From 5eb0b0bdba3374cee96006cd1006603bbe13e36b Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 5 Feb 2020 06:30:11 -0600
Subject: gn: ratspub: Update to 0.1.

---
 gn/packages/ratspub.scm | 126 ++++++++++++++++++++++++------------------------
 1 file changed, 62 insertions(+), 64 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index da6df5f..81959a0 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -11,73 +11,71 @@
   #:use-module (gn packages web))
 
 (define-public ratspub
-  (let ((commit "88ab6a3a21fcc2715c9a7528d8b4d15bb7ea85ed")
-        (revision "2"))
-    (package
-      (name "ratspub")
-      (version (git-version "0.0.0" revision commit)) ; Aug 30, 2019
-      (source (origin
-               (method git-fetch)
-               (uri (git-reference
-                     (url "https://github.com/chen42/ratspub.git")
-                     (commit commit)))
-               (file-name (git-file-name name version))
-               (sha256
-                (base32
-                 "0gg2wikajbz248qgg7vyclrmjhdw01wb721zvzgil9qd2gm0g4c6"))))
-      (build-system python-build-system)
-      (arguments
-       `(#:tests? #f ; no test suite
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (delete 'build)
-           (add-after 'unpack 'patch-sources
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let ((out       (assoc-ref outputs "out"))
-                     (cytoscape (assoc-ref inputs "cytoscape"))
-                     (bootstrap (assoc-ref inputs "bootstrap"))
-                     (inetutils (assoc-ref inputs "inetutils")))
-                 ;; Source cannot find the substituted css currently.
-                 ;(substitute* "templates/cytoscape.html"
-                 ;  (("script src=.*")
-                 ;   (string-append "script src=\"" cytoscape
-                 ;                  "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n")))
-                 ;(substitute* "templates/layout.html"
-                 ;  (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
-                 ;   (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n")))
-                 (substitute* "ratspub.py"
-                   (("hostname") (string-append inetutils "/bin/hostname"))))
-               #t))
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((out (assoc-ref outputs "out")))
-                 (copy-recursively "." out))
-               #t))
-           (add-after 'install 'wrap-executable
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let ((out  (assoc-ref outputs "out"))
-                     (path (getenv "PYTHONPATH")))
-                 (wrap-program (string-append out "/server.py")
-                   `("PATH" ":" prefix (,(dirname (which "edirect.pl"))))
-                   `("PYTHONPATH" ":" prefix (,path))))
-               #t)))))
-      (inputs
-       `(("edirect" ,edirect-gn)
-         ("inetutils" ,inetutils)
-         ("python-flask" ,python-flask)
-         ("python-nltk" ,python-nltk)))
-      (native-inputs
-       `(("cytoscape" ,javascript-cytoscape)
-         ("bootstrap" ,web-bootstrap)))
-      (home-page "http://rats.pub/")
-      (synopsis "Relationship with Addiction Through Searches of PubMed")
-      (description
-       "RatsPub searches PubMed to find sentences that contain the query terms
+  (package
+    (name "ratspub")
+    (version "0.1")
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/chen42/ratspub.git")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "0cm9g38fxpa52458mdmhzhghj5c7b8l3k1b764zs9hdrki5s7wi7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (add-after 'unpack 'patch-sources
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out       (assoc-ref outputs "out"))
+                   (cytoscape (assoc-ref inputs "cytoscape"))
+                   (bootstrap (assoc-ref inputs "bootstrap"))
+                   (inetutils (assoc-ref inputs "inetutils")))
+               ;; Source cannot find the substituted css currently.
+               ;(substitute* "templates/cytoscape.html"
+               ;  (("script src=.*")
+               ;   (string-append "script src=\"" cytoscape
+               ;                  "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n")))
+               ;(substitute* "templates/layout.html"
+               ;  (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
+               ;   (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n")))
+               (substitute* "ratspub.py"
+                 (("hostname") (string-append inetutils "/bin/hostname"))))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (copy-recursively "." out))
+             #t))
+         (add-after 'install 'wrap-executable
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out  (assoc-ref outputs "out"))
+                   (path (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/server.py")
+                 `("PATH" ":" prefix (,(dirname (which "edirect.pl"))))
+                 `("PYTHONPATH" ":" prefix (,path))))
+             #t)))))
+    (inputs
+     `(("edirect" ,edirect-gn)
+       ("inetutils" ,inetutils)
+       ("python-flask" ,python-flask)
+       ("python-nltk" ,python-nltk)))
+    (native-inputs
+     `(("cytoscape" ,javascript-cytoscape)
+       ("bootstrap" ,web-bootstrap)))
+    (home-page "http://rats.pub/")
+    (synopsis "Relationship with Addiction Through Searches of PubMed")
+    (description
+     "RatsPub searches PubMed to find sentences that contain the query terms
 (i.e., gene symbols) and drug addiction-related keywords.  These gene-keyword
 relationships are presented as an interactive graph that can efficiently answer
 the question \"What do we know about these genes and addiction?\".  Data from
 @acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association
 Studies} catalog are also included in the search to better answer this
 question.")
-      (license #f))))
+    (license #f)))
-- 
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