ratspub: remove definitions as they are replaced by genecup

1 files changed, 0 insertions, 152 deletions

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index d797e8a..c530979 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -20,135 +20,6 @@
   #:use-module (gn packages python)
   #:use-module (gn packages web))
 
-(define-public ratspub
-  (package
-    (name "ratspub")
-    (version "0.4.5")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/chen42/ratspub")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              ;; Keep the service running on port 4200.
-              (modules '((guix build utils)))
-              (snippet
-               '(begin (substitute* "server.py"
-                         (("4201") "4200"))))
-              (sha256
-               (base32
-                "1y89rkqdxcnl2jjsy1wfp9p8qkgh6nzqs1r37wyhc8y7r3dva7kf"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f  ; no test suite
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (delete 'build)
-         (add-after 'unpack 'make-files-writable
-           (lambda _
-             (for-each make-file-writable (find-files "."))))
-         (add-after 'unpack 'patch-datadir
-           (lambda _
-             (substitute* "server.py"
-               (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))))
-         (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")
-                 (("https.*FileSaver.js.*\\\">") "/static/FileSaver.js\">")
-                 (("https.*cytoscape-svg.js.*\\\">") "/static/cytoscape-svg.js\">")
-                 (("https.*cytoscape.min.js.*\\\">") "/static/cytoscape.min.js\">"))
-               (substitute* "templates/layout.html"
-                 (("https.*bootstrap.min.css.*\\\">") "/static/bootstrap.min.css\">")
-                 (("https.*4.*bootstrap.min.js.*\\\">") "/static/bootstrap.min.js\">")
-                 (("https.*4.7.0/css/font-awesome.min.css") "/static/font-awesome.min.css")
-                 (("https.*jquery-3.2.1.slim.min.js.*\\\">") "/static/jquery.slim.min.js\">")
-                 (("https.*1.12.9/umd/popper.min.js.*\\\">") "/static/popper.min.js\">"))
-               (substitute* "ratspub.py"
-                 (("hostname") (string-append inetutils "/bin/hostname"))))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (copy-recursively "." out))))
-         (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"))
-                   (cytoscape-svg (assoc-ref inputs "cytoscape-svg"))
-                   (jquery    (assoc-ref inputs "jquery"))
-                   (js-filesaver (assoc-ref inputs "js-filesaver"))
-                   (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 cytoscape-svg
-                                       "/share/javascript/cytoscape-svg.js")
-                        (string-append out "/static/cytoscape-svg.js"))
-               (symlink (string-append jquery
-                                       "/share/web/jquery/jquery.slim.min.js")
-                        (string-append out "/static/jquery.slim.min.js"))
-               (symlink (string-append js-filesaver
-                                       "/share/javascript/FileSaver.js")
-                        (string-append out "/static/FileSaver.js"))
-               (symlink (string-append js-popper
-                                       "/share/javascript/popper.min.js")
-                        (string-append out "/static/popper.min.js")))))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out  (assoc-ref outputs "out"))
-                   (path (getenv "GUIX_PYTHONPATH")))
-               (wrap-program (string-append out "/server.py")
-                `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
-                                      ,(dirname (which "dirname"))
-                                      ,(dirname (which "grep"))
-                                      ,(dirname (which "sed"))))
-                `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
-    (inputs
-     `(("edirect" ,edirect)
-       ("inetutils" ,inetutils)
-       ("python-bcrypt" ,python-bcrypt)
-       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
-       ("python-keras" ,python-keras-for-ratspub)
-       ("python-nltk" ,python-nltk)
-       ("tensorflow" ,tensorflow)))
-    (native-inputs
-     `(("bootstrap" ,web-bootstrap)
-       ("cytoscape" ,javascript-cytoscape-3.17)
-       ;("cytoscape-svg" ,js-cytoscape-svg-0.3.1)   ; TODO
-       ("cytoscape-svg" ,js-cytoscape-svg-vendor-0.3.1)
-       ("font-awesome" ,web-font-awesome)
-       ("jquery" ,web-jquery)
-       ("js-filesaver" ,js-filesaver-1.3.2)
-       ("js-popper" ,js-popper-1.12.9)))
-    (home-page "https://rats.pub/")
-    (synopsis "Relationship with Addiction Through Searches of PubMed")
-    (description
-     "RatsPub is a tool to efficiently and comprehensively answer the question
-\"What do we know about these genes and addiction?\".  RatsPub answers this
-question by searching PubMed to find sentences containing the query terms (i.e.,
-gene symbols) and over 300 drug addiction-related keywords that are organized
-into six categories.  Data from @url{https://www.ebi.ac.uk/gwas/,
-@acronym{NHGRI-EBI GWAS, European Bioinformatics Institute Genome-Wide
-Association Studies}} catalog are also included in the search.  These
-gene-keyword relationships are presented as an interactive graph and a table.")
-    (license license:expat)))
-
 (define use-corrected-inputs
   (package-input-rewriting/spec
     ;; Tensorflow-native provides much improved speeds. python-h5py@2 provides
@@ -156,29 +27,6 @@ gene-keyword relationships are presented as an interactive graph and a table.")
     `(("tensorflow" . ,(const tensorflow-native))
       ("python-h5py" . ,(const python-h5py-2)))))
 
-(define-public ratspub-with-tensorflow-native
-  (package
-    (inherit
-      (tensowflow-native-instead-of-tensorflow ratspub))
-    (name "ratspub-with-tensorflow-native")))
-
-;; We want a copy of python-keras with the AUC optimizer backported.
-;; We skip the tests because we "test in production".
-;; That's a lie. The test suite just takes a long time to run.
-(define-public python-keras-for-ratspub
-  (hidden-package
-    (package
-      (inherit python-keras)
-      (source
-        (origin
-          (inherit (package-source python-keras))
-          (patches (search-patches "keras-auc-optimizer.patch"))))
-      (arguments
-       (substitute-keyword-arguments (package-arguments python-keras)
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (delete 'check))))))))
-
 (define-public python-keras-no-tests
   (hidden-package
     (package