From 14dc7e6f85f204d01fc5a96e986469c0355e87fb Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 15 Mar 2020 04:33:59 -0500
Subject: gn: ratspub: Update to 0.2.2.

---
 gn/packages/ratspub.scm | 80 ++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 59 insertions(+), 21 deletions(-)

(limited to 'gn/packages/ratspub.scm')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 694379a..3e5727c 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -6,6 +6,8 @@
   #:use-module (gnu packages admin)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
+  #:use-module (gnu packages time)
+  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gn packages web))
@@ -13,16 +15,16 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.1")
+    (version "0.2.2")
     (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"))))
+              (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
+                "0q111fsch69kjv96d0pld9agqpwazh9p47vsvig63hmmjp72wa84"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no test suite
@@ -34,12 +36,24 @@
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out       (assoc-ref outputs "out"))
                    (inetutils (assoc-ref inputs "inetutils")))
-               (substitute* "templates/cytoscape.html"
+               (substitute* '("templates/cytoscape.html"
+                              "templates/tableview.html"
+                              "templates/tableview0.html"
+                              "templates/userarchive.html")
                  (("script src=.*")
                   "script src=\"/static/cytoscape.min.js\"></script>\n"))
                (substitute* "templates/layout.html"
-                 (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
-                  "/static/bootstrap.min.css\">\n"))
+                 (("https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css.*")
+                  "/static/bootstrap.min.css\">\n")
+                 (("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
+                  "/static/bootstrap.min.js\"></script>\n")
+                 (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css")
+                  "/static/font-awesome.min.css")
+                 (("https://code.jquery.com/jquery-3.2.1.slim.min.js.*")
+                  "/static/jquery.slim.min.js\"></script>\n")
+                 ;(("https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js.*")
+                 ; "/static/popper.min.js\"></script>\n")
+                 )
                (substitute* "ratspub.py"
                  (("hostname") (string-append inetutils "/bin/hostname"))))
              #t))
@@ -51,34 +65,58 @@
          (add-after 'install 'install-javascript
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out       (assoc-ref outputs "out"))
+                   (awesome   (assoc-ref inputs "font-awesome"))
+                   (bootstrap (assoc-ref inputs "bootstrap"))
                    (cytoscape (assoc-ref inputs "cytoscape"))
-                   (bootstrap (assoc-ref inputs "bootstrap")))
+                   (jquery    (assoc-ref inputs "jquery"))
+                   ;(js-popper (assoc-ref inputs "js-popper"))
+                   )
+               (symlink (string-append awesome
+                                       "/share/web/font-awesomecss/font-awesome.min.css")
+                        (string-append out "/static/font-awesome.min.css"))
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/css/bootstrap.min.css")
+                        (string-append out "/static/bootstrap.min.css"))
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/js/bootstrap.min.js")
+                        (string-append out "/static/bootstrap.min.js"))
                (symlink (string-append cytoscape
                                        "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
                         (string-append out "/static/cytoscape.min.js"))
-               (symlink (string-append bootstrap
-                                       "/share/web/bootstrap/css/bootstrap.min.css")
-                        (string-append out "/static/bootstrap.min.css")))
+               (symlink (string-append jquery
+                                       "/share/web/jquery/jquery.slim.min.js")
+                        (string-append out "/static/jquery.slim.min.js"))
+               ;(symlink (string-append js-popper
+               ;                        "/share/web/popper/popper.min.js")
+               ;         (string-append out "/static/popper.min.js"))
+               )
              #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"))
+                `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
                                       ,(dirname (which "dirname"))
                                       ,(dirname (which "grep"))
                                       ,(dirname (which "sed"))))
-                 `("PYTHONPATH" ":" prefix (,path))))
+                `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
      `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
+       ("python-bcrypt" ,python-bcrypt)
        ("python-flask" ,python-flask)
-       ("python-nltk" ,python-nltk)))
+       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+       ("python-nltk" ,python-nltk)
+       ("python-pytz" ,python-pytz)))
     (native-inputs
-     `(("cytoscape" ,javascript-cytoscape)
-       ("bootstrap" ,web-bootstrap)))
+     `(("bootstrap" ,web-bootstrap)
+       ("cytoscape" ,javascript-cytoscape)
+       ("font-awesome" ,web-font-awesome)
+       ("jquery" ,web-jquery)
+       ;("js-popper" ,js-popper)
+       ))
     (home-page "http://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
     (description
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