indexList = $entityData->{Indexes};
986                my $n = scalar @{$indexList};
987                Trace("Searching $n indexes in index list for $entityName.") if T(2);
988                # We use an indexed FOR here because we're returning an
989                # index number instead of an object. We do THAT so we can
990                # delete the index from the list if needed.
991                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
992                    my $index = $indexList->[$i];
993                    my $fields = $index->{IndexFields};
994                    # Technically this IF should be safe (that is, we are guaranteed
995                    # the existence of a "$fields->[0]"), because when we load the XML
996                    # we have SuppressEmpty specified.
997                    if ($fields->[0]->{name} eq $attributeName) {
998                        $retVal = $i;
999                  }                  }
1000          }          }
         # 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);  
1001          }          }
1002          # Add the duration of the load to the statistical object.      }
1003          $retVal->Add('duration', gettimeofday - $startTime);      Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
1004          # Return the accumulated statistics.      Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
1005        # Return the result.
1006          return $retVal;          return $retVal;
1007  }  }
1008    
1009  =head3 GetTableNames  =head3 CreateTables
1010    
1011  C<< my @names = $database->GetTableNames; >>      $erdb->CreateTables();
1012    
1013  Return a list of the relations required to implement this database.  This method creates the tables for the database from the metadata structure loaded by the
1014    constructor. It is expected this function will only be used on rare occasions, when the
1015    user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
1016    used by itself with the truncate flag turned on.
1017    
1018  =cut  =cut
1019    
1020  sub GetTableNames {  sub CreateTables {
1021          # Get the parameters.          # Get the parameters.
1022          my ($self) = @_;          my ($self) = @_;
1023          # Get the relation list from the metadata.      # Get the relation names.
1024          my $relationTable = $self->{_metaData}->{RelationTable};      my @relNames = $self->GetTableNames();
1025          # Return the relation names.      # Loop through the relations.
1026          return keys %{$relationTable};      for my $relationName (@relNames) {
1027            # Create a table for this relation.
1028            $self->CreateTable($relationName, 1);
1029            Trace("Relation $relationName created.") if T(2);
1030        }
1031  }  }
1032    
1033  =head3 GetEntityTypes  =head3 CreateTable
1034    
1035  C<< my @names = $database->GetEntityTypes; >>      $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
1036    
1037  Return a list of the entity type names.  Create the table for a relation and optionally create its indexes.
1038    
1039    =over 4
1040    
1041    =item relationName
1042    
1043    Name of the relation (which will also be the table name).
1044    
1045    =item indexFlag
1046    
1047    TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
1048    L</CreateIndexes> must be called later to bring the indexes into existence.
1049    
1050    =item estimatedRows (optional)
1051    
1052    If specified, the estimated maximum number of rows for the relation. This
1053    information allows the creation of tables using storage engines that are
1054    faster but require size estimates, such as MyISAM.
1055    
1056    =back
1057    
1058  =cut  =cut
1059    
1060  sub GetEntityTypes {  sub CreateTable {
1061          # Get the database object.      # Get the parameters.
1062          my ($self) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
1063          # Get the entity list from the metadata object.      # Get the database handle.
1064          my $entityList = $self->{_metaData}->{Entities};      my $dbh = $self->{_dbh};
1065          # Return the list of entity names in alphabetical order.      # Get the relation data and determine whether or not the relation is primary.
1066          return sort keys %{$entityList};      my $relationData = $self->_FindRelation($relationName);
1067        my $rootFlag = $self->_IsPrimary($relationName);
1068        # Create a list of the field data.
1069        my @fieldList;
1070        for my $fieldData (@{$relationData->{Fields}}) {
1071            # Assemble the field name and type.
1072            my $fieldName = _FixName($fieldData->{name});
1073            my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
1074            # Push the result into the field list.
1075            push @fieldList, $fieldString;
1076        }
1077        # Convert the field list into a comma-delimited string.
1078        my $fieldThing = join(', ', @fieldList);
1079        # Insure the table is not already there.
1080        $dbh->drop_table(tbl => $relationName);
1081        Trace("Table $relationName dropped.") if T(2);
1082        # If there are estimated rows, create an estimate so we can take advantage of
1083        # faster DB technologies.
1084        my $estimation = undef;
1085        if ($estimatedRows) {
1086            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1087            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1088        }
1089        # Create the table.
1090        Trace("Creating table $relationName: $fieldThing") if T(2);
1091        $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
1092        Trace("Relation $relationName created in database.") if T(2);
1093        # If we want to build the indexes, we do it here. Note that the full-text search
1094        # index will not be built until the table has been loaded.
1095        if ($indexFlag) {
1096            $self->CreateIndex($relationName);
1097        }
1098  }  }
1099    
1100  =head3 Get  =head3 VerifyFields
1101    
1102  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
1103    
1104  This method returns a query object for entities of a specified type using a specified filter.  Run through the list of proposed field values, insuring that all the character fields are
1105  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  below the maximum length. If any fields are too long, they will be truncated in place.
 field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the  
 following call requests all B<Genome> objects for the genus specified in the variable  
 $genus.  
1106    
1107  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  =over 4
1108    
1109  The WHERE clause contains a single question mark, so there is a single additional  =item relName
 parameter representing the parameter value. It would also be possible to code  
1110    
1111  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  Name of the relation for which the specified fields are destined.
1112    
1113  however, this version of the call would generate a syntax error if there were any quote  =item fieldList
 characters inside the variable C<$genus>.  
1114    
1115  The use of the strange parenthesized notation for field names enables us to distinguish  Reference to a list, in order, of the fields to be put into the relation.
 hyphens contained within field names from minus signs that participate in the computation  
 of the WHERE clause. All of the methods that manipulate fields will use this same notation.  
1116    
1117  It is possible to specify multiple entity and relationship names in order to retrieve more than  =item RETURN
 one object's data at the same time, which allows highly complex joined queries. For example,  
1118    
1119  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  Returns the number of fields truncated.
1120    
1121  If multiple names are specified, then the query processor will automatically determine a  =back
1122  join path between the entities and relationships. The algorithm used is very simplistic.  
1123  In particular, you can't specify any entity or relationship more than once, and if a  =cut
1124  relationship is recursive, the path is determined by the order in which the entity  
1125  and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  sub VerifyFields {
1126  which relates B<People> objects to other B<People> objects. If the join path is      # Get the parameters.
1127  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,      my ($self, $relName, $fieldList) = @_;
1128  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.      # Initialize the return value.
1129        my $retVal = 0;
1130        # Get the relation definition.
1131        my $relData = $self->_FindRelation($relName);
1132        # Get the list of field descriptors.
1133        my $fieldTypes = $relData->{Fields};
1134        my $fieldCount = scalar @{$fieldTypes};
1135        # Loop through the two lists.
1136        for (my $i = 0; $i < $fieldCount; $i++) {
1137            # Get the type of the current field.
1138            my $fieldType = $fieldTypes->[$i]->{type};
1139            # If it's a character field, verify the length.
1140            if ($fieldType =~ /string/) {
1141                my $maxLen = $TypeTable{$fieldType}->{maxLen};
1142                my $oldString = $fieldList->[$i];
1143                if (length($oldString) > $maxLen) {
1144                    # Here it's too big, so we truncate it.
1145                    Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1146                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
1147                    $retVal++;
1148                }
1149            }
1150        }
1151        # Return the truncation count.
1152        return $retVal;
1153    }
1154    
1155    =head3 DigestFields
1156    
1157        $erdb->DigestFields($relName, $fieldList);
1158    
1159    Digest the strings in the field list that correspond to data type C<hash-string> in the
1160    specified relation.
1161    
1162  =over 4  =over 4
1163    
1164  =item objectNames  =item relName
1165    
1166  List containing the names of the entity and relationship objects to be retrieved.  Name of the relation to which the fields belong.
1167    
1168  =item filterClause  =item fieldList
1169    
1170  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  List of field contents to be loaded into the relation.
 be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  
 specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  
 in the filter clause should be added to the parameter list as additional parameters. The  
 fields in a filter clause can come from primary entity relations, relationship relations,  
 or secondary entity relations; however, all of the entities and relationships involved must  
 be included in the list of object names.  
1171    
1172  The filter clause can also specify a sort order. To do this, simply follow the filter string  =back
1173  with an ORDER BY clause. For example, the following filter string gets all genomes for a  
1174  particular genus and sorts them by species name.  =cut
1175    #: Return Type ;
1176    sub DigestFields {
1177        # Get the parameters.
1178        my ($self, $relName, $fieldList) = @_;
1179        # Get the relation definition.
1180        my $relData = $self->_FindRelation($relName);
1181        # Get the list of field descriptors.
1182        my $fieldTypes = $relData->{Fields};
1183        my $fieldCount = scalar @{$fieldTypes};
1184        # Loop through the two lists.
1185        for (my $i = 0; $i < $fieldCount; $i++) {
1186            # Get the type of the current field.
1187            my $fieldType = $fieldTypes->[$i]->{type};
1188            # If it's a hash string, digest it in place.
1189            if ($fieldType eq 'hash-string') {
1190                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1191            }
1192        }
1193    }
1194    
1195  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  =head3 DigestKey
1196    
1197  The rules for field references in a sort order are the same as those for field references in the      my $digested = $erdb->DigestKey($keyValue);
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
1198    
1199  =item param1, param2, ..., paramN  Return the digested value of a symbolic key. The digested value can then be plugged into a
1200    key-based search into a table with key-type hash-string.
1201    
1202  Parameter values to be substituted into the filter clause.  Currently the digesting process is independent of the database structure, but that may not
1203    always be the case, so this is an instance method instead of a static method.
1204    
1205    =over 4
1206    
1207    =item keyValue
1208    
1209    Key value to digest.
1210    
1211  =item RETURN  =item RETURN
1212    
1213  Returns a B<DBQuery> that can be used to iterate through all of the results.  Digested value of the key.
1214    
1215  =back  =back
1216    
1217  =cut  =cut
1218    
1219  sub Get {  sub DigestKey {
1220          # Get the parameters.          # Get the parameters.
1221          my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $keyValue) = @_;
1222          # Construct the SELECT statement. The general pattern is      # Compute the digest.
1223          #      my $retVal = md5_base64($keyValue);
1224          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN      # Return the result.
1225          #      return $retVal;
         my $dbh = $self->{_dbh};  
         my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .  
                                 join(', ', @{$objectNames});  
         # Check for a filter clause.  
         if ($filterClause) {  
                 # Here we have one, so we convert its field names and add it to the query. First,  
                 # We create a copy of the filter string we can work with.  
                 my $filterString = $filterClause;  
                 # Next, we sort the object names by length. This helps protect us from finding  
                 # object names inside other object names when we're doing our search and replace.  
                 my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
                 # We will also keep a list of conditions to add to the WHERE clause in order to link  
                 # entities and relationships as well as primary relations to secondary ones.  
                 my @joinWhere = ();  
                 # The final preparatory step is to create a hash table of relation names. The  
                 # table begins with the relation names already in the SELECT command.  
                 my %fromNames = ();  
                 for my $objectName (@sortedNames) {  
                         $fromNames{$objectName} = 1;  
                 }  
                 # We are ready to begin. We loop through the object names, replacing each  
                 # object name's field references by the corresponding SQL field reference.  
                 # Along the way, if we find a secondary relation, we will need to add it  
                 # to the FROM clause.  
                 for my $objectName (@sortedNames) {  
                         # Get the length of the object name plus 2. This is the value we add to the  
                         # size of the field name to determine the size of the field reference as a  
                         # whole.  
                         my $nameLength = 2 + length $objectName;  
                         # Get the object's field list.  
                         my $fieldList = $self->_GetFieldTable($objectName);  
                         # Find the field references for this object.  
                         while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                                 # At this point, $1 contains the field name, and the current position  
                                 # is set immediately after the final parenthesis. We pull out the name of  
                                 # the field and the position and length of the field reference as a whole.  
                                 my $fieldName = $1;  
                                 my $len = $nameLength + length $fieldName;  
                                 my $pos = pos($filterString) - $len;  
                                 # Insure the field exists.  
                                 if (!exists $fieldList->{$fieldName}) {  
                                         Confess("Field $fieldName not found for object $objectName.");  
                                 } else {  
                                         # Get the field's relation.  
                                         my $relationName = $fieldList->{$fieldName}->{relation};  
                                         # Insure the relation is in the FROM clause.  
                                         if (!exists $fromNames{$relationName}) {  
                                                 # Add the relation to the FROM clause.  
                                                 $command .= ", $relationName";  
                                                 # Create its join sub-clause.  
                                                 push @joinWhere, "$objectName.id = $relationName.id";  
                                                 # Denote we have it available for future fields.  
                                                 $fromNames{$relationName} = 1;  
                                         }  
                                         # Form an SQL field reference from the relation name and the field name.  
                                         my $sqlReference = "$relationName." . _FixName($fieldName);  
                                         # Put it into the filter string in place of the old value.  
                                         substr($filterString, $pos, $len) = $sqlReference;  
                                         # Reposition the search.  
                                         pos $filterString = $pos + length $sqlReference;  
1226                                  }                                  }
1227    
1228    =head3 CreateIndex
1229    
1230        $erdb->CreateIndex($relationName);
1231    
1232    Create the indexes for a relation. If a table is being loaded from a large source file (as
1233    is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
1234    If that is the case, then L</CreateTable> should be called with the index flag set to
1235    FALSE, and this method used after the load to create the indexes for the table.
1236    
1237    =cut
1238    
1239    sub CreateIndex {
1240        # Get the parameters.
1241        my ($self, $relationName) = @_;
1242        # Get the relation's descriptor.
1243        my $relationData = $self->_FindRelation($relationName);
1244        # Get the database handle.
1245        my $dbh = $self->{_dbh};
1246        # Now we need to create this relation's indexes. We do this by looping through its index table.
1247        my $indexHash = $relationData->{Indexes};
1248        for my $indexName (keys %{$indexHash}) {
1249            my $indexData = $indexHash->{$indexName};
1250            # Get the index's field list.
1251            my @rawFields = @{$indexData->{IndexFields}};
1252            # Get a hash of the relation's field types.
1253            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1254            # We need to check for text fields so we can append a length limitation for them. To do
1255            # that, we need the relation's field list.
1256            my $relFields = $relationData->{Fields};
1257            for (my $i = 0; $i <= $#rawFields; $i++) {
1258                # Get the field type.
1259                my $field = $rawFields[$i];
1260                my $type = $types{$field};
1261                # Ask if it requires using prefix notation for the index.
1262                my $mod = $TypeTable{$type}->{indexMod};
1263                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1264                if ($mod) {
1265                    # Append the prefix length to the field name,
1266                    $rawFields[$i] .= "($mod)";
1267                          }                          }
1268                  }                  }
1269                  # The next step is to join the objects together. We only need to do this if there          my @fieldList = _FixNames(@rawFields);
1270                  # is more than one object in the object list. We start with the first object and          my $flds = join(', ', @fieldList);
1271                  # run through the objects after it. Note also that we make a safety copy of the          # Get the index's uniqueness flag.
1272                  # list before running through it.          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1273                  my @objectList = @{$objectNames};          # Create the index.
1274                  my $lastObject = shift @objectList;          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1275                  # Get the join table.                                      flds => $flds, kind => $unique);
1276                  my $joinTable = $self->{_metaData}->{Joins};          if ($rv) {
1277                  # Loop through the object list.              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
                 for my $thisObject (@objectList) {  
                         # Look for a join.  
                         my $joinKey = "$lastObject/$thisObject";  
                         if (!exists $joinTable->{$joinKey}) {  
                                 # Here there's no join, so we throw an error.  
                                 Confess("No join exists to connect from $lastObject to $thisObject.");  
1278                          } else {                          } else {
1279                                  # Get the join clause and add it to the WHERE list.              Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
                                 push @joinWhere, $joinTable->{$joinKey};  
                                 # Save this object as the last object for the next iteration.  
                                 $lastObject = $thisObject;  
1280                          }                          }
1281                  }                  }
                 # Now we need to handle the whole ORDER BY thing. We'll put the order by clause  
                 # in the following variable.  
                 my $orderClause = "";  
                 # Locate the ORDER BY verb (if any).  
                 if ($filterString =~ m/^(.*)ORDER BY/g) {  
                         # Here we have an ORDER BY verb. Split it off of the filter string.  
                         my $pos = pos $filterString;  
                         $orderClause = substr($filterString, $pos);  
                         $filterString = $1;  
1282                  }                  }
1283                  # Add the filter and the join clauses (if any) to the SELECT command.  
1284                  if ($filterString) {  =head3 GetSecondaryFields
1285                          push @joinWhere, "($filterString)";  
1286        my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1287    
1288    This method will return a list of the name and type of each of the secondary
1289    fields for a specified entity. Secondary fields are stored in two-column tables
1290    in addition to the primary entity table. This enables the field to have no value
1291    or to have multiple values.
1292    
1293    =over 4
1294    
1295    =item entityName
1296    
1297    Name of the entity whose secondary fields are desired.
1298    
1299    =item RETURN
1300    
1301    Returns a hash mapping the field names to their field types.
1302    
1303    =back
1304    
1305    =cut
1306    
1307    sub GetSecondaryFields {
1308        # Get the parameters.
1309        my ($self, $entityName) = @_;
1310        # Declare the return variable.
1311        my %retVal = ();
1312        # Look for the entity.
1313        my $table = $self->GetFieldTable($entityName);
1314        # Loop through the fields, pulling out the secondaries.
1315        for my $field (sort keys %{$table}) {
1316            if ($table->{$field}->{relation} ne $entityName) {
1317                # Here we have a secondary field.
1318                $retVal{$field} = $table->{$field}->{type};
1319            }
1320        }
1321        # Return the result.
1322        return %retVal;
1323    }
1324    
1325    =head3 GetFieldRelationName
1326    
1327        my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1328    
1329    Return the name of the relation containing a specified field.
1330    
1331    =over 4
1332    
1333    =item objectName
1334    
1335    Name of the entity or relationship containing the field.
1336    
1337    =item fieldName
1338    
1339    Name of the relevant field in that entity or relationship.
1340    
1341    =item RETURN
1342    
1343    Returns the name of the database relation containing the field, or C<undef> if
1344    the field does not exist.
1345    
1346    =back
1347    
1348    =cut
1349    
1350    sub GetFieldRelationName {
1351        # Get the parameters.
1352        my ($self, $objectName, $fieldName) = @_;
1353        # Declare the return variable.
1354        my $retVal;
1355        # Get the object field table.
1356        my $table = $self->GetFieldTable($objectName);
1357        # Only proceed if the field exists.
1358        if (exists $table->{$fieldName}) {
1359            # Determine the name of the relation that contains this field.
1360            $retVal = $table->{$fieldName}->{relation};
1361        }
1362        # Return the result.
1363        return $retVal;
1364    }
1365    
1366    =head3 DeleteValue
1367    
1368        my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1369    
1370    Delete secondary field values from the database. This method can be used to delete all
1371    values of a specified field for a particular entity instance, or only a single value.
1372    
1373    Secondary fields are stored in two-column relations separate from an entity's primary
1374    table, and as a result a secondary field can legitimately have no value or multiple
1375    values. Therefore, it makes sense to talk about deleting secondary fields where it
1376    would not make sense for primary fields.
1377    
1378    =over 4
1379    
1380    =item entityName
1381    
1382    Name of the entity from which the fields are to be deleted.
1383    
1384    =item id
1385    
1386    ID of the entity instance to be processed. If the instance is not found, this
1387    method will have no effect. If C<undef> is specified, all values for all of
1388    the entity instances will be deleted.
1389    
1390    =item fieldName
1391    
1392    Name of the field whose values are to be deleted.
1393    
1394    =item fieldValue (optional)
1395    
1396    Value to be deleted. If not specified, then all values of the specified field
1397    will be deleted for the entity instance. If specified, then only the values which
1398    match this parameter will be deleted.
1399    
1400    =item RETURN
1401    
1402    Returns the number of rows deleted.
1403    
1404    =back
1405    
1406    =cut
1407    
1408    sub DeleteValue {
1409        # Get the parameters.
1410        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1411        # Declare the return value.
1412        my $retVal = 0;
1413        # We need to set up an SQL command to do the deletion. First, we
1414        # find the name of the field's relation.
1415        my $table = $self->GetFieldTable($entityName);
1416        my $field = $table->{$fieldName};
1417        my $relation = $field->{relation};
1418        # Make sure this is a secondary field.
1419        if ($relation eq $entityName) {
1420            Confess("Cannot delete values of $fieldName for $entityName.");
1421        } else {
1422            # Set up the SQL command to delete all values.
1423            my $sql = "DELETE FROM $relation";
1424            # Build the filter.
1425            my @filters = ();
1426            my @parms = ();
1427            # Check for a filter by ID.
1428            if (defined $id) {
1429                push @filters, "id = ?";
1430                push @parms, $id;
1431            }
1432            # Check for a filter by value.
1433            if (defined $fieldValue) {
1434                push @filters, "$fieldName = ?";
1435                push @parms, $fieldValue;
1436            }
1437            # Append the filters to the command.
1438            if (@filters) {
1439                $sql .= " WHERE " . join(" AND ", @filters);
1440            }
1441            # Execute the command.
1442            my $dbh = $self->{_dbh};
1443            $retVal = $dbh->SQL($sql, 0, @parms);
1444        }
1445        # Return the result.
1446        return $retVal;
1447    }
1448    
1449    =head3 LoadTables
1450    
1451        my $stats = $erdb->LoadTables($directoryName, $rebuild);
1452    
1453    This method will load the database tables from a directory. The tables must already have been created
1454    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1455    all of the relations to be loaded must have a file in the directory with the same name as the relation
1456    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1457    line of the file will be loaded as a row of the target relation table. The field values should be in
1458    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1459    erased before the new data is loaded in.
1460    
1461    A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1462    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1463    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1464    
1465    =over 4
1466    
1467    =item directoryName
1468    
1469    Name of the directory containing the relation files to be loaded.
1470    
1471    =item rebuild
1472    
1473    TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1474    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1475    by all of the DB engines we use.
1476    
1477    =item RETURN
1478    
1479    Returns a statistical object describing the number of records read and a list of the error messages.
1480    
1481    =back
1482    
1483    =cut
1484    
1485    sub LoadTables {
1486        # Get the parameters.
1487        my ($self, $directoryName, $rebuild) = @_;
1488        # Start the timer.
1489        my $startTime = gettimeofday;
1490        # Clean any trailing slash from the directory name.
1491        $directoryName =~ s!/\\$!!;
1492        # Declare the return variable.
1493        my $retVal = Stats->new();
1494        # Get the relation names.
1495        my @relNames = $self->GetTableNames();
1496        for my $relationName (@relNames) {
1497            # Try to load this relation.
1498            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1499            # Accumulate the statistics.
1500            $retVal->Accumulate($result);
1501        }
1502        # Add the duration of the load to the statistical object.
1503        $retVal->Add('duration', gettimeofday - $startTime);
1504        # Return the accumulated statistics.
1505        return $retVal;
1506    }
1507    
1508    
1509    =head3 GetTableNames
1510    
1511        my @names = $erdb->GetTableNames;
1512    
1513    Return a list of the relations required to implement this database.
1514    
1515    =cut
1516    
1517    sub GetTableNames {
1518        # Get the parameters.
1519        my ($self) = @_;
1520        # Get the relation list from the metadata.
1521        my $relationTable = $self->{_metaData}->{RelationTable};
1522        # Return the relation names.
1523        return keys %{$relationTable};
1524    }
1525    
1526    =head3 GetEntityTypes
1527    
1528        my @names = $erdb->GetEntityTypes;
1529    
1530    Return a list of the entity type names.
1531    
1532    =cut
1533    
1534    sub GetEntityTypes {
1535        # Get the database object.
1536        my ($self) = @_;
1537        # Get the entity list from the metadata object.
1538        my $entityList = $self->{_metaData}->{Entities};
1539        # Return the list of entity names in alphabetical order.
1540        return sort keys %{$entityList};
1541    }
1542    
1543    
1544    =head3 GetConnectingRelationships
1545    
1546        my @list = $erdb->GetConnectingRelationships($entityName);
1547    
1548    Return a list of the relationships connected to the specified entity.
1549    
1550    =over 4
1551    
1552    =item entityName
1553    
1554    Entity whose connected relationships are desired.
1555    
1556    =item RETURN
1557    
1558    Returns a list of the relationships that originate from the entity.
1559    If the entity is on the from end, it will return the relationship
1560    name. If the entity is on the to end it will return the converse of
1561    the relationship name.
1562    
1563    =back
1564    
1565    =cut
1566    
1567    sub GetConnectingRelationships {
1568        # Get the parameters.
1569        my ($self, $entityName) = @_;
1570        # Declare the return variable.
1571        my @retVal;
1572        # Get the relationship list.
1573        my $relationships = $self->{_metaData}->{Relationships};
1574        # Find the entity.
1575        my $entity = $self->{_metaData}->{Entities}->{$entityName};
1576        # Only proceed if the entity exists.
1577        if (! defined $entity) {
1578            Trace("Entity $entityName not found.") if T(3);
1579        } else {
1580            # Loop through the relationships.
1581            my @rels = keys %$relationships;
1582            Trace(scalar(@rels) . " relationships found in connection search.") if T(3);
1583            for my $relationshipName (@rels) {
1584                my $relationship = $relationships->{$relationshipName};
1585                if ($relationship->{from} eq $entityName) {
1586                    # Here we have a forward relationship.
1587                    push @retVal, $relationshipName;
1588                } elsif ($relationship->{to} eq $entityName) {
1589                    # Here we have a backward relationship. In this case, the
1590                    # converse relationship name is preferred if it exists.
1591                    my $converse = $relationship->{converse} || $relationshipName;
1592                    push @retVal, $converse;
1593                }
1594            }
1595        }
1596        # Return the result.
1597        return @retVal;
1598    }
1599    
1600    
1601    =head3 GetDataTypes
1602    
1603        my %types = ERDB::GetDataTypes();
1604    
1605    Return a table of ERDB data types. The table returned is a hash of hashes.
1606    The keys of the big hash are the datatypes. Each smaller hash has several
1607    values used to manage the data. The most interesting is the SQL type (key
1608    C<sqlType>) and the descriptive node (key C<notes>).
1609    
1610    Note that changing the values in the smaller hashes will seriously break
1611    things, so this data should be treated as read-only.
1612    
1613    =cut
1614    
1615    sub GetDataTypes {
1616        return %TypeTable;
1617    }
1618    
1619    
1620    =head3 IsEntity
1621    
1622        my $flag = $erdb->IsEntity($entityName);
1623    
1624    Return TRUE if the parameter is an entity name, else FALSE.
1625    
1626    =over 4
1627    
1628    =item entityName
1629    
1630    Object name to be tested.
1631    
1632    =item RETURN
1633    
1634    Returns TRUE if the specified string is an entity name, else FALSE.
1635    
1636    =back
1637    
1638    =cut
1639    
1640    sub IsEntity {
1641        # Get the parameters.
1642        my ($self, $entityName) = @_;
1643        # Test to see if it's an entity.
1644        return exists $self->{_metaData}->{Entities}->{$entityName};
1645    }
1646    
1647    =head3 Get
1648    
1649        my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1650    
1651    This method returns a query object for entities of a specified type using a specified filter.
1652    The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1653    field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1654    following call requests all B<Genome> objects for the genus specified in the variable
1655    $genus.
1656    
1657        $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1658    
1659    The WHERE clause contains a single question mark, so there is a single additional
1660    parameter representing the parameter value. It would also be possible to code
1661    
1662        $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1663    
1664    however, this version of the call would generate a syntax error if there were any quote
1665    characters inside the variable C<$genus>.
1666    
1667    The use of the strange parenthesized notation for field names enables us to distinguish
1668    hyphens contained within field names from minus signs that participate in the computation
1669    of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1670    
1671    It is possible to specify multiple entity and relationship names in order to retrieve more than
1672    one object's data at the same time, which allows highly complex joined queries. For example,
1673    
1674        $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1675    
1676    If multiple names are specified, then the query processor will automatically determine a
1677    join path between the entities and relationships. The algorithm used is very simplistic.
1678    In particular, if a relationship is recursive, the path is determined by the order in which
1679    the entity and the relationship appear. For example, consider a recursive relationship
1680    B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1681    coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1682    the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1683    
1684    If an entity or relationship is mentioned twice, the name for the second occurrence will
1685    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1686    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1687    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1688    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1689    
1690    =over 4
1691    
1692    =item objectNames
1693    
1694    List containing the names of the entity and relationship objects to be retrieved.
1695    
1696    =item filterClause
1697    
1698    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1699    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1700    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1701    in the filter clause should be added to the parameter list as additional parameters. The
1702    fields in a filter clause can come from primary entity relations, relationship relations,
1703    or secondary entity relations; however, all of the entities and relationships involved must
1704    be included in the list of object names.
1705    
1706    The filter clause can also specify a sort order. To do this, simply follow the filter string
1707    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1708    particular genus and sorts them by species name.
1709    
1710        "Genome(genus) = ? ORDER BY Genome(species)"
1711    
1712    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1713    be processed. The idea is to make it less likely to find the verb by accident.
1714    
1715    The rules for field references in a sort order are the same as those for field references in the
1716    filter clause in general; however, odd things may happen if a sort field is from a secondary
1717    relation.
1718    
1719    Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1720    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1721    a positive number. So, for example
1722    
1723        "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1724    
1725    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1726    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1727    use
1728    
1729        "LIMIT 10"
1730    
1731    =item params
1732    
1733    Reference to a list of parameter values to be substituted into the filter clause.
1734    
1735    =item RETURN
1736    
1737    Returns a B<DBQuery> that can be used to iterate through all of the results.
1738    
1739    =back
1740    
1741    =cut
1742    
1743    sub Get {
1744        # Get the parameters.
1745        my ($self, $objectNames, $filterClause, $params) = @_;
1746        # Process the SQL stuff.
1747        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1748            $self->_SetupSQL($objectNames, $filterClause);
1749        # Create the query.
1750        my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1751            ".* $suffix";
1752        my $sth = $self->_GetStatementHandle($command, $params);
1753        # Now we create the relation map, which enables DBQuery to determine the order, name
1754        # and mapped name for each object in the query.
1755        my @relationMap = ();
1756        for my $mappedName (@{$mappedNameListRef}) {
1757            push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1758        }
1759        # Return the statement object.
1760        my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1761        return $retVal;
1762    }
1763    
1764    
1765    
1766    =head3 Search
1767    
1768        my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1769    
1770    Perform a full text search with filtering. The search will be against a specified object
1771    in the object name list. That object will get an extra field containing the search
1772    relevance. Note that except for the search expression, the parameters of this method are
1773    the same as those for L</Get> and follow the same rules.
1774    
1775    =over 4
1776    
1777    =item searchExpression
1778    
1779    Boolean search expression for the text fields of the target object. The default mode for
1780    a Boolean search expression is OR, but we want the default to be AND, so we will
1781    add a C<+> operator to each word with no other operator before it.
1782    
1783    =item idx
1784    
1785    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1786    
1787    =item objectNames
1788    
1789    List containing the names of the entity and relationship objects to be retrieved.
1790    
1791    =item filterClause
1792    
1793    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1794    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1795    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1796    in the filter clause should be added to the parameter list as additional parameters. The
1797    fields in a filter clause can come from primary entity relations, relationship relations,
1798    or secondary entity relations; however, all of the entities and relationships involved must
1799    be included in the list of object names.
1800    
1801    =item params
1802    
1803    Reference to a list of parameter values to be substituted into the filter clause.
1804    
1805    =item RETURN
1806    
1807    Returns a query object for the specified search.
1808    
1809    =back
1810    
1811    =cut
1812    
1813    sub Search {
1814        # Get the parameters.
1815        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1816        # Declare the return variable.
1817        my $retVal;
1818        # Create a safety copy of the parameter list. Note we have to be careful to insure
1819        # a parameter list exists before we copy it.
1820        my @myParams = ();
1821        if (defined $params) {
1822            @myParams = @{$params};
1823        }
1824        # Get the first object's structure so we have access to the searchable fields.
1825        my $object1Name = $objectNames->[$idx];
1826        my $object1Structure = $self->_GetStructure($object1Name);
1827        # Get the field list.
1828        if (! exists $object1Structure->{searchFields}) {
1829            Confess("No searchable index for $object1Name.");
1830        } else {
1831            # Get the field list.
1832            my @fields = @{$object1Structure->{searchFields}};
1833            # Clean the search expression.
1834            my $actualKeywords = $self->CleanKeywords($searchExpression);
1835            # Prefix a "+" to each uncontrolled word. This converts the default
1836            # search mode from OR to AND.
1837            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1838            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1839            # We need two match expressions, one for the filter clause and one in the
1840            # query itself. Both will use a parameter mark, so we need to push the
1841            # search expression onto the front of the parameter list twice.
1842            unshift @myParams, $actualKeywords, $actualKeywords;
1843            # Build the match expression.
1844            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1845            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1846            # Process the SQL stuff.
1847            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1848                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1849            # Create the query. Note that the match clause is inserted at the front of
1850            # the select fields.
1851            my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1852                ".* $suffix";
1853            my $sth = $self->_GetStatementHandle($command, \@myParams);
1854            # Now we create the relation map, which enables DBQuery to determine the order, name
1855            # and mapped name for each object in the query.
1856            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1857            # Return the statement object.
1858            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1859        }
1860        return $retVal;
1861    }
1862    
1863    =head3 GetFlat
1864    
1865        my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1866    
1867    This is a variation of L</GetAll> that asks for only a single field per record and
1868    returns a single flattened list.
1869    
1870    =over 4
1871    
1872    =item objectNames
1873    
1874    List containing the names of the entity and relationship objects to be retrieved.
1875    
1876    =item filterClause
1877    
1878    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1879    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1880    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1881    parameter list as additional parameters. The fields in a filter clause can come from primary
1882    entity relations, relationship relations, or secondary entity relations; however, all of the
1883    entities and relationships involved must be included in the list of object names.
1884    
1885    =item parameterList
1886    
1887    List of the parameters to be substituted in for the parameters marks in the filter clause.
1888    
1889    =item field
1890    
1891    Name of the field to be used to get the elements of the list returned.
1892    
1893    =item RETURN
1894    
1895    Returns a list of values.
1896    
1897    =back
1898    
1899    =cut
1900    #: Return Type @;
1901    sub GetFlat {
1902        # Get the parameters.
1903        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1904        # Construct the query.
1905        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1906        # Create the result list.
1907        my @retVal = ();
1908        # Loop through the records, adding the field values found to the result list.
1909        while (my $row = $query->Fetch()) {
1910            push @retVal, $row->Value($field);
1911        }
1912        # Return the list created.
1913        return @retVal;
1914    }
1915    
1916    =head3 SpecialFields
1917    
1918        my %specials = $erdb->SpecialFields($entityName);
1919    
1920    Return a hash mapping special fields in the specified entity to the value of their
1921    C<special> attribute. This enables the subclass to get access to the special field
1922    attributes without needed to plumb the internal ERDB data structures.
1923    
1924    =over 4
1925    
1926    =item entityName
1927    
1928    Name of the entity whose special fields are desired.
1929    
1930    =item RETURN
1931    
1932    Returns a hash. The keys of the hash are the special field names, and the values
1933    are the values from each special field's C<special> attribute.
1934    
1935    =back
1936    
1937    =cut
1938    
1939    sub SpecialFields {
1940        # Get the parameters.
1941        my ($self, $entityName) = @_;
1942        # Declare the return variable.
1943        my %retVal = ();
1944        # Find the entity's data structure.
1945        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1946        # Loop through its fields, adding each special field to the return hash.
1947        my $fieldHash = $entityData->{Fields};
1948        for my $fieldName (keys %{$fieldHash}) {
1949            my $fieldData = $fieldHash->{$fieldName};
1950            if (exists $fieldData->{special}) {
1951                $retVal{$fieldName} = $fieldData->{special};
1952            }
1953        }
1954        # Return the result.
1955        return %retVal;
1956    }
1957    
1958    =head3 Delete
1959    
1960        my $stats = $erdb->Delete($entityName, $objectID, %options);
1961    
1962    Delete an entity instance from the database. The instance is deleted along with all entity and
1963    relationship instances dependent on it. The definition of I<dependence> is recursive.
1964    
1965    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1966    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1967    dependent relationship.
1968    
1969    =over 4
1970    
1971    =item entityName
1972    
1973    Name of the entity type for the instance being deleted.
1974    
1975    =item objectID
1976    
1977    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1978    then it is presumed to by a LIKE pattern.
1979    
1980    =item options
1981    
1982    A hash detailing the options for this delete operation.
1983    
1984    =item RETURN
1985    
1986    Returns a statistics object indicating how many records of each particular table were
1987    deleted.
1988    
1989    =back
1990    
1991    The permissible options for this method are as follows.
1992    
1993    =over 4
1994    
1995    =item testMode
1996    
1997    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1998    
1999    =item keepRoot
2000    
2001    If TRUE, then the entity instances will not be deleted, only the dependent records.
2002    
2003    =back
2004    
2005    =cut
2006    #: Return Type $%;
2007    sub Delete {
2008        # Get the parameters.
2009        my ($self, $entityName, $objectID, %options) = @_;
2010        # Declare the return variable.
2011        my $retVal = Stats->new();
2012        # Get the DBKernel object.
2013        my $db = $self->{_dbh};
2014        # We're going to generate all the paths branching out from the starting entity. One of
2015        # the things we have to be careful about is preventing loops. We'll use a hash to
2016        # determine if we've hit a loop.
2017        my %alreadyFound = ();
2018        # These next lists will serve as our result stack. We start by pushing object lists onto
2019        # the stack, and then popping them off to do the deletes. This means the deletes will
2020        # start with the longer paths before getting to the shorter ones. That, in turn, makes
2021        # sure we don't delete records that might be needed to forge relationships back to the
2022        # original item. We have two lists-- one for TO-relationships, and one for
2023        # FROM-relationships and entities.
2024        my @fromPathList = ();
2025        my @toPathList = ();
2026        # This final list is used to remember what work still needs to be done. We push paths
2027        # onto the list, then pop them off to extend the paths. We prime it with the starting
2028        # point. Note that we will work hard to insure that the last item on a path in the
2029        # to-do list is always an entity.
2030        my @todoList = ([$entityName]);
2031        while (@todoList) {
2032            # Get the current path.
2033            my $current = pop @todoList;
2034            # Copy it into a list.
2035            my @stackedPath = @{$current};
2036            # Pull off the last item on the path. It will always be an entity.
2037            my $myEntityName = pop @stackedPath;
2038            # Add it to the alreadyFound list.
2039            $alreadyFound{$myEntityName} = 1;
2040            # Figure out if we need to delete this entity.
2041            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
2042                # Get the entity data.
2043                my $entityData = $self->_GetStructure($myEntityName);
2044                # Loop through the entity's relations. A DELETE command will be needed for each of them.
2045                my $relations = $entityData->{Relations};
2046                for my $relation (keys %{$relations}) {
2047                    my @augmentedList = (@stackedPath, $relation);
2048                    push @fromPathList, \@augmentedList;
2049                }
2050            }
2051            # Now we need to look for relationships connected to this entity.
2052            my $relationshipList = $self->{_metaData}->{Relationships};
2053            for my $relationshipName (keys %{$relationshipList}) {
2054                my $relationship = $relationshipList->{$relationshipName};
2055                # Check the FROM field. We're only interested if it's us.
2056                if ($relationship->{from} eq $myEntityName) {
2057                    # Add the path to this relationship.
2058                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2059                    push @fromPathList, \@augmentedList;
2060                    # Check the arity. If it's MM we're done. If it's 1M
2061                    # and the target hasn't been seen yet, we want to
2062                    # stack the entity for future processing.
2063                    if ($relationship->{arity} eq '1M') {
2064                        my $toEntity = $relationship->{to};
2065                        if (! exists $alreadyFound{$toEntity}) {
2066                            # Here we have a new entity that's dependent on
2067                            # the current entity, so we need to stack it.
2068                            my @stackList = (@augmentedList, $toEntity);
2069                            push @fromPathList, \@stackList;
2070                        } else {
2071                            Trace("$toEntity ignored because it occurred previously.") if T(4);
2072                        }
2073                    }
2074                }
2075                # Now check the TO field. In this case only the relationship needs
2076                # deletion.
2077                if ($relationship->{to} eq $myEntityName) {
2078                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2079                    push @toPathList, \@augmentedList;
2080                }
2081            }
2082        }
2083        # Create the first qualifier for the WHERE clause. This selects the
2084        # keys of the primary entity records to be deleted. When we're deleting
2085        # from a dependent table, we construct a join path from the first qualifier
2086        # to the table containing the dependent records to delete.
2087        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
2088        # We need to make two passes. The first is through the to-list, and
2089        # the second through the from-list. The from-list is second because
2090        # the to-list may need to pass through some of the entities the
2091        # from-list would delete.
2092        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
2093        # Now it's time to do the deletes. We do it in two passes.
2094        for my $keyName ('to_link', 'from_link') {
2095            # Get the list for this key.
2096            my @pathList = @{$stackList{$keyName}};
2097            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
2098            # Loop through this list.
2099            while (my $path = pop @pathList) {
2100                # Get the table whose rows are to be deleted.
2101                my @pathTables = @{$path};
2102                # Start the DELETE statement. We need to call DBKernel because the
2103                # syntax of a DELETE-USING varies among DBMSs.
2104                my $target = $pathTables[$#pathTables];
2105                my $stmt = $db->SetUsing(@pathTables);
2106                # Now start the WHERE. The first thing is the ID field from the starting table. That
2107                # starting table will either be the entity relation or one of the entity's
2108                # sub-relations.
2109                $stmt .= " WHERE $pathTables[0].id $qualifier";
2110                # Now we run through the remaining entities in the path, connecting them up.
2111                for (my $i = 1; $i <= $#pathTables; $i += 2) {
2112                    # Connect the current relationship to the preceding entity.
2113                    my ($entity, $rel) = @pathTables[$i-1,$i];
2114                    # The style of connection depends on the direction of the relationship.
2115                    $stmt .= " AND $entity.id = $rel.$keyName";
2116                    if ($i + 1 <= $#pathTables) {
2117                        # Here there's a next entity, so connect that to the relationship's
2118                        # to-link.
2119                        my $entity2 = $pathTables[$i+1];
2120                        $stmt .= " AND $rel.to_link = $entity2.id";
2121                    }
2122                }
2123                # Now we have our desired DELETE statement.
2124                if ($options{testMode}) {
2125                    # Here the user wants to trace without executing.
2126                    Trace($stmt) if T(0);
2127                } else {
2128                    # Here we can delete. Note that the SQL method dies with a confession
2129                    # if an error occurs, so we just go ahead and do it.
2130                    Trace("Executing delete from $target using '$objectID'.") if T(3);
2131                    my $rv = $db->SQL($stmt, 0, $objectID);
2132                    # Accumulate the statistics for this delete. The only rows deleted
2133                    # are from the target table, so we use its name to record the
2134                    # statistic.
2135                    $retVal->Add($target, $rv);
2136                }
2137            }
2138        }
2139        # Return the result.
2140        return $retVal;
2141    }
2142    
2143    =head3 Disconnect
2144    
2145        $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2146    
2147    Disconnect an entity instance from all the objects to which it is related. This
2148    will delete each relationship instance that connects to the specified entity.
2149    
2150    =over 4
2151    
2152    =item relationshipName
2153    
2154    Name of the relationship whose instances are to be deleted.
2155    
2156    =item originEntityName
2157    
2158    Name of the entity that is to be disconnected.
2159    
2160    =item originEntityID
2161    
2162    ID of the entity that is to be disconnected.
2163    
2164    =back
2165    
2166    =cut
2167    
2168    sub Disconnect {
2169        # Get the parameters.
2170        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
2171        # Get the relationship descriptor.
2172        my $structure = $self->_GetStructure($relationshipName);
2173        # Insure we have a relationship.
2174        if (! exists $structure->{from}) {
2175            Confess("$relationshipName is not a relationship in the database.");
2176        } else {
2177            # Get the database handle.
2178            my $dbh = $self->{_dbh};
2179            # We'll set this value to 1 if we find our entity.
2180            my $found = 0;
2181            # Loop through the ends of the relationship.
2182            for my $dir ('from', 'to') {
2183                if ($structure->{$dir} eq $originEntityName) {
2184                    $found = 1;
2185                    # Here we want to delete all relationship instances on this side of the
2186                    # entity instance.
2187                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2188                    # We do this delete in batches to keep it from dragging down the
2189                    # server.
2190                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2191                    my $done = 0;
2192                    while (! $done) {
2193                        # Do the delete.
2194                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2195                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2196                        $done = ($rows == 0 || ! $limitClause);
2197                    }
2198                }
2199            }
2200            # Insure we found the entity on at least one end.
2201            if (! $found) {
2202                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2203            }
2204        }
2205    }
2206    
2207    =head3 DeleteRow
2208    
2209        $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2210    
2211    Delete a row from a relationship. In most cases, only the from-link and to-link are
2212    needed; however, for relationships with intersection data values can be specified
2213    for the other fields using a hash.
2214    
2215    =over 4
2216    
2217    =item relationshipName
2218    
2219    Name of the relationship from which the row is to be deleted.
2220    
2221    =item fromLink
2222    
2223    ID of the entity instance in the From direction.
2224    
2225    =item toLink
2226    
2227    ID of the entity instance in the To direction.
2228    
2229    =item values
2230    
2231    Reference to a hash of other values to be used for filtering the delete.
2232    
2233    =back
2234    
2235    =cut
2236    
2237    sub DeleteRow {
2238        # Get the parameters.
2239        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2240        # Create a hash of all the filter information.
2241        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2242        if (defined $values) {
2243            for my $key (keys %{$values}) {
2244                $filter{$key} = $values->{$key};
2245            }
2246        }
2247        # Build an SQL statement out of the hash.
2248        my @filters = ();
2249        my @parms = ();
2250        for my $key (keys %filter) {
2251            push @filters, _FixName($key) . " = ?";
2252            push @parms, $filter{$key};
2253        }
2254        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2255        my $command = "DELETE FROM $relationshipName WHERE " .
2256                      join(" AND ", @filters);
2257        # Execute it.
2258        my $dbh = $self->{_dbh};
2259        $dbh->SQL($command, undef, @parms);
2260    }
2261    
2262    =head3 DeleteLike
2263    
2264        my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2265    
2266    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2267    filter, only fields from the relationship itself can be used.
2268    
2269    =over 4
2270    
2271    =item relName
2272    
2273    Name of the relationship whose records are to be deleted.
2274    
2275    =item filter
2276    
2277    A filter clause (L</Get>-style) for the delete query.
2278    
2279    =item parms
2280    
2281    Reference to a list of parameters for the filter clause.
2282    
2283    =item RETURN
2284    
2285    Returns a count of the number of rows deleted.
2286    
2287    =back
2288    
2289    =cut
2290    
2291    sub DeleteLike {
2292        # Get the parameters.
2293        my ($self, $objectName, $filter, $parms) = @_;
2294        # Declare the return variable.
2295        my $retVal;
2296        # Insure the parms argument is an array reference if the caller left it off.
2297        if (! defined($parms)) {
2298            $parms = [];
2299        }
2300        # Insure we have a relationship. The main reason for this is if we delete an entity
2301        # instance we have to yank out a bunch of other stuff with it.
2302        if ($self->IsEntity($objectName)) {
2303            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2304        } else {
2305            # Create the SQL command suffix to get the desierd records.
2306            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2307            # Convert it to a DELETE command.
2308            my $command = "DELETE $suffix";
2309            # Execute the command.
2310            my $dbh = $self->{_dbh};
2311            my $result = $dbh->SQL($command, 0, @{$parms});
2312            # Check the results. Note we convert the "0D0" result to a real zero.
2313            # A failure causes an abnormal termination, so the caller isn't going to
2314            # worry about it.
2315            if (! defined $result) {
2316                Confess("Error deleting from $objectName: " . $dbh->errstr());
2317            } elsif ($result == 0) {
2318                $retVal = 0;
2319            } else {
2320                $retVal = $result;
2321            }
2322        }
2323        # Return the result count.
2324        return $retVal;
2325    }
2326    
2327    =head3 SortNeeded
2328    
2329        my $parms = $erdb->SortNeeded($relationName);
2330    
2331    Return the pipe command for the sort that should be applied to the specified
2332    relation when creating the load file.
2333    
2334    For example, if the load file should be sorted ascending by the first
2335    field, this method would return
2336    
2337        sort -k1 -t"\t"
2338    
2339    If the first field is numeric, the method would return
2340    
2341        sort -k1n -t"\t"
2342    
2343    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2344    keys using a sort.
2345    
2346    =over 4
2347    
2348    =item relationName
2349    
2350    Name of the relation to be examined.
2351    
2352    =item
2353    
2354    Returns the sort command to use for sorting the relation, suitable for piping.
2355    
2356    =back
2357    
2358    =cut
2359    #: Return Type $;
2360    sub SortNeeded {
2361        # Get the parameters.
2362        my ($self, $relationName) = @_;
2363        # Declare a descriptor to hold the names of the key fields.
2364        my @keyNames = ();
2365        # Get the relation structure.
2366        my $relationData = $self->_FindRelation($relationName);
2367        # Find out if the relation is a primary entity relation,
2368        # a relationship relation, or a secondary entity relation.
2369        my $entityTable = $self->{_metaData}->{Entities};
2370        my $relationshipTable = $self->{_metaData}->{Relationships};
2371        if (exists $entityTable->{$relationName}) {
2372            # Here we have a primary entity relation.
2373            push @keyNames, "id";
2374        } elsif (exists $relationshipTable->{$relationName}) {
2375            # Here we have a relationship. We sort using the FROM index.
2376            my $relationshipData = $relationshipTable->{$relationName};
2377            my $index = $relationData->{Indexes}->{idxFrom};
2378            push @keyNames, @{$index->{IndexFields}};
2379        } else {
2380            # Here we have a secondary entity relation, so we have a sort on the ID field.
2381            push @keyNames, "id";
2382        }
2383        # Now we parse the key names into sort parameters. First, we prime the return
2384        # string.
2385        my $retVal = "sort -S 1G -T\"$FIG_Config::temp\" -t\"\t\" ";
2386        # Get the relation's field list.
2387        my @fields = @{$relationData->{Fields}};
2388        # Loop through the keys.
2389        for my $keyData (@keyNames) {
2390            # Get the key and the ordering.
2391            my ($keyName, $ordering);
2392            if ($keyData =~ /^([^ ]+) DESC/) {
2393                ($keyName, $ordering) = ($1, "descending");
2394            } else {
2395                ($keyName, $ordering) = ($keyData, "ascending");
2396            }
2397            # Find the key's position and type.
2398            my $fieldSpec;
2399            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2400                my $thisField = $fields[$i];
2401                if ($thisField->{name} eq $keyName) {
2402                    # Get the sort modifier for this field type. The modifier
2403                    # decides whether we're using a character, numeric, or
2404                    # floating-point sort.
2405                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2406                    # If the index is descending for this field, denote we want
2407                    # to reverse the sort order on this field.
2408                    if ($ordering eq 'descending') {
2409                        $modifier .= "r";
2410                    }
2411                    # Store the position and modifier into the field spec, which
2412                    # will stop the inner loop. Note that the field number is
2413                    # 1-based in the sort command, so we have to increment the
2414                    # index.
2415                    my $realI = $i + 1;
2416                    $fieldSpec = "$realI,$realI$modifier";
2417                }
2418            }
2419            # Add this field to the sort command.
2420            $retVal .= " -k$fieldSpec";
2421        }
2422        # Return the result.
2423        return $retVal;
2424    }
2425    
2426    =head3 GetList
2427    
2428        my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2429    
2430    Return a list of object descriptors for the specified objects as determined by the
2431    specified filter clause.
2432    
2433    This method is essentially the same as L</Get> except it returns a list of objects rather
2434    than a query object that can be used to get the results one record at a time.
2435    
2436    =over 4
2437    
2438    =item objectNames
2439    
2440    List containing the names of the entity and relationship objects to be retrieved.
2441    
2442    =item filterClause
2443    
2444    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2445    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2446    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2447    in the filter clause should be added to the parameter list as additional parameters. The
2448    fields in a filter clause can come from primary entity relations, relationship relations,
2449    or secondary entity relations; however, all of the entities and relationships involved must
2450    be included in the list of object names.
2451    
2452    The filter clause can also specify a sort order. To do this, simply follow the filter string
2453    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2454    particular genus and sorts them by species name.
2455    
2456        "Genome(genus) = ? ORDER BY Genome(species)"
2457    
2458    The rules for field references in a sort order are the same as those for field references in the
2459    filter clause in general; however, odd things may happen if a sort field is from a secondary
2460    relation.
2461    
2462    =item params
2463    
2464    Reference to a list of parameter values to be substituted into the filter clause.
2465    
2466    =item RETURN
2467    
2468    Returns a list of B<ERDBObject>s that satisfy the query conditions.
2469    
2470    =back
2471    
2472    =cut
2473    #: Return Type @%
2474    sub GetList {
2475        # Get the parameters.
2476        my ($self, $objectNames, $filterClause, $params) = @_;
2477        # Declare the return variable.
2478        my @retVal = ();
2479        # Perform the query.
2480        my $query = $self->Get($objectNames, $filterClause, $params);
2481        # Loop through the results.
2482        while (my $object = $query->Fetch) {
2483            push @retVal, $object;
2484        }
2485        # Return the result.
2486        return @retVal;
2487    }
2488    
2489    =head3 GetCount
2490    
2491        my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2492    
2493    Return the number of rows found by a specified query. This method would
2494    normally be used to count the records in a single table. For example, in a
2495    genetics database
2496    
2497        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2498    
2499    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2500    to use it to return records based on a join. For example,
2501    
2502        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2503                                    ['homo %']);
2504    
2505    would return the number of features for genomes in the genus I<homo>. Note that
2506    only the rows from the first table are counted. If the above command were
2507    
2508        my $count = $erdb->GetCount(['Genome', 'HasFeature'], 'Genome(genus-species) LIKE ?',
2509                                    ['homo %']);
2510    
2511    it would return the number of genomes, not the number of genome/feature pairs.
2512    
2513    =over 4
2514    
2515    =item objectNames
2516    
2517    Reference to a list of the objects (entities and relationships) included in the
2518    query.
2519    
2520    =item filter
2521    
2522    A filter clause for restricting the query. The rules are the same as for the L</Get>
2523    method.
2524    
2525    =item params
2526    
2527    Reference to a list of the parameter values to be substituted for the parameter marks
2528    in the filter.
2529    
2530    =item RETURN
2531    
2532    Returns a count of the number of records in the first table that would satisfy
2533    the query.
2534    
2535    =back
2536    
2537    =cut
2538    
2539    sub GetCount {
2540        # Get the parameters.
2541        my ($self, $objectNames, $filter, $params) = @_;
2542        # Insure the params argument is an array reference if the caller left it off.
2543        if (! defined($params)) {
2544            $params = [];
2545        }
2546        # Declare the return variable.
2547        my $retVal;
2548        # Find out if we're counting an entity or a relationship.
2549        my $countedField;
2550        if ($self->IsEntity($objectNames->[0])) {
2551            $countedField = "id";
2552        } else {
2553            # For a relationship we count the to-link because it's usually more
2554            # numerous. Note we're automatically converting to the SQL form
2555            # of the field name (to_link vs. to-link).
2556            $countedField = "to_link";
2557        }
2558        # Create the SQL command suffix to get the desired records.
2559        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2560                                                                                $filter);
2561        # Prefix it with text telling it we want a record count.
2562        my $firstObject = $mappedNameListRef->[0];
2563        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2564        # Prepare and execute the command.
2565        my $sth = $self->_GetStatementHandle($command, $params);
2566        # Get the count value.
2567        ($retVal) = $sth->fetchrow_array();
2568        # Check for a problem.
2569        if (! defined($retVal)) {
2570            if ($sth->err) {
2571                # Here we had an SQL error.
2572                Confess("Error retrieving row count: " . $sth->errstr());
2573            } else {
2574                # Here we have no result.
2575                Confess("No result attempting to retrieve row count.");
2576            }
2577        }
2578        # Return the result.
2579        return $retVal;
2580    }
2581    
2582    =head3 ComputeObjectSentence
2583    
2584        my $sentence = $erdb->ComputeObjectSentence($objectName);
2585    
2586    Check an object name, and if it is a relationship convert it to a relationship sentence.
2587    
2588    =over 4
2589    
2590    =item objectName
2591    
2592    Name of the entity or relationship.
2593    
2594    =item RETURN
2595    
2596    Returns a string containing the entity name or a relationship sentence.
2597    
2598    =back
2599    
2600    =cut
2601    
2602    sub ComputeObjectSentence {
2603        # Get the parameters.
2604        my ($self, $objectName) = @_;
2605        # Set the default return value.
2606        my $retVal = $objectName;
2607        # Look for the object as a relationship.
2608        my $relTable = $self->{_metaData}->{Relationships};
2609        if (exists $relTable->{$objectName}) {
2610            # Get the relationship sentence.
2611            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2612        }
2613        # Return the result.
2614        return $retVal;
2615    }
2616    
2617    =head3 DumpRelations
2618    
2619        $erdb->DumpRelations($outputDirectory);
2620    
2621    Write the contents of all the relations to tab-delimited files in the specified directory.
2622    Each file will have the same name as the relation dumped, with an extension of DTX.
2623    
2624    =over 4
2625    
2626    =item outputDirectory
2627    
2628    Name of the directory into which the relation files should be dumped.
2629    
2630    =back
2631    
2632    =cut
2633    
2634    sub DumpRelations {
2635        # Get the parameters.
2636        my ($self, $outputDirectory) = @_;
2637        # Now we need to run through all the relations. First, we loop through the entities.
2638        my $metaData = $self->{_metaData};
2639        my $entities = $metaData->{Entities};
2640        for my $entityName (keys %{$entities}) {
2641            my $entityStructure = $entities->{$entityName};
2642            # Get the entity's relations.
2643            my $relationList = $entityStructure->{Relations};
2644            # Loop through the relations, dumping them.
2645            for my $relationName (keys %{$relationList}) {
2646                my $relation = $relationList->{$relationName};
2647                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2648            }
2649        }
2650        # Next, we loop through the relationships.
2651        my $relationships = $metaData->{Relationships};
2652        for my $relationshipName (keys %{$relationships}) {
2653            my $relationshipStructure = $relationships->{$relationshipName};
2654            # Dump this relationship's relation.
2655            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2656        }
2657    }
2658    
2659    =head3 InsertValue
2660    
2661        $erdb->InsertValue($entityID, $fieldName, $value);
2662    
2663    This method will insert a new value into the database. The value must be one
2664    associated with a secondary relation, since primary values cannot be inserted:
2665    they occur exactly once. Secondary values, on the other hand, can be missing
2666    or multiply-occurring.
2667    
2668    =over 4
2669    
2670    =item entityID
2671    
2672    ID of the object that is to receive the new value.
2673    
2674    =item fieldName
2675    
2676    Field name for the new value-- this includes the entity name, since
2677    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2678    
2679    =item value
2680    
2681    New value to be put in the field.
2682    
2683    =back
2684    
2685    =cut
2686    
2687    sub InsertValue {
2688        # Get the parameters.
2689        my ($self, $entityID, $fieldName, $value) = @_;
2690        # Parse the entity name and the real field name.
2691        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2692            my $entityName = $1;
2693            my $fieldTitle = $2;
2694            # Get its descriptor.
2695            if (!$self->IsEntity($entityName)) {
2696                Confess("$entityName is not a valid entity.");
2697            } else {
2698                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2699                # Find the relation containing this field.
2700                my $fieldHash = $entityData->{Fields};
2701                if (! exists $fieldHash->{$fieldTitle}) {
2702                    Confess("$fieldTitle not found in $entityName.");
2703                } else {
2704                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2705                    if ($relation eq $entityName) {
2706                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2707                    } else {
2708                        # Now we can create an INSERT statement.
2709                        my $dbh = $self->{_dbh};
2710                        my $fixedName = _FixName($fieldTitle);
2711                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2712                        # Execute the command.
2713                        $dbh->SQL($statement, 0, $entityID, $value);
2714                    }
2715                }
2716            }
2717        } else {
2718            Confess("$fieldName is not a valid field name.");
2719        }
2720    }
2721    
2722    =head3 InsertObject
2723    
2724        $erdb->InsertObject($objectType, \%fieldHash);
2725    
2726    Insert an object into the database. The object is defined by a type name and then a hash
2727    of field names to values. Field values in the primary relation are represented by scalars.
2728    (Note that for relationships, the primary relation is the B<only> relation.)
2729    Field values for the other relations comprising the entity are always list references. For
2730    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2731    C<ZP_00210270.1> and C<gi|46206278>.
2732    
2733        $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2734    
2735    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2736    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2737    
2738        $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2739    
2740    =over 4
2741    
2742    =item newObjectType
2743    
2744    Type name of the object to insert.
2745    
2746    =item fieldHash
2747    
2748    Hash of field names to values.
2749    
2750    =back
2751    
2752    =cut
2753    
2754    sub InsertObject {
2755        # Get the parameters.
2756        my ($self, $newObjectType, $fieldHash) = @_;
2757        # Denote that so far we appear successful.
2758        my $retVal = 1;
2759        # Get the database handle.
2760        my $dbh = $self->{_dbh};
2761        # Get the relation list.
2762        my $relationTable = $self->_GetRelationTable($newObjectType);
2763        # Loop through the relations. We'll build insert statements for each one. If a relation is
2764        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2765        # stop the loop.
2766        my @relationList = keys %{$relationTable};
2767        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2768            my $relationName = $relationList[$i];
2769            my $relationDefinition = $relationTable->{$relationName};
2770            # Get the relation's fields. For each field we will collect a value in the corresponding
2771            # position of the @valueList array. If one of the fields is missing, we will add it to the
2772            # @missing list.
2773            my @fieldList = @{$relationDefinition->{Fields}};
2774            my @fieldNameList = ();
2775            my @valueList = ();
2776            my @missing = ();
2777            my $recordCount = 1;
2778            for my $fieldDescriptor (@fieldList) {
2779                # Get the field name and save it. Note we need to fix it up so the hyphens
2780                # are converted to underscores.
2781                my $fieldName = $fieldDescriptor->{name};
2782                push @fieldNameList, _FixName($fieldName);
2783                # Look for the named field in the incoming structure. Note that we are looking
2784                # for the real field name, not the fixed-up one!
2785                if (exists $fieldHash->{$fieldName}) {
2786                    # Here we found the field. Stash it in the value list.
2787                    my $value = $fieldHash->{$fieldName};
2788                    push @valueList, $value;
2789                    # If the value is a list, we may need to increment the record count.
2790                    if (ref $value eq "ARRAY") {
2791                        my $thisCount = @{$value};
2792                        if ($recordCount == 1) {
2793                            # Here we have our first list, so we save its count.
2794                            $recordCount = $thisCount;
2795                        } elsif ($recordCount != $thisCount) {
2796                            # Here we have a second list, so its length has to match the
2797                            # previous lists.
2798                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2799                            $retVal = 0;
2800                        }
2801                    }
2802                } else {
2803                    # Here the field is not present. Flag it as missing.
2804                    push @missing, $fieldName;
2805                }
2806            }
2807            # Only proceed if there are no missing fields.
2808            if (@missing > 0) {
2809                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2810                    join(' ', @missing)) if T(1);
2811            } else {
2812                # Build the INSERT statement.
2813                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2814                    ") VALUES (";
2815                # Create a marker list of the proper size and put it in the statement.
2816                my @markers = ();
2817                while (@markers < @fieldNameList) { push @markers, '?'; }
2818                $statement .= join(', ', @markers) . ")";
2819                # We have the insert statement, so prepare it.
2820                my $sth = $dbh->prepare_command($statement);
2821                Trace("Insert statement prepared: $statement") if T(3);
2822                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2823                # a list, we use the current element. The values are stored in the @parameterList array.
2824                my $done = 0;
2825                for (my $i = 0; $i < $recordCount; $i++) {
2826                    # Clear the parameter list array.
2827                    my @parameterList = ();
2828                    # Loop through the values.
2829                    for my $value (@valueList) {
2830                        # Check to see if this is a scalar value.
2831                        if (ref $value eq "ARRAY") {
2832                            # Here we have a list value. Pull the current entry.
2833                            push @parameterList, $value->[$i];
2834                        } else {
2835                            # Here we have a scalar value. Use it unmodified.
2836                            push @parameterList, $value;
2837                        }
2838                    }
2839                    # Execute the INSERT statement with the specified parameter list.
2840                    $retVal = $sth->execute(@parameterList);
2841                    if (!$retVal) {
2842                        my $errorString = $sth->errstr();
2843                        Confess("Error inserting into $relationName: $errorString");
2844                    } else {
2845                        Trace("Insert successful using $parameterList[0].") if T(3);
2846                    }
2847                }
2848            }
2849        }
2850        # Return a 1 for backward compatability.
2851        return 1;
2852    }
2853    
2854    =head3 UpdateEntity
2855    
2856        $erdb->UpdateEntity($entityName, $id, \%fields);
2857    
2858    Update the values of an entity. This is an unprotected update, so it should only be
2859    done if the database resides on a database server.
2860    
2861    =over 4
2862    
2863    =item entityName
2864    
2865    Name of the entity to update. (This is the entity type.)
2866    
2867    =item id
2868    
2869    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2870    
2871    =item fields
2872    
2873    Reference to a hash mapping field names to their new values. All of the fields named
2874    must be in the entity's primary relation, and they cannot any of them be the ID field.
2875    
2876    =back
2877    
2878    =cut
2879    
2880    sub UpdateEntity {
2881        # Get the parameters.
2882        my ($self, $entityName, $id, $fields) = @_;
2883        # Get a list of the field names being updated.
2884        my @fieldList = keys %{$fields};
2885        # Verify that the fields exist.
2886        my $checker = $self->GetFieldTable($entityName);
2887        for my $field (@fieldList) {
2888            if ($field eq 'id') {
2889                Confess("Cannot update the ID field for entity $entityName.");
2890            } elsif ($checker->{$field}->{relation} ne $entityName) {
2891                Confess("Cannot find $field in primary relation of $entityName.");
2892            }
2893        }
2894        # Build the SQL statement.
2895        my @sets = ();
2896        my @valueList = ();
2897        for my $field (@fieldList) {
2898            push @sets, _FixName($field) . " = ?";
2899            push @valueList, $fields->{$field};
2900        }
2901        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2902        # Add the ID to the list of binding values.
2903        push @valueList, $id;
2904        # Call SQL to do the work.
2905        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2906        # Check for errors.
2907        if ($rows == 0) {
2908            Confess("Entity $id of type $entityName not found.");
2909        }
2910    }
2911    
2912    =head3 LoadTable
2913    
2914        my $results = $erdb->LoadTable($fileName, $relationName, %options);
2915    
2916    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2917    first.
2918    
2919    =over 4
2920    
2921    =item fileName
2922    
2923    Name of the file from which the table data should be loaded.
2924    
2925    =item relationName
2926    
2927    Name of the relation to be loaded. This is the same as the table name.
2928    
2929    =item options
2930    
2931    A hash of load options.
2932    
2933    =item RETURN
2934    
2935    Returns a statistical object containing a list of the error messages.
2936    
2937    =back
2938    
2939    The permissible options are as follows.
2940    
2941    =over 4
2942    
2943    =item truncate
2944    
2945    If TRUE, then the table will be erased before loading.
2946    
2947    =item mode
2948    
2949    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2950    This option is only applicable to a MySQL database.
2951    
2952    =item partial
2953    
2954    If TRUE, then it is assumed that this is a partial load, and the table will not
2955    be analyzed and compacted at the end.
2956    
2957    =back
2958    
2959    =cut
2960    sub LoadTable {
2961        # Get the parameters.
2962        my ($self, $fileName, $relationName, %options) = @_;
2963        # Create the statistical return object.
2964        my $retVal = _GetLoadStats();
2965        # Trace the fact of the load.
2966        Trace("Loading table $relationName from $fileName") if T(2);
2967        # Get the database handle.
2968        my $dbh = $self->{_dbh};
2969        # Get the input file size.
2970        my $fileSize = -s $fileName;
2971        # Get the relation data.
2972        my $relation = $self->_FindRelation($relationName);
2973        # Check the truncation flag.
2974        if ($options{truncate}) {
2975            Trace("Creating table $relationName") if T(2);
2976            # Compute the row count estimate. We take the size of the load file,
2977            # divide it by the estimated row size, and then multiply by 2 to
2978            # leave extra room. We postulate a minimum row count of 1000 to
2979            # prevent problems with incoming empty load files.
2980            my $rowSize = $self->EstimateRowSize($relationName);
2981            my $estimate = $fileSize * 8 / $rowSize;
2982            if ($estimate < 1000) {
2983                $estimate = 1000;
2984            }
2985            # Re-create the table without its index.
2986            $self->CreateTable($relationName, 0, $estimate);
2987            # If this is a pre-index DBMS, create the index here.
2988            if ($dbh->{_preIndex}) {
2989                eval {
2990                    $self->CreateIndex($relationName);
2991                };
2992                if ($@) {
2993                    $retVal->AddMessage($@);
2994                }
2995            }
2996        }
2997        # Load the table.
2998        my $rv;
2999        eval {
3000            $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
3001        };
3002        if (!defined $rv) {
3003            $retVal->AddMessage($@) if ($@);
3004            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
3005            Trace("Table load failed for $relationName.") if T(1);
3006        } else {
3007            # Here we successfully loaded the table.
3008            $retVal->Add("tables");
3009            my $size = -s $fileName;
3010            Trace("$size bytes loaded into $relationName.") if T(2);
3011            $retVal->Add("bytes", $size);
3012            # If we're rebuilding, we need to create the table indexes.
3013            if ($options{truncate}) {
3014                # Indexes are created here for PostGres. For PostGres, indexes are
3015                # best built at the end. For MySQL, the reverse is true.
3016                if (! $dbh->{_preIndex}) {
3017                    eval {
3018                        $self->CreateIndex($relationName);
3019                    };
3020                    if ($@) {
3021                        $retVal->AddMessage($@);
3022                    }
3023                }
3024                # The full-text index (if any) is always built last, even for MySQL.
3025                # First we need to see if this table has a full-text index. Only
3026                # primary relations are allowed that privilege.
3027                Trace("Checking for full-text index on $relationName.") if T(2);
3028                if ($self->_IsPrimary($relationName)) {
3029                    $self->CreateSearchIndex($relationName);
3030                }
3031            }
3032        }
3033        # Analyze the table to improve performance.
3034        if (! $options{partial}) {
3035            Trace("Analyzing and compacting $relationName.") if T(3);
3036            $self->Analyze($relationName);
3037        }
3038        Trace("$relationName load completed.") if T(3);
3039        # Return the statistics.
3040        return $retVal;
3041    }
3042    
3043    =head3 Analyze
3044    
3045        $erdb->Analyze($tableName);
3046    
3047    Analyze and compact a table in the database. This is useful after a load
3048    to improve the performance of the indexes.
3049    
3050    =over 4
3051    
3052    =item tableName
3053    
3054    Name of the table to be analyzed and compacted.
3055    
3056    =back
3057    
3058    =cut
3059    
3060    sub Analyze {
3061        # Get the parameters.
3062        my ($self, $tableName) = @_;
3063        # Analyze the table.
3064        $self->{_dbh}->vacuum_it($tableName);
3065    }
3066    
3067    =head3 TruncateTable
3068    
3069        $erdb->TruncateTable($table);
3070    
3071    Delete all rows from a table quickly. This uses the built-in SQL
3072    C<TRUNCATE> statement, which effectively drops and re-creates a table
3073    with all its settings intact.
3074    
3075    =over 4
3076    
3077    =item table
3078    
3079    Name of the table to be cleared.
3080    
3081    =back
3082    
3083    =cut
3084    
3085    sub TruncateTable {
3086        # Get the parameters.
3087        my ($self, $table) = @_;
3088        # Get the database handle.
3089        my $dbh = $self->{_dbh};
3090        # Execute a truncation comment.
3091        $dbh->SQL("TRUNCATE TABLE $table");
3092    }
3093    
3094    
3095    =head3 CreateSearchIndex
3096    
3097        $erdb->CreateSearchIndex($objectName);
3098    
3099    Check for a full-text search index on the specified entity or relationship object, and
3100    if one is required, rebuild it.
3101    
3102    =over 4
3103    
3104    =item objectName
3105    
3106    Name of the entity or relationship to be indexed.
3107    
3108    =back
3109    
3110    =cut
3111    
3112    sub CreateSearchIndex {
3113        # Get the parameters.
3114        my ($self, $objectName) = @_;
3115        # Get the relation's entity/relationship structure.
3116        my $structure = $self->_GetStructure($objectName);
3117        # Get the database handle.
3118        my $dbh = $self->{_dbh};
3119        Trace("Checking for search fields in $objectName.") if T(3);
3120        # Check for a searchable fields list.
3121        if (exists $structure->{searchFields}) {
3122            # Here we know that we need to create a full-text search index.
3123            # Get an SQL-formatted field name list.
3124            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
3125            # Create the index. If it already exists, it will be dropped.
3126            $dbh->create_index(tbl => $objectName, idx => "search_idx",
3127                               flds => $fields, kind => 'fulltext');
3128            Trace("Index created for $fields in $objectName.") if T(2);
3129        }
3130    }
3131    
3132    =head3 DropRelation
3133    
3134        $erdb->DropRelation($relationName);
3135    
3136    Physically drop a relation from the database.
3137    
3138    =over 4
3139    
3140    =item relationName
3141    
3142    Name of the relation to drop. If it does not exist, this method will have
3143    no effect.
3144    
3145    =back
3146    
3147    =cut
3148    
3149    sub DropRelation {
3150        # Get the parameters.
3151        my ($self, $relationName) = @_;
3152        # Get the database handle.
3153        my $dbh = $self->{_dbh};
3154        # Drop the relation. The method used here has no effect if the relation
3155        # does not exist.
3156        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
3157        $dbh->drop_table(tbl => $relationName);
3158    }
3159    
3160    =head3 MatchSqlPattern
3161    
3162        my $matched = ERDB::MatchSqlPattern($value, $pattern);
3163    
3164    Determine whether or not a specified value matches an SQL pattern. An SQL
3165    pattern has two wild card characters: C<%> that matches multiple characters,
3166    and C<_> that matches a single character. These can be escaped using a
3167    backslash (C<\>). We pull this off by converting the SQL pattern to a
3168    PERL regular expression. As per SQL rules, the match is case-insensitive.
3169    
3170    =over 4
3171    
3172    =item value
3173    
3174    Value to be matched against the pattern. Note that an undefined or empty
3175    value will not match anything.
3176    
3177    =item pattern
3178    
3179    SQL pattern against which to match the value. An undefined or empty pattern will
3180    match everything.
3181    
3182    =item RETURN
3183    
3184    Returns TRUE if the value and pattern match, else FALSE.
3185    
3186    =back
3187    
3188    =cut
3189    
3190    sub MatchSqlPattern {
3191        # Get the parameters.
3192        my ($value, $pattern) = @_;
3193        # Declare the return variable.
3194        my $retVal;
3195        # Insure we have a pattern.
3196        if (! defined($pattern) || $pattern eq "") {
3197            $retVal = 1;
3198        } else {
3199            # Break the pattern into pieces around the wildcard characters. Because we
3200            # use parentheses in the split function's delimiter expression, we'll get
3201            # list elements for the delimiters as well as the rest of the string.
3202            my @pieces = split /([_%]|\\[_%])/, $pattern;
3203            # Check some fast special cases.
3204            if ($pattern eq '%') {
3205                # A null pattern matches everything.
3206                $retVal = 1;
3207            } elsif (@pieces == 1) {
3208                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
3209                $retVal = (lc($value) eq lc($pattern));
3210            } elsif (@pieces == 2 && $pieces[1] eq '%') {
3211                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
3212                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
3213            } else {
3214                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
3215                my $realPattern = "";
3216                for my $piece (@pieces) {
3217                    # Determine the type of piece.
3218                    if ($piece eq "") {
3219                        # Empty pieces are ignored.
3220                    } elsif ($piece eq "%") {
3221                        # Here we have a multi-character wildcard. Note that it can match
3222                        # zero or more characters.
3223                        $realPattern .= ".*"
3224                    } elsif ($piece eq "_") {
3225                        # Here we have a single-character wildcard.
3226                        $realPattern .= ".";
3227                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
3228                        # This is an escape sequence (which is a rare thing, actually).
3229                        $realPattern .= substr($piece, 1, 1);
3230                    } else {
3231                        # Here we have raw text.
3232                        $realPattern .= quotemeta($piece);
3233                    }
3234                }
3235                # Do the match.
3236                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
3237            }
3238        }
3239        # Return the result.
3240        return $retVal;
3241    }
3242    
3243    =head3 GetEntity
3244    
3245        my $entityObject = $erdb->GetEntity($entityType, $ID);
3246    
3247    Return an object describing the entity instance with a specified ID.
3248    
3249    =over 4
3250    
3251    =item entityType
3252    
3253    Entity type name.
3254    
3255    =item ID
3256    
3257    ID of the desired entity.
3258    
3259    =item RETURN
3260    
3261    Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
3262    instance is found with the specified key.
3263    
3264    =back
3265    
3266    =cut
3267    
3268    sub GetEntity {
3269        # Get the parameters.
3270        my ($self, $entityType, $ID) = @_;
3271        # Create a query.
3272        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3273        # Get the first (and only) object.
3274        my $retVal = $query->Fetch();
3275        if (T(3)) {
3276            if ($retVal) {
3277                Trace("Entity $entityType \"$ID\" found.");
3278            } else {
3279                Trace("Entity $entityType \"$ID\" not found.");
3280            }
3281        }
3282        # Return the result.
3283        return $retVal;
3284    }
3285    
3286    =head3 GetChoices
3287    
3288        my @values = $erdb->GetChoices($entityName, $fieldName);
3289    
3290    Return a list of all the values for the specified field that are represented in the
3291    specified entity.
3292    
3293    Note that if the field is not indexed, then this will be a very slow operation.
3294    
3295    =over 4
3296    
3297    =item entityName
3298    
3299    Name of an entity in the database.
3300    
3301    =item fieldName
3302    
3303    Name of a field belonging to the entity. This is a raw field name without
3304    the standard parenthesized notation used in most calls.
3305    
3306    =item RETURN
3307    
3308    Returns a list of the distinct values for the specified field in the database.
3309    
3310    =back
3311    
3312    =cut
3313    
3314    sub GetChoices {
3315        # Get the parameters.
3316        my ($self, $entityName, $fieldName) = @_;
3317        # Declare the return variable.
3318        my @retVal;
3319        # Get the entity data structure.
3320        my $entityData = $self->_GetStructure($entityName);
3321        # Get the field.
3322        my $fieldHash = $entityData->{Fields};
3323        if (! exists $fieldHash->{$fieldName}) {
3324            Confess("$fieldName not found in $entityName.");
3325        } else {
3326            # Get the name of the relation containing the field.
3327            my $relation = $fieldHash->{$fieldName}->{relation};
3328            # Fix up the field name.
3329            my $realName = _FixName($fieldName);
3330            # Get the database handle.
3331            my $dbh = $self->{_dbh};
3332            # Query the database.
3333            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
3334            # Clean the results. They are stored as a list of lists, and we just want the one list.
3335            @retVal = sort map { $_->[0] } @{$results};
3336        }
3337        # Return the result.
3338        return @retVal;
3339    }
3340    
3341    =head3 GetEntityValues
3342    
3343        my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3344    
3345    Return a list of values from a specified entity instance. If the entity instance
3346    does not exist, an empty list is returned.
3347    
3348    =over 4
3349    
3350    =item entityType
3351    
3352    Entity type name.
3353    
3354    =item ID
3355    
3356    ID of the desired entity.
3357    
3358    =item fields
3359    
3360    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
3361    
3362    =item RETURN
3363    
3364    Returns a flattened list of the values of the specified fields for the specified entity.
3365    
3366    =back
3367    
3368    =cut
3369    
3370    sub GetEntityValues {
3371        # Get the parameters.
3372        my ($self, $entityType, $ID, $fields) = @_;
3373        # Get the specified entity.
3374        my $entity = $self->GetEntity($entityType, $ID);
3375        # Declare the return list.
3376        my @retVal = ();
3377        # If we found the entity, push the values into the return list.
3378        if ($entity) {
3379            push @retVal, $entity->Values($fields);
3380        }
3381        # Return the result.
3382        return @retVal;
3383    }
3384    
3385    =head3 GetAll
3386    
3387        my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3388    
3389    Return a list of values taken from the objects returned by a query. The first three
3390    parameters correspond to the parameters of the L</Get> method. The final parameter is
3391    a list of the fields desired from each record found by the query. The field name
3392    syntax is the standard syntax used for fields in the B<ERDB> system--
3393    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
3394    or relationship and I<fieldName> is the name of the field.
3395    
3396    The list returned will be a list of lists. Each element of the list will contain
3397    the values returned for the fields specified in the fourth parameter. If one of the
3398    fields specified returns multiple values, they are flattened in with the rest. For
3399    example, the following call will return a list of the features in a particular
3400    spreadsheet cell, and each feature will be represented by a list containing the
3401    feature ID followed by all of its essentiality determinations.
3402    
3403        @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']);
3404    
3405    =over 4
3406    
3407    =item objectNames
3408    
3409    List containing the names of the entity and relationship objects to be retrieved.
3410    
3411    =item filterClause
3412    
3413    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
3414    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
3415    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
3416    parameter list as additional parameters. The fields in a filter clause can come from primary
3417    entity relations, relationship relations, or secondary entity relations; however, all of the
3418    entities and relationships involved must be included in the list of object names.
3419    
3420    =item parameterList
3421    
3422    List of the parameters to be substituted in for the parameters marks in the filter clause.
3423    
3424    =item fields
3425    
3426    List of the fields to be returned in each element of the list returned.
3427    
3428    =item count
3429    
3430    Maximum number of records to return. If omitted or 0, all available records will be returned.
3431    
3432    =item RETURN
3433    
3434    Returns a list of list references. Each element of the return list contains the values for the
3435    fields specified in the B<fields> parameter.
3436    
3437    =back
3438    
3439    =cut
3440    #: Return Type @@;
3441    sub GetAll {
3442        # Get the parameters.
3443        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3444        # Translate the parameters from a list reference to a list. If the parameter
3445        # list is a scalar we convert it into a singleton list.
3446        my @parmList = ();
3447        if (ref $parameterList eq "ARRAY") {
3448            Trace("GetAll parm list is an array.") if T(4);
3449            @parmList = @{$parameterList};
3450        } else {
3451            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3452            push @parmList, $parameterList;
3453        }
3454        # Insure the counter has a value.
3455        if (!defined $count) {
3456            $count = 0;
3457        }
3458        # Add the row limit to the filter clause.
3459        if ($count > 0) {
3460            $filterClause .= " LIMIT $count";
3461        }
3462        # Create the query.
3463        my $query = $self->Get($objectNames, $filterClause, \@parmList);
3464        # Set up a counter of the number of records read.
3465        my $fetched = 0;
3466        # Loop through the records returned, extracting the fields. Note that if the
3467        # counter is non-zero, we stop when the number of records read hits the count.
3468        my @retVal = ();
3469        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3470            my @rowData = $row->Values($fields);
3471            push @retVal, \@rowData;
3472            $fetched++;
3473                  }                  }
3474                  if (@joinWhere) {      # Return the resulting list.
3475                          $command .= " WHERE " . join(' AND ', @joinWhere);      return @retVal;
3476                  }                  }
3477                  # Add the sort clause (if any) to the SELECT command.  
3478                  if ($orderClause) {  =head3 Exists
3479                          $command .= " ORDER BY $orderClause";  
3480        my $found = $sprout->Exists($entityName, $entityID);
3481    
3482    Return TRUE if an entity exists, else FALSE.
3483    
3484    =over 4
3485    
3486    =item entityName
3487    
3488    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3489    
3490    =item entityID
3491    
3492    ID of the entity instance whose existence is to be checked.
3493    
3494    =item RETURN
3495    
3496    Returns TRUE if the entity instance exists, else FALSE.
3497    
3498    =back
3499    
3500    =cut
3501    #: Return Type $;
3502    sub Exists {
3503        # Get the parameters.
3504        my ($self, $entityName, $entityID) = @_;
3505        # Check for the entity instance.
3506        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3507        my $testInstance = $self->GetEntity($entityName, $entityID);
3508        # Return an existence indicator.
3509        my $retVal = ($testInstance ? 1 : 0);
3510        return $retVal;
3511    }
3512    
3513    =head3 EstimateRowSize
3514    
3515        my $rowSize = $erdb->EstimateRowSize($relName);
3516    
3517    Estimate the row size of the specified relation. The estimated row size is computed by adding
3518    up the average length for each data type.
3519    
3520    =over 4
3521    
3522    =item relName
3523    
3524    Name of the relation whose estimated row size is desired.
3525    
3526    =item RETURN
3527    
3528    Returns an estimate of the row size for the specified relation.
3529    
3530    =back
3531    
3532    =cut
3533    #: Return Type $;
3534    sub EstimateRowSize {
3535        # Get the parameters.
3536        my ($self, $relName) = @_;
3537        # Declare the return variable.
3538        my $retVal = 0;
3539        # Find the relation descriptor.
3540        my $relation = $self->_FindRelation($relName);
3541        # Get the list of fields.
3542        for my $fieldData (@{$relation->{Fields}}) {
3543            # Get the field type and add its length.
3544            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3545            $retVal += $fieldLen;
3546                  }                  }
3547        # Return the result.
3548        return $retVal;
3549          }          }
3550          Trace("SQL query: $command") if T(2);  
3551          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));  =head3 GetFieldTable
3552          my $sth = $dbh->prepare_command($command);  
3553          # Execute it with the parameters bound in.      my $fieldHash = $self->GetFieldTable($objectnName);
3554          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
3555          # Return the statement object.  Get the field structure for a specified entity or relationship.
3556          my $retVal = DBQuery::_new($self, $sth, @{$objectNames});  
3557    =over 4
3558    
3559    =item objectName
3560    
3561    Name of the desired entity or relationship.
3562    
3563    =item RETURN
3564    
3565    The table containing the field descriptors for the specified object.
3566    
3567    =back
3568    
3569    =cut
3570    
3571    sub GetFieldTable {
3572        # Get the parameters.
3573        my ($self, $objectName) = @_;
3574        # Get the descriptor from the metadata.
3575        my $objectData = $self->_GetStructure($objectName);
3576        # Return the object's field table.
3577        return $objectData->{Fields};
3578    }
3579    
3580    =head3 SplitKeywords
3581    
3582        my @keywords = ERDB::SplitKeywords($keywordString);
3583    
3584    This method returns a list of the positive keywords in the specified
3585    keyword string. All of the operators will have been stripped off,
3586    and if the keyword is preceded by a minus operator (C<->), it will
3587    not be in the list returned. The idea here is to get a list of the
3588    keywords the user wants to see. The list will be processed to remove
3589    duplicates.
3590    
3591    It is possible to create a string that confuses this method. For example
3592    
3593        frog toad -frog
3594    
3595    would return both C<frog> and C<toad>. If this is a problem we can deal
3596    with it later.
3597    
3598    =over 4
3599    
3600    =item keywordString
3601    
3602    The keyword string to be parsed.
3603    
3604    =item RETURN
3605    
3606    Returns a list of the words in the keyword string the user wants to
3607    see.
3608    
3609    =back
3610    
3611    =cut
3612    
3613    sub SplitKeywords {
3614        # Get the parameters.
3615        my ($keywordString) = @_;
3616        # Make a safety copy of the string. (This helps during debugging.)
3617        my $workString = $keywordString;
3618        # Convert operators we don't care about to spaces.
3619        $workString =~ tr/+"()<>/ /;
3620        # Split the rest of the string along space boundaries. Note that we
3621        # eliminate any words that are zero length or begin with a minus sign.
3622        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3623        # Use a hash to remove duplicates.
3624        my %words = map { $_ => 1 } @wordList;
3625        # Return the result.
3626        return sort keys %words;
3627    }
3628    
3629    =head3 ValidateFieldName
3630    
3631        my $okFlag = ERDB::ValidateFieldName($fieldName);