diff options
| -rwxr-xr-x | examples/dataset-metadata.scm | 8 | ||||
| -rwxr-xr-x | examples/generif.scm | 10 | ||||
| -rwxr-xr-x | examples/genotype.scm | 10 | ||||
| -rwxr-xr-x | examples/phenotype.scm | 8 | ||||
| -rwxr-xr-x | examples/probeset-data.scm | 8 | ||||
| -rwxr-xr-x | examples/probeset.scm | 8 | ||||
| -rwxr-xr-x | examples/publication.scm | 8 | ||||
| -rwxr-xr-x | examples/species-metadata.scm | 8 | ||||
| -rwxr-xr-x | examples/tissue.scm | 8 | ||||
| -rwxr-xr-x | json-dump.scm | 2 | ||||
| -rw-r--r-- | tests.scm | 16 | ||||
| -rw-r--r-- | transform/schema-dump.scm (renamed from dump/schema-dump.scm) | 10 | ||||
| -rw-r--r-- | transform/special-forms.scm (renamed from dump/special-forms.scm) | 22 | ||||
| -rw-r--r-- | transform/sql.scm (renamed from dump/sql.scm) | 2 | ||||
| -rw-r--r-- | transform/string-similarity.scm (renamed from dump/string-similarity.scm) | 2 | ||||
| -rw-r--r-- | transform/strings.scm (renamed from dump/strings.scm) | 2 | ||||
| -rw-r--r-- | transform/table.scm (renamed from dump/table.scm) | 12 | ||||
| -rw-r--r-- | transform/triples.scm (renamed from dump/triples.scm) | 4 | ||||
| -rwxr-xr-x | visualize-schema.scm | 16 |
19 files changed, 82 insertions, 82 deletions
diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm index 5680a2b..783b2b7 100755 --- a/examples/dataset-metadata.scm +++ b/examples/dataset-metadata.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/generif.scm b/examples/generif.scm index 0b3c8e4..76f55ee 100755 --- a/examples/generif.scm +++ b/examples/generif.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) @@ -64,7 +64,7 @@ 'gn:geneWikiEntry)) (set gnt:wikiEntryOfSpecies (string->binomial-name (field Species FullName))) - ;; This only dumps symbols not present in the GeneRIF_BASIC table + ;; This only transforms symbols not present in the GeneRIF_BASIC table (set gnt:symbol (let ([geneid (field GeneRIF_BASIC GeneId)]) (if (eq? geneid 0) (field GeneRIF symbol) diff --git a/examples/genotype.scm b/examples/genotype.scm index 63b85a7..6fe60c9 100755 --- a/examples/genotype.scm +++ b/examples/genotype.scm @@ -7,10 +7,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) @@ -86,7 +86,7 @@ '^^xsd:double)) (set gnt:hasSequence (field Geno Sequence)) (set gnt:hasSource (field Geno Source)) - ;; Only dump Source2 if it differs from Source + ;; Only transform Source2 if it differs from Source (set gnt:hasAltSourceName (field ("IF((Source2 = Source), NULL, Source2)" Source2))) diff --git a/examples/phenotype.scm b/examples/phenotype.scm index 1c68159..31d7972 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -7,10 +7,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/probeset-data.scm b/examples/probeset-data.scm index d46bcda..ebb6a92 100755 --- a/examples/probeset-data.scm +++ b/examples/probeset-data.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/probeset.scm b/examples/probeset.scm index 68ddb59..2dfdbc2 100755 --- a/examples/probeset.scm +++ b/examples/probeset.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/publication.scm b/examples/publication.scm index 313ee96..d9e2aa5 100755 --- a/examples/publication.scm +++ b/examples/publication.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm index f3794b8..b67c0bc 100755 --- a/examples/species-metadata.scm +++ b/examples/species-metadata.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/examples/tissue.scm b/examples/tissue.scm index 8ce96c8..22b715e 100755 --- a/examples/tissue.scm +++ b/examples/tissue.scm @@ -5,10 +5,10 @@ (srfi srfi-26) (ice-9 match) (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms)) diff --git a/json-dump.scm b/json-dump.scm index 8625139..0a054c5 100755 --- a/json-dump.scm +++ b/json-dump.scm @@ -4,7 +4,7 @@ (use-modules (json) (ice-9 ftw) (ice-9 match) - (dump triples)) + (transform triples)) diff --git a/tests.scm b/tests.scm index 7ba4261..1dfa2ac 100644 --- a/tests.scm +++ b/tests.scm @@ -1,9 +1,9 @@ (use-modules (srfi srfi-64) (ice-9 match) - (dump sql) - (dump string-similarity) - (dump strings) - (dump special-forms)) + (transform sql) + (transform string-similarity) + (transform strings) + (transform special-forms)) (test-begin "sql") @@ -24,23 +24,23 @@ (test-equal "trigrams of a string" (list "coe" "oef" "eff" "ffi" "fic" "ici" "cie" "ien" "ent") - ((@@ (dump string-similarity) trigrams) "coefficient")) + ((@@ (transform string-similarity) trigrams) "coefficient")) (test-equal "Jaccard index" 0.4 - ((@@ (dump string-similarity) jaccard-index) + ((@@ (transform string-similarity) jaccard-index) (list 0 1 2 5 6 8 9) (list 0 2 3 4 5 7 9))) (test-equal "Jaccard index of equal sets" 1.0 - ((@@ (dump string-similarity) jaccard-index) + ((@@ (transform string-similarity) jaccard-index) (iota 10) (iota 10))) (test-equal "Jaccard index of disjoint sets" 0.0 - ((@@ (dump string-similarity) jaccard-index) + ((@@ (transform string-similarity) jaccard-index) (iota 10) (iota 10 10))) diff --git a/dump/schema-dump.scm b/transform/schema-dump.scm index 525bf65..bf7f8cb 100644 --- a/dump/schema-dump.scm +++ b/transform/schema-dump.scm @@ -1,10 +1,10 @@ -(define-module (dump schema) +(define-module (transform schema) #:use-module (ice-9 match) #:use-module (ice-9 srfi-26) - #:use-module (dump sql) - #:use-module (dump triples) - #:use-module (dump strings) - #:use-module (dump table)) + #:use-module (transform sql) + #:use-module (transform triples) + #:use-module (transform strings) + #:use-module (transform table)) (define (table-fields db table) diff --git a/dump/special-forms.scm b/transform/special-forms.scm index 2650580..4b69337 100644 --- a/dump/special-forms.scm +++ b/transform/special-forms.scm @@ -1,10 +1,10 @@ -(define-module (dump special-forms) +(define-module (transform 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) + #:use-module (transform sql) + #:use-module (transform table) + #:use-module (transform triples) #:export (translate-forms collect-forms collect-keys @@ -279,7 +279,7 @@ ALIST field-name) forms." (define (id table predicate) (symbol->string (string->identifier - "dump" + "transform" (string-append table "_" (remove-namespace (symbol->string predicate))))))) @@ -344,7 +344,7 @@ literals is optional. So, (define-syntax define-transformer (lambda (x) - "Define FUNCTION-NAME, a function that dumps a view of the database. + "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. @@ -357,7 +357,7 @@ schema-triples and triples---in the form shown below. (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 +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 @@ -367,9 +367,9 @@ string. This is usually something like 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. +once when the transform starts. -The triples clause specifies the triples to be dumped once for each +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. @@ -409,11 +409,11 @@ must be remedied." (map (lambda (predicate-clause) (syntax-case predicate-clause () ((_ predicate _) - ;; Dump metadata about the dump itself. + ;; Dump metadata about the transform itself. #`(begin (scm->triples (map-alist '() - (set rdf:type 'gn-id:dump) + (set rdf:type 'gn-id:transform) (set gn-term:createsPredicate 'predicate) (filter-set gn-term:forSubjectType #,subject-type) (multiset gn-term:dependsOn diff --git a/dump/sql.scm b/transform/sql.scm index 9e6b21a..a8962c8 100644 --- a/dump/sql.scm +++ b/transform/sql.scm @@ -3,7 +3,7 @@ ;;; Most of these functions should have been a part of ;;; guile-dbi. Never too late to contribute upstream! -(define-module (dump sql) +(define-module (transform sql) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (ice-9 match) diff --git a/dump/string-similarity.scm b/transform/string-similarity.scm index 4bcdf7c..c715856 100644 --- a/dump/string-similarity.scm +++ b/transform/string-similarity.scm @@ -1,4 +1,4 @@ -(define-module (dump string-similarity) +(define-module (transform string-similarity) #:use-module (srfi srfi-1) #:export (jaccard-string-similar?)) diff --git a/dump/strings.scm b/transform/strings.scm index e965f03..98f828f 100644 --- a/dump/strings.scm +++ b/transform/strings.scm @@ -1,4 +1,4 @@ -(define-module (dump strings) +(define-module (transform strings) #:use-module (srfi srfi-1) #:use-module (srfi srfi-19) #:use-module (ice-9 match) diff --git a/dump/table.scm b/transform/table.scm index 834c4fd..e6254d0 100644 --- a/dump/table.scm +++ b/transform/table.scm @@ -1,4 +1,4 @@ -(define-module (dump table) +(define-module (transform table) #:use-module (srfi srfi-9 gnu) #:export (make-table table-name @@ -8,7 +8,7 @@ make-column column-name column-type - column-dumped?)) + column-transformed?)) (define-immutable-record-type <table> (make-table name size columns) @@ -18,11 +18,11 @@ (columns table-columns set-table-columns)) (define-immutable-record-type <column> - (column-constructor name type dumped?) + (column-constructor name type transformed?) column? (name column-name) (type column-type) - (dumped? column-dumped?)) + (transformed? column-transformed?)) -(define* (make-column name type #:optional dumped?) - (column-constructor name type dumped?)) +(define* (make-column name type #:optional transformed?) + (column-constructor name type transformed?)) diff --git a/dump/triples.scm b/transform/triples.scm index b0eb1e4..8a64c5b 100644 --- a/dump/triples.scm +++ b/transform/triples.scm @@ -1,7 +1,7 @@ -(define-module (dump triples) +(define-module (transform triples) #:use-module (ice-9 regex) #:use-module (ice-9 match) - #:use-module (dump strings) + #:use-module (transform strings) #:export (ontology string->identifier prefix diff --git a/visualize-schema.scm b/visualize-schema.scm index 6850cb8..92f9272 100755 --- a/visualize-schema.scm +++ b/visualize-schema.scm @@ -12,8 +12,8 @@ (sparql driver) (sparql lang) (sparql util) - (dump string-similarity) - (dump table)) + (transform string-similarity) + (transform table)) (define rdfs (prefix "http://www.w3.org/2000/01/rdf-schema#")) @@ -83,7 +83,7 @@ "Return HTML string label for TABLE." (sxml->graphviz-html `(table (@ (cellborder 0) - (bgcolor ,(if (any column-dumped? + (bgcolor ,(if (any column-transformed? (table-columns table)) "lightgrey" "white"))) @@ -94,7 +94,7 @@ (human-units (table-size table))))) ,@(map (lambda (column) `(tr (td (@ (port ,(column-name column)) - ,@(if (column-dumped? column) + ,@(if (column-transformed? column) `((bgcolor "green")) '())) ,(column-name column)))) @@ -140,17 +140,17 @@ return #f. ALL-TABLES is a list of all tables in the database." "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-dumped) + ((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-dumped #\,)))))) + (string-split field-transformed #\,)))))) (sparql-query-records "PREFIX gn: <http://genenetwork.org/> -SELECT SAMPLE(?tablename) SAMPLE(?size) GROUP_CONCAT(?fieldname ; separator=\",\") GROUP_CONCAT(?fieldtype ; separator=\",\") GROUP_CONCAT(EXISTS{ ?dump rdf:type gn:dump . ?dump gn:dependsOn ?field .} ; separator=\",\") +SELECT SAMPLE(?tablename) SAMPLE(?size) GROUP_CONCAT(?fieldname ; separator=\",\") GROUP_CONCAT(?fieldtype ; separator=\",\") GROUP_CONCAT(EXISTS{ ?transform rdf:type gn:transform . ?transform gn:dependsOn ?field .} ; separator=\",\") WHERE { ?table rdf:type gn:sqlTable ; @@ -239,7 +239,7 @@ WHERE { ?predicate rdfs:domain ?type ; rdfs:range rdfs:Literal . - ?dump rdf:type gn:dump ; + ?transform rdf:type gn:transform ; gn:createsPredicate ?predicate ; gn:forSubjectType ?type ; gn:dependsOn ?field . |