Unite importing GeneRIF with dumping SQL data.

* README.md: Document generif-data-file parameter in connection
settings.
* dump.scm: Import (srfi srfi-171), (ice-9 regex) and (zlib).
(decode-html-entities, import-generif): New functions.
(main): Call import-generif.
* import-generif.scm: Delete file.

3 files changed, 57 insertions, 77 deletions

diff --git a/README.md b/README.md
index b9084fa..c4276e6 100644
--- a/README.md
+++ b/README.md
@@ -26,7 +26,8 @@ shown below. Take care to replace the placeholders within angle brackets
 with the appropriate values.
 
 ``` scheme
-((sql-username . "<sql-username-here>")
+((generif-data-file . "/path/to/generifs_basic.gz")
+ (sql-username . "<sql-username-here>")
  (sql-password . "<sql-password-here>")
  (sql-database . "<sql-database-name-here>")
  (sql-host . "<sql-hostname-here>")
diff --git a/dump.scm b/dump.scm
index 295bf1e..e26cdd7 100755
--- a/dump.scm
+++ b/dump.scm
@@ -5,12 +5,15 @@
              (rnrs io ports)
              (srfi srfi-1)
              (srfi srfi-26)
+             (srfi srfi-171)
              (ice-9 match)
+             (ice-9 regex)
              (ice-9 string-fun)
              (dump sql)
              (dump table)
              (dump triples)
-             (dump utils))
+             (dump utils)
+             (zlib))
 
 
 ;;; GeneNetwork database connection parameters and dump path
@@ -768,6 +771,55 @@ is a <table> object."
     (set gn:species (field Species Name))))
 
 
+;; Import GeneRIF
+
+(define decode-html-entities
+  (cut regexp-substitute/global
+       #f
+       ;; We tolerate the absence of the trailing semicolon.
+       "&#([[:digit:]]+);{0,1}"
+       <>
+       'pre
+       (compose string integer->char string->number (cut match:substring <> 1))
+       'post))
+
+(define (import-generif generif-data-file)
+  ;; TODO: Link to gene objects, not merely literal Gene IDs.
+  (triple 'gn:geneId 'rdfs:domain 'gn:geneRIF)
+  (triple 'gn:geneId 'rdfs:range 'rdfs:Literal)
+  ;; TODO: Link to gn:publication objects, not merely literal PubMed
+  ;; IDs.
+  (triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:domain 'gn:geneRIF)
+  (triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:range 'rdfs:Literal)
+  (triple 'gn:geneRIFText 'rdfs:domain 'gn:geneRIF)
+  (triple 'gn:geneRIFText 'rdfs:range 'rdfs:Literal)
+
+  (call-with-gzip-input-port (open-input-file generif-data-file)
+    (lambda (port)
+      ;; Read and discard header.
+      (get-line port)
+      ;; Dump other lines.
+      (port-transduce
+       (compose (tenumerate)
+                (tmap (match-lambda
+                        ;; Is there a better way to identify GeneRIF
+                        ;; entries instead of merely enumerating them?
+                        ((i . line)
+                         (match (string-split line #\tab)
+                           ((_ gene-id pubmed-id _ text)
+                            (scm->triples
+                             `((rdf:type . gn:geneRIF)
+                               (gn:geneId . ,(string->number gene-id))
+                               (gn:pubMedId . ,(string->number pubmed-id))
+                               ;; Some text has HTML entities. Decode
+                               ;; them.
+                               (gn:geneRIFText . ,(decode-html-entities text)))
+                             (string->identifier "geneRIF" (number->string i)))))))))
+       (const #t)
+       get-line
+       port))))
+
+
 ;; Main function
 
 (call-with-genenetwork-database
@@ -793,4 +845,5 @@ is a <table> object."
        (dump-info-files db)
        (dump-schema db)
        (dump-case-attributes db)
-       (dump-groups db)))))
+       (dump-groups db)
+       (import-generif (assq-ref %connection-settings 'generif-data-file))))))
diff --git a/import-generif.scm b/import-generif.scm
deleted file mode 100755
index 69a5f78..0000000
--- a/import-generif.scm
+++ /dev/null
@@ -1,74 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-;; This script imports GeneRIF data downloaded from
-;; https://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz into RDF.
-
-(use-modules (rnrs io ports)
-             (srfi srfi-26)
-             (srfi srfi-171)
-             (ice-9 match)
-             (ice-9 regex)
-             (dump triples)
-             (dump utils)
-             (zlib))
-
-(define decode-html-entities
-  (cut regexp-substitute/global
-       #f
-       ;; We tolerate the absence of the trailing semicolon.
-       "&#([[:digit:]]+);{0,1}"
-       <>
-       'pre
-       (compose string integer->char string->number (cut match:substring <> 1))
-       'post))
-
-(define (main generif-data-file dump-directory)
-  (with-output-to-file (string-append dump-directory "/generif.ttl")
-    (lambda ()
-      (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-      (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-      (prefix "gn:" "<http://genenetwork.org/>")
-      (newline)
-      ;; TODO: Link to gene objects, not merely literal Gene IDs.
-      (triple 'gn:geneId 'rdfs:domain 'gn:geneRIF)
-      (triple 'gn:geneId 'rdfs:range 'rdfs:Literal)
-      ;; TODO: Link to gn:publication objects, not merely literal
-      ;; PubMed IDs.
-      (triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:domain 'gn:geneRIF)
-      (triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:range 'rdfs:Literal)
-      (triple 'gn:geneRIFText 'rdfs:domain 'gn:geneRIF)
-      (triple 'gn:geneRIFText 'rdfs:range 'rdfs:Literal)
-
-      (call-with-gzip-input-port (open-input-file generif-data-file)
-        (lambda (port)
-          ;; Read and discard header.
-          (get-line port)
-          ;; Dump other lines.
-          (port-transduce
-           (compose (tenumerate)
-                    (tmap (match-lambda
-                            ;; Is there a better way to identify
-                            ;; GeneRIF entries instead of merely
-                            ;; enumerating them?
-                            ((i . line)
-                             (match (string-split line #\tab)
-                               ((_ gene-id pubmed-id _ text)
-                                (scm->triples
-                                 `((rdf:type . gn:geneRIF)
-                                   (gn:geneId . ,(string->number gene-id))
-                                   (gn:pubMedId . ,(string->number pubmed-id))
-                                   ;; Some text has HTML
-                                   ;; entities. Decode them.
-                                   (gn:geneRIFText . ,(decode-html-entities text)))
-                                 (string->identifier "geneRIF" (number->string i)))))))))
-           (const #t)
-           get-line
-           port))))))
-
-(match (command-line)
-  ((arg0 generif-data-file dump-directory)
-   (main generif-data-file dump-directory))
-  ((arg0 _ ...)
-   (format (current-error-port) "Usage: ~a GENERIF-DATA-FILE DUMP-DIRECTORY~%" arg0)
-   (exit #f)))