WIP: update ratspub to 0.2-1.1b516eewip-ratspub

As a package it is ready, but it tries to write to files in it's
directory, which is in the store, meaning the service will need to be
rewritten.

1 files changed, 109 insertions, 73 deletions

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 290b9e2..3394592 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -6,87 +6,123 @@
   #:use-module (gnu packages admin)
   #:use-module (gn 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))
 
 (define-public ratspub
-  (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"))
-                   (inetutils (assoc-ref inputs "inetutils")))
-               (substitute* "templates/cytoscape.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"))
-               (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 'install-javascript
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out       (assoc-ref outputs "out"))
-                   (cytoscape (assoc-ref inputs "cytoscape"))
-                   (bootstrap (assoc-ref inputs "bootstrap")))
-               (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")))
-             #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"))
-                                      ,(dirname (which "dirname"))
-                                      ,(dirname (which "grep"))
-                                      ,(dirname (which "sed"))))
-                 `("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
+  (let ((commit "1b516ee692248f4cd75570d9750b14f78554b41f")
+        (revision "1"))
+    (package
+      (name "ratspub")
+      (version (git-version "0.2" revision commit))
+      (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
+                  "16zr89993h1idkazradivm9yjgl695wdr34d2qbwj4nmaxfrg8dy"))))
+      (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"))
+                     (inetutils (assoc-ref inputs "inetutils")))
+                 (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/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/poppler.js\"></script>\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 '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"))
+                     (jquery    (assoc-ref inputs "jquery"))
+                     (js-poppler (assoc-ref inputs "js-poppler")))
+                 (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 jquery
+                                         "/share/web/jquery/jquery.slim.min.js")
+                          (string-append out "/static/jquery.slim.min.js"))
+                 (symlink (string-append js-poppler
+                                         "/share/web/poppler/poppler.min.js")
+                          (string-append out "/static/poppler.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"))
+                                                     ,(dirname (which "dirname"))
+                                                     ,(dirname (which "grep"))
+                                                     ,(dirname (which "sed"))))
+                               `("PYTHONPATH" ":" prefix (,path))))
+               #t)))))
+      (inputs
+       `(("edirect" ,edirect-gn)
+         ("inetutils" ,inetutils)
+         ("python-bcrypt" ,python-bcrypt)
+         ("python-flask" ,python-flask)
+         ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+         ("python-nltk" ,python-nltk)
+         ("python-pytz" ,python-pytz)))
+      (native-inputs
+       `(("bootstrap" ,web-bootstrap)
+         ("cytoscape" ,javascript-cytoscape)
+         ("font-awesome" ,web-font-awesome)
+         ("jquery" ,web-jquery)
+         ("js-poppler" ,js-poppler)))
+      (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))))