diff options
| -rwxr-xr-x | dump.scm | 366 | ||||
| -rw-r--r-- | dump/schema-dump.scm | 120 | ||||
| -rw-r--r-- | dump/special-forms.scm | 430 | ||||
| -rw-r--r-- | dump/sql.scm | 13 | ||||
| -rw-r--r-- | dump/strings.scm | 88 | ||||
| -rw-r--r-- | dump/triples.scm | 35 | ||||
| -rw-r--r-- | dump/utils.scm | 208 |
7 files changed, 678 insertions, 582 deletions
@@ -5,15 +5,12 @@ (rnrs io ports) (srfi srfi-1) (srfi srfi-26) - (srfi srfi-171) (ice-9 match) (ice-9 regex) - (ice-9 string-fun) + (dump strings) (dump sql) - (dump table) (dump triples) - (dump utils) - (zlib)) + (dump special-forms)) ;;; GeneNetwork database connection parameters and dump path @@ -22,371 +19,12 @@ (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 (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 (string-null? string-field) - "" - (string->symbol - (format #f "~s~a" string-field schema))))) - -(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" . "")))) - -(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 (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 (dump-id dump-table predicate) - (symbol->string - (string->identifier - "dump" - (string-append - dump-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-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 #:optional (table-metadata? #f)) - #,(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))) - (when table-metadata? - #,@(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)))) - (((query alias)) - (datum->syntax - x (column-id query (symbol->string alias)))))) - (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" <>)) diff --git a/dump/schema-dump.scm b/dump/schema-dump.scm new file mode 100644 index 0000000..cda3fd0 --- /dev/null +++ b/dump/schema-dump.scm @@ -0,0 +1,120 @@ +(define-module (dump schema) + #:use-module (ice-9 match) + #:use-module (dump sql)) + + +(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 (get-tables-from-comments db) + (sql-map (match-lambda + ((("TableName" . table)) table)) + db + (select-query ((TableComments TableName)) + (TableComments)))) + +(define (dump-schema-annotations db) + (call-with-genenetwork-database + (lambda (db) + (for-each (cut dump-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 (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-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))) diff --git a/dump/special-forms.scm b/dump/special-forms.scm new file mode 100644 index 0000000..9b295ba --- /dev/null +++ b/dump/special-forms.scm @@ -0,0 +1,430 @@ +(define-module (dump special-forms) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:use-module (srfi srfi-26) + #:use-module (dump sql) + #:use-module (dump table) + #:use-module (dump triples) + #:export (translate-forms + collect-forms + collect-keys + field->key + field->assoc-ref + collect-fields + find-clause + remove-namespace + column-id + dump-id + syntax-let + blank-node + define-dump)) + +(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 eval) + (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 (dump-id dump-table predicate) + (symbol->string + (string->identifier + "dump" + (string-append + dump-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-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 #:optional (table-metadata? #f)) + #,(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))) + (when table-metadata? + #,@(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)))) + (((query alias)) + (datum->syntax + x (column-id query (symbol->string alias)))))) + (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)))))) diff --git a/dump/sql.scm b/dump/sql.scm index 76c9e0e..9e6b21a 100644 --- a/dump/sql.scm +++ b/dump/sql.scm @@ -10,6 +10,7 @@ #:use-module (dbi dbi) #:export (select-query call-with-database + call-with-target-database sql-exec sql-fold sql-map @@ -99,3 +100,15 @@ (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/dump/strings.scm b/dump/strings.scm new file mode 100644 index 0000000..c67d7fc --- /dev/null +++ b/dump/strings.scm @@ -0,0 +1,88 @@ +(define-module (dump strings) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-19) + #:use-module (ice-9 match) + #:use-module (ice-9 string-fun) + #:export (string-blank? + time-unix->string + string-blank? + string-split-substring + delete-substrings + replace-substrings + sanitize-rdf-string + snake->lower-camel)) + +(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" . "")))) + +(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))))) diff --git a/dump/triples.scm b/dump/triples.scm index 32cd243..a0f8213 100644 --- a/dump/triples.scm +++ b/dump/triples.scm @@ -1,24 +1,39 @@ (define-module (dump triples) #:use-module (ice-9 regex) #:use-module (ice-9 match) - #:use-module (dump utils) + #:use-module (dump strings) #:export (ontology string->identifier prefix triple - scm->triples)) + scm->triples + annotate-field)) + +(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 (string-null? string-field) + "" + (string->symbol + (format #f "~s~a" string-field schema))))) (define (string->identifier prefix str) "Convert STR to a turtle identifier after replacing illegal characters with an underscore and prefixing with gn:PREFIX." - (string->symbol - (string-append "gn:" prefix "_" - (string-map (lambda (c) - (case c - ((#\/ #\< #\> #\+ #\( #\) #\space #\@) #\_) - (else c))) - (string-downcase - (string-trim-right str #\.)))))) + (if (string-null? str) + "" + (string->symbol + (string-append "gn:" prefix "_" + (string-map (lambda (c) + (case c + ((#\/ #\< #\> #\+ #\( #\) #\space #\@) #\_) + (else c))) + (string-downcase + (string-trim-right str #\.))))))) (define (prefix prefix iri) (format #t "@prefix ~a ~a .~%" prefix iri)) diff --git a/dump/utils.scm b/dump/utils.scm deleted file mode 100644 index 8544eec..0000000 --- a/dump/utils.scm +++ /dev/null @@ -1,208 +0,0 @@ -(define-module (dump utils) - #:use-module (srfi srfi-1) - #:use-module (srfi srfi-19) - #:use-module (srfi srfi-26) - #:use-module (ice-9 match) - #:export (string-blank? - translate-forms - collect-forms - map-alist - time-unix->string)) - - -(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 (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 (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 (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 (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-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 ...))))))))))) |