1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
|
#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(srfi srfi-1)
(srfi srfi-26)
(srfi srfi-171)
(ice-9 match)
(ice-9 regex)
(ice-9 string-fun)
(dump sql)
(dump table)
(dump triples)
(dump utils)
(zlib))
;;; GeneNetwork database connection parameters and dump path
(define %connection-settings
(call-with-input-file (list-ref (command-line) 1)
read))
(define (call-with-genenetwork-database proc)
(call-with-database "mysql" (string-join
(list (assq-ref %connection-settings 'sql-username)
(assq-ref %connection-settings 'sql-password)
(assq-ref %connection-settings 'sql-database)
"tcp"
(assq-ref %connection-settings 'sql-host)
(number->string
(assq-ref %connection-settings 'sql-port)))
":")
proc))
(define %dump-directory
(list-ref (command-line) 2))
(define (call-with-dump-file filename proc)
(let ((absolute-path (string-append %dump-directory filename)))
(display absolute-path)
(newline)
(call-with-output-file absolute-path proc)))
;; Dump schema annotations to org
(define (get-tables-from-comments db)
(sql-map (match-lambda
((("TableName" . table)) table))
db
(select-query ((TableComments TableName))
(TableComments))))
(define (dump-table-fields db table)
(format #t "* ~a~%" table)
(match (sql-find db
(select-query ((TableComments Comment))
(TableComments)
(format #f "WHERE TableName = '~a'" table)))
((("Comment" . comment))
(format #t "~a~%" comment)))
(sql-for-each (lambda (row)
(match row
((("TableField" . table-field)
("Foreign_Key" . foreign-key)
("Annotation" . annotation))
(format #t "** ~a~%" (substring table-field (1+ (string-length table))))
(unless (string-null? foreign-key)
(format #t "Foreign key to ~a~%" foreign-key))
(unless (string-null? annotation)
(display annotation)
(newline)))))
db
(select-query ((TableFieldAnnotation TableField)
(TableFieldAnnotation Foreign_Key)
(TableFieldAnnotation Annotation))
(TableFieldAnnotation)
(format #f "WHERE TableField LIKE '~a.%'" table)))
(newline))
(define (dump-schema-annotations db)
(call-with-genenetwork-database
(lambda (db)
(for-each (cut dump-table-fields db <>)
(get-tables-from-comments db)))))
;;; Dump tables
(define (delete-substrings str . substrings)
"Delete SUBSTRINGS, a list of strings, from STR."
(fold (lambda (substring result)
(string-replace-substring result substring ""))
str
substrings))
(define (replace-substrings str replacement-alist)
"Replace substrings in STR according to REPLACEMENT-ALIST, an
association list mapping substrings to their replacements."
(fold (match-lambda*
(((substring . replacement) str)
(string-replace-substring str substring replacement)))
str
replacement-alist))
(define (snake->lower-camel str)
(let ((char-list (string->list str)))
(call-with-output-string
(lambda (port)
(put-char port (char-downcase (string-ref str 0)))
(map (lambda (char previous-char)
(unless (char=? char #\_)
(put-char port (if (char=? previous-char #\_)
(char-upcase char)
char))))
(drop char-list 1)
char-list)))))
(eval-when (expand load eval)
(define (field->key x)
(translate-forms 'field
(lambda (x)
#`(key #,(symbol->string
(syntax->datum
((syntax-rules (field)
((field table column) column)
((field table column alias) alias))
x)))))
x))
(define (field->assoc-ref alist x)
"Recursively translate field references in source X to (assoc-ref
ALIST field-name) forms."
(translate-forms 'field
(lambda (x)
#`(assoc-ref #,alist
#,(symbol->string
(syntax->datum
((syntax-rules (field)
((field table column) column)
((field table column alias) alias))
x)))))
x))
(define (collect-fields x)
(map (syntax-rules (field)
((field reference ...)
(reference ...)))
(collect-forms 'field x)))
(define (find-clause clauses key)
"Find (KEY ...) clause among CLAUSES, a list of syntax forms."
(find (lambda (x)
(syntax-case x ()
((clause-key _ ...)
(eq? (syntax->datum #'clause-key)
key))))
clauses))
(define (remove-namespace str)
"Remove RDF namespace prefix from STR."
(substring str (1+ (string-index str #\:))))
(define (column-id table-name column-name)
(string->identifier
"field" (string-append
;; We downcase table names in identifiers. So, we
;; distinguish between the user and User tables.
(if (string=? table-name "User")
"user2" table-name)
"__" column-name)))
(define (dump-id dump-table predicate)
(symbol->string
(string->identifier
"dump"
(string-append
dump-table "_" (remove-namespace (symbol->string predicate)))))))
(define-syntax syntax-let
(syntax-rules ()
"Like match-let, but for syntax.
(syntax-let ((pattern literals expression))
body ...)
≡
(syntax-case expression ()
(pattern literals
body ...))
literals is optional. So,
(syntax-let ((pattern expression))
body ...)
≡
(syntax-case expression ()
(pattern
body ...))
"
((_ () body ...)
(begin body ...))
((_ ((pattern expression)
bindings ...)
body ...)
(syntax-case expression ()
(pattern
(syntax-let (bindings ...)
body ...))))
((_ ((pattern literals expression)
bindings ...)
body ...)
(syntax-case expression literals
(pattern
(syntax-let (bindings ...)
body ...))))))
(define-syntax define-dump
(lambda (x)
"Define FUNCTION-NAME, a function that dumps a view of the database.
define-dump consists of three order-agnostic clauses---tables,
schema-triples and triples---in the form shown below.
(define-dump function-name
(tables (table ...) raw-forms ...)
(schema-triples
(subject predicate object) ...)
(triples subject
(verb predicate object) ...))
The tables clause specifies the database tables to be joined to
construct the view to be dumped. TABLE must be either of the form
TABLE-NAME or of the form (JOIN-OPERATOR TABLE-NAME
RAW-CONDITION). TABLE-NAME must, obviously, be the name of the
table. JOIN-OPERATOR must be one of join, left-join and
inner-join. RAW-CONDITION should be the join condition as a raw
string. This is usually something like
\"USING (SpeciesId)\". RAW-FORMS are expressions that must evaluate to
strings to be appended to the SQL query.
The schema-triples clause specifies the list of triples to be written
once when the dump starts.
The triples clause specifies the triples to be dumped once for each
row in the view. All triples have a common SUBJECT. The (verb
predicate object) clauses are described below.
VERB must either be set or multiset. For the set VERB, a single triple
(SUBJECT PREDICATE OBJECT-VALUE) is written where OBJECT-VALUE is the
result of evaluating OBJECT. For the multiset VERB, OBJECT must
evaluate to a list, and a triple (SUBJECT PREDICATE
OBJECT-VALUE-ELEMENT) is created for each element OBJECT-VALUE-ELEMENT
of that list.
The SUBJECT and OBJECT expressions in the triples clause must
reference database fields using a (field TABLE COLUMN) clause where
TABLE and COLUMN refer to the table and column of the field being
referenced. Database fields can also be referenced using (field TABLE
COLUMN ALIAS) where ALIAS is an alias for that column in the SQL
query. Specification of ALIAS is indeed a leak in the abstraction, and
must be remedied."
(syntax-case x (tables schema-triples triples)
((_ name clauses ...)
(syntax-let (((tables (primary-table other-tables ...) tables-raw ...) (tables)
(find-clause #'(clauses ...) 'tables))
(schema-triples-clause (or (find-clause #'(clauses ...) 'schema-triples)
#'(schema-triples)))
((triples subject predicate-clauses ...) (triples)
(find-clause #'(clauses ...) 'triples)))
#`(define (name db)
#,(syntax-case #'schema-triples-clause (schema-triples)
((schema-triples (triple-subject triple-predicate triple-object) ...)
#`(for-each triple
(list 'triple-subject ...)
(list 'triple-predicate ...)
(list 'triple-object ...)))
(_ (error "Invalid schema triples clause:" #'schema-triples-clause)))
#,@(let ((dump-table (symbol->string (syntax->datum #'primary-table)))
(subject-type (any (lambda (predicate)
(syntax-case predicate (rdf:type)
((_ rdf:type type) #'type)
(_ #f)))
#'(predicate-clauses ...))))
(map (lambda (predicate-clause)
(syntax-case predicate-clause ()
((_ predicate _)
;; Dump metadata about the dump itself.
#`(begin
(scm->triples
(map-alist '()
(set rdf:type 'gn:dump)
(set gn:createsPredicate 'predicate)
(filter-set gn:forSubjectType #,subject-type)
(multiset gn:dependsOn
'#,(map (lambda (field)
(match (syntax->datum field)
((table-name column-name _ ...)
(datum->syntax
x (column-id (symbol->string table-name)
(symbol->string column-name))))))
(collect-fields predicate-clause))))
#,(dump-id dump-table (syntax->datum #'predicate)))
;; Automatically create domain triples
;; for predicates.
(when #,subject-type
(triple 'predicate 'rdfs:domain #,subject-type))))
(_ (error "Invalid predicate clause:" predicate-clause))))
#'(predicate-clauses ...)))
(sql-for-each (lambda (row)
(scm->triples
(map-alist row #,@(field->key #'(predicate-clauses ...)))
#,(field->assoc-ref #'row #'subject)))
db
(select-query #,(collect-fields #'(subject predicate-clauses ...))
(primary-table other-tables ...)
tables-raw ...)))))
(_ (error "Invalid define-dump syntax:" (syntax->datum x))))))
(define binomial-name->species-id
(cut string->identifier "species" <>))
(define-dump dump-species
(tables (Species))
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:menuname rdfs:range rdfs:Literal)
(gn:binomialName rdfs:range rdfs:Literal))
(triples (binomial-name->species-id (field Species FullName))
(set rdf:type 'gn:species)
(set gn:name (field Species SpeciesName))
(set gn:menuName (field Species MenuName))
(set gn:binomialName (field Species FullName))))
(define-dump dump-strain
(tables (Strain
(join Species "ON Strain.SpeciesId = Species.SpeciesId")))
(schema-triples
(gn:strainOfSpecies rdfs:domain gn:strain)
(gn:strainOfSpecies rdfs:range gn:species)
(gn:name rdfs:range rdfs:Literal)
(gn:alias rdfs:range rdfs:Literal)
(gn:symbol rdfs:range rdfs:Literal))
(triples (string->identifier "strain" (field Strain Name))
(set rdf:type 'gn:strain)
(set gn:strainOfSpecies
(binomial-name->species-id (field Species FullName)))
;; Name, and maybe a second name
(set gn:name (field Strain Name))
(set gn:name (field Strain Name2))
(set gn:alias (field Strain Alias))
(set gn:symbol (field Strain Symbol))))
;; TODO: This function is unused. Remove if not required.
(define mapping-method-name->id
(cut string->identifier "mappingMethod" <>))
;; TODO: This function is unused. Remove if not required.
(define-dump dump-mapping-method
(tables (MappingMethod))
(triples (string->identifier "mappingMethod" (field MappingMethod Name))
(set rdf:type 'gn:mappingMethod)))
(define inbred-set-name->id
(cut string->identifier "inbredSet" <>))
(define-dump dump-inbred-set
(tables (InbredSet
(inner-join Species "USING (SpeciesId)")))
(schema-triples
(gn:fullName rdfs:range rdfs:Literal)
(gn:geneticType rdfs:range rdfs:Literal)
(gn:family rdfs:range rdfs:Literal)
(gn:inbredSetOfSpecies rdfs:range gn:species))
(triples (inbred-set-name->id (field InbredSet Name))
(set rdf:type 'gn:inbredSet)
(set gn:fullName (field InbredSet FullName))
(set gn:geneticType (field InbredSet GeneticType))
(set gn:family (field InbredSet Family))
(set gn:inbredSetOfSpecies
(binomial-name->species-id (field Species FullName BinomialName)))))
(define (phenotype-id->id id)
(string->identifier "phenotype" (number->string id)))
(define-dump dump-phenotype
(tables (Phenotype))
(schema-triples
(gn:prePublicationDescription rdfs:range rdfs:Literal)
(gn:postPublicationDescription rdfs:range rdfs:Literal)
(gn:originalDescription rdfs:range rdfs:Literal)
(gn:labCode rdfs:range rdfs:Literal)
(gn:submitter rdfs:range rdfs:Literal)
(gn:owner rdfs:range rdfs:Literal)
(gn:authorizedUsers rdfs:range rdfs:Literal)
(gn:units rdfs:range rdfs:Literal))
(triples (phenotype-id->id (field Phenotype Id))
(set rdf:type 'gn:phenotype)
(set gn:prePublicationDescription (field Phenotype Pre_publication_description))
(set gn:postPublicationDescription (field Phenotype Post_publication_description))
(set gn:originalDescription (field Phenotype Original_description))
(set gn:labCode (field Phenotype Lab_code))
(set gn:submitter (field Phenotype Submitter))
(set gn:owner (field Phenotype Owner))
(set gn:authorizedUsers (field Phenotype Authorized_Users))
(set gn:units (and (string-ci=? (field Phenotype Units) "unknown")
(field Phenotype Units)))))
(define-dump dump-publication
(tables (Publication))
(schema-triples
(gn:pubMedId rdfs:range rdfs:Literal)
(gn:title rdfs:range rdfs:Literal)
(gn:journal rdfs:range rdfs:Literal)
(gn:volume rdfs:range rdfs:Literal)
(gn:pages rdfs:range rdfs:Literal)
(gn:month rdfs:range rdfs:Literal)
(gn:year rdfs:range rdfs:Literal)
(gn:author rdfs:range rdfs:Literal)
(gn:abstract rdfs:range rdfs:Literal))
(triples (string->identifier "publication"
(number->string (field Publication Id)))
(set rdf:type 'gn:publication)
(set gn:pubMedId (field Publication PubMed_ID))
(set gn:title (field Publication Title))
(set gn:journal (field Publication Journal))
(set gn:volume (field Publication Volume))
(set gn:pages (field Publication Pages))
(set gn:month (field Publication Month))
(set gn:year (field Publication Year))
(multiset gn:author
;; The authors field is a comma
;; separated list. Split it.
(map string-trim (string-split (field Publication Authors) #\,)))
(set gn:abstract
;; TODO: Why are there unprintable characters?
(delete-substrings (field Publication Abstract)
"\x01"
;; \v is a vertical tab
;; character. Microsoft Word probably
;; still uses this.
"\v"))))
(define-dump dump-publish-xref
(tables (PublishXRef
(inner-join InbredSet "USING (InbredSetId)")))
(schema-triples
(gn:phenotypeOfSpecies rdfs:domain gn:phenotype)
(gn:phenotypeOfSpecies rdfs:range gn:species))
(triples (phenotype-id->id (field PublishXRef PhenotypeId))
(set gn:phenotypeOfSpecies (inbred-set-name->id (field InbredSet Name)))
(set gn:traitId (field PublishXRef id))
(set gn:publicationId
(string->identifier "publication"
(number->string (field PublishXRef PublicationId))))))
(define tissue-short-name->id
(cut string->identifier "tissue" <>))
(define-dump dump-tissue
;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
;; and BIRN_lex_Name are mostly NULL.
(tables (Tissue))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
;; Hopefully the Short_Name field is distinct and can be used as an
;; identifier.
(triples (tissue-short-name->id (field Tissue Short_Name))
(set rdf:type 'gn:tissue)
(set gn:name (field Tissue Name))))
;; One email ID in the Investigators table has spaces in it. This
;; function fixes that.
(define (fix-email-id email)
(string-delete #\space email))
(define (investigator-attributes->id first-name last-name email)
;; There is just one record corresponding to "Evan Williams" which
;; does not have an email ID. To accommodate that record, we
;; construct the investigator ID from not just the email ID, but
;; also the first and the last names. It would be preferable to just
;; find Evan Williams' email ID and insert it into the database.
(string->identifier "investigator"
(string-join
;; Add special case for Yohan Bossé whose name
;; has unprintable characters.
;; TODO: Fix Yohan Bossé's name in the database.
(let ((last-name (if (string=? first-name "Yohan")
"Bosse"
last-name)))
(list first-name last-name (fix-email-id email)))
"_")))
(define-dump dump-investigators
;; There are a few duplicate entries. We group by email to
;; deduplicate.
(tables (Investigators)
"GROUP BY Email")
(schema-triples
;; TODO: Are ranges required for FOAF predicates? Can they not be
;; obtained from the FOAF spec?
(foaf:name rdfs:range rdfs:Literal)
(foaf:givenName rdfs:range rdfs:Literal)
(foaf:familyName rdfs:range rdfs:Literal)
(foaf:phone rdfs:range rdfs:Literal)
(foaf:mbox rdfs:range rdfs:Literal)
(foaf:homepage rdfs:range rdfs:Literal)
(gn:address rdfs:range rdfs:Literal)
(gn:city rdfs:range rdfs:Literal)
(gn:state rdfs:range rdfs:Literal)
(gn:zipCode rdfs:range rdfs:Literal)
(gn:country rdfs:range rdfs:Literal))
(triples (investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email))
(set rdf:type 'foaf:Person)
;; Special case Yohan Bossé's name since the last name has
;; unprintable characters.
(set foaf:name (string-append (field Investigators FirstName) " "
(if (string=? (field Investigators FirstName) "Yohan")
"Bossé"
(field Investigators LastName))))
(set foaf:givenName (field Investigators FirstName))
;; Special case Yohan Bossé's name since the last name has
;; unprintable characters.
(set foaf:familyName (if (string=? (field Investigators FirstName) "Yohan")
"Bossé"
(field Investigators LastName)))
(set foaf:phone (field Investigators Phone))
(set foaf:mbox (fix-email-id (field Investigators Email)))
(set foaf:homepage (field Investigators Url))
(set gn:address (field Investigators Address))
(set gn:city (field Investigators City))
(set gn:state (field Investigators State))
(set gn:zipCode (field Investigators ZipCode))
(set gn:country (field Investigators Country))))
(define avg-method-name->id
(cut string->identifier "avgmethod" <>))
(define-dump dump-avg-method
;; The Name and Normalization fields seem to be the same. Dump only
;; the Name field.
(tables (AvgMethod))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
(triples (avg-method-name->id (field AvgMethod Name))
(set rdf:type 'gn:avgMethod)
(set gn:name (field AvgMethod Name))))
(define gene-chip-name->id
(cut string->identifier "platform" <>))
(define-dump dump-gene-chip
(tables (GeneChip))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
(triples (gene-chip-name->id (field GeneChip Name))
(set rdf:type 'gn:platform)
(set gn:name (field GeneChip GeneChipName))))
;; TODO: Double check Platforms. It doesn't seem to match up.
(define-dump dump-info-files
(tables (InfoFiles
(left-join Datasets "USING (DatasetId)")
(left-join DatasetStatus "USING (DatasetStatusId)")
(left-join Species "USING (SpeciesId)")
(left-join InbredSet "USING (InbredSetId)")
(left-join Tissue "USING (TissueId)")
(left-join Investigators "USING (InvestigatorId)")
(left-join AvgMethod "USING (AvgMethodId)")
(left-join GeneChip "USING (GeneChipId)"))
"WHERE GN_AccesionId IS NOT NULL")
(schema-triples
(gn:datasetOfInvestigator rdfs:domain gn:dataset)
(gn:datasetOfInvestigator rdfs:range foaf:Person)
(gn:datasetOfSpecies rdfs:domain gn:dataset)
(gn:datasetOfSpecies rdfs:range gn:species)
(gn:datasetOfInbredSet rdfs:domain gn:dataset)
(gn:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn:datasetOfTissue rdfs:domain gn:dataset)
(gn:datasetOfTissue rdfs:range gn:tissue)
(gn:normalization rdfs:domain gn:dataset)
(gn:normalization rdfs:range gn:avgMethod)
(gn:datasetOfPlatform rdfs:domain gn:dataset)
(gn:datasetOfPlatform rdfs:range gn:geneChip)
(gn:accessionId rdfs:range rdfs:Literal)
(gn:datasetStatusName rdfs:range rdfs:Literal)
(gn:summary rdfs:range rdfs:Literal)
(gn:aboutTissue rdfs:range rdfs:Literal)
(gn:geoSeries rdfs:range rdfs:Literal)
(gn:name rdfs:range rdfs:Literal)
(gn:title rdfs:range rdfs:Literal)
(gn:specifics rdfs:range rdfs:Literal)
(gn:datasetGroup rdfs:range rdfs:Literal)
(gn:aboutCases rdfs:range rdfs:Literal)
(gn:aboutPlatform rdfs:range rdfs:Literal)
(gn:aboutDataProcessing rdfs:range rdfs:Literal)
(gn:notes rdfs:range rdfs:Literal)
(gn:experimentDesign rdfs:range rdfs:Literal)
(gn:contributors rdfs:range rdfs:Literal)
(gn:citation rdfs:range rdfs:Literal)
(gn:acknowledgment rdfs:range rdfs:Literal))
(triples (string->identifier "dataset"
(number->string (field InfoFiles GN_AccesionId)))
(set rdf:type 'gn:dataset)
(set gn:datasetOfInvestigator
(investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email)))
(set gn:accessionId (string-append "GN" (number->string
(field InfoFiles GN_AccesionId))))
(set gn:datasetStatusName (string-downcase
(field DatasetStatus DatasetStatusName)))
(set gn:datasetOfSpecies (binomial-name->species-id
(field Species FullName BinomialName)))
(set gn:datasetOfInbredSet (inbred-set-name->id (field InbredSet Name InbredSetName)))
(set gn:datasetOfTissue (tissue-short-name->id (field Tissue Short_Name)))
(set gn:normalization
(avg-method-name->id
;; If AvgMethodName is NULL, assume N/A.
(if (string-blank? (field AvgMethod Name AvgMethodName))
"N/A" (field AvgMethod Name AvgMethodName))))
(set gn:datasetOfPlatform (gene-chip-name->id (field GeneChip Name GeneChip)))
(set gn:summary
;; TODO: Why are there unprintable characters?
(delete-substrings (field Datasets Summary)
"\x01" "\x03"))
(set gn:aboutTissue
;; TODO: Why are there unprintable characters?
(delete-substrings (field Datasets AboutTissue)
"\x01" "\x03"))
(set gn:geoSeries
(and (not (string-prefix-ci? "no geo series"
(field Datasets GeoSeries)))
(field Datasets GeoSeries)))
(set gn:name (field InfoFiles InfoPageName))
(set gn:title (field InfoFiles Title))
(set gn:specifics (field InfoFiles Specifics))
(set gn:datasetGroup (field Datasets DatasetName DatasetGroup))
(set gn:aboutCases (field Datasets AboutCases))
(set gn:aboutPlatform (field Datasets AboutPlatform))
(set gn:aboutDataProcessing (field Datasets AboutDataProcessing))
(set gn:notes (field Datasets Notes))
(set gn:experimentDesign (field Datasets ExperimentDesign))
(set gn:contributors (field Datasets Contributors))
(set gn:citation (field Datasets Citation))
(set gn:acknowledgment (field Datasets Acknowledgment))))
(define (dump-data-table db table-name data-field)
(let ((dump-directory (string-append %dump-directory "/" table-name))
(port #f)
(current-strain-id #f))
(unless (file-exists? dump-directory)
(mkdir dump-directory))
(sql-for-each (match-lambda
(((_ . strain-id)
(_ . value))
;; Close file if new strain.
(when (and port
(not (= current-strain-id strain-id)))
(close-port port)
(set! port #f))
;; If no file is open, open new file.
(unless port
(set! current-strain-id strain-id)
(let ((filename (string-append dump-directory
"/" (number->string strain-id))))
(display filename (current-error-port))
(newline (current-error-port))
(set! port (open-output-file filename))))
(display value port)
(newline port)))
db
(format #f "SELECT StrainId, ~a FROM ~a ORDER BY StrainId"
data-field table-name))
(close-port port)))
;;; Dump schema
(define (tables db)
"Return list of all tables in DB. Each element of the returned list
is a <table> object."
(map (lambda (table)
(set-table-columns table
(sql-map (lambda (row)
(make-column (assoc-ref row "Field")
(assoc-ref row "Type")))
db
(format #f "SHOW COLUMNS FROM ~a" (table-name table)))))
(sql-map (lambda (row)
(make-table (assoc-ref row "table_name")
;; FIXME: This is probably correct only for
;; MyISAM tables.
(assoc-ref row "data_length")
#f))
db
(select-query ((information_schema.tables table_name)
(information_schema.tables data_length))
(information_schema.tables)
(format #f "WHERE table_schema = '~a'"
(assq-ref %connection-settings 'sql-database))))))
(define (dump-schema db)
(let ((tables (tables db)))
(for-each (lambda (table)
(let ((table-id (string->identifier
"table"
;; We downcase table names in
;; identifiers. So, we distinguish
;; between the user and User tables.
(if (string=? (table-name table) "User")
"user2"
(table-name table)))))
(triple table-id 'rdf:type 'gn:sqlTable)
(triple table-id 'gn:name (table-name table))
(triple table-id 'gn:hasSize (table-size table))
(for-each (lambda (column)
(let ((column-id (column-id (table-name table)
(column-name column))))
(triple column-id 'rdf:type 'gn:sqlTableField)
(triple column-id 'gn:name (column-name column))
(triple column-id 'gn:sqlFieldType (column-type column))
(triple table-id 'gn:hasField column-id)))
(table-columns table))))
tables)))
(define-dump dump-groups
(tables (InbredSet
(left-join Species "USING (SpeciesId)"))
(string-join
'("WHERE Species.Name IN "
"(SELECT Name FROM Species ORDER BY OrderId) "
"GROUP BY InbredSet.Name "
"ORDER BY "
"IFNULL(InbredSet.FamilyOrder, InbredSet.FullName) "
"ASC, IFNULL(InbredSet.Family, InbredSet.FullName) "
"ASC, InbredSet.FullName ASC, InbredSet.MenuOrderId ASC")))
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:binomialName rdfs:range rdfs:Literal)
(gn:species rdfs:range gn:species))
(triples (string->identifier "inbredSet" (field InbredSet Name))
(set gn:name (field InbredSet Name))
(set gn:binomialName (field InbredSet fullName))
(set gn:species (field Species Name))))
;; Import GeneRIF
;; Download GeneRIF data from
;; https://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz
(define decode-html-entities
(cut regexp-substitute/global
#f
;; We tolerate the absence of the trailing semicolon.
"&#([[:digit:]]+);{0,1}"
<>
'pre
(compose string integer->char string->number (cut match:substring <> 1))
'post))
(define (import-generif generif-data-file)
;; TODO: Link to gene objects, not merely literal Gene IDs.
(triple 'gn:geneId 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneId 'rdfs:range 'rdfs:Literal)
;; TODO: Link to gn:publication objects, not merely literal PubMed
;; IDs.
(triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:range 'rdfs:Literal)
(triple 'gn:geneRIFText 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneRIFText 'rdfs:range 'rdfs:Literal)
(call-with-gzip-input-port (open-input-file generif-data-file)
(lambda (port)
;; Read and discard header.
(get-line port)
;; Dump other lines.
(port-transduce
(compose (tenumerate)
(tmap (match-lambda
;; Is there a better way to identify GeneRIF
;; entries instead of merely enumerating them?
((i . line)
(match (string-split line #\tab)
((_ gene-id pubmed-id _ text)
(scm->triples
`((rdf:type . gn:geneRIF)
(gn:geneId . ,(string->number gene-id))
(gn:pubMedId . ,(string->number pubmed-id))
;; Some text has HTML entities. Decode
;; them.
(gn:geneRIFText . ,(decode-html-entities text)))
(string->identifier "geneRIF" (number->string i)))))))))
(const #t)
get-line
port))))
;; Main function
(call-with-genenetwork-database
(lambda (db)
(with-output-to-file (string-append %dump-directory "/dump.ttl")
(lambda ()
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
(prefix "gn:" "<http://genenetwork.org/>")
(newline)
(dump-species db)
(dump-strain db)
(dump-mapping-method db)
(dump-inbred-set db)
(dump-phenotype db)
(dump-publication db)
(dump-publish-xref db)
(dump-tissue db)
(dump-investigators db)
(dump-avg-method db)
(dump-gene-chip db)
(dump-info-files db)
(dump-schema db)
(dump-groups db)
(import-generif (assq-ref %connection-settings 'generif-data-file))))))
|