Move investigators transform to its own file.

* examples/dataset-metadata.scm (investigators): Delete.
(option-spec)[investigators]: Delete
* transform/strings.scm (fix-email-id, investigator-attributes->id):
Move these ...
* examples/investigators.scm: ... here.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 93 insertions, 0 deletions

diff --git a/examples/investigators.scm b/examples/investigators.scm
new file mode 100755
index 0000000..8d31974
--- /dev/null
+++ b/examples/investigators.scm
@@ -0,0 +1,93 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 getopt-long)
+             (ice-9 match)
+             (ice-9 regex)
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
+
+
+;; One email ID in the Investigators table has spaces in it. This
+;; function fixes that.
+(define (fix-email-id email)
+  (string-delete #\space email))
+
+(define (investigator-attributes->id first-name last-name email)
+  ;; There is just one record corresponding to "Evan Williams" which
+  ;; does not have an email ID. To accommodate that record, we
+  ;; construct the investigator ID from not just the email ID, but
+  ;; also the first and the last names. It would be preferable to just
+  ;; find Evan Williams' email ID and insert it into the database.
+  (string->identifier "investigator"
+                      (string-join
+                       (list first-name last-name (fix-email-id email))
+                       "_")
+                      #:separator "_"))
+
+
+(define-transformer investigators
+  ;; There are a few duplicate entries. We group by email to
+  ;; deduplicate.
+  (tables (Investigators)
+          "GROUP BY Email")
+  (triples (investigator-attributes->id (field Investigators FirstName)
+                                        (field Investigators LastName)
+                                        "")
+    (set rdf:type 'foaf:Person)
+    (set foaf:name (string-append (field Investigators FirstName) " "
+                                  (field Investigators LastName)))
+    (set foaf:givenName
+         (field Investigators FirstName))
+    (set foaf:familyName
+         (field Investigators LastName))
+    (set foaf:homepage (field Investigators Url))
+    (set v:adr (field Investigators Address))
+    (set v:locality (field Investigators City))
+    (set v:region (field Investigators State))
+    (set v:postal-code (field Investigators ZipCode))
+    (set v:country-name (field Investigators Country))))
+
+
+(let* ((option-spec
+        '((settings (single-char #\s) (value #t))
+          (output (single-char #\o) (value #t))
+          (documentation (single-char #\d) (value #t))))
+       (options (getopt-long (command-line) option-spec))
+       (settings (option-ref options 'settings #f))
+       (output (option-ref options 'output #f))
+       (documentation (option-ref options 'documentation #f))
+       (%connection-settings
+        (call-with-input-file settings
+          read)))
+  (with-documentation
+   (name "Info files / Investigators Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(
+      ("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("foaf:" "<http://xmlns.com/foaf/0.1/#term_>")
+      ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
+      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
+      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
+      ("v:" "<http://www.w3.org/2006/vcard/ns#>")
+      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ))
+   (inputs
+    (list investigators))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))