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revision 1.2, Tue Jan 25 01:00:20 2005 UTC revision 1.87, Sun Feb 18 21:28:19 2007 UTC
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1  package ERDB;  package ERDB;
2    
3          use strict;          use strict;
         use Carp;  
4          use Tracer;          use Tracer;
5          use DBKernel;      use DBrtns;
6          use Data::Dumper;          use Data::Dumper;
7          use XML::Simple;          use XML::Simple;
8          use DBQuery;          use DBQuery;
9          use DBObject;          use DBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13        use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 33  Line 35 
35  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36  The B<FEATURE> entity also contains an optional virulence number. This is implemented  The B<FEATURE> entity also contains an optional virulence number. This is implemented
37  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in the  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39  C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence number.  the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40  If the virulence of I<ABC> is not known, there will not be any rows for it in C<FeatureVirulence>.  number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41    C<FeatureVirulence>.
42    
43  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
44  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
# Line 57  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
76  To facilitate testing, the ERDB module supports automatic generation of test data. This process  =head2 XML Database Description
77  is described in the L</GenerateEntity> and L</GenerateConnection> methods.  
78    =head3 Data Types
79    
80    The ERDB system supports the following data types. Note that there are numerous string
81    types depending on the maximum length. Some database packages limit the total number of
82    characters you have in an index key; to insure the database works in all environments,
83    the type of string should be the shortest one possible that supports all the known values.
84    
85    =over 4
86    
87    =item char
88    
89    single ASCII character
90    
91    =item int
92    
93    32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99    =item date
100    
101    64-bit unsigned integer, representing a PERL date/time value
102    
103    =item text
104    
105    long string; Text fields cannot be used in indexes or sorting and do not support the
106    normal syntax of filter clauses, but can be up to a billion character in length
107    
108    =item float
109    
110    double-precision floating-point number
111    
112    =item boolean
113    
114    single-bit numeric value; The value is stored as a 16-bit signed integer (for
115    compatability with certain database packages), but the only values supported are
116    0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122    =item key-string
123    
124    variable-length string, maximum 40 characters
125    
126    =item name-string
127    
128    variable-length string, maximum 80 characters
129    
130    =item medium-string
131    
132    variable-length string, maximum 160 characters
133    
134    =item string
135    
136    variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142    =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151    =head3 Global Tags
152    
153    The entire database definition must be inside a B<Database> tag. The display name of
154    the database is given by the text associated with the B<Title> tag. The display name
155    is only used in the automated documentation. It has no other effect. The entities and
156    relationships are listed inside the B<Entities> and B<Relationships> tags,
157    respectively. None of these tags have attributes.
158    
159        <Database>
160            <Title>... display title here...</Title>
161            <Entities>
162                ... entity definitions here ...
163            </Entities>
164            <Relationships>
165                ... relationship definitions here...
166            </Relationships>
167        </Database>
168    
169    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170    The text inside the B<Notes> tag contains comments that will appear when the database
171    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173    
174    =head3 Fields
175    
176    Both entities and relationships have fields described by B<Field> tags. A B<Field>
177    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178    object mus be inside B<Fields> tags.
179    
180        <Entity ... >
181            <Fields>
182                ... Field tags ...
183            </Fields>
184        </Entity>
185    
186    The attributes for the B<Field> tag are as follows.
187    
188    =over 4
189    
190    =item name
191    
192    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193    and the first character should be a letter. Most underlying databases are case-insensitive
194    with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198    =item type
199    
200    Data type of the field. The legal data types are given above.
201    
202    =item relation
203    
204    Name of the relation containing the field. This should only be specified for entity
205    fields. The ERDB system does not support optional fields or multi-occurring fields
206    in the primary relation of an entity. Instead, they are put into secondary relations.
207    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208    grouping used to select a subset of the genomes. A given genome may not be in any
209    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210    value. The relation name specified must be a valid table name. By convention, it is
211    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212    entity, the fields without a relation attribute are said to belong to the
213    I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227    =back
228    
229    =head3 Indexes
230    
231    An entity can have multiple alternate indexes associated with it. The fields in an
232    index must all be from the same relation. The alternate indexes assist in searching
233    on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
234    I<from-index> that 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. In addition, it can have zero or more alternate
238    indexes. A relationship's index must specify only fields in
239    the relationship.
240    
241    The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
242    The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
243    specified using the B<ToIndex> tag.
244    
245    Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
246    tag containing the B<IndexField> tags. These specify, in order, the fields used in
247    the index. The attributes of an B<IndexField> tag are as follows.
248    
249    =over 4
250    
251    =item name
252    
253    Name of the field.
254    
255    =item order
256    
257    Sort order of the field-- C<ascending> or C<descending>.
258    
259    =back
260    
261    The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
262    have a B<Unique> attribute. If specified, the index will be generated as a unique
263    index.
264    
265    =head3 Object and Field Names
266    
267    By convention entity and relationship names use capital casing (e.g. C<Genome> or
268    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
269    with respect to relation names, converting them internally to all-upper case or
270    all-lower case.
271    
272    If syntax or parsing errors occur when you try to load or use an ERDB database, the
273    most likely reason is that one of your objects has an SQL reserved word as its name.
274    The list of SQL reserved words keeps increasing; however, most are unlikely to show
275    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
276    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
277    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
278    
279    Every entity has a field called C<id> that acts as its primary key. Every relationship
280    has fields called C<from-link> and C<to-link> that contain copies of the relevant
281    entity IDs. These are essentially ERDB's reserved words, and should not be used
282    for user-defined field names.
283    
284    =head3 Entities
285    
286    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
287    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
288    containing one or more fields. The attributes of the B<Entity> tag are as follows.
289    
290    =over 4
291    
292    =item name
293    
294    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
295    or C<GroupBlock>) and should be a noun or noun phrase.
296    
297    =item keyType
298    
299    Data type of the primary key. The primary key is always named C<id>.
300    
301    =back
302    
303    =head3 Relationships
304    
305    A relationship is described by the C<Relationship> tag. Within a relationship,
306    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
307    fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
308    the to-index, and an C<Indexes> tag containing the alternate indexes.
309    
310    The C<Relationship> tag has the following attributes.
311    
312    =over 4
313    
314    =item name
315    
316    Name of the relationship. The relationship name, by convention, uses capital casing
317    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
318    phrase, designed to fit between the from-entity and the to-entity (e.g.
319    Block C<ContainsRegionIn> Genome).
320    
321    =item from
322    
323    Name of the entity from which the relationship starts.
324    
325    =item to
326    
327    Name of the entity to which the relationship proceeds.
328    
329    =item arity
330    
331    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
332    
333    =back
334    
335  =cut  =cut
336    
# Line 75  Line 338 
338    
339  # 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.
340  # "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
341  # 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
342   #string is specified in the field definition.  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
343  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
344                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  # index
345                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
346                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "single ASCII character"},
347                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
348                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
349                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
350                                   indexMod =>   0, notes => "unsigned 32-bit integer"},
351                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
352                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
353                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
354                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
355                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
356                                   indexMod =>   0, notes => "signed, 64-bit integer"},
357                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
358                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
359                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
360                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
361                     'hash-string' =>
362                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
363                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
364                     'id-string' =>
365                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
367                               'key-string' =>                               'key-string' =>
368                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
370                                   'name-string' =>                                   'name-string' =>
371                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
373                                   'medium-string' =>                                   'medium-string' =>
374                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
375                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
376                                  );                                  );
377    
378  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 98  Line 381 
381                                     'MM' => 'many-to-many'                                     'MM' => 'many-to-many'
382                                   );                                   );
383    
384  # Table for interpreting string patterns.  # Options for XML input and output.
385    
386    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
387                                      Entities => 'Entity',
388                                      Fields => 'Field',
389                                      Indexes => 'Index',
390                                      IndexFields => 'IndexField'
391                                    },
392                      KeyAttr =>    { Relationship => 'name',
393                                      Entity => 'name',
394                                      Field => 'name'
395                                    },
396                      SuppressEmpty => 1,
397                     );
398    
399  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
400                                           '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
401                                           'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
402                                           'V' => "aeiou",                    NormalizeSpace => 2,
403                                           'K' => "bcdfghjklmnoprstvwxyz"                   );
404    my %XmlOutOpts = (
405                      RootName => 'Database',
406                      XMLDecl => 1,
407                                     );                                     );
408    
409    
410  =head2 Public Methods  =head2 Public Methods
411    
412  =head3 new  =head3 new
413    
414  C<< my $database = ERDB::new($dbh, $metaFileName); >>  C<< my $database = ERDB->new($dbh, $metaFileName); >>
415    
416  Create a new ERDB object.  Create a new ERDB object.
417    
# Line 136  Line 436 
436          my $metaData = _LoadMetaData($metaFileName);          my $metaData = _LoadMetaData($metaFileName);
437          # Create the object.          # Create the object.
438          my $self = { _dbh => $dbh,          my $self = { _dbh => $dbh,
439                                   _metaData => $metaData,                   _metaData => $metaData
                                  _options => $options,  
440                             };                             };
441          # Bless and return it.          # Bless and return it.
442          bless $self;      bless $self, $class;
443          return $self;          return $self;
444  }  }
445    
446  =head3 ShowMetaData  =head3 ShowMetaData
447    
448  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
449    
450  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
451  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 163  Line 462 
462    
463  sub ShowMetaData {  sub ShowMetaData {
464          # Get the parameters.          # Get the parameters.
465          my $self = shift @_;      my ($self, $filename) = @_;
         my ($filename) = @_;  
466          # Get the metadata and the title string.          # Get the metadata and the title string.
467          my $metadata = $self->{_metaData};          my $metadata = $self->{_metaData};
468          # Get the title string.          # Get the title string.
# Line 174  Line 472 
472          my $relationshipList = $metadata->{Relationships};          my $relationshipList = $metadata->{Relationships};
473          # Open the output file.          # Open the output file.
474          open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");          open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
475        Trace("Building MetaData table of contents.") if T(4);
476          # Write the HTML heading stuff.          # Write the HTML heading stuff.
477          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
478          print HTMLOUT "</head>\n<body>\n";          print HTMLOUT "</head>\n<body>\n";
479        # Write the documentation.
480        print HTMLOUT $self->DisplayMetaData();
481        # Close the document.
482        print HTMLOUT "</body>\n</html>\n";
483        # Close the file.
484        close HTMLOUT;
485    }
486    
487    =head3 DisplayMetaData
488    
489    C<< my $html = $erdb->DisplayMetaData(); >>
490    
491    Return an HTML description of the database. This description can be used to help users create
492    the data to be loaded into the relations and form queries. The output is raw includable HTML
493    without any HEAD or BODY tags.
494    
495    =over 4
496    
497    =item filename
498    
499    The name of the output file.
500    
501    =back
502    
503    =cut
504    
505    sub DisplayMetaData {
506        # Get the parameters.
507        my ($self) = @_;
508        # Get the metadata and the title string.
509        my $metadata = $self->{_metaData};
510        # Get the title string.
511        my $title = $metadata->{Title};
512        # Get the entity and relationship lists.
513        my $entityList = $metadata->{Entities};
514        my $relationshipList = $metadata->{Relationships};
515        # Declare the return variable.
516        my $retVal = "";
517        # Open the output file.
518        Trace("Building MetaData table of contents.") if T(4);
519          # 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
520          # section contains an ordered list of entity or relationship subsections.          # section contains an ordered list of entity or relationship subsections.
521          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";
522          # Loop through the Entities, displaying a list item for each.          # Loop through the Entities, displaying a list item for each.
523          foreach my $key (sort keys %{$entityList}) {          foreach my $key (sort keys %{$entityList}) {
524                  # Display this item.                  # Display this item.
525                  print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
526          }          }
527          # Close off the entity section and start the relationship section.          # Close off the entity section and start the relationship section.
528          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";
529          # Loop through the Relationships.          # Loop through the Relationships.
530          foreach my $key (sort keys %{$relationshipList}) {          foreach my $key (sort keys %{$relationshipList}) {
531                  # Display this item.                  # Display this item.
532                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
533                  print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
534          }          }
535          # Close off the relationship section and list the join table section.          # Close off the relationship section and list the join table section.
536          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";
537          # Close off the table of contents itself.          # Close off the table of contents itself.
538          print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
539          # 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.
540          print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
541          # Loop through the entities.          # Loop through the entities.
542          for my $key (sort keys %{$entityList}) {          for my $key (sort keys %{$entityList}) {
543            Trace("Building MetaData entry for $key entity.") if T(4);
544                  # Create the entity header. It contains a bookmark and the entity name.                  # Create the entity header. It contains a bookmark and the entity name.
545                  print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
546                  # Get the entity data.                  # Get the entity data.
547                  my $entityData = $entityList->{$key};                  my $entityData = $entityList->{$key};
548                  # If there's descriptive text, display it.                  # If there's descriptive text, display it.
549                  if (my $notes = $entityData->{Notes}) {                  if (my $notes = $entityData->{Notes}) {
550                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
551                  }                  }
552                  # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
553                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
554            if ($relCount > 0) {
555                # First, we set up the relationship subsection.
556                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
557                  # Loop through the relationships.                  # Loop through the relationships.
558                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
559                          # Get the relationship data.                          # Get the relationship data.
# Line 220  Line 563 
563                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
564                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
565                                  # Display the relationship data.                                  # Display the relationship data.
566                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
567                          }                          }
568                  }                  }
569                  # Close off the relationship list.                  # Close off the relationship list.
570                  print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
571            }
572                  # Get the entity's relations.                  # Get the entity's relations.
573                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
574                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
575                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
576                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
577                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
578                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
579                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
580                  }                  }
581          }          }
582          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
583          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
584          # Loop through the relationships.          # Loop through the relationships.
585          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
586            Trace("Building MetaData entry for $key relationship.") if T(4);
587                  # Get the relationship's structure.                  # Get the relationship's structure.
588                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
589                  # Create the relationship header.                  # Create the relationship header.
590                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
591                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
592                  # Get the entity names.                  # Get the entity names.
593                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
594                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 253  Line 598 
598                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
599                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
600                  if ($arity eq "11") {                  if ($arity eq "11") {
601                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
602                  } else {                  } else {
603                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
604                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
605                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
606                          }                          }
607                  }                  }
608                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
609                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
610                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
611                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
612                  }                  }
613                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
614                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
615                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
616          }          }
617        Trace("Building MetaData join table.") if T(4);
618          # Denote we're starting the join table.          # Denote we're starting the join table.
619          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
620          # Create a table header.          # Create a table header.
621          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
622          # Loop through the joins.          # Loop through the joins.
623          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
624          for my $joinKey (sort keys %{$joinTable}) {      my @joinKeys = keys %{$joinTable};
625        for my $joinKey (sort @joinKeys) {
626                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
627                  $joinKey =~ m!([^/]*)/(.*)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
628                  my ($source, $target, $clause) = ($self->ComputeObjectSentence($1),          my ($sourceRelation, $targetRelation) = ($1, $2);
629                                                                                    $self->ComputeObjectSentence($2),          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
630                                                                                    $joinTable->{$joinKey});          my $source = $self->ComputeObjectSentence($sourceRelation);
631            my $target = $self->ComputeObjectSentence($targetRelation);
632            my $clause = $joinTable->{$joinKey};
633                  # Display them in a table row.                  # Display them in a table row.
634                  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";
635          }          }
636          # Close the table.          # Close the table.
637          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
638          # Close the document.      Trace("Built MetaData HTML.") if T(3);
639          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
640          # Close the file.      return $retVal;
         close HTMLOUT;  
641  }  }
642    
643  =head3 DumpMetaData  =head3 DumpMetaData
644    
645  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
646    
647  Return a dump of the metadata structure.  Return a dump of the metadata structure.
648    
# Line 302  Line 650 
650    
651  sub DumpMetaData {  sub DumpMetaData {
652          # Get the parameters.          # Get the parameters.
653          my $self = shift @_;      my ($self) = @_;
654          # Dump the meta-data.          # Dump the meta-data.
655          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
656  }  }
657    
658    =head3 FindIndexForEntity
659    
660    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
661    
662    This method locates the entry in an entity's index list that begins with the
663    specified attribute name. If the entity has no index list, one will be
664    created. This method works on raw XML, not a live ERDB object.
665    
666    =over 4
667    
668    =item xml
669    
670    The raw XML structure defining the database.
671    
672    =item entityName
673    
674    The name of the relevant entity.
675    
676    =item attributeName
677    
678    The name of the attribute relevant to the search.
679    
680    =item RETURN
681    
682    The numerical index in the index list of the index entry for the specified entity and
683    attribute, or C<undef> if no such index exists.
684    
685    =back
686    
687    =cut
688    
689    sub FindIndexForEntity {
690        # Get the parameters.
691        my ($xml, $entityName, $attributeName) = @_;
692        # Declare the return variable.
693        my $retVal;
694        # Get the named entity.
695        my $entityData = $xml->{Entities}->{$entityName};
696        if (! $entityData) {
697            Confess("Entity $entityName not found in DBD structure.");
698        } else {
699            # Insure it has an index list.
700            if (! exists $entityData->{Indexes}) {
701                $entityData->{Indexes} = [];
702            } else {
703                # Search for the desired index.
704                my $indexList = $entityData->{Indexes};
705                my $n = scalar @{$indexList};
706                Trace("Searching $n indexes in index list for $entityName.") if T(2);
707                # We use an indexed FOR here because we're returning an
708                # index number instead of an object. We do THAT so we can
709                # delete the index from the list if needed.
710                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
711                    my $index = $indexList->[$i];
712                    my $fields = $index->{IndexFields};
713                    # Technically this IF should be safe (that is, we are guaranteed
714                    # the existence of a "$fields->[0]"), because when we load the XML
715                    # we have SuppressEmpty specified.
716                    if ($fields->[0]->{name} eq $attributeName) {
717                        $retVal = $i;
718                    }
719                }
720            }
721        }
722        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
723        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
724        # Return the result.
725        return $retVal;
726    }
727    
728  =head3 CreateTables  =head3 CreateTables
729    
730  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
731    
732  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
733  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 320  Line 738 
738    
739  sub CreateTables {  sub CreateTables {
740          # Get the parameters.          # Get the parameters.
741          my $self = shift @_;      my ($self) = @_;
742          my $metadata = $self->{_metaData};      # Get the relation names.
743          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
744          # Loop through the entities.      # Loop through the relations.
745          while (my ($entityName, $entityData) = each %{$metadata->{Entities}}) {      for my $relationName (@relNames) {
                 # Tell the user what we're doing.  
                 Trace("Creating relations for entity $entityName.") if T(1);  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entityData->{Relations}}) {  
746                          # Create a table for this relation.                          # Create a table for this relation.
747                          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
748                          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);  
749          }          }
750  }  }
751    
752  =head3 CreateTable  =head3 CreateTable
753    
754  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
755    
756  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
757    
# Line 355  Line 761 
761    
762  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
763    
764  =item $indexFlag  =item indexFlag
765    
766  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,
767  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
768    
769    =item estimatedRows (optional)
770    
771    If specified, the estimated maximum number of rows for the relation. This
772    information allows the creation of tables using storage engines that are
773    faster but require size estimates, such as MyISAM.
774    
775  =back  =back
776    
777  =cut  =cut
778    
779  sub CreateTable {  sub CreateTable {
780          # Get the parameters.          # Get the parameters.
781          my $self = shift @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
         my ($relationName, $indexFlag) = @_;  
782          # Get the database handle.          # Get the database handle.
783          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
784          # Get the relation data and determine whether or not the relation is primary.          # Get the relation data and determine whether or not the relation is primary.
# Line 391  Line 802 
802          # Insure the table is not already there.          # Insure the table is not already there.
803          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
804          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
805        # If there are estimated rows, create an estimate so we can take advantage of
806        # faster DB technologies.
807        my $estimation = undef;
808        if ($estimatedRows) {
809            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
810        }
811          # Create the table.          # Create the table.
812          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
813          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
814          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
815          # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
816        # index will not be built until the table has been loaded.
817          if ($indexFlag) {          if ($indexFlag) {
818                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
819          }          }
820  }  }
821    
822  =head3 CreateIndex  =head3 VerifyFields
   
 C<< $database->CreateIndex($relationName); >>  
   
 Create the indexes for a relation. If a table is being loaded from a large source file (as  
 is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  
 the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  
 method used after the load to create the indexes for the table.  
   
 =cut  
   
 sub CreateIndex {  
         # Get the parameters.  
         my $self = shift @_;  
         my ($relationName) = @_;  
         # Get the relation's descriptor.  
         my $relationData = $self->_FindRelation($relationName);  
         # Get the database handle.  
         my $dbh = $self->{_dbh};  
         # Now we need to create this relation's indexes. We do this by looping through its index table.  
         while (my ($indexName, $indexData) = each %{$relationData->{Indexes}}) {  
                 # Get the index's field list.  
                 my @fieldList = _FixNames(@{$indexData->{IndexFields}});  
                 my $flds = join(', ', @fieldList);  
                 # Get the index's uniqueness flag.  
                 my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');  
                 # Create the index.  
                 $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);  
                 Trace("Index created: $indexName for $relationName ($flds)") if T(1);  
         }  
 }  
   
 =head3 LoadTables  
   
 C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  
823    
824  This method will load the database tables from a directory. The tables must already have been created  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
 in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  
 all of the relations to be loaded must have a file in the directory with the same name as the relation  
 (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each  
 line of the file will be loaded as a row of the target relation table. The field values should be in  
 the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is  
 erased before the new data is loaded in.  
825    
826  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and  Run through the list of proposed field values, insuring that all the character fields are
827  tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must  below the maximum length. If any fields are too long, they will be truncated in place.
 be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.  
828    
829  =over 4  =over 4
830    
831  =item directoryName  =item relName
832    
833  Name of the directory containing the relation files to be loaded.  Name of the relation for which the specified fields are destined.
834    
835  =item rebuild  =item fieldList
836    
837  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the  Reference to a list, in order, of the fields to be put into the relation.
 only way to erase existing data in the tables, since the TRUNCATE command is not supported  
 by all of the DB engines we use.  
838    
839  =item RETURN  =item RETURN
840    
841  Returns a statistical object describing the number of records read and a list of the error messages.  Returns the number of fields truncated.
842    
843  =back  =back
844    
845  =cut  =cut
846    
847  sub LoadTables {  sub VerifyFields {
848          # Get the parameters.          # Get the parameters.
849          my $self = shift @_;      my ($self, $relName, $fieldList) = @_;
850          my ($directoryName, $rebuild) = @_;      # Initialize the return value.
851          # Start the timer.      my $retVal = 0;
852          my $startTime = gettimeofday;      # Get the relation definition.
853          # Clean any trailing slash from the directory name.      my $relData = $self->_FindRelation($relName);
854          $directoryName =~ s!/\\$!!;      # Get the list of field descriptors.
855          # Declare the return variable.      my $fieldTypes = $relData->{Fields};
856          my $retVal = Stats->new();      my $fieldCount = scalar @{$fieldTypes};
857          # Get the metadata structure.      # Loop through the two lists.
858          my $metaData = $self->{_metaData};      for (my $i = 0; $i < $fieldCount; $i++) {
859          # Loop through the entities.          # Get the type of the current field.
860          for my $entity (values %{$metaData->{Entities}}) {          my $fieldType = $fieldTypes->[$i]->{type};
861                  # Loop through the entity's relations.          # If it's a character field, verify the length.
862                  for my $relationName (keys %{$entity->{Relations}}) {          if ($fieldType =~ /string/) {
863                          # Try to load this relation.              my $maxLen = $TypeTable{$fieldType}->{maxLen};
864                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $oldString = $fieldList->[$i];
865                          # Accumulate the statistics.              if (length($oldString) > $maxLen) {
866                          $retVal->Accumulate($result);                  # Here it's too big, so we truncate it.
867                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
868                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
869                    $retVal++;
870                  }                  }
871          }          }
         # 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);  
872          }          }
873          # Add the duration of the load to the statistical object.      # Return the truncation count.
         $retVal->Add('duration', gettimeofday - $startTime);  
         # Return the accumulated statistics.  
874          return $retVal;          return $retVal;
875  }  }
876    
877  =head3 GetTableNames  =head3 DigestFields
878    
879  C<< my @names = $database->GetTableNames; >>  C<< $erdb->DigestFields($relName, $fieldList); >>
880    
881  Return a list of the relations required to implement this database.  Digest the strings in the field list that correspond to data type C<hash-string> in the
882    specified relation.
883    
884  =cut  =over 4
885    
886  sub GetTableNames {  =item relName
         # Get the parameters.  
         my $self = shift @_;  
         # Get the relation list from the metadata.  
         my $relationTable = $self->{_metaData}->{RelationTable};  
         # Return the relation names.  
         return keys %{$relationTable};  
 }  
887    
888  =head3 GetEntityTypes  Name of the relation to which the fields belong.
889    
890  C<< my @names = $database->GetEntityTypes; >>  =item fieldList
891    
892  Return a list of the entity type names.  List of field contents to be loaded into the relation.
893    
894  =cut  =back
895    
896  sub GetEntityTypes {  =cut
897          # Get the database object.  #: Return Type ;
898          my $self = shift @_;  sub DigestFields {
899          # Get the entity list from the metadata object.      # Get the parameters.
900          my $entityList = $self->{_metaData}->{Entities};      my ($self, $relName, $fieldList) = @_;
901          # Return the list of entity names in alphabetical order.      # Get the relation definition.
902          return sort keys %{$entityList};      my $relData = $self->_FindRelation($relName);
903        # Get the list of field descriptors.
904        my $fieldTypes = $relData->{Fields};
905        my $fieldCount = scalar @{$fieldTypes};
906        # Loop through the two lists.
907        for (my $i = 0; $i < $fieldCount; $i++) {
908            # Get the type of the current field.
909            my $fieldType = $fieldTypes->[$i]->{type};
910            # If it's a hash string, digest it in place.
911            if ($fieldType eq 'hash-string') {
912                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
913            }
914        }
915  }  }
916    
917  =head3 Get  =head3 DigestKey
918    
919  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $digested = $erdb->DigestKey($keyValue); >>
920    
921  This method returns a query object for entities of a specified type using a specified filter.  Return the digested value of a symbolic key. The digested value can then be plugged into a
922  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  key-based search into a table with key-type hash-string.
 field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the  
 following call requests all B<Genome> objects for the genus specified in the variable  
 $genus.  
923    
924  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  Currently the digesting process is independent of the database structure, but that may not
925    always be the case, so this is an instance method instead of a static method.
926    
927  The WHERE clause contains a single question mark, so there is a single additional  =over 4
 parameter representing the parameter value. It would also be possible to code  
928    
929  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  =item keyValue
930    
931  however, this version of the call would generate a syntax error if there were any quote  Key value to digest.
 characters inside the variable C<$genus>.  
932    
933  The use of the strange parenthesized notation for field names enables us to distinguish  =item RETURN
 hyphens contained within field names from minus signs that participate in the computation  
 of the WHERE clause. All of the methods that manipulate fields will use this same notation.  
934    
935  It is possible to specify multiple entity and relationship names in order to retrieve more than  Digested value of the key.
 one object's data at the same time, which allows highly complex joined queries. For example,  
936    
937  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  =back
938    
939  If multiple names are specified, then the query processor will automatically determine a  =cut
 join path between the entities and relationships. The algorithm used is very simplistic.  
 In particular, you can't specify any entity or relationship more than once, and if a  
 relationship is recursive, the path is determined by the order in which the entity  
 and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  
 which relates B<People> objects to other B<People> objects. If the join path is  
 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  
 the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  
940    
941  =over 4  sub DigestKey {
942        # Get the parameters.
943        my ($self, $keyValue) = @_;
944        # Compute the digest.
945        my $retVal = md5_base64($keyValue);
946        # Return the result.
947        return $retVal;
948    }
949    
950  =item objectNames  =head3 CreateIndex
951    
952  List containing the names of the entity and relationship objects to be retrieved.  C<< $erdb->CreateIndex($relationName); >>
953    
954  =item filterClause  Create the indexes for a relation. If a table is being loaded from a large source file (as
955    is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
956    If that is the case, then L</CreateTable> should be called with the index flag set to
957    FALSE, and this method used after the load to create the indexes for the table.
958    
959  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  =cut
 be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  
 specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  
 in the filter clause should be added to the parameter list as additional parameters. The  
 fields in a filter clause can come from primary entity relations, relationship relations,  
 or secondary entity relations; however, all of the entities and relationships involved must  
 be included in the list of object names.  
960    
961  The filter clause can also specify a sort order. To do this, simply follow the filter string  sub CreateIndex {
962  with an ORDER BY clause. For example, the following filter string gets all genomes for a      # Get the parameters.
963  particular genus and sorts them by species name.      my ($self, $relationName) = @_;
964        # Get the relation's descriptor.
965        my $relationData = $self->_FindRelation($relationName);
966        # Get the database handle.
967        my $dbh = $self->{_dbh};
968        # Now we need to create this relation's indexes. We do this by looping through its index table.
969        my $indexHash = $relationData->{Indexes};
970        for my $indexName (keys %{$indexHash}) {
971            my $indexData = $indexHash->{$indexName};
972            # Get the index's field list.
973            my @rawFields = @{$indexData->{IndexFields}};
974            # Get a hash of the relation's field types.
975            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
976            # We need to check for text fields so we can append a length limitation for them. To do
977            # that, we need the relation's field list.
978            my $relFields = $relationData->{Fields};
979            for (my $i = 0; $i <= $#rawFields; $i++) {
980                # Get the field type.
981                my $field = $rawFields[$i];
982                my $type = $types{$field};
983                # Ask if it requires using prefix notation for the index.
984                my $mod = $TypeTable{$type}->{indexMod};
985                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
986                if ($mod) {
987                    # Append the prefix length to the field name,
988                    $rawFields[$i] .= "($mod)";
989                }
990            }
991            my @fieldList = _FixNames(@rawFields);
992            my $flds = join(', ', @fieldList);
993            # Get the index's uniqueness flag.
994            my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
995            # Create the index.
996            my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
997                                        flds => $flds, kind => $unique);
998            if ($rv) {
999                Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1000            } else {
1001                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
1002            }
1003        }
1004    }
1005    
1006  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  =head3 GetSecondaryFields
1007    
1008  The rules for field references in a sort order are the same as those for field references in the  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1009  filter clause in general; however, odd things may happen if a sort field is from a secondary  
1010  relation.  This method will return a list of the name and type of each of the secondary
1011    fields for a specified entity. Secondary fields are stored in two-column tables
1012    in addition to the primary entity table. This enables the field to have no value
1013    or to have multiple values.
1014    
1015    =over 4
1016    
1017  =item param1, param2, ..., paramN  =item entityName
1018    
1019  Parameter values to be substituted into the filter clause.  Name of the entity whose secondary fields are desired.
1020    
1021  =item RETURN  =item RETURN
1022    
1023  Returns a B<DBQuery> that can be used to iterate through all of the results.  Returns a hash mapping the field names to their field types.
1024    
1025  =back  =back
1026    
1027  =cut  =cut
1028    
1029  sub Get {  sub GetSecondaryFields {
1030          # Get the parameters.          # Get the parameters.
1031          my $self = shift @_;      my ($self, $entityName) = @_;
1032          my ($objectNames, $filterClause, @params) = @_;      # Declare the return variable.
1033          # Construct the SELECT statement. The general pattern is      my %retVal = ();
1034          #      # Look for the entity.
1035          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN      my $table = $self->GetFieldTable($entityName);
1036          #      # Loop through the fields, pulling out the secondaries.
1037          my $dbh = $self->{_dbh};      for my $field (sort keys %{$table}) {
1038          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          if ($table->{$field}->{relation} ne $entityName) {
1039                                  join(', ', @{$objectNames});              # Here we have a secondary field.
1040          # Check for a filter clause.              $retVal{$field} = $table->{$field}->{type};
         if ($filterClause) {  
                 # Here we have one, so we convert its field names and add it to the query. First,  
                 # We create a copy of the filter string we can work with.  
                 my $filterString = $filterClause;  
                 # Next, we sort the object names by length. This helps protect us from finding  
                 # object names inside other object names when we're doing our search and replace.  
                 my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
                 # We will also keep a list of conditions to add to the WHERE clause in order to link  
                 # entities and relationships as well as primary relations to secondary ones.  
                 my @joinWhere = ();  
                 # The final preparatory step is to create a hash table of relation names. The  
                 # table begins with the relation names already in the SELECT command.  
                 my %fromNames = ();  
                 for my $objectName (@sortedNames) {  
                         $fromNames{$objectName} = 1;  
                 }  
                 # We are ready to begin. We loop through the object names, replacing each  
                 # object name's field references by the corresponding SQL field reference.  
                 # Along the way, if we find a secondary relation, we will need to add it  
                 # to the FROM clause.  
                 for my $objectName (@sortedNames) {  
                         # Get the length of the object name plus 2. This is the value we add to the  
                         # size of the field name to determine the size of the field reference as a  
                         # whole.  
                         my $nameLength = 2 + length $objectName;  
                         # Get the object's field list.  
                         my $fieldList = $self->_GetFieldTable($objectName);  
                         # Find the field references for this object.  
                         while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                                 # At this point, $1 contains the field name, and the current position  
                                 # is set immediately after the final parenthesis. We pull out the name of  
                                 # the field and the position and length of the field reference as a whole.  
                                 my $fieldName = $1;  
                                 my $len = $nameLength + length $fieldName;  
                                 my $pos = pos($filterString) - $len;  
                                 # Insure the field exists.  
                                 if (!exists $fieldList->{$fieldName}) {  
                                         Confess("Field $fieldName not found for object $objectName.");  
                                 } else {  
                                         # Get the field's relation.  
                                         my $relationName = $fieldList->{$fieldName}->{relation};  
                                         # Insure the relation is in the FROM clause.  
                                         if (!exists $fromNames{$relationName}) {  
                                                 # Add the relation to the FROM clause.  
                                                 $command .= ", $relationName";  
                                                 # Create its join sub-clause.  
                                                 push @joinWhere, "$objectName.id = $relationName.id";  
                                                 # Denote we have it available for future fields.  
                                                 $fromNames{$relationName} = 1;  
                                         }  
                                         # Form an SQL field reference from the relation name and the field name.  
                                         my $sqlReference = "$relationName." . _FixName($fieldName);  
                                         # Put it into the filter string in place of the old value.  
                                         substr($filterString, $pos, $len) = $sqlReference;  
                                         # Reposition the search.  
                                         pos $filterString = $pos + length $sqlReference;  
                                 }  
                         }  
                 }  
                 # The next step is to join the objects together. We only need to do this if there  
                 # is more than one object in the object list. We start with the first object and  
                 # run through the objects after it. Note also that we make a safety copy of the  
                 # list before running through it.  
                 my @objectList = @{$objectNames};  
                 my $lastObject = shift @objectList;  
                 # Get the join table.  
                 my $joinTable = $self->{_metaData}->{Joins};  
                 # Loop through the object list.  
                 for my $thisObject (@objectList) {  
                         # Look for a join.  
                         my $joinKey = "$lastObject/$thisObject";  
                         if (!exists $joinTable->{$joinKey}) {  
                                 # Here there's no join, so we throw an error.  
                                 Confess("No join exists to connect from $lastObject to $thisObject.");  
                         } else {  
                                 # Get the join clause and add it to the WHERE list.  
                                 push @joinWhere, $joinTable->{$joinKey};  
                                 # Save this object as the last object for the next iteration.  
                                 $lastObject = $thisObject;  
                         }  
                 }  
                 # Now we need to handle the whole ORDER BY thing. We'll put the order by clause  
                 # in the following variable.  
                 my $orderClause = "";  
                 # Locate the ORDER BY verb (if any).  
                 if ($filterString =~ m/^(.*)ORDER BY/g) {  
                         # Here we have an ORDER BY verb. Split it off of the filter string.  
                         my $pos = pos $filterString;  
                         $orderClause = substr($filterString, $pos);  
                         $filterString = $1;  
                 }  
                 # Add the filter and the join clauses (if any) to the SELECT command.  
                 if ($filterString) {  
                         push @joinWhere, "($filterString)";  
                 }  
                 if (@joinWhere) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
                 }  
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
1041                  }                  }
1042          }          }
1043          Trace("SQL query: $command") if T(2);      # Return the result.
1044          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      return %retVal;
         my $sth = $dbh->prepare_command($command);  
         # Execute it with the parameters bound in.  
         $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
         # Return the statement object.  
         my $retVal = DBQuery::_new($self, $sth, @{$objectNames});  
         return $retVal;  
1045  }  }
1046    
1047  =head3 ComputeObjectSentence  =head3 GetFieldRelationName
1048    
1049  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1050    
1051  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return the name of the relation containing a specified field.
1052    
1053  =over 4  =over 4
1054    
1055  =item objectName  =item objectName
1056    
1057  Name of the entity or relationship.  Name of the entity or relationship containing the field.
1058    
1059    =item fieldName
1060    
1061    Name of the relevant field in that entity or relationship.
1062    
1063  =item RETURN  =item RETURN
1064    
1065  Returns a string containing the entity name or a relationship sentence.  Returns the name of the database relation containing the field, or C<undef> if
1066    the field does not exist.
1067    
1068  =back  =back
1069    
1070  =cut  =cut
1071    
1072  sub ComputeObjectSentence {  sub GetFieldRelationName {
1073          # Get the parameters.          # Get the parameters.
1074          my $self = shift @_;      my ($self, $objectName, $fieldName) = @_;
1075          my ($objectName) = @_;      # Declare the return variable.
1076          # Set the default return value.      my $retVal;
1077          my $retVal = $objectName;      # Get the object field table.
1078          # Look for the object as a relationship.      my $table = $self->GetFieldTable($objectName);
1079          my $relTable = $self->{_metaData}->{Relationships};      # Only proceed if the field exists.
1080          if (exists $relTable->{$objectName}) {      if (exists $table->{$fieldName}) {
1081                  # Get the relationship sentence.          # Determine the name of the relation that contains this field.
1082                  $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          $retVal = $table->{$fieldName}->{relation};
1083          }          }
1084          # Return the result.          # Return the result.
1085          return $retVal;          return $retVal;
1086  }  }
1087    
1088  =head3 DumpRelations  =head3 DeleteValue
1089    
1090  C<< $database->DumpRelations($outputDirectory); >>  C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1091    
1092  Write the contents of all the relations to tab-delimited files in the specified directory.  Delete secondary field values from the database. This method can be used to delete all
1093  Each file will have the same name as the relation dumped, with an extension of DTX.  values of a specified field for a particular entity instance, or only a single value.
1094    
1095    Secondary fields are stored in two-column relations separate from an entity's primary
1096    table, and as a result a secondary field can legitimately have no value or multiple
1097    values. Therefore, it makes sense to talk about deleting secondary fields where it
1098    would not make sense for primary fields.
1099    
1100  =over 4  =over 4
1101    
1102  =item outputDirectory  =item entityName
1103    
1104  Name of the directory into which the relation files should be dumped.  Name of the entity from which the fields are to be deleted.
1105    
1106    =item id
1107    
1108    ID of the entity instance to be processed. If the instance is not found, this
1109    method will have no effect. If C<undef> is specified, all values for all of
1110    the entity instances will be deleted.
1111    
1112    =item fieldName
1113    
1114    Name of the field whose values are to be deleted.
1115    
1116    =item fieldValue (optional)
1117    
1118    Value to be deleted. If not specified, then all values of the specified field
1119    will be deleted for the entity instance. If specified, then only the values which
1120    match this parameter will be deleted.
1121    
1122    =item RETURN
1123    
1124    Returns the number of rows deleted.
1125    
1126  =back  =back
1127    
1128  =cut  =cut
1129    
1130  sub DumpRelations {  sub DeleteValue {
1131          # Get the parameters.          # Get the parameters.
1132          my $self = shift @_;      my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1133          my ($outputDirectory) = @_;      # Declare the return value.
1134          # Now we need to run through all the relations. First, we loop through the entities.      my $retVal = 0;
1135          my $metaData = $self->{_metaData};      # We need to set up an SQL command to do the deletion. First, we
1136          my $entities = $metaData->{Entities};      # find the name of the field's relation.
1137          while (my ($entityName, $entityStructure) = each %{$entities}) {      my $table = $self->GetFieldTable($entityName);
1138                  # Get the entity's relations.      my $field = $table->{$fieldName};
1139                  my $relationList = $entityStructure->{Relations};      my $relation = $field->{relation};
1140                  # Loop through the relations, dumping them.      # Make sure this is a secondary field.
1141                  while (my ($relationName, $relation) = each %{$relationList}) {      if ($relation eq $entityName) {
1142                          $self->_DumpRelation($outputDirectory, $relationName, $relation);          Confess("Cannot delete values of $fieldName for $entityName.");
1143                  }      } else {
1144            # Set up the SQL command to delete all values.
1145            my $sql = "DELETE FROM $relation";
1146            # Build the filter.
1147            my @filters = ();
1148            my @parms = ();
1149            # Check for a filter by ID.
1150            if (defined $id) {
1151                push @filters, "id = ?";
1152                push @parms, $id;
1153            }
1154            # Check for a filter by value.
1155            if (defined $fieldValue) {
1156                push @filters, "$fieldName = ?";
1157                push @parms, $fieldValue;
1158            }
1159            # Append the filters to the command.
1160            if (@filters) {
1161                $sql .= " WHERE " . join(" AND ", @filters);
1162          }          }
1163          # Next, we loop through the relationships.          # Execute the command.
1164          my $relationships = $metaData->{Relationships};          my $dbh = $self->{_dbh};
1165          while (my ($relationshipName, $relationshipStructure) = each %{$relationships}) {          $retVal = $dbh->SQL($sql, 0, @parms);
                 # Dump this relationship's relation.  
                 $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
1166          }          }
1167        # Return the result.
1168        return $retVal;
1169  }  }
1170    
1171  =head3 InsertObject  =head3 LoadTables
   
 C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  
   
 Insert an object into the database. The object is defined by a type name and then a hash  
 of field names to values. Field values in the primary relation are represented by scalars.  
 (Note that for relationships, the primary relation is the B<only> relation.)  
 Field values for the other relations comprising the entity are always list references. For  
 example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  
 C<ZP_00210270.1> and C<gi|46206278>.  
1172    
1173  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1174    
1175  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  This method will load the database tables from a directory. The tables must already have been created
1176  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1177    all of the relations to be loaded must have a file in the directory with the same name as the relation
1178    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1179    line of the file will be loaded as a row of the target relation table. The field values should be in
1180    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1181    erased before the new data is loaded in.
1182    
1183  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1184    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1185    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1186    
1187  =over 4  =over 4
1188    
1189  =item newObjectType  =item directoryName
1190    
1191  Type name of the object to insert.  Name of the directory containing the relation files to be loaded.
1192    
1193  =item fieldHash  =item rebuild
1194    
1195  Hash of field names to values.  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1196    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1197    by all of the DB engines we use.
1198    
1199  =item RETURN  =item RETURN
1200    
1201  Returns 1 if successful, 0 if an error occurred.  Returns a statistical object describing the number of records read and a list of the error messages.
1202    
1203  =back  =back
1204    
1205  =cut  =cut
1206    
1207  sub InsertObject {  sub LoadTables {
1208          # Get the parameters.          # Get the parameters.
1209          my $self = shift @_;      my ($self, $directoryName, $rebuild) = @_;
1210          my ($newObjectType, $fieldHash) = @_;      # Start the timer.
1211          # Denote that so far we appear successful.      my $startTime = gettimeofday;
1212          my $retVal = 1;      # Clean any trailing slash from the directory name.
1213          # Get the database handle.      $directoryName =~ s!/\\$!!;
1214          my $dbh = $self->{_dbh};      # Declare the return variable.
1215        my $retVal = Stats->new();
1216        # Get the relation names.
1217        my @relNames = $self->GetTableNames();
1218        for my $relationName (@relNames) {
1219            # Try to load this relation.
1220            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1221            # Accumulate the statistics.
1222            $retVal->Accumulate($result);
1223        }
1224        # Add the duration of the load to the statistical object.
1225        $retVal->Add('duration', gettimeofday - $startTime);
1226        # Return the accumulated statistics.
1227        return $retVal;
1228    }
1229    
1230    
1231    =head3 GetTableNames
1232    
1233    C<< my @names = $erdb->GetTableNames; >>
1234    
1235    Return a list of the relations required to implement this database.
1236    
1237    =cut
1238    
1239    sub GetTableNames {
1240        # Get the parameters.
1241        my ($self) = @_;
1242        # Get the relation list from the metadata.
1243        my $relationTable = $self->{_metaData}->{RelationTable};
1244        # Return the relation names.
1245        return keys %{$relationTable};
1246    }
1247    
1248    =head3 GetEntityTypes
1249    
1250    C<< my @names = $erdb->GetEntityTypes; >>
1251    
1252    Return a list of the entity type names.
1253    
1254    =cut
1255    
1256    sub GetEntityTypes {
1257        # Get the database object.
1258        my ($self) = @_;
1259        # Get the entity list from the metadata object.
1260        my $entityList = $self->{_metaData}->{Entities};
1261        # Return the list of entity names in alphabetical order.
1262        return sort keys %{$entityList};
1263    }
1264    
1265    =head3 GetDataTypes
1266    
1267    C<< my %types = ERDB::GetDataTypes(); >>
1268    
1269    Return a table of ERDB data types. The table returned is a hash of hashes.
1270    The keys of the big hash are the datatypes. Each smaller hash has several
1271    values used to manage the data. The most interesting is the SQL type (key
1272    C<sqlType>) and the descriptive node (key C<notes>).
1273    
1274    Note that changing the values in the smaller hashes will seriously break
1275    things, so this data should be treated as read-only.
1276    
1277    =cut
1278    
1279    sub GetDataTypes {
1280        return %TypeTable;
1281    }
1282    
1283    
1284    =head3 IsEntity
1285    
1286    C<< my $flag = $erdb->IsEntity($entityName); >>
1287    
1288    Return TRUE if the parameter is an entity name, else FALSE.
1289    
1290    =over 4
1291    
1292    =item entityName
1293    
1294    Object name to be tested.
1295    
1296    =item RETURN
1297    
1298    Returns TRUE if the specified string is an entity name, else FALSE.
1299    
1300    =back
1301    
1302    =cut
1303    
1304    sub IsEntity {
1305        # Get the parameters.
1306        my ($self, $entityName) = @_;
1307        # Test to see if it's an entity.
1308        return exists $self->{_metaData}->{Entities}->{$entityName};
1309    }
1310    
1311    =head3 Get
1312    
1313    C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1314    
1315    This method returns a query object for entities of a specified type using a specified filter.
1316    The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1317    field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1318    following call requests all B<Genome> objects for the genus specified in the variable
1319    $genus.
1320    
1321    C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1322    
1323    The WHERE clause contains a single question mark, so there is a single additional
1324    parameter representing the parameter value. It would also be possible to code
1325    
1326    C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1327    
1328    however, this version of the call would generate a syntax error if there were any quote
1329    characters inside the variable C<$genus>.
1330    
1331    The use of the strange parenthesized notation for field names enables us to distinguish
1332    hyphens contained within field names from minus signs that participate in the computation
1333    of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1334    
1335    It is possible to specify multiple entity and relationship names in order to retrieve more than
1336    one object's data at the same time, which allows highly complex joined queries. For example,
1337    
1338    C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1339    
1340    If multiple names are specified, then the query processor will automatically determine a
1341    join path between the entities and relationships. The algorithm used is very simplistic.
1342    In particular, if a relationship is recursive, the path is determined by the order in which
1343    the entity and the relationship appear. For example, consider a recursive relationship
1344    B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1345    coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1346    the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1347    
1348    If an entity or relationship is mentioned twice, the name for the second occurrence will
1349    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1350    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1351    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1352    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1353    
1354    =over 4
1355    
1356    =item objectNames
1357    
1358    List containing the names of the entity and relationship objects to be retrieved.
1359    
1360    =item filterClause
1361    
1362    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1363    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1364    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1365    in the filter clause should be added to the parameter list as additional parameters. The
1366    fields in a filter clause can come from primary entity relations, relationship relations,
1367    or secondary entity relations; however, all of the entities and relationships involved must
1368    be included in the list of object names.
1369    
1370    The filter clause can also specify a sort order. To do this, simply follow the filter string
1371    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1372    particular genus and sorts them by species name.
1373    
1374    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1375    
1376    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1377    be processed. The idea is to make it less likely to find the verb by accident.
1378    
1379    The rules for field references in a sort order are the same as those for field references in the
1380    filter clause in general; however, odd things may happen if a sort field is from a secondary
1381    relation.
1382    
1383    Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1384    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1385    a positive number. So, for example
1386    
1387    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1388    
1389    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1390    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1391    use
1392    
1393    C<< "LIMIT 10" >>
1394    
1395    =item params
1396    
1397    Reference to a list of parameter values to be substituted into the filter clause.
1398    
1399    =item RETURN
1400    
1401    Returns a B<DBQuery> that can be used to iterate through all of the results.
1402    
1403    =back
1404    
1405    =cut
1406    
1407    sub Get {
1408        # Get the parameters.
1409        my ($self, $objectNames, $filterClause, $params) = @_;
1410        # Process the SQL stuff.
1411        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1412            $self->_SetupSQL($objectNames, $filterClause);
1413        # Create the query.
1414        my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1415            ".* $suffix";
1416        my $sth = $self->_GetStatementHandle($command, $params);
1417        # Now we create the relation map, which enables DBQuery to determine the order, name
1418        # and mapped name for each object in the query.
1419        my @relationMap = ();
1420        for my $mappedName (@{$mappedNameListRef}) {
1421            push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1422        }
1423        # Return the statement object.
1424        my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1425        return $retVal;
1426    }
1427    
1428    
1429    
1430    =head3 Search
1431    
1432    C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1433    
1434    Perform a full text search with filtering. The search will be against a specified object
1435    in the object name list. That object will get an extra field containing the search
1436    relevance. Note that except for the search expression, the parameters of this method are
1437    the same as those for L</Get> and follow the same rules.
1438    
1439    =over 4
1440    
1441    =item searchExpression
1442    
1443    Boolean search expression for the text fields of the target object. The default mode for
1444    a Boolean search expression is OR, but we want the default to be AND, so we will
1445    add a C<+> operator to each word with no other operator before it.
1446    
1447    =item idx
1448    
1449    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1450    
1451    =item objectNames
1452    
1453    List containing the names of the entity and relationship objects to be retrieved.
1454    
1455    =item filterClause
1456    
1457    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1458    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1459    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1460    in the filter clause should be added to the parameter list as additional parameters. The
1461    fields in a filter clause can come from primary entity relations, relationship relations,
1462    or secondary entity relations; however, all of the entities and relationships involved must
1463    be included in the list of object names.
1464    
1465    =item params
1466    
1467    Reference to a list of parameter values to be substituted into the filter clause.
1468    
1469    =item RETURN
1470    
1471    Returns a query object for the specified search.
1472    
1473    =back
1474    
1475    =cut
1476    
1477    sub Search {
1478        # Get the parameters.
1479        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1480        # Declare the return variable.
1481        my $retVal;
1482        # Create a safety copy of the parameter list. Note we have to be careful to insure
1483        # a parameter list exists before we copy it.
1484        my @myParams = ();
1485        if (defined $params) {
1486            @myParams = @{$params};
1487        }
1488        # Get the first object's structure so we have access to the searchable fields.
1489        my $object1Name = $objectNames->[$idx];
1490        my $object1Structure = $self->_GetStructure($object1Name);
1491        # Get the field list.
1492        if (! exists $object1Structure->{searchFields}) {
1493            Confess("No searchable index for $object1Name.");
1494        } else {
1495            # Get the field list.
1496            my @fields = @{$object1Structure->{searchFields}};
1497            # Clean the search expression.
1498            my $actualKeywords = $self->CleanKeywords($searchExpression);
1499            # Prefix a "+" to each uncontrolled word. This converts the default
1500            # search mode from OR to AND.
1501            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1502            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1503            # We need two match expressions, one for the filter clause and one in the
1504            # query itself. Both will use a parameter mark, so we need to push the
1505            # search expression onto the front of the parameter list twice.
1506            unshift @myParams, $actualKeywords, $actualKeywords;
1507            # Build the match expression.
1508            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1509            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1510            # Process the SQL stuff.
1511            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1512                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1513            # Create the query. Note that the match clause is inserted at the front of
1514            # the select fields.
1515            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1516                ".* $suffix";
1517            my $sth = $self->_GetStatementHandle($command, \@myParams);
1518            # Now we create the relation map, which enables DBQuery to determine the order, name
1519            # and mapped name for each object in the query.
1520            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1521            # Return the statement object.
1522            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1523        }
1524        return $retVal;
1525    }
1526    
1527    =head3 GetFlat
1528    
1529    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1530    
1531    This is a variation of L</GetAll> that asks for only a single field per record and
1532    returns a single flattened list.
1533    
1534    =over 4
1535    
1536    =item objectNames
1537    
1538    List containing the names of the entity and relationship objects to be retrieved.
1539    
1540    =item filterClause
1541    
1542    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1543    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1544    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1545    parameter list as additional parameters. The fields in a filter clause can come from primary
1546    entity relations, relationship relations, or secondary entity relations; however, all of the
1547    entities and relationships involved must be included in the list of object names.
1548    
1549    =item parameterList
1550    
1551    List of the parameters to be substituted in for the parameters marks in the filter clause.
1552    
1553    =item field
1554    
1555    Name of the field to be used to get the elements of the list returned.
1556    
1557    =item RETURN
1558    
1559    Returns a list of values.
1560    
1561    =back
1562    
1563    =cut
1564    #: Return Type @;
1565    sub GetFlat {
1566        # Get the parameters.
1567        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1568        # Construct the query.
1569        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1570        # Create the result list.
1571        my @retVal = ();
1572        # Loop through the records, adding the field values found to the result list.
1573        while (my $row = $query->Fetch()) {
1574            push @retVal, $row->Value($field);
1575        }
1576        # Return the list created.
1577        return @retVal;
1578    }
1579    
1580    =head3 SpecialFields
1581    
1582    C<< my %specials = $erdb->SpecialFields($entityName); >>
1583    
1584    Return a hash mapping special fields in the specified entity to the value of their
1585    C<special> attribute. This enables the subclass to get access to the special field
1586    attributes without needed to plumb the internal ERDB data structures.
1587    
1588    =over 4
1589    
1590    =item entityName
1591    
1592    Name of the entity whose special fields are desired.
1593    
1594    =item RETURN
1595    
1596    Returns a hash. The keys of the hash are the special field names, and the values
1597    are the values from each special field's C<special> attribute.
1598    
1599    =back
1600    
1601    =cut
1602    
1603    sub SpecialFields {
1604        # Get the parameters.
1605        my ($self, $entityName) = @_;
1606        # Declare the return variable.
1607        my %retVal = ();
1608        # Find the entity's data structure.
1609        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1610        # Loop through its fields, adding each special field to the return hash.
1611        my $fieldHash = $entityData->{Fields};
1612        for my $fieldName (keys %{$fieldHash}) {
1613            my $fieldData = $fieldHash->{$fieldName};
1614            if (exists $fieldData->{special}) {
1615                $retVal{$fieldName} = $fieldData->{special};
1616            }
1617        }
1618        # Return the result.
1619        return %retVal;
1620    }
1621    
1622    =head3 Delete
1623    
1624    C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1625    
1626    Delete an entity instance from the database. The instance is deleted along with all entity and
1627    relationship instances dependent on it. The definition of I<dependence> is recursive.
1628    
1629    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1630    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1631    dependent relationship.
1632    
1633    =over 4
1634    
1635    =item entityName
1636    
1637    Name of the entity type for the instance being deleted.
1638    
1639    =item objectID
1640    
1641    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1642    then it is presumed to by a LIKE pattern.
1643    
1644    =item options
1645    
1646    A hash detailing the options for this delete operation.
1647    
1648    =item RETURN
1649    
1650    Returns a statistics object indicating how many records of each particular table were
1651    deleted.
1652    
1653    =back
1654    
1655    The permissible options for this method are as follows.
1656    
1657    =over 4
1658    
1659    =item testMode
1660    
1661    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1662    
1663    =item keepRoot
1664    
1665    If TRUE, then the entity instances will not be deleted, only the dependent records.
1666    
1667    =back
1668    
1669    =cut
1670    #: Return Type $%;
1671    sub Delete {
1672        # Get the parameters.
1673        my ($self, $entityName, $objectID, %options) = @_;
1674        # Declare the return variable.
1675        my $retVal = Stats->new();
1676        # Get the DBKernel object.
1677        my $db = $self->{_dbh};
1678        # We're going to generate all the paths branching out from the starting entity. One of
1679        # the things we have to be careful about is preventing loops. We'll use a hash to
1680        # determine if we've hit a loop.
1681        my %alreadyFound = ();
1682        # These next lists will serve as our result stack. We start by pushing object lists onto
1683        # the stack, and then popping them off to do the deletes. This means the deletes will
1684        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1685        # sure we don't delete records that might be needed to forge relationships back to the
1686        # original item. We have two lists-- one for TO-relationships, and one for
1687        # FROM-relationships and entities.
1688        my @fromPathList = ();
1689        my @toPathList = ();
1690        # This final list is used to remember what work still needs to be done. We push paths
1691        # onto the list, then pop them off to extend the paths. We prime it with the starting
1692        # point. Note that we will work hard to insure that the last item on a path in the
1693        # to-do list is always an entity.
1694        my @todoList = ([$entityName]);
1695        while (@todoList) {
1696            # Get the current path.
1697            my $current = pop @todoList;
1698            # Copy it into a list.
1699            my @stackedPath = @{$current};
1700            # Pull off the last item on the path. It will always be an entity.
1701            my $myEntityName = pop @stackedPath;
1702            # Add it to the alreadyFound list.
1703            $alreadyFound{$myEntityName} = 1;
1704            # Figure out if we need to delete this entity.
1705            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1706                # Get the entity data.
1707                my $entityData = $self->_GetStructure($myEntityName);
1708                # Loop through the entity's relations. A DELETE command will be needed for each of them.
1709                my $relations = $entityData->{Relations};
1710                for my $relation (keys %{$relations}) {
1711                    my @augmentedList = (@stackedPath, $relation);
1712                    push @fromPathList, \@augmentedList;
1713                }
1714            }
1715            # Now we need to look for relationships connected to this entity.
1716            my $relationshipList = $self->{_metaData}->{Relationships};
1717            for my $relationshipName (keys %{$relationshipList}) {
1718                my $relationship = $relationshipList->{$relationshipName};
1719                # Check the FROM field. We're only interested if it's us.
1720                if ($relationship->{from} eq $myEntityName) {
1721                    # Add the path to this relationship.
1722                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1723                    push @fromPathList, \@augmentedList;
1724                    # Check the arity. If it's MM we're done. If it's 1M
1725                    # and the target hasn't been seen yet, we want to
1726                    # stack the entity for future processing.
1727                    if ($relationship->{arity} eq '1M') {
1728                        my $toEntity = $relationship->{to};
1729                        if (! exists $alreadyFound{$toEntity}) {
1730                            # Here we have a new entity that's dependent on
1731                            # the current entity, so we need to stack it.
1732                            my @stackList = (@augmentedList, $toEntity);
1733                            push @fromPathList, \@stackList;
1734                        } else {
1735                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1736                        }
1737                    }
1738                }
1739                # Now check the TO field. In this case only the relationship needs
1740                # deletion.
1741                if ($relationship->{to} eq $myEntityName) {
1742                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1743                    push @toPathList, \@augmentedList;
1744                }
1745            }
1746        }
1747        # Create the first qualifier for the WHERE clause. This selects the
1748        # keys of the primary entity records to be deleted. When we're deleting
1749        # from a dependent table, we construct a join path from the first qualifier
1750        # to the table containing the dependent records to delete.
1751        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1752        # We need to make two passes. The first is through the to-list, and
1753        # the second through the from-list. The from-list is second because
1754        # the to-list may need to pass through some of the entities the
1755        # from-list would delete.
1756        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1757        # Now it's time to do the deletes. We do it in two passes.
1758        for my $keyName ('to_link', 'from_link') {
1759            # Get the list for this key.
1760            my @pathList = @{$stackList{$keyName}};
1761            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1762            # Loop through this list.
1763            while (my $path = pop @pathList) {
1764                # Get the table whose rows are to be deleted.
1765                my @pathTables = @{$path};
1766                # Start the DELETE statement. We need to call DBKernel because the
1767                # syntax of a DELETE-USING varies among DBMSs.
1768                my $target = $pathTables[$#pathTables];
1769                my $stmt = $db->SetUsing(@pathTables);
1770                # Now start the WHERE. The first thing is the ID field from the starting table. That
1771                # starting table will either be the entity relation or one of the entity's
1772                # sub-relations.
1773                $stmt .= " WHERE $pathTables[0].id $qualifier";
1774                # Now we run through the remaining entities in the path, connecting them up.
1775                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1776                    # Connect the current relationship to the preceding entity.
1777                    my ($entity, $rel) = @pathTables[$i-1,$i];
1778                    # The style of connection depends on the direction of the relationship.
1779                    $stmt .= " AND $entity.id = $rel.$keyName";
1780                    if ($i + 1 <= $#pathTables) {
1781                        # Here there's a next entity, so connect that to the relationship's
1782                        # to-link.
1783                        my $entity2 = $pathTables[$i+1];
1784                        $stmt .= " AND $rel.to_link = $entity2.id";
1785                    }
1786                }
1787                # Now we have our desired DELETE statement.
1788                if ($options{testMode}) {
1789                    # Here the user wants to trace without executing.
1790                    Trace($stmt) if T(0);
1791                } else {
1792                    # Here we can delete. Note that the SQL method dies with a confession
1793                    # if an error occurs, so we just go ahead and do it.
1794                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1795                    my $rv = $db->SQL($stmt, 0, $objectID);
1796                    # Accumulate the statistics for this delete. The only rows deleted
1797                    # are from the target table, so we use its name to record the
1798                    # statistic.
1799                    $retVal->Add($target, $rv);
1800                }
1801            }
1802        }
1803        # Return the result.
1804        return $retVal;
1805    }
1806    
1807    =head3 Disconnect
1808    
1809    C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1810    
1811    Disconnect an entity instance from all the objects to which it is related. This
1812    will delete each relationship instance that connects to the specified entity.
1813    
1814    =over 4
1815    
1816    =item relationshipName
1817    
1818    Name of the relationship whose instances are to be deleted.
1819    
1820    =item originEntityName
1821    
1822    Name of the entity that is to be disconnected.
1823    
1824    =item originEntityID
1825    
1826    ID of the entity that is to be disconnected.
1827    
1828    =back
1829    
1830    =cut
1831    
1832    sub Disconnect {
1833        # Get the parameters.
1834        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1835        # Get the relationship descriptor.
1836        my $structure = $self->_GetStructure($relationshipName);
1837        # Insure we have a relationship.
1838        if (! exists $structure->{from}) {
1839            Confess("$relationshipName is not a relationship in the database.");
1840        } else {
1841            # Get the database handle.
1842            my $dbh = $self->{_dbh};
1843            # We'll set this value to 1 if we find our entity.
1844            my $found = 0;
1845            # Loop through the ends of the relationship.
1846            for my $dir ('from', 'to') {
1847                if ($structure->{$dir} eq $originEntityName) {
1848                    # Delete all relationship instances on this side of the entity instance.
1849                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
1850                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1851                    $found = 1;
1852                }
1853            }
1854            # Insure we found the entity on at least one end.
1855            if (! $found) {
1856                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1857            }
1858        }
1859    }
1860    
1861    =head3 DeleteRow
1862    
1863    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1864    
1865    Delete a row from a relationship. In most cases, only the from-link and to-link are
1866    needed; however, for relationships with intersection data values can be specified
1867    for the other fields using a hash.
1868    
1869    =over 4
1870    
1871    =item relationshipName
1872    
1873    Name of the relationship from which the row is to be deleted.
1874    
1875    =item fromLink
1876    
1877    ID of the entity instance in the From direction.
1878    
1879    =item toLink
1880    
1881    ID of the entity instance in the To direction.
1882    
1883    =item values
1884    
1885    Reference to a hash of other values to be used for filtering the delete.
1886    
1887    =back
1888    
1889    =cut
1890    
1891    sub DeleteRow {
1892        # Get the parameters.
1893        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1894        # Create a hash of all the filter information.
1895        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1896        if (defined $values) {
1897            for my $key (keys %{$values}) {
1898                $filter{$key} = $values->{$key};
1899            }
1900        }
1901        # Build an SQL statement out of the hash.
1902        my @filters = ();
1903        my @parms = ();
1904        for my $key (keys %filter) {
1905            push @filters, _FixName($key) . " = ?";
1906            push @parms, $filter{$key};
1907        }
1908        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1909        my $command = "DELETE FROM $relationshipName WHERE " .
1910                      join(" AND ", @filters);
1911        # Execute it.
1912        my $dbh = $self->{_dbh};
1913        $dbh->SQL($command, undef, @parms);
1914    }
1915    
1916    =head3 SortNeeded
1917    
1918    C<< my $parms = $erdb->SortNeeded($relationName); >>
1919    
1920    Return the pipe command for the sort that should be applied to the specified
1921    relation when creating the load file.
1922    
1923    For example, if the load file should be sorted ascending by the first
1924    field, this method would return
1925    
1926        sort -k1 -t"\t"
1927    
1928    If the first field is numeric, the method would return
1929    
1930        sort -k1n -t"\t"
1931    
1932    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1933    keys using a sort.
1934    
1935    =over 4
1936    
1937    =item relationName
1938    
1939    Name of the relation to be examined.
1940    
1941    =item
1942    
1943    Returns the sort command to use for sorting the relation, suitable for piping.
1944    
1945    =back
1946    
1947    =cut
1948    #: Return Type $;
1949    sub SortNeeded {
1950        # Get the parameters.
1951        my ($self, $relationName) = @_;
1952        # Declare a descriptor to hold the names of the key fields.
1953        my @keyNames = ();
1954        # Get the relation structure.
1955        my $relationData = $self->_FindRelation($relationName);
1956        # Find out if the relation is a primary entity relation,
1957        # a relationship relation, or a secondary entity relation.
1958        my $entityTable = $self->{_metaData}->{Entities};
1959        my $relationshipTable = $self->{_metaData}->{Relationships};
1960        if (exists $entityTable->{$relationName}) {
1961            # Here we have a primary entity relation.
1962            push @keyNames, "id";
1963        } elsif (exists $relationshipTable->{$relationName}) {
1964            # Here we have a relationship. We sort using the FROM index.
1965            my $relationshipData = $relationshipTable->{$relationName};
1966            my $index = $relationData->{Indexes}->{idxFrom};
1967            push @keyNames, @{$index->{IndexFields}};
1968        } else {
1969            # Here we have a secondary entity relation, so we have a sort on the ID field.
1970            push @keyNames, "id";
1971        }
1972        # Now we parse the key names into sort parameters. First, we prime the return
1973        # string.
1974        my $retVal = "sort -t\"\t\" ";
1975        # Get the relation's field list.
1976        my @fields = @{$relationData->{Fields}};
1977        # Loop through the keys.
1978        for my $keyData (@keyNames) {
1979            # Get the key and the ordering.
1980            my ($keyName, $ordering);
1981            if ($keyData =~ /^([^ ]+) DESC/) {
1982                ($keyName, $ordering) = ($1, "descending");
1983            } else {
1984                ($keyName, $ordering) = ($keyData, "ascending");
1985            }
1986            # Find the key's position and type.
1987            my $fieldSpec;
1988            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1989                my $thisField = $fields[$i];
1990                if ($thisField->{name} eq $keyName) {
1991                    # Get the sort modifier for this field type. The modifier
1992                    # decides whether we're using a character, numeric, or
1993                    # floating-point sort.
1994                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1995                    # If the index is descending for this field, denote we want
1996                    # to reverse the sort order on this field.
1997                    if ($ordering eq 'descending') {
1998                        $modifier .= "r";
1999                    }
2000                    # Store the position and modifier into the field spec, which
2001                    # will stop the inner loop. Note that the field number is
2002                    # 1-based in the sort command, so we have to increment the
2003                    # index.
2004                    $fieldSpec = ($i + 1) . $modifier;
2005                }
2006            }
2007            # Add this field to the sort command.
2008            $retVal .= " -k$fieldSpec";
2009        }
2010        # Return the result.
2011        return $retVal;
2012    }
2013    
2014    =head3 GetList
2015    
2016    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2017    
2018    Return a list of object descriptors for the specified objects as determined by the
2019    specified filter clause.
2020    
2021    This method is essentially the same as L</Get> except it returns a list of objects rather
2022    than a query object that can be used to get the results one record at a time.
2023    
2024    =over 4
2025    
2026    =item objectNames
2027    
2028    List containing the names of the entity and relationship objects to be retrieved.
2029    
2030    =item filterClause
2031    
2032    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2033    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2034    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2035    in the filter clause should be added to the parameter list as additional parameters. The
2036    fields in a filter clause can come from primary entity relations, relationship relations,
2037    or secondary entity relations; however, all of the entities and relationships involved must
2038    be included in the list of object names.
2039    
2040    The filter clause can also specify a sort order. To do this, simply follow the filter string
2041    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2042    particular genus and sorts them by species name.
2043    
2044    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2045    
2046    The rules for field references in a sort order are the same as those for field references in the
2047    filter clause in general; however, odd things may happen if a sort field is from a secondary
2048    relation.
2049    
2050    =item params
2051    
2052    Reference to a list of parameter values to be substituted into the filter clause.
2053    
2054    =item RETURN
2055    
2056    Returns a list of B<DBObject>s that satisfy the query conditions.
2057    
2058    =back
2059    
2060    =cut
2061    #: Return Type @%
2062    sub GetList {
2063        # Get the parameters.
2064        my ($self, $objectNames, $filterClause, $params) = @_;
2065        # Declare the return variable.
2066        my @retVal = ();
2067        # Perform the query.
2068        my $query = $self->Get($objectNames, $filterClause, $params);
2069        # Loop through the results.
2070        while (my $object = $query->Fetch) {
2071            push @retVal, $object;
2072        }
2073        # Return the result.
2074        return @retVal;
2075    }
2076    
2077    =head3 GetCount
2078    
2079    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2080    
2081    Return the number of rows found by a specified query. This method would
2082    normally be used to count the records in a single table. For example, in a
2083    genetics database
2084    
2085        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2086    
2087    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2088    to use it to return records based on a join. For example,
2089    
2090        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2091                                    ['homo %']);
2092    
2093    would return the number of features for genomes in the genus I<homo>. Note that
2094    only the rows from the first table are counted. If the above command were
2095    
2096        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2097                                    ['homo %']);
2098    
2099    it would return the number of genomes, not the number of genome/feature pairs.
2100    
2101    =over 4
2102    
2103    =item objectNames
2104    
2105    Reference to a list of the objects (entities and relationships) included in the
2106    query.
2107    
2108    =item filter
2109    
2110    A filter clause for restricting the query. The rules are the same as for the L</Get>
2111    method.
2112    
2113    =item params
2114    
2115    Reference to a list of the parameter values to be substituted for the parameter marks
2116    in the filter.
2117    
2118    =item RETURN
2119    
2120    Returns a count of the number of records in the first table that would satisfy
2121    the query.
2122    
2123    =back
2124    
2125    =cut
2126    
2127    sub GetCount {
2128        # Get the parameters.
2129        my ($self, $objectNames, $filter, $params) = @_;
2130        # Insure the params argument is an array reference if the caller left it off.
2131        if (! defined($params)) {
2132            $params = [];
2133        }
2134        # Declare the return variable.
2135        my $retVal;
2136        # Find out if we're counting an entity or a relationship.
2137        my $countedField;
2138        if ($self->IsEntity($objectNames->[0])) {
2139            $countedField = "id";
2140        } else {
2141            # For a relationship we count the to-link because it's usually more
2142            # numerous. Note we're automatically converting to the SQL form
2143            # of the field name (to_link vs. to-link).
2144            $countedField = "to_link";
2145        }
2146        # Create the SQL command suffix to get the desired records.
2147        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2148                                                                                $filter);
2149        # Prefix it with text telling it we want a record count.
2150        my $firstObject = $mappedNameListRef->[0];
2151        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2152        # Prepare and execute the command.
2153        my $sth = $self->_GetStatementHandle($command, $params);
2154        # Get the count value.
2155        ($retVal) = $sth->fetchrow_array();
2156        # Check for a problem.
2157        if (! defined($retVal)) {
2158            if ($sth->err) {
2159                # Here we had an SQL error.
2160                Confess("Error retrieving row count: " . $sth->errstr());
2161            } else {
2162                # Here we have no result.
2163                Confess("No result attempting to retrieve row count.");
2164            }
2165        }
2166        # Return the result.
2167        return $retVal;
2168    }
2169    
2170    =head3 ComputeObjectSentence
2171    
2172    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2173    
2174    Check an object name, and if it is a relationship convert it to a relationship sentence.
2175    
2176    =over 4
2177    
2178    =item objectName
2179    
2180    Name of the entity or relationship.
2181    
2182    =item RETURN
2183    
2184    Returns a string containing the entity name or a relationship sentence.
2185    
2186    =back
2187    
2188    =cut
2189    
2190    sub ComputeObjectSentence {
2191        # Get the parameters.
2192        my ($self, $objectName) = @_;
2193        # Set the default return value.
2194        my $retVal = $objectName;
2195        # Look for the object as a relationship.
2196        my $relTable = $self->{_metaData}->{Relationships};
2197        if (exists $relTable->{$objectName}) {
2198            # Get the relationship sentence.
2199            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2200        }
2201        # Return the result.
2202        return $retVal;
2203    }
2204    
2205    =head3 DumpRelations
2206    
2207    C<< $erdb->DumpRelations($outputDirectory); >>
2208    
2209    Write the contents of all the relations to tab-delimited files in the specified directory.
2210    Each file will have the same name as the relation dumped, with an extension of DTX.
2211    
2212    =over 4
2213    
2214    =item outputDirectory
2215    
2216    Name of the directory into which the relation files should be dumped.
2217    
2218    =back
2219    
2220    =cut
2221    
2222    sub DumpRelations {
2223        # Get the parameters.
2224        my ($self, $outputDirectory) = @_;
2225        # Now we need to run through all the relations. First, we loop through the entities.
2226        my $metaData = $self->{_metaData};
2227        my $entities = $metaData->{Entities};
2228        for my $entityName (keys %{$entities}) {
2229            my $entityStructure = $entities->{$entityName};
2230            # Get the entity's relations.
2231            my $relationList = $entityStructure->{Relations};
2232            # Loop through the relations, dumping them.
2233            for my $relationName (keys %{$relationList}) {
2234                my $relation = $relationList->{$relationName};
2235                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2236            }
2237        }
2238        # Next, we loop through the relationships.
2239        my $relationships = $metaData->{Relationships};
2240        for my $relationshipName (keys %{$relationships}) {
2241            my $relationshipStructure = $relationships->{$relationshipName};
2242            # Dump this relationship's relation.
2243            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2244        }
2245    }
2246    
2247    =head3 InsertValue
2248    
2249    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2250    
2251    This method will insert a new value into the database. The value must be one
2252    associated with a secondary relation, since primary values cannot be inserted:
2253    they occur exactly once. Secondary values, on the other hand, can be missing
2254    or multiply-occurring.
2255    
2256    =over 4
2257    
2258    =item entityID
2259    
2260    ID of the object that is to receive the new value.
2261    
2262    =item fieldName
2263    
2264    Field name for the new value-- this includes the entity name, since
2265    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2266    
2267    =item value
2268    
2269    New value to be put in the field.
2270    
2271    =back
2272    
2273    =cut
2274    
2275    sub InsertValue {
2276        # Get the parameters.
2277        my ($self, $entityID, $fieldName, $value) = @_;
2278        # Parse the entity name and the real field name.
2279        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2280            my $entityName = $1;
2281            my $fieldTitle = $2;
2282            # Get its descriptor.
2283            if (!$self->IsEntity($entityName)) {
2284                Confess("$entityName is not a valid entity.");
2285            } else {
2286                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2287                # Find the relation containing this field.
2288                my $fieldHash = $entityData->{Fields};
2289                if (! exists $fieldHash->{$fieldTitle}) {
2290                    Confess("$fieldTitle not found in $entityName.");
2291                } else {
2292                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2293                    if ($relation eq $entityName) {
2294                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2295                    } else {
2296                        # Now we can create an INSERT statement.
2297                        my $dbh = $self->{_dbh};
2298                        my $fixedName = _FixName($fieldTitle);
2299                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2300                        # Execute the command.
2301                        $dbh->SQL($statement, 0, $entityID, $value);
2302                    }
2303                }
2304            }
2305        } else {
2306            Confess("$fieldName is not a valid field name.");
2307        }
2308    }
2309    
2310    =head3 InsertObject
2311    
2312    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2313    
2314    Insert an object into the database. The object is defined by a type name and then a hash
2315    of field names to values. Field values in the primary relation are represented by scalars.
2316    (Note that for relationships, the primary relation is the B<only> relation.)
2317    Field values for the other relations comprising the entity are always list references. For
2318    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2319    C<ZP_00210270.1> and C<gi|46206278>.
2320    
2321    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2322    
2323    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2324    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2325    
2326    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2327    
2328    =over 4
2329    
2330    =item newObjectType
2331    
2332    Type name of the object to insert.
2333    
2334    =item fieldHash
2335    
2336    Hash of field names to values.
2337    
2338    =back
2339    
2340    =cut
2341    
2342    sub InsertObject {
2343        # Get the parameters.
2344        my ($self, $newObjectType, $fieldHash) = @_;
2345        # Denote that so far we appear successful.
2346        my $retVal = 1;
2347        # Get the database handle.
2348        my $dbh = $self->{_dbh};
2349          # Get the relation list.          # Get the relation list.
2350          my $relationTable = $self->_GetRelationTable($newObjectType);          my $relationTable = $self->_GetRelationTable($newObjectType);
2351          # Loop through the relations. We'll build insert statements for each one. If a relation is          # Loop through the relations. We'll build insert statements for each one. If a relation is
2352          # secondary, we may end up generating multiple insert statements. If an error occurs, we          # secondary, we may end up generating multiple insert statements. If an error occurs, we
2353          # stop the loop.          # stop the loop.
2354          while ($retVal && (my ($relationName, $relationDefinition) = each %{$relationTable})) {      my @relationList = keys %{$relationTable};
2355        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2356            my $relationName = $relationList[$i];
2357            my $relationDefinition = $relationTable->{$relationName};
2358                  # Get the relation's fields. For each field we will collect a value in the corresponding                  # Get the relation's fields. For each field we will collect a value in the corresponding
2359                  # position of the @valueList array. If one of the fields is missing, we will add it to the                  # position of the @valueList array. If one of the fields is missing, we will add it to the
2360                  # @missing list.                  # @missing list.
# Line 897  Line 2387 
2387                                                  $retVal = 0;                                                  $retVal = 0;
2388                                          }                                          }
2389                                  }                                  }
2390                          } else {              } else {
2391                                  # Here the field is not present. Flag it as missing.                  # Here the field is not present. Flag it as missing.
2392                                  push @missing, $fieldName;                  push @missing, $fieldName;
2393                }
2394            }
2395            # If we are the primary relation, add the new-record flag.
2396            if ($relationName eq $newObjectType) {
2397                push @valueList, 1;
2398                push @fieldNameList, "new_record";
2399            }
2400            # Only proceed if there are no missing fields.
2401            if (@missing > 0) {
2402                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2403                    join(' ', @missing)) if T(1);
2404            } else {
2405                # Build the INSERT statement.
2406                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2407                    ") VALUES (";
2408                # Create a marker list of the proper size and put it in the statement.
2409                my @markers = ();
2410                while (@markers < @fieldNameList) { push @markers, '?'; }
2411                $statement .= join(', ', @markers) . ")";
2412                # We have the insert statement, so prepare it.
2413                my $sth = $dbh->prepare_command($statement);
2414                Trace("Insert statement prepared: $statement") if T(3);
2415                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2416                # a list, we use the current element. The values are stored in the @parameterList array.
2417                my $done = 0;
2418                for (my $i = 0; $i < $recordCount; $i++) {
2419                    # Clear the parameter list array.
2420                    my @parameterList = ();
2421                    # Loop through the values.
2422                    for my $value (@valueList) {
2423                        # Check to see if this is a scalar value.
2424                        if (ref $value eq "ARRAY") {
2425                            # Here we have a list value. Pull the current entry.
2426                            push @parameterList, $value->[$i];
2427                        } else {
2428                            # Here we have a scalar value. Use it unmodified.
2429                            push @parameterList, $value;
2430                        }
2431                    }
2432                    # Execute the INSERT statement with the specified parameter list.
2433                    $retVal = $sth->execute(@parameterList);
2434                    if (!$retVal) {
2435                        my $errorString = $sth->errstr();
2436                        Confess("Error inserting into $relationName: $errorString");
2437                    } else {
2438                        Trace("Insert successful using $parameterList[0].") if T(3);
2439                    }
2440                }
2441            }
2442        }
2443        # Return a 1 for backward compatability.
2444        return 1;
2445    }
2446    
2447    =head3 UpdateEntity
2448    
2449    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2450    
2451    Update the values of an entity. This is an unprotected update, so it should only be
2452    done if the database resides on a database server.
2453    
2454    =over 4
2455    
2456    =item entityName
2457    
2458    Name of the entity to update. (This is the entity type.)
2459    
2460    =item id
2461    
2462    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2463    
2464    =item fields
2465    
2466    Reference to a hash mapping field names to their new values. All of the fields named
2467    must be in the entity's primary relation, and they cannot any of them be the ID field.
2468    
2469    =back
2470    
2471    =cut
2472    
2473    sub UpdateEntity {
2474        # Get the parameters.
2475        my ($self, $entityName, $id, $fields) = @_;
2476        # Get a list of the field names being updated.
2477        my @fieldList = keys %{$fields};
2478        # Verify that the fields exist.
2479        my $checker = $self->GetFieldTable($entityName);
2480        for my $field (@fieldList) {
2481            if ($field eq 'id') {
2482                Confess("Cannot update the ID field for entity $entityName.");
2483            } elsif ($checker->{$field}->{relation} ne $entityName) {
2484                Confess("Cannot find $field in primary relation of $entityName.");
2485            }
2486        }
2487        # Build the SQL statement.
2488        my @sets = ();
2489        my @valueList = ();
2490        for my $field (@fieldList) {
2491            push @sets, _FixName($field) . " = ?";
2492            push @valueList, $fields->{$field};
2493        }
2494        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2495        # Add the ID to the list of binding values.
2496        push @valueList, $id;
2497        # Call SQL to do the work.
2498        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2499        # Check for errors.
2500        if ($rows == 0) {
2501            Confess("Entity $id of type $entityName not found.");
2502        }
2503    }
2504    
2505    =head3 LoadTable
2506    
2507    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2508    
2509    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2510    first.
2511    
2512    =over 4
2513    
2514    =item fileName
2515    
2516    Name of the file from which the table data should be loaded.
2517    
2518    =item relationName
2519    
2520    Name of the relation to be loaded. This is the same as the table name.
2521    
2522    =item truncateFlag
2523    
2524    TRUE if the table should be dropped and re-created, else FALSE
2525    
2526    =item RETURN
2527    
2528    Returns a statistical object containing a list of the error messages.
2529    
2530    =back
2531    
2532    =cut
2533    sub LoadTable {
2534        # Get the parameters.
2535        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2536        # Create the statistical return object.
2537        my $retVal = _GetLoadStats();
2538        # Trace the fact of the load.
2539        Trace("Loading table $relationName from $fileName") if T(2);
2540        # Get the database handle.
2541        my $dbh = $self->{_dbh};
2542        # Get the input file size.
2543        my $fileSize = -s $fileName;
2544        # Get the relation data.
2545        my $relation = $self->_FindRelation($relationName);
2546        # Check the truncation flag.
2547        if ($truncateFlag) {
2548            Trace("Creating table $relationName") if T(2);
2549            # Compute the row count estimate. We take the size of the load file,
2550            # divide it by the estimated row size, and then multiply by 1.5 to
2551            # leave extra room. We postulate a minimum row count of 1000 to
2552            # prevent problems with incoming empty load files.
2553            my $rowSize = $self->EstimateRowSize($relationName);
2554            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2555            # Re-create the table without its index.
2556            $self->CreateTable($relationName, 0, $estimate);
2557            # If this is a pre-index DBMS, create the index here.
2558            if ($dbh->{_preIndex}) {
2559                eval {
2560                    $self->CreateIndex($relationName);
2561                };
2562                if ($@) {
2563                    $retVal->AddMessage($@);
2564                }
2565            }
2566        }
2567        # Load the table.
2568        my $rv;
2569        eval {
2570            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2571        };
2572        if (!defined $rv) {
2573            $retVal->AddMessage($@) if ($@);
2574            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2575            Trace("Table load failed for $relationName.") if T(1);
2576        } else {
2577            # Here we successfully loaded the table.
2578            $retVal->Add("tables");
2579            my $size = -s $fileName;
2580            Trace("$size bytes loaded into $relationName.") if T(2);
2581            # If we're rebuilding, we need to create the table indexes.
2582            if ($truncateFlag) {
2583                # Indexes are created here for PostGres. For PostGres, indexes are
2584                # best built at the end. For MySQL, the reverse is true.
2585                if (! $dbh->{_preIndex}) {
2586                    eval {
2587                        $self->CreateIndex($relationName);
2588                    };
2589                    if ($@) {
2590                        $retVal->AddMessage($@);
2591                    }
2592                }
2593                # The full-text index (if any) is always built last, even for MySQL.
2594                # First we need to see if this table has a full-text index. Only
2595                # primary relations are allowed that privilege.
2596                Trace("Checking for full-text index on $relationName.") if T(2);
2597                if ($self->_IsPrimary($relationName)) {
2598                    $self->CreateSearchIndex($relationName);
2599                }
2600            }
2601        }
2602        # Analyze the table to improve performance.
2603        Trace("Analyzing and compacting $relationName.") if T(3);
2604        $dbh->vacuum_it($relationName);
2605        Trace("$relationName load completed.") if T(3);
2606        # Return the statistics.
2607        return $retVal;
2608    }
2609    
2610    =head3 CreateSearchIndex
2611    
2612    C<< $erdb->CreateSearchIndex($objectName); >>
2613    
2614    Check for a full-text search index on the specified entity or relationship object, and
2615    if one is required, rebuild it.
2616    
2617    =over 4
2618    
2619    =item objectName
2620    
2621    Name of the entity or relationship to be indexed.
2622    
2623    =back
2624    
2625    =cut
2626    
2627    sub CreateSearchIndex {
2628        # Get the parameters.
2629        my ($self, $objectName) = @_;
2630        # Get the relation's entity/relationship structure.
2631        my $structure = $self->_GetStructure($objectName);
2632        # Get the database handle.
2633        my $dbh = $self->{_dbh};
2634        Trace("Checking for search fields in $objectName.") if T(3);
2635        # Check for a searchable fields list.
2636        if (exists $structure->{searchFields}) {
2637            # Here we know that we need to create a full-text search index.
2638            # Get an SQL-formatted field name list.
2639            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2640            # Create the index. If it already exists, it will be dropped.
2641            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2642                               flds => $fields, kind => 'fulltext');
2643            Trace("Index created for $fields in $objectName.") if T(2);
2644        }
2645    }
2646    
2647    =head3 DropRelation
2648    
2649    C<< $erdb->DropRelation($relationName); >>
2650    
2651    Physically drop a relation from the database.
2652    
2653    =over 4
2654    
2655    =item relationName
2656    
2657    Name of the relation to drop. If it does not exist, this method will have
2658    no effect.
2659    
2660    =back
2661    
2662    =cut
2663    
2664    sub DropRelation {
2665        # Get the parameters.
2666        my ($self, $relationName) = @_;
2667        # Get the database handle.
2668        my $dbh = $self->{_dbh};
2669        # Drop the relation. The method used here has no effect if the relation
2670        # does not exist.
2671        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2672        $dbh->drop_table(tbl => $relationName);
2673    }
2674    
2675    =head3 MatchSqlPattern
2676    
2677    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2678    
2679    Determine whether or not a specified value matches an SQL pattern. An SQL
2680    pattern has two wild card characters: C<%> that matches multiple characters,
2681    and C<_> that matches a single character. These can be escaped using a
2682    backslash (C<\>). We pull this off by converting the SQL pattern to a
2683    PERL regular expression. As per SQL rules, the match is case-insensitive.
2684    
2685    =over 4
2686    
2687    =item value
2688    
2689    Value to be matched against the pattern. Note that an undefined or empty
2690    value will not match anything.
2691    
2692    =item pattern
2693    
2694    SQL pattern against which to match the value. An undefined or empty pattern will
2695    match everything.
2696    
2697    =item RETURN
2698    
2699    Returns TRUE if the value and pattern match, else FALSE.
2700    
2701    =back
2702    
2703    =cut
2704    
2705    sub MatchSqlPattern {
2706        # Get the parameters.
2707        my ($value, $pattern) = @_;
2708        # Declare the return variable.
2709        my $retVal;
2710        # Insure we have a pattern.
2711        if (! defined($pattern) || $pattern eq "") {
2712            $retVal = 1;
2713        } else {
2714            # Break the pattern into pieces around the wildcard characters. Because we
2715            # use parentheses in the split function's delimiter expression, we'll get
2716            # list elements for the delimiters as well as the rest of the string.
2717            my @pieces = split /([_%]|\\[_%])/, $pattern;
2718            # Check some fast special cases.
2719            if ($pattern eq '%') {
2720                # A null pattern matches everything.
2721                $retVal = 1;
2722            } elsif (@pieces == 1) {
2723                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2724                $retVal = (lc($value) eq lc($pattern));
2725            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2726                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2727                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2728            } else {
2729                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2730                my $realPattern = "";
2731                for my $piece (@pieces) {
2732                    # Determine the type of piece.
2733                    if ($piece eq "") {
2734                        # Empty pieces are ignored.
2735                    } elsif ($piece eq "%") {
2736                        # Here we have a multi-character wildcard. Note that it can match
2737                        # zero or more characters.
2738                        $realPattern .= ".*"
2739                    } elsif ($piece eq "_") {
2740                        # Here we have a single-character wildcard.
2741                        $realPattern .= ".";
2742                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2743                        # This is an escape sequence (which is a rare thing, actually).
2744                        $realPattern .= substr($piece, 1, 1);
2745                    } else {
2746                        # Here we have raw text.
2747                        $realPattern .= quotemeta($piece);
2748                    }
2749                }
2750                # Do the match.
2751                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2752            }
2753        }
2754        # Return the result.
2755        return $retVal;
2756    }
2757    
2758    =head3 GetEntity
2759    
2760    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2761    
2762    Return an object describing the entity instance with a specified ID.
2763    
2764    =over 4
2765    
2766    =item entityType
2767    
2768    Entity type name.
2769    
2770    =item ID
2771    
2772    ID of the desired entity.
2773    
2774    =item RETURN
2775    
2776    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2777    instance is found with the specified key.
2778    
2779    =back
2780    
2781    =cut
2782    
2783    sub GetEntity {
2784        # Get the parameters.
2785        my ($self, $entityType, $ID) = @_;
2786        # Create a query.
2787        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2788        # Get the first (and only) object.
2789        my $retVal = $query->Fetch();
2790        # Return the result.
2791        return $retVal;
2792    }
2793    
2794    =head3 GetChoices
2795    
2796    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2797    
2798    Return a list of all the values for the specified field that are represented in the
2799    specified entity.
2800    
2801    Note that if the field is not indexed, then this will be a very slow operation.
2802    
2803    =over 4
2804    
2805    =item entityName
2806    
2807    Name of an entity in the database.
2808    
2809    =item fieldName
2810    
2811    Name of a field belonging to the entity. This is a raw field name without
2812    the standard parenthesized notation used in most calls.
2813    
2814    =item RETURN
2815    
2816    Returns a list of the distinct values for the specified field in the database.
2817    
2818    =back
2819    
2820    =cut
2821    
2822    sub GetChoices {
2823        # Get the parameters.
2824        my ($self, $entityName, $fieldName) = @_;
2825        # Declare the return variable.
2826        my @retVal;
2827        # Get the entity data structure.
2828        my $entityData = $self->_GetStructure($entityName);
2829        # Get the field.
2830        my $fieldHash = $entityData->{Fields};
2831        if (! exists $fieldHash->{$fieldName}) {
2832            Confess("$fieldName not found in $entityName.");
2833        } else {
2834            # Get the name of the relation containing the field.
2835            my $relation = $fieldHash->{$fieldName}->{relation};
2836            # Fix up the field name.
2837            my $realName = _FixName($fieldName);
2838            # Get the database handle.
2839            my $dbh = $self->{_dbh};
2840            # Query the database.
2841            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2842            # Clean the results. They are stored as a list of lists, and we just want the one list.
2843            @retVal = sort map { $_->[0] } @{$results};
2844        }
2845        # Return the result.
2846        return @retVal;
2847    }
2848    
2849    =head3 GetEntityValues
2850    
2851    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2852    
2853    Return a list of values from a specified entity instance. If the entity instance
2854    does not exist, an empty list is returned.
2855    
2856    =over 4
2857    
2858    =item entityType
2859    
2860    Entity type name.
2861    
2862    =item ID
2863    
2864    ID of the desired entity.
2865    
2866    =item fields
2867    
2868    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2869    
2870    =item RETURN
2871    
2872    Returns a flattened list of the values of the specified fields for the specified entity.
2873    
2874    =back
2875    
2876    =cut
2877    
2878    sub GetEntityValues {
2879        # Get the parameters.
2880        my ($self, $entityType, $ID, $fields) = @_;
2881        # Get the specified entity.
2882        my $entity = $self->GetEntity($entityType, $ID);
2883        # Declare the return list.
2884        my @retVal = ();
2885        # If we found the entity, push the values into the return list.
2886        if ($entity) {
2887            push @retVal, $entity->Values($fields);
2888        }
2889        # Return the result.
2890        return @retVal;
2891    }
2892    
2893    =head3 GetAll
2894    
2895    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2896    
2897    Return a list of values taken from the objects returned by a query. The first three
2898    parameters correspond to the parameters of the L</Get> method. The final parameter is
2899    a list of the fields desired from each record found by the query. The field name
2900    syntax is the standard syntax used for fields in the B<ERDB> system--
2901    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2902    or relationship and I<fieldName> is the name of the field.
2903    
2904    The list returned will be a list of lists. Each element of the list will contain
2905    the values returned for the fields specified in the fourth parameter. If one of the
2906    fields specified returns multiple values, they are flattened in with the rest. For
2907    example, the following call will return a list of the features in a particular
2908    spreadsheet cell, and each feature will be represented by a list containing the
2909    feature ID followed by all of its aliases.
2910    
2911    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2912    
2913    =over 4
2914    
2915    =item objectNames
2916    
2917    List containing the names of the entity and relationship objects to be retrieved.
2918    
2919    =item filterClause
2920    
2921    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2922    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2923    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2924    parameter list as additional parameters. The fields in a filter clause can come from primary
2925    entity relations, relationship relations, or secondary entity relations; however, all of the
2926    entities and relationships involved must be included in the list of object names.
2927    
2928    =item parameterList
2929    
2930    List of the parameters to be substituted in for the parameters marks in the filter clause.
2931    
2932    =item fields
2933    
2934    List of the fields to be returned in each element of the list returned.
2935    
2936    =item count
2937    
2938    Maximum number of records to return. If omitted or 0, all available records will be returned.
2939    
2940    =item RETURN
2941    
2942    Returns a list of list references. Each element of the return list contains the values for the
2943    fields specified in the B<fields> parameter.
2944    
2945    =back
2946    
2947    =cut
2948    #: Return Type @@;
2949    sub GetAll {
2950        # Get the parameters.
2951        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2952        # Translate the parameters from a list reference to a list. If the parameter
2953        # list is a scalar we convert it into a singleton list.
2954        my @parmList = ();
2955        if (ref $parameterList eq "ARRAY") {
2956            Trace("GetAll parm list is an array.") if T(4);
2957            @parmList = @{$parameterList};
2958        } else {
2959            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2960            push @parmList, $parameterList;
2961        }
2962        # Insure the counter has a value.
2963        if (!defined $count) {
2964            $count = 0;
2965        }
2966        # Add the row limit to the filter clause.
2967        if ($count > 0) {
2968            $filterClause .= " LIMIT $count";
2969        }
2970        # Create the query.
2971        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2972        # Set up a counter of the number of records read.
2973        my $fetched = 0;
2974        # Loop through the records returned, extracting the fields. Note that if the
2975        # counter is non-zero, we stop when the number of records read hits the count.
2976        my @retVal = ();
2977        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2978            my @rowData = $row->Values($fields);
2979            push @retVal, \@rowData;
2980            $fetched++;
2981        }
2982        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2983        # Return the resulting list.
2984        return @retVal;
2985    }
2986    
2987    =head3 Exists
2988    
2989    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2990    
2991    Return TRUE if an entity exists, else FALSE.
2992    
2993    =over 4
2994    
2995    =item entityName
2996    
2997    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2998    
2999    =item entityID
3000    
3001    ID of the entity instance whose existence is to be checked.
3002    
3003    =item RETURN
3004    
3005    Returns TRUE if the entity instance exists, else FALSE.
3006    
3007    =back
3008    
3009    =cut
3010    #: Return Type $;
3011    sub Exists {
3012        # Get the parameters.
3013        my ($self, $entityName, $entityID) = @_;
3014        # Check for the entity instance.
3015        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3016        my $testInstance = $self->GetEntity($entityName, $entityID);
3017        # Return an existence indicator.
3018        my $retVal = ($testInstance ? 1 : 0);
3019        return $retVal;
3020    }
3021    
3022    =head3 EstimateRowSize
3023    
3024    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3025    
3026    Estimate the row size of the specified relation. The estimated row size is computed by adding
3027    up the average length for each data type.
3028    
3029    =over 4
3030    
3031    =item relName
3032    
3033    Name of the relation whose estimated row size is desired.
3034    
3035    =item RETURN
3036    
3037    Returns an estimate of the row size for the specified relation.
3038    
3039    =back
3040    
3041    =cut
3042    #: Return Type $;
3043    sub EstimateRowSize {
3044        # Get the parameters.
3045        my ($self, $relName) = @_;
3046        # Declare the return variable.
3047        my $retVal = 0;
3048        # Find the relation descriptor.
3049        my $relation = $self->_FindRelation($relName);
3050        # Get the list of fields.
3051        for my $fieldData (@{$relation->{Fields}}) {
3052            # Get the field type and add its length.
3053            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3054            $retVal += $fieldLen;
3055        }
3056        # Return the result.
3057        return $retVal;
3058                          }                          }
3059    
3060    =head3 GetFieldTable
3061    
3062    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3063    
3064    Get the field structure for a specified entity or relationship.
3065    
3066    =over 4
3067    
3068    =item objectName
3069    
3070    Name of the desired entity or relationship.
3071    
3072    =item RETURN
3073    
3074    The table containing the field descriptors for the specified object.
3075    
3076    =back
3077    
3078    =cut
3079    
3080    sub GetFieldTable {
3081        # Get the parameters.
3082        my ($self, $objectName) = @_;
3083        # Get the descriptor from the metadata.
3084        my $objectData = $self->_GetStructure($objectName);
3085        # Return the object's field table.
3086        return $objectData->{Fields};
3087                  }                  }
3088                  # If we are the primary relation, add the new-record flag.  
3089                  if ($relationName eq $newObjectType) {  =head3 SplitKeywords
3090                          push @valueList, 1;  
3091                          push @fieldNameList, "new_record";  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3092    
3093    This method returns a list of the positive keywords in the specified
3094    keyword string. All of the operators will have been stripped off,
3095    and if the keyword is preceded by a minus operator (C<->), it will
3096    not be in the list returned. The idea here is to get a list of the
3097    keywords the user wants to see. The list will be processed to remove
3098    duplicates.
3099    
3100    It is possible to create a string that confuses this method. For example
3101    
3102        frog toad -frog
3103    
3104    would return both C<frog> and C<toad>. If this is a problem we can deal
3105    with it later.
3106    
3107    =over 4
3108    
3109    =item keywordString
3110    
3111    The keyword string to be parsed.
3112    
3113    =item RETURN
3114    
3115    Returns a list of the words in the keyword string the user wants to
3116    see.
3117    
3118    =back
3119    
3120    =cut
3121    
3122    sub SplitKeywords {
3123        # Get the parameters.
3124        my ($keywordString) = @_;
3125        # Make a safety copy of the string. (This helps during debugging.)
3126        my $workString = $keywordString;
3127        # Convert operators we don't care about to spaces.
3128        $workString =~ tr/+"()<>/ /;
3129        # Split the rest of the string along space boundaries. Note that we
3130        # eliminate any words that are zero length or begin with a minus sign.
3131        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3132        # Use a hash to remove duplicates.
3133        my %words = map { $_ => 1 } @wordList;
3134        # Return the result.
3135        return sort keys %words;
3136                  }                  }
3137                  # Only proceed if there are no missing fields.  
3138                  if (@missing > 0) {  =head3 ValidateFieldName
3139                          Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .  
3140                                  join(' ', @missing)) if T(1);  C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3141                  } else {  
3142                          # Build the INSERT statement.  Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3143                          my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .  be hyphenated words subject to certain restrictions.
3144                                  ") VALUES (";  
3145                          # Create a marker list of the proper size and put it in the statement.  =over 4
3146                          my @markers = ();  
3147                          while (@markers < @fieldNameList) { push @markers, '?'; }  =item fieldName
3148                          $statement .= join(', ', @markers) . ")";  
3149                          # We have the insert statement, so prepare it.  Field name to be validated.
3150                          my $sth = $dbh->prepare_command($statement);  
3151                          Trace("Insert statement prepared: $statement") if T(3);  =item RETURN
3152                          # Now we loop through the values. If a value is scalar, we use it unmodified. If it's  
3153                          # a list, we use the current element. The values are stored in the @parameterList array.  Returns TRUE if the field name is valid, else FALSE.
3154                          my $done = 0;  
3155                          for (my $i = 0; $i < $recordCount; $i++) {  =back
3156                                  # Clear the parameter list array.  
3157                                  my @parameterList = ();  =cut
3158                                  # Loop through the values.  
3159                                  for my $value (@valueList) {  sub ValidateFieldName {
3160                                          # Check to see if this is a scalar value.      # Get the parameters.
3161                                          if (ref $value eq "ARRAY") {      my ($fieldName) = @_;
3162                                                  # Here we have a list value. Pull the current entry.      # Declare the return variable. The field name is valid until we hear
3163                                                  push @parameterList, $value->[$i];      # differently.
3164        my $retVal = 1;
3165        # Compute the maximum name length.
3166        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3167        # Look for bad stuff in the name.
3168        if ($fieldName =~ /--/) {
3169            # Here we have a doubled minus sign.
3170            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3171            $retVal = 0;
3172        } elsif ($fieldName !~ /^[A-Za-z]/) {
3173            # Here the field name is missing the initial letter.
3174            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3175            $retVal = 0;
3176        } elsif (length($fieldName) > $maxLen) {
3177            # Here the field name is too long.
3178            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3179                                          } else {                                          } else {
3180                                                  # Here we have a scalar value. Use it unmodified.          # Strip out the minus signs. Everything remaining must be a letter,
3181                                                  push @parameterList, $value;          # underscore, or digit.
3182            my $strippedName = $fieldName;
3183            $strippedName =~ s/-//g;
3184            if ($strippedName !~ /^(\w|\d)+$/) {
3185                Trace("Field name $fieldName contains illegal characters.") if T(1);
3186                $retVal = 0;
3187                                          }                                          }
3188                                  }                                  }
3189                                  # Execute the INSERT statement with the specified parameter list.      # Return the result.
3190                                  $retVal = $sth->execute(@parameterList);      return $retVal;
3191                                  if (!$retVal) {  }
3192                                          my $errorString = $sth->errstr();  
3193                                          Trace("Insert error: $errorString.") if T(0);  =head3 ReadMetaXML
3194    
3195    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3196    
3197    This method reads a raw database definition XML file and returns it.
3198    Normally, the metadata used by the ERDB system has been processed and
3199    modified to make it easier to load and retrieve the data; however,
3200    this method can be used to get the data in its raw form.
3201    
3202    =over 4
3203    
3204    =item fileName
3205    
3206    Name of the XML file to read.
3207    
3208    =item RETURN
3209    
3210    Returns a hash reference containing the raw XML data from the specified file.
3211    
3212    =back
3213    
3214    =cut
3215    
3216    sub ReadMetaXML {
3217        # Get the parameters.
3218        my ($fileName) = @_;
3219        # Read the XML.
3220        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3221        Trace("XML metadata loaded from file $fileName.") if T(1);
3222        # Return the result.
3223        return $retVal;
3224                                  }                                  }
3225    
3226    =head3 GetEntityFieldHash
3227    
3228    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3229    
3230    Get the field hash of the named entity in the specified raw XML structure.
3231    The field hash may not exist, in which case we need to create it.
3232    
3233    =over 4
3234    
3235    =item structure
3236    
3237    Raw XML structure defininng the database. This is not the run-time XML used by
3238    an ERDB object, since that has all sorts of optimizations built-in.
3239    
3240    =item entityName
3241    
3242    Name of the entity whose field structure is desired.
3243    
3244    =item RETURN
3245    
3246    Returns the field hash used to define the entity's fields.
3247    
3248    =back
3249    
3250    =cut
3251    
3252    sub GetEntityFieldHash {
3253        # Get the parameters.
3254        my ($structure, $entityName) = @_;
3255        # Get the entity structure.
3256        my $entityData = $structure->{Entities}->{$entityName};
3257        # Look for a field structure.
3258        my $retVal = $entityData->{Fields};
3259        # If it doesn't exist, create it.
3260        if (! defined($retVal)) {
3261            $entityData->{Fields} = {};
3262            $retVal = $entityData->{Fields};
3263                          }                          }
3264        # Return the result.
3265        return $retVal;
3266                  }                  }
3267    
3268    =head3 WriteMetaXML
3269    
3270    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3271    
3272    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3273    used to update the database definition. It must be used with care, however, since it
3274    will only work on a raw structure, not on the processed structure created by an ERDB
3275    constructor.
3276    
3277    =over 4
3278    
3279    =item structure
3280    
3281    XML structure to be written to the file.
3282    
3283    =item fileName
3284    
3285    Name of the output file to which the updated XML should be stored.
3286    
3287    =back
3288    
3289    =cut
3290    
3291    sub WriteMetaXML {
3292        # Get the parameters.
3293        my ($structure, $fileName) = @_;
3294        # Compute the output.
3295        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3296        # Write it to the file.
3297        my $xmlOut = Open(undef, ">$fileName");
3298        print $xmlOut $fileString;
3299          }          }
3300          # Return the success indicator.  
3301    
3302    =head3 HTMLNote
3303    
3304    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3305    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3306    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3307    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3308    
3309    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3310    
3311    =over 4
3312    
3313    =item dataString
3314    
3315    String to convert to HTML.
3316    
3317    =item RETURN
3318    
3319    An HTML string derived from the input string.
3320    
3321    =back
3322    
3323    =cut
3324    
3325    sub HTMLNote {
3326        # Get the parameter.
3327        my ($dataString) = @_;
3328        # HTML-escape the text.
3329        my $retVal = CGI::escapeHTML($dataString);
3330        # Substitute the bulletin board codes.
3331        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3332        $retVal =~ s!\[p\]!</p><p>!g;
3333        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3334        $retVal =~ s!\[/link\]!</a>!g;
3335        # Return the result.
3336          return $retVal;          return $retVal;
3337  }  }
3338    
3339  =head3 LoadTable  =head3 BeginTran
3340    
3341    C<< $erdb->BeginTran(); >>
3342    
3343    Start a database transaction.
3344    
3345    =cut
3346    
3347    sub BeginTran {
3348        my ($self) = @_;
3349        $self->{_dbh}->begin_tran();
3350    
3351    }
3352    
3353    =head3 CommitTran
3354    
3355    C<< $erdb->CommitTran(); >>
3356    
3357    Commit an active database transaction.
3358    
3359    =cut
3360    
3361    sub CommitTran {
3362        my ($self) = @_;
3363        $self->{_dbh}->commit_tran();
3364    }
3365    
3366    =head3 RollbackTran
3367    
3368    C<< $erdb->RollbackTran(); >>
3369    
3370    Roll back an active database transaction.
3371    
3372    =cut
3373    
3374    sub RollbackTran {
3375        my ($self) = @_;
3376        $self->{_dbh}->roll_tran();
3377    }
3378    
3379    
3380    =head2 Data Mining Methods
3381    
3382    =head3 GetUsefulCrossValues
3383    
3384    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3385    
3386    Return a list of the useful attributes that would be returned by a B<Cross> call
3387    from an entity of the source entity type through the specified relationship. This
3388    means it will return the fields of the target entity type and the intersection data
3389    fields in the relationship. Only primary table fields are returned. In other words,
3390    the field names returned will be for fields where there is always one and only one
3391    value.
3392    
3393    =over 4
3394    
3395    =item sourceEntity
3396    
3397    Name of the entity from which the relationship crossing will start.
3398    
3399    =item relationship
3400    
3401    Name of the relationship being crossed.
3402    
3403    =item RETURN
3404    
3405    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3406    
3407    =back
3408    
3409  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  =cut
3410    #: Return Type @;
3411    sub GetUsefulCrossValues {
3412        # Get the parameters.
3413        my ($self, $sourceEntity, $relationship) = @_;
3414        # Declare the return variable.
3415        my @retVal = ();
3416        # Determine the target entity for the relationship. This is whichever entity is not
3417        # the source entity. So, if the source entity is the FROM, we'll get the name of
3418        # the TO, and vice versa.
3419        my $relStructure = $self->_GetStructure($relationship);
3420        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3421        my $targetEntity = $relStructure->{$targetEntityType};
3422        # Get the field table for the entity.
3423        my $entityFields = $self->GetFieldTable($targetEntity);
3424        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3425        # For the entity fields, the key aspect of the target structure is that the {relation} value
3426        # must match the entity name.
3427        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3428                            keys %{$entityFields};
3429        # Push the fields found onto the return variable.
3430        push @retVal, sort @fieldList;
3431        # Get the field table for the relationship.
3432        my $relationshipFields = $self->GetFieldTable($relationship);
3433        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3434        # This may end up being an empty set.
3435        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3436                            keys %{$relationshipFields};
3437        # Push these onto the return list.
3438        push @retVal, sort @fieldList2;
3439        # Return the result.
3440        return @retVal;
3441    }
3442    
3443  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  =head3 FindColumn
3444    
3445  =over 4  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3446    
3447  =item fileName  Return the location a desired column in a data mining header line. The data
3448    mining header line is a tab-separated list of column names. The column
3449    identifier is either the numerical index of a column or the actual column
3450    name.
3451    
3452  Name of the file from which the table data should be loaded.  =over 4
3453    
3454  =item relationName  =item headerLine
3455    
3456  Name of the relation to be loaded. This is the same as the table name.  The header line from a data mining command, which consists of a tab-separated
3457    list of column names.
3458    
3459  =item truncateFlag  =item columnIdentifier
3460    
3461  TRUE if the table should be dropped and re-created, else FALSE  Either the ordinal number of the desired column (1-based), or the name of the
3462    desired column.
3463    
3464  =item RETURN  =item RETURN
3465    
3466  Returns a statistical object containing the number of records read and a list of the error messages.  Returns the array index (0-based) of the desired column.
3467    
3468  =back  =back
3469    
3470  =cut  =cut
3471  sub LoadTable {  
3472    sub FindColumn {
3473          # Get the parameters.          # Get the parameters.
3474          my $self = shift @_;      my ($headerLine, $columnIdentifier) = @_;
3475          my ($fileName, $relationName, $truncateFlag) = @_;      # Declare the return variable.
3476          # Create the statistical return object.      my $retVal;
3477          my $retVal = _GetLoadStats();      # Split the header line into column names.
3478          # Trace the fact of the load.      my @headers = ParseColumns($headerLine);
3479          Trace("Loading table $relationName from $fileName") if T(1);      # Determine whether we have a number or a name.
3480          # Get the database handle.      if ($columnIdentifier =~ /^\d+$/) {
3481          my $dbh = $self->{_dbh};          # Here we have a number. Subtract 1 and validate the result.
3482          # Get the relation data.          $retVal = $columnIdentifier - 1;
3483          my $relation = $self->_FindRelation($relationName);          if ($retVal < 0 || $retVal > $#headers) {
3484          # Check the truncation flag.              Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
         if ($truncateFlag) {  
                 Trace("Creating table $relationName") if T(1);  
                 # Re-create the table without its index.  
                 $self->CreateTable($relationName, 0);  
3485          }          }
         # 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');  
         }  
         }  
         # Close the files.  
         close TABLEIN;  
         close TABLEOUT;  
         # Load the table.  
         my $rv;  
         eval {  
                 $rv = $dbh->load_table(file => $tempName, tbl => $relationName);  
         };  
         if (!defined $rv) {  
                 $retVal->AddMessage("Table load failed for $relationName.");  
                 Trace("Table load failed for $relationName.") if T(1);  
3486          } else {          } else {
3487                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we have a name. We need to find it in the list.
3488                  Trace("$retVal->{records} records read for $relationName.") if T(1);          for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3489                  # If we're rebuilding, we need to create the table indexes.              if ($headers[$i] eq $columnIdentifier) {
3490                  if ($truncateFlag) {                  $retVal = $i;
                         eval {  
                                 $self->CreateIndex($relationName);  
                         };  
                         if ($@) {  
                                 $retVal->AddMessage($@);  
3491                          }                          }
3492                  }                  }
3493            if (! defined($retVal)) {
3494                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3495          }          }
3496          # Commit the database changes.      }
3497          $dbh->commit_tran;      # Return the result.
         # Delete the temporary file.  
         unlink $tempName;  
         # Return the statistics.  
3498          return $retVal;          return $retVal;
3499  }  }
3500    
3501  =head3 GenerateEntity  =head3 ParseColumns
3502    
3503  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3504    
3505  Generate the data for a new entity instance. This method creates a field hash suitable for  Convert the specified data line to a list of columns.
 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.  
3506    
3507  =over 4  =over 4
3508    
3509  =item id  =item line
   
 ID to assign to the new entity.  
   
 =item type  
3510    
3511  Type name for the new entity.  A data mining input, consisting of a tab-separated list of columns terminated by a
3512    new-line.
3513    
3514  =item values  =item RETURN
3515    
3516  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a list consisting of the column values.
3517    
3518  =back  =back
3519    
3520  =cut  =cut
3521    
3522  sub GenerateEntity {  sub ParseColumns {
3523          # Get the parameters.          # Get the parameters.
3524          my $self = shift @_;      my ($line) = @_;
3525          my ($id, $type, $values) = @_;      # Chop off the line-end.
3526          # Create the return hash.      chomp $line;
3527          my $this = { id => $id };      # Split it into a list.
3528          # Get the metadata structure.      my @retVal = split(/\t/, $line);
3529          my $metadata = $self->{_metaData};      # Return the result.
3530          # Get this entity's list of fields.      return @retVal;
         if (!exists $metadata->{Entities}->{$type}) {  
                 Confess("Unrecognized entity type $type in GenerateEntity.");  
         } else {  
                 my $entity = $metadata->{Entities}->{$type};  
                 my $fields = $entity->{Fields};  
                 # Generate data from the fields.  
                 _GenerateFields($this, $fields, $type, $values);  
         }  
         # Return the hash created.  
         return $this;  
3531  }  }
3532    
3533    =head2 Virtual Methods
3534    
3535  =head2 Internal Utility Methods  =head3 CleanKeywords
3536    
3537  =head3 GetLoadStats  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3538    
3539  Return a blank statistics object for use by the load methods.  Clean up a search expression or keyword list. This is a virtual method that may
3540    be overridden by the subclass. The base-class method removes extra spaces
3541    and converts everything to lower case.
3542    
3543  This is a static method.  =over 4
3544    
3545    =item searchExpression
3546    
3547    Search expression or keyword list to clean. Note that a search expression may
3548    contain boolean operators which need to be preserved. This includes leading
3549    minus signs.
3550    
3551    =item RETURN
3552    
3553    Cleaned expression or keyword list.
3554    
3555    =back
3556    
3557  =cut  =cut
3558    
3559  sub _GetLoadStats {  sub CleanKeywords {
3560          return Stats->new('records');      # Get the parameters.
3561        my ($self, $searchExpression) = @_;
3562        # Lower-case the expression and copy it into the return variable. Note that we insure we
3563        # don't accidentally end up with an undefined value.
3564        my $retVal = lc($searchExpression || "");
3565        # Remove extra spaces.
3566        $retVal =~ s/\s+/ /g;
3567        $retVal =~ s/(^\s+)|(\s+$)//g;
3568        # Return the result.
3569        return $retVal;
3570  }  }
3571    
3572  =head3 GenerateFields  =head3 GetSourceObject
3573    
3574  Generate fie