#! /usr/bin/env guile
!#
(use-modules (rnrs io ports)
(srfi srfi-1)
(srfi srfi-26)
(srfi srfi-28)
(srfi srfi-71)
(srfi srfi-171)
(ice-9 match)
(sxml simple)
(sparql driver)
(sparql lang)
(sparql util)
(transform string-similarity)
(transform table))
(define rdfs
(prefix "http://www.w3.org/2000/01/rdf-schema#"))
(define rdf
(prefix "http://www.w3.org/1999/02/22-rdf-syntax-ns#"))
(define gn
(prefix "http://rdf.genenetwork.org/v1/"))
(define graph (@@ (ccwl graphviz) graph))
(define graph-node (@@ (ccwl graphviz) graph-node))
(define graph-edge (@@ (ccwl graphviz) graph-edge))
(define graph-port (@@ (ccwl graphviz) graph-port))
(define html-string (@@ (ccwl graphviz) html-string))
(define graph->dot (@@ (ccwl graphviz) graph->dot))
(define %sparql-host
(make-parameter #f))
(define %sparql-port
(make-parameter #f))
(define (sparql-query-records . args)
;; TODO: Use the JSON query results so that types can be converted
;; correctly.
(query-results->list (apply sparql-query
(append args
(list #:host (%sparql-host)
#:port (%sparql-port))))
#t))
(define (floor-log1024 x)
"Return the floor of the base 1024 logarithm of X."
(if (< x 1024)
0
(1+ (floor-log1024 (/ x 1024)))))
(define (human-units bytes)
"Return number of BYTES as a string with human-readable units."
(let* ((integer-log (floor-log1024 bytes)))
(format "~a ~a"
(round-quotient bytes (expt 1024 (min integer-log 3)))
(case integer-log
((0) "B")
((1) "KiB")
((2) "MiB")
(else "GiB")))))
(define (human-units-color bytes)
"Return the table header color coding for a table of size BYTES."
(let* ((color-scheme "purd4"))
(format "/~a/~a"
color-scheme
(1+ (min (floor-log1024 bytes) 3)))))
(define (sxml->xml-string tree)
"Serialize sxml TREE to a string. Return the serialized string."
(call-with-output-string
(cut sxml->xml tree <>)))
(define (sxml->graphviz-html tree)
"Convert sxml TREE to a graphviz <html-string>, and return it."
(html-string (sxml->xml-string tree)))
(define (table-label table)
"Return HTML string label for TABLE."
(sxml->graphviz-html
`(table (@ (cellborder 0)
(bgcolor ,(if (any column-transformed?
(table-columns table))
"lightgrey"
"white")))
(tr (td (@ (border 1)
(bgcolor ,(human-units-color (table-size table))))
,(format "~a (~a)"
(table-name table)
(human-units (table-size table)))))
,@(map (lambda (column)
`(tr (td (@ (port ,(column-name column))
,@(if (column-transformed? column)
`((bgcolor "green"))
'()))
,(column-name column))))
(table-columns table)))))
(define (string-remove-suffix-ci suffix str)
"Remove SUFFIX from STR if present. Suffix check is
case-insensitive."
(if (string-suffix-ci? suffix str)
(substring str 0 (- (string-length str)
(string-length suffix)))
str))
(define (column->foreign-table table column all-tables)
"If COLUMN in TABLE is a foreign key, return the table it refers to. Else,
return #f. ALL-TABLES is a list of all tables in the database."
(cond
((and (string=? (column-name column) "UserId")
(string=? (table-name table) "UserPrivilege"))
'User)
((string-ci=? (column-name column) "GenbankID")
'Genbank)
((not (or (string-prefix? "int" (column-type column))
(string-prefix? "smallint" (column-type column))))
#f)
((let ((string-similarity-threshold 0.8)
(target-table
(or (and=> (find (lambda (suffix)
(string-suffix-ci? suffix (column-name column)))
(list "id1" "id2" "_id" "id"))
(cut string-remove-suffix-ci <> (column-name column)))
(column-name column))))
(and (not (jaccard-string-similar? target-table
(table-name table)))
(find (lambda (table)
(jaccard-string-similar?
target-table (table-name table)))
all-tables)))
=> table-name)
(else #f)))
(define (tables)
"Return list of all tables in DB. Each element of the returned list
is a <table> object."
(map (match-lambda
((table size fields field-types field-transformed)
(make-table table
(string->number size)
(map make-column
(string-split fields #\,)
(string-split field-types #\,)
(map (cut string=? <> "1")
(string-split field-transformed #\,))))))
(sparql-query-records
"PREFIX gn: <http://rdf.genenetwork.org/v1/>
SELECT SAMPLE(?tablename) SAMPLE(?size) GROUP_CONCAT(?fieldname ; separator=\",\") GROUP_CONCAT(?fieldtype ; separator=\",\") GROUP_CONCAT(EXISTS{ ?transform rdf:type gn:transform . ?transform gn:depends_on ?field .} ; separator=\",\")
WHERE
{
?table rdf:type gn:sqlTable ;
gn:name ?tablename ;
gn:has_size ?size ;
gn:has_field ?field .
?field rdf:type gn:sql_table_field ;
gn:name ?fieldname ;
gn:sql_field_type ?fieldtype .
} GROUP BY ?table")))
(define (foreign-key-graphviz-edges tables)
"Return the list of graphviz edges representing foreign key
relations in TABLES."
(append-map (lambda (table)
(filter-map (lambda (column)
(and=> (column->foreign-table table column tables)
(cut cons
(graph-port (table-name table)
(column-name column))
<>)))
(table-columns table)))
tables))
(define (write-sql-visualization port)
"Write a visualization of the SQL schema in graphviz dot syntax to
PORT."
(let ((all-tables (tables)))
(graph->dot
(graph 'schema
#:nodes (map (lambda (table)
(graph-node
(table-name table)
`((shape . "none")
(label . ,(table-label table)))))
all-tables)
#:edges (foreign-key-graphviz-edges all-tables))
port)))
(define (literal-node-id domain predicate)
"Return the graphviz node identifier for an RDF literal node which
is the range of PREDICATE. The domain of PREDICATE is DOMAIN."
(string-append "literal_node__"
(basename domain)
"_"
(basename predicate)))
(define (rdf-type-nodes)
"Return the list of all graphviz nodes representing types."
(map (match-lambda
((type)
(graph-node (basename type)
`((fillcolor . lightgreen)
(style . filled)))))
(sparql-query-records
"SELECT DISTINCT ?type
WHERE {
{ ?predicate rdfs:domain ?type }
UNION
{ ?predicate rdfs:range ?type }
MINUS
{ ?predicate rdfs:range rdfs:Literal }
}")))
(define (rdf-literal-nodes)
"Return the list of all graphviz nodes representing literal
properties."
(map (match-lambda
((type predicate tables fields)
(graph-node
(literal-node-id type predicate)
`((shape . box)
(style . filled)
(fillcolor . gold)
(label . ,(basename predicate))
(tooltip . ,(string-join
(map (lambda (table field)
(string-append table "." field))
(string-split tables #\,)
(string-split fields #\,))
", "))))))
(sparql-query-records
"PREFIX gn: <http://rdf.genenetwork.org/v1/>
SELECT ?type ?predicate GROUP_CONCAT(?tablename ; separator=\",\") GROUP_CONCAT(?fieldname ; separator=\",\")
WHERE
{
?predicate rdfs:domain ?type ;
rdfs:range rdfs:Literal .
?transform rdf:type gn:transform ;
gn:creates_predicate ?predicate ;
gn:for_subject_type ?type ;
gn:depends_on ?field .
?field rdf:type gn:sql_table_field ;
gn:name ?fieldname .
?table rdf:type gn:sqlTable ;
gn:has_field ?field ;
gn:name ?tablename .
} GROUP BY ?type ?predicate
")))
(define (rdf-edges)
"Return the list of all graphviz edges in the RDF visualization."
(map (match-lambda
((type predicate range)
(if (string=? range (string-trim-both (rdfs "Literal")
(char-set #\< #\>)))
;; Literal properties
(graph-edge (basename type)
(literal-node-id type predicate))
;; Relations between classes
(graph-edge (basename type)
(basename range)))))
(sparql-query-records
(select '(type predicate range)
`((predicate ,(rdfs "domain") type)
(predicate ,(rdfs "range") range))))))
(define (write-rdf-visualization port)
"Write a visualization of the RDF schema in graphviz dot syntax to
PORT."
(graph->dot
(graph 'rdf
#:nodes (append (rdf-type-nodes)
(rdf-literal-nodes))
#:edges (rdf-edges))
port))
(define main
(match-lambda*
((_ connection-settings-file)
(let ((connection-settings (call-with-input-file connection-settings-file
read)))
(parameterize ((%sparql-host (assq-ref connection-settings 'sparql-host))
(%sparql-port (assq-ref connection-settings 'sparql-port)))
(call-with-output-file "sql.dot"
write-sql-visualization)
(call-with-output-file "rdf.dot"
write-rdf-visualization))))
((arg0 _ ...)
(display (format "Usage: ~a CONNECTION-SETTINGS-FILE~%" arg0)
(current-error-port))
(exit #f))))
(apply main (command-line))
