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revision 1.6, Wed May 4 03:24:43 2005 UTC revision 1.77, Mon Nov 20 05:53:02 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<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
261    
262    =head3 Object and Field Names
263    
264    By convention entity and relationship names use capital casing (e.g. C<Genome> or
265    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
266    with respect to relation names, converting them internally to all-upper case or
267    all-lower case.
268    
269    If syntax or parsing errors occur when you try to load or use an ERDB database, the
270    most likely reason is that one of your objects has an SQL reserved word as its name.
271    The list of SQL reserved words keeps increasing; however, most are unlikely to show
272    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
273    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
274    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
275    
276    Every entity has a field called C<id> that acts as its primary key. Every relationship
277    has fields called C<from-link> and C<to-link> that contain copies of the relevant
278    entity IDs. These are essentially ERDB's reserved words, and should not be used
279    for user-defined field names.
280    
281    =head3 Entities
282    
283    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
284    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
285    containing one or more fields. The attributes of the B<Entity> tag are as follows.
286    
287    =over 4
288    
289    =item name
290    
291    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
292    or C<GroupBlock>) and should be a noun or noun phrase.
293    
294    =item keyType
295    
296    Data type of the primary key. The primary key is always named C<id>.
297    
298    =back
299    
300    =head3 Relationships
301    
302    A relationship is described by the C<Relationship> tag. Within a relationship,
303    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
304    fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
305    the to-index.
306    
307    The C<Relationship> tag has the following attributes.
308    
309    =over 4
310    
311    =item name
312    
313    Name of the relationship. The relationship name, by convention, uses capital casing
314    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
315    phrase, designed to fit between the from-entity and the to-entity (e.g.
316    Block C<ContainsRegionIn> Genome).
317    
318    =item from
319    
320    Name of the entity from which the relationship starts.
321    
322    =item to
323    
324    Name of the entity to which the relationship proceeds.
325    
326    =item arity
327    
328    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
329    
330    =back
331    
332  =cut  =cut
333    
# Line 75  Line 335 
335    
336  # 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.
337  # "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
338  # 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
339   #string is specified in the field definition.  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
340  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
341                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  # index
342                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
343                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "single ASCII character"},
344                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
345                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
346                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
347                                   indexMod =>   0, notes => "unsigned 32-bit integer"},
348                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
349                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
350                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
351                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
352                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
353                                   indexMod =>   0, notes => "signed, 64-bit integer"},
354                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
355                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
356                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
357                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
358                     'hash-string' =>
359                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
360                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
361                     'id-string' =>
362                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
363                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
364                               'key-string' =>                               'key-string' =>
365                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
367                                   'name-string' =>                                   'name-string' =>
368                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
370                                   'medium-string' =>                                   'medium-string' =>
371                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
373                                  );                                  );
374    
375  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 98  Line 378 
378                                     'MM' => 'many-to-many'                                     'MM' => 'many-to-many'
379                                   );                                   );
380    
381  # Table for interpreting string patterns.  # Options for XML input and output.
382    
383    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
384                                      Entities => 'Entity',
385                                      Fields => 'Field',
386                                      Indexes => 'Index',
387                                      IndexFields => 'IndexField'
388                                    },
389                      KeyAttr =>    { Relationship => 'name',
390                                      Entity => 'name',
391                                      Field => 'name'
392                                    },
393                      SuppressEmpty => 1,
394                     );
395    
396  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
397                                           '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField'],
398                                           'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
399                                           'V' => "aeiou",                    NormalizeSpace => 2,
                                          'K' => "bcdfghjklmnoprstvwxyz"  
400                                     );                                     );
401    my %XmlOutOpts = (
402                      RootName => 'Database',
403                      XMLDecl => 1,
404                     );
405    
406    
407  =head2 Public Methods  =head2 Public Methods
408    
# Line 145  Line 442 
442    
443  =head3 ShowMetaData  =head3 ShowMetaData
444    
445  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
446    
447  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
448  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 176  Line 473 
473          # Write the HTML heading stuff.          # Write the HTML heading stuff.
474          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
475          print HTMLOUT "</head>\n<body>\n";          print HTMLOUT "</head>\n<body>\n";
476        # Write the documentation.
477        print HTMLOUT $self->DisplayMetaData();
478        # Close the document.
479        print HTMLOUT "</body>\n</html>\n";
480        # Close the file.
481        close HTMLOUT;
482    }
483    
484    =head3 DisplayMetaData
485    
486    C<< my $html = $erdb->DisplayMetaData(); >>
487    
488    Return an HTML description of the database. This description can be used to help users create
489    the data to be loaded into the relations and form queries. The output is raw includable HTML
490    without any HEAD or BODY tags.
491    
492    =over 4
493    
494    =item filename
495    
496    The name of the output file.
497    
498    =back
499    
500    =cut
501    
502    sub DisplayMetaData {
503        # Get the parameters.
504        my ($self) = @_;
505        # Get the metadata and the title string.
506        my $metadata = $self->{_metaData};
507        # Get the title string.
508        my $title = $metadata->{Title};
509        # Get the entity and relationship lists.
510        my $entityList = $metadata->{Entities};
511        my $relationshipList = $metadata->{Relationships};
512        # Declare the return variable.
513        my $retVal = "";
514        # Open the output file.
515        Trace("Building MetaData table of contents.") if T(4);
516          # 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
517          # section contains an ordered list of entity or relationship subsections.          # section contains an ordered list of entity or relationship subsections.
518          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";
519          # Loop through the Entities, displaying a list item for each.          # Loop through the Entities, displaying a list item for each.
520          foreach my $key (sort keys %{$entityList}) {          foreach my $key (sort keys %{$entityList}) {
521                  # Display this item.                  # Display this item.
522                  print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
523          }          }
524          # Close off the entity section and start the relationship section.          # Close off the entity section and start the relationship section.
525          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";
526          # Loop through the Relationships.          # Loop through the Relationships.
527          foreach my $key (sort keys %{$relationshipList}) {          foreach my $key (sort keys %{$relationshipList}) {
528                  # Display this item.                  # Display this item.
529                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
530                  print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
531          }          }
532          # Close off the relationship section and list the join table section.          # Close off the relationship section and list the join table section.
533          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";
534          # Close off the table of contents itself.          # Close off the table of contents itself.
535          print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
536          # 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.
537          print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
538          # Loop through the entities.          # Loop through the entities.
539          for my $key (sort keys %{$entityList}) {          for my $key (sort keys %{$entityList}) {
540                  Trace("Building MetaData entry for $key entity.") if T(4);                  Trace("Building MetaData entry for $key entity.") if T(4);
541                  # Create the entity header. It contains a bookmark and the entity name.                  # Create the entity header. It contains a bookmark and the entity name.
542                  print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
543                  # Get the entity data.                  # Get the entity data.
544                  my $entityData = $entityList->{$key};                  my $entityData = $entityList->{$key};
545                  # If there's descriptive text, display it.                  # If there's descriptive text, display it.
546                  if (my $notes = $entityData->{Notes}) {                  if (my $notes = $entityData->{Notes}) {
547                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
548                  }                  }
549                  # 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.
550                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
551                  # Loop through the relationships.                  # Loop through the relationships.
552                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
553                          # Get the relationship data.                          # Get the relationship data.
# Line 220  Line 557 
557                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
558                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
559                                  # Display the relationship data.                                  # Display the relationship data.
560                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
561                          }                          }
562                  }                  }
563                  # Close off the relationship list.                  # Close off the relationship list.
564                  print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
565                  # Get the entity's relations.                  # Get the entity's relations.
566                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
567                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
568                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
569                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
570                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
571                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
572                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
573                  }                  }
574          }          }
575          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
576          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
577          # Loop through the relationships.          # Loop through the relationships.
578          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
579                  Trace("Building MetaData entry for $key relationship.") if T(4);                  Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 244  Line 581 
581                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
582                  # Create the relationship header.                  # Create the relationship header.
583                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
584                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
585                  # Get the entity names.                  # Get the entity names.
586                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
587                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 254  Line 591 
591                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
592                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
593                  if ($arity eq "11") {                  if ($arity eq "11") {
594                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
595                  } else {                  } else {
596                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
597                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
598                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
599                          }                          }
600                  }                  }
601                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
602                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
603                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
604                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
605                  }                  }
606                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
607                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
608                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
609          }          }
610          Trace("Building MetaData join table.") if T(4);          Trace("Building MetaData join table.") if T(4);
611          # Denote we're starting the join table.          # Denote we're starting the join table.
612          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
613          # Create a table header.          # Create a table header.
614          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
615          # Loop through the joins.          # Loop through the joins.
616          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
617          my @joinKeys = keys %{$joinTable};          my @joinKeys = keys %{$joinTable};
# Line 282  Line 619 
619                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
620                  $joinKey =~ m!^([^/]+)/(.+)$!;                  $joinKey =~ m!^([^/]+)/(.+)$!;
621                  my ($sourceRelation, $targetRelation) = ($1, $2);                  my ($sourceRelation, $targetRelation) = ($1, $2);
622                  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);
623                  my $source = $self->ComputeObjectSentence($sourceRelation);                  my $source = $self->ComputeObjectSentence($sourceRelation);
624                  my $target = $self->ComputeObjectSentence($targetRelation);                  my $target = $self->ComputeObjectSentence($targetRelation);
625                  my $clause = $joinTable->{$joinKey};                  my $clause = $joinTable->{$joinKey};
626                  # Display them in a table row.                  # Display them in a table row.
627                  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";
628          }          }
629          # Close the table.          # Close the table.
630          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
631          # Close the document.      Trace("Built MetaData HTML.") if T(3);
632          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
633          # Close the file.      return $retVal;
         close HTMLOUT;  
         Trace("Built MetaData web page.") if T(3);  
634  }  }
635    
636  =head3 DumpMetaData  =head3 DumpMetaData
637    
638  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
639    
640  Return a dump of the metadata structure.  Return a dump of the metadata structure.
641    
# Line 313  Line 648 
648          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
649  }  }
650    
651    =head3 FindIndexForEntity
652    
653    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
654    
655    This method locates the entry in an entity's index list that begins with the
656    specified attribute name. If the entity has no index list, one will be
657    created. This method works on raw XML, not a live ERDB object.
658    
659    =over 4
660    
661    =item xml
662    
663    The raw XML structure defining the database.
664    
665    =item entityName
666    
667    The name of the relevant entity.
668    
669    =item attributeName
670    
671    The name of the attribute relevant to the search.
672    
673    =item RETURN
674    
675    The numerical index in the index list of the index entry for the specified entity and
676    attribute, or C<undef> if no such index exists.
677    
678    =back
679    
680    =cut
681    
682    sub FindIndexForEntity {
683        # Get the parameters.
684        my ($xml, $entityName, $attributeName) = @_;
685        # Declare the return variable.
686        my $retVal;
687        # Get the named entity.
688        my $entityData = $xml->{Entities}->{$entityName};
689        if (! $entityData) {
690            Confess("Entity $entityName not found in DBD structure.");
691        } else {
692            # Insure it has an index list.
693            if (! exists $entityData->{Indexes}) {
694                $entityData->{Indexes} = [];
695            } else {
696                # Search for the desired index.
697                my $indexList = $entityData->{Indexes};
698                my $n = scalar @{$indexList};
699                Trace("Searching $n indexes in index list for $entityName.") if T(2);
700                # We use an indexed FOR here because we're returning an
701                # index number instead of an object. We do THAT so we can
702                # delete the index from the list if needed.
703                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
704                    my $index = $indexList->[$i];
705                    my $fields = $index->{IndexFields};
706                    # Technically this IF should be safe (that is, we are guaranteed
707                    # the existence of a "$fields->[0]"), because when we load the XML
708                    # we have SuppressEmpty specified.
709                    if ($fields->[0]->{name} eq $attributeName) {
710                        $retVal = $i;
711                    }
712                }
713            }
714        }
715        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
716        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
717        # Return the result.
718        return $retVal;
719    }
720    
721  =head3 CreateTables  =head3 CreateTables
722    
723  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
724    
725  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
726  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 327  Line 732 
732  sub CreateTables {  sub CreateTables {
733          # Get the parameters.          # Get the parameters.
734          my ($self) = @_;          my ($self) = @_;
735          my $metadata = $self->{_metaData};      # Get the relation names.
736          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
737          # Loop through the entities.      # Loop through the relations.
738          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}}) {  
739                          # Create a table for this relation.                          # Create a table for this relation.
740                          $self->CreateTable($relationName);                          $self->CreateTable($relationName);
741                          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);  
742          }          }
743  }  }
744    
745  =head3 CreateTable  =head3 CreateTable
746    
747  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
748    
749  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
750    
# Line 363  Line 754 
754    
755  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
756    
757  =item $indexFlag  =item indexFlag
758    
759  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
760  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
761    
762    =item estimatedRows (optional)
763    
764    If specified, the estimated maximum number of rows for the relation. This
765    information allows the creation of tables using storage engines that are
766    faster but require size estimates, such as MyISAM.
767    
768  =back  =back
769    
770  =cut  =cut
771    
772  sub CreateTable {  sub CreateTable {
773          # Get the parameters.          # Get the parameters.
774          my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
775          # Get the database handle.          # Get the database handle.
776          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
777          # 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 795 
795          # Insure the table is not already there.          # Insure the table is not already there.
796          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
797          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
798        # If there are estimated rows, create an estimate so we can take advantage of
799        # faster DB technologies.
800        my $estimation = undef;
801        if ($estimatedRows) {
802            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
803        }
804          # Create the table.          # Create the table.
805          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
806          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
807          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
808          # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
809        # index will not be built until the table has been loaded.
810          if ($indexFlag) {          if ($indexFlag) {
811                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
812          }          }
813  }  }
814    
815    =head3 VerifyFields
816    
817    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
818    
819    Run through the list of proposed field values, insuring that all the character fields are
820    below the maximum length. If any fields are too long, they will be truncated in place.
821    
822    =over 4
823    
824    =item relName
825    
826    Name of the relation for which the specified fields are destined.
827    
828    =item fieldList
829    
830    Reference to a list, in order, of the fields to be put into the relation.
831    
832    =item RETURN
833    
834    Returns the number of fields truncated.
835    
836    =back
837    
838    =cut
839    
840    sub VerifyFields {
841        # Get the parameters.
842        my ($self, $relName, $fieldList) = @_;
843        # Initialize the return value.
844        my $retVal = 0;
845        # Get the relation definition.
846        my $relData = $self->_FindRelation($relName);
847        # Get the list of field descriptors.
848        my $fieldTypes = $relData->{Fields};
849        my $fieldCount = scalar @{$fieldTypes};
850        # Loop through the two lists.
851        for (my $i = 0; $i < $fieldCount; $i++) {
852            # Get the type of the current field.
853            my $fieldType = $fieldTypes->[$i]->{type};
854            # If it's a character field, verify the length.
855            if ($fieldType =~ /string/) {
856                my $maxLen = $TypeTable{$fieldType}->{maxLen};
857                my $oldString = $fieldList->[$i];
858                if (length($oldString) > $maxLen) {
859                    # Here it's too big, so we truncate it.
860                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
861                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
862                    $retVal++;
863                }
864            }
865        }
866        # Return the truncation count.
867        return $retVal;
868    }
869    
870    =head3 DigestFields
871    
872    C<< $erdb->DigestFields($relName, $fieldList); >>
873    
874    Digest the strings in the field list that correspond to data type C<hash-string> in the
875    specified relation.
876    
877    =over 4
878    
879    =item relName
880    
881    Name of the relation to which the fields belong.
882    
883    =item fieldList
884    
885    List of field contents to be loaded into the relation.
886    
887    =back
888    
889    =cut
890    #: Return Type ;
891    sub DigestFields {
892        # Get the parameters.
893        my ($self, $relName, $fieldList) = @_;
894        # Get the relation definition.
895        my $relData = $self->_FindRelation($relName);
896        # Get the list of field descriptors.
897        my $fieldTypes = $relData->{Fields};
898        my $fieldCount = scalar @{$fieldTypes};
899        # Loop through the two lists.
900        for (my $i = 0; $i < $fieldCount; $i++) {
901            # Get the type of the current field.
902            my $fieldType = $fieldTypes->[$i]->{type};
903            # If it's a hash string, digest it in place.
904            if ($fieldType eq 'hash-string') {
905                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
906            }
907        }
908    }
909    
910    =head3 DigestKey
911    
912    C<< my $digested = $erdb->DigestKey($keyValue); >>
913    
914    Return the digested value of a symbolic key. The digested value can then be plugged into a
915    key-based search into a table with key-type hash-string.
916    
917    Currently the digesting process is independent of the database structure, but that may not
918    always be the case, so this is an instance method instead of a static method.
919    
920    =over 4
921    
922    =item keyValue
923    
924    Key value to digest.
925    
926    =item RETURN
927    
928    Digested value of the key.
929    
930    =back
931    
932    =cut
933    
934    sub DigestKey {
935        # Get the parameters.
936        my ($self, $keyValue) = @_;
937        # Compute the digest.
938        my $retVal = md5_base64($keyValue);
939        # Return the result.
940        return $retVal;
941    }
942    
943  =head3 CreateIndex  =head3 CreateIndex
944    
945  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
946    
947  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
948  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.
949  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
950  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.
951    
952  =cut  =cut
953    
# Line 431  Line 963 
963          for my $indexName (keys %{$indexHash}) {          for my $indexName (keys %{$indexHash}) {
964                  my $indexData = $indexHash->{$indexName};                  my $indexData = $indexHash->{$indexName};
965                  # Get the index's field list.                  # Get the index's field list.
966                  my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
967            # Get a hash of the relation's field types.
968            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
969            # We need to check for text fields. We need a append a length limitation for them. To do
970            # that, we need the relation's field list.
971            my $relFields = $relationData->{Fields};
972            for (my $i = 0; $i <= $#rawFields; $i++) {
973                # Get the field type.
974                my $field = $rawFields[$i];
975                my $type = $types{$field};
976                # Ask if it requires using prefix notation for the index.
977                my $mod = $TypeTable{$type}->{indexMod};
978                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
979                if ($mod) {
980                    # Append the prefix length to the field name,
981                    $rawFields[$i] .= "($mod)";
982                }
983            }
984            my @fieldList = _FixNames(@rawFields);
985                  my $flds = join(', ', @fieldList);                  my $flds = join(', ', @fieldList);
986                  # Get the index's uniqueness flag.                  # Get the index's uniqueness flag.
987                  my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
988                  # Create the index.                  # Create the index.
989                  $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
990                                        flds => $flds, kind => $unique);
991            if ($rv) {
992                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);                  Trace("Index created: $indexName for $relationName ($flds)") if T(1);
993            } else {
994                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
995            }
996          }          }
997  }  }
998    
999  =head3 LoadTables  =head3 GetSecondaryFields
1000    
1001  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1002    
1003  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
1004  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
1005    in addition to the primary entity table. This enables the field to have no value
1006    or to have multiple values.
1007    
1008    =over 4
1009    
1010    =item entityName
1011    
1012    Name of the entity whose secondary fields are desired.
1013    
1014    =item RETURN
1015    
1016    Returns a hash mapping the field names to their field types.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub GetSecondaryFields {
1023        # Get the parameters.
1024        my ($self, $entityName) = @_;
1025        # Declare the return variable.
1026        my %retVal = ();
1027        # Look for the entity.
1028        my $table = $self->GetFieldTable($entityName);
1029        # Loop through the fields, pulling out the secondaries.
1030        for my $field (sort keys %{$table}) {
1031            if ($table->{$field}->{relation} ne $entityName) {
1032                # Here we have a secondary field.
1033                $retVal{$field} = $table->{$field}->{type};
1034            }
1035        }
1036        # Return the result.
1037        return %retVal;
1038    }
1039    
1040    =head3 GetFieldRelationName
1041    
1042    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1043    
1044    Return the name of the relation containing a specified field.
1045    
1046    =over 4
1047    
1048    =item objectName
1049    
1050    Name of the entity or relationship containing the field.
1051    
1052    =item fieldName
1053    
1054    Name of the relevant field in that entity or relationship.
1055    
1056    =item RETURN
1057    
1058    Returns the name of the database relation containing the field, or C<undef> if
1059    the field does not exist.
1060    
1061    =back
1062    
1063    =cut
1064    
1065    sub GetFieldRelationName {
1066        # Get the parameters.
1067        my ($self, $objectName, $fieldName) = @_;
1068        # Declare the return variable.
1069        my $retVal;
1070        # Get the object field table.
1071        my $table = $self->GetFieldTable($objectName);
1072        # Only proceed if the field exists.
1073        if (exists $table->{$fieldName}) {
1074            # Determine the name of the relation that contains this field.
1075            $retVal = $table->{$fieldName}->{relation};
1076        }
1077        # Return the result.
1078        return $retVal;
1079    }
1080    
1081    =head3 DeleteValue
1082    
1083    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1084    
1085    Delete secondary field values from the database. This method can be used to delete all
1086    values of a specified field for a particular entity instance, or only a single value.
1087    
1088    Secondary fields are stored in two-column relations separate from an entity's primary
1089    table, and as a result a secondary field can legitimately have no value or multiple
1090    values. Therefore, it makes sense to talk about deleting secondary fields where it
1091    would not make sense for primary fields.
1092    
1093    =over 4
1094    
1095    =item entityName
1096    
1097    Name of the entity from which the fields are to be deleted.
1098    
1099    =item id
1100    
1101    ID of the entity instance to be processed. If the instance is not found, this
1102    method will have no effect. If C<undef> is specified, all values for all of
1103    the entity instances will be deleted.
1104    
1105    =item fieldName
1106    
1107    Name of the field whose values are to be deleted.
1108    
1109    =item fieldValue (optional)
1110    
1111    Value to be deleted. If not specified, then all values of the specified field
1112    will be deleted for the entity instance. If specified, then only the values which
1113    match this parameter will be deleted.
1114    
1115    =item RETURN
1116    
1117    Returns the number of rows deleted.
1118    
1119    =back
1120    
1121    =cut
1122    
1123    sub DeleteValue {
1124        # Get the parameters.
1125        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1126        # Declare the return value.
1127        my $retVal = 0;
1128        # We need to set up an SQL command to do the deletion. First, we
1129        # find the name of the field's relation.
1130        my $table = $self->GetFieldTable($entityName);
1131        my $field = $table->{$fieldName};
1132        my $relation = $field->{relation};
1133        # Make sure this is a secondary field.
1134        if ($relation eq $entityName) {
1135            Confess("Cannot delete values of $fieldName for $entityName.");
1136        } else {
1137            # Set up the SQL command to delete all values.
1138            my $sql = "DELETE FROM $relation";
1139            # Build the filter.
1140            my @filters = ();
1141            my @parms = ();
1142            # Check for a filter by ID.
1143            if (defined $id) {
1144                push @filters, "id = ?";
1145                push @parms, $id;
1146            }
1147            # Check for a filter by value.
1148            if (defined $fieldValue) {
1149                push @filters, "$fieldName = ?";
1150                push @parms, $fieldValue;
1151            }
1152            # Append the filters to the command.
1153            if (@filters) {
1154                $sql .= " WHERE " . join(" AND ", @filters);
1155            }
1156            # Execute the command.
1157            my $dbh = $self->{_dbh};
1158            $retVal = $dbh->SQL($sql, 0, @parms);
1159        }
1160        # Return the result.
1161        return $retVal;
1162    }
1163    
1164    =head3 LoadTables
1165    
1166    C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1167    
1168    This method will load the database tables from a directory. The tables must already have been created
1169    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1170  all of the relations to be loaded must have a file in the directory with the same name as the relation  all of the relations to be loaded must have a file in the directory with the same name as the relation
1171  (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
1172  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
# Line 486  Line 1206 
1206          $directoryName =~ s!/\\$!!;          $directoryName =~ s!/\\$!!;
1207          # Declare the return variable.          # Declare the return variable.
1208          my $retVal = Stats->new();          my $retVal = Stats->new();
1209          # Get the metadata structure.      # Get the relation names.
1210          my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
1211          # 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}}) {  
1212                          # Try to load this relation.                          # Try to load this relation.
1213                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1214                          # Accumulate the statistics.                          # Accumulate the statistics.
1215                          $retVal->Accumulate($result);                          $retVal->Accumulate($result);
1216                  }                  }
         }  
         # 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);  
         }  
1217          # Add the duration of the load to the statistical object.          # Add the duration of the load to the statistical object.
1218          $retVal->Add('duration', gettimeofday - $startTime);          $retVal->Add('duration', gettimeofday - $startTime);
1219          # Return the accumulated statistics.          # Return the accumulated statistics.
1220          return $retVal;          return $retVal;
1221  }  }
1222    
1223    
1224  =head3 GetTableNames  =head3 GetTableNames
1225    
1226  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
1227    
1228  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1229    
# Line 530  Line 1240 
1240    
1241  =head3 GetEntityTypes  =head3 GetEntityTypes
1242    
1243  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
1244    
1245  Return a list of the entity type names.  Return a list of the entity type names.
1246    
# Line 545  Line 1255 
1255          return sort keys %{$entityList};          return sort keys %{$entityList};
1256  }  }
1257    
1258    =head3 GetDataTypes
1259    
1260    C<< my %types = ERDB::GetDataTypes(); >>
1261    
1262    Return a table of ERDB data types. The table returned is a hash of hashes.
1263    The keys of the big hash are the datatypes. Each smaller hash has several
1264    values used to manage the data. The most interesting is the SQL type (key
1265    C<sqlType>) and the descriptive node (key C<notes>).
1266    
1267    Note that changing the values in the smaller hashes will seriously break
1268    things, so this data should be treated as read-only.
1269    
1270    =cut
1271    
1272    sub GetDataTypes {
1273        return %TypeTable;
1274    }
1275    
1276    
1277    =head3 IsEntity
1278    
1279    C<< my $flag = $erdb->IsEntity($entityName); >>
1280    
1281    Return TRUE if the parameter is an entity name, else FALSE.
1282    
1283    =over 4
1284    
1285    =item entityName
1286    
1287    Object name to be tested.
1288    
1289    =item RETURN
1290    
1291    Returns TRUE if the specified string is an entity name, else FALSE.
1292    
1293    =back
1294    
1295    =cut
1296    
1297    sub IsEntity {
1298        # Get the parameters.
1299        my ($self, $entityName) = @_;
1300        # Test to see if it's an entity.
1301        return exists $self->{_metaData}->{Entities}->{$entityName};
1302    }
1303    
1304  =head3 Get  =head3 Get
1305    
1306  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1307    
1308  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.
1309  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 1311 
1311  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
1312  $genus.  $genus.
1313    
1314  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1315    
1316  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
1317  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1318    
1319  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1320    
1321  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
1322  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 572  Line 1328 
1328  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
1329  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,
1330    
1331  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1332    
1333  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
1334  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.
1335  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
1336  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
1337  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  
1338  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,
1339  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.
1340    
1341    If an entity or relationship is mentioned twice, the name for the second occurrence will
1342    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1343    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1344    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1345    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1346    
1347  =over 4  =over 4
1348    
1349  =item objectNames  =item objectNames
# Line 605  Line 1366 
1366    
1367  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1368    
1369    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1370    be processed. The idea is to make it less likely to find the verb by accident.
1371    
1372  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
1373  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
1374  relation.  relation.
1375    
1376  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1377    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1378    a positive number. So, for example
1379    
1380    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1381    
1382  Parameter values to be substituted into the filter clause.  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1383    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1384    use
1385    
1386    C<< "LIMIT 10" >>
1387    
1388    =item params
1389    
1390    Reference to a list of parameter values to be substituted into the filter clause.
1391    
1392  =item RETURN  =item RETURN
1393    
# Line 623  Line 1399 
1399    
1400  sub Get {  sub Get {
1401          # Get the parameters.          # Get the parameters.
1402          my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1403          # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1404          #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1405          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1406          #      # Create the query.
1407          my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1408          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1409                                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1410          # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1411          if ($filterClause) {      # and mapped name for each object in the query.
1412                  # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1413                  # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1414                  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) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
                 }  
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
                 }  
1415          }          }
         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());  
1416          # Return the statement object.          # Return the statement object.
1417          my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1418          return $retVal;          return $retVal;
1419  }  }
1420    
1421  =head3 GetList  =head3 Search
   
 C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1422    
1423  Return a list of object descriptors for the specified objects as determined by the  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
 specified filter clause.  
1424    
1425  This method is essentially the same as L</Get> except it returns a list of objects rather  Perform a full text search with filtering. The search will be against a specified object
1426  that a query object that can be used to get the results one record at a time.  in the object name list. That object will get an extra field containing the search
1427    relevance. Note that except for the search expression, the parameters of this method are
1428    the same as those for L</Get> and follow the same rules.
1429    
1430  =over 4  =over 4
1431    
1432  =over 4  =item searchExpression
1433    
1434    Boolean search expression for the text fields of the target object. The default mode for
1435    a Boolean search expression is OR, but we want the default to be AND, so we will
1436    add a C<+> operator to each word with no other operator before it.
1437    
1438    =item idx
1439    
1440    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1441    
1442  =item objectNames  =item objectNames
1443    
# Line 773  Line 1453 
1453  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
1454  be included in the list of object names.  be included in the list of object names.
1455    
1456  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.  
1457    
1458  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  Reference to a list of parameter values to be substituted into the filter clause.
1459    
1460  The rules for field references in a sort order are the same as those for field references in the  =item RETURN
1461  filter clause in general; however, odd things may happen if a sort field is from a secondary  
1462  relation.  Returns a query object for the specified search.
1463    
1464    =back
1465    
1466    =cut
1467    
1468    sub Search {
1469        # Get the parameters.
1470        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1471        # Declare the return variable.
1472        my $retVal;
1473        # Create a safety copy of the parameter list. Note we have to be careful to insure
1474        # a parameter list exists before we copy it.
1475        my @myParams = ();
1476        if (defined $params) {
1477            @myParams = @{$params};
1478        }
1479        # Get the first object's structure so we have access to the searchable fields.
1480        my $object1Name = $objectNames->[$idx];
1481        my $object1Structure = $self->_GetStructure($object1Name);
1482        # Get the field list.
1483        if (! exists $object1Structure->{searchFields}) {
1484            Confess("No searchable index for $object1Name.");
1485        } else {
1486            # Get the field list.
1487            my @fields = @{$object1Structure->{searchFields}};
1488            # Clean the search expression.
1489            my $actualKeywords = $self->CleanKeywords($searchExpression);
1490            # Prefix a "+" to each uncontrolled word. This converts the default
1491            # search mode from OR to AND.
1492            $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;
1493            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1494            # We need two match expressions, one for the filter clause and one in the
1495            # query itself. Both will use a parameter mark, so we need to push the
1496            # search expression onto the front of the parameter list twice.
1497            unshift @myParams, $actualKeywords, $actualKeywords;
1498            # Build the match expression.
1499            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1500            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1501            # Process the SQL stuff.
1502            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1503                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1504            # Create the query. Note that the match clause is inserted at the front of
1505            # the select fields.
1506            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1507                ".* $suffix";
1508            my $sth = $self->_GetStatementHandle($command, \@myParams);
1509            # Now we create the relation map, which enables DBQuery to determine the order, name
1510            # and mapped name for each object in the query.
1511            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1512            # Return the statement object.
1513            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1514        }
1515        return $retVal;
1516    }
1517    
1518    =head3 GetFlat
1519    
1520    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1521    
1522    This is a variation of L</GetAll> that asks for only a single field per record and
1523    returns a single flattened list.
1524    
1525    =over 4
1526    
1527    =item objectNames
1528    
1529    List containing the names of the entity and relationship objects to be retrieved.
1530    
1531    =item filterClause
1532    
1533    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1534    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1535    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1536    parameter list as additional parameters. The fields in a filter clause can come from primary
1537    entity relations, relationship relations, or secondary entity relations; however, all of the
1538    entities and relationships involved must be included in the list of object names.
1539    
1540    =item parameterList
1541    
1542  =item param1, param2, ..., paramN  List of the parameters to be substituted in for the parameters marks in the filter clause.
1543    
1544  Parameter values to be substituted into the filter clause.  =item field
1545    
1546    Name of the field to be used to get the elements of the list returned.
1547    
1548  =item RETURN  =item RETURN
1549    
1550  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of values.
1551    
1552  =back  =back
1553    
1554  =cut  =cut
1555  #: Return Type @%  #: Return Type @;
1556  sub GetList {  sub GetFlat {
1557      # Get the parameters.      # Get the parameters.
1558      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1559          # Declare the return variable.      # Construct the query.
1560        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1561        # Create the result list.
1562          my @retVal = ();          my @retVal = ();
1563          # Perform the query.      # Loop through the records, adding the field values found to the result list.
1564          my $query = $self->Get($objectNames, $filterClause, @params);      while (my $row = $query->Fetch()) {
1565          # Loop through the results.          push @retVal, $row->Value($field);
         while (my $object = $query->Fetch) {  
                 push @retVal, $object;  
1566          }          }
1567      # Return the result.      # Return the list created.
1568      return @retVal;      return @retVal;
1569  }  }
1570    
1571  =head3 ComputeObjectSentence  =head3 SpecialFields
1572    
1573  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my %specials = $erdb->SpecialFields($entityName); >>
1574    
1575  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return a hash mapping special fields in the specified entity to the value of their
1576    C<special> attribute. This enables the subclass to get access to the special field
1577    attributes without needed to plumb the internal ERDB data structures.
1578    
1579  =over 4  =over 4
1580    
1581  =item objectName  =item entityName
1582    
1583  Name of the entity or relationship.  Name of the entity whose special fields are desired.
1584    
1585  =item RETURN  =item RETURN
1586    
1587  Returns a string containing the entity name or a relationship sentence.  Returns a hash. The keys of the hash are the special field names, and the values
1588    are the values from each special field's C<special> attribute.
1589    
1590    =back
1591    
1592    =cut
1593    
1594    sub SpecialFields {
1595        # Get the parameters.
1596        my ($self, $entityName) = @_;
1597        # Declare the return variable.
1598        my %retVal = ();
1599        # Find the entity's data structure.
1600        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1601        # Loop through its fields, adding each special field to the return hash.
1602        my $fieldHash = $entityData->{Fields};
1603        for my $fieldName (keys %{$fieldHash}) {
1604            my $fieldData = $fieldHash->{$fieldName};
1605            if (exists $fieldData->{special}) {
1606                $retVal{$fieldName} = $fieldData->{special};
1607            }
1608        }
1609        # Return the result.
1610        return %retVal;
1611    }
1612    
1613    =head3 Delete
1614    
1615    C<< my $stats = $erdb->Delete($entityName, $objectID, $testFlag); >>
1616    
1617    Delete an entity instance from the database. The instance is deleted along with all entity and
1618    relationship instances dependent on it. The definition of I<dependence> is recursive.
1619    
1620    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1621    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1622    dependent relationship.
1623    
1624    =over 4
1625    
1626    =item entityName
1627    
1628    Name of the entity type for the instance being deleted.
1629    
1630    =item objectID
1631    
1632    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1633    then it is presumed to by a LIKE pattern.
1634    
1635    =item testFlag
1636    
1637    If TRUE, the delete statements will be traced without being executed.
1638    
1639    =item RETURN
1640    
1641    Returns a statistics object indicating how many records of each particular table were
1642    deleted.
1643    
1644    =back
1645    
1646    =cut
1647    #: Return Type $%;
1648    sub Delete {
1649        # Get the parameters.
1650        my ($self, $entityName, $objectID, $testFlag) = @_;
1651        # Declare the return variable.
1652        my $retVal = Stats->new();
1653        # Get the DBKernel object.
1654        my $db = $self->{_dbh};
1655        # We're going to generate all the paths branching out from the starting entity. One of
1656        # the things we have to be careful about is preventing loops. We'll use a hash to
1657        # determine if we've hit a loop.
1658        my %alreadyFound = ();
1659        # These next lists will serve as our result stack. We start by pushing object lists onto
1660        # the stack, and then popping them off to do the deletes. This means the deletes will
1661        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1662        # sure we don't delete records that might be needed to forge relationships back to the
1663        # original item. We have two lists-- one for TO-relationships, and one for
1664        # FROM-relationships and entities.
1665        my @fromPathList = ();
1666        my @toPathList = ();
1667        # This final hash is used to remember what work still needs to be done. We push paths
1668        # onto the list, then pop them off to extend the paths. We prime it with the starting
1669        # point. Note that we will work hard to insure that the last item on a path in the
1670        # to-do list is always an entity.
1671        my @todoList = ([$entityName]);
1672        while (@todoList) {
1673            # Get the current path.
1674            my $current = pop @todoList;
1675            # Copy it into a list.
1676            my @stackedPath = @{$current};
1677            # Pull off the last item on the path. It will always be an entity.
1678            my $entityName = pop @stackedPath;
1679            # Add it to the alreadyFound list.
1680            $alreadyFound{$entityName} = 1;
1681            # Get the entity data.
1682            my $entityData = $self->_GetStructure($entityName);
1683            # The first task is to loop through the entity's relation. A DELETE command will
1684            # be needed for each of them.
1685            my $relations = $entityData->{Relations};
1686            for my $relation (keys %{$relations}) {
1687                my @augmentedList = (@stackedPath, $relation);
1688                push @fromPathList, \@augmentedList;
1689            }
1690            # Now we need to look for relationships connected to this entity.
1691            my $relationshipList = $self->{_metaData}->{Relationships};
1692            for my $relationshipName (keys %{$relationshipList}) {
1693                my $relationship = $relationshipList->{$relationshipName};
1694                # Check the FROM field. We're only interested if it's us.
1695                if ($relationship->{from} eq $entityName) {
1696                    # Add the path to this relationship.
1697                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1698                    push @fromPathList, \@augmentedList;
1699                    # Check the arity. If it's MM we're done. If it's 1M
1700                    # and the target hasn't been seen yet, we want to
1701                    # stack the entity for future processing.
1702                    if ($relationship->{arity} eq '1M') {
1703                        my $toEntity = $relationship->{to};
1704                        if (! exists $alreadyFound{$toEntity}) {
1705                            # Here we have a new entity that's dependent on
1706                            # the current entity, so we need to stack it.
1707                            my @stackList = (@augmentedList, $toEntity);
1708                            push @fromPathList, \@stackList;
1709                        } else {
1710                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1711                        }
1712                    }
1713                }
1714                # Now check the TO field. In this case only the relationship needs
1715                # deletion.
1716                if ($relationship->{to} eq $entityName) {
1717                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1718                    push @toPathList, \@augmentedList;
1719                }
1720            }
1721        }
1722        # Create the first qualifier for the WHERE clause. This selects the
1723        # keys of the primary entity records to be deleted. When we're deleting
1724        # from a dependent table, we construct a join page from the first qualifier
1725        # to the table containing the dependent records to delete.
1726        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1727        # We need to make two passes. The first is through the to-list, and
1728        # the second through the from-list. The from-list is second because
1729        # the to-list may need to pass through some of the entities the
1730        # from-list would delete.
1731        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1732        # Now it's time to do the deletes. We do it in two passes.
1733        for my $keyName ('to_link', 'from_link') {
1734            # Get the list for this key.
1735            my @pathList = @{$stackList{$keyName}};
1736            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1737            # Loop through this list.
1738            while (my $path = pop @pathList) {
1739                # Get the table whose rows are to be deleted.
1740                my @pathTables = @{$path};
1741                # Start the DELETE statement. We need to call DBKernel because the
1742                # syntax of a DELETE-USING varies among DBMSs.
1743                my $target = $pathTables[$#pathTables];
1744                my $stmt = $db->SetUsing(@pathTables);
1745                # Now start the WHERE. The first thing is the ID field from the starting table. That
1746                # starting table will either be the entity relation or one of the entity's
1747                # sub-relations.
1748                $stmt .= " WHERE $pathTables[0].id $qualifier";
1749                # Now we run through the remaining entities in the path, connecting them up.
1750                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1751                    # Connect the current relationship to the preceding entity.
1752                    my ($entity, $rel) = @pathTables[$i-1,$i];
1753                    # The style of connection depends on the direction of the relationship.
1754                    $stmt .= " AND $entity.id = $rel.$keyName";
1755                    if ($i + 1 <= $#pathTables) {
1756                        # Here there's a next entity, so connect that to the relationship's
1757                        # to-link.
1758                        my $entity2 = $pathTables[$i+1];
1759                        $stmt .= " AND $rel.to_link = $entity2.id";
1760                    }
1761                }
1762                # Now we have our desired DELETE statement.
1763                if ($testFlag) {
1764                    # Here the user wants to trace without executing.
1765                    Trace($stmt) if T(0);
1766                } else {
1767                    # Here we can delete. Note that the SQL method dies with a confession
1768                    # if an error occurs, so we just go ahead and do it.
1769                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1770                    my $rv = $db->SQL($stmt, 0, $objectID);
1771                    # Accumulate the statistics for this delete. The only rows deleted
1772                    # are from the target table, so we use its name to record the
1773                    # statistic.
1774                    $retVal->Add($target, $rv);
1775                }
1776            }
1777        }
1778        # Return the result.
1779        return $retVal;
1780    }
1781    
1782    =head3 SortNeeded
1783    
1784    C<< my $parms = $erdb->SortNeeded($relationName); >>
1785    
1786    Return the pipe command for the sort that should be applied to the specified
1787    relation when creating the load file.
1788    
1789    For example, if the load file should be sorted ascending by the first
1790    field, this method would return
1791    
1792        sort -k1 -t"\t"
1793    
1794    If the first field is numeric, the method would return
1795    
1796        sort -k1n -t"\t"
1797    
1798    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1799    keys using a sort.
1800    
1801    =over 4
1802    
1803    =item relationName
1804    
1805    Name of the relation to be examined.
1806    
1807    =item
1808    
1809    Returns the sort command to use for sorting the relation, suitable for piping.
1810    
1811    =back
1812    
1813    =cut
1814    #: Return Type $;
1815    sub SortNeeded {
1816        # Get the parameters.
1817        my ($self, $relationName) = @_;
1818        # Declare a descriptor to hold the names of the key fields.
1819        my @keyNames = ();
1820        # Get the relation structure.
1821        my $relationData = $self->_FindRelation($relationName);
1822        # Find out if the relation is a primary entity relation,
1823        # a relationship relation, or a secondary entity relation.
1824        my $entityTable = $self->{_metaData}->{Entities};
1825        my $relationshipTable = $self->{_metaData}->{Relationships};
1826        if (exists $entityTable->{$relationName}) {
1827            # Here we have a primary entity relation.
1828            push @keyNames, "id";
1829        } elsif (exists $relationshipTable->{$relationName}) {
1830            # Here we have a relationship. We sort using the FROM index.
1831            my $relationshipData = $relationshipTable->{$relationName};
1832            my $index = $relationData->{Indexes}->{idxFrom};
1833            push @keyNames, @{$index->{IndexFields}};
1834        } else {
1835            # Here we have a secondary entity relation, so we have a sort on the ID field.
1836            push @keyNames, "id";
1837        }
1838        # Now we parse the key names into sort parameters. First, we prime the return
1839        # string.
1840        my $retVal = "sort -t\"\t\" ";
1841        # Get the relation's field list.
1842        my @fields = @{$relationData->{Fields}};
1843        # Loop through the keys.
1844        for my $keyData (@keyNames) {
1845            # Get the key and the ordering.
1846            my ($keyName, $ordering);
1847            if ($keyData =~ /^([^ ]+) DESC/) {
1848                ($keyName, $ordering) = ($1, "descending");
1849            } else {
1850                ($keyName, $ordering) = ($keyData, "ascending");
1851            }
1852            # Find the key's position and type.
1853            my $fieldSpec;
1854            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1855                my $thisField = $fields[$i];
1856                if ($thisField->{name} eq $keyName) {
1857                    # Get the sort modifier for this field type. The modifier
1858                    # decides whether we're using a character, numeric, or
1859                    # floating-point sort.
1860                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1861                    # If the index is descending for this field, denote we want
1862                    # to reverse the sort order on this field.
1863                    if ($ordering eq 'descending') {
1864                        $modifier .= "r";
1865                    }
1866                    # Store the position and modifier into the field spec, which
1867                    # will stop the inner loop. Note that the field number is
1868                    # 1-based in the sort command, so we have to increment the
1869                    # index.
1870                    $fieldSpec = ($i + 1) . $modifier;
1871                }
1872            }
1873            # Add this field to the sort command.
1874            $retVal .= " -k$fieldSpec";
1875        }
1876        # Return the result.
1877        return $retVal;
1878    }
1879    
1880    =head3 GetList
1881    
1882    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1883    
1884    Return a list of object descriptors for the specified objects as determined by the
1885    specified filter clause.
1886    
1887    This method is essentially the same as L</Get> except it returns a list of objects rather
1888    than a query object that can be used to get the results one record at a time.
1889    
1890    =over 4
1891    
1892    =item objectNames
1893    
1894    List containing the names of the entity and relationship objects to be retrieved.
1895    
1896    =item filterClause
1897    
1898    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1899    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1900    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1901    in the filter clause should be added to the parameter list as additional parameters. The
1902    fields in a filter clause can come from primary entity relations, relationship relations,
1903    or secondary entity relations; however, all of the entities and relationships involved must
1904    be included in the list of object names.
1905    
1906    The filter clause can also specify a sort order. To do this, simply follow the filter string
1907    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1908    particular genus and sorts them by species name.
1909    
1910    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1911    
1912    The rules for field references in a sort order are the same as those for field references in the
1913    filter clause in general; however, odd things may happen if a sort field is from a secondary
1914    relation.
1915    
1916    =item params
1917    
1918    Reference to a list of parameter values to be substituted into the filter clause.
1919    
1920    =item RETURN
1921    
1922    Returns a list of B<DBObject>s that satisfy the query conditions.
1923    
1924    =back
1925    
1926    =cut
1927    #: Return Type @%
1928    sub GetList {
1929        # Get the parameters.
1930        my ($self, $objectNames, $filterClause, $params) = @_;
1931        # Declare the return variable.
1932        my @retVal = ();
1933        # Perform the query.
1934        my $query = $self->Get($objectNames, $filterClause, $params);
1935        # Loop through the results.
1936        while (my $object = $query->Fetch) {
1937            push @retVal, $object;
1938        }
1939        # Return the result.
1940        return @retVal;
1941    }
1942    
1943    =head3 GetCount
1944    
1945    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1946    
1947    Return the number of rows found by a specified query. This method would
1948    normally be used to count the records in a single table. For example, in a
1949    genetics database
1950    
1951        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1952    
1953    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1954    to use it to return records based on a join. For example,
1955    
1956        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1957                                    ['homo %']);
1958    
1959    would return the number of features for genomes in the genus I<homo>. Note that
1960    only the rows from the first table are counted. If the above command were
1961    
1962        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1963                                    ['homo %']);
1964    
1965    it would return the number of genomes, not the number of genome/feature pairs.
1966    
1967    =over 4
1968    
1969    =item objectNames
1970    
1971    Reference to a list of the objects (entities and relationships) included in the
1972    query.
1973    
1974    =item filter
1975    
1976    A filter clause for restricting the query. The rules are the same as for the L</Get>
1977    method.
1978    
1979    =item params
1980    
1981    Reference to a list of the parameter values to be substituted for the parameter marks
1982    in the filter.
1983    
1984    =item RETURN
1985    
1986    Returns a count of the number of records in the first table that would satisfy
1987    the query.
1988    
1989    =back
1990    
1991    =cut
1992    
1993    sub GetCount {
1994        # Get the parameters.
1995        my ($self, $objectNames, $filter, $params) = @_;
1996        # Insure the params argument is an array reference if the caller left it off.
1997        if (! defined($params)) {
1998            $params = [];
1999        }
2000        # Declare the return variable.
2001        my $retVal;
2002        # Find out if we're counting an entity or a relationship.
2003        my $countedField;
2004        if ($self->IsEntity($objectNames->[0])) {
2005            $countedField = "id";
2006        } else {
2007            # For a relationship we count the to-link because it's usually more
2008            # numerous. Note we're automatically converting to the SQL form
2009            # of the field name (to_link vs. to-link).
2010            $countedField = "to_link";
2011        }
2012        # Create the SQL command suffix to get the desired records.
2013        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2014                                                                                $filter);
2015        # Prefix it with text telling it we want a record count.
2016        my $firstObject = $mappedNameListRef->[0];
2017        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2018        # Prepare and execute the command.
2019        my $sth = $self->_GetStatementHandle($command, $params);
2020        # Get the count value.
2021        ($retVal) = $sth->fetchrow_array();
2022        # Check for a problem.
2023        if (! defined($retVal)) {
2024            if ($sth->err) {
2025                # Here we had an SQL error.
2026                Confess("Error retrieving row count: " . $sth->errstr());
2027            } else {
2028                # Here we have no result.
2029                Confess("No result attempting to retrieve row count.");
2030            }
2031        }
2032        # Return the result.
2033        return $retVal;
2034    }
2035    
2036    =head3 ComputeObjectSentence
2037    
2038    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2039    
2040    Check an object name, and if it is a relationship convert it to a relationship sentence.
2041    
2042    =over 4
2043    
2044    =item objectName
2045    
2046    Name of the entity or relationship.
2047    
2048    =item RETURN
2049    
2050    Returns a string containing the entity name or a relationship sentence.
2051    
2052  =back  =back
2053    
# Line 847  Line 2070 
2070    
2071  =head3 DumpRelations  =head3 DumpRelations
2072    
2073  C<< $database->DumpRelations($outputDirectory); >>  C<< $erdb->DumpRelations($outputDirectory); >>
2074    
2075  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
2076  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 887  Line 2110 
2110          }          }
2111  }  }
2112    
2113    =head3 InsertValue
2114    
2115    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2116    
2117    This method will insert a new value into the database. The value must be one
2118    associated with a secondary relation, since primary values cannot be inserted:
2119    they occur exactly once. Secondary values, on the other hand, can be missing
2120    or multiply-occurring.
2121    
2122    =over 4
2123    
2124    =item entityID
2125    
2126    ID of the object that is to receive the new value.
2127    
2128    =item fieldName
2129    
2130    Field name for the new value-- this includes the entity name, since
2131    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2132    
2133    =item value
2134    
2135    New value to be put in the field.
2136    
2137    =back
2138    
2139    =cut
2140    
2141    sub InsertValue {
2142        # Get the parameters.
2143        my ($self, $entityID, $fieldName, $value) = @_;
2144        # Parse the entity name and the real field name.
2145        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2146            my $entityName = $1;
2147            my $fieldTitle = $2;
2148            # Get its descriptor.
2149            if (!$self->IsEntity($entityName)) {
2150                Confess("$entityName is not a valid entity.");
2151            } else {
2152                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2153                # Find the relation containing this field.
2154                my $fieldHash = $entityData->{Fields};
2155                if (! exists $fieldHash->{$fieldTitle}) {
2156                    Confess("$fieldTitle not found in $entityName.");
2157                } else {
2158                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2159                    if ($relation eq $entityName) {
2160                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2161                    } else {
2162                        # Now we can create an INSERT statement.
2163                        my $dbh = $self->{_dbh};
2164                        my $fixedName = _FixName($fieldTitle);
2165                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2166                        # Execute the command.
2167                        $dbh->SQL($statement, 0, $entityID, $value);
2168                    }
2169                }
2170            }
2171        } else {
2172            Confess("$fieldName is not a valid field name.");
2173        }
2174    }
2175    
2176  =head3 InsertObject  =head3 InsertObject
2177    
2178  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2179    
2180  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2181  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 898  Line 2184 
2184  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2185  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2186    
2187  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2188    
2189  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2190  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2191    
2192  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2193    
2194  =over 4  =over 4
2195    
# Line 1028  Line 2314 
2314    
2315  =head3 LoadTable  =head3 LoadTable
2316    
2317  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2318    
2319  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2320    first.
2321    
2322  =over 4  =over 4
2323    
# Line 1048  Line 2335 
2335    
2336  =item RETURN  =item RETURN
2337    
2338  Returns a statistical object containing the number of records read and a list of the error messages.  Returns a statistical object containing a list of the error messages.
2339    
2340  =back  =back
2341    
# Line 1059  Line 2346 
2346          # Create the statistical return object.          # Create the statistical return object.
2347          my $retVal = _GetLoadStats();          my $retVal = _GetLoadStats();
2348          # Trace the fact of the load.          # Trace the fact of the load.
2349          Trace("Loading table $relationName from $fileName") if T(1);      Trace("Loading table $relationName from $fileName") if T(2);
2350          # Get the database handle.          # Get the database handle.
2351          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
2352        # Get the input file size.
2353        my $fileSize = -s $fileName;
2354          # Get the relation data.          # Get the relation data.
2355          my $relation = $self->_FindRelation($relationName);          my $relation = $self->_FindRelation($relationName);
2356          # Check the truncation flag.          # Check the truncation flag.
2357          if ($truncateFlag) {          if ($truncateFlag) {
2358                  Trace("Creating table $relationName") if T(1);          Trace("Creating table $relationName") if T(2);
2359            # Compute the row count estimate. We take the size of the load file,
2360            # divide it by the estimated row size, and then multiply by 1.5 to
2361            # leave extra room. We postulate a minimum row count of 1000 to
2362            # prevent problems with incoming empty load files.
2363            my $rowSize = $self->EstimateRowSize($relationName);
2364            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2365                  # Re-create the table without its index.                  # Re-create the table without its index.
2366                  $self->CreateTable($relationName, 0);          $self->CreateTable($relationName, 0, $estimate);
2367            # If this is a pre-index DBMS, create the index here.
2368            if ($dbh->{_preIndex}) {
2369                eval {
2370                    $self->CreateIndex($relationName);
2371                };
2372                if ($@) {
2373                    $retVal->AddMessage($@);
2374                }
2375            }
2376          }          }
         # 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);  
2377      # Load the table.      # Load the table.
2378          my $rv;          my $rv;
2379          eval {          eval {
2380                  $rv = $dbh->load_table(file => $tempName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2381          };          };
2382          if (!defined $rv) {          if (!defined $rv) {
2383          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
2384          $retVal->AddMessage("Table load failed for $relationName using $tempName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2385                  Trace("Table load failed for $relationName.") if T(1);                  Trace("Table load failed for $relationName.") if T(1);
2386          } else {          } else {
2387                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we successfully loaded the table.
2388                  Trace("$retVal->{records} records read for $relationName.") if T(1);          $retVal->Add("tables");
2389            my $size = -s $fileName;
2390            Trace("$size bytes loaded into $relationName.") if T(2);
2391                  # If we're rebuilding, we need to create the table indexes.                  # If we're rebuilding, we need to create the table indexes.
2392                  if ($truncateFlag) {                  if ($truncateFlag) {
2393                # Indexes are created here for PostGres. For PostGres, indexes are
2394                # best built at the end. For MySQL, the reverse is true.
2395                if (! $dbh->{_preIndex}) {
2396                          eval {                          eval {
2397                                  $self->CreateIndex($relationName);                                  $self->CreateIndex($relationName);
2398                          };                          };
# Line 1133  Line 2400 
2400                                  $retVal->AddMessage($@);                                  $retVal->AddMessage($@);
2401                          }                          }
2402                  }                  }
2403                # The full-text index (if any) is always built last, even for MySQL.
2404                # First we need to see if this table has a full-text index. Only
2405                # primary relations are allowed that privilege.
2406                if ($self->_IsPrimary($relationName)) {
2407                    # Get the relation's entity/relationship structure.
2408                    my $structure = $self->_GetStructure($relationName);
2409                    # Check for a searchable fields list.
2410                    if (exists $structure->{searchFields}) {
2411                        # Here we know that we need to create a full-text search index.
2412                        # Get an SQL-formatted field name list.
2413                        my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2414                        # Create the index.
2415                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2416                                           flds => $fields, kind => 'fulltext');
2417                    }
2418                }
2419          }          }
2420          # Commit the database changes.      }
2421          $dbh->commit_tran;      # Analyze the table to improve performance.
2422          # Delete the temporary file.      Trace("Analyzing and compacting $relationName.") if T(3);
2423          unlink $tempName;      $dbh->vacuum_it($relationName);
2424        Trace("$relationName load completed.") if T(3);
2425          # Return the statistics.          # Return the statistics.
2426          return $retVal;          return $retVal;
2427  }  }
2428    
2429  =head3 GenerateEntity  =head3 DropRelation
2430    
2431  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< $erdb->DropRelation($relationName); >>
2432    
2433  Generate the data for a new entity instance. This method creates a field hash suitable for  Physically drop a relation from the database.
 passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  
 of the fields are generated using information in the database schema.  
   
 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.  
2434    
2435  =over 4  =over 4
2436    
2437  =item id  =item relationName
   
 ID to assign to the new entity.  
   
 =item type  
   
 Type name for the new entity.  
   
 =item values  
2438    
2439  Hash containing additional values that might be needed by the data generation methods (optional).  Name of the relation to drop. If it does not exist, this method will have
2440    no effect.
2441    
2442  =back  =back
2443    
2444  =cut  =cut
2445    
2446  sub GenerateEntity {  sub DropRelation {
2447          # Get the parameters.          # Get the parameters.
2448          my ($self, $id, $type, $values) = @_;      my ($self, $relationName) = @_;
2449          # Create the return hash.      # Get the database handle.
2450          my $this = { id => $id };      my $dbh = $self->{_dbh};
2451          # Get the metadata structure.      # Drop the relation. The method used here has no effect if the relation
2452          my $metadata = $self->{_metaData};      # does not exist.
2453          # Get this entity's list of fields.      Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2454          if (!exists $metadata->{Entities}->{$type}) {      $dbh->drop_table(tbl => $relationName);
                 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);  
         }  
         # Return the hash created.  
         return $this;  
2455  }  }
2456    
2457  =head3 GetEntity  =head3 GetEntity
2458    
2459  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2460    
2461  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
2462    
# Line 1229  Line 2483 
2483          # Get the parameters.          # Get the parameters.
2484          my ($self, $entityType, $ID) = @_;          my ($self, $entityType, $ID) = @_;
2485          # Create a query.          # Create a query.
2486          my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2487          # Get the first (and only) object.          # Get the first (and only) object.
2488          my $retVal = $query->Fetch();          my $retVal = $query->Fetch();
2489          # Return the result.          # Return the result.
2490          return $retVal;          return $retVal;
2491  }  }
2492    
2493  =head3 GetEntityValues  =head3 GetChoices
2494    
2495  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2496    
2497  Return a list of values from a specified entity instance.  Return a list of all the values for the specified field that are represented in the
2498    specified entity.
2499    
2500    Note that if the field is not indexed, then this will be a very slow operation.
2501    
2502  =over 4  =over 4
2503    
2504  =item entityType  =item entityName
2505    
2506  Entity type name.  Name of an entity in the database.
2507    
2508  =item ID  =item fieldName
2509    
2510  ID of the desired entity.  Name of a field belonging to the entity. This is a raw field name without
2511    the standard parenthesized notation used in most calls.
2512    
2513    =item RETURN
2514    
2515    Returns a list of the distinct values for the specified field in the database.
2516    
2517    =back
2518    
2519    =cut
2520    
2521    sub GetChoices {
2522        # Get the parameters.
2523        my ($self, $entityName, $fieldName) = @_;
2524        # Declare the return variable.
2525        my @retVal;
2526        # Get the entity data structure.
2527        my $entityData = $self->_GetStructure($entityName);
2528        # Get the field.
2529        my $fieldHash = $entityData->{Fields};
2530        if (! exists $fieldHash->{$fieldName}) {
2531            Confess("$fieldName not found in $entityName.");
2532        } else {
2533            # Get the name of the relation containing the field.
2534            my $relation = $fieldHash->{$fieldName}->{relation};
2535            # Fix up the field name.
2536            my $realName = _FixName($fieldName);
2537            # Get the database handle.
2538            my $dbh = $self->{_dbh};
2539            # Query the database.
2540            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2541            # Clean the results. They are stored as a list of lists, and we just want the one list.
2542            @retVal = sort map { $_->[0] } @{$results};
2543        }
2544        # Return the result.
2545        return @retVal;
2546    }
2547    
2548    =head3 GetEntityValues
2549    
2550    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2551    
2552    Return a list of values from a specified entity instance. If the entity instance
2553    does not exist, an empty list is returned.
2554    
2555    =over 4
2556    
2557    =item entityType
2558    
2559    Entity type name.
2560    
2561    =item ID
2562    
2563    ID of the desired entity.
2564    
2565  =item fields  =item fields
2566    
# Line 1279  Line 2589 
2589          return @retVal;          return @retVal;
2590  }  }
2591    
2592  =head2 Internal Utility Methods  =head3 GetAll
2593    
2594  =head3 GetLoadStats  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2595    
2596  Return a blank statistics object for use by the load methods.  Return a list of values taken from the objects returned by a query. The first three
2597    parameters correspond to the parameters of the L</Get> method. The final parameter is
2598    a list of the fields desired from each record found by the query. The field name
2599    syntax is the standard syntax used for fields in the B<ERDB> system--
2600    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2601    or relationship and I<fieldName> is the name of the field.
2602    
2603    The list returned will be a list of lists. Each element of the list will contain
2604    the values returned for the fields specified in the fourth parameter. If one of the
2605    fields specified returns multiple values, they are flattened in with the rest. For
2606    example, the following call will return a list of the features in a particular
2607    spreadsheet cell, and each feature will be represented by a list containing the
2608    feature ID followed by all of its aliases.
2609    
2610  This is a static method.  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2611    
2612    =over 4
2613    
2614    =item objectNames
2615    
2616    List containing the names of the entity and relationship objects to be retrieved.
2617    
2618    =item filterClause
2619    
2620    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2621    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2622    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2623    parameter list as additional parameters. The fields in a filter clause can come from primary
2624    entity relations, relationship relations, or secondary entity relations; however, all of the
2625    entities and relationships involved must be included in the list of object names.
2626    
2627    =item parameterList
2628    
2629    List of the parameters to be substituted in for the parameters marks in the filter clause.
2630    
2631    =item fields
2632    
2633    List of the fields to be returned in each element of the list returned.
2634    
2635    =item count
2636    
2637    Maximum number of records to return. If omitted or 0, all available records will be returned.
2638    
2639    =item RETURN
2640    
2641    Returns a list of list references. Each element of the return list contains the values for the
2642    fields specified in the B<fields> parameter.
2643    
2644    =back
2645    
2646    =cut
2647    #: Return Type @@;
2648    sub GetAll {
2649        # Get the parameters.
2650        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2651        # Translate the parameters from a list reference to a list. If the parameter
2652        # list is a scalar we convert it into a singleton list.
2653        my @parmList = ();
2654        if (ref $parameterList eq "ARRAY") {
2655            Trace("GetAll parm list is an array.") if T(4);
2656            @parmList = @{$parameterList};
2657        } else {
2658            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2659            push @parmList, $parameterList;
2660        }
2661        # Insure the counter has a value.
2662        if (!defined $count) {
2663            $count = 0;
2664        }
2665        # Add the row limit to the filter clause.
2666        if ($count > 0) {
2667            $filterClause .= " LIMIT $count";
2668        }
2669        # Create the query.
2670        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2671        # Set up a counter of the number of records read.
2672        my $fetched = 0;
2673        # Loop through the records returned, extracting the fields. Note that if the
2674        # counter is non-zero, we stop when the number of records read hits the count.
2675        my @retVal = ();
2676        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2677            my @rowData = $row->Values($fields);
2678            push @retVal, \@rowData;
2679            $fetched++;
2680        }
2681        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2682        # Return the resulting list.
2683        return @retVal;
2684    }
2685    
2686    =head3 Exists
2687    
2688    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2689    
2690    Return TRUE if an entity exists, else FALSE.
2691    
2692    =over 4
2693    
2694    =item entityName
2695    
2696    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2697    
2698    =item entityID
2699    
2700    ID of the entity instance whose existence is to be checked.
2701    
2702    =item RETURN
2703    
2704    Returns TRUE if the entity instance exists, else FALSE.
2705    
2706    =back
2707    
2708  =cut  =cut
2709    #: Return Type $;
2710    sub Exists {
2711        # Get the parameters.
2712        my ($self, $entityName, $entityID) = @_;
2713        # Check for the entity instance.
2714        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2715        my $testInstance = $self->GetEntity($entityName, $entityID);
2716        # Return an existence indicator.
2717        my $retVal = ($testInstance ? 1 : 0);
2718        return $retVal;
2719    }
2720    
2721  sub _GetLoadStats {  =head3 EstimateRowSize
2722          return Stats->new('records');  
2723    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2724    
2725    Estimate the row size of the specified relation. The estimated row size is computed by adding
2726    up the average length for each data type.
2727    
2728    =over 4
2729    
2730    =item relName
2731    
2732    Name of the relation whose estimated row size is desired.
2733    
2734    =item RETURN
2735    
2736    Returns an estimate of the row size for the specified relation.
2737    
2738    =back
2739    
2740    =cut
2741    #: Return Type $;
2742    sub EstimateRowSize {
2743        # Get the parameters.
2744        my ($self, $relName) = @_;
2745        # Declare the return variable.
2746        my $retVal = 0;
2747        # Find the relation descriptor.
2748        my $relation = $self->_FindRelation($relName);
2749        # Get the list of fields.
2750        for my $fieldData (@{$relation->{Fields}}) {
2751            # Get the field type and add its length.
2752            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2753            $retVal += $fieldLen;
2754        }
2755        # Return the result.
2756        return $retVal;
2757  }  }
2758    
2759  =head3 GenerateFields  =head3 GetFieldTable
2760    
2761  Generate field values from a field structure and store in a specified table. The field names  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
 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.  
2762    
2763  This is a static method.  Get the field structure for a specified entity or relationship.
2764    
2765  =over 4  =over 4
2766    
2767  =item this  =item objectName
2768    
2769  Hash table into which the field values should be placed.  Name of the desired entity or relationship.
2770    
2771  =item fields  =item RETURN
2772    
2773  Field structure from which the field descriptors should be taken.  The table containing the field descriptors for the specified object.
2774    
2775  =item type  =back
2776    
2777    =cut
2778    
2779    sub GetFieldTable {
2780        # Get the parameters.
2781        my ($self, $objectName) = @_;
2782        # Get the descriptor from the metadata.
2783        my $objectData = $self->_GetStructure($objectName);
2784        # Return the object's field table.
2785        return $objectData->{Fields};
2786    }
2787    
2788    =head3 SplitKeywords
2789    
2790    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2791    
2792    This method returns a list of the positive keywords in the specified
2793    keyword string. All of the operators will have been stripped off,
2794    and if the keyword is preceded by a minus operator (C<->), it will
2795    not be in the list returned. The idea here is to get a list of the
2796    keywords the user wants to see. The list will be processed to remove
2797    duplicates.
2798    
2799    It is possible to create a string that confuses this method. For example
2800    
2801        frog toad -frog
2802    
2803    would return both C<frog> and C<toad>. If this is a problem we can deal
2804    with it later.
2805    
2806    =over 4
2807    
2808    =item keywordString
2809    
2810    The keyword string to be parsed.
2811    
2812    =item RETURN
2813    
2814    Returns a list of the words in the keyword string the user wants to
2815    see.
2816    
2817    =back
2818    
2819    =cut
2820    
2821    sub SplitKeywords {
2822        # Get the parameters.
2823        my ($keywordString) = @_;
2824        # Make a safety copy of the string. (This helps during debugging.)
2825        my $workString = $keywordString;
2826        # Convert operators we don't care about to spaces.
2827        $workString =~ tr/+"()<>/ /;
2828        # Split the rest of the string along space boundaries. Note that we
2829        # eliminate any words that are zero length or begin with a minus sign.
2830        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2831        # Use a hash to remove duplicates.
2832        my %words = map { $_ => 1 } @wordList;
2833        # Return the result.
2834        return sort keys %words;
2835    }
2836    
2837    =head3 ValidateFieldName
2838    
2839    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2840    
2841    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2842    be hyphenated words subject to certain restrictions.
2843    
2844    =over 4
2845    
2846    =item fieldName
2847    
2848    Field name to be validated.
2849    
2850    =item RETURN
2851    
2852    Returns TRUE if the field name is valid, else FALSE.
2853    
2854    =back
2855    
2856    =cut
2857    
2858    sub ValidateFieldName {
2859        # Get the parameters.
2860        my ($fieldName) = @_;
2861        # Declare the return variable. The field name is valid until we hear
2862        # differently.
2863        my $retVal = 1;
2864        # Look for bad stuff in the name.
2865        if ($fieldName =~ /--/) {
2866            # Here we have a doubled minus sign.
2867            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2868            $retVal = 0;
2869        } elsif ($fieldName !~ /^[A-Za-z]/) {
2870            # Here the field name is missing the initial letter.
2871            Trace("Field name $fieldName does not begin with a letter.") if T(1);
2872            $retVal = 0;
2873        } else {
2874            # Strip out the minus signs. Everything remaining must be a letter,
2875            # underscore, or digit.
2876            my $strippedName = $fieldName;
2877            $strippedName =~ s/-//g;
2878            if ($strippedName !~ /^(\w|\d)+$/) {
2879                Trace("Field name $fieldName contains illegal characters.") if T(1);
2880                $retVal = 0;
2881            }
2882        }
2883        # Return the result.
2884        return $retVal;
2885    }
2886    
2887    =head3 ReadMetaXML
2888    
2889    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2890    
2891    This method reads a raw database definition XML file and returns it.
2892    Normally, the metadata used by the ERDB system has been processed and
2893    modified to make it easier to load and retrieve the data; however,
2894    this method can be used to get the data in its raw form.
2895    
2896    =over 4
2897    
2898    =item fileName
2899    
2900    Name of the XML file to read.
2901    
2902    =item RETURN
2903    
2904    Returns a hash reference containing the raw XML data from the specified file.
2905    
2906    =back
2907    
2908    =cut
2909    
2910    sub ReadMetaXML {
2911        # Get the parameters.
2912        my ($fileName) = @_;
2913        # Read the XML.
2914        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2915        Trace("XML metadata loaded from file $fileName.") if T(1);
2916        # Return the result.
2917        return $retVal;
2918    }
2919    
2920    =head3 GetEntityFieldHash
2921    
2922    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2923    
2924    Get the field hash of the named entity in the specified raw XML structure.
2925    The field hash may not exist, in which case we need to create it.
2926    
2927    =over 4
2928    
2929    =item structure
2930    
2931    Raw XML structure defininng the database. This is not the run-time XML used by
2932    an ERDB object, since that has all sorts of optimizations built-in.
2933    
2934    =item entityName
2935    
2936    Name of the entity whose field structure is desired.
2937    
2938    =item RETURN
2939    
2940    Returns the field hash used to define the entity's fields.
2941    
2942    =back
2943    
2944    =cut
2945    
2946    sub GetEntityFieldHash {
2947        # Get the parameters.
2948        my ($structure, $entityName) = @_;
2949        # Get the entity structure.
2950        my $entityData = $structure->{Entities}->{$entityName};
2951        # Look for a field structure.
2952        my $retVal = $entityData->{Fields};
2953        # If it doesn't exist, create it.
2954        if (! defined($retVal)) {
2955            $entityData->{Fields} = {};
2956            $retVal = $entityData->{Fields};
2957        }
2958        # Return the result.
2959        return $retVal;
2960    }
2961    
2962    =head3 WriteMetaXML
2963    
2964    C<< ERDB::WriteMetaXML($structure, $fileName); >>
2965    
2966    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2967    used to update the database definition. It must be used with care, however, since it
2968    will only work on a raw structure, not on the processed structure created by an ERDB
2969    constructor.
2970    
2971    =over 4
2972    
2973    =item structure
2974    
2975    XML structure to be written to the file.
2976    
2977    =item fileName
2978    
2979    Name of the output file to which the updated XML should be stored.
2980    
2981    =back
2982    
2983    =cut
2984    
2985    sub WriteMetaXML {
2986        # Get the parameters.
2987        my ($structure, $fileName) = @_;
2988        # Compute the output.
2989        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2990        # Write it to the file.
2991        my $xmlOut = Open(undef, ">$fileName");
2992        print $xmlOut $fileString;
2993    }
2994    
2995    
2996    =head3 HTMLNote
2997    
2998    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2999    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3000    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3001    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3002    
3003    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3004    
3005    =over 4
3006    
3007    =item dataString
3008    
3009    String to convert to HTML.
3010    
3011  Type name of the object whose fields are being generated.  =item RETURN
3012    
3013    An HTML string derived from the input string.
3014    
3015    =back
3016    
3017    =cut
3018    
3019    sub HTMLNote {
3020        # Get the parameter.
3021        my ($dataString) = @_;
3022        # HTML-escape the text.
3023        my $retVal = CGI::escapeHTML($dataString);
3024        # Substitute the bulletin board codes.
3025        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3026        $retVal =~ s!\[p\]!</p><p>!g;
3027        # Return the result.
3028        return $retVal;
3029    }
3030    
3031    
3032    =head2 Data Mining Methods
3033    
3034    =head3 GetUsefulCrossValues
3035    
3036    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3037    
3038    Return a list of the useful attributes that would be returned by a B<Cross> call
3039    from an entity of the source entity type through the specified relationship. This
3040    means it will return the fields of the target entity type and the intersection data
3041    fields in the relationship. Only primary table fields are returned. In other words,
3042    the field names returned will be for fields where there is always one and only one
3043    value.
3044    
3045    =over 4
3046    
3047    =item sourceEntity
3048    
3049    Name of the entity from which the relationship crossing will start.
3050    
3051    =item relationship
3052    
3053    Name of the relationship being crossed.
3054    
3055    =item RETURN
3056    
3057    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3058    
3059    =back
3060    
3061    =cut
3062    #: Return Type @;
3063    sub GetUsefulCrossValues {
3064        # Get the parameters.
3065        my ($self, $sourceEntity, $relationship) = @_;
3066        # Declare the return variable.
3067        my @retVal = ();
3068        # Determine the target entity for the relationship. This is whichever entity is not
3069        # the source entity. So, if the source entity is the FROM, we'll get the name of
3070        # the TO, and vice versa.
3071        my $relStructure = $self->_GetStructure($relationship);
3072        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3073        my $targetEntity = $relStructure->{$targetEntityType};
3074        # Get the field table for the entity.
3075        my $entityFields = $self->GetFieldTable($targetEntity);
3076        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3077        # For the entity fields, the key aspect of the target structure is that the {relation} value
3078        # must match the entity name.
3079        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3080                            keys %{$entityFields};
3081        # Push the fields found onto the return variable.
3082        push @retVal, sort @fieldList;
3083        # Get the field table for the relationship.
3084        my $relationshipFields = $self->GetFieldTable($relationship);
3085        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3086        # This may end up being an empty set.
3087        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3088                            keys %{$relationshipFields};
3089        # Push these onto the return list.
3090        push @retVal, sort @fieldList2;
3091        # Return the result.
3092        return @retVal;
3093    }
3094    
3095    =head3 FindColumn
3096    
3097    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3098    
3099    Return the location a desired column in a data mining header line. The data
3100    mining header line is a tab-separated list of column names. The column
3101    identifier is either the numerical index of a column or the actual column
3102    name.
3103    
3104    =over 4
3105    
3106    =item headerLine
3107    
3108    The header line from a data mining command, which consists of a tab-separated
3109    list of column names.
3110    
3111    =item columnIdentifier
3112    
3113    Either the ordinal number of the desired column (1-based), or the name of the
3114    desired column.
3115    
3116    =item RETURN
3117    
3118    Returns the array index (0-based) of the desired column.
3119    
3120    =back
3121    
3122    =cut
3123    
3124    sub FindColumn {
3125        # Get the parameters.
3126        my ($headerLine, $columnIdentifier) = @_;
3127        # Declare the return variable.
3128        my $retVal;
3129        # Split the header line into column names.
3130        my @headers = ParseColumns($headerLine);
3131        # Determine whether we have a number or a name.
3132        if ($columnIdentifier =~ /^\d+$/) {
3133            # Here we have a number. Subtract 1 and validate the result.
3134            $retVal = $columnIdentifier - 1;
3135            if ($retVal < 0 || $retVal > $#headers) {
3136                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3137            }
3138        } else {
3139            # Here we have a name. We need to find it in the list.
3140            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3141                if ($headers[$i] eq $columnIdentifier) {
3142                    $retVal = $i;
3143                }
3144            }
3145            if (! defined($retVal)) {
3146                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3147            }
3148        }
3149        # Return the result.
3150        return $retVal;
3151    }
3152    
3153    =head3 ParseColumns
3154    
3155    C<< my @columns = ERDB::ParseColumns($line); >>
3156    
3157    Convert the specified data line to a list of columns.
3158    
3159    =over 4
3160    
3161    =item line
3162    
3163    A data mining input, consisting of a tab-separated list of columns terminated by a
3164    new-line.
3165    
3166    =item RETURN
3167    
3168    Returns a list consisting of the column values.
3169    
3170    =back
3171    
3172    =cut
3173    
3174    sub ParseColumns {
3175        # Get the parameters.
3176        my ($line) = @_;
3177        # Chop off the line-end.
3178        chomp $line;
3179        # Split it into a list.
3180        my @retVal = split(/\t/, $line);
3181        # Return the result.
3182        return @retVal;
3183    }
3184    
3185    =head2 Virtual Methods
3186    
3187    =head3 CleanKeywords
3188    
3189  =item values (optional)  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3190    
3191  Reference to a value structure from which additional values can be taken.  Clean up a search expression or keyword list. This is a virtual method that may
3192    be overridden by the subclass. The base-class method removes extra spaces
3193    and converts everything to lower case.
3194    
3195  =item from (optiona)  =over 4
3196    
3197    =item searchExpression
3198    
3199  Reference to the source entity instance if relationship data is being generated.  Search expression or keyword list to clean. Note that a search expression may
3200    contain boolean operators which need to be preserved. This includes leading
3201    minus signs.
3202    
3203  =item to (optional)  =item RETURN
3204    
3205  Reference to the target entity instance if relationship data is being generated.  Cleaned expression or keyword list.
3206    
3207  =back  =back
3208    
3209  =cut  =cut
3210    
3211  sub _GenerateFields {  sub CleanKeywords {
3212          # Get the parameters.          # Get the parameters.
3213          my ($this, $fields, $type, $values, $from, $to) = @_;      my ($self, $searchExpression) = @_;
3214          # Sort the field names by pass number.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3215          my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};      # don't accidentally end up with an undefined value.
3216          # Loop through the field names, generating data.      my $retVal = lc($searchExpression || "");
3217          for my $name (@fieldNames) {      # Remove extra spaces.
3218                  # Only proceed if this field needs to be generated.      $retVal =~ s/\s+/ /g;
3219                  if (!exists $this->{$name}) {      $retVal =~ s/(^\s+)|(\s+$)//g;
3220                          # Get this field's data generation descriptor.      # Return the result.
3221                          my $fieldDescriptor = $fields->{$name};      return $retVal;
3222                          my $data = $fieldDescriptor->{DataGen};  }
3223                          # Get the code to generate the field value.  
3224                          my $codeString = $data->{content};  =head3 GetSourceObject
3225                          # Determine whether or not this field is in the primary relation.  
3226                          if ($fieldDescriptor->{relation} eq $type) {  C<< my $source = $erdb->GetSourceObject($entityName); >>
3227                                  # Here we have a primary relation field. Store the field value as  
3228                                  # a scalar.  Return the object to be used in loading special attributes of the specified entity. The
3229                                  $this->{$name} = eval($codeString);  algorithm for loading special attributes is stored in the C<DataGen> elements of the
3230    XML
3231    
3232    =head2 Internal Utility Methods
3233    
3234    =head3 _RelationMap
3235    
3236    C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3237    
3238    Create the relation map for an SQL query. The relation map is used by B<DBObject>
3239    to determine how to interpret the results of the query.
3240    
3241    =over 4
3242    
3243    =item mappedNameHashRef
3244    
3245    Reference to a hash that maps modified object names to real object names.
3246    
3247    =item mappedNameListRef
3248    
3249    Reference to a list of modified object names in the order they appear in the
3250    SELECT list.
3251    
3252    =item RETURN
3253    
3254    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3255    query followed by the actual name of that object. This enables the B<DBObject> to
3256    determine the order of the tables in the query and which object name belongs to each
3257    mapped object name. Most of the time these two values are the same; however, if a
3258    relation occurs twice in the query, the relation name in the field list and WHERE
3259    clause will use a mapped name (generally the actual relation name with a numeric
3260    suffix) that does not match the actual relation name.
3261    
3262    =back
3263    
3264    =cut
3265    
3266    sub _RelationMap {
3267        # Get the parameters.
3268        my ($mappedNameHashRef, $mappedNameListRef) = @_;
3269        # Declare the return variable.
3270        my @retVal = ();
3271        # Build the map.
3272        for my $mappedName (@{$mappedNameListRef}) {
3273            push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3274        }
3275        # Return it.
3276        return @retVal;
3277    }
3278    
3279    
3280    =head3 _SetupSQL
3281    
3282    Process a list of object names and a filter clause so that they can be used to
3283    build an SQL statement. This method takes in a reference to a list of object names
3284    and a filter clause. It will return a corrected filter clause, a list of mapped
3285    names and the mapped name hash.
3286    
3287    This is an instance method.
3288    
3289    =over 4
3290    
3291    =item objectNames
3292    
3293    Reference to a list of the object names to be included in the query.
3294    
3295    =item filterClause
3296    
3297    A string containing the WHERE clause for the query (without the C<WHERE>) and also
3298    optionally the C<ORDER BY> and C<LIMIT> clauses.
3299    
3300    =item matchClause
3301    
3302    An optional full-text search clause. If specified, it will be inserted at the
3303    front of the WHERE clause. It should already be SQL-formatted; that is, the
3304    field names should be in the form I<table>C<.>I<fieldName>.
3305    
3306    =item RETURN
3307    
3308    Returns a three-element list. The first element is the SQL statement suffix, beginning
3309    with the FROM clause. The second element is a reference to a list of the names to be
3310    used in retrieving the fields. The third element is a hash mapping the names to the
3311    objects they represent.
3312    
3313    =back
3314    
3315    =cut
3316    
3317    sub _SetupSQL {
3318        my ($self, $objectNames, $filterClause, $matchClause) = @_;
3319        # Adjust the list of object names to account for multiple occurrences of the
3320        # same object. We start with a hash table keyed on object name that will
3321        # return the object suffix. The first time an object is encountered it will
3322        # not be found in the hash. The next time the hash will map the object name
3323        # to 2, then 3, and so forth.
3324        my %objectHash = ();
3325        # This list will contain the object names as they are to appear in the
3326        # FROM list.
3327        my @fromList = ();
3328        # This list contains the suffixed object name for each object. It is exactly
3329        # parallel to the list in the $objectNames parameter.
3330        my @mappedNameList = ();
3331        # Finally, this hash translates from a mapped name to its original object name.
3332        my %mappedNameHash = ();
3333        # Now we create the lists. Note that for every single name we push something into
3334        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3335        # parallel to $objectNames.
3336        for my $objectName (@{$objectNames}) {
3337            # Get the next suffix for this object.
3338            my $suffix = $objectHash{$objectName};
3339            if (! $suffix) {
3340                # Here we are seeing the object for the first time. The object name
3341                # is used as is.
3342                push @mappedNameList, $objectName;
3343                push @fromList, $objectName;
3344                $mappedNameHash{$objectName} = $objectName;
3345                # Denote the next suffix will be 2.
3346                $objectHash{$objectName} = 2;
3347            } else {
3348                # Here we've seen the object before. We construct a new name using
3349                # the suffix from the hash and update the hash.
3350                my $mappedName = "$objectName$suffix";
3351                $objectHash{$objectName} = $suffix + 1;
3352                # The FROM list has the object name followed by the mapped name. This
3353                # tells SQL it's still the same table, but we're using a different name
3354                # for it to avoid confusion.
3355                push @fromList, "$objectName $mappedName";
3356                # The mapped-name list contains the real mapped name.
3357                push @mappedNameList, $mappedName;
3358                # Finally, enable us to get back from the mapped name to the object name.
3359                $mappedNameHash{$mappedName} = $objectName;
3360            }
3361        }
3362        # Begin the SELECT suffix. It starts with
3363        #
3364        # FROM name1, name2, ... nameN
3365        #
3366        my $suffix = "FROM " . join(', ', @fromList);
3367        # Now for the WHERE. First, we need a place for the filter string.
3368        my $filterString = "";
3369        # We will also keep a list of conditions to add to the WHERE clause in order to link
3370        # entities and relationships as well as primary relations to secondary ones.
3371        my @joinWhere = ();
3372        # Check for a filter clause.
3373        if ($filterClause) {
3374            # Here we have one, so we convert its field names and add it to the query. First,
3375            # We create a copy of the filter string we can work with.
3376            $filterString = $filterClause;
3377            # Next, we sort the object names by length. This helps protect us from finding
3378            # object names inside other object names when we're doing our search and replace.
3379            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3380            # The final preparatory step is to create a hash table of relation names. The
3381            # table begins with the relation names already in the SELECT command. We may
3382            # need to add relations later if there is filtering on a field in a secondary
3383            # relation. The secondary relations are the ones that contain multiply-
3384            # occurring or optional fields.
3385            my %fromNames = map { $_ => 1 } @sortedNames;
3386            # We are ready to begin. We loop through the object names, replacing each
3387            # object name's field references by the corresponding SQL field reference.
3388            # Along the way, if we find a secondary relation, we will need to add it
3389            # to the FROM clause.
3390            for my $mappedName (@sortedNames) {
3391                # Get the length of the object name plus 2. This is the value we add to the
3392                # size of the field name to determine the size of the field reference as a
3393                # whole.
3394                my $nameLength = 2 + length $mappedName;
3395                # Get the real object name for this mapped name.
3396                my $objectName = $mappedNameHash{$mappedName};
3397                Trace("Processing $mappedName for object $objectName.") if T(4);
3398                # Get the object's field list.
3399                my $fieldList = $self->GetFieldTable($objectName);
3400                # Find the field references for this object.
3401                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3402                    # At this point, $1 contains the field name, and the current position
3403                    # is set immediately after the final parenthesis. We pull out the name of
3404                    # the field and the position and length of the field reference as a whole.
3405                    my $fieldName = $1;
3406                    my $len = $nameLength + length $fieldName;
3407                    my $pos = pos($filterString) - $len;
3408                    # Insure the field exists.
3409                    if (!exists $fieldList->{$fieldName}) {
3410                        Confess("Field $fieldName not found for object $objectName.");
3411                    } else {
3412                        Trace("Processing $fieldName at position $pos.") if T(4);
3413                        # Get the field's relation.
3414                        my $relationName = $fieldList->{$fieldName}->{relation};
3415                        # Now we have a secondary relation. We need to insure it matches the
3416                        # mapped name of the primary relation. First we peel off the suffix
3417                        # from the mapped name.
3418                        my $mappingSuffix = substr $mappedName, length($objectName);
3419                        # Put the mapping suffix onto the relation name to get the
3420                        # mapped relation name.
3421                        my $mappedRelationName = "$relationName$mappingSuffix";
3422                        # Insure the relation is in the FROM clause.
3423                        if (!exists $fromNames{$mappedRelationName}) {
3424                            # Add the relation to the FROM clause.
3425                            if ($mappedRelationName eq $relationName) {
3426                                # The name is un-mapped, so we add it without
3427                                # any frills.
3428                                $suffix .= ", $relationName";
3429                                push @joinWhere, "$objectName.id = $relationName.id";
3430                            } else {
3431                                # Here we have a mapping situation.
3432                                $suffix .= ", $relationName $mappedRelationName";
3433                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3434                            }
3435                            # Denote we have this relation available for future fields.
3436                            $fromNames{$mappedRelationName} = 1;
3437                        }
3438                        # Form an SQL field reference from the relation name and the field name.
3439                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3440                        # Put it into the filter string in place of the old value.
3441                        substr($filterString, $pos, $len) = $sqlReference;
3442                        # Reposition the search.
3443                        pos $filterString = $pos + length $sqlReference;
3444                    }
3445                }
3446            }
3447        }
3448        # The next step is to join the objects together. We only need to do this if there
3449        # is more than one object in the object list. We start with the first object and
3450        # run through the objects after it. Note also that we make a safety copy of the
3451        # list before running through it, because we shift off the first object before
3452        # processing the rest.
3453        my @mappedObjectList = @mappedNameList;
3454        my $lastMappedObject = shift @mappedObjectList;
3455        # Get the join table.
3456        my $joinTable = $self->{_metaData}->{Joins};
3457        # Loop through the object list.
3458        for my $thisMappedObject (@mappedObjectList) {
3459            # Look for a join using the real object names.
3460            my $lastObject = $mappedNameHash{$lastMappedObject};
3461            my $thisObject = $mappedNameHash{$thisMappedObject};
3462            my $joinKey = "$lastObject/$thisObject";
3463            if (!exists $joinTable->{$joinKey}) {
3464                # Here there's no join, so we throw an error.
3465                Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3466                          } else {                          } else {
3467                                  # Here we have a secondary relation field. Create a null list              # Get the join clause.
3468                                  # and push the desired number of field values onto it.              my $unMappedJoin = $joinTable->{$joinKey};
3469                                  my @fieldValues = ();              # Fix the names.
3470                                  my $count = IntGen(0,$data->{testCount});              $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3471                                  for (my $i = 0; $i < $count; $i++) {              $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3472                                          my $newValue = eval($codeString);              push @joinWhere, $unMappedJoin;
3473                                          push @fieldValues, $newValue;              # Save this object as the last object for the next iteration.
3474                $lastMappedObject = $thisMappedObject;
3475            }
3476        }
3477        # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3478        # here is we want the filter clause to be empty if there's no WHERE filter.
3479        # We'll put the ORDER BY / LIMIT clauses in the following variable.
3480        my $orderClause = "";
3481        # This is only necessary if we have a filter string in which the ORDER BY
3482        # and LIMIT clauses can live.
3483        if ($filterString) {
3484            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3485            # operator so that we find the first occurrence of either verb.
3486            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3487                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3488                my $pos = pos $filterString;
3489                $orderClause = $2 . substr($filterString, $pos);
3490                $filterString = $1;
3491                                  }                                  }
                                 # Store the value list in the main hash.  
                                 $this->{$name} = \@fieldValues;  
3492                          }                          }
3493        # All the things that are supposed to be in the WHERE clause of the
3494        # SELECT command need to be put into @joinWhere so we can string them
3495        # together. We begin with the match clause. This is important,
3496        # because the match clause's parameter mark must precede any parameter
3497        # marks in the filter string.
3498        if ($matchClause) {
3499            push @joinWhere, $matchClause;
3500                  }                  }
3501        # Add the filter string. We put it in parentheses to avoid operator
3502        # precedence problems with the match clause or the joins.
3503        if ($filterString) {
3504            Trace("Filter string is \"$filterString\".") if T(4);
3505            push @joinWhere, "($filterString)";
3506        }
3507        # String it all together into a big filter clause.
3508        if (@joinWhere) {
3509            $suffix .= " WHERE " . join(' AND ', @joinWhere);
3510          }          }
3511        # Add the sort or limit clause (if any).
3512        if ($orderClause) {
3513            $suffix .= " $orderClause";
3514        }
3515        # Return the suffix, the mapped name list, and the mapped name hash.
3516        return ($suffix, \@mappedNameList, \%mappedNameHash);
3517    }
3518    
3519    =head3 _GetStatementHandle
3520    
3521    This method will prepare and execute an SQL query, returning the statement handle.
3522    The main reason for doing this here is so that everybody who does SQL queries gets
3523    the benefit of tracing.
3524    
3525    This is an instance method.
3526    
3527    =over 4
3528    
3529    =item command
3530    
3531    Command to prepare and execute.
3532    
3533    =item params
3534    
3535    Reference to a list of the values to be substituted in for the parameter marks.
3536    
3537    =item RETURN
3538    
3539    Returns a prepared and executed statement handle from which the caller can extract
3540    results.
3541    
3542    =back
3543    
3544    =cut
3545    
3546    sub _GetStatementHandle {
3547        # Get the parameters.
3548        my ($self, $command, $params) = @_;
3549        # Trace the query.
3550        Trace("SQL query: $command") if T(SQL => 3);
3551        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3552        # Get the database handle.
3553        my $dbh = $self->{_dbh};
3554        # Prepare the command.
3555        my $sth = $dbh->prepare_command($command);
3556        # Execute it with the parameters bound in.
3557        $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
3558        # Return the statement handle.
3559        return $sth;
3560    }
3561    
3562    =head3 _GetLoadStats
3563    
3564    Return a blank statistics object for use by the load methods.
3565    
3566    This is a static method.
3567    
3568    =cut
3569    
3570    sub _GetLoadStats{
3571        return Stats->new();
3572  }  }
3573    
3574  =head3 DumpRelation  =head3 _DumpRelation
3575    
3576  Dump the specified relation's to the specified output file in tab-delimited format.  Dump the specified relation to the specified output file in tab-delimited format.
3577    
3578  This is an instance method.  This is an instance method.
3579    
# Line 1417  Line 3621 
3621          close DTXOUT;          close DTXOUT;
3622  }  }
3623    
3624  =head3 GetStructure  =head3 _GetStructure
3625    
3626  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
3627    
# Line 1456  Line 3660 
3660          return $retVal;          return $retVal;
3661  }  }
3662    
3663  =head3 GetRelationTable  
3664    
3665    =head3 _GetRelationTable
3666    
3667  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
3668    
# Line 1485  Line 3691 
3691          return $objectData->{Relations};          return $objectData->{Relations};
3692  }  }
3693    
3694  =head3 GetFieldTable  =head3 _ValidateFieldNames
   
 Get the field structure for a specified entity or relationship.  
   
 This is an instance method.  
   
 =over 4  
   
 =item objectName  
   
 Name of the desired entity or relationship.  
   
 =item RETURN  
   
 The table containing the field descriptors for the specified object.  
   
 =back  
   
 =cut  
   
 sub _GetFieldTable {  
         # Get the parameters.  
         my ($self, $objectName) = @_;  
         # Get the descriptor from the metadata.  
         my $objectData = $self->_GetStructure($objectName);  
         # Return the object's field table.  
         return $objectData->{Fields};  
 }  
   
 =head3 ValidateFieldNames  
3695    
3696  Determine whether or not the field names are valid. A description of the problems with the names  Determine whether or not the field names are valid. A description of the problems with the names
3697  will be written to the standard error output. If there is an error, this method will abort. This is  will be written to the standard error output. If there is an error, this method will abort. This is
# Line 1541  Line 3718 
3718                  for my $object (values %{$metadata->{$section}}) {                  for my $object (values %{$metadata->{$section}}) {
3719                          # Loop through the object's fields.                          # Loop through the object's fields.
3720                          for my $fieldName (keys %{$object->{Fields}}) {                          for my $fieldName (keys %{$object->{Fields}}) {
3721                                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
3722                                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
3723                                          # Here we have a doubled minus sign.                  if (! ValidateFieldName($fieldName)) {
                                         print STDERR "Field name $fieldName has a doubled hyphen.\n";  
                                         $retVal = 0;  
                                 } elsif ($fieldName !~ /^[A-Za-z]/) {  
                                         # Here the field name is missing the initial letter.  
                                         print STDERR "Field name $fieldName does not begin with a letter.\n";  
                                         $retVal = 0;  
                                 } else {  
                                         # Strip out the minus signs. Everything remaining must be a letter  
                                         # or digit.  
                                         my $strippedName = $fieldName;  
                                         $strippedName =~ s/-//g;  
                                         if ($strippedName !~ /^[A-Za-z0-9]+$/) {  
                                                 print STDERR "Field name $fieldName contains illegal characters.\n";  
3724                                                  $retVal = 0;                                                  $retVal = 0;
3725                                          }                                          }
3726                                  }                                  }
3727                          }                          }
3728                  }                  }
         }  
3729          # If an error was found, fail.          # If an error was found, fail.
3730          if ($retVal  == 0) {          if ($retVal  == 0) {
3731                  Confess("Errors found in field names.");                  Confess("Errors found in field names.");
3732          }          }
3733  }  }
3734    
3735  =head3 LoadRelation  =head3 _LoadRelation
3736    
3737  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
3738  file with the same name as the relation exists in the specified directory.  file with the same name as the relation exists in the specified directory.
# Line 1629  Line 3792 
3792          return $retVal;          return $retVal;
3793  }  }
3794    
3795  =head3 LoadMetaData  
3796    =head3 _LoadMetaData
3797    
3798  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
3799  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 1654  Line 3818 
3818  sub _LoadMetaData {  sub _LoadMetaData {
3819          # Get the parameters.          # Get the parameters.
3820          my ($filename) = @_;          my ($filename) = @_;
3821        Trace("Reading DBD from $filename.") if T(2);
3822          # Slurp the XML file into a variable. Extensive use of options is used to insure we          # Slurp the XML file into a variable. Extensive use of options is used to insure we
3823          # get the exact structure we want.          # get the exact structure we want.
3824          my $metadata = XML::Simple::XMLin($filename,      my $metadata = ReadMetaXML($filename);
                                                                           GroupTags => { Relationships => 'Relationship',  
                                                                                                      Entities => 'Entity',  
                                                                                                          Fields => 'Field',  
                                                                                                          Indexes => 'Index',  
                                                                                                          IndexFields => 'IndexField'},  
                                                                           KeyAttr => { Relationship => 'name',  
                                                                                                    Entity => 'name',  
                                                                                                    Field => 'name'},  
                                                                           ForceArray => ['Field', 'Index', 'IndexField'],  
                                                                           ForceContent => 1,  
                                                                           NormalizeSpace => 2  
                                                                           );  
         Trace("XML metadata loaded from file $filename.") if T(1);  
3825          # Before we go any farther, we need to validate the field and object names. If an error is found,          # Before we go any farther, we need to validate the field and object names. If an error is found,
3826          # the method below will fail.          # the method below will fail.
3827          _ValidateFieldNames($metadata);          _ValidateFieldNames($metadata);
# Line 1681  Line 3833 
3833          for my $entityName (keys %{$entityList}) {          for my $entityName (keys %{$entityList}) {
3834                  my $entityStructure = $entityList->{$entityName};                  my $entityStructure = $entityList->{$entityName};
3835                  #                  #
3836                  # The first step is to run creating all the entity's default values. For C<Field> elements,          # The first step is to create all the entity's default values. For C<Field> elements,
3837                  # the relation name must be added where it is not specified. For relationships,                  # the relation name must be added where it is not specified. For relationships,
3838                  # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>                  # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
3839                  # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute                  # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
# Line 1799  Line 3951 
3951                          my $count = 0;                          my $count = 0;
3952                          for my $index (@{$indexList}) {                          for my $index (@{$indexList}) {
3953                                  # Add this index to the index table.                                  # Add this index to the index table.
3954                                  _AddIndex("idx$relationName$count", $relation, $index);                  _AddIndex("idx$count", $relation, $index);
3955                                  # Increment the counter so that the next index has a different name.                                  # Increment the counter so that the next index has a different name.
3956                                  $count++;                                  $count++;
3957                          }                          }
# Line 1860  Line 4012 
4012                  my @fromList = ();                  my @fromList = ();
4013                  my @toList = ();                  my @toList = ();
4014                  my @bothList = ();                  my @bothList = ();
4015                  Trace("Join table build for $entityName.") if T(3);          Trace("Join table build for $entityName.") if T(metadata => 4);
4016                  for my $relationshipName (keys %{$relationshipList}) {                  for my $relationshipName (keys %{$relationshipList}) {
4017                          my $relationship = $relationshipList->{$relationshipName};                          my $relationship = $relationshipList->{$relationshipName};
4018                          # Determine if this relationship has our entity in one of its link fields.                          # Determine if this relationship has our entity in one of its link fields.
4019                          my $fromEntity = $relationship->{from};                          my $fromEntity = $relationship->{from};
4020                          my $toEntity = $relationship->{to};                          my $toEntity = $relationship->{to};
4021                          Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(3);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4022                          if ($fromEntity eq $entityName) {                          if ($fromEntity eq $entityName) {
4023                                  if ($toEntity eq $entityName) {                                  if ($toEntity eq $entityName) {
4024                                          # Here the relationship is recursive.                                          # Here the relationship is recursive.
4025                                          push @bothList, $relationshipName;                                          push @bothList, $relationshipName;
4026                                          Trace("Relationship $relationshipName put in both-list.") if T(3);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
4027                                  } else {                                  } else {
4028                                          # Here the relationship comes from the entity.                                          # Here the relationship comes from the entity.
4029                                          push @fromList, $relationshipName;                                          push @fromList, $relationshipName;
4030                                          Trace("Relationship $relationshipName put in from-list.") if T(3);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
4031                                  }                                  }
4032                          } elsif ($toEntity eq $entityName) {                          } elsif ($toEntity eq $entityName) {
4033                                  # Here the relationship goes to the entity.                                  # Here the relationship goes to the entity.
4034                                  push @toList, $relationshipName;                                  push @toList, $relationshipName;
4035                                  Trace("Relationship $relationshipName put in to-list.") if T(3);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
4036                          }                          }
4037                  }                  }
4038                  # Create the nonrecursive joins. Note that we build two hashes for running                  # Create the nonrecursive joins. Note that we build two hashes for running
# Line 1896  Line 4048 
4048                                  # Create joins between the entity and this relationship.                                  # Create joins between the entity and this relationship.
4049                                  my $linkField = "$relationshipName.${linkType}_link";                                  my $linkField = "$relationshipName.${linkType}_link";
4050                                  my $joinClause = "$entityName.id = $linkField";                                  my $joinClause = "$entityName.id = $linkField";
4051                                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(4);                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
4052                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
4053                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
4054                                  # Create joins between this relationship and the other relationships.                                  # Create joins between this relationship and the other relationships.
# Line 1917  Line 4069 
4069                                                          # relationship and itself are prohibited.                                                          # relationship and itself are prohibited.
4070                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";                                                          my $relJoinClause = "$otherName.${otherType}_link = $linkField";
4071                                                          $joinTable{$joinKey} = $relJoinClause;                                                          $joinTable{$joinKey} = $relJoinClause;
4072                                                          Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
4073                                                  }                                                  }
4074                                          }                                          }
4075                                  }                                  }
# Line 1926  Line 4078 
4078                                  # relationship can only be ambiguous with another recursive relationship,                                  # relationship can only be ambiguous with another recursive relationship,
4079                                  # and the incoming relationship from the outer loop is never recursive.                                  # and the incoming relationship from the outer loop is never recursive.
4080                                  for my $otherName (@bothList) {                                  for my $otherName (@bothList) {
4081                                          Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(3);                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
4082                                          # Join from the left.                                          # Join from the left.
4083                                          $joinTable{"$relationshipName/$otherName"} =                                          $joinTable{"$relationshipName/$otherName"} =
4084                                                  "$linkField = $otherName.from_link";                                                  "$linkField = $otherName.from_link";
# Line 1941  Line 4093 
4093                  # rise to situations where we can't create the path we want; however, it is always                  # rise to situations where we can't create the path we want; however, it is always
4094                  # possible to get the same effect using multiple queries.                  # possible to get the same effect using multiple queries.
4095                  for my $relationshipName (@bothList) {                  for my $relationshipName (@bothList) {
4096                          Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(3);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
4097                          # Join to the entity from each direction.                          # Join to the entity from each direction.
4098                          $joinTable{"$entityName/$relationshipName"} =                          $joinTable{"$entityName/$relationshipName"} =
4099                                  "$entityName.id = $relationshipName.from_link";                                  "$entityName.id = $relationshipName.from_link";
# Line 1955  Line 4107 
4107          return $metadata;          return $metadata;
4108  }  }
4109    
4110  =head3 CreateRelationshipIndex  =head3 _CreateRelationshipIndex
4111    
4112  Create an index for a relationship's relation.  Create an index for a relationship's relation.
4113    
# Line 1992  Line 4144 
4144          # index descriptor does not exist, it will be created automatically so we can add          # index descriptor does not exist, it will be created automatically so we can add
4145          # the field to it.          # the field to it.
4146          unshift @{$newIndex->{IndexFields}}, $firstField;          unshift @{$newIndex->{IndexFields}}, $firstField;
4147        # If this is a one-to-many relationship, the "To" index is unique.
4148        if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
4149            $newIndex->{Unique} = 'true';
4150        }
4151          # Add the index to the relation.          # Add the index to the relation.
4152          _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4153  }  }
4154    
4155  =head3 AddIndex  =head3 _AddIndex
4156    
4157  Add an index to a relation structure.  Add an index to a relation structure.
4158    
# Line 2042  Line 4198 
4198          $relationStructure->{Indexes}->{$indexName} = $newIndex;          $relationStructure->{Indexes}->{$indexName} = $newIndex;
4199  }  }
4200    
4201  =head3 FixupFields  =head3 _FixupFields
4202    
4203  This method fixes the field list for an entity or relationship. It will add the caller-specified  This method fixes the field list for an entity or relationship. It will add the caller-specified
4204  relation name to fields that do not have a name and set the C<PrettySort> value as specified.  relation name to fields that do not have a name and set the C<PrettySort> value as specified.
# Line 2080  Line 4236 
4236                  # Here it doesn't, so we create a new one.                  # Here it doesn't, so we create a new one.
4237                  $structure->{Fields} = { };                  $structure->{Fields} = { };
4238          } else {          } else {
4239                  # Here we have a field list. Loop through its fields.          # Here we have a field list. We need to track the searchable fields, so we
4240            # create a list for stashing them.
4241            my @textFields = ();
4242            # Loop through the fields.
4243                  my $fieldStructures = $structure->{Fields};                  my $fieldStructures = $structure->{Fields};
4244                  for my $fieldName (keys %{$fieldStructures}) {                  for my $fieldName (keys %{$fieldStructures}) {
4245                Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
4246                          my $fieldData = $fieldStructures->{$fieldName};                          my $fieldData = $fieldStructures->{$fieldName};
4247                          # Get the field type.                          # Get the field type.
4248                          my $type = $fieldData->{type};                          my $type = $fieldData->{type};
4249                          # Plug in a relation name if it is needed.                          # Plug in a relation name if it is needed.
4250                          Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });                          Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4251                          # Plug in a data generator if we need one.              # Check for searchability.
4252                          if (!exists $fieldData->{DataGen}) {              if ($fieldData->{searchable}) {
4253                                  # The data generator will use the default for the field's type.                  # Only allow this for a primary relation.
4254                                  $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };                  if ($fieldData->{relation} ne $defaultRelationName) {
4255                        Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4256                    } else {
4257                        push @textFields, $fieldName;
4258                    }
4259                          }                          }
                         # Plug in the defaults for the optional data generation parameters.  
                         Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
4260                          # Add the PrettySortValue.                          # Add the PrettySortValue.
4261                          $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);                          $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4262                  }                  }
4263            # If there are searchable fields, remember the fact.
4264            if (@textFields) {
4265                $structure->{searchFields} = \@textFields;
4266            }
4267          }          }
4268  }  }
4269    
4270  =head3 FixName  =head3 _FixName
4271    
4272  Fix the incoming field name so that it is a legal SQL column name.  Fix the incoming field name so that it is a legal SQL column name.
4273    
# Line 2130  Line 4296 
4296          return $fieldName;          return $fieldName;
4297  }  }
4298    
4299  =head3 FixNames  =head3 _FixNames
4300    
4301  Fix all the field names in a list.  Fix all the field names in a list.
4302    
# Line 2161  Line 4327 
4327          return @result;          return @result;
4328  }  }
4329    
4330  =head3