[Bio] / Sprout / ERDB.pm Repository:
ViewVC logotype

Diff of /Sprout/ERDB.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.2, Tue Jan 25 01:00:20 2005 UTC revision 1.84, Wed Jan 24 10:22:22 2007 UTC
# Line 1  Line 1 
1  package ERDB;  package ERDB;
2    
3          use strict;          use strict;
         use Carp;  
4          use Tracer;          use Tracer;
5          use DBKernel;      use DBrtns;
6          use Data::Dumper;          use Data::Dumper;
7          use XML::Simple;          use XML::Simple;
8          use DBQuery;          use DBQuery;
9          use DBObject;          use DBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13        use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 33  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 57  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.  
78    =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 cannot be used in indexes or sorting and do not support the
106    normal syntax of filter clauses, but can be up to a billion character in length
107    
108    =item float
109    
110    double-precision floating-point number
111    
112    =item boolean
113    
114    single-bit numeric value; The value is stored as a 16-bit signed integer (for
115    compatability with certain database packages), but the only values supported are
116    0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122    =item key-string
123    
124    variable-length string, maximum 40 characters
125    
126    =item name-string
127    
128    variable-length string, maximum 80 characters
129    
130    =item medium-string
131    
132    variable-length string, maximum 160 characters
133    
134    =item string
135    
136    variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142    =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151    =head3 Global Tags
152    
153    The entire database definition must be inside a B<Database> tag. The display name of
154    the database is given by the text associated with the B<Title> tag. The display name
155    is only used in the automated documentation. It has no other effect. The entities and
156    relationships are listed inside the B<Entities> and B<Relationships> tags,
157    respectively. None of these tags have attributes.
158    
159        <Database>
160            <Title>... display title here...</Title>
161            <Entities>
162                ... entity definitions here ...
163            </Entities>
164            <Relationships>
165                ... relationship definitions here...
166            </Relationships>
167        </Database>
168    
169    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170    The text inside the B<Notes> tag contains comments that will appear when the database
171    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173    
174    =head3 Fields
175    
176    Both entities and relationships have fields described by B<Field> tags. A B<Field>
177    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178    object mus be inside B<Fields> tags.
179    
180        <Entity ... >
181            <Fields>
182                ... Field tags ...
183            </Fields>
184        </Entity>
185    
186    The attributes for the B<Field> tag are as follows.
187    
188    =over 4
189    
190    =item name
191    
192    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193    and the first character should be a letter. Most underlying databases are case-insensitive
194    with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198    =item type
199    
200    Data type of the field. The legal data types are given above.
201    
202    =item relation
203    
204    Name of the relation containing the field. This should only be specified for entity
205    fields. The ERDB system does not support optional fields or multi-occurring fields
206    in the primary relation of an entity. Instead, they are put into secondary relations.
207    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208    grouping used to select a subset of the genomes. A given genome may not be in any
209    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210    value. The relation name specified must be a valid table name. By convention, it is
211    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212    entity, the fields without a relation attribute are said to belong to the
213    I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227    =back
228    
229    =head3 Indexes
230    
231    An entity can have multiple alternate indexes associated with it. The fields must
232    all be from the same relation. The alternate indexes assist in ordering results
233    from a query. A relationship can have up to two indexes-- a I<to-index> and a
234    I<from-index>. These order the results when crossing the relationship. For
235    example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236    from-index would order the contigs of a ganome, and the to-index would order
237    the genomes of a contig. A relationship's index must specify only fields in
238    the relationship.
239    
240    The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
241    of a relationship is specified using the B<FromIndex> tag; the to-index is specified
242    using the B<ToIndex> tag.
243    
244    Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245    tag containing the B<IndexField> tags. These specify, in order, the fields used in
246    the index. The attributes of an B<IndexField> tag are as follows.
247    
248    =over 4
249    
250    =item name
251    
252    Name of the field.
253    
254    =item order
255    
256    Sort order of the field-- C<ascending> or C<descending>.
257    
258    =back
259    
260    The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
261    have a B<Unique> attribute. If specified, the index will be generated as a unique
262    index.
263    
264    =head3 Object and Field Names
265    
266    By convention entity and relationship names use capital casing (e.g. C<Genome> or
267    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
268    with respect to relation names, converting them internally to all-upper case or
269    all-lower case.
270    
271    If syntax or parsing errors occur when you try to load or use an ERDB database, the
272    most likely reason is that one of your objects has an SQL reserved word as its name.
273    The list of SQL reserved words keeps increasing; however, most are unlikely to show
274    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
275    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
276    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
277    
278    Every entity has a field called C<id> that acts as its primary key. Every relationship
279    has fields called C<from-link> and C<to-link> that contain copies of the relevant
280    entity IDs. These are essentially ERDB's reserved words, and should not be used
281    for user-defined field names.
282    
283    =head3 Entities
284    
285    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
286    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
287    containing one or more fields. The attributes of the B<Entity> tag are as follows.
288    
289    =over 4
290    
291    =item name
292    
293    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
294    or C<GroupBlock>) and should be a noun or noun phrase.
295    
296    =item keyType
297    
298    Data type of the primary key. The primary key is always named C<id>.
299    
300    =back
301    
302    =head3 Relationships
303    
304    A relationship is described by the C<Relationship> tag. Within a relationship,
305    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306    fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
307    the to-index.
308    
309    The C<Relationship> tag has the following attributes.
310    
311    =over 4
312    
313    =item name
314    
315    Name of the relationship. The relationship name, by convention, uses capital casing
316    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
317    phrase, designed to fit between the from-entity and the to-entity (e.g.
318    Block C<ContainsRegionIn> Genome).
319    
320    =item from
321    
322    Name of the entity from which the relationship starts.
323    
324    =item to
325    
326    Name of the entity to which the relationship proceeds.
327    
328    =item arity
329    
330    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
331    
332    =back
333    
334  =cut  =cut
335    
# Line 75  Line 337 
337    
338  # 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.
339  # "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
340  # 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
341   #string is specified in the field definition.  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
342  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
343                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  # index
344                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
345                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "single ASCII character"},
346                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
347                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
348                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
349                                   indexMod =>   0, notes => "unsigned 32-bit integer"},
350                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
351                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
352                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
353                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
355                                   indexMod =>   0, notes => "signed, 64-bit integer"},
356                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
357                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
358                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
359                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
360                     'hash-string' =>
361                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
362                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
363                     'id-string' =>
364                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
365                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
366                               'key-string' =>                               'key-string' =>
367                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
368                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
369                                   'name-string' =>                                   'name-string' =>
370                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
371                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
372                                   'medium-string' =>                                   'medium-string' =>
373                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                                  );                                  );
376    
377  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 98  Line 380 
380                                     'MM' => 'many-to-many'                                     'MM' => 'many-to-many'
381                                   );                                   );
382    
383  # Table for interpreting string patterns.  # Options for XML input and output.
384    
385    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
386                                      Entities => 'Entity',
387                                      Fields => 'Field',
388                                      Indexes => 'Index',
389                                      IndexFields => 'IndexField'
390                                    },
391                      KeyAttr =>    { Relationship => 'name',
392                                      Entity => 'name',
393                                      Field => 'name'
394                                    },
395                      SuppressEmpty => 1,
396                     );
397    
398  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
399                                           '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
400                                           'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
401                                           'V' => "aeiou",                    NormalizeSpace => 2,
402                                           'K' => "bcdfghjklmnoprstvwxyz"                   );
403    my %XmlOutOpts = (
404                      RootName => 'Database',
405                      XMLDecl => 1,
406                                     );                                     );
407    
408    
409  =head2 Public Methods  =head2 Public Methods
410    
411  =head3 new  =head3 new
412    
413  C<< my $database = ERDB::new($dbh, $metaFileName); >>  C<< my $database = ERDB->new($dbh, $metaFileName); >>
414    
415  Create a new ERDB object.  Create a new ERDB object.
416    
# Line 136  Line 435 
435          my $metaData = _LoadMetaData($metaFileName);          my $metaData = _LoadMetaData($metaFileName);
436          # Create the object.          # Create the object.
437          my $self = { _dbh => $dbh,          my $self = { _dbh => $dbh,
438                                   _metaData => $metaData,                   _metaData => $metaData
                                  _options => $options,  
439                             };                             };
440          # Bless and return it.          # Bless and return it.
441          bless $self;      bless $self, $class;
442          return $self;          return $self;
443  }  }
444    
445  =head3 ShowMetaData  =head3 ShowMetaData
446    
447  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
448    
449  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
450  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 163  Line 461 
461    
462  sub ShowMetaData {  sub ShowMetaData {
463          # Get the parameters.          # Get the parameters.
464          my $self = shift @_;      my ($self, $filename) = @_;
         my ($filename) = @_;  
465          # Get the metadata and the title string.          # Get the metadata and the title string.
466          my $metadata = $self->{_metaData};          my $metadata = $self->{_metaData};
467          # Get the title string.          # Get the title string.
# Line 174  Line 471 
471          my $relationshipList = $metadata->{Relationships};          my $relationshipList = $metadata->{Relationships};
472          # Open the output file.          # Open the output file.
473          open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");          open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
474        Trace("Building MetaData table of contents.") if T(4);
475          # Write the HTML heading stuff.          # Write the HTML heading stuff.
476          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
477          print HTMLOUT "</head>\n<body>\n";          print HTMLOUT "</head>\n<body>\n";
478        # Write the documentation.
479        print HTMLOUT $self->DisplayMetaData();
480        # Close the document.
481        print HTMLOUT "</body>\n</html>\n";
482        # Close the file.
483        close HTMLOUT;
484    }
485    
486    =head3 DisplayMetaData
487    
488    C<< my $html = $erdb->DisplayMetaData(); >>
489    
490    Return an HTML description of the database. This description can be used to help users create
491    the data to be loaded into the relations and form queries. The output is raw includable HTML
492    without any HEAD or BODY tags.
493    
494    =over 4
495    
496    =item filename
497    
498    The name of the output file.
499    
500    =back
501    
502    =cut
503    
504    sub DisplayMetaData {
505        # Get the parameters.
506        my ($self) = @_;
507        # Get the metadata and the title string.
508        my $metadata = $self->{_metaData};
509        # Get the title string.
510        my $title = $metadata->{Title};
511        # Get the entity and relationship lists.
512        my $entityList = $metadata->{Entities};
513        my $relationshipList = $metadata->{Relationships};
514        # Declare the return variable.
515        my $retVal = "";
516        # Open the output file.
517        Trace("Building MetaData table of contents.") if T(4);
518          # 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
519          # section contains an ordered list of entity or relationship subsections.          # section contains an ordered list of entity or relationship subsections.
520          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";
521          # Loop through the Entities, displaying a list item for each.          # Loop through the Entities, displaying a list item for each.
522          foreach my $key (sort keys %{$entityList}) {          foreach my $key (sort keys %{$entityList}) {
523                  # Display this item.                  # Display this item.
524                  print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
525          }          }
526          # Close off the entity section and start the relationship section.          # Close off the entity section and start the relationship section.
527          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";
528          # Loop through the Relationships.          # Loop through the Relationships.
529          foreach my $key (sort keys %{$relationshipList}) {          foreach my $key (sort keys %{$relationshipList}) {
530                  # Display this item.                  # Display this item.
531                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
532                  print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
533          }          }
534          # Close off the relationship section and list the join table section.          # Close off the relationship section and list the join table section.
535          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";
536          # Close off the table of contents itself.          # Close off the table of contents itself.
537          print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
538          # 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.
539          print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
540          # Loop through the entities.          # Loop through the entities.
541          for my $key (sort keys %{$entityList}) {          for my $key (sort keys %{$entityList}) {
542            Trace("Building MetaData entry for $key entity.") if T(4);
543                  # Create the entity header. It contains a bookmark and the entity name.                  # Create the entity header. It contains a bookmark and the entity name.
544                  print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
545                  # Get the entity data.                  # Get the entity data.
546                  my $entityData = $entityList->{$key};                  my $entityData = $entityList->{$key};
547                  # If there's descriptive text, display it.                  # If there's descriptive text, display it.
548                  if (my $notes = $entityData->{Notes}) {                  if (my $notes = $entityData->{Notes}) {
549                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
550                  }                  }
551                  # 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.
552                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
553            if ($relCount > 0) {
554                # First, we set up the relationship subsection.
555                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
556                  # Loop through the relationships.                  # Loop through the relationships.
557                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
558                          # Get the relationship data.                          # Get the relationship data.
# Line 220  Line 562 
562                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
563                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
564                                  # Display the relationship data.                                  # Display the relationship data.
565                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
566                          }                          }
567                  }                  }
568                  # Close off the relationship list.                  # Close off the relationship list.
569                  print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
570            }
571                  # Get the entity's relations.                  # Get the entity's relations.
572                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
573                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
574                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
575                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
576                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
577                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
578                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
579                  }                  }
580          }          }
581          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
582          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
583          # Loop through the relationships.          # Loop through the relationships.
584          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
585            Trace("Building MetaData entry for $key relationship.") if T(4);
586                  # Get the relationship's structure.                  # Get the relationship's structure.
587                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
588                  # Create the relationship header.                  # Create the relationship header.
589                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
590                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
591                  # Get the entity names.                  # Get the entity names.
592                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
593                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 253  Line 597 
597                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
598                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
599                  if ($arity eq "11") {                  if ($arity eq "11") {
600                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
601                  } else {                  } else {
602                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
603                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
604                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
605                          }                          }
606                  }                  }
607                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
608                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
609                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
610                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
611                  }                  }
612                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
613                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
614                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
615          }          }
616        Trace("Building MetaData join table.") if T(4);
617          # Denote we're starting the join table.          # Denote we're starting the join table.
618          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
619          # Create a table header.          # Create a table header.
620          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
621          # Loop through the joins.          # Loop through the joins.
622          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
623          for my $joinKey (sort keys %{$joinTable}) {      my @joinKeys = keys %{$joinTable};
624        for my $joinKey (sort @joinKeys) {
625                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
626                  $joinKey =~ m!([^/]*)/(.*)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
627                  my ($source, $target, $clause) = ($self->ComputeObjectSentence($1),          my ($sourceRelation, $targetRelation) = ($1, $2);
628                                                                                    $self->ComputeObjectSentence($2),          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
629                                                                                    $joinTable->{$joinKey});          my $source = $self->ComputeObjectSentence($sourceRelation);
630            my $target = $self->ComputeObjectSentence($targetRelation);
631            my $clause = $joinTable->{$joinKey};
632                  # Display them in a table row.                  # Display them in a table row.
633                  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";
634          }          }
635          # Close the table.          # Close the table.
636          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
637          # Close the document.      Trace("Built MetaData HTML.") if T(3);
638          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
639          # Close the file.      return $retVal;
         close HTMLOUT;  
640  }  }
641    
642  =head3 DumpMetaData  =head3 DumpMetaData
643    
644  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
645    
646  Return a dump of the metadata structure.  Return a dump of the metadata structure.
647    
# Line 302  Line 649 
649    
650  sub DumpMetaData {  sub DumpMetaData {
651          # Get the parameters.          # Get the parameters.
652          my $self = shift @_;      my ($self) = @_;
653          # Dump the meta-data.          # Dump the meta-data.
654          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
655  }  }
656    
657    =head3 FindIndexForEntity
658    
659    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
660    
661    This method locates the entry in an entity's index list that begins with the
662    specified attribute name. If the entity has no index list, one will be
663    created. This method works on raw XML, not a live ERDB object.
664    
665    =over 4
666    
667    =item xml
668    
669    The raw XML structure defining the database.
670    
671    =item entityName
672    
673    The name of the relevant entity.
674    
675    =item attributeName
676    
677    The name of the attribute relevant to the search.
678    
679    =item RETURN
680    
681    The numerical index in the index list of the index entry for the specified entity and
682    attribute, or C<undef> if no such index exists.
683    
684    =back
685    
686    =cut
687    
688    sub FindIndexForEntity {
689        # Get the parameters.
690        my ($xml, $entityName, $attributeName) = @_;
691        # Declare the return variable.
692        my $retVal;
693        # Get the named entity.
694        my $entityData = $xml->{Entities}->{$entityName};
695        if (! $entityData) {
696            Confess("Entity $entityName not found in DBD structure.");
697        } else {
698            # Insure it has an index list.
699            if (! exists $entityData->{Indexes}) {
700                $entityData->{Indexes} = [];
701            } else {
702                # Search for the desired index.
703                my $indexList = $entityData->{Indexes};
704                my $n = scalar @{$indexList};
705                Trace("Searching $n indexes in index list for $entityName.") if T(2);
706                # We use an indexed FOR here because we're returning an
707                # index number instead of an object. We do THAT so we can
708                # delete the index from the list if needed.
709                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
710                    my $index = $indexList->[$i];
711                    my $fields = $index->{IndexFields};
712                    # Technically this IF should be safe (that is, we are guaranteed
713                    # the existence of a "$fields->[0]"), because when we load the XML
714                    # we have SuppressEmpty specified.
715                    if ($fields->[0]->{name} eq $attributeName) {
716                        $retVal = $i;
717                    }
718                }
719            }
720        }
721        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
722        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
723        # Return the result.
724        return $retVal;
725    }
726    
727  =head3 CreateTables  =head3 CreateTables
728    
729  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
730    
731  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
732  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 320  Line 737 
737    
738  sub CreateTables {  sub CreateTables {
739          # Get the parameters.          # Get the parameters.
740          my $self = shift @_;      my ($self) = @_;
741          my $metadata = $self->{_metaData};      # Get the relation names.
742          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
743          # Loop through the entities.      # Loop through the relations.
744          while (my ($entityName, $entityData) = each %{$metadata->{Entities}}) {      for my $relationName (@relNames) {
                 # Tell the user what we're doing.  
                 Trace("Creating relations for entity $entityName.") if T(1);  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entityData->{Relations}}) {  
745                          # Create a table for this relation.                          # Create a table for this relation.
746                          $self->CreateTable($relationName);                          $self->CreateTable($relationName);
747                          Trace("Relation $relationName created.") if T(1);          Trace("Relation $relationName created.") if T(2);
                 }  
         }  
         # Loop through the relationships.  
         my $relationshipTable = $metadata->{Relationships};  
         for my $relationshipName (keys %{$metadata->{Relationships}}) {  
                 # Create a table for this relationship.  
                 Trace("Creating relationship $relationshipName.") if T(1);  
                 $self->CreateTable($relationshipName);  
748          }          }
749  }  }
750    
751  =head3 CreateTable  =head3 CreateTable
752    
753  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
754    
755  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
756    
# Line 355  Line 760 
760    
761  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
762    
763  =item $indexFlag  =item indexFlag
764    
765  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
766  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
767    
768    =item estimatedRows (optional)
769    
770    If specified, the estimated maximum number of rows for the relation. This
771    information allows the creation of tables using storage engines that are
772    faster but require size estimates, such as MyISAM.
773    
774  =back  =back
775    
776  =cut  =cut
777    
778  sub CreateTable {  sub CreateTable {
779          # Get the parameters.          # Get the parameters.
780          my $self = shift @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
         my ($relationName, $indexFlag) = @_;  
781          # Get the database handle.          # Get the database handle.
782          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
783          # Get the relation data and determine whether or not the relation is primary.          # Get the relation data and determine whether or not the relation is primary.
# Line 391  Line 801 
801          # Insure the table is not already there.          # Insure the table is not already there.
802          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
803          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
804        # If there are estimated rows, create an estimate so we can take advantage of
805        # faster DB technologies.
806        my $estimation = undef;
807        if ($estimatedRows) {
808            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
809        }
810          # Create the table.          # Create the table.
811          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
812          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
813          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
814          # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
815        # index will not be built until the table has been loaded.
816          if ($indexFlag) {          if ($indexFlag) {
817                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
818          }          }
819  }  }
820    
821  =head3 CreateIndex  =head3 VerifyFields
   
 C<< $database->CreateIndex($relationName); >>  
   
 Create the indexes for a relation. If a table is being loaded from a large source file (as  
 is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  
 the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  
 method used after the load to create the indexes for the table.  
   
 =cut  
   
 sub CreateIndex {  
         # Get the parameters.  
         my $self = shift @_;  
         my ($relationName) = @_;  
         # Get the relation's descriptor.  
         my $relationData = $self->_FindRelation($relationName);  
         # Get the database handle.  
         my $dbh = $self->{_dbh};  
         # Now we need to create this relation's indexes. We do this by looping through its index table.  
         while (my ($indexName, $indexData) = each %{$relationData->{Indexes}}) {  
                 # 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);  
         }  
 }  
   
 =head3 LoadTables  
   
 C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  
822    
823  This method will load the database tables from a directory. The tables must already have been created  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
 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.  
824    
825  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and  Run through the list of proposed field values, insuring that all the character fields are
826  tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must  below the maximum length. If any fields are too long, they will be truncated in place.
 be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.  
827    
828  =over 4  =over 4
829    
830  =item directoryName  =item relName
831    
832  Name of the directory containing the relation files to be loaded.  Name of the relation for which the specified fields are destined.
833    
834  =item rebuild  =item fieldList
835    
836  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the  Reference to a list, in order, of the fields to be put into the relation.
 only way to erase existing data in the tables, since the TRUNCATE command is not supported  
 by all of the DB engines we use.  
837    
838  =item RETURN  =item RETURN
839    
840  Returns a statistical object describing the number of records read and a list of the error messages.  Returns the number of fields truncated.
841    
842  =back  =back
843    
844  =cut  =cut
845    
846  sub LoadTables {  sub VerifyFields {
847          # Get the parameters.          # Get the parameters.
848          my $self = shift @_;      my ($self, $relName, $fieldList) = @_;
849          my ($directoryName, $rebuild) = @_;      # Initialize the return value.
850          # Start the timer.      my $retVal = 0;
851          my $startTime = gettimeofday;      # Get the relation definition.
852          # Clean any trailing slash from the directory name.      my $relData = $self->_FindRelation($relName);
853          $directoryName =~ s!/\\$!!;      # Get the list of field descriptors.
854          # Declare the return variable.      my $fieldTypes = $relData->{Fields};
855          my $retVal = Stats->new();      my $fieldCount = scalar @{$fieldTypes};
856          # Get the metadata structure.      # Loop through the two lists.
857          my $metaData = $self->{_metaData};      for (my $i = 0; $i < $fieldCount; $i++) {
858          # Loop through the entities.          # Get the type of the current field.
859          for my $entity (values %{$metaData->{Entities}}) {          my $fieldType = $fieldTypes->[$i]->{type};
860                  # Loop through the entity's relations.          # If it's a character field, verify the length.
861                  for my $relationName (keys %{$entity->{Relations}}) {          if ($fieldType =~ /string/) {
862                          # Try to load this relation.              my $maxLen = $TypeTable{$fieldType}->{maxLen};
863                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $oldString = $fieldList->[$i];
864                          # Accumulate the statistics.              if (length($oldString) > $maxLen) {
865                          $retVal->Accumulate($result);                  # Here it's too big, so we truncate it.
866                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
867                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
868                    $retVal++;
869                  }                  }
870          }          }
         # 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);  
871          }          }
872          # Add the duration of the load to the statistical object.      # Return the truncation count.
         $retVal->Add('duration', gettimeofday - $startTime);  
         # Return the accumulated statistics.  
873          return $retVal;          return $retVal;
874  }  }
875    
876  =head3 GetTableNames  =head3 DigestFields
877    
878  C<< my @names = $database->GetTableNames; >>  C<< $erdb->DigestFields($relName, $fieldList); >>
879    
880  Return a list of the relations required to implement this database.  Digest the strings in the field list that correspond to data type C<hash-string> in the
881    specified relation.
882    
883  =cut  =over 4
884    
885  sub GetTableNames {  =item relName
         # Get the parameters.  
         my $self = shift @_;  
         # Get the relation list from the metadata.  
         my $relationTable = $self->{_metaData}->{RelationTable};  
         # Return the relation names.  
         return keys %{$relationTable};  
 }  
886    
887  =head3 GetEntityTypes  Name of the relation to which the fields belong.
888    
889  C<< my @names = $database->GetEntityTypes; >>  =item fieldList
890    
891  Return a list of the entity type names.  List of field contents to be loaded into the relation.
892    
893  =cut  =back
894    
895  sub GetEntityTypes {  =cut
896          # Get the database object.  #: Return Type ;
897          my $self = shift @_;  sub DigestFields {
898          # Get the entity list from the metadata object.      # Get the parameters.
899          my $entityList = $self->{_metaData}->{Entities};      my ($self, $relName, $fieldList) = @_;
900          # Return the list of entity names in alphabetical order.      # Get the relation definition.
901          return sort keys %{$entityList};      my $relData = $self->_FindRelation($relName);
902        # Get the list of field descriptors.
903        my $fieldTypes = $relData->{Fields};
904        my $fieldCount = scalar @{$fieldTypes};
905        # Loop through the two lists.
906        for (my $i = 0; $i < $fieldCount; $i++) {
907            # Get the type of the current field.
908            my $fieldType = $fieldTypes->[$i]->{type};
909            # If it's a hash string, digest it in place.
910            if ($fieldType eq 'hash-string') {
911                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
912            }
913        }
914  }  }
915    
916  =head3 Get  =head3 DigestKey
917    
918  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $digested = $erdb->DigestKey($keyValue); >>
919    
920  This method returns a query object for entities of a specified type using a specified filter.  Return the digested value of a symbolic key. The digested value can then be plugged into a
921  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  key-based search into a table with key-type hash-string.
 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.  
922    
923  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  Currently the digesting process is independent of the database structure, but that may not
924    always be the case, so this is an instance method instead of a static method.
925    
926  The WHERE clause contains a single question mark, so there is a single additional  =over 4
 parameter representing the parameter value. It would also be possible to code  
927    
928  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  =item keyValue
929    
930  however, this version of the call would generate a syntax error if there were any quote  Key value to digest.
 characters inside the variable C<$genus>.  
931    
932  The use of the strange parenthesized notation for field names enables us to distinguish  =item RETURN
 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.  
933    
934  It is possible to specify multiple entity and relationship names in order to retrieve more than  Digested value of the key.
 one object's data at the same time, which allows highly complex joined queries. For example,  
935    
936  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  =back
937    
938  If multiple names are specified, then the query processor will automatically determine a  =cut
 join path between the entities and relationships. The algorithm used is very simplistic.  
 In particular, you can't specify any entity or relationship more than once, and if a  
 relationship is recursive, the path is determined by the order in which the entity  
 and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  
 which relates B<People> objects to other B<People> objects. If the join path is  
 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  
 the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  
939    
940  =over 4  sub DigestKey {
941        # Get the parameters.
942        my ($self, $keyValue) = @_;
943        # Compute the digest.
944        my $retVal = md5_base64($keyValue);
945        # Return the result.
946        return $retVal;
947    }
948    
949  =item objectNames  =head3 CreateIndex
950    
951  List containing the names of the entity and relationship objects to be retrieved.  C<< $erdb->CreateIndex($relationName); >>
952    
953  =item filterClause  Create the indexes for a relation. If a table is being loaded from a large source file (as
954    is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
955    If that is the case, then L</CreateTable> should be called with the index flag set to
956    FALSE, and this method used after the load to create the indexes for the table.
957    
958  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  =cut
 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.  
959    
960  The filter clause can also specify a sort order. To do this, simply follow the filter string  sub CreateIndex {
961  with an ORDER BY clause. For example, the following filter string gets all genomes for a      # Get the parameters.
962  particular genus and sorts them by species name.      my ($self, $relationName) = @_;
963        # Get the relation's descriptor.
964        my $relationData = $self->_FindRelation($relationName);
965        # Get the database handle.
966        my $dbh = $self->{_dbh};
967        # Now we need to create this relation's indexes. We do this by looping through its index table.
968        my $indexHash = $relationData->{Indexes};
969        for my $indexName (keys %{$indexHash}) {
970            my $indexData = $indexHash->{$indexName};
971            # Get the index's field list.
972            my @rawFields = @{$indexData->{IndexFields}};
973            # Get a hash of the relation's field types.
974            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
975            # We need to check for text fields so we can append a length limitation for them. To do
976            # that, we need the relation's field list.
977            my $relFields = $relationData->{Fields};
978            for (my $i = 0; $i <= $#rawFields; $i++) {
979                # Get the field type.
980                my $field = $rawFields[$i];
981                my $type = $types{$field};
982                # Ask if it requires using prefix notation for the index.
983                my $mod = $TypeTable{$type}->{indexMod};
984                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
985                if ($mod) {
986                    # Append the prefix length to the field name,
987                    $rawFields[$i] .= "($mod)";
988                }
989            }
990            my @fieldList = _FixNames(@rawFields);
991            my $flds = join(', ', @fieldList);
992            # Get the index's uniqueness flag.
993            my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
994            # Create the index.
995            my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
996                                        flds => $flds, kind => $unique);
997            if ($rv) {
998                Trace("Index created: $indexName for $relationName ($flds)") if T(1);
999            } else {
1000                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
1001            }
1002        }
1003    }
1004    
1005  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  =head3 GetSecondaryFields
1006    
1007  The rules for field references in a sort order are the same as those for field references in the  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
1008    
1009  =item param1, param2, ..., paramN  This method will return a list of the name and type of each of the secondary
1010    fields for a specified entity. Secondary fields are stored in two-column tables
1011    in addition to the primary entity table. This enables the field to have no value
1012    or to have multiple values.
1013    
1014  Parameter values to be substituted into the filter clause.  =over 4
1015    
1016    =item entityName
1017    
1018    Name of the entity whose secondary fields are desired.
1019    
1020  =item RETURN  =item RETURN
1021    
1022  Returns a B<DBQuery> that can be used to iterate through all of the results.  Returns a hash mapping the field names to their field types.
1023    
1024  =back  =back
1025    
1026  =cut  =cut
1027    
1028  sub Get {  sub GetSecondaryFields {
1029          # Get the parameters.          # Get the parameters.
1030          my $self = shift @_;      my ($self, $entityName) = @_;
1031          my ($objectNames, $filterClause, @params) = @_;      # Declare the return variable.
1032          # Construct the SELECT statement. The general pattern is      my %retVal = ();
1033          #      # Look for the entity.
1034          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN      my $table = $self->GetFieldTable($entityName);
1035          #      # Loop through the fields, pulling out the secondaries.
1036          my $dbh = $self->{_dbh};      for my $field (sort keys %{$table}) {
1037          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          if ($table->{$field}->{relation} ne $entityName) {
1038                                  join(', ', @{$objectNames});              # Here we have a secondary field.
1039          # Check for a filter clause.              $retVal{$field} = $table->{$field}->{type};
         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 $sqlReference;  
                                 }  
                         }  
                 }  
                 # The next step is to join the objects together. We only need to do this if there  
                 # is more than one object in the object list. We start with the first object and  
                 # run through the objects after it. Note also that we make a safety copy of the  
                 # list before running through it.  
                 my @objectList = @{$objectNames};  
                 my $lastObject = shift @objectList;  
                 # Get the join table.  
                 my $joinTable = $self->{_metaData}->{Joins};  
                 # Loop through the object list.  
                 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.");  
                         } else {  
                                 # Get the join clause and add it to the WHERE list.  
                                 push @joinWhere, $joinTable->{$joinKey};  
                                 # Save this object as the last object for the next iteration.  
                                 $lastObject = $thisObject;  
                         }  
                 }  
                 # 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 = $1;  
                 }  
                 # Add the filter and the join clauses (if any) to the SELECT command.  
                 if ($filterString) {  
                         push @joinWhere, "($filterString)";  
                 }  
                 if (@joinWhere) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
                 }  
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
1040                  }                  }
1041          }          }
1042          Trace("SQL query: $command") if T(2);      # Return the result.
1043          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      return %retVal;
         my $sth = $dbh->prepare_command($command);  
         # Execute it with the parameters bound in.  
         $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
         # Return the statement object.  
         my $retVal = DBQuery::_new($self, $sth, @{$objectNames});  
         return $retVal;  
1044  }  }
1045    
1046  =head3 ComputeObjectSentence  =head3 GetFieldRelationName
1047    
1048  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1049    
1050  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return the name of the relation containing a specified field.
1051    
1052  =over 4  =over 4
1053    
1054  =item objectName  =item objectName
1055    
1056  Name of the entity or relationship.  Name of the entity or relationship containing the field.
1057    
1058    =item fieldName
1059    
1060    Name of the relevant field in that entity or relationship.
1061    
1062  =item RETURN  =item RETURN
1063    
1064  Returns a string containing the entity name or a relationship sentence.  Returns the name of the database relation containing the field, or C<undef> if
1065    the field does not exist.
1066    
1067  =back  =back
1068    
1069  =cut  =cut
1070    
1071  sub ComputeObjectSentence {  sub GetFieldRelationName {
1072          # Get the parameters.          # Get the parameters.
1073          my $self = shift @_;      my ($self, $objectName, $fieldName) = @_;
1074          my ($objectName) = @_;      # Declare the return variable.
1075          # Set the default return value.      my $retVal;
1076          my $retVal = $objectName;      # Get the object field table.
1077          # Look for the object as a relationship.      my $table = $self->GetFieldTable($objectName);
1078          my $relTable = $self->{_metaData}->{Relationships};      # Only proceed if the field exists.
1079          if (exists $relTable->{$objectName}) {      if (exists $table->{$fieldName}) {
1080                  # Get the relationship sentence.          # Determine the name of the relation that contains this field.
1081                  $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          $retVal = $table->{$fieldName}->{relation};
1082          }          }
1083          # Return the result.          # Return the result.
1084          return $retVal;          return $retVal;
1085  }  }
1086    
1087  =head3 DumpRelations  =head3 DeleteValue
1088    
1089  C<< $database->DumpRelations($outputDirectory); >>  C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1090    
1091  Write the contents of all the relations to tab-delimited files in the specified directory.  Delete secondary field values from the database. This method can be used to delete all
1092  Each file will have the same name as the relation dumped, with an extension of DTX.  values of a specified field for a particular entity instance, or only a single value.
1093    
1094    Secondary fields are stored in two-column relations separate from an entity's primary
1095    table, and as a result a secondary field can legitimately have no value or multiple
1096    values. Therefore, it makes sense to talk about deleting secondary fields where it
1097    would not make sense for primary fields.
1098    
1099  =over 4  =over 4
1100    
1101  =item outputDirectory  =item entityName
1102    
1103  Name of the directory into which the relation files should be dumped.  Name of the entity from which the fields are to be deleted.
1104    
1105    =item id
1106    
1107    ID of the entity instance to be processed. If the instance is not found, this
1108    method will have no effect. If C<undef> is specified, all values for all of
1109    the entity instances will be deleted.
1110    
1111    =item fieldName
1112    
1113    Name of the field whose values are to be deleted.
1114    
1115    =item fieldValue (optional)
1116    
1117    Value to be deleted. If not specified, then all values of the specified field
1118    will be deleted for the entity instance. If specified, then only the values which
1119    match this parameter will be deleted.
1120    
1121    =item RETURN
1122    
1123    Returns the number of rows deleted.
1124    
1125  =back  =back
1126    
1127  =cut  =cut
1128    
1129  sub DumpRelations {  sub DeleteValue {
1130          # Get the parameters.          # Get the parameters.
1131          my $self = shift @_;      my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1132          my ($outputDirectory) = @_;      # Declare the return value.
1133          # Now we need to run through all the relations. First, we loop through the entities.      my $retVal = 0;
1134          my $metaData = $self->{_metaData};      # We need to set up an SQL command to do the deletion. First, we
1135          my $entities = $metaData->{Entities};      # find the name of the field's relation.
1136          while (my ($entityName, $entityStructure) = each %{$entities}) {      my $table = $self->GetFieldTable($entityName);
1137                  # Get the entity's relations.      my $field = $table->{$fieldName};
1138                  my $relationList = $entityStructure->{Relations};      my $relation = $field->{relation};
1139                  # Loop through the relations, dumping them.      # Make sure this is a secondary field.
1140                  while (my ($relationName, $relation) = each %{$relationList}) {      if ($relation eq $entityName) {
1141                          $self->_DumpRelation($outputDirectory, $relationName, $relation);          Confess("Cannot delete values of $fieldName for $entityName.");
1142                  }      } else {
1143            # Set up the SQL command to delete all values.
1144            my $sql = "DELETE FROM $relation";
1145            # Build the filter.
1146            my @filters = ();
1147            my @parms = ();
1148            # Check for a filter by ID.
1149            if (defined $id) {
1150                push @filters, "id = ?";
1151                push @parms, $id;
1152            }
1153            # Check for a filter by value.
1154            if (defined $fieldValue) {
1155                push @filters, "$fieldName = ?";
1156                push @parms, $fieldValue;
1157            }
1158            # Append the filters to the command.
1159            if (@filters) {
1160                $sql .= " WHERE " . join(" AND ", @filters);
1161          }          }
1162          # Next, we loop through the relationships.          # Execute the command.
1163          my $relationships = $metaData->{Relationships};          my $dbh = $self->{_dbh};
1164          while (my ($relationshipName, $relationshipStructure) = each %{$relationships}) {          $retVal = $dbh->SQL($sql, 0, @parms);
                 # Dump this relationship's relation.  
                 $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
1165          }          }
1166        # Return the result.
1167        return $retVal;
1168  }  }
1169    
1170  =head3 InsertObject  =head3 LoadTables
   
 C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  
   
 Insert an object into the database. The object is defined by a type name and then a hash  
 of field names to values. Field values in the primary relation are represented by scalars.  
 (Note that for relationships, the primary relation is the B<only> relation.)  
 Field values for the other relations comprising the entity are always list references. For  
 example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  
 C<ZP_00210270.1> and C<gi|46206278>.  
1171    
1172  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1173    
1174  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  This method will load the database tables from a directory. The tables must already have been created
1175  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1176    all of the relations to be loaded must have a file in the directory with the same name as the relation
1177    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1178    line of the file will be loaded as a row of the target relation table. The field values should be in
1179    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1180    erased before the new data is loaded in.
1181    
1182  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1183    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1184    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1185    
1186  =over 4  =over 4
1187    
1188  =item newObjectType  =item directoryName
1189    
1190  Type name of the object to insert.  Name of the directory containing the relation files to be loaded.
1191    
1192  =item fieldHash  =item rebuild
1193    
1194  Hash of field names to values.  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1195    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1196    by all of the DB engines we use.
1197    
1198  =item RETURN  =item RETURN
1199    
1200  Returns 1 if successful, 0 if an error occurred.  Returns a statistical object describing the number of records read and a list of the error messages.
1201    
1202  =back  =back
1203    
1204  =cut  =cut
1205    
1206  sub InsertObject {  sub LoadTables {
1207          # Get the parameters.          # Get the parameters.
1208          my $self = shift @_;      my ($self, $directoryName, $rebuild) = @_;
1209          my ($newObjectType, $fieldHash) = @_;      # Start the timer.
1210          # Denote that so far we appear successful.      my $startTime = gettimeofday;
1211          my $retVal = 1;      # Clean any trailing slash from the directory name.
1212          # Get the database handle.      $directoryName =~ s!/\\$!!;
1213          my $dbh = $self->{_dbh};      # Declare the return variable.
1214          # Get the relation list.      my $retVal = Stats->new();
1215        # Get the relation names.
1216        my @relNames = $self->GetTableNames();
1217        for my $relationName (@relNames) {
1218            # Try to load this relation.
1219            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1220            # Accumulate the statistics.
1221            $retVal->Accumulate($result);
1222        }
1223        # Add the duration of the load to the statistical object.
1224        $retVal->Add('duration', gettimeofday - $startTime);
1225        # Return the accumulated statistics.
1226        return $retVal;
1227    }
1228    
1229    
1230    =head3 GetTableNames
1231    
1232    C<< my @names = $erdb->GetTableNames; >>
1233    
1234    Return a list of the relations required to implement this database.
1235    
1236    =cut
1237    
1238    sub GetTableNames {
1239        # Get the parameters.
1240        my ($self) = @_;
1241        # Get the relation list from the metadata.
1242        my $relationTable = $self->{_metaData}->{RelationTable};
1243        # Return the relation names.
1244        return keys %{$relationTable};
1245    }
1246    
1247    =head3 GetEntityTypes
1248    
1249    C<< my @names = $erdb->GetEntityTypes; >>
1250    
1251    Return a list of the entity type names.
1252    
1253    =cut
1254    
1255    sub GetEntityTypes {
1256        # Get the database object.
1257        my ($self) = @_;
1258        # Get the entity list from the metadata object.
1259        my $entityList = $self->{_metaData}->{Entities};
1260        # Return the list of entity names in alphabetical order.
1261        return sort keys %{$entityList};
1262    }
1263    
1264    =head3 GetDataTypes
1265    
1266    C<< my %types = ERDB::GetDataTypes(); >>
1267    
1268    Return a table of ERDB data types. The table returned is a hash of hashes.
1269    The keys of the big hash are the datatypes. Each smaller hash has several
1270    values used to manage the data. The most interesting is the SQL type (key
1271    C<sqlType>) and the descriptive node (key C<notes>).
1272    
1273    Note that changing the values in the smaller hashes will seriously break
1274    things, so this data should be treated as read-only.
1275    
1276    =cut
1277    
1278    sub GetDataTypes {
1279        return %TypeTable;
1280    }
1281    
1282    
1283    =head3 IsEntity
1284    
1285    C<< my $flag = $erdb->IsEntity($entityName); >>
1286    
1287    Return TRUE if the parameter is an entity name, else FALSE.
1288    
1289    =over 4
1290    
1291    =item entityName
1292    
1293    Object name to be tested.
1294    
1295    =item RETURN
1296    
1297    Returns TRUE if the specified string is an entity name, else FALSE.
1298    
1299    =back
1300    
1301    =cut
1302    
1303    sub IsEntity {
1304        # Get the parameters.
1305        my ($self, $entityName) = @_;
1306        # Test to see if it's an entity.
1307        return exists $self->{_metaData}->{Entities}->{$entityName};
1308    }
1309    
1310    =head3 Get
1311    
1312    C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1313    
1314    This method returns a query object for entities of a specified type using a specified filter.
1315    The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1316    field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1317    following call requests all B<Genome> objects for the genus specified in the variable
1318    $genus.
1319    
1320    C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1321    
1322    The WHERE clause contains a single question mark, so there is a single additional
1323    parameter representing the parameter value. It would also be possible to code
1324    
1325    C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1326    
1327    however, this version of the call would generate a syntax error if there were any quote
1328    characters inside the variable C<$genus>.
1329    
1330    The use of the strange parenthesized notation for field names enables us to distinguish
1331    hyphens contained within field names from minus signs that participate in the computation
1332    of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1333    
1334    It is possible to specify multiple entity and relationship names in order to retrieve more than
1335    one object's data at the same time, which allows highly complex joined queries. For example,
1336    
1337    C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1338    
1339    If multiple names are specified, then the query processor will automatically determine a
1340    join path between the entities and relationships. The algorithm used is very simplistic.
1341    In particular, if a relationship is recursive, the path is determined by the order in which
1342    the entity and the relationship appear. For example, consider a recursive relationship
1343    B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1344    coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1345    the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1346    
1347    If an entity or relationship is mentioned twice, the name for the second occurrence will
1348    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1349    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1350    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1351    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1352    
1353    =over 4
1354    
1355    =item objectNames
1356    
1357    List containing the names of the entity and relationship objects to be retrieved.
1358    
1359    =item filterClause
1360    
1361    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1362    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1363    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1364    in the filter clause should be added to the parameter list as additional parameters. The
1365    fields in a filter clause can come from primary entity relations, relationship relations,
1366    or secondary entity relations; however, all of the entities and relationships involved must
1367    be included in the list of object names.
1368    
1369    The filter clause can also specify a sort order. To do this, simply follow the filter string
1370    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1371    particular genus and sorts them by species name.
1372    
1373    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1374    
1375    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1376    be processed. The idea is to make it less likely to find the verb by accident.
1377    
1378    The rules for field references in a sort order are the same as those for field references in the
1379    filter clause in general; however, odd things may happen if a sort field is from a secondary
1380    relation.
1381    
1382    Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1383    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1384    a positive number. So, for example
1385    
1386    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1387    
1388    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1389    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1390    use
1391    
1392    C<< "LIMIT 10" >>
1393    
1394    =item params
1395    
1396    Reference to a list of parameter values to be substituted into the filter clause.
1397    
1398    =item RETURN
1399    
1400    Returns a B<DBQuery> that can be used to iterate through all of the results.
1401    
1402    =back
1403    
1404    =cut
1405    
1406    sub Get {
1407        # Get the parameters.
1408        my ($self, $objectNames, $filterClause, $params) = @_;
1409        # Process the SQL stuff.
1410        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1411            $self->_SetupSQL($objectNames, $filterClause);
1412        # Create the query.
1413        my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1414            ".* $suffix";
1415        my $sth = $self->_GetStatementHandle($command, $params);
1416        # Now we create the relation map, which enables DBQuery to determine the order, name
1417        # and mapped name for each object in the query.
1418        my @relationMap = ();
1419        for my $mappedName (@{$mappedNameListRef}) {
1420            push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1421        }
1422        # Return the statement object.
1423        my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1424        return $retVal;
1425    }
1426    
1427    
1428    
1429    =head3 Search
1430    
1431    C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1432    
1433    Perform a full text search with filtering. The search will be against a specified object
1434    in the object name list. That object will get an extra field containing the search
1435    relevance. Note that except for the search expression, the parameters of this method are
1436    the same as those for L</Get> and follow the same rules.
1437    
1438    =over 4
1439    
1440    =item searchExpression
1441    
1442    Boolean search expression for the text fields of the target object. The default mode for
1443    a Boolean search expression is OR, but we want the default to be AND, so we will
1444    add a C<+> operator to each word with no other operator before it.
1445    
1446    =item idx
1447    
1448    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1449    
1450    =item objectNames
1451    
1452    List containing the names of the entity and relationship objects to be retrieved.
1453    
1454    =item filterClause
1455    
1456    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1457    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1458    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1459    in the filter clause should be added to the parameter list as additional parameters. The
1460    fields in a filter clause can come from primary entity relations, relationship relations,
1461    or secondary entity relations; however, all of the entities and relationships involved must
1462    be included in the list of object names.
1463    
1464    =item params
1465    
1466    Reference to a list of parameter values to be substituted into the filter clause.
1467    
1468    =item RETURN
1469    
1470    Returns a query object for the specified search.
1471    
1472    =back
1473    
1474    =cut
1475    
1476    sub Search {
1477        # Get the parameters.
1478        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1479        # Declare the return variable.
1480        my $retVal;
1481        # Create a safety copy of the parameter list. Note we have to be careful to insure
1482        # a parameter list exists before we copy it.
1483        my @myParams = ();
1484        if (defined $params) {
1485            @myParams = @{$params};
1486        }
1487        # Get the first object's structure so we have access to the searchable fields.
1488        my $object1Name = $objectNames->[$idx];
1489        my $object1Structure = $self->_GetStructure($object1Name);
1490        # Get the field list.
1491        if (! exists $object1Structure->{searchFields}) {
1492            Confess("No searchable index for $object1Name.");
1493        } else {
1494            # Get the field list.
1495            my @fields = @{$object1Structure->{searchFields}};
1496            # Clean the search expression.
1497            my $actualKeywords = $self->CleanKeywords($searchExpression);
1498            # Prefix a "+" to each uncontrolled word. This converts the default
1499            # search mode from OR to AND.
1500            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1501            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1502            # We need two match expressions, one for the filter clause and one in the
1503            # query itself. Both will use a parameter mark, so we need to push the
1504            # search expression onto the front of the parameter list twice.
1505            unshift @myParams, $actualKeywords, $actualKeywords;
1506            # Build the match expression.
1507            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1508            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1509            # Process the SQL stuff.
1510            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1511                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1512            # Create the query. Note that the match clause is inserted at the front of
1513            # the select fields.
1514            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1515                ".* $suffix";
1516            my $sth = $self->_GetStatementHandle($command, \@myParams);
1517            # Now we create the relation map, which enables DBQuery to determine the order, name
1518            # and mapped name for each object in the query.
1519            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1520            # Return the statement object.
1521            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1522        }
1523        return $retVal;
1524    }
1525    
1526    =head3 GetFlat
1527    
1528    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1529    
1530    This is a variation of L</GetAll> that asks for only a single field per record and
1531    returns a single flattened list.
1532    
1533    =over 4
1534    
1535    =item objectNames
1536    
1537    List containing the names of the entity and relationship objects to be retrieved.
1538    
1539    =item filterClause
1540    
1541    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1542    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1543    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1544    parameter list as additional parameters. The fields in a filter clause can come from primary
1545    entity relations, relationship relations, or secondary entity relations; however, all of the
1546    entities and relationships involved must be included in the list of object names.
1547    
1548    =item parameterList
1549    
1550    List of the parameters to be substituted in for the parameters marks in the filter clause.
1551    
1552    =item field
1553    
1554    Name of the field to be used to get the elements of the list returned.
1555    
1556    =item RETURN
1557    
1558    Returns a list of values.
1559    
1560    =back
1561    
1562    =cut
1563    #: Return Type @;
1564    sub GetFlat {
1565        # Get the parameters.
1566        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1567        # Construct the query.
1568        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1569        # Create the result list.
1570        my @retVal = ();
1571        # Loop through the records, adding the field values found to the result list.
1572        while (my $row = $query->Fetch()) {
1573            push @retVal, $row->Value($field);
1574        }
1575        # Return the list created.
1576        return @retVal;
1577    }
1578    
1579    =head3 SpecialFields
1580    
1581    C<< my %specials = $erdb->SpecialFields($entityName); >>
1582    
1583    Return a hash mapping special fields in the specified entity to the value of their
1584    C<special> attribute. This enables the subclass to get access to the special field
1585    attributes without needed to plumb the internal ERDB data structures.
1586    
1587    =over 4
1588    
1589    =item entityName
1590    
1591    Name of the entity whose special fields are desired.
1592    
1593    =item RETURN
1594    
1595    Returns a hash. The keys of the hash are the special field names, and the values
1596    are the values from each special field's C<special> attribute.
1597    
1598    =back
1599    
1600    =cut
1601    
1602    sub SpecialFields {
1603        # Get the parameters.
1604        my ($self, $entityName) = @_;
1605        # Declare the return variable.
1606        my %retVal = ();
1607        # Find the entity's data structure.
1608        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1609        # Loop through its fields, adding each special field to the return hash.
1610        my $fieldHash = $entityData->{Fields};
1611        for my $fieldName (keys %{$fieldHash}) {
1612            my $fieldData = $fieldHash->{$fieldName};
1613            if (exists $fieldData->{special}) {
1614                $retVal{$fieldName} = $fieldData->{special};
1615            }
1616        }
1617        # Return the result.
1618        return %retVal;
1619    }
1620    
1621    =head3 Delete
1622    
1623    C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1624    
1625    Delete an entity instance from the database. The instance is deleted along with all entity and
1626    relationship instances dependent on it. The definition of I<dependence> is recursive.
1627    
1628    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1629    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1630    dependent relationship.
1631    
1632    =over 4
1633    
1634    =item entityName
1635    
1636    Name of the entity type for the instance being deleted.
1637    
1638    =item objectID
1639    
1640    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1641    then it is presumed to by a LIKE pattern.
1642    
1643    =item options
1644    
1645    A hash detailing the options for this delete operation.
1646    
1647    =item RETURN
1648    
1649    Returns a statistics object indicating how many records of each particular table were
1650    deleted.
1651    
1652    =back
1653    
1654    The permissible options for this method are as follows.
1655    
1656    =over 4
1657    
1658    =item testMode
1659    
1660    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1661    
1662    =item keepRoot
1663    
1664    If TRUE, then the entity instances will not be deleted, only the dependent records.
1665    
1666    =back
1667    
1668    =cut
1669    #: Return Type $%;
1670    sub Delete {
1671        # Get the parameters.
1672        my ($self, $entityName, $objectID, %options) = @_;
1673        # Declare the return variable.
1674        my $retVal = Stats->new();
1675        # Get the DBKernel object.
1676        my $db = $self->{_dbh};
1677        # We're going to generate all the paths branching out from the starting entity. One of
1678        # the things we have to be careful about is preventing loops. We'll use a hash to
1679        # determine if we've hit a loop.
1680        my %alreadyFound = ();
1681        # These next lists will serve as our result stack. We start by pushing object lists onto
1682        # the stack, and then popping them off to do the deletes. This means the deletes will
1683        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1684        # sure we don't delete records that might be needed to forge relationships back to the
1685        # original item. We have two lists-- one for TO-relationships, and one for
1686        # FROM-relationships and entities.
1687        my @fromPathList = ();
1688        my @toPathList = ();
1689        # This final list is used to remember what work still needs to be done. We push paths
1690        # onto the list, then pop them off to extend the paths. We prime it with the starting
1691        # point. Note that we will work hard to insure that the last item on a path in the
1692        # to-do list is always an entity.
1693        my @todoList = ([$entityName]);
1694        while (@todoList) {
1695            # Get the current path.
1696            my $current = pop @todoList;
1697            # Copy it into a list.
1698            my @stackedPath = @{$current};
1699            # Pull off the last item on the path. It will always be an entity.
1700            my $myEntityName = pop @stackedPath;
1701            # Add it to the alreadyFound list.
1702            $alreadyFound{$myEntityName} = 1;
1703            # Figure out if we need to delete this entity.
1704            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1705                # Get the entity data.
1706                my $entityData = $self->_GetStructure($myEntityName);
1707                # Loop through the entity's relations. A DELETE command will be needed for each of them.
1708                my $relations = $entityData->{Relations};
1709                for my $relation (keys %{$relations}) {
1710                    my @augmentedList = (@stackedPath, $relation);
1711                    push @fromPathList, \@augmentedList;
1712                }
1713            }
1714            # Now we need to look for relationships connected to this entity.
1715            my $relationshipList = $self->{_metaData}->{Relationships};
1716            for my $relationshipName (keys %{$relationshipList}) {
1717                my $relationship = $relationshipList->{$relationshipName};
1718                # Check the FROM field. We're only interested if it's us.
1719                if ($relationship->{from} eq $myEntityName) {
1720                    # Add the path to this relationship.
1721                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1722                    push @fromPathList, \@augmentedList;
1723                    # Check the arity. If it's MM we're done. If it's 1M
1724                    # and the target hasn't been seen yet, we want to
1725                    # stack the entity for future processing.
1726                    if ($relationship->{arity} eq '1M') {
1727                        my $toEntity = $relationship->{to};
1728                        if (! exists $alreadyFound{$toEntity}) {
1729                            # Here we have a new entity that's dependent on
1730                            # the current entity, so we need to stack it.
1731                            my @stackList = (@augmentedList, $toEntity);
1732                            push @fromPathList, \@stackList;
1733                        } else {
1734                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1735                        }
1736                    }
1737                }
1738                # Now check the TO field. In this case only the relationship needs
1739                # deletion.
1740                if ($relationship->{to} eq $myEntityName) {
1741                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1742                    push @toPathList, \@augmentedList;
1743                }
1744            }
1745        }
1746        # Create the first qualifier for the WHERE clause. This selects the
1747        # keys of the primary entity records to be deleted. When we're deleting
1748        # from a dependent table, we construct a join path from the first qualifier
1749        # to the table containing the dependent records to delete.
1750        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1751        # We need to make two passes. The first is through the to-list, and
1752        # the second through the from-list. The from-list is second because
1753        # the to-list may need to pass through some of the entities the
1754        # from-list would delete.
1755        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1756        # Now it's time to do the deletes. We do it in two passes.
1757        for my $keyName ('to_link', 'from_link') {
1758            # Get the list for this key.
1759            my @pathList = @{$stackList{$keyName}};
1760            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1761            # Loop through this list.
1762            while (my $path = pop @pathList) {
1763                # Get the table whose rows are to be deleted.
1764                my @pathTables = @{$path};
1765                # Start the DELETE statement. We need to call DBKernel because the
1766                # syntax of a DELETE-USING varies among DBMSs.
1767                my $target = $pathTables[$#pathTables];
1768                my $stmt = $db->SetUsing(@pathTables);
1769                # Now start the WHERE. The first thing is the ID field from the starting table. That
1770                # starting table will either be the entity relation or one of the entity's
1771                # sub-relations.
1772                $stmt .= " WHERE $pathTables[0].id $qualifier";
1773                # Now we run through the remaining entities in the path, connecting them up.
1774                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1775                    # Connect the current relationship to the preceding entity.
1776                    my ($entity, $rel) = @pathTables[$i-1,$i];
1777                    # The style of connection depends on the direction of the relationship.
1778                    $stmt .= " AND $entity.id = $rel.$keyName";
1779                    if ($i + 1 <= $#pathTables) {
1780                        # Here there's a next entity, so connect that to the relationship's
1781                        # to-link.
1782                        my $entity2 = $pathTables[$i+1];
1783                        $stmt .= " AND $rel.to_link = $entity2.id";
1784                    }
1785                }
1786                # Now we have our desired DELETE statement.
1787                if ($options{testMode}) {
1788                    # Here the user wants to trace without executing.
1789                    Trace($stmt) if T(0);
1790                } else {
1791                    # Here we can delete. Note that the SQL method dies with a confession
1792                    # if an error occurs, so we just go ahead and do it.
1793                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1794                    my $rv = $db->SQL($stmt, 0, $objectID);
1795                    # Accumulate the statistics for this delete. The only rows deleted
1796                    # are from the target table, so we use its name to record the
1797                    # statistic.
1798                    $retVal->Add($target, $rv);
1799                }
1800            }
1801        }
1802        # Return the result.
1803        return $retVal;
1804    }
1805    
1806    =head3 Disconnect
1807    
1808    C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1809    
1810    Disconnect an entity instance from all the objects to which it is related. This
1811    will delete each relationship instance that connects to the specified entity.
1812    
1813    =over 4
1814    
1815    =item relationshipName
1816    
1817    Name of the relationship whose instances are to be deleted.
1818    
1819    =item originEntityName
1820    
1821    Name of the entity that is to be disconnected.
1822    
1823    =item originEntityID
1824    
1825    ID of the entity that is to be disconnected.
1826    
1827    =back
1828    
1829    =cut
1830    
1831    sub Disconnect {
1832        # Get the parameters.
1833        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1834        # Get the relationship descriptor.
1835        my $structure = $self->_GetStructure($relationshipName);
1836        # Insure we have a relationship.
1837        if (! exists $structure->{from}) {
1838            Confess("$relationshipName is not a relationship in the database.");
1839        } else {
1840            # Get the database handle.
1841            my $dbh = $self->{_dbh};
1842            # We'll set this value to 1 if we find our entity.
1843            my $found = 0;
1844            # Loop through the ends of the relationship.
1845            for my $dir ('from', 'to') {
1846                if ($structure->{$dir} eq $originEntityName) {
1847                    # Delete all relationship instances on this side of the entity instance.
1848                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
1849                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1850                    $found = 1;
1851                }
1852            }
1853            # Insure we found the entity on at least one end.
1854            if (! $found) {
1855                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1856            }
1857        }
1858    }
1859    
1860    =head3 DeleteRow
1861    
1862    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1863    
1864    Delete a row from a relationship. In most cases, only the from-link and to-link are
1865    needed; however, for relationships with intersection data values can be specified
1866    for the other fields using a hash.
1867    
1868    =over 4
1869    
1870    =item relationshipName
1871    
1872    Name of the relationship from which the row is to be deleted.
1873    
1874    =item fromLink
1875    
1876    ID of the entity instance in the From direction.
1877    
1878    =item toLink
1879    
1880    ID of the entity instance in the To direction.
1881    
1882    =item values
1883    
1884    Reference to a hash of other values to be used for filtering the delete.
1885    
1886    =back
1887    
1888    =cut
1889    
1890    sub DeleteRow {
1891        # Get the parameters.
1892        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1893        # Create a hash of all the filter information.
1894        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1895        if (defined $values) {
1896            for my $key (keys %{$values}) {
1897                $filter{$key} = $values->{$key};
1898            }
1899        }
1900        # Build an SQL statement out of the hash.
1901        my @filters = ();
1902        my @parms = ();
1903        for my $key (keys %filter) {
1904            push @filters, _FixName($key) . " = ?";
1905            push @parms, $filter{$key};
1906        }
1907        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1908        my $command = "DELETE FROM $relationshipName WHERE " .
1909                      join(" AND ", @filters);
1910        # Execute it.
1911        my $dbh = $self->{_dbh};
1912        $dbh->SQL($command, undef, @parms);
1913    }
1914    
1915    =head3 SortNeeded
1916    
1917    C<< my $parms = $erdb->SortNeeded($relationName); >>
1918    
1919    Return the pipe command for the sort that should be applied to the specified
1920    relation when creating the load file.
1921    
1922    For example, if the load file should be sorted ascending by the first
1923    field, this method would return
1924    
1925        sort -k1 -t"\t"
1926    
1927    If the first field is numeric, the method would return
1928    
1929        sort -k1n -t"\t"
1930    
1931    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1932    keys using a sort.
1933    
1934    =over 4
1935    
1936    =item relationName
1937    
1938    Name of the relation to be examined.
1939    
1940    =item
1941    
1942    Returns the sort command to use for sorting the relation, suitable for piping.
1943    
1944    =back
1945    
1946    =cut
1947    #: Return Type $;
1948    sub SortNeeded {
1949        # Get the parameters.
1950        my ($self, $relationName) = @_;
1951        # Declare a descriptor to hold the names of the key fields.
1952        my @keyNames = ();
1953        # Get the relation structure.
1954        my $relationData = $self->_FindRelation($relationName);
1955        # Find out if the relation is a primary entity relation,
1956        # a relationship relation, or a secondary entity relation.
1957        my $entityTable = $self->{_metaData}->{Entities};
1958        my $relationshipTable = $self->{_metaData}->{Relationships};
1959        if (exists $entityTable->{$relationName}) {
1960            # Here we have a primary entity relation.
1961            push @keyNames, "id";
1962        } elsif (exists $relationshipTable->{$relationName}) {
1963            # Here we have a relationship. We sort using the FROM index.
1964            my $relationshipData = $relationshipTable->{$relationName};
1965            my $index = $relationData->{Indexes}->{idxFrom};
1966            push @keyNames, @{$index->{IndexFields}};
1967        } else {
1968            # Here we have a secondary entity relation, so we have a sort on the ID field.
1969            push @keyNames, "id";
1970        }
1971        # Now we parse the key names into sort parameters. First, we prime the return
1972        # string.
1973        my $retVal = "sort -t\"\t\" ";
1974        # Get the relation's field list.
1975        my @fields = @{$relationData->{Fields}};
1976        # Loop through the keys.
1977        for my $keyData (@keyNames) {
1978            # Get the key and the ordering.
1979            my ($keyName, $ordering);
1980            if ($keyData =~ /^([^ ]+) DESC/) {
1981                ($keyName, $ordering) = ($1, "descending");
1982            } else {
1983                ($keyName, $ordering) = ($keyData, "ascending");
1984            }
1985            # Find the key's position and type.
1986            my $fieldSpec;
1987            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1988                my $thisField = $fields[$i];
1989                if ($thisField->{name} eq $keyName) {
1990                    # Get the sort modifier for this field type. The modifier
1991                    # decides whether we're using a character, numeric, or
1992                    # floating-point sort.
1993                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1994                    # If the index is descending for this field, denote we want
1995                    # to reverse the sort order on this field.
1996                    if ($ordering eq 'descending') {
1997                        $modifier .= "r";
1998                    }
1999                    # Store the position and modifier into the field spec, which
2000                    # will stop the inner loop. Note that the field number is
2001                    # 1-based in the sort command, so we have to increment the
2002                    # index.
2003                    $fieldSpec = ($i + 1) . $modifier;
2004                }
2005            }
2006            # Add this field to the sort command.
2007            $retVal .= " -k$fieldSpec";
2008        }
2009        # Return the result.
2010        return $retVal;
2011    }
2012    
2013    =head3 GetList
2014    
2015    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2016    
2017    Return a list of object descriptors for the specified objects as determined by the
2018    specified filter clause.
2019    
2020    This method is essentially the same as L</Get> except it returns a list of objects rather
2021    than a query object that can be used to get the results one record at a time.
2022    
2023    =over 4
2024    
2025    =item objectNames
2026    
2027    List containing the names of the entity and relationship objects to be retrieved.
2028    
2029    =item filterClause
2030    
2031    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2032    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2033    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2034    in the filter clause should be added to the parameter list as additional parameters. The
2035    fields in a filter clause can come from primary entity relations, relationship relations,
2036    or secondary entity relations; however, all of the entities and relationships involved must
2037    be included in the list of object names.
2038    
2039    The filter clause can also specify a sort order. To do this, simply follow the filter string
2040    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2041    particular genus and sorts them by species name.
2042    
2043    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2044    
2045    The rules for field references in a sort order are the same as those for field references in the
2046    filter clause in general; however, odd things may happen if a sort field is from a secondary
2047    relation.
2048    
2049    =item params
2050    
2051    Reference to a list of parameter values to be substituted into the filter clause.
2052    
2053    =item RETURN
2054    
2055    Returns a list of B<DBObject>s that satisfy the query conditions.
2056    
2057    =back
2058    
2059    =cut
2060    #: Return Type @%
2061    sub GetList {
2062        # Get the parameters.
2063        my ($self, $objectNames, $filterClause, $params) = @_;
2064        # Declare the return variable.
2065        my @retVal = ();
2066        # Perform the query.
2067        my $query = $self->Get($objectNames, $filterClause, $params);
2068        # Loop through the results.
2069        while (my $object = $query->Fetch) {
2070            push @retVal, $object;
2071        }
2072        # Return the result.
2073        return @retVal;
2074    }
2075    
2076    =head3 GetCount
2077    
2078    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2079    
2080    Return the number of rows found by a specified query. This method would
2081    normally be used to count the records in a single table. For example, in a
2082    genetics database
2083    
2084        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2085    
2086    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2087    to use it to return records based on a join. For example,
2088    
2089        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2090                                    ['homo %']);
2091    
2092    would return the number of features for genomes in the genus I<homo>. Note that
2093    only the rows from the first table are counted. If the above command were
2094    
2095        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2096                                    ['homo %']);
2097    
2098    it would return the number of genomes, not the number of genome/feature pairs.
2099    
2100    =over 4
2101    
2102    =item objectNames
2103    
2104    Reference to a list of the objects (entities and relationships) included in the
2105    query.
2106    
2107    =item filter
2108    
2109    A filter clause for restricting the query. The rules are the same as for the L</Get>
2110    method.
2111    
2112    =item params
2113    
2114    Reference to a list of the parameter values to be substituted for the parameter marks
2115    in the filter.
2116    
2117    =item RETURN
2118    
2119    Returns a count of the number of records in the first table that would satisfy
2120    the query.
2121    
2122    =back
2123    
2124    =cut
2125    
2126    sub GetCount {
2127        # Get the parameters.
2128        my ($self, $objectNames, $filter, $params) = @_;
2129        # Insure the params argument is an array reference if the caller left it off.
2130        if (! defined($params)) {
2131            $params = [];
2132        }
2133        # Declare the return variable.
2134        my $retVal;
2135        # Find out if we're counting an entity or a relationship.
2136        my $countedField;
2137        if ($self->IsEntity($objectNames->[0])) {
2138            $countedField = "id";
2139        } else {
2140            # For a relationship we count the to-link because it's usually more
2141            # numerous. Note we're automatically converting to the SQL form
2142            # of the field name (to_link vs. to-link).
2143            $countedField = "to_link";
2144        }
2145        # Create the SQL command suffix to get the desired records.
2146        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2147                                                                                $filter);
2148        # Prefix it with text telling it we want a record count.
2149        my $firstObject = $mappedNameListRef->[0];
2150        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2151        # Prepare and execute the command.
2152        my $sth = $self->_GetStatementHandle($command, $params);
2153        # Get the count value.
2154        ($retVal) = $sth->fetchrow_array();
2155        # Check for a problem.
2156        if (! defined($retVal)) {
2157            if ($sth->err) {
2158                # Here we had an SQL error.
2159                Confess("Error retrieving row count: " . $sth->errstr());
2160            } else {
2161                # Here we have no result.
2162                Confess("No result attempting to retrieve row count.");
2163            }
2164        }
2165        # Return the result.
2166        return $retVal;
2167    }
2168    
2169    =head3 ComputeObjectSentence
2170    
2171    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2172    
2173    Check an object name, and if it is a relationship convert it to a relationship sentence.
2174    
2175    =over 4
2176    
2177    =item objectName
2178    
2179    Name of the entity or relationship.
2180    
2181    =item RETURN
2182    
2183    Returns a string containing the entity name or a relationship sentence.
2184    
2185    =back
2186    
2187    =cut
2188    
2189    sub ComputeObjectSentence {
2190        # Get the parameters.
2191        my ($self, $objectName) = @_;
2192        # Set the default return value.
2193        my $retVal = $objectName;
2194        # Look for the object as a relationship.
2195        my $relTable = $self->{_metaData}->{Relationships};
2196        if (exists $relTable->{$objectName}) {
2197            # Get the relationship sentence.
2198            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2199        }
2200        # Return the result.
2201        return $retVal;
2202    }
2203    
2204    =head3 DumpRelations
2205    
2206    C<< $erdb->DumpRelations($outputDirectory); >>
2207    
2208    Write the contents of all the relations to tab-delimited files in the specified directory.
2209    Each file will have the same name as the relation dumped, with an extension of DTX.
2210    
2211    =over 4
2212    
2213    =item outputDirectory
2214    
2215    Name of the directory into which the relation files should be dumped.
2216    
2217    =back
2218    
2219    =cut
2220    
2221    sub DumpRelations {
2222        # Get the parameters.
2223        my ($self, $outputDirectory) = @_;
2224        # Now we need to run through all the relations. First, we loop through the entities.
2225        my $metaData = $self->{_metaData};
2226        my $entities = $metaData->{Entities};
2227        for my $entityName (keys %{$entities}) {
2228            my $entityStructure = $entities->{$entityName};
2229            # Get the entity's relations.
2230            my $relationList = $entityStructure->{Relations};
2231            # Loop through the relations, dumping them.
2232            for my $relationName (keys %{$relationList}) {
2233                my $relation = $relationList->{$relationName};
2234                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2235            }
2236        }
2237        # Next, we loop through the relationships.
2238        my $relationships = $metaData->{Relationships};
2239        for my $relationshipName (keys %{$relationships}) {
2240            my $relationshipStructure = $relationships->{$relationshipName};
2241            # Dump this relationship's relation.
2242            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2243        }
2244    }
2245    
2246    =head3 InsertValue
2247    
2248    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2249    
2250    This method will insert a new value into the database. The value must be one
2251    associated with a secondary relation, since primary values cannot be inserted:
2252    they occur exactly once. Secondary values, on the other hand, can be missing
2253    or multiply-occurring.
2254    
2255    =over 4
2256    
2257    =item entityID
2258    
2259    ID of the object that is to receive the new value.
2260    
2261    =item fieldName
2262    
2263    Field name for the new value-- this includes the entity name, since
2264    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2265    
2266    =item value
2267    
2268    New value to be put in the field.
2269    
2270    =back
2271    
2272    =cut
2273    
2274    sub InsertValue {
2275        # Get the parameters.
2276        my ($self, $entityID, $fieldName, $value) = @_;
2277        # Parse the entity name and the real field name.
2278        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2279            my $entityName = $1;
2280            my $fieldTitle = $2;
2281            # Get its descriptor.
2282            if (!$self->IsEntity($entityName)) {
2283                Confess("$entityName is not a valid entity.");
2284            } else {
2285                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2286                # Find the relation containing this field.
2287                my $fieldHash = $entityData->{Fields};
2288                if (! exists $fieldHash->{$fieldTitle}) {
2289                    Confess("$fieldTitle not found in $entityName.");
2290                } else {
2291                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2292                    if ($relation eq $entityName) {
2293                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2294                    } else {
2295                        # Now we can create an INSERT statement.
2296                        my $dbh = $self->{_dbh};
2297                        my $fixedName = _FixName($fieldTitle);
2298                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2299                        # Execute the command.
2300                        $dbh->SQL($statement, 0, $entityID, $value);
2301                    }
2302                }
2303            }
2304        } else {
2305            Confess("$fieldName is not a valid field name.");
2306        }
2307    }
2308    
2309    =head3 InsertObject
2310    
2311    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2312    
2313    Insert an object into the database. The object is defined by a type name and then a hash
2314    of field names to values. Field values in the primary relation are represented by scalars.
2315    (Note that for relationships, the primary relation is the B<only> relation.)
2316    Field values for the other relations comprising the entity are always list references. For
2317    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2318    C<ZP_00210270.1> and C<gi|46206278>.
2319    
2320    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2321    
2322    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2323    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2324    
2325    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2326    
2327    =over 4
2328    
2329    =item newObjectType
2330    
2331    Type name of the object to insert.
2332    
2333    =item fieldHash
2334    
2335    Hash of field names to values.
2336    
2337    =back
2338    
2339    =cut
2340    
2341    sub InsertObject {
2342        # Get the parameters.
2343        my ($self, $newObjectType, $fieldHash) = @_;
2344        # Denote that so far we appear successful.
2345        my $retVal = 1;
2346        # Get the database handle.
2347        my $dbh = $self->{_dbh};
2348        # Get the relation list.
2349          my $relationTable = $self->_GetRelationTable($newObjectType);          my $relationTable = $self->_GetRelationTable($newObjectType);
2350          # Loop through the relations. We'll build insert statements for each one. If a relation is          # Loop through the relations. We'll build insert statements for each one. If a relation is
2351          # secondary, we may end up generating multiple insert statements. If an error occurs, we          # secondary, we may end up generating multiple insert statements. If an error occurs, we
2352          # stop the loop.          # stop the loop.
2353          while ($retVal && (my ($relationName, $relationDefinition) = each %{$relationTable})) {      my @relationList = keys %{$relationTable};
2354        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2355            my $relationName = $relationList[$i];
2356            my $relationDefinition = $relationTable->{$relationName};
2357                  # Get the relation's fields. For each field we will collect a value in the corresponding                  # Get the relation's fields. For each field we will collect a value in the corresponding
2358                  # position of the @valueList array. If one of the fields is missing, we will add it to the                  # position of the @valueList array. If one of the fields is missing, we will add it to the
2359                  # @missing list.                  # @missing list.
# Line 886  Line 2375 
2375                                  push @valueList, $value;                                  push @valueList, $value;
2376                                  # If the value is a list, we may need to increment the record count.                                  # If the value is a list, we may need to increment the record count.
2377                                  if (ref $value eq "ARRAY") {                                  if (ref $value eq "ARRAY") {
2378                                          my $thisCount = @{$value};                      my $thisCount = @{$value};
2379                                          if ($recordCount == 1) {                      if ($recordCount == 1) {
2380                                                  # Here we have our first list, so we save its count.                          # Here we have our first list, so we save its count.
2381                                                  $recordCount = $thisCount;                          $recordCount = $thisCount;
2382                                          } elsif ($recordCount != $thisCount) {                      } elsif ($recordCount != $thisCount) {
2383                                                  # Here we have a second list, so its length has to match the                          # Here we have a second list, so its length has to match the
2384                                                  # previous lists.                          # previous lists.
2385                                                  Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);                          Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2386                                                  $retVal = 0;                          $retVal = 0;
2387                        }
2388                    }
2389                } else {
2390                    # Here the field is not present. Flag it as missing.
2391                    push @missing, $fieldName;
2392                }
2393            }
2394            # If we are the primary relation, add the new-record flag.
2395            if ($relationName eq $newObjectType) {
2396                push @valueList, 1;
2397                push @fieldNameList, "new_record";
2398            }
2399            # Only proceed if there are no missing fields.
2400            if (@missing > 0) {
2401                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2402                    join(' ', @missing)) if T(1);
2403            } else {
2404                # Build the INSERT statement.
2405                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2406                    ") VALUES (";
2407                # Create a marker list of the proper size and put it in the statement.
2408                my @markers = ();
2409                while (@markers < @fieldNameList) { push @markers, '?'; }
2410                $statement .= join(', ', @markers) . ")";
2411                # We have the insert statement, so prepare it.
2412                my $sth = $dbh->prepare_command($statement);
2413                Trace("Insert statement prepared: $statement") if T(3);
2414                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2415                # a list, we use the current element. The values are stored in the @parameterList array.
2416                my $done = 0;
2417                for (my $i = 0; $i < $recordCount; $i++) {
2418                    # Clear the parameter list array.
2419                    my @parameterList = ();
2420                    # Loop through the values.
2421                    for my $value (@valueList) {
2422                        # Check to see if this is a scalar value.
2423                        if (ref $value eq "ARRAY") {
2424                            # Here we have a list value. Pull the current entry.
2425                            push @parameterList, $value->[$i];
2426                        } else {
2427                            # Here we have a scalar value. Use it unmodified.
2428                            push @parameterList, $value;
2429                        }
2430                    }
2431                    # Execute the INSERT statement with the specified parameter list.
2432                    $retVal = $sth->execute(@parameterList);
2433                    if (!$retVal) {
2434                        my $errorString = $sth->errstr();
2435                        Confess("Error inserting into $relationName: $errorString");
2436                    }
2437                }
2438            }
2439        }
2440        # Return a 1 for backward compatability.
2441        return 1;
2442    }
2443    
2444    =head3 UpdateEntity
2445    
2446    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2447    
2448    Update the values of an entity. This is an unprotected update, so it should only be
2449    done if the database resides on a database server.
2450    
2451    =over 4
2452    
2453    =item entityName
2454    
2455    Name of the entity to update. (This is the entity type.)
2456    
2457    =item id
2458    
2459    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2460    
2461    =item fields
2462    
2463    Reference to a hash mapping field names to their new values. All of the fields named
2464    must be in the entity's primary relation, and they cannot any of them be the ID field.
2465    
2466    =back
2467    
2468    =cut
2469    
2470    sub UpdateEntity {
2471        # Get the parameters.
2472        my ($self, $entityName, $id, $fields) = @_;
2473        # Get a list of the field names being updated.
2474        my @fieldList = keys %{$fields};
2475        # Verify that the fields exist.
2476        my $checker = $self->GetFieldTable($entityName);
2477        for my $field (@fieldList) {
2478            if ($field eq 'id') {
2479                Confess("Cannot update the ID field for entity $entityName.");
2480            } elsif ($checker->{$field}->{relation} ne $entityName) {
2481                Confess("Cannot find $field in primary relation of $entityName.");
2482            }
2483        }
2484        # Build the SQL statement.
2485        my @sets = ();
2486        my @valueList = ();
2487        for my $field (@fieldList) {
2488            push @sets, _FixName($field) . " = ?";
2489            push @valueList, $fields->{$field};
2490        }
2491        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2492        # Add the ID to the list of binding values.
2493        push @valueList, $id;
2494        # Call SQL to do the work.
2495        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2496        # Check for errors.
2497        if ($rows == 0) {
2498            Confess("Entity $id of type $entityName not found.");
2499        }
2500    }
2501    
2502    =head3 LoadTable
2503    
2504    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2505    
2506    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2507    first.
2508    
2509    =over 4
2510    
2511    =item fileName
2512    
2513    Name of the file from which the table data should be loaded.
2514    
2515    =item relationName
2516    
2517    Name of the relation to be loaded. This is the same as the table name.
2518    
2519    =item truncateFlag
2520    
2521    TRUE if the table should be dropped and re-created, else FALSE
2522    
2523    =item RETURN
2524    
2525    Returns a statistical object containing a list of the error messages.
2526    
2527    =back
2528    
2529    =cut
2530    sub LoadTable {
2531        # Get the parameters.
2532        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2533        # Create the statistical return object.
2534        my $retVal = _GetLoadStats();
2535        # Trace the fact of the load.
2536        Trace("Loading table $relationName from $fileName") if T(2);
2537        # Get the database handle.
2538        my $dbh = $self->{_dbh};
2539        # Get the input file size.
2540        my $fileSize = -s $fileName;
2541        # Get the relation data.
2542        my $relation = $self->_FindRelation($relationName);
2543        # Check the truncation flag.
2544        if ($truncateFlag) {
2545            Trace("Creating table $relationName") if T(2);
2546            # Compute the row count estimate. We take the size of the load file,
2547            # divide it by the estimated row size, and then multiply by 1.5 to
2548            # leave extra room. We postulate a minimum row count of 1000 to
2549            # prevent problems with incoming empty load files.
2550            my $rowSize = $self->EstimateRowSize($relationName);
2551            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2552            # Re-create the table without its index.
2553            $self->CreateTable($relationName, 0, $estimate);
2554            # If this is a pre-index DBMS, create the index here.
2555            if ($dbh->{_preIndex}) {
2556                eval {
2557                    $self->CreateIndex($relationName);
2558                };
2559                if ($@) {
2560                    $retVal->AddMessage($@);
2561                }
2562            }
2563        }
2564        # Load the table.
2565        my $rv;
2566        eval {
2567            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2568        };
2569        if (!defined $rv) {
2570            $retVal->AddMessage($@) if ($@);
2571            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2572            Trace("Table load failed for $relationName.") if T(1);
2573        } else {
2574            # Here we successfully loaded the table.
2575            $retVal->Add("tables");
2576            my $size = -s $fileName;
2577            Trace("$size bytes loaded into $relationName.") if T(2);
2578            # If we're rebuilding, we need to create the table indexes.
2579            if ($truncateFlag) {
2580                # Indexes are created here for PostGres. For PostGres, indexes are
2581                # best built at the end. For MySQL, the reverse is true.
2582                if (! $dbh->{_preIndex}) {
2583                    eval {
2584                        $self->CreateIndex($relationName);
2585                    };
2586                    if ($@) {
2587                        $retVal->AddMessage($@);
2588                    }
2589                }
2590                # The full-text index (if any) is always built last, even for MySQL.
2591                # First we need to see if this table has a full-text index. Only
2592                # primary relations are allowed that privilege.
2593                Trace("Checking for full-text index on $relationName.") if T(2);
2594                if ($self->_IsPrimary($relationName)) {
2595                    $self->CreateSearchIndex($relationName);
2596                }
2597            }
2598        }
2599        # Analyze the table to improve performance.
2600        Trace("Analyzing and compacting $relationName.") if T(3);
2601        $dbh->vacuum_it($relationName);
2602        Trace("$relationName load completed.") if T(3);
2603        # Return the statistics.
2604        return $retVal;
2605    }
2606    
2607    =head3 CreateSearchIndex
2608    
2609    C<< $erdb->CreateSearchIndex($objectName); >>
2610    
2611    Check for a full-text search index on the specified entity or relationship object, and
2612    if one is required, rebuild it.
2613    
2614    =over 4
2615    
2616    =item objectName
2617    
2618    Name of the entity or relationship to be indexed.
2619    
2620    =back
2621    
2622    =cut
2623    
2624    sub CreateSearchIndex {
2625        # Get the parameters.
2626        my ($self, $objectName) = @_;
2627        # Get the relation's entity/relationship structure.
2628        my $structure = $self->_GetStructure($objectName);
2629        # Get the database handle.
2630        my $dbh = $self->{_dbh};
2631        Trace("Checking for search fields in $objectName.") if T(3);
2632        # Check for a searchable fields list.
2633        if (exists $structure->{searchFields}) {
2634            # Here we know that we need to create a full-text search index.
2635            # Get an SQL-formatted field name list.
2636            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2637            # Create the index. If it already exists, it will be dropped.
2638            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2639                               flds => $fields, kind => 'fulltext');
2640            Trace("Index created for $fields in $objectName.") if T(2);
2641        }
2642    }
2643    
2644    =head3 DropRelation
2645    
2646    C<< $erdb->DropRelation($relationName); >>
2647    
2648    Physically drop a relation from the database.
2649    
2650    =over 4
2651    
2652    =item relationName
2653    
2654    Name of the relation to drop. If it does not exist, this method will have
2655    no effect.
2656    
2657    =back
2658    
2659    =cut
2660    
2661    sub DropRelation {
2662        # Get the parameters.
2663        my ($self, $relationName) = @_;
2664        # Get the database handle.
2665        my $dbh = $self->{_dbh};
2666        # Drop the relation. The method used here has no effect if the relation
2667        # does not exist.
2668        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2669        $dbh->drop_table(tbl => $relationName);
2670    }
2671    
2672    =head3 MatchSqlPattern
2673    
2674    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2675    
2676    Determine whether or not a specified value matches an SQL pattern. An SQL
2677    pattern has two wild card characters: C<%> that matches multiple characters,
2678    and C<_> that matches a single character. These can be escaped using a
2679    backslash (C<\>). We pull this off by converting the SQL pattern to a
2680    PERL regular expression. As per SQL rules, the match is case-insensitive.
2681    
2682    =over 4
2683    
2684    =item value
2685    
2686    Value to be matched against the pattern. Note that an undefined or empty
2687    value will not match anything.
2688    
2689    =item pattern
2690    
2691    SQL pattern against which to match the value. An undefined or empty pattern will
2692    match everything.
2693    
2694    =item RETURN
2695    
2696    Returns TRUE if the value and pattern match, else FALSE.
2697    
2698    =back
2699    
2700    =cut
2701    
2702    sub MatchSqlPattern {
2703        # Get the parameters.
2704        my ($value, $pattern) = @_;
2705        # Declare the return variable.
2706        my $retVal;
2707        # Insure we have a pattern.
2708        if (! defined($pattern) || $pattern eq "") {
2709            $retVal = 1;
2710        } else {
2711            # Break the pattern into pieces around the wildcard characters. Because we
2712            # use parentheses in the split function's delimiter expression, we'll get
2713            # list elements for the delimiters as well as the rest of the string.
2714            my @pieces = split /([_%]|\\[_%])/, $pattern;
2715            # Check some fast special cases.
2716            if ($pattern eq '%') {
2717                # A null pattern matches everything.
2718                $retVal = 1;
2719            } elsif (@pieces == 1) {
2720                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2721                $retVal = (lc($value) eq lc($pattern));
2722            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2723                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2724                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2725            } else {
2726                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2727                my $realPattern = "";
2728                for my $piece (@pieces) {
2729                    # Determine the type of piece.
2730                    if ($piece eq "") {
2731                        # Empty pieces are ignored.
2732                    } elsif ($piece eq "%") {
2733                        # Here we have a multi-character wildcard. Note that it can match
2734                        # zero or more characters.
2735                        $realPattern .= ".*"
2736                    } elsif ($piece eq "_") {
2737                        # Here we have a single-character wildcard.
2738                        $realPattern .= ".";
2739                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2740                        # This is an escape sequence (which is a rare thing, actually).
2741                        $realPattern .= substr($piece, 1, 1);
2742                    } else {
2743                        # Here we have raw text.
2744                        $realPattern .= quotemeta($piece);
2745                    }
2746                }
2747                # Do the match.
2748                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2749            }
2750        }
2751        # Return the result.
2752        return $retVal;
2753    }
2754    
2755    =head3 GetEntity
2756    
2757    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2758    
2759    Return an object describing the entity instance with a specified ID.
2760    
2761    =over 4
2762    
2763    =item entityType
2764    
2765    Entity type name.
2766    
2767    =item ID
2768    
2769    ID of the desired entity.
2770    
2771    =item RETURN
2772    
2773    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2774    instance is found with the specified key.
2775    
2776    =back
2777    
2778    =cut
2779    
2780    sub GetEntity {
2781        # Get the parameters.
2782        my ($self, $entityType, $ID) = @_;
2783        # Create a query.
2784        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2785        # Get the first (and only) object.
2786        my $retVal = $query->Fetch();
2787        # Return the result.
2788        return $retVal;
2789    }
2790    
2791    =head3 GetChoices
2792    
2793    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2794    
2795    Return a list of all the values for the specified field that are represented in the
2796    specified entity.
2797    
2798    Note that if the field is not indexed, then this will be a very slow operation.
2799    
2800    =over 4
2801    
2802    =item entityName
2803    
2804    Name of an entity in the database.
2805    
2806    =item fieldName
2807    
2808    Name of a field belonging to the entity. This is a raw field name without
2809    the standard parenthesized notation used in most calls.
2810    
2811    =item RETURN
2812    
2813    Returns a list of the distinct values for the specified field in the database.
2814    
2815    =back
2816    
2817    =cut
2818    
2819    sub GetChoices {
2820        # Get the parameters.
2821        my ($self, $entityName, $fieldName) = @_;
2822        # Declare the return variable.
2823        my @retVal;
2824        # Get the entity data structure.
2825        my $entityData = $self->_GetStructure($entityName);
2826        # Get the field.
2827        my $fieldHash = $entityData->{Fields};
2828        if (! exists $fieldHash->{$fieldName}) {
2829            Confess("$fieldName not found in $entityName.");
2830        } else {
2831            # Get the name of the relation containing the field.
2832            my $relation = $fieldHash->{$fieldName}->{relation};
2833            # Fix up the field name.
2834            my $realName = _FixName($fieldName);
2835            # Get the database handle.
2836            my $dbh = $self->{_dbh};
2837            # Query the database.
2838            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2839            # Clean the results. They are stored as a list of lists, and we just want the one list.
2840            @retVal = sort map { $_->[0] } @{$results};
2841        }
2842        # Return the result.
2843        return @retVal;
2844    }
2845    
2846    =head3 GetEntityValues
2847    
2848    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2849    
2850    Return a list of values from a specified entity instance. If the entity instance
2851    does not exist, an empty list is returned.
2852    
2853    =over 4
2854    
2855    =item entityType
2856    
2857    Entity type name.
2858    
2859    =item ID
2860    
2861    ID of the desired entity.
2862    
2863    =item fields
2864    
2865    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2866    
2867    =item RETURN
2868    
2869    Returns a flattened list of the values of the specified fields for the specified entity.
2870    
2871    =back
2872    
2873    =cut
2874    
2875    sub GetEntityValues {
2876        # Get the parameters.
2877        my ($self, $entityType, $ID, $fields) = @_;
2878        # Get the specified entity.
2879        my $entity = $self->GetEntity($entityType, $ID);
2880        # Declare the return list.
2881        my @retVal = ();
2882        # If we found the entity, push the values into the return list.
2883        if ($entity) {
2884            push @retVal, $entity->Values($fields);
2885                                          }                                          }
2886        # Return the result.
2887        return @retVal;
2888                                  }                                  }
2889    
2890    =head3 GetAll
2891    
2892    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2893    
2894    Return a list of values taken from the objects returned by a query. The first three
2895    parameters correspond to the parameters of the L</Get> method. The final parameter is
2896    a list of the fields desired from each record found by the query. The field name
2897    syntax is the standard syntax used for fields in the B<ERDB> system--
2898    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2899    or relationship and I<fieldName> is the name of the field.
2900    
2901    The list returned will be a list of lists. Each element of the list will contain
2902    the values returned for the fields specified in the fourth parameter. If one of the
2903    fields specified returns multiple values, they are flattened in with the rest. For
2904    example, the following call will return a list of the features in a particular
2905    spreadsheet cell, and each feature will be represented by a list containing the
2906    feature ID followed by all of its aliases.
2907    
2908    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2909    
2910    =over 4
2911    
2912    =item objectNames
2913    
2914    List containing the names of the entity and relationship objects to be retrieved.
2915    
2916    =item filterClause
2917    
2918    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2919    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2920    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2921    parameter list as additional parameters. The fields in a filter clause can come from primary
2922    entity relations, relationship relations, or secondary entity relations; however, all of the
2923    entities and relationships involved must be included in the list of object names.
2924    
2925    =item parameterList
2926    
2927    List of the parameters to be substituted in for the parameters marks in the filter clause.
2928    
2929    =item fields
2930    
2931    List of the fields to be returned in each element of the list returned.
2932    
2933    =item count
2934    
2935    Maximum number of records to return. If omitted or 0, all available records will be returned.
2936    
2937    =item RETURN
2938    
2939    Returns a list of list references. Each element of the return list contains the values for the
2940    fields specified in the B<fields> parameter.
2941    
2942    =back
2943    
2944    =cut
2945    #: Return Type @@;
2946    sub GetAll {
2947        # Get the parameters.
2948        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2949        # Translate the parameters from a list reference to a list. If the parameter
2950        # list is a scalar we convert it into a singleton list.
2951        my @parmList = ();
2952        if (ref $parameterList eq "ARRAY") {
2953            Trace("GetAll parm list is an array.") if T(4);
2954            @parmList = @{$parameterList};
2955                          } else {                          } else {
2956                                  # Here the field is not present. Flag it as missing.          Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2957                                  push @missing, $fieldName;          push @parmList, $parameterList;
2958                          }                          }
2959        # Insure the counter has a value.
2960        if (!defined $count) {
2961            $count = 0;
2962        }
2963        # Add the row limit to the filter clause.
2964        if ($count > 0) {
2965            $filterClause .= " LIMIT $count";
2966        }
2967        # Create the query.
2968        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2969        # Set up a counter of the number of records read.
2970        my $fetched = 0;
2971        # Loop through the records returned, extracting the fields. Note that if the
2972        # counter is non-zero, we stop when the number of records read hits the count.
2973        my @retVal = ();
2974        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2975            my @rowData = $row->Values($fields);
2976            push @retVal, \@rowData;
2977            $fetched++;
2978                  }                  }
2979                  # If we are the primary relation, add the new-record flag.      Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2980                  if ($relationName eq $newObjectType) {      # Return the resulting list.
2981                          push @valueList, 1;      return @retVal;
                         push @fieldNameList, "new_record";  
2982                  }                  }
2983                  # Only proceed if there are no missing fields.  
2984                  if (@missing > 0) {  =head3 Exists
2985                          Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .  
2986                                  join(' ', @missing)) if T(1);  C<< my $found = $sprout->Exists($entityName, $entityID); >>
2987                  } else {  
2988                          # Build the INSERT statement.  Return TRUE if an entity exists, else FALSE.
2989                          my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .  
2990                                  ") VALUES (";  =over 4
2991                          # Create a marker list of the proper size and put it in the statement.  
2992                          my @markers = ();  =item entityName
2993                          while (@markers < @fieldNameList) { push @markers, '?'; }  
2994                          $statement .= join(', ', @markers) . ")";  Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2995                          # We have the insert statement, so prepare it.  
2996                          my $sth = $dbh->prepare_command($statement);  =item entityID
2997                          Trace("Insert statement prepared: $statement") if T(3);  
2998                          # Now we loop through the values. If a value is scalar, we use it unmodified. If it's  ID of the entity instance whose existence is to be checked.
2999                          # a list, we use the current element. The values are stored in the @parameterList array.  
3000                          my $done = 0;  =item RETURN
3001                          for (my $i = 0; $i < $recordCount; $i++) {  
3002                                  # Clear the parameter list array.  Returns TRUE if the entity instance exists, else FALSE.
3003                                  my @parameterList = ();  
3004                                  # Loop through the values.  =back
3005                                  for my $value (@valueList) {  
3006                                          # Check to see if this is a scalar value.  =cut
3007                                          if (ref $value eq "ARRAY") {  #: Return Type $;
3008                                                  # Here we have a list value. Pull the current entry.  sub Exists {
3009                                                  push @parameterList, $value->[$i];      # Get the parameters.
3010        my ($self, $entityName, $entityID) = @_;
3011        # Check for the entity instance.
3012        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3013        my $testInstance = $self->GetEntity($entityName, $entityID);
3014        # Return an existence indicator.
3015        my $retVal = ($testInstance ? 1 : 0);
3016        return $retVal;
3017    }
3018    
3019    =head3 EstimateRowSize
3020    
3021    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3022    
3023    Estimate the row size of the specified relation. The estimated row size is computed by adding
3024    up the average length for each data type.
3025    
3026    =over 4
3027    
3028    =item relName
3029    
3030    Name of the relation whose estimated row size is desired.
3031    
3032    =item RETURN
3033    
3034    Returns an estimate of the row size for the specified relation.
3035    
3036    =back
3037    
3038    =cut
3039    #: Return Type $;
3040    sub EstimateRowSize {
3041        # Get the parameters.
3042        my ($self, $relName) = @_;
3043        # Declare the return variable.
3044        my $retVal = 0;
3045        # Find the relation descriptor.
3046        my $relation = $self->_FindRelation($relName);
3047        # Get the list of fields.
3048        for my $fieldData (@{$relation->{Fields}}) {
3049            # Get the field type and add its length.
3050            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3051            $retVal += $fieldLen;
3052        }
3053        # Return the result.
3054        return $retVal;
3055    }
3056    
3057    =head3 GetFieldTable
3058    
3059    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3060    
3061    Get the field structure for a specified entity or relationship.
3062    
3063    =over 4
3064    
3065    =item objectName
3066    
3067    Name of the desired entity or relationship.
3068    
3069    =item RETURN
3070    
3071    The table containing the field descriptors for the specified object.
3072    
3073    =back
3074    
3075    =cut
3076    
3077    sub GetFieldTable {
3078        # Get the parameters.
3079        my ($self, $objectName) = @_;
3080        # Get the descriptor from the metadata.
3081        my $objectData = $self->_GetStructure($objectName);
3082        # Return the object's field table.
3083        return $objectData->{Fields};
3084    }
3085    
3086    =head3 SplitKeywords
3087    
3088    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3089    
3090    This method returns a list of the positive keywords in the specified
3091    keyword string. All of the operators will have been stripped off,
3092    and if the keyword is preceded by a minus operator (C<->), it will
3093    not be in the list returned. The idea here is to get a list of the
3094    keywords the user wants to see. The list will be processed to remove
3095    duplicates.
3096    
3097    It is possible to create a string that confuses this method. For example
3098    
3099        frog toad -frog
3100    
3101    would return both C<frog> and C<toad>. If this is a problem we can deal
3102    with it later.
3103    
3104    =over 4
3105    
3106    =item keywordString
3107    
3108    The keyword string to be parsed.
3109    
3110    =item RETURN
3111    
3112    Returns a list of the words in the keyword string the user wants to
3113    see.
3114    
3115    =back
3116    
3117    =cut
3118    
3119    sub SplitKeywords {
3120        # Get the parameters.
3121        my ($keywordString) = @_;
3122        # Make a safety copy of the string. (This helps during debugging.)
3123        my $workString = $keywordString;
3124        # Convert operators we don't care about to spaces.
3125        $workString =~ tr/+"()<>/ /;
3126        # Split the rest of the string along space boundaries. Note that we
3127        # eliminate any words that are zero length or begin with a minus sign.
3128        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3129        # Use a hash to remove duplicates.
3130        my %words = map { $_ => 1 } @wordList;
3131        # Return the result.
3132        return sort keys %words;
3133    }
3134    
3135    =head3 ValidateFieldName
3136    
3137    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3138    
3139    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3140    be hyphenated words subject to certain restrictions.
3141    
3142    =over 4
3143    
3144    =item fieldName
3145    
3146    Field name to be validated.
3147    
3148    =item RETURN
3149    
3150    Returns TRUE if the field name is valid, else FALSE.
3151    
3152    =back
3153    
3154    =cut
3155    
3156    sub ValidateFieldName {
3157        # Get the parameters.
3158        my ($fieldName) = @_;
3159        # Declare the return variable. The field name is valid until we hear
3160        # differently.
3161        my $retVal = 1;
3162        # Compute the maximum name length.
3163        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3164        # Look for bad stuff in the name.
3165        if ($fieldName =~ /--/) {
3166            # Here we have a doubled minus sign.
3167            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3168            $retVal = 0;
3169        } elsif ($fieldName !~ /^[A-Za-z]/) {
3170            # Here the field name is missing the initial letter.
3171            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3172            $retVal = 0;
3173        } elsif (length($fieldName) > $maxLen) {
3174            # Here the field name is too long.
3175            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3176                                          } else {                                          } else {
3177                                                  # Here we have a scalar value. Use it unmodified.          # Strip out the minus signs. Everything remaining must be a letter,
3178                                                  push @parameterList, $value;          # underscore, or digit.
3179            my $strippedName = $fieldName;
3180            $strippedName =~ s/-//g;
3181            if ($strippedName !~ /^(\w|\d)+$/) {
3182                Trace("Field name $fieldName contains illegal characters.") if T(1);
3183                $retVal = 0;
3184                                          }                                          }
3185                                  }                                  }
3186                                  # Execute the INSERT statement with the specified parameter list.      # Return the result.
3187                                  $retVal = $sth->execute(@parameterList);      return $retVal;
3188                                  if (!$retVal) {  }
3189                                          my $errorString = $sth->errstr();  
3190                                          Trace("Insert error: $errorString.") if T(0);  =head3 ReadMetaXML
3191    
3192    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3193    
3194    This method reads a raw database definition XML file and returns it.
3195    Normally, the metadata used by the ERDB system has been processed and
3196    modified to make it easier to load and retrieve the data; however,
3197    this method can be used to get the data in its raw form.
3198    
3199    =over 4
3200    
3201    =item fileName
3202    
3203    Name of the XML file to read.
3204    
3205    =item RETURN
3206    
3207    Returns a hash reference containing the raw XML data from the specified file.
3208    
3209    =back
3210    
3211    =cut
3212    
3213    sub ReadMetaXML {
3214        # Get the parameters.
3215        my ($fileName) = @_;
3216        # Read the XML.
3217        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3218        Trace("XML metadata loaded from file $fileName.") if T(1);
3219        # Return the result.
3220        return $retVal;
3221                                  }                                  }
3222    
3223    =head3 GetEntityFieldHash
3224    
3225    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3226    
3227    Get the field hash of the named entity in the specified raw XML structure.
3228    The field hash may not exist, in which case we need to create it.
3229    
3230    =over 4
3231    
3232    =item structure
3233    
3234    Raw XML structure defininng the database. This is not the run-time XML used by
3235    an ERDB object, since that has all sorts of optimizations built-in.
3236    
3237    =item entityName
3238    
3239    Name of the entity whose field structure is desired.
3240    
3241    =item RETURN
3242    
3243    Returns the field hash used to define the entity's fields.
3244    
3245    =back
3246    
3247    =cut
3248    
3249    sub GetEntityFieldHash {
3250        # Get the parameters.
3251        my ($structure, $entityName) = @_;
3252        # Get the entity structure.
3253        my $entityData = $structure->{Entities}->{$entityName};
3254        # Look for a field structure.
3255        my $retVal = $entityData->{Fields};
3256        # If it doesn't exist, create it.
3257        if (! defined($retVal)) {
3258            $entityData->{Fields} = {};
3259            $retVal = $entityData->{Fields};
3260                          }                          }
3261        # Return the result.
3262        return $retVal;
3263                  }                  }
3264    
3265    =head3 WriteMetaXML
3266    
3267    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3268    
3269    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3270    used to update the database definition. It must be used with care, however, since it
3271    will only work on a raw structure, not on the processed structure created by an ERDB
3272    constructor.
3273    
3274    =over 4
3275    
3276    =item structure
3277    
3278    XML structure to be written to the file.
3279    
3280    =item fileName
3281    
3282    Name of the output file to which the updated XML should be stored.
3283    
3284    =back
3285    
3286    =cut
3287    
3288    sub WriteMetaXML {
3289        # Get the parameters.
3290        my ($structure, $fileName) = @_;
3291        # Compute the output.
3292        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3293        # Write it to the file.
3294        my $xmlOut = Open(undef, ">$fileName");
3295        print $xmlOut $fileString;
3296          }          }
3297          # Return the success indicator.  
3298    
3299    =head3 HTMLNote
3300    
3301    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3302    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3303    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3304    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3305    
3306    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3307    
3308    =over 4
3309    
3310    =item dataString
3311    
3312    String to convert to HTML.
3313    
3314    =item RETURN
3315    
3316    An HTML string derived from the input string.
3317    
3318    =back
3319    
3320    =cut
3321    
3322    sub HTMLNote {
3323        # Get the parameter.
3324        my ($dataString) = @_;
3325        # HTML-escape the text.
3326        my $retVal = CGI::escapeHTML($dataString);
3327        # Substitute the bulletin board codes.
3328        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3329        $retVal =~ s!\[p\]!</p><p>!g;
3330        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3331        $retVal =~ s!\[/link\]!</a>!g;
3332        # Return the result.
3333          return $retVal;          return $retVal;
3334  }  }
3335    
 =head3 LoadTable  
3336    
3337  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  =head2 Data Mining Methods
3338    
3339    =head3 GetUsefulCrossValues
3340    
3341  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3342    
3343    Return a list of the useful attributes that would be returned by a B<Cross> call
3344    from an entity of the source entity type through the specified relationship. This
3345    means it will return the fields of the target entity type and the intersection data
3346    fields in the relationship. Only primary table fields are returned. In other words,
3347    the field names returned will be for fields where there is always one and only one
3348    value.
3349    
3350  =over 4  =over 4
3351    
3352  =item fileName  =item sourceEntity
3353    
3354  Name of the file from which the table data should be loaded.  Name of the entity from which the relationship crossing will start.
3355    
3356  =item relationName  =item relationship
3357    
3358  Name of the relation to be loaded. This is the same as the table name.  Name of the relationship being crossed.
3359    
3360  =item truncateFlag  =item RETURN
3361    
3362  TRUE if the table should be dropped and re-created, else FALSE  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3363    
3364    =back
3365    
3366    =cut
3367    #: Return Type @;
3368    sub GetUsefulCrossValues {
3369        # Get the parameters.
3370        my ($self, $sourceEntity, $relationship) = @_;
3371        # Declare the return variable.
3372        my @retVal = ();
3373        # Determine the target entity for the relationship. This is whichever entity is not
3374        # the source entity. So, if the source entity is the FROM, we'll get the name of
3375        # the TO, and vice versa.
3376        my $relStructure = $self->_GetStructure($relationship);
3377        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3378        my $targetEntity = $relStructure->{$targetEntityType};
3379        # Get the field table for the entity.
3380        my $entityFields = $self->GetFieldTable($targetEntity);
3381        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3382        # For the entity fields, the key aspect of the target structure is that the {relation} value
3383        # must match the entity name.
3384        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3385                            keys %{$entityFields};
3386        # Push the fields found onto the return variable.
3387        push @retVal, sort @fieldList;
3388        # Get the field table for the relationship.
3389        my $relationshipFields = $self->GetFieldTable($relationship);
3390        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3391        # This may end up being an empty set.
3392        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3393                            keys %{$relationshipFields};
3394