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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.81, Wed Dec 20 20:03:25 2006 UTC
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2    
3          use strict;          use strict;
4          use Tracer;          use Tracer;
5          use DBKernel;      use DBrtns;
6          use Data::Dumper;          use Data::Dumper;
7          use XML::Simple;          use XML::Simple;
8          use DBQuery;          use DBQuery;
9          use DBObject;          use DBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use 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 32  Line 35 
35  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36  The B<FEATURE> entity also contains an optional virulence number. This is implemented  The B<FEATURE> entity also contains an optional virulence number. This is implemented
37  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in the  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39  C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence number.  the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40  If the virulence of I<ABC> is not known, there will not be any rows for it in C<FeatureVirulence>.  number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41    C<FeatureVirulence>.
42    
43  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
44  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
# Line 56  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
76  To facilitate testing, the ERDB module supports automatic generation of test data. This process  =head2 XML Database Description
77  is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
78  fully implemented.  =head3 Data Types
79    
80    The ERDB system supports the following data types. Note that there are numerous string
81    types depending on the maximum length. Some database packages limit the total number of
82    characters you have in an index key; to insure the database works in all environments,
83    the type of string should be the shortest one possible that supports all the known values.
84    
85    =over 4
86    
87    =item char
88    
89    single ASCII character
90    
91    =item int
92    
93    32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99    =item date
100    
101    64-bit unsigned integer, representing a PERL date/time value
102    
103    =item text
104    
105    long string; Text fields 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
# Line 145  Line 444 
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 176  Line 475 
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);                  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.                  # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
552                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
553                  # Loop through the relationships.                  # Loop through the relationships.
554                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
555                          # Get the relationship data.                          # Get the relationship data.
# Line 220  Line 559 
559                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
560                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
561                                  # Display the relationship data.                                  # Display the relationship data.
562                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
563                          }                          }
564                  }                  }
565                  # Close off the relationship list.                  # Close off the relationship list.
566                  print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
567                  # Get the entity's relations.                  # Get the entity's relations.
568                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
569                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
570                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
571                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
572                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
573                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
574                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
575                  }                  }
576          }          }
577          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
578          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
579          # Loop through the relationships.          # Loop through the relationships.
580          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
581                  Trace("Building MetaData entry for $key relationship.") if T(4);                  Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 244  Line 583 
583                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
584                  # Create the relationship header.                  # Create the relationship header.
585                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
586                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
587                  # Get the entity names.                  # Get the entity names.
588                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
589                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 254  Line 593 
593                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
594                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
595                  if ($arity eq "11") {                  if ($arity eq "11") {
596                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
597                  } else {                  } else {
598                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
599                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
600                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
601                          }                          }
602                  }                  }
603                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
604                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
605                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
606                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
607                  }                  }
608                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
609                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
610                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
611          }          }
612          Trace("Building MetaData join table.") if T(4);          Trace("Building MetaData join table.") if T(4);
613          # Denote we're starting the join table.          # Denote we're starting the join table.
614          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
615          # Create a table header.          # Create a table header.
616          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
617          # Loop through the joins.          # Loop through the joins.
618          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
619          my @joinKeys = keys %{$joinTable};          my @joinKeys = keys %{$joinTable};
# Line 282  Line 621 
621                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
622                  $joinKey =~ m!^([^/]+)/(.+)$!;                  $joinKey =~ m!^([^/]+)/(.+)$!;
623                  my ($sourceRelation, $targetRelation) = ($1, $2);                  my ($sourceRelation, $targetRelation) = ($1, $2);
624                  Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
625                  my $source = $self->ComputeObjectSentence($sourceRelation);                  my $source = $self->ComputeObjectSentence($sourceRelation);
626                  my $target = $self->ComputeObjectSentence($targetRelation);                  my $target = $self->ComputeObjectSentence($targetRelation);
627                  my $clause = $joinTable->{$joinKey};                  my $clause = $joinTable->{$joinKey};
628                  # Display them in a table row.                  # Display them in a table row.
629                  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";
630          }          }
631          # Close the table.          # Close the table.
632          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
633          # Close the document.      Trace("Built MetaData HTML.") if T(3);
634          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
635          # Close the file.      return $retVal;
         close HTMLOUT;  
         Trace("Built MetaData web page.") if T(3);  
636  }  }
637    
638  =head3 DumpMetaData  =head3 DumpMetaData
639    
640  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
641    
642  Return a dump of the metadata structure.  Return a dump of the metadata structure.
643    
# Line 313  Line 650 
650          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
651  }  }
652    
653    =head3 FindIndexForEntity
654    
655    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
656    
657    This method locates the entry in an entity's index list that begins with the
658    specified attribute name. If the entity has no index list, one will be
659    created. This method works on raw XML, not a live ERDB object.
660    
661    =over 4
662    
663    =item xml
664    
665    The raw XML structure defining the database.
666    
667    =item entityName
668    
669    The name of the relevant entity.
670    
671    =item attributeName
672    
673    The name of the attribute relevant to the search.
674    
675    =item RETURN
676    
677    The numerical index in the index list of the index entry for the specified entity and
678    attribute, or C<undef> if no such index exists.
679    
680    =back
681    
682    =cut
683    
684    sub FindIndexForEntity {
685        # Get the parameters.
686        my ($xml, $entityName, $attributeName) = @_;
687        # Declare the return variable.
688        my $retVal;
689        # Get the named entity.
690        my $entityData = $xml->{Entities}->{$entityName};
691        if (! $entityData) {
692            Confess("Entity $entityName not found in DBD structure.");
693        } else {
694            # Insure it has an index list.
695            if (! exists $entityData->{Indexes}) {
696                $entityData->{Indexes} = [];
697            } else {
698                # Search for the desired index.
699                my $indexList = $entityData->{Indexes};
700                my $n = scalar @{$indexList};
701                Trace("Searching $n indexes in index list for $entityName.") if T(2);
702                # We use an indexed FOR here because we're returning an
703                # index number instead of an object. We do THAT so we can
704                # delete the index from the list if needed.
705                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
706                    my $index = $indexList->[$i];
707                    my $fields = $index->{IndexFields};
708                    # Technically this IF should be safe (that is, we are guaranteed
709                    # the existence of a "$fields->[0]"), because when we load the XML
710                    # we have SuppressEmpty specified.
711                    if ($fields->[0]->{name} eq $attributeName) {
712                        $retVal = $i;
713                    }
714                }
715            }
716        }
717        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
718        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
719        # Return the result.
720        return $retVal;
721    }
722    
723  =head3 CreateTables  =head3 CreateTables
724    
725  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
726    
727  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
728  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 327  Line 734 
734  sub CreateTables {  sub CreateTables {
735          # Get the parameters.          # Get the parameters.
736          my ($self) = @_;          my ($self) = @_;
737          my $metadata = $self->{_metaData};      # Get the relation names.
738          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
739          # Loop through the entities.      # Loop through the relations.
740          my $entityHash = $metadata->{Entities};      for my $relationName (@relNames) {
         for my $entityName (keys %{$entityHash}) {  
                 my $entityData = $entityHash->{$entityName};  
                 # Tell the user what we're doing.  
                 Trace("Creating relations for entity $entityName.") if T(1);  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entityData->{Relations}}) {  
741                          # Create a table for this relation.                          # Create a table for this relation.
742                          $self->CreateTable($relationName);                          $self->CreateTable($relationName);
743                          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);  
744          }          }
745  }  }
746    
747  =head3 CreateTable  =head3 CreateTable
748    
749  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
750    
751  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
752    
# Line 363  Line 756 
756    
757  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
758    
759  =item $indexFlag  =item indexFlag
760    
761  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
762  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
763    
764    =item estimatedRows (optional)
765    
766    If specified, the estimated maximum number of rows for the relation. This
767    information allows the creation of tables using storage engines that are
768    faster but require size estimates, such as MyISAM.
769    
770  =back  =back
771    
772  =cut  =cut
773    
774  sub CreateTable {  sub CreateTable {
775          # Get the parameters.          # Get the parameters.
776          my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
777          # Get the database handle.          # Get the database handle.
778          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
779          # Get the relation data and determine whether or not the relation is primary.          # Get the relation data and determine whether or not the relation is primary.
# Line 398  Line 797 
797          # Insure the table is not already there.          # Insure the table is not already there.
798          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
799          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
800        # If there are estimated rows, create an estimate so we can take advantage of
801        # faster DB technologies.
802        my $estimation = undef;
803        if ($estimatedRows) {
804            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
805        }
806          # Create the table.          # Create the table.
807          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
808          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
809          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
810          # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
811        # index will not be built until the table has been loaded.
812          if ($indexFlag) {          if ($indexFlag) {
813                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
814          }          }
815  }  }
816    
817    =head3 VerifyFields
818    
819    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
820    
821    Run through the list of proposed field values, insuring that all the character fields are
822    below the maximum length. If any fields are too long, they will be truncated in place.
823    
824    =over 4
825    
826    =item relName
827    
828    Name of the relation for which the specified fields are destined.
829    
830    =item fieldList
831    
832    Reference to a list, in order, of the fields to be put into the relation.
833    
834    =item RETURN
835    
836    Returns the number of fields truncated.
837    
838    =back
839    
840    =cut
841    
842    sub VerifyFields {
843        # Get the parameters.
844        my ($self, $relName, $fieldList) = @_;
845        # Initialize the return value.
846        my $retVal = 0;
847        # Get the relation definition.
848        my $relData = $self->_FindRelation($relName);
849        # Get the list of field descriptors.
850        my $fieldTypes = $relData->{Fields};
851        my $fieldCount = scalar @{$fieldTypes};
852        # Loop through the two lists.
853        for (my $i = 0; $i < $fieldCount; $i++) {
854            # Get the type of the current field.
855            my $fieldType = $fieldTypes->[$i]->{type};
856            # If it's a character field, verify the length.
857            if ($fieldType =~ /string/) {
858                my $maxLen = $TypeTable{$fieldType}->{maxLen};
859                my $oldString = $fieldList->[$i];
860                if (length($oldString) > $maxLen) {
861                    # Here it's too big, so we truncate it.
862                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
863                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
864                    $retVal++;
865                }
866            }
867        }
868        # Return the truncation count.
869        return $retVal;
870    }
871    
872    =head3 DigestFields
873    
874    C<< $erdb->DigestFields($relName, $fieldList); >>
875    
876    Digest the strings in the field list that correspond to data type C<hash-string> in the
877    specified relation.
878    
879    =over 4
880    
881    =item relName
882    
883    Name of the relation to which the fields belong.
884    
885    =item fieldList
886    
887    List of field contents to be loaded into the relation.
888    
889    =back
890    
891    =cut
892    #: Return Type ;
893    sub DigestFields {
894        # Get the parameters.
895        my ($self, $relName, $fieldList) = @_;
896        # Get the relation definition.
897        my $relData = $self->_FindRelation($relName);
898        # Get the list of field descriptors.
899        my $fieldTypes = $relData->{Fields};
900        my $fieldCount = scalar @{$fieldTypes};
901        # Loop through the two lists.
902        for (my $i = 0; $i < $fieldCount; $i++) {
903            # Get the type of the current field.
904            my $fieldType = $fieldTypes->[$i]->{type};
905            # If it's a hash string, digest it in place.
906            if ($fieldType eq 'hash-string') {
907                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
908            }
909        }
910    }
911    
912    =head3 DigestKey
913    
914    C<< my $digested = $erdb->DigestKey($keyValue); >>
915    
916    Return the digested value of a symbolic key. The digested value can then be plugged into a
917    key-based search into a table with key-type hash-string.
918    
919    Currently the digesting process is independent of the database structure, but that may not
920    always be the case, so this is an instance method instead of a static method.
921    
922    =over 4
923    
924    =item keyValue
925    
926    Key value to digest.
927    
928    =item RETURN
929    
930    Digested value of the key.
931    
932    =back
933    
934    =cut
935    
936    sub DigestKey {
937        # Get the parameters.
938        my ($self, $keyValue) = @_;
939        # Compute the digest.
940        my $retVal = md5_base64($keyValue);
941        # Return the result.
942        return $retVal;
943    }
944    
945  =head3 CreateIndex  =head3 CreateIndex
946    
947  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
948    
949  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
950  is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
951  the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  If that is the case, then L</CreateTable> should be called with the index flag set to
952  method used after the load to create the indexes for the table.  FALSE, and this method used after the load to create the indexes for the table.
953    
954  =cut  =cut
955    
# Line 431  Line 965 
965          for my $indexName (keys %{$indexHash}) {          for my $indexName (keys %{$indexHash}) {
966                  my $indexData = $indexHash->{$indexName};                  my $indexData = $indexHash->{$indexName};
967                  # Get the index's field list.                  # Get the index's field list.
968                  my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
969            # Get a hash of the relation's field types.
970            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
971            # We need to check for text fields so we can append a length limitation for them. To do
972            # that, we need the relation's field list.
973            my $relFields = $relationData->{Fields};
974            for (my $i = 0; $i <= $#rawFields; $i++) {
975                # Get the field type.
976                my $field = $rawFields[$i];
977                my $type = $types{$field};
978                # Ask if it requires using prefix notation for the index.
979                my $mod = $TypeTable{$type}->{indexMod};
980                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
981                if ($mod) {
982                    # Append the prefix length to the field name,
983                    $rawFields[$i] .= "($mod)";
984                }
985            }
986            my @fieldList = _FixNames(@rawFields);
987                  my $flds = join(', ', @fieldList);                  my $flds = join(', ', @fieldList);
988                  # Get the index's uniqueness flag.                  # Get the index's uniqueness flag.
989                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
990                  # Create the index.                  # Create the index.
991                  $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
992                                        flds => $flds, kind => $unique);
993            if ($rv) {
994                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);
995            } else {
996                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
997            }
998          }          }
999  }  }
1000    
1001  =head3 LoadTables  =head3 GetSecondaryFields
1002    
1003  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1004    
1005  This method will load the database tables from a directory. The tables must already have been created  This method will return a list of the name and type of each of the secondary
1006  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  fields for a specified entity. Secondary fields are stored in two-column tables
1007  all of the relations to be loaded must have a file in the directory with the same name as the relation  in addition to the primary entity table. This enables the field to have no value
1008    or to have multiple values.
1009    
1010    =over 4
1011    
1012    =item entityName
1013    
1014    Name of the entity whose secondary fields are desired.
1015    
1016    =item RETURN
1017    
1018    Returns a hash mapping the field names to their field types.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub GetSecondaryFields {
1025        # Get the parameters.
1026        my ($self, $entityName) = @_;
1027        # Declare the return variable.
1028        my %retVal = ();
1029        # Look for the entity.
1030        my $table = $self->GetFieldTable($entityName);
1031        # Loop through the fields, pulling out the secondaries.
1032        for my $field (sort keys %{$table}) {
1033            if ($table->{$field}->{relation} ne $entityName) {
1034                # Here we have a secondary field.
1035                $retVal{$field} = $table->{$field}->{type};
1036            }
1037        }
1038        # Return the result.
1039        return %retVal;
1040    }
1041    
1042    =head3 GetFieldRelationName
1043    
1044    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1045    
1046    Return the name of the relation containing a specified field.
1047    
1048    =over 4
1049    
1050    =item objectName
1051    
1052    Name of the entity or relationship containing the field.
1053    
1054    =item fieldName
1055    
1056    Name of the relevant field in that entity or relationship.
1057    
1058    =item RETURN
1059    
1060    Returns the name of the database relation containing the field, or C<undef> if
1061    the field does not exist.
1062    
1063    =back
1064    
1065    =cut
1066    
1067    sub GetFieldRelationName {
1068        # Get the parameters.
1069        my ($self, $objectName, $fieldName) = @_;
1070        # Declare the return variable.
1071        my $retVal;
1072        # Get the object field table.
1073        my $table = $self->GetFieldTable($objectName);
1074        # Only proceed if the field exists.
1075        if (exists $table->{$fieldName}) {
1076            # Determine the name of the relation that contains this field.
1077            $retVal = $table->{$fieldName}->{relation};
1078        }
1079        # Return the result.
1080        return $retVal;
1081    }
1082    
1083    =head3 DeleteValue
1084    
1085    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1086    
1087    Delete secondary field values from the database. This method can be used to delete all
1088    values of a specified field for a particular entity instance, or only a single value.
1089    
1090    Secondary fields are stored in two-column relations separate from an entity's primary
1091    table, and as a result a secondary field can legitimately have no value or multiple
1092    values. Therefore, it makes sense to talk about deleting secondary fields where it
1093    would not make sense for primary fields.
1094    
1095    =over 4
1096    
1097    =item entityName
1098    
1099    Name of the entity from which the fields are to be deleted.
1100    
1101    =item id
1102    
1103    ID of the entity instance to be processed. If the instance is not found, this
1104    method will have no effect. If C<undef> is specified, all values for all of
1105    the entity instances will be deleted.
1106    
1107    =item fieldName
1108    
1109    Name of the field whose values are to be deleted.
1110    
1111    =item fieldValue (optional)
1112    
1113    Value to be deleted. If not specified, then all values of the specified field
1114    will be deleted for the entity instance. If specified, then only the values which
1115    match this parameter will be deleted.
1116    
1117    =item RETURN
1118    
1119    Returns the number of rows deleted.
1120    
1121    =back
1122    
1123    =cut
1124    
1125    sub DeleteValue {
1126        # Get the parameters.
1127        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1128        # Declare the return value.
1129        my $retVal = 0;
1130        # We need to set up an SQL command to do the deletion. First, we
1131        # find the name of the field's relation.
1132        my $table = $self->GetFieldTable($entityName);
1133        my $field = $table->{$fieldName};
1134        my $relation = $field->{relation};
1135        # Make sure this is a secondary field.
1136        if ($relation eq $entityName) {
1137            Confess("Cannot delete values of $fieldName for $entityName.");
1138        } else {
1139            # Set up the SQL command to delete all values.
1140            my $sql = "DELETE FROM $relation";
1141            # Build the filter.
1142            my @filters = ();
1143            my @parms = ();
1144            # Check for a filter by ID.
1145            if (defined $id) {
1146                push @filters, "id = ?";
1147                push @parms, $id;
1148            }
1149            # Check for a filter by value.
1150            if (defined $fieldValue) {
1151                push @filters, "$fieldName = ?";
1152                push @parms, $fieldValue;
1153            }
1154            # Append the filters to the command.
1155            if (@filters) {
1156                $sql .= " WHERE " . join(" AND ", @filters);
1157            }
1158            # Execute the command.
1159            my $dbh = $self->{_dbh};
1160            $retVal = $dbh->SQL($sql, 0, @parms);
1161        }
1162        # Return the result.
1163        return $retVal;
1164    }
1165    
1166    =head3 LoadTables
1167    
1168    C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1169    
1170    This method will load the database tables from a directory. The tables must already have been created
1171    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1172    all of the relations to be loaded must have a file in the directory with the same name as the relation
1173  (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each  (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1174  line of the file will be loaded as a row of the target relation table. The field values should be in  line of the file will be loaded as a row of the target relation table. The field values should be in
1175  the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is  the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
# Line 486  Line 1208 
1208          $directoryName =~ s!/\\$!!;          $directoryName =~ s!/\\$!!;
1209          # Declare the return variable.          # Declare the return variable.
1210          my $retVal = Stats->new();          my $retVal = Stats->new();
1211          # Get the metadata structure.      # Get the relation names.
1212          my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
1213          # Loop through the entities.      for my $relationName (@relNames) {
         for my $entity (values %{$metaData->{Entities}}) {  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entity->{Relations}}) {  
1214                          # Try to load this relation.                          # Try to load this relation.
1215                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1216                          # Accumulate the statistics.                          # Accumulate the statistics.
1217                          $retVal->Accumulate($result);                          $retVal->Accumulate($result);
1218                  }                  }
         }  
         # 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);  
         }  
1219          # Add the duration of the load to the statistical object.          # Add the duration of the load to the statistical object.
1220          $retVal->Add('duration', gettimeofday - $startTime);          $retVal->Add('duration', gettimeofday - $startTime);
1221          # Return the accumulated statistics.          # Return the accumulated statistics.
1222          return $retVal;          return $retVal;
1223  }  }
1224    
1225    
1226  =head3 GetTableNames  =head3 GetTableNames
1227    
1228  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
1229    
1230  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1231    
# Line 530  Line 1242 
1242    
1243  =head3 GetEntityTypes  =head3 GetEntityTypes
1244    
1245  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
1246    
1247  Return a list of the entity type names.  Return a list of the entity type names.
1248    
# Line 545  Line 1257 
1257          return sort keys %{$entityList};          return sort keys %{$entityList};
1258  }  }
1259    
1260    =head3 GetDataTypes
1261    
1262    C<< my %types = ERDB::GetDataTypes(); >>
1263    
1264    Return a table of ERDB data types. The table returned is a hash of hashes.
1265    The keys of the big hash are the datatypes. Each smaller hash has several
1266    values used to manage the data. The most interesting is the SQL type (key
1267    C<sqlType>) and the descriptive node (key C<notes>).
1268    
1269    Note that changing the values in the smaller hashes will seriously break
1270    things, so this data should be treated as read-only.
1271    
1272    =cut
1273    
1274    sub GetDataTypes {
1275        return %TypeTable;
1276    }
1277    
1278    
1279    =head3 IsEntity
1280    
1281    C<< my $flag = $erdb->IsEntity($entityName); >>
1282    
1283    Return TRUE if the parameter is an entity name, else FALSE.
1284    
1285    =over 4
1286    
1287    =item entityName
1288    
1289    Object name to be tested.
1290    
1291    =item RETURN
1292    
1293    Returns TRUE if the specified string is an entity name, else FALSE.
1294    
1295    =back
1296    
1297    =cut
1298    
1299    sub IsEntity {
1300        # Get the parameters.
1301        my ($self, $entityName) = @_;
1302        # Test to see if it's an entity.
1303        return exists $self->{_metaData}->{Entities}->{$entityName};
1304    }
1305    
1306  =head3 Get  =head3 Get
1307    
1308  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1309    
1310  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
1311  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 555  Line 1313 
1313  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
1314  $genus.  $genus.
1315    
1316  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1317    
1318  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
1319  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1320    
1321  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1322    
1323  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1324  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 572  Line 1330 
1330  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
1331  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
1332    
1333  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1334    
1335  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
1336  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
1337  In particular, you can't specify any entity or relationship more than once, and if a  In particular, if a relationship is recursive, the path is determined by the order in which
1338  relationship is recursive, the path is determined by the order in which the entity  the entity and the relationship appear. For example, consider a recursive relationship
1339  and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
 which relates B<People> objects to other B<People> objects. If the join path is  
1340  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1341  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1342    
1343    If an entity or relationship is mentioned twice, the name for the second occurrence will
1344    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1345    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1346    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1347    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1348    
1349  =over 4  =over 4
1350    
1351  =item objectNames  =item objectNames
# Line 605  Line 1368 
1368    
1369  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1370    
1371    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1372    be processed. The idea is to make it less likely to find the verb by accident.
1373    
1374  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
1375  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1376  relation.  relation.
1377    
1378  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1379    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1380    a positive number. So, for example
1381    
1382  Parameter values to be substituted into the filter clause.  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1383    
1384    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1385    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1386    use
1387    
1388    C<< "LIMIT 10" >>
1389    
1390    =item params
1391    
1392    Reference to a list of parameter values to be substituted into the filter clause.
1393    
1394  =item RETURN  =item RETURN
1395    
# Line 623  Line 1401 
1401    
1402  sub Get {  sub Get {
1403          # Get the parameters.          # Get the parameters.
1404          my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1405          # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1406          #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1407          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1408          #      # Create the query.
1409          my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1410          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1411                                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1412          # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1413          if ($filterClause) {      # and mapped name for each object in the query.
1414                  # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1415                  # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1416                  my $filterString = $filterClause;          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
                 # 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) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
1417                  }                  }
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
                 }  
         }  
         Trace("SQL query: $command") if T(2);  
         Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));  
         my $sth = $dbh->prepare_command($command);  
         # Execute it with the parameters bound in.  
         $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1418          # Return the statement object.          # Return the statement object.
1419          my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1420          return $retVal;          return $retVal;
1421  }  }
1422    
 =head3 GetList  
1423    
 C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1424    
1425  Return a list of object descriptors for the specified objects as determined by the  =head3 Search
 specified filter clause.  
1426    
1427  This method is essentially the same as L</Get> except it returns a list of objects rather  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
 that a query object that can be used to get the results one record at a time.  
1428    
1429  =over 4  Perform a full text search with filtering. The search will be against a specified object
1430    in the object name list. That object will get an extra field containing the search
1431    relevance. Note that except for the search expression, the parameters of this method are
1432    the same as those for L</Get> and follow the same rules.
1433    
1434  =over 4  =over 4
1435    
1436    =item searchExpression
1437    
1438    Boolean search expression for the text fields of the target object. The default mode for
1439    a Boolean search expression is OR, but we want the default to be AND, so we will
1440    add a C<+> operator to each word with no other operator before it.
1441    
1442    =item idx
1443    
1444    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1445    
1446  =item objectNames  =item objectNames
1447    
1448  List containing the names of the entity and relationship objects to be retrieved.  List containing the names of the entity and relationship objects to be retrieved.
# Line 773  Line 1457 
1457  or secondary entity relations; however, all of the entities and relationships involved must  or secondary entity relations; however, all of the entities and relationships involved must
1458  be included in the list of object names.  be included in the list of object names.
1459    
1460  The filter clause can also specify a sort order. To do this, simply follow the filter string  =item params
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
   
 C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  
   
 The rules for field references in a sort order are the same as those for field references in the  
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
   
 =item param1, param2, ..., paramN  
1461    
1462  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1463    
1464  =item RETURN  =item RETURN
1465    
1466  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a query object for the specified search.
1467    
1468  =back  =back
1469    
1470  =cut  =cut
1471  #: Return Type @%  
1472  sub GetList {  sub Search {
1473      # Get the parameters.      # Get the parameters.
1474      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1475          # Declare the return variable.          # Declare the return variable.
1476          my @retVal = ();      my $retVal;
1477          # Perform the query.      # Create a safety copy of the parameter list. Note we have to be careful to insure
1478          my $query = $self->Get($objectNames, $filterClause, @params);      # a parameter list exists before we copy it.
1479          # Loop through the results.      my @myParams = ();
1480          while (my $object = $query->Fetch) {      if (defined $params) {
1481                  push @retVal, $object;          @myParams = @{$params};
1482        }
1483        # Get the first object's structure so we have access to the searchable fields.
1484        my $object1Name = $objectNames->[$idx];
1485        my $object1Structure = $self->_GetStructure($object1Name);
1486        # Get the field list.
1487        if (! exists $object1Structure->{searchFields}) {
1488            Confess("No searchable index for $object1Name.");
1489        } else {
1490            # Get the field list.
1491            my @fields = @{$object1Structure->{searchFields}};
1492            # Clean the search expression.
1493            my $actualKeywords = $self->CleanKeywords($searchExpression);
1494            # Prefix a "+" to each uncontrolled word. This converts the default
1495            # search mode from OR to AND.
1496            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1497            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1498            # We need two match expressions, one for the filter clause and one in the
1499            # query itself. Both will use a parameter mark, so we need to push the
1500            # search expression onto the front of the parameter list twice.
1501            unshift @myParams, $actualKeywords, $actualKeywords;
1502            # Build the match expression.
1503            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1504            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1505            # Process the SQL stuff.
1506            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1507                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1508            # Create the query. Note that the match clause is inserted at the front of
1509            # the select fields.
1510            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1511                ".* $suffix";
1512            my $sth = $self->_GetStatementHandle($command, \@myParams);
1513            # Now we create the relation map, which enables DBQuery to determine the order, name
1514            # and mapped name for each object in the query.
1515            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1516            # Return the statement object.
1517            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1518          }          }
1519      # Return the result.      return $retVal;
     return @retVal;  
1520  }  }
1521    
1522  =head3 ComputeObjectSentence  =head3 GetFlat
1523    
1524  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1525    
1526  Check an object name, and if it is a relationship convert it to a relationship sentence.  This is a variation of L</GetAll> that asks for only a single field per record and
1527    returns a single flattened list.
1528    
1529  =over 4  =over 4
1530    
1531  =item objectName  =item objectNames
1532    
1533  Name of the entity or relationship.  List containing the names of the entity and relationship objects to be retrieved.
1534    
1535    =item filterClause
1536    
1537    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1538    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1539    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1540    parameter list as additional parameters. The fields in a filter clause can come from primary
1541    entity relations, relationship relations, or secondary entity relations; however, all of the
1542    entities and relationships involved must be included in the list of object names.
1543    
1544    =item parameterList
1545    
1546    List of the parameters to be substituted in for the parameters marks in the filter clause.
1547    
1548    =item field
1549    
1550    Name of the field to be used to get the elements of the list returned.
1551    
1552  =item RETURN  =item RETURN
1553    
1554  Returns a string containing the entity name or a relationship sentence.  Returns a list of values.
1555    
1556  =back  =back
1557    
1558  =cut  =cut
1559    #: Return Type @;
1560  sub ComputeObjectSentence {  sub GetFlat {
1561          # Get the parameters.          # Get the parameters.
1562          my ($self, $objectName) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1563          # Set the default return value.      # Construct the query.
1564          my $retVal = $objectName;      my $query = $self->Get($objectNames, $filterClause, $parameterList);
1565          # Look for the object as a relationship.      # Create the result list.
1566          my $relTable = $self->{_metaData}->{Relationships};      my @retVal = ();
1567          if (exists $relTable->{$objectName}) {      # Loop through the records, adding the field values found to the result list.
1568                  # Get the relationship sentence.      while (my $row = $query->Fetch()) {
1569                  $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          push @retVal, $row->Value($field);
1570          }      }
1571          # Return the result.      # Return the list created.
1572          return $retVal;      return @retVal;
1573  }  }
1574    
1575  =head3 DumpRelations  =head3 SpecialFields
1576    
1577  C<< $database->DumpRelations($outputDirectory); >>  C<< my %specials = $erdb->SpecialFields($entityName); >>
1578    
1579  Write the contents of all the relations to tab-delimited files in the specified directory.  Return a hash mapping special fields in the specified entity to the value of their
1580  Each file will have the same name as the relation dumped, with an extension of DTX.  C<special> attribute. This enables the subclass to get access to the special field
1581    attributes without needed to plumb the internal ERDB data structures.
1582    
1583  =over 4  =over 4
1584    
1585  =item outputDirectory  =item entityName
1586    
1587  Name of the directory into which the relation files should be dumped.  Name of the entity whose special fields are desired.
1588    
1589    =item RETURN
1590    
1591    Returns a hash. The keys of the hash are the special field names, and the values
1592    are the values from each special field's C<special> attribute.
1593    
1594  =back  =back
1595    
1596  =cut  =cut
1597    
1598  sub DumpRelations {  sub SpecialFields {
1599          # Get the parameters.          # Get the parameters.
1600          my ($self, $outputDirectory) = @_;      my ($self, $entityName) = @_;
1601          # Now we need to run through all the relations. First, we loop through the entities.      # Declare the return variable.
1602          my $metaData = $self->{_metaData};      my %retVal = ();
1603          my $entities = $metaData->{Entities};      # Find the entity's data structure.
1604          for my $entityName (keys %{$entities}) {      my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1605                  my $entityStructure = $entities->{$entityName};      # Loop through its fields, adding each special field to the return hash.
1606                  # Get the entity's relations.      my $fieldHash = $entityData->{Fields};
1607                  my $relationList = $entityStructure->{Relations};      for my $fieldName (keys %{$fieldHash}) {
1608                  # Loop through the relations, dumping them.          my $fieldData = $fieldHash->{$fieldName};
1609                  for my $relationName (keys %{$relationList}) {          if (exists $fieldData->{special}) {
1610                          my $relation = $relationList->{$relationName};              $retVal{$fieldName} = $fieldData->{special};
                         $self->_DumpRelation($outputDirectory, $relationName, $relation);  
                 }  
1611          }          }
         # Next, we loop through the relationships.  
         my $relationships = $metaData->{Relationships};  
         for my $relationshipName (keys %{$relationships}) {  
                 my $relationshipStructure = $relationships->{$relationshipName};  
                 # Dump this relationship's relation.  
                 $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
1612          }          }
1613        # Return the result.
1614        return %retVal;
1615  }  }
1616    
1617  =head3 InsertObject  =head3 Delete
1618    
1619  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1620    
1621  Insert an object into the database. The object is defined by a type name and then a hash  Delete an entity instance from the database. The instance is deleted along with all entity and
1622  of field names to values. Field values in the primary relation are represented by scalars.  relationship instances dependent on it. The definition of I<dependence> is recursive.
 (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>.  
1623    
1624  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1625    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1626    dependent relationship.
1627    
1628  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  =over 4
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
1629    
1630  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  =item entityName
1631    
1632  =over 4  Name of the entity type for the instance being deleted.
1633    
1634  =item newObjectType  =item objectID
1635    
1636  Type name of the object to insert.  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1637    then it is presumed to by a LIKE pattern.
1638    
1639  =item fieldHash  =item options
1640    
1641  Hash of field names to values.  A hash detailing the options for this delete operation.
1642    
1643  =item RETURN  =item RETURN
1644    
1645  Returns 1 if successful, 0 if an error occurred.  Returns a statistics object indicating how many records of each particular table were
1646    deleted.
1647    
1648  =back  =back
1649    
1650  =cut  The permissible options for this method are as follows.
1651    
1652  sub InsertObject {  =over 4
1653    
1654    =item testMode
1655    
1656    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1657    
1658    =item keepRoot
1659    
1660    If TRUE, then the entity instances will not be deleted, only the dependent records.
1661    
1662    =back
1663    
1664    =cut
1665    #: Return Type $%;
1666    sub Delete {
1667          # Get the parameters.          # Get the parameters.
1668          my ($self, $newObjectType, $fieldHash) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1669          # Denote that so far we appear successful.      # Declare the return variable.
1670          my $retVal = 1;      my $retVal = Stats->new();
1671          # Get the database handle.      # Get the DBKernel object.
1672          my $dbh = $self->{_dbh};      my $db = $self->{_dbh};
1673          # Get the relation list.      # We're going to generate all the paths branching out from the starting entity. One of
1674          my $relationTable = $self->_GetRelationTable($newObjectType);      # the things we have to be careful about is preventing loops. We'll use a hash to
1675          # Loop through the relations. We'll build insert statements for each one. If a relation is      # determine if we've hit a loop.
1676          # secondary, we may end up generating multiple insert statements. If an error occurs, we      my %alreadyFound = ();
1677          # stop the loop.      # These next lists will serve as our result stack. We start by pushing object lists onto
1678          my @relationList = keys %{$relationTable};      # the stack, and then popping them off to do the deletes. This means the deletes will
1679          for (my $i = 0; $retVal && $i <= $#relationList; $i++) {      # start with the longer paths before getting to the shorter ones. That, in turn, makes
1680                  my $relationName = $relationList[$i];      # sure we don't delete records that might be needed to forge relationships back to the
1681                  my $relationDefinition = $relationTable->{$relationName};      # original item. We have two lists-- one for TO-relationships, and one for
1682                  # Get the relation's fields. For each field we will collect a value in the corresponding      # FROM-relationships and entities.
1683                  # position of the @valueList array. If one of the fields is missing, we will add it to the      my @fromPathList = ();
1684                  # @missing list.      my @toPathList = ();
1685                  my @fieldList = @{$relationDefinition->{Fields}};      # This final list is used to remember what work still needs to be done. We push paths
1686                  my @fieldNameList = ();      # onto the list, then pop them off to extend the paths. We prime it with the starting
1687                  my @valueList = ();      # point. Note that we will work hard to insure that the last item on a path in the
1688                  my @missing = ();      # to-do list is always an entity.
1689                  my $recordCount = 1;      my @todoList = ([$entityName]);
1690                  for my $fieldDescriptor (@fieldList) {      while (@todoList) {
1691                          # Get the field name and save it. Note we need to fix it up so the hyphens          # Get the current path.
1692                          # are converted to underscores.          my $current = pop @todoList;
1693                          my $fieldName = $fieldDescriptor->{name};          # Copy it into a list.
1694                          push @fieldNameList, _FixName($fieldName);          my @stackedPath = @{$current};
1695                          # Look for the named field in the incoming structure. Note that we are looking          # Pull off the last item on the path. It will always be an entity.
1696                          # for the real field name, not the fixed-up one!          my $myEntityName = pop @stackedPath;
1697                          if (exists $fieldHash->{$fieldName}) {          # Add it to the alreadyFound list.
1698                                  # Here we found the field. Stash it in the value list.          $alreadyFound{$myEntityName} = 1;
1699                                  my $value = $fieldHash->{$fieldName};          # Figure out if we need to delete this entity.
1700                                  push @valueList, $value;          if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1701                                  # If the value is a list, we may need to increment the record count.              # Get the entity data.
1702                                  if (ref $value eq "ARRAY") {              my $entityData = $self->_GetStructure($myEntityName);
1703                                          my $thisCount = @{$value};              # Loop through the entity's relations. A DELETE command will be needed for each of them.
1704                                          if ($recordCount == 1) {              my $relations = $entityData->{Relations};
1705                                                  # Here we have our first list, so we save its count.              for my $relation (keys %{$relations}) {
1706                                                  $recordCount = $thisCount;                  my @augmentedList = (@stackedPath, $relation);
1707                                          } elsif ($recordCount != $thisCount) {                  push @fromPathList, \@augmentedList;
                                                 # Here we have a second list, so its length has to match the  
                                                 # previous lists.  
                                                 Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);  
                                                 $retVal = 0;  
1708                                          }                                          }
1709                                  }                                  }
1710            # Now we need to look for relationships connected to this entity.
1711            my $relationshipList = $self->{_metaData}->{Relationships};
1712            for my $relationshipName (keys %{$relationshipList}) {
1713                my $relationship = $relationshipList->{$relationshipName};
1714                # Check the FROM field. We're only interested if it's us.
1715                if ($relationship->{from} eq $myEntityName) {
1716                    # Add the path to this relationship.
1717                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1718                    push @fromPathList, \@augmentedList;
1719                    # Check the arity. If it's MM we're done. If it's 1M
1720                    # and the target hasn't been seen yet, we want to
1721                    # stack the entity for future processing.
1722                    if ($relationship->{arity} eq '1M') {
1723                        my $toEntity = $relationship->{to};
1724                        if (! exists $alreadyFound{$toEntity}) {
1725                            # Here we have a new entity that's dependent on
1726                            # the current entity, so we need to stack it.
1727                            my @stackList = (@augmentedList, $toEntity);
1728                            push @fromPathList, \@stackList;
1729                          } else {                          } else {
1730                                  # Here the field is not present. Flag it as missing.                          Trace("$toEntity ignored because it occurred previously.") if T(4);
                                 push @missing, $fieldName;  
1731                          }                          }
1732                  }                  }
                 # If we are the primary relation, add the new-record flag.  
                 if ($relationName eq $newObjectType) {  
                         push @valueList, 1;  
                         push @fieldNameList, "new_record";  
1733                  }                  }
1734                  # Only proceed if there are no missing fields.              # Now check the TO field. In this case only the relationship needs
1735                  if (@missing > 0) {              # deletion.
1736                          Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .              if ($relationship->{to} eq $myEntityName) {
1737                                  join(' ', @missing)) if T(1);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1738                  } else {                  push @toPathList, \@augmentedList;
                         # Build the INSERT statement.  
                         my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .  
                                 ") VALUES (";  
                         # Create a marker list of the proper size and put it in the statement.  
                         my @markers = ();  
                         while (@markers < @fieldNameList) { push @markers, '?'; }  
                         $statement .= join(', ', @markers) . ")";  
                         # We have the insert statement, so prepare it.  
                         my $sth = $dbh->prepare_command($statement);  
                         Trace("Insert statement prepared: $statement") if T(3);  
                         # Now we loop through the values. If a value is scalar, we use it unmodified. If it's  
                         # a list, we use the current element. The values are stored in the @parameterList array.  
                         my $done = 0;  
                         for (my $i = 0; $i < $recordCount; $i++) {  
                                 # Clear the parameter list array.  
                                 my @parameterList = ();  
                                 # Loop through the values.  
                                 for my $value (@valueList) {  
                                         # Check to see if this is a scalar value.  
                                         if (ref $value eq "ARRAY") {  
                                                 # Here we have a list value. Pull the current entry.  
                                                 push @parameterList, $value->[$i];  
                                         } else {  
                                                 # Here we have a scalar value. Use it unmodified.  
                                                 push @parameterList, $value;  
1739                                          }                                          }
1740                                  }                                  }
                                 # Execute the INSERT statement with the specified parameter list.  
                                 $retVal = $sth->execute(@parameterList);  
                                 if (!$retVal) {  
                                         my $errorString = $sth->errstr();  
                                         Trace("Insert error: $errorString.") if T(0);  
1741                                  }                                  }
1742        # Create the first qualifier for the WHERE clause. This selects the
1743        # keys of the primary entity records to be deleted. When we're deleting
1744        # from a dependent table, we construct a join path from the first qualifier
1745        # to the table containing the dependent records to delete.
1746        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1747        # We need to make two passes. The first is through the to-list, and
1748        # the second through the from-list. The from-list is second because
1749        # the to-list may need to pass through some of the entities the
1750        # from-list would delete.
1751        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1752        # Now it's time to do the deletes. We do it in two passes.
1753        for my $keyName ('to_link', 'from_link') {
1754            # Get the list for this key.
1755            my @pathList = @{$stackList{$keyName}};
1756            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1757            # Loop through this list.
1758            while (my $path = pop @pathList) {
1759                # Get the table whose rows are to be deleted.
1760                my @pathTables = @{$path};
1761                # Start the DELETE statement. We need to call DBKernel because the
1762                # syntax of a DELETE-USING varies among DBMSs.
1763                my $target = $pathTables[$#pathTables];
1764                my $stmt = $db->SetUsing(@pathTables);
1765                # Now start the WHERE. The first thing is the ID field from the starting table. That
1766                # starting table will either be the entity relation or one of the entity's
1767                # sub-relations.
1768                $stmt .= " WHERE $pathTables[0].id $qualifier";
1769                # Now we run through the remaining entities in the path, connecting them up.
1770                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1771                    # Connect the current relationship to the preceding entity.
1772                    my ($entity, $rel) = @pathTables[$i-1,$i];
1773                    # The style of connection depends on the direction of the relationship.
1774                    $stmt .= " AND $entity.id = $rel.$keyName";
1775                    if ($i + 1 <= $#pathTables) {
1776                        # Here there's a next entity, so connect that to the relationship's
1777                        # to-link.
1778                        my $entity2 = $pathTables[$i+1];
1779                        $stmt .= " AND $rel.to_link = $entity2.id";
1780                    }
1781                }
1782                # Now we have our desired DELETE statement.
1783                if ($options{testMode}) {
1784                    # Here the user wants to trace without executing.
1785                    Trace($stmt) if T(0);
1786                } else {
1787                    # Here we can delete. Note that the SQL method dies with a confession
1788                    # if an error occurs, so we just go ahead and do it.
1789                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1790                    my $rv = $db->SQL($stmt, 0, $objectID);
1791                    # Accumulate the statistics for this delete. The only rows deleted
1792                    # are from the target table, so we use its name to record the
1793                    # statistic.
1794                    $retVal->Add($target, $rv);
1795                          }                          }
1796                  }                  }
1797          }          }
1798          # Return the success indicator.      # Return the result.
1799          return $retVal;          return $retVal;
1800  }  }
1801    
1802  =head3 LoadTable  =head3 Disconnect
1803    
1804  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1805    
1806  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  Disconnect an entity instance from all the objects to which it is related. This
1807    will delete each relationship instance that connects to the specified entity.
1808    
1809  =over 4  =over 4
1810    
1811  =item fileName  =item relationshipName
   
 Name of the file from which the table data should be loaded.  
   
 =item relationName  
1812    
1813  Name of the relation to be loaded. This is the same as the table name.  Name of the relationship whose instances are to be deleted.
1814    
1815  =item truncateFlag  =item originEntityName
1816    
1817  TRUE if the table should be dropped and re-created, else FALSE  Name of the entity that is to be disconnected.
1818    
1819  =item RETURN  =item originEntityID
1820    
1821  Returns a statistical object containing the number of records read and a list of the error messages.  ID of the entity that is to be disconnected.
1822    
1823  =back  =back
1824    
1825  =cut  =cut
1826  sub LoadTable {  
1827    sub Disconnect {
1828          # Get the parameters.          # Get the parameters.
1829          my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1830          # Create the statistical return object.      # Get the relationship descriptor.
1831          my $retVal = _GetLoadStats();      my $structure = $self->_GetStructure($relationshipName);
1832          # Trace the fact of the load.      # Insure we have a relationship.
1833          Trace("Loading table $relationName from $fileName") if T(1);      if (! exists $structure->{from}) {
1834            Confess("$relationshipName is not a relationship in the database.");
1835        } else {
1836          # Get the database handle.          # Get the database handle.
1837          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
1838          # Get the relation data.          # We'll set this value to 1 if we find our entity.
1839          my $relation = $self->_FindRelation($relationName);          my $found = 0;
1840          # Check the truncation flag.          # Loop through the ends of the relationship.
1841          if ($truncateFlag) {          for my $dir ('from', 'to') {
1842                  Trace("Creating table $relationName") if T(1);              if ($structure->{$dir} eq $originEntityName) {
1843                  # Re-create the table without its index.                  # Delete all relationship instances on this side of the entity instance.
1844                  $self->CreateTable($relationName, 0);                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1845                    $found = 1;
1846          }          }
         # Determine whether or not this is a primary relation. Primary relations have an extra  
         # field indicating whether or not a given object is new or was loaded from the flat files.  
         my $primary = $self->_IsPrimary($relationName);  
         # Get the number of fields in this relation.  
         my @fieldList = @{$relation->{Fields}};  
         my $fieldCount = @fieldList;  
         # Record the number of expected fields.  
         my $expectedFields = $fieldCount + ($primary ? 1 : 0);  
         # Start a database transaction.  
         $dbh->begin_tran;  
         # Open the relation file. We need to create a cleaned-up copy before loading.  
         open TABLEIN, '<', $fileName;  
         my $tempName = "$fileName.tbl";  
         open TABLEOUT, '>', $tempName;  
         # Loop through the file.  
         while (<TABLEIN>) {  
                 # Chop off the new-line character.  
                 my $record = $_;  
                 chomp $record;  
         # Only proceed if the record is non-blank.  
         if ($record) {  
             # Escape all the backslashes found in the line.  
             $record =~ s/\\/\\\\/g;  
             # Eliminate any trailing tabs.  
             chop $record while substr($record, -1) eq "\t";  
             # If this is a primary relation, add a 0 for the new-record flag (indicating that  
             # this record is not new, but part of the original load).  
             if ($primary) {  
                 $record .= "\t0";  
             }  
             # Write the record.  
             print TABLEOUT "$record\n";  
             # Count the record read.  
             my $count = $retVal->Add('records');  
             my $len = length $record;  
             Trace("Record $count written with $len characters.") if T(4);  
         }  
         }  
         # Close the files.  
         close TABLEIN;  
         close TABLEOUT;  
     Trace("Temporary file $tempName created.") if T(4);  
     # Load the table.  
         my $rv;  
         eval {  
                 $rv = $dbh->load_table(file => $tempName, tbl => $relationName);  
         };  
         if (!defined $rv) {  
         $retVal->AddMessage($@) if ($@);  
         $retVal->AddMessage("Table load failed for $relationName using $tempName.");  
                 Trace("Table load failed for $relationName.") if T(1);  
         } else {  
                 # Here we successfully loaded the table. Trace the number of records loaded.  
                 Trace("$retVal->{records} records read for $relationName.") if T(1);  
                 # If we're rebuilding, we need to create the table indexes.  
                 if ($truncateFlag) {  
                         eval {  
                                 $self->CreateIndex($relationName);  
                         };  
                         if ($@) {  
                                 $retVal->AddMessage($@);  
1847                          }                          }
1848            # Insure we found the entity on at least one end.
1849            if (! $found) {
1850                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1851                  }                  }
1852          }          }
         # Commit the database changes.  
         $dbh->commit_tran;  
         # Delete the temporary file.  
         unlink $tempName;  
         # Return the statistics.  
         return $retVal;  
1853  }  }
1854    
1855  =head3 GenerateEntity  =head3 DeleteRow
1856    
1857  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1858    
1859  Generate the data for a new entity instance. This method creates a field hash suitable for  Delete a row from a relationship. In most cases, only the from-link and to-link are
1860  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  needed; however, for relationships with intersection data values can be specified
1861  of the fields are generated using information in the database schema.  for the other fields using a hash.
   
 Each data type has a default algorithm for generating random test data. This can be overridden  
 by including a B<DataGen> element in the field. If this happens, the content of the element is  
 executed as a PERL program in the context of this module. The element may make use of a C<$this>  
 variable which contains the field hash as it has been built up to the current point. If any  
 fields are dependent on other fields, the C<pass> attribute can be used to control the order  
 in which the fields are generated. A field with a high data pass number will be generated after  
 a field with a lower one. If any external values are needed, they should be passed in via the  
 optional third parameter, which will be available to the data generation script under the name  
 C<$value>. Several useful utility methods are provided for generating random values, including  
 L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated  
 in the form of a timestamp number rather than a string.  
1862    
1863  =over 4  =over 4
1864    
1865  =item id  =item relationshipName
1866    
1867  ID to assign to the new entity.  Name of the relationship from which the row is to be deleted.
1868    
1869  =item type  =item fromLink
1870    
1871    ID of the entity instance in the From direction.
1872    
1873  Type name for the new entity.  =item toLink
1874    
1875    ID of the entity instance in the To direction.
1876    
1877  =item values  =item values
1878    
1879  Hash containing additional values that might be needed by the data generation methods (optional).  Reference to a hash of other values to be used for filtering the delete.
1880    
1881  =back  =back
1882    
1883  =cut  =cut
1884    
1885  sub GenerateEntity {  sub DeleteRow {
1886          # Get the parameters.          # Get the parameters.
1887          my ($self, $id, $type, $values) = @_;      my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1888          # Create the return hash.      # Create a hash of all the filter information.
1889          my $this = { id => $id };      my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1890          # Get the metadata structure.      if (defined $values) {
1891          my $metadata = $self->{_metaData};          for my $key (keys %{$values}) {
1892          # Get this entity's list of fields.              $filter{$key} = $values->{$key};
1893          if (!exists $metadata->{Entities}->{$type}) {          }
                 Confess("Unrecognized entity type $type in GenerateEntity.");  
         } else {  
                 my $entity = $metadata->{Entities}->{$type};  
                 my $fields = $entity->{Fields};  
                 # Generate data from the fields.  
                 _GenerateFields($this, $fields, $type, $values);  
1894          }          }
1895          # Return the hash created.      # Build an SQL statement out of the hash.
1896          return $this;      my @filters = ();
1897        my @parms = ();
1898        for my $key (keys %filter) {
1899            push @filters, _FixName($key) . " = ?";
1900            push @parms, $filter{$key};
1901        }
1902        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1903        my $command = "DELETE FROM $relationshipName WHERE " .
1904                      join(" AND ", @filters);
1905        # Execute it.
1906        my $dbh = $self->{_dbh};
1907        $dbh->SQL($command, undef, @parms);
1908  }  }
1909    
1910  =head3 GetEntity  =head3 SortNeeded
1911    
1912  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $parms = $erdb->SortNeeded($relationName); >>
1913    
1914  Return an object describing the entity instance with a specified ID.  Return the pipe command for the sort that should be applied to the specified
1915    relation when creating the load file.
1916    
1917  =over 4  For example, if the load file should be sorted ascending by the first
1918    field, this method would return
1919    
1920  =item entityType      sort -k1 -t"\t"
1921    
1922  Entity type name.  If the first field is numeric, the method would return
1923    
1924  =item ID      sort -k1n -t"\t"
1925    
1926  ID of the desired entity.  Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1927    keys using a sort.
1928    
1929  =item RETURN  =over 4
1930    
1931  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  =item relationName
1932  instance is found with the specified key.  
1933    Name of the relation to be examined.
1934    
1935    =item
1936    
1937    Returns the sort command to use for sorting the relation, suitable for piping.
1938    
1939  =back  =back
1940    
1941  =cut  =cut
1942    #: Return Type $;
1943  sub GetEntity {  sub SortNeeded {
1944          # Get the parameters.          # Get the parameters.
1945          my ($self, $entityType, $ID) = @_;      my ($self, $relationName) = @_;
1946          # Create a query.      # Declare a descriptor to hold the names of the key fields.
1947          my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my @keyNames = ();
1948          # Get the first (and only) object.      # Get the relation structure.
1949          my $retVal = $query->Fetch();      my $relationData = $self->_FindRelation($relationName);
1950        # Find out if the relation is a primary entity relation,
1951        # a relationship relation, or a secondary entity relation.
1952        my $entityTable = $self->{_metaData}->{Entities};
1953        my $relationshipTable = $self->{_metaData}->{Relationships};
1954        if (exists $entityTable->{$relationName}) {
1955            # Here we have a primary entity relation.
1956            push @keyNames, "id";
1957        } elsif (exists $relationshipTable->{$relationName}) {
1958            # Here we have a relationship. We sort using the FROM index.
1959            my $relationshipData = $relationshipTable->{$relationName};
1960            my $index = $relationData->{Indexes}->{idxFrom};
1961            push @keyNames, @{$index->{IndexFields}};
1962        } else {
1963            # Here we have a secondary entity relation, so we have a sort on the ID field.
1964            push @keyNames, "id";
1965        }
1966        # Now we parse the key names into sort parameters. First, we prime the return
1967        # string.
1968        my $retVal = "sort -t\"\t\" ";
1969        # Get the relation's field list.
1970        my @fields = @{$relationData->{Fields}};
1971        # Loop through the keys.
1972        for my $keyData (@keyNames) {
1973            # Get the key and the ordering.
1974            my ($keyName, $ordering);
1975            if ($keyData =~ /^([^ ]+) DESC/) {
1976                ($keyName, $ordering) = ($1, "descending");
1977            } else {
1978                ($keyName, $ordering) = ($keyData, "ascending");
1979            }
1980            # Find the key's position and type.
1981            my $fieldSpec;
1982            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1983                my $thisField = $fields[$i];
1984                if ($thisField->{name} eq $keyName) {
1985                    # Get the sort modifier for this field type. The modifier
1986                    # decides whether we're using a character, numeric, or
1987                    # floating-point sort.
1988                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1989                    # If the index is descending for this field, denote we want
1990                    # to reverse the sort order on this field.
1991                    if ($ordering eq 'descending') {
1992                        $modifier .= "r";
1993                    }
1994                    # Store the position and modifier into the field spec, which
1995                    # will stop the inner loop. Note that the field number is
1996                    # 1-based in the sort command, so we have to increment the
1997                    # index.
1998                    $fieldSpec = ($i + 1) . $modifier;
1999                }
2000            }
2001            # Add this field to the sort command.
2002            $retVal .= " -k$fieldSpec";
2003        }
2004          # Return the result.          # Return the result.
2005          return $retVal;          return $retVal;
2006  }  }
2007    
2008  =head3 GetEntityValues  =head3 GetList
   
 C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  
2009    
2010  Return a list of values from a specified entity instance.  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2011    
2012  =over 4  Return a list of object descriptors for the specified objects as determined by the
2013    specified filter clause.
2014    
2015  =item entityType  This method is essentially the same as L</Get> except it returns a list of objects rather
2016    than a query object that can be used to get the results one record at a time.
2017    
2018  Entity type name.  =over 4
2019    
2020  =item ID  =item objectNames
2021    
2022  ID of the desired entity.  List containing the names of the entity and relationship objects to be retrieved.
2023    
2024  =item fields  =item filterClause
2025    
2026  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2027    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2028    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2029    in the filter clause should be added to the parameter list as additional parameters. The
2030    fields in a filter clause can come from primary entity relations, relationship relations,
2031    or secondary entity relations; however, all of the entities and relationships involved must
2032    be included in the list of object names.
2033    
2034    The filter clause can also specify a sort order. To do this, simply follow the filter string
2035    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2036    particular genus and sorts them by species name.
2037    
2038    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2039    
2040    The rules for field references in a sort order are the same as those for field references in the
2041    filter clause in general; however, odd things may happen if a sort field is from a secondary
2042    relation.
2043    
2044    =item params
2045    
2046    Reference to a list of parameter values to be substituted into the filter clause.
2047    
2048    =item RETURN
2049    
2050    Returns a list of B<DBObject>s that satisfy the query conditions.
2051    
2052    =back
2053    
2054    =cut
2055    #: Return Type @%
2056    sub GetList {
2057        # Get the parameters.
2058        my ($self, $objectNames, $filterClause, $params) = @_;
2059        # Declare the return variable.
2060        my @retVal = ();
2061        # Perform the query.
2062        my $query = $self->Get($objectNames, $filterClause, $params);
2063        # Loop through the results.
2064        while (my $object = $query->Fetch) {
2065            push @retVal, $object;
2066        }
2067        # Return the result.
2068        return @retVal;
2069    }
2070    
2071    =head3 GetCount
2072    
2073    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2074    
2075    Return the number of rows found by a specified query. This method would
2076    normally be used to count the records in a single table. For example, in a
2077    genetics database
2078    
2079        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2080    
2081    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2082    to use it to return records based on a join. For example,
2083    
2084        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2085                                    ['homo %']);
2086    
2087    would return the number of features for genomes in the genus I<homo>. Note that
2088    only the rows from the first table are counted. If the above command were
2089    
2090        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2091                                    ['homo %']);
2092    
2093    it would return the number of genomes, not the number of genome/feature pairs.
2094    
2095    =over 4
2096    
2097    =item objectNames
2098    
2099    Reference to a list of the objects (entities and relationships) included in the
2100    query.
2101    
2102    =item filter
2103    
2104    A filter clause for restricting the query. The rules are the same as for the L</Get>
2105    method.
2106    
2107    =item params
2108    
2109    Reference to a list of the parameter values to be substituted for the parameter marks
2110    in the filter.
2111    
2112    =item RETURN
2113    
2114    Returns a count of the number of records in the first table that would satisfy
2115    the query.
2116    
2117    =back
2118    
2119    =cut
2120    
2121    sub GetCount {
2122        # Get the parameters.
2123        my ($self, $objectNames, $filter, $params) = @_;
2124        # Insure the params argument is an array reference if the caller left it off.
2125        if (! defined($params)) {
2126            $params = [];
2127        }
2128        # Declare the return variable.
2129        my $retVal;
2130        # Find out if we're counting an entity or a relationship.
2131        my $countedField;
2132        if ($self->IsEntity($objectNames->[0])) {
2133            $countedField = "id";
2134        } else {
2135            # For a relationship we count the to-link because it's usually more
2136            # numerous. Note we're automatically converting to the SQL form
2137            # of the field name (to_link vs. to-link).
2138            $countedField = "to_link";
2139        }
2140        # Create the SQL command suffix to get the desired records.
2141        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2142                                                                                $filter);
2143        # Prefix it with text telling it we want a record count.
2144        my $firstObject = $mappedNameListRef->[0];
2145        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2146        # Prepare and execute the command.
2147        my $sth = $self->_GetStatementHandle($command, $params);
2148        # Get the count value.
2149        ($retVal) = $sth->fetchrow_array();
2150        # Check for a problem.
2151        if (! defined($retVal)) {
2152            if ($sth->err) {
2153                # Here we had an SQL error.
2154                Confess("Error retrieving row count: " . $sth->errstr());
2155            } else {
2156                # Here we have no result.
2157                Confess("No result attempting to retrieve row count.");
2158            }
2159        }
2160        # Return the result.
2161        return $retVal;
2162    }
2163    
2164    =head3 ComputeObjectSentence
2165    
2166    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2167    
2168    Check an object name, and if it is a relationship convert it to a relationship sentence.
2169    
2170    =over 4
2171    
2172    =item objectName
2173    
2174    Name of the entity or relationship.
2175    
2176    =item RETURN
2177    
2178    Returns a string containing the entity name or a relationship sentence.
2179    
2180    =back
2181    
2182    =cut
2183    
2184    sub ComputeObjectSentence {
2185        # Get the parameters.
2186        my ($self, $objectName) = @_;
2187        # Set the default return value.
2188        my $retVal = $objectName;
2189        # Look for the object as a relationship.
2190        my $relTable = $self->{_metaData}->{Relationships};
2191        if (exists $relTable->{$objectName}) {
2192            # Get the relationship sentence.
2193            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2194        }
2195        # Return the result.
2196        return $retVal;
2197    }
2198    
2199    =head3 DumpRelations
2200    
2201    C<< $erdb->DumpRelations($outputDirectory); >>
2202    
2203    Write the contents of all the relations to tab-delimited files in the specified directory.
2204    Each file will have the same name as the relation dumped, with an extension of DTX.
2205    
2206    =over 4
2207    
2208    =item outputDirectory
2209    
2210    Name of the directory into which the relation files should be dumped.
2211    
2212    =back
2213    
2214    =cut
2215    
2216    sub DumpRelations {
2217        # Get the parameters.
2218        my ($self, $outputDirectory) = @_;
2219        # Now we need to run through all the relations. First, we loop through the entities.
2220        my $metaData = $self->{_metaData};
2221        my $entities = $metaData->{Entities};
2222        for my $entityName (keys %{$entities}) {
2223            my $entityStructure = $entities->{$entityName};
2224            # Get the entity's relations.
2225            my $relationList = $entityStructure->{Relations};
2226            # Loop through the relations, dumping them.
2227            for my $relationName (keys %{$relationList}) {
2228                my $relation = $relationList->{$relationName};
2229                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2230            }
2231        }
2232        # Next, we loop through the relationships.
2233        my $relationships = $metaData->{Relationships};
2234        for my $relationshipName (keys %{$relationships}) {
2235            my $relationshipStructure = $relationships->{$relationshipName};
2236            # Dump this relationship's relation.
2237            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2238        }
2239    }
2240    
2241    =head3 InsertValue
2242    
2243    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2244    
2245    This method will insert a new value into the database. The value must be one
2246    associated with a secondary relation, since primary values cannot be inserted:
2247    they occur exactly once. Secondary values, on the other hand, can be missing
2248    or multiply-occurring.
2249    
2250    =over 4
2251    
2252    =item entityID
2253    
2254    ID of the object that is to receive the new value.
2255    
2256    =item fieldName
2257    
2258    Field name for the new value-- this includes the entity name, since
2259    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2260    
2261    =item value
2262    
2263    New value to be put in the field.
2264    
2265    =back
2266    
2267    =cut
2268    
2269    sub InsertValue {
2270        # Get the parameters.
2271        my ($self, $entityID, $fieldName, $value) = @_;
2272        # Parse the entity name and the real field name.
2273        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2274            my $entityName = $1;
2275            my $fieldTitle = $2;
2276            # Get its descriptor.
2277            if (!$self->IsEntity($entityName)) {
2278                Confess("$entityName is not a valid entity.");
2279            } else {
2280                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2281                # Find the relation containing this field.
2282                my $fieldHash = $entityData->{Fields};
2283                if (! exists $fieldHash->{$fieldTitle}) {
2284                    Confess("$fieldTitle not found in $entityName.");
2285                } else {
2286                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2287                    if ($relation eq $entityName) {
2288                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2289                    } else {
2290                        # Now we can create an INSERT statement.
2291                        my $dbh = $self->{_dbh};
2292                        my $fixedName = _FixName($fieldTitle);
2293                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2294                        # Execute the command.
2295                        $dbh->SQL($statement, 0, $entityID, $value);
2296                    }
2297                }
2298            }
2299        } else {
2300            Confess("$fieldName is not a valid field name.");
2301        }
2302    }
2303    
2304    =head3 InsertObject
2305    
2306    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2307    
2308    Insert an object into the database. The object is defined by a type name and then a hash
2309    of field names to values. Field values in the primary relation are represented by scalars.
2310    (Note that for relationships, the primary relation is the B<only> relation.)
2311    Field values for the other relations comprising the entity are always list references. For
2312    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2313    C<ZP_00210270.1> and C<gi|46206278>.
2314    
2315    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2316    
2317    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2318    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2319    
2320    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2321    
2322    =over 4
2323    
2324    =item newObjectType
2325    
2326    Type name of the object to insert.
2327    
2328    =item fieldHash
2329    
2330    Hash of field names to values.
2331    
2332    =back
2333    
2334    =cut
2335    
2336    sub InsertObject {
2337        # Get the parameters.
2338        my ($self, $newObjectType, $fieldHash) = @_;
2339        # Denote that so far we appear successful.
2340        my $retVal = 1;
2341        # Get the database handle.
2342        my $dbh = $self->{_dbh};
2343        # Get the relation list.
2344        my $relationTable = $self->_GetRelationTable($newObjectType);
2345        # Loop through the relations. We'll build insert statements for each one. If a relation is
2346        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2347        # stop the loop.
2348        my @relationList = keys %{$relationTable};
2349        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2350            my $relationName = $relationList[$i];
2351            my $relationDefinition = $relationTable->{$relationName};
2352            # Get the relation's fields. For each field we will collect a value in the corresponding
2353            # position of the @valueList array. If one of the fields is missing, we will add it to the
2354            # @missing list.
2355            my @fieldList = @{$relationDefinition->{Fields}};
2356            my @fieldNameList = ();
2357            my @valueList = ();
2358            my @missing = ();
2359            my $recordCount = 1;
2360            for my $fieldDescriptor (@fieldList) {
2361                # Get the field name and save it. Note we need to fix it up so the hyphens
2362                # are converted to underscores.
2363                my $fieldName = $fieldDescriptor->{name};
2364                push @fieldNameList, _FixName($fieldName);
2365                # Look for the named field in the incoming structure. Note that we are looking
2366                # for the real field name, not the fixed-up one!
2367                if (exists $fieldHash->{$fieldName}) {
2368                    # Here we found the field. Stash it in the value list.
2369                    my $value = $fieldHash->{$fieldName};
2370                    push @valueList, $value;
2371                    # If the value is a list, we may need to increment the record count.
2372                    if (ref $value eq "ARRAY") {
2373                        my $thisCount = @{$value};
2374                        if ($recordCount == 1) {
2375                            # Here we have our first list, so we save its count.
2376                            $recordCount = $thisCount;
2377                        } elsif ($recordCount != $thisCount) {
2378                            # Here we have a second list, so its length has to match the
2379                            # previous lists.
2380                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2381                            $retVal = 0;
2382                        }
2383                    }
2384                } else {
2385                    # Here the field is not present. Flag it as missing.
2386                    push @missing, $fieldName;
2387                }
2388            }
2389            # If we are the primary relation, add the new-record flag.
2390            if ($relationName eq $newObjectType) {
2391                push @valueList, 1;
2392                push @fieldNameList, "new_record";
2393            }
2394            # Only proceed if there are no missing fields.
2395            if (@missing > 0) {
2396                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2397                    join(' ', @missing)) if T(1);
2398            } else {
2399                # Build the INSERT statement.
2400                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2401                    ") VALUES (";
2402                # Create a marker list of the proper size and put it in the statement.
2403                my @markers = ();
2404                while (@markers < @fieldNameList) { push @markers, '?'; }
2405                $statement .= join(', ', @markers) . ")";
2406                # We have the insert statement, so prepare it.
2407                my $sth = $dbh->prepare_command($statement);
2408                Trace("Insert statement prepared: $statement") if T(3);
2409                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2410                # a list, we use the current element. The values are stored in the @parameterList array.
2411                my $done = 0;
2412                for (my $i = 0; $i < $recordCount; $i++) {
2413                    # Clear the parameter list array.
2414                    my @parameterList = ();
2415                    # Loop through the values.
2416                    for my $value (@valueList) {
2417                        # Check to see if this is a scalar value.
2418                        if (ref $value eq "ARRAY") {
2419                            # Here we have a list value. Pull the current entry.
2420                            push @parameterList, $value->[$i];
2421                        } else {
2422                            # Here we have a scalar value. Use it unmodified.
2423                            push @parameterList, $value;
2424                        }
2425                    }
2426                    # Execute the INSERT statement with the specified parameter list.
2427                    $retVal = $sth->execute(@parameterList);
2428                    if (!$retVal) {
2429                        my $errorString = $sth->errstr();
2430                        Confess("Error inserting into $relationName: $errorString");
2431                    }
2432                }
2433            }
2434        }
2435        # Return a 1 for backward compatability.
2436        return 1;
2437    }
2438    
2439    =head3 UpdateEntity
2440    
2441    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2442    
2443    Update the values of an entity. This is an unprotected update, so it should only be
2444    done if the database resides on a database server.
2445    
2446    =over 4
2447    
2448    =item entityName
2449    
2450    Name of the entity to update. (This is the entity type.)
2451    
2452    =item id
2453    
2454    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2455    
2456    =item fields
2457    
2458    Reference to a hash mapping field names to their new values. All of the fields named
2459    must be in the entity's primary relation, and they cannot any of them be the ID field.
2460    
2461    =back
2462    
2463    =cut
2464    
2465    sub UpdateEntity {
2466        # Get the parameters.
2467        my ($self, $entityName, $id, $fields) = @_;
2468        # Get a list of the field names being updated.
2469        my @fieldList = keys %{$fields};
2470        # Verify that the fields exist.
2471        my $checker = $self->GetFieldTable($entityName);
2472        for my $field (@fieldList) {
2473            if ($field eq 'id') {
2474                Confess("Cannot update the ID field for entity $entityName.");
2475            } elsif ($checker->{$field}->{relation} ne $entityName) {
2476                Confess("Cannot find $field in primary relation of $entityName.");
2477            }
2478        }
2479        # Build the SQL statement.
2480        my @sets = ();
2481        my @valueList = ();
2482        for my $field (@fieldList) {
2483            push @sets, _FixName($field) . " = ?";
2484            push @valueList, $fields->{$field};
2485        }
2486        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2487        # Add the ID to the list of binding values.
2488        push @valueList, $id;
2489        # Call SQL to do the work.
2490        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2491        # Check for errors.
2492        if ($rows == 0) {
2493            Confess("Entity $id of type $entityName not found.");
2494        }
2495    }
2496    
2497    =head3 LoadTable
2498    
2499    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2500    
2501    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2502    first.
2503    
2504    =over 4
2505    
2506    =item fileName
2507    
2508    Name of the file from which the table data should be loaded.
2509    
2510    =item relationName
2511    
2512    Name of the relation to be loaded. This is the same as the table name.
2513    
2514    =item truncateFlag
2515    
2516    TRUE if the table should be dropped and re-created, else FALSE
2517    
2518    =item RETURN
2519    
2520    Returns a statistical object containing a list of the error messages.
2521    
2522    =back
2523    
2524    =cut
2525    sub LoadTable {
2526        # Get the parameters.
2527        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2528        # Create the statistical return object.
2529        my $retVal = _GetLoadStats();
2530        # Trace the fact of the load.
2531        Trace("Loading table $relationName from $fileName") if T(2);
2532        # Get the database handle.
2533        my $dbh = $self->{_dbh};
2534        # Get the input file size.
2535        my $fileSize = -s $fileName;
2536        # Get the relation data.
2537        my $relation = $self->_FindRelation($relationName);
2538        # Check the truncation flag.
2539        if ($truncateFlag) {
2540            Trace("Creating table $relationName") if T(2);
2541            # Compute the row count estimate. We take the size of the load file,
2542            # divide it by the estimated row size, and then multiply by 1.5 to
2543            # leave extra room. We postulate a minimum row count of 1000 to
2544            # prevent problems with incoming empty load files.
2545            my $rowSize = $self->EstimateRowSize($relationName);
2546            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2547            # Re-create the table without its index.
2548            $self->CreateTable($relationName, 0, $estimate);
2549            # If this is a pre-index DBMS, create the index here.
2550            if ($dbh->{_preIndex}) {
2551                eval {
2552                    $self->CreateIndex($relationName);
2553                };
2554                if ($@) {
2555                    $retVal->AddMessage($@);
2556                }
2557            }
2558        }
2559        # Load the table.
2560        my $rv;
2561        eval {
2562            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2563        };
2564        if (!defined $rv) {
2565            $retVal->AddMessage($@) if ($@);
2566            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2567            Trace("Table load failed for $relationName.") if T(1);
2568        } else {
2569            # Here we successfully loaded the table.
2570            $retVal->Add("tables");
2571            my $size = -s $fileName;
2572            Trace("$size bytes loaded into $relationName.") if T(2);
2573            # If we're rebuilding, we need to create the table indexes.
2574            if ($truncateFlag) {
2575                # Indexes are created here for PostGres. For PostGres, indexes are
2576                # best built at the end. For MySQL, the reverse is true.
2577                if (! $dbh->{_preIndex}) {
2578                    eval {
2579                        $self->CreateIndex($relationName);
2580                    };
2581                    if ($@) {
2582                        $retVal->AddMessage($@);
2583                    }
2584                }
2585                # The full-text index (if any) is always built last, even for MySQL.
2586                # First we need to see if this table has a full-text index. Only
2587                # primary relations are allowed that privilege.
2588                Trace("Checking for full-text index on $relationName.") if T(2);
2589                if ($self->_IsPrimary($relationName)) {
2590                    # Get the relation's entity/relationship structure.
2591                    my $structure = $self->_GetStructure($relationName);
2592                    Trace("Checking for search fields in $relationName.") if T(3);
2593                    # Check for a searchable fields list.
2594                    if (exists $structure->{searchFields}) {
2595                        # Here we know that we need to create a full-text search index.
2596                        # Get an SQL-formatted field name list.
2597                        my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2598                        # Create the index.
2599                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2600                                           flds => $fields, kind => 'fulltext');
2601                        Trace("Index created for $fields in $relationName.") if T(2);
2602                    }
2603                }
2604            }
2605        }
2606        # Analyze the table to improve performance.
2607        Trace("Analyzing and compacting $relationName.") if T(3);
2608        $dbh->vacuum_it($relationName);
2609        Trace("$relationName load completed.") if T(3);
2610        # Return the statistics.
2611        return $retVal;
2612    }
2613    
2614    =head3 DropRelation
2615    
2616    C<< $erdb->DropRelation($relationName); >>
2617    
2618    Physically drop a relation from the database.
2619    
2620    =over 4
2621    
2622    =item relationName
2623    
2624    Name of the relation to drop. If it does not exist, this method will have
2625    no effect.
2626    
2627    =back
2628    
2629    =cut
2630    
2631    sub DropRelation {
2632        # Get the parameters.
2633        my ($self, $relationName) = @_;
2634        # Get the database handle.
2635        my $dbh = $self->{_dbh};
2636        # Drop the relation. The method used here has no effect if the relation
2637        # does not exist.
2638        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2639        $dbh->drop_table(tbl => $relationName);
2640    }
2641    
2642    =head3 MatchSqlPattern
2643    
2644    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2645    
2646    Determine whether or not a specified value matches an SQL pattern. An SQL
2647    pattern has two wild card characters: C<%> that matches multiple characters,
2648    and C<_> that matches a single character. These can be escaped using a
2649    backslash (C<\>). We pull this off by converting the SQL pattern to a
2650    PERL regular expression. As per SQL rules, the match is case-insensitive.
2651    
2652    =over 4
2653    
2654    =item value
2655    
2656    Value to be matched against the pattern. Note that an undefined or empty
2657    value will not match anything.
2658    
2659    =item pattern
2660    
2661    SQL pattern against which to match the value. An undefined or empty pattern will
2662    match everything.
2663    
2664    =item RETURN
2665    
2666    Returns TRUE if the value and pattern match, else FALSE.
2667    
2668    =back
2669    
2670    =cut
2671    
2672    sub MatchSqlPattern {
2673        # Get the parameters.
2674        my ($value, $pattern) = @_;
2675        # Declare the return variable.
2676        my $retVal;
2677        # Insure we have a pattern.
2678        if (! defined($pattern) || $pattern eq "") {
2679            $retVal = 1;
2680        } else {
2681            # Break the pattern into pieces around the wildcard characters. Because we
2682            # use parentheses in the split function's delimiter expression, we'll get
2683            # list elements for the delimiters as well as the rest of the string.
2684            my @pieces = split /([_%]|\\[_%])/, $pattern;
2685            # Check some fast special cases.
2686            if ($pattern eq '%') {
2687                # A null pattern matches everything.
2688                $retVal = 1;
2689            } elsif (@pieces == 1) {
2690                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2691                $retVal = (lc($value) eq lc($pattern));
2692            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2693                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2694                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2695            } else {
2696                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2697                my $realPattern = "";
2698                for my $piece (@pieces) {
2699                    # Determine the type of piece.
2700                    if ($piece eq "") {
2701                        # Empty pieces are ignored.
2702                    } elsif ($piece eq "%") {
2703                        # Here we have a multi-character wildcard. Note that it can match
2704                        # zero or more characters.
2705                        $realPattern .= ".*"
2706                    } elsif ($piece eq "_") {
2707                        # Here we have a single-character wildcard.
2708                        $realPattern .= ".";
2709                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2710                        # This is an escape sequence (which is a rare thing, actually).
2711                        $realPattern .= substr($piece, 1, 1);
2712                    } else {
2713                        # Here we have raw text.
2714                        $realPattern .= quotemeta($piece);
2715                    }
2716                }
2717                # Do the match.
2718                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2719            }
2720        }
2721        # Return the result.
2722        return $retVal;
2723    }
2724    
2725    =head3 GetEntity
2726    
2727    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2728    
2729    Return an object describing the entity instance with a specified ID.
2730    
2731    =over 4
2732    
2733    =item entityType
2734    
2735    Entity type name.
2736    
2737    =item ID
2738    
2739    ID of the desired entity.
2740    
2741    =item RETURN
2742    
2743    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2744    instance is found with the specified key.
2745    
2746    =back
2747    
2748    =cut
2749    
2750    sub GetEntity {
2751        # Get the parameters.
2752        my ($self, $entityType, $ID) = @_;
2753        # Create a query.
2754        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2755        # Get the first (and only) object.
2756        my $retVal = $query->Fetch();
2757        # Return the result.
2758        return $retVal;
2759    }
2760    
2761    =head3 GetChoices
2762    
2763    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2764    
2765    Return a list of all the values for the specified field that are represented in the
2766    specified entity.
2767    
2768    Note that if the field is not indexed, then this will be a very slow operation.
2769    
2770    =over 4
2771    
2772    =item entityName
2773    
2774    Name of an entity in the database.
2775    
2776    =item fieldName
2777    
2778    Name of a field belonging to the entity. This is a raw field name without
2779    the standard parenthesized notation used in most calls.
2780    
2781    =item RETURN
2782    
2783    Returns a list of the distinct values for the specified field in the database.
2784    
2785    =back
2786    
2787    =cut
2788    
2789    sub GetChoices {
2790        # Get the parameters.
2791        my ($self, $entityName, $fieldName) = @_;
2792        # Declare the return variable.
2793        my @retVal;
2794        # Get the entity data structure.
2795        my $entityData = $self->_GetStructure($entityName);
2796        # Get the field.
2797        my $fieldHash = $entityData->{Fields};
2798        if (! exists $fieldHash->{$fieldName}) {
2799            Confess("$fieldName not found in $entityName.");
2800        } else {
2801            # Get the name of the relation containing the field.
2802            my $relation = $fieldHash->{$fieldName}->{relation};
2803            # Fix up the field name.
2804            my $realName = _FixName($fieldName);
2805            # Get the database handle.
2806            my $dbh = $self->{_dbh};
2807            # Query the database.
2808            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2809            # Clean the results. They are stored as a list of lists, and we just want the one list.
2810            @retVal = sort map { $_->[0] } @{$results};
2811        }
2812        # Return the result.
2813        return @retVal;
2814    }
2815    
2816    =head3 GetEntityValues
2817    
2818    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2819    
2820    Return a list of values from a specified entity instance. If the entity instance
2821    does not exist, an empty list is returned.
2822    
2823    =over 4
2824    
2825    =item entityType
2826    
2827    Entity type name.
2828    
2829    =item ID
2830    
2831    ID of the desired entity.
2832    
2833    =item fields
2834    
2835    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2836    
2837    =item RETURN
2838    
2839    Returns a flattened list of the values of the specified fields for the specified entity.
2840    
2841    =back
2842    
2843    =cut
2844    
2845    sub GetEntityValues {
2846        # Get the parameters.
2847        my ($self, $entityType, $ID, $fields) = @_;
2848        # Get the specified entity.
2849        my $entity = $self->GetEntity($entityType, $ID);
2850        # Declare the return list.
2851        my @retVal = ();
2852        # If we found the entity, push the values into the return list.
2853        if ($entity) {
2854            push @retVal, $entity->Values($fields);
2855        }
2856        # Return the result.
2857        return @retVal;
2858    }
2859    
2860    =head3 GetAll
2861    
2862    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2863    
2864    Return a list of values taken from the objects returned by a query. The first three
2865    parameters correspond to the parameters of the L</Get> method. The final parameter is
2866    a list of the fields desired from each record found by the query. The field name
2867    syntax is the standard syntax used for fields in the B<ERDB> system--
2868    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2869    or relationship and I<fieldName> is the name of the field.
2870    
2871    The list returned will be a list of lists. Each element of the list will contain
2872    the values returned for the fields specified in the fourth parameter. If one of the
2873    fields specified returns multiple values, they are flattened in with the rest. For
2874    example, the following call will return a list of the features in a particular
2875    spreadsheet cell, and each feature will be represented by a list containing the
2876    feature ID followed by all of its aliases.
2877    
2878    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2879    
2880    =over 4
2881    
2882    =item objectNames
2883    
2884    List containing the names of the entity and relationship objects to be retrieved.
2885    
2886    =item filterClause
2887    
2888    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2889    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2890    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2891    parameter list as additional parameters. The fields in a filter clause can come from primary
2892    entity relations, relationship relations, or secondary entity relations; however, all of the
2893    entities and relationships involved must be included in the list of object names.
2894    
2895    =item parameterList
2896    
2897    List of the parameters to be substituted in for the parameters marks in the filter clause.
2898    
2899    =item fields
2900    
2901    List of the fields to be returned in each element of the list returned.
2902    
2903    =item count
2904    
2905    Maximum number of records to return. If omitted or 0, all available records will be returned.
2906    
2907    =item RETURN
2908    
2909    Returns a list of list references. Each element of the return list contains the values for the
2910    fields specified in the B<fields> parameter.
2911    
2912    =back
2913    
2914    =cut
2915    #: Return Type @@;
2916    sub GetAll {
2917        # Get the parameters.
2918        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2919        # Translate the parameters from a list reference to a list. If the parameter
2920        # list is a scalar we convert it into a singleton list.
2921        my @parmList = ();
2922        if (ref $parameterList eq "ARRAY") {
2923            Trace("GetAll parm list is an array.") if T(4);
2924            @parmList = @{$parameterList};
2925        } else {
2926            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2927            push @parmList, $parameterList;
2928        }
2929        # Insure the counter has a value.
2930        if (!defined $count) {
2931            $count = 0;
2932        }
2933        # Add the row limit to the filter clause.
2934        if ($count > 0) {
2935            $filterClause .= " LIMIT $count";
2936        }
2937        # Create the query.
2938        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2939        # Set up a counter of the number of records read.
2940        my $fetched = 0;
2941        # Loop through the records returned, extracting the fields. Note that if the
2942        # counter is non-zero, we stop when the number of records read hits the count.
2943        my @retVal = ();
2944        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2945            my @rowData = $row->Values($fields);
2946            push @retVal, \@rowData;
2947            $fetched++;
2948        }
2949        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2950        # Return the resulting list.
2951        return @retVal;
2952    }
2953    
2954    =head3 Exists
2955    
2956    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2957    
2958    Return TRUE if an entity exists, else FALSE.
2959    
2960    =over 4
2961    
2962    =item entityName
2963    
2964    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2965    
2966    =item entityID
2967    
2968    ID of the entity instance whose existence is to be checked.
2969    
2970    =item RETURN
2971    
2972    Returns TRUE if the entity instance exists, else FALSE.
2973    
2974    =back
2975    
2976    =cut
2977    #: Return Type $;
2978    sub Exists {
2979        # Get the parameters.
2980        my ($self, $entityName, $entityID) = @_;
2981        # Check for the entity instance.
2982        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2983        my $testInstance = $self->GetEntity($entityName, $entityID);
2984        # Return an existence indicator.
2985        my $retVal = ($testInstance ? 1 : 0);
2986        return $retVal;
2987    }
2988    
2989    =head3 EstimateRowSize
2990    
2991    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2992    
2993    Estimate the row size of the specified relation. The estimated row size is computed by adding
2994    up the average length for each data type.
2995    
2996    =over 4
2997    
2998    =item relName
2999    
3000    Name of the relation whose estimated row size is desired.
3001    
3002    =item RETURN
3003    
3004    Returns an estimate of the row size for the specified relation.
3005    
3006    =back
3007    
3008    =cut
3009    #: Return Type $;
3010    sub EstimateRowSize {
3011        # Get the parameters.
3012        my ($self, $relName) = @_;
3013        # Declare the return variable.
3014        my $retVal = 0;
3015        # Find the relation descriptor.
3016        my $relation = $self->_FindRelation($relName);
3017        # Get the list of fields.
3018        for my $fieldData (@{$relation->{Fields}}) {
3019            # Get the field type and add its length.
3020            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3021            $retVal += $fieldLen;
3022        }
3023        # Return the result.
3024        return $retVal;
3025    }
3026    
3027    =head3 GetFieldTable
3028    
3029    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3030    
3031    Get the field structure for a specified entity or relationship.
3032    
3033    =over 4
3034    
3035    =item objectName
3036    
3037    Name of the desired entity or relationship.
3038    
3039    =item RETURN
3040    
3041    The table containing the field descriptors for the specified object.
3042    
3043    =back
3044    
3045    =cut
3046    
3047    sub GetFieldTable {
3048        # Get the parameters.
3049        my ($self, $objectName) = @_;
3050        # Get the descriptor from the metadata.
3051        my $objectData = $self->_GetStructure($objectName);
3052        # Return the object's field table.
3053        return $objectData->{Fields};
3054    }
3055    
3056    =head3 SplitKeywords
3057    
3058    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3059    
3060    This method returns a list of the positive keywords in the specified
3061    keyword string. All of the operators will have been stripped off,
3062    and if the keyword is preceded by a minus operator (C<->), it will
3063    not be in the list returned. The idea here is to get a list of the
3064    keywords the user wants to see. The list will be processed to remove
3065    duplicates.
3066    
3067    It is possible to create a string that confuses this method. For example
3068    
3069        frog toad -frog
3070    
3071    would return both C<frog> and C<toad>. If this is a problem we can deal
3072    with it later.
3073    
3074    =over 4
3075    
3076    =item keywordString
3077    
3078    The keyword string to be parsed.
3079    
3080    =item RETURN
3081    
3082    Returns a list of the words in the keyword string the user wants to
3083    see.
3084    
3085    =back
3086    
3087    =cut
3088    
3089    sub SplitKeywords {
3090        # Get the parameters.
3091        my ($keywordString) = @_;
3092        # Make a safety copy of the string. (This helps during debugging.)
3093        my $workString = $keywordString;
3094        # Convert operators we don't care about to spaces.
3095        $workString =~ tr/+"()<>/ /;
3096        # Split the rest of the string along space boundaries. Note that we
3097        # eliminate any words that are zero length or begin with a minus sign.
3098        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3099        # Use a hash to remove duplicates.
3100        my %words = map { $_ => 1 } @wordList;
3101        # Return the result.
3102        return sort keys %words;
3103    }
3104    
3105    =head3 ValidateFieldName
3106    
3107    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3108    
3109    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3110    be hyphenated words subject to certain restrictions.
3111    
3112    =over 4
3113    
3114    =item fieldName
3115    
3116    Field name to be validated.
3117    
3118    =item RETURN
3119    
3120    Returns TRUE if the field name is valid, else FALSE.
3121    
3122    =back
3123    
3124    =cut
3125    
3126    sub ValidateFieldName {
3127        # Get the parameters.
3128        my ($fieldName) = @_;
3129        # Declare the return variable. The field name is valid until we hear
3130        # differently.
3131        my $retVal = 1;
3132        # Compute the maximum name length.
3133        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3134        # Look for bad stuff in the name.
3135        if ($fieldName =~ /--/) {
3136            # Here we have a doubled minus sign.
3137            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3138            $retVal = 0;
3139        } elsif ($fieldName !~ /^[A-Za-z]/) {
3140            # Here the field name is missing the initial letter.
3141            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3142            $retVal = 0;
3143        } elsif (length($fieldName) > $maxLen) {
3144            # Here the field name is too long.
3145            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3146        } else {
3147            # Strip out the minus signs. Everything remaining must be a letter,
3148            # underscore, or digit.
3149            my $strippedName = $fieldName;
3150            $strippedName =~ s/-//g;
3151            if ($strippedName !~ /^(\w|\d)+$/) {
3152                Trace("Field name $fieldName contains illegal characters.") if T(1);
3153                $retVal = 0;
3154            }
3155        }
3156        # Return the result.
3157        return $retVal;
3158    }
3159    
3160    =head3 ReadMetaXML
3161    
3162    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3163    
3164    This method reads a raw database definition XML file and returns it.
3165    Normally, the metadata used by the ERDB system has been processed and
3166    modified to make it easier to load and retrieve the data; however,
3167    this method can be used to get the data in its raw form.
3168    
3169    =over 4
3170    
3171    =item fileName
3172    
3173    Name of the XML file to read.
3174    
3175    =item RETURN
3176    
3177    Returns a hash reference containing the raw XML data from the specified file.
3178    
3179    =back
3180    
3181    =cut
3182    
3183    sub ReadMetaXML {
3184        # Get the parameters.
3185        my ($fileName) = @_;
3186        # Read the XML.
3187        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3188        Trace("XML metadata loaded from file $fileName.") if T(1);
3189        # Return the result.
3190        return $retVal;
3191    }
3192    
3193    =head3 GetEntityFieldHash
3194    
3195    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3196    
3197    Get the field hash of the named entity in the specified raw XML structure.
3198    The field hash may not exist, in which case we need to create it.
3199    
3200    =over 4
3201    
3202    =item structure
3203    
3204    Raw XML structure defininng the database. This is not the run-time XML used by
3205    an ERDB object, since that has all sorts of optimizations built-in.
3206    
3207    =item entityName
3208    
3209    Name of the entity whose field structure is desired.
3210    
3211    =item RETURN
3212    
3213    Returns the field hash used to define the entity's fields.
3214    
3215    =back
3216    
3217    =cut
3218    
3219    sub GetEntityFieldHash {
3220        # Get the parameters.
3221        my ($structure, $entityName) = @_;
3222        # Get the entity structure.
3223        my $entityData = $structure->{Entities}->{$entityName};
3224        # Look for a field structure.
3225        my $retVal = $entityData->{Fields};
3226        # If it doesn't exist, create it.
3227        if (! defined($retVal)) {
3228            $entityData->{Fields} = {};
3229            $retVal = $entityData->{Fields};
3230        }
3231        # Return the result.
3232        return $retVal;
3233    }
3234    
3235    =head3 WriteMetaXML
3236    
3237    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3238    
3239    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3240    used to update the database definition. It must be used with care, however, since it
3241    will only work on a raw structure, not on the processed structure created by an ERDB
3242    constructor.
3243    
3244    =over 4
3245    
3246    =item structure
3247    
3248    XML structure to be written to the file.
3249    
3250    =item fileName
3251    
3252    Name of the output file to which the updated XML should be stored.
3253    
3254    =back
3255    
3256    =cut
3257    
3258    sub WriteMetaXML {
3259        # Get the parameters.
3260        my ($structure, $fileName) = @_;
3261        # Compute the output.
3262        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3263        # Write it to the file.
3264        my $xmlOut = Open(undef, ">$fileName");
3265        print $xmlOut $fileString;
3266    }
3267    
3268    
3269    =head3 HTMLNote
3270    
3271    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3272    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3273    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3274    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3275    
3276    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3277    
3278    =over 4
3279    
3280    =item dataString
3281    
3282    String to convert to HTML.
3283    
3284  =item RETURN  =item RETURN
3285    
3286  Returns a flattened list of the values of the specified fields for the specified entity.  An HTML string derived from the input string.
3287    
3288  =back  =back
3289    
3290  =cut  =cut
3291    
3292  sub GetEntityValues {  sub HTMLNote {
3293        # Get the parameter.
3294        my ($dataString) = @_;
3295        # HTML-escape the text.
3296        my $retVal = CGI::escapeHTML($dataString);
3297        # Substitute the bulletin board codes.
3298        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3299        $retVal =~ s!\[p\]!</p><p>!g;
3300        # Return the result.
3301        return $retVal;
3302    }
3303    
3304    
3305    =head2 Data Mining Methods
3306    
3307    =head3 GetUsefulCrossValues
3308    
3309    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3310    
3311    Return a list of the useful attributes that would be returned by a B<Cross> call
3312    from an entity of the source entity type through the specified relationship. This
3313    means it will return the fields of the target entity type and the intersection data
3314    fields in the relationship. Only primary table fields are returned. In other words,
3315    the field names returned will be for fields where there is always one and only one
3316    value.
3317    
3318    =over 4
3319    
3320    =item sourceEntity
3321    
3322    Name of the entity from which the relationship crossing will start.
3323    
3324    =item relationship
3325    
3326    Name of the relationship being crossed.
3327    
3328    =item RETURN
3329    
3330    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3331    
3332    =back
3333    
3334    =cut
3335    #: Return Type @;
3336    sub GetUsefulCrossValues {
3337          # Get the parameters.          # Get the parameters.
3338          my ($self, $entityType, $ID, $fields) = @_;      my ($self, $sourceEntity, $relationship) = @_;
3339          # Get the specified entity.      # Declare the return variable.
         my $entity = $self->GetEntity($entityType, $ID);  
         # Declare the return list.  
3340          my @retVal = ();          my @retVal = ();
3341          # If we found the entity, push the values into the return list.      # Determine the target entity for the relationship. This is whichever entity is not
3342          if ($entity) {      # the source entity. So, if the source entity is the FROM, we'll get the name of
3343                  push @retVal, $entity->Values($fields);      # the TO, and vice versa.
3344          }      my $relStructure = $self->_GetStructure($relationship);
3345        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3346        my $targetEntity = $relStructure->{$targetEntityType};
3347        # Get the field table for the entity.
3348        my $entityFields = $self->GetFieldTable($targetEntity);
3349        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3350        # For the entity fields, the key aspect of the target structure is that the {relation} value
3351        # must match the entity name.
3352        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3353                            keys %{$entityFields};
3354        # Push the fields found onto the return variable.
3355        push @retVal, sort @fieldList;
3356        # Get the field table for the relationship.
3357        my $relationshipFields = $self->GetFieldTable($relationship);
3358        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3359        # This may end up being an empty set.
3360        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3361                            keys %{$relationshipFields};
3362        # Push these onto the return list.
3363        push @retVal, sort @fieldList2;
3364          # Return the result.          # Return the result.
3365          return @retVal;          return @retVal;
3366  }  }
3367    
3368  =head2 Internal Utility Methods  =head3 FindColumn
3369    
3370  =head3 GetLoadStats  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3371    
3372  Return a blank statistics object for use by the load methods.  Return the location a desired column in a data mining header line. The data
3373    mining header line is a tab-separated list of column names. The column
3374    identifier is either the numerical index of a column or the actual column
3375    name.
3376    
3377  This is a static method.  =over 4
3378    
3379    =item headerLine
3380    
3381    The header line from a data mining command, which consists of a tab-separated
3382    list of column names.
3383    
3384    =item columnIdentifier
3385    
3386    Either the ordinal number of the desired column (1-based), or the name of the
3387    desired column.
3388    
3389    =item RETURN
3390    
3391    Returns the array index (0-based) of the desired column.
3392    
3393    =back
3394    
3395  =cut  =cut
3396    
3397  sub _GetLoadStats {  sub FindColumn {
3398          return Stats->new('records');      # Get the parameters.
3399        my ($headerLine, $columnIdentifier) = @_;
3400        # Declare the return variable.
3401        my $retVal;
3402        # Split the header line into column names.
3403        my @headers = ParseColumns($headerLine);
3404        # Determine whether we have a number or a name.
3405        if ($columnIdentifier =~ /^\d+$/) {
3406            # Here we have a number. Subtract 1 and validate the result.
3407            $retVal = $columnIdentifier - 1;
3408            if ($retVal < 0 || $retVal > $#headers) {
3409                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3410            }
3411        } else {
3412            # Here we have a name. We need to find it in the list.
3413            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3414                if ($headers[$i] eq $columnIdentifier) {
3415                    $retVal = $i;
3416                }
3417            }
3418            if (! defined($retVal)) {
3419                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3420            }
3421        }
3422        # Return the result.
3423        return $retVal;
3424  }  }
3425    
3426  =head3 GenerateFields  =head3 ParseColumns
3427    
3428  Generate field values from a field structure and store in a specified table. The field names  C<< my @columns = ERDB::ParseColumns($line); >>
 are first sorted by pass count, certain pre-defined fields are removed from the list, and  
 then we rip through them evaluation the data generation string. Fields in the primary relation  
 are stored as scalars; fields in secondary relations are stored as value lists.  
3429    
3430  This is a static method.  Convert the specified data line to a list of columns.
3431    
3432  =over 4  =over 4
3433    
3434  =item this  =item line
3435    
3436  Hash table into which the field values should be placed.  A data mining input, consisting of a tab-separated list of columns terminated by a
3437    new-line.
3438    
3439  =item fields  =item RETURN
3440    
3441  Field structure from which the field descriptors should be taken.  Returns a list consisting of the column values.
3442    
3443  =item type  =back
3444    
3445    =cut
3446    
3447    sub ParseColumns {
3448        # Get the parameters.
3449        my ($line) = @_;
3450        # Chop off the line-end.
3451        chomp $line;
3452        # Split it into a list.
3453        my @retVal = split(/\t/, $line);
3454        # Return the result.
3455        return @retVal;
3456    }
3457    
3458    =head2 Virtual Methods
3459    
3460    =head3 CleanKeywords
3461    
3462    C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3463    
3464    Clean up a search expression or keyword list. This is a virtual method that may
3465    be overridden by the subclass. The base-class method removes extra spaces
3466    and converts everything to lower case.
3467    
3468    =over 4
3469    
3470  Type name of the object whose fields are being generated.  =item searchExpression
3471    
3472  =item values (optional)  Search expression or keyword list to clean. Note that a search expression may
3473    contain boolean operators which need to be preserved. This includes leading
3474    minus signs.
3475    
3476  Reference to a value structure from which additional values can be taken.  =item RETURN
3477    
3478    Cleaned expression or keyword list.
3479    
3480    =back
3481    
3482    =cut
3483    
3484    sub CleanKeywords {
3485        # Get the parameters.
3486        my ($self, $searchExpression) = @_;
3487        # Lower-case the expression and copy it into the return variable. Note that we insure we
3488        # don't accidentally end up with an undefined value.
3489        my $retVal = lc($searchExpression || "");
3490        # Remove extra spaces.
3491        $retVal =~ s/\s+/ /g;
3492        $retVal =~ s/(^\s+)|(\s+$)//g;
3493        # Return the result.
3494        return $retVal;
3495    }
3496    
3497    =head3 GetSourceObject
3498    
3499    C<< my $source = $erdb->GetSourceObject($entityName); >>
3500    
3501    Return the object to be used in loading special attributes of the specified entity. The
3502    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3503    XML
3504    
3505    =head2 Internal Utility Methods
3506    
3507  =item from (optiona)  =head3 _RelationMap
3508    
3509  Reference to the source entity instance if relationship data is being generated.  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3510    
3511  =item to (optional)  Create the relation map for an SQL query. The relation map is used by B<DBObject>
3512    to determine how to interpret the results of the query.
3513    
3514  Reference to the target entity instance if relationship data is being generated.  =over 4
3515    
3516    =item mappedNameHashRef
3517    
3518    Reference to a hash that maps modified object names to real object names.
3519    
3520    =item mappedNameListRef
3521    
3522    Reference to a list of modified object names in the order they appear in the
3523    SELECT list.
3524    
3525    =item RETURN
3526    
3527    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3528    query followed by the actual name of that object. This enables the B<DBObject> to
3529    determine the order of the tables in the query and which object name belongs to each
3530    mapped object name. Most of the time these two values are the same; however, if a
3531    relation occurs twice in the query, the relation name in the field list and WHERE
3532    clause will use a mapped name (generally the actual relation name with a numeric
3533    suffix) that does not match the actual relation name.
3534    
3535  =back  =back
3536    
3537  =cut  =cut
3538    
3539  sub _GenerateFields {  sub _RelationMap {
3540          # Get the parameters.          # Get the parameters.
3541          my ($this, $fields, $type, $values, $from, $to) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
3542          # Sort the field names by pass number.      # Declare the return variable.
3543          my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};      my @retVal = ();
3544          # Loop through the field names, generating data.      # Build the map.
3545          for my $name (@fieldNames) {      for my $mappedName (@{$mappedNameListRef}) {
3546                  # Only proceed if this field needs to be generated.          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3547                  if (!exists $this->{$name}) {      }
3548                          # Get this field's data generation descriptor.      # Return it.
3549                          my $fieldDescriptor = $fields->{$name};      return @retVal;
3550                          my $data = $fieldDescriptor->{DataGen};  }
3551                          # Get the code to generate the field value.  
3552                          my $codeString = $data->{content};  
3553                          # Determine whether or not this field is in the primary relation.  =head3 _SetupSQL
3554                          if ($fieldDescriptor->{relation} eq $type) {  
3555                                  # Here we have a primary relation field. Store the field value as  Process a list of object names and a filter clause so that they can be used to
3556                                  # a scalar.  build an SQL statement. This method takes in a reference to a list of object names
3557                                  $this->{$name} = eval($codeString);  and a filter clause. It will return a corrected filter clause, a list of mapped
3558    names and the mapped name hash.
3559    
3560    This is an instance method.
3561    
3562    =over 4
3563    
3564    =item objectNames
3565    
3566    Reference to a list of the object names to be included in the query.
3567    
3568    =item filterClause
3569    
3570    A string containing the WHERE clause for the query (without the C<WHERE>) and also
3571    optionally the C<ORDER BY> and C<LIMIT> clauses.
3572    
3573    =item matchClause
3574    
3575    An optional full-text search clause. If specified, it will be inserted at the
3576    front of the WHERE clause. It should already be SQL-formatted; that is, the
3577    field names should be in the form I<table>C<.>I<fieldName>.
3578    
3579    =item RETURN
3580    
3581    Returns a three-element list. The first element is the SQL statement suffix, beginning
3582    with the FROM clause. The second element is a reference to a list of the names to be
3583    used in retrieving the fields. The third element is a hash mapping the names to the
3584    objects they represent.
3585    
3586    =back
3587    
3588    =cut
3589    
3590    sub _SetupSQL {
3591        my ($self, $objectNames, $filterClause, $matchClause) = @_;
3592        # Adjust the list of object names to account for multiple occurrences of the
3593        # same object. We start with a hash table keyed on object name that will
3594        # return the object suffix. The first time an object is encountered it will
3595        # not be found in the hash. The next time the hash will map the object name
3596        # to 2, then 3, and so forth.
3597        my %objectHash = ();
3598        # This list will contain the object names as they are to appear in the
3599        # FROM list.
3600        my @fromList = ();
3601        # This list contains the suffixed object name for each object. It is exactly
3602        # parallel to the list in the $objectNames parameter.
3603        my @mappedNameList = ();
3604        # Finally, this hash translates from a mapped name to its original object name.
3605        my %mappedNameHash = ();
3606        # Now we create the lists. Note that for every single name we push something into
3607        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3608        # parallel to $objectNames.
3609        for my $objectName (@{$objectNames}) {
3610            # Get the next suffix for this object.
3611            my $suffix = $objectHash{$objectName};
3612            if (! $suffix) {
3613                # Here we are seeing the object for the first time. The object name
3614                # is used as is.
3615                push @mappedNameList, $objectName;
3616                push @fromList, $objectName;
3617                $mappedNameHash{$objectName} = $objectName;
3618                # Denote the next suffix will be 2.
3619                $objectHash{$objectName} = 2;
3620            } else {
3621                # Here we've seen the object before. We construct a new name using
3622                # the suffix from the hash and update the hash.
3623                my $mappedName = "$objectName$suffix";
3624                $objectHash{$objectName} = $suffix + 1;
3625                # The FROM list has the object name followed by the mapped name. This
3626                # tells SQL it's still the same table, but we're using a different name
3627                # for it to avoid confusion.
3628                push @fromList, "$objectName $mappedName";
3629                # The mapped-name list contains the real mapped name.
3630                push @mappedNameList, $mappedName;
3631                # Finally, enable us to get back from the mapped name to the object name.
3632                $mappedNameHash{$mappedName} = $objectName;
3633            }
3634        }
3635        # Begin the SELECT suffix. It starts with
3636        #
3637        # FROM name1, name2, ... nameN
3638        #
3639        my $suffix = "FROM " . join(', ', @fromList);
3640        # Now for the WHERE. First, we need a place for the filter string.
3641        my $filterString = "";
3642        # We will also keep a list of conditions to add to the WHERE clause in order to link
3643        # entities and relationships as well as primary relations to secondary ones.
3644        my @joinWhere = ();
3645        # Check for a filter clause.
3646        if ($filterClause) {
3647