diff options
Diffstat (limited to 'transform')
| -rw-r--r-- | transform/schema-dump.scm | 125 | ||||
| -rw-r--r-- | transform/special-forms.scm | 599 | ||||
| -rw-r--r-- | transform/sql.scm | 114 | ||||
| -rw-r--r-- | transform/string-similarity.scm | 37 | ||||
| -rw-r--r-- | transform/strings.scm | 101 | ||||
| -rw-r--r-- | transform/table.scm | 28 | ||||
| -rw-r--r-- | transform/triples.scm | 110 |
7 files changed, 1114 insertions, 0 deletions
diff --git a/transform/schema-dump.scm b/transform/schema-dump.scm new file mode 100644 index 0000000..bf7f8cb --- /dev/null +++ b/transform/schema-dump.scm @@ -0,0 +1,125 @@ +(define-module (transform schema) + #:use-module (ice-9 match) + #:use-module (ice-9 srfi-26) + #:use-module (transform sql) + #:use-module (transform triples) + #:use-module (transform strings) + #:use-module (transform table)) + + +(define (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 (get-tables-from-comments db) + (sql-map (match-lambda + ((("TableName" . table)) table)) + db + (select-query ((TableComments TableName)) + (TableComments)))) + +(define (schema-annotations db) + (call-with-target-database + (lambda (db) + (for-each (cut table-fields db <>) + (get-tables-from-comments db))))) + +(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 (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* (data-table db table-name data-field + #:optional (default-directory "")) + (let ((directory (string-append default-directory "/" table-name)) + (port #f) + (current-strain-id #f)) + (unless (file-exists? directory) + (mkdir 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 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))) diff --git a/transform/special-forms.scm b/transform/special-forms.scm new file mode 100644 index 0000000..4b69337 --- /dev/null +++ b/transform/special-forms.scm @@ -0,0 +1,599 @@ +(define-module (transform special-forms) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:use-module (srfi srfi-26) + #:use-module (transform sql) + #:use-module (transform table) + #:use-module (transform triples) + #:export (translate-forms + collect-forms + collect-keys + field->key + field->assoc-ref + collect-fields + find-clause + remove-namespace + column-id + id + syntax-let + blank-node + map-alist + with-documentation + define-transformer)) + +(define (key->assoc-ref alist x) + "Recursively translate (key k) forms in source X to (assoc-ref ALIST +k) forms." + (translate-forms 'key + ;; (syntax-rules (key) + ;; ((key k) (assoc-ref alist k))) + (lambda (x) + (syntax-case x (key) + ((key k) #`(assoc-ref #,alist 'k)))) + x)) + +(define (alist-delete* alist keys) + "Delete entries from ALIST whose key is equal (in the sense of +equal?) to any in KEYS, a list." + (remove (match-lambda + ((key . value) + (member key keys)) + (x (error "malformed alist element" x))) + alist)) + +(define (translate-forms from translator x) + "Recursively pass (FROM ...) forms in source X to TRANSLATOR, and +replace them with the return value." + (syntax-case x () + ;; Handle translation base case. + ((head tail ...) (eq? (syntax->datum #'head) + from) + (translator x)) + ;; Recurse. + ((head tail ...) + (cons (translate-forms from translator #'head) + (map (cut translate-forms from translator <>) + #'(tail ...)))) + ;; Handle leaf base case. + (leaf #'leaf))) + +(define (collect-forms target x) + "Recursively collect (TARGET ...) forms in source X and return them +as a list." + (syntax-case x () + ;; Handle collection base case. + ((head tail ...) (eq? (syntax->datum #'head) + target) + (list x)) + ;; Recurse. + ((head tail ...) + (append (collect-forms target #'head) + (append-map (cut collect-forms target <>) #'(tail ...)))) + ;; Handle leaf base case. + (leaf (list)))) + +(define (collect-keys x) + "Recursively collect (key k) forms from source X and return as a +list of all K." + (map (syntax-rules (key) + ((key k) 'k)) + (collect-forms 'key x))) + +(define-syntax map-alist + (lambda (x) + "Transform (aka map) ALIST, an association list, into another +association list. The returned association list may contain multiple +associations for the same key. equal? is used in all association list +key comparisons. + +Syntax: + +(map-alist alist + (verb key expression) ... + (else=> proc)) + +VERB must be one of set, filter-set, multiset and remove. + +For the set VERB, KEY is set to the result of evaluating +EXPRESSION. Multiple set verbs on the same key will result in multiple +associations for that key. + +For the filter-set VERB, KEY is set to the result of evaluating +EXPRESSION only if that result is not #f. + +For the multiset VERB, EXPRESSION must return a list and KEY is +associated multiple times once with each element of the returned list. + +For the remove VERB, KEY is discarded. + +EXPRESSIONs must reference elements of ALIST using (key k) forms where +K is the key to be referenced from ALIST. K must not be quoted. That +is, if K is the symbol 'bar, it must be referenced as (key bar), not +as (key 'bar). + +The else=> clause is optional. + +If the else=> clause is present, PROC is passed all pairs of ALIST +that are not set by an earlier (verb key expression) action. PROC must +return #f or a pair to replace its input pair. If PROC returns #f, +that pair is discarded. + +If the else=> clause is absent, all unset pairs are discarded. + +Example: + +(map-alist '((\"foo\" . 1) + (bar . 2) + (foobar . 5) + (fubar . 3)) + (set spam (1+ (key \"foo\"))) + (set ham (* 2 (key bar))) + (set eggs (* 3 (key bar))) + (set aal (+ (key \"foo\") + (key bar))) + (multiset vel (iota (* 2 (key bar)))) + (remove foobar) + (else=> (match-lambda + ((key . value) + (cons key (expt 2 value)))))) +=> ((spam . 2) (ham . 4) (eggs . 6) (aal . 3) + (vel . 0) (vel . 1) (vel . 2) (vel . 3) (fubar . 8))" + (syntax-case x () + ((_ alist actions ...) + ;; TODO: Check that all actions are valid. + #`(let ((evaluated-alist alist)) + (append (remove (match-lambda + ;; Filter out results of filter-set actions. + ((key . #f) + (member key '#,(filter-map (lambda (action) + (syntax-case action (filter-set) + ((filter-set key expression) #'key) + (_ #f))) + #'(actions ...)))) + (_ #f)) + ;; Do set and filter-set. + `#,(filter-map (lambda (action) + (syntax-case action (set filter-set) + ((set key expression) + #`(key . ,#,(key->assoc-ref #'evaluated-alist #'expression))) + ((filter-set key expression) + #`(key . ,#,(key->assoc-ref #'evaluated-alist #'expression))) + (_ #f))) + #'(actions ...))) + ;; Do multiset. + #,@(filter-map (lambda (action) + (syntax-case action (multiset) + ((multiset key expression) + #`(map (cut cons 'key <>) + #,(key->assoc-ref #'evaluated-alist #'expression))) + (_ #f))) + #'(actions ...)) + ;; Apply else=> procedure on unspecified keys. If + ;; no else=> procedure is specified, delete + ;; unspecified keys. + (filter-map #,(or (any (lambda (action) + (syntax-case action (else=>) + ((else=> proc) #'proc) + (_ #f))) + #'(actions ...)) + #'(const #f)) + ;; The unspecified part of the input + ;; alist + (alist-delete* evaluated-alist + (list + ;; Keys that were referenced + #,@(append-map (lambda (action) + (syntax-case action () + ((_ key expression) + (collect-keys #'expression)) + (_ '()))) + #'(actions ...)) + ;; Keys that were deleted + #,@(filter-map (lambda (action) + (syntax-case action (remove) + ((remove key) #''key) + (_ #f))) + #'(actions ...)) + ;; Keys that were set + #,@(filter-map (lambda (action) + (syntax-case action () + ((_ key expression) #''key) + (_ #f))) + #'(actions ...))))))))))) + + + +(eval-when (expand load ) + (define (field->datum x) + (translate-forms + 'field + (lambda (x) + (syntax-case x (field) + ((field (query alias)) + #`(format #f "~a" (syntax->datum #'alias))) + ((field table column) + #`(format #f "~a(~a)" + (syntax->datum #'table) + (syntax->datum #'column))) + ((field table column alias) + #`(format #f "~a(~a)" + (syntax->datum #'table) + (syntax->datum #'alias))))) + x)) + + (define (field->key x) + (translate-forms 'field + (lambda (x) + #`(key #,(symbol->string + (syntax->datum + ((syntax-rules (field) + ((field (query alias)) alias) + ((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 (query alias)) alias) + ((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 (id table predicate) + (symbol->string + (string->identifier + "transform" + (string-append + table "_" (remove-namespace (symbol->string predicate))))))) + +(define-syntax blank-node + (syntax-rules () + "Allow having set and multiset within the context of a blank-node" + [(_ (op predicate object) ...) + (let [(node (string-join + (filter-map (match-lambda + ((pred . obj) + (match obj + ((and (? string? obj) + (? string-null? obj)) + #f) + ((? symbol? obj) + (format #f "~a ~a" pred (symbol->string obj))) + (_ + (format #f "~a ~s" pred obj))))) + (map-alist '() + (op predicate object) ...)) + " ; "))] + (if (string-null? node) + "" + (format #f "[ ~a ]" node)))])) + +(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-transformer + (lambda (x) + "Define FUNCTION-NAME, a function that transforms a view of the database. + +define-transformer consists of three order-agnostic clauses---tables, +schema-triples and triples---in the form shown below. + +(define-transformer 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 transformed. 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 transform starts. + +The triples clause specifies the triples to be transformed 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 #:key + (metadata? #f) + (data? #t) + (documentation? #f)) + (when metadata? + #,@(let ((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 transform itself. + #`(begin + (scm->triples + (map-alist '() + (set rdf:type 'gn-id:transform) + (set gn-term:createsPredicate 'predicate) + (filter-set gn-term:forSubjectType #,subject-type) + (multiset gn-term: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)))) + (((query alias)) + (datum->syntax + x (column-id query (symbol->string alias)))))) + (collect-fields predicate-clause)))) + #,(id 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 ...)))) + (when documentation? + (format #t "~%## '~a'~%~%" (syntax->datum #'name)) + #,(syntax-case #'schema-triples-clause (schema-triples) + ((schema-triples (triple-subject triple-predicate triple-object) ...) + #`(begin + (when (not (list 'triple-subject ...)) + (format #t "## Schema Triples:~%~%```text~%") + (for-each (lambda (s p o) + (format #t "~a -> ~a -> ~a~%" s p o)) + (list 'triple-subject ...) + (list 'triple-predicate ...) + (list 'triple-object ...)) + (format #t "```")))) + (_ (error "Invalid schema triples clause:" #'schema-triples-clause))) + (format #t "## Generated Triples: + +The following SQL query was executed: + +```sql +~a +``` + +The above query results to triples that have the form: + +```text +" + (select-query #,(collect-fields #'(subject predicate-clauses ...)) + (primary-table other-tables ...) + tables-raw ...)) + (for-each (match-lambda + ((predicate . object) + (format #t "~a -> ~a -> ~a ~%" + (if (symbol? #,(field->datum #'subject)) + (symbol->string #,(field->datum #'subject)) + #,(field->datum #'subject)) + predicate + (if (symbol? object) + (symbol->string object) + object)))) + (map-alist + '() + #,@(field->datum #'(predicate-clauses ...)))) + (format #t "```~%Here's an example query:~%~%```sparql~%") + (documentation?) + (newline) + (let* ((result + (map-alist (sql-find + db + (format #f "~a LIMIT 1" + (select-query #,(collect-fields #'(subject predicate-clauses ...)) + (primary-table other-tables ...) + tables-raw ...))) + #,@(field->key #'(predicate-clauses ...)))) + (first-n (list-head result + (let ((n + (min 4 (truncate + (+ (exact-integer-sqrt (length result)) 1))))) + (if (< n 3) + (length result) + n))))) + (format #t "SELECT * WHERE { ~%") + (for-each (match-lambda + ((predicate . object) + (match object + ((or (? symbol? object) + (? (lambda (el) (string-match "^\\[ .* \\]$" el)) object)) + (format #t " ?s ~a ~a .~%" predicate object)) + ((and (? string? object) + (? (lambda (el) (not (string-null? el))) object)) + (format #t " ?s ~a \"~a\" .~%" predicate object)) + (_ "")))) + first-n) + (format #t " ?s ?p ?o .~%}~%```~%")) + (format #t "~%Expected Result:~%~%```rdf~%") + (sql-for-each (lambda (row) + (scm->triples + (map-alist row #,@(field->key #'(predicate-clauses ...))) + #,(field->assoc-ref #'row #'subject) + (lambda (s p o) + (triple s p o)))) + db + (format #f "~a LIMIT 1" + (select-query #,(collect-fields #'(subject predicate-clauses ...)) + (primary-table other-tables ...) + tables-raw ...))) + (format #t "```~%~%")) + (when data? + #,(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))) + (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-transformer syntax:" (syntax->datum x)))))) + +(define (get-keyword-value args keyword default) + (let ((kv (memq keyword args))) + (if (and kv (>= (length kv) 2)) + (cadr kv) + default))) + +(define-syntax with-documentation + (syntax-rules () + ((_ (key value) ...) + (let* ((alist `((key . ,value) ...)) + (name (assoc-ref alist 'name)) + (connection (assoc-ref alist 'connection)) + (table-metadata? (assoc-ref alist 'table-metadata?)) + (prefixes (assoc-ref alist 'prefixes)) + (inputs (assoc-ref alist 'inputs)) + (outputs (assoc-ref alist 'outputs)) + (rdf-path (get-keyword-value outputs #:rdf "")) + (doc-path (get-keyword-value outputs #:documentation ""))) + (call-with-target-database + connection + (lambda (db) + (with-output-to-file ; + doc-path + (lambda () + (format #t "# ~a" name) + (for-each + (lambda (proc) + (proc db + #:metadata? #f + #:data? #f + #:documentation? + (lambda () (for-each + (match-lambda + ((k v) + (begin + (prefix k v #f)))) + prefixes)))) + inputs)) + #:encoding "UTF-8") + + ;; Dumping the actual data + (with-output-to-file + rdf-path + (lambda () + ;; Add the prefixes + (for-each + (match-lambda + ((k v) + (begin + (prefix k v)))) + prefixes) + (newline) + (for-each + (lambda (proc) + (proc db #:metadata? table-metadata?)) + inputs)) + #:encoding "UTF-8"))))))) + diff --git a/transform/sql.scm b/transform/sql.scm new file mode 100644 index 0000000..a8962c8 --- /dev/null +++ b/transform/sql.scm @@ -0,0 +1,114 @@ +;;; Database helpers +;;; +;;; Most of these functions should have been a part of +;;; guile-dbi. Never too late to contribute upstream! + +(define-module (transform sql) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) + #:use-module (ice-9 match) + #:use-module (dbi dbi) + #:export (select-query + call-with-database + call-with-target-database + sql-exec + sql-fold + sql-map + sql-for-each + sql-find)) + +;; A half-baked macro to make SQL SELECT queries a bit more +;; S-expression friendly +(define-syntax select-query + (lambda (x) + (syntax-case x () + ((_ fields tables raw-forms ...) + #`(string-append "SELECT " + #,(syntax-case #'fields (distinct) + ((distinct _ ...) + "DISTINCT ") + (_ "")) + #,(string-join (filter-map (match-lambda + ('distinct #f) + (((query alias)) + (format #f "~a AS ~a" query alias)) + ((table column) + (format #f "~a.~a" table column)) + ((table column alias) + (format #f "~a.~a AS ~a" table column alias)) + (field-spec + (error "Invalid field specification" field-spec))) + (syntax->datum #'fields)) + ", ") + " FROM " + #,(string-join (map (match-lambda + ((join table condition) + (format #f "~a ~a ~a" + (case join + ((join) "JOIN") + ((left-join) "LEFT JOIN") + ((inner-join) "INNER JOIN") + (else (error "Invalid join operator" join))) + table condition)) + ((? symbol? table) + (symbol->string table)) + (table-spec + (error "Invalid table specification" table-spec))) + (syntax->datum #'tables)) + " ") + #,(syntax-case #'(raw-forms ...) () + (() "") + (_ " ")) + raw-forms ...)) + (_ (error "Invalid SQL select query" (syntax->datum x)))))) + +(define (call-with-database backend connection-string proc) + (let ((db #f)) + (dynamic-wind (lambda () + (set! db (dbi-open backend connection-string))) + (cut proc db) + (cut dbi-close db)))) + +(define (database-check-status db) + (match (dbi-get_status db) + ((code . str) + (unless (zero? code) + (error str))))) + +(define (sql-exec db statement) + (dbi-query db statement) + (database-check-status db)) + +(define (sql-fold proc init db statement) + (sql-exec db statement) + (let loop ((result init)) + (let ((row (dbi-get_row db))) + (if row + (loop (proc row result)) + result)))) + +(define (sql-map proc db statement) + (sql-fold (lambda (row result) + (cons (proc row) result)) + (list) db statement)) + +(define (sql-for-each proc db statement) + (sql-fold (lambda (row _) + (proc row)) + #f db statement)) + +(define (sql-find db statement) + (sql-exec db statement) + (dbi-get_row db)) + +(define (call-with-target-database connection-settings 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)) diff --git a/transform/string-similarity.scm b/transform/string-similarity.scm new file mode 100644 index 0000000..c715856 --- /dev/null +++ b/transform/string-similarity.scm @@ -0,0 +1,37 @@ +(define-module (transform string-similarity) + #:use-module (srfi srfi-1) + #:export (jaccard-string-similar?)) + +(define (trigrams str) + "Return all trigrams in STR." + (if (< (string-length str) 3) + '() + (map (lambda (start) + (substring str start (+ start 3))) + (iota (- (string-length str) 2))))) + +(define (jaccard-index set1 set2) + "Return the Jaccard similarity coefficient between lists SET1 and +SET2. Similarity between null sets is defined to be 0." + (if (and (null? set1) + (null? set2)) + 0 + (let ((length-of-intersection (length (lset-intersection equal? set1 set2)))) + (exact->inexact + (/ length-of-intersection + (- (+ (length set1) (length set2)) + length-of-intersection)))))) + +(define (jaccard-string-similarity str1 str2) + "Return the trigram similarity between strings STR1 and STR2 as +defined by the Jaccard index." + (jaccard-index (trigrams (string-downcase str1)) + (trigrams (string-downcase str2)))) + +(define (jaccard-string-similar? str1 str2) + "Return #t if STR1 and STR2 have a trigram similarity greater than +0.8. Else, return #f. The Jaccard index is used as the similarity +metric." + (let ((similarity-threshold 0.8)) + (> (jaccard-string-similarity str1 str2) + similarity-threshold))) diff --git a/transform/strings.scm b/transform/strings.scm new file mode 100644 index 0000000..98f828f --- /dev/null +++ b/transform/strings.scm @@ -0,0 +1,101 @@ +(define-module (transform strings) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-19) + #:use-module (ice-9 match) + #:use-module (ice-9 string-fun) + #:use-module (ice-9 textual-ports) + #:export (string-blank? + time-unix->string + string-blank? + string-split-substring + delete-substrings + replace-substrings + sanitize-rdf-string + snake->lower-camel + string-capitalize-first)) + +(define (time-unix->string seconds . maybe-format) + "Given an integer saying the number of seconds since the Unix +epoch (1970-01-01 00:00:00), SECONDS, format it as a human readable +date and time-string, possible using the MAYBE-FORMAT." + (letrec ([time-unix->time-utc + (lambda (seconds) + (add-duration + (date->time-utc (make-date 0 0 0 0 1 1 1970 0)) + (make-time time-duration 0 seconds)))]) + (apply date->string + (time-utc->date (time-unix->time-utc seconds)) + maybe-format))) + +(define (string-blank? str) + "Return non-#f if STR consists only of whitespace characters." + (string-every char-set:whitespace str)) + +(define (string-split-substring str substr) + "Split the string @var{str} into a list of substrings delimited by the +substring @var{substr}." + + (define substrlen (string-length substr)) + (define strlen (string-length str)) + + (define (loop index start) + (cond + ((>= start strlen) (list "")) + ((not index) (list (substring str start))) + (else + (cons (substring str start index) + (let ((new-start (+ index substrlen))) + (loop (string-contains str substr new-start) + new-start)))))) + + (cond + ((string-contains str substr) => (lambda (idx) (loop idx 0))) + (else (list str)))) + +(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 (sanitize-rdf-string str) + (replace-substrings + (string-trim-both str) + '(("\r" . "\\r") + ("\n" . "\\n") + ("\"" . "'") + ("\v" . "") + ("\xad" . "") + ("\x28" . "") + ("\x29" . "") + ("\xa0" . " ") + ("\x02" . "") + ("\x01" . "")))) + +(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))))) + +(define (string-capitalize-first string) + (string-titlecase + (string-downcase string) 0 1)) + diff --git a/transform/table.scm b/transform/table.scm new file mode 100644 index 0000000..e6254d0 --- /dev/null +++ b/transform/table.scm @@ -0,0 +1,28 @@ +(define-module (transform table) + #:use-module (srfi srfi-9 gnu) + #:export (make-table + table-name + table-size + table-columns + set-table-columns + make-column + column-name + column-type + column-transformed?)) + +(define-immutable-record-type <table> + (make-table name size columns) + table? + (name table-name) + (size table-size) + (columns table-columns set-table-columns)) + +(define-immutable-record-type <column> + (column-constructor name type transformed?) + column? + (name column-name) + (type column-type) + (transformed? column-transformed?)) + +(define* (make-column name type #:optional transformed?) + (column-constructor name type transformed?)) diff --git a/transform/triples.scm b/transform/triples.scm new file mode 100644 index 0000000..8a64c5b --- /dev/null +++ b/transform/triples.scm @@ -0,0 +1,110 @@ +(define-module (transform triples) + #:use-module (ice-9 regex) + #:use-module (ice-9 match) + #:use-module (transform strings) + #:export (ontology + string->identifier + prefix + triple + scm->triples + annotate-field + string->binomial-name)) + +(define (annotate-field field schema) + (let ([schema (cond ((symbol? schema) + (symbol->string schema)) + ((string? schema) schema) + (else + (error "Use a string/symbol")))] + [string-field (if (number? field) (number->string field) field)]) + (if (or (and (string? string-field) (string-null? string-field)) + (eq? string-field #f)) + "" + (string->symbol + (format #f "~s~a" string-field schema))))) + +(define* (string->identifier prefix str + #:optional #:key + (ontology "gn:") + (separator "_") + (proc string-downcase)) + "Convert STR to a turtle identifier after replacing illegal +characters with an underscore and prefixing with gn:PREFIX." + (if (or (and (string? str) (string-null? str)) + (eq? str #f)) + "" + (string->symbol + (string-append ontology prefix separator + (string-delete + (lambda (c) + (eq? c #\))) + (string-map (lambda (c) + (case c + ((#\/ #\< #\> #\+ #\( #\space #\@) #\_) + (else c))) + (proc + (string-trim-right str #\.)))))))) + + +(define* (prefix prefix iri #:optional (ttl? #t)) + (format #t + (if ttl? + "@prefix ~a ~a .~%" + "PREFIX ~a ~a ~%") + prefix iri)) + +(define (ontology prefix value) + (if (and (string? value) (string-null? value)) + "" + (string->symbol + `,(format #f "~a~a" prefix value)))) + +(define (triple subject predicate object) + (unless (or (string? subject) + (symbol? subject)) + (error "Triple subject not a string or symbol:" + (list subject predicate object))) + (unless (or (string? predicate) + (symbol? predicate)) + (error "Triple predicate not a string or symbol:" + (list subject predicate object))) + (unless (or (string? object) + (symbol? object) + (number? object)) + (error "Triple object not a string, symbol or number:" + (list subject predicate object))) + (let ([pattern (match object + ((or (? symbol? object) + (? (lambda (el) (string-match "^\\[ .* \\]$" el)) object)) + "~a ~a ~a .~%") + (_ "~a ~a \"~a\" .~%"))]) + (format #t pattern subject predicate + (if (symbol? object) (symbol->string object) object)))) + +(define* (scm->triples alist id + #:optional + (fn triple)) + (for-each (match-lambda + ((predicate . object) + (when (cond + ((string? object) + (not (string-blank? object))) + (else object)) + (fn id predicate object)))) + alist)) + +(define (string->binomial-name name) + (let ((binomial? + (string-match + "\\\(.+\\)" + name))) + (string->identifier + "" + (if binomial? + (regexp-substitute/global + #f "[^[:space:]A-Za-z0-9:]" + (match:substring binomial?) + 'pre "" 'post) + name) + #:separator "" + #:proc string-capitalize-first))) |