(define-module (gn packages genecup)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix git)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (guix packages)
  #:use-module (guix git-download)
  #:use-module (guix build-system python)
  #:use-module (gnu packages admin)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages javascript)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gn packages javascript)
  #:use-module (gn packages machine-learning)
  #:use-module (gn packages python)
  #:use-module (gn packages web))

(define use-corrected-inputs
  (package-input-rewriting/spec
    ;; Tensorflow-native provides much improved speeds. python-h5py@2 provides
    ;; compatibility with our version of tensorflow.
    `(("tensorflow" . ,(const tensorflow-native))
      ("python-h5py" . ,(const python-h5py-2)))))

(define-public python-keras-no-tests
  (hidden-package
    (package
      (inherit python-keras)
      (source
        (origin
          (inherit (package-source python-keras))))
      (arguments
       (substitute-keyword-arguments (package-arguments python-keras)
         ((#:phases phases)
          `(modify-phases ,phases
             (delete 'check))))))))


(define-public hrdp-project
  (package
    (name "hrdp-project")
    (version "0.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                     (url "https://github.com/noderboarder/hrdp-project")
                     (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1ag7jm43p35yh0cqcn53wg4iw7sgfypw10mxq5klxvhgj3r6cf7i"))))
    (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 _
             (substitute* "./app/templates/layout.html"
               (("https://.*.bootstrapcdn.com/bootstrap/4.*/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://code.jquery.com/jquery-3.*.slim.min.js.*")
                "/static/jquery.slim.min.js\"></script>\n")
               ;(("https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js.*")
               ; "/static/popper.min.js\"></script>\n")
               )))
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (python (assoc-ref inputs "python")))
               (delete-file "main.py")
               (with-output-to-file "main.py"
                 (lambda ()
                   (format #t "#!~a/bin/python
from app import create_app

app = create_app()

if __name__ == '__main__':
    app.run(debug=True, port=4222)~%"
                   python)))
               (chmod "main.py" #o555)
               (copy-recursively "." out))))
         (add-after 'install 'install-javascript
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out       (assoc-ref outputs "out"))
                   (bootstrap (assoc-ref inputs "bootstrap"))
                   (jquery    (assoc-ref inputs "jquery"))
                   ;(js-popper (assoc-ref inputs "js-popper"))
                   )
               (symlink (string-append bootstrap
                                       "/share/web/bootstrap/css/bootstrap.min.css")
                        (string-append out "/app/static/bootstrap.min.css"))
               (symlink (string-append bootstrap
                                       "/share/web/bootstrap/js/bootstrap.min.js")
                        (string-append out "/app/static/bootstrap.min.js"))
               (symlink (string-append jquery
                                       "/share/web/jquery/jquery.slim.min.js")
                        (string-append out "/app/static/jquery.slim.min.js"))
               ;(symlink (string-append js-popper
               ;                        "/share/web/popper/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 "/main.py")
                `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
    (inputs
     `(("python" ,python)
       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)))
    (native-inputs
     `(("bootstrap" ,web-bootstrap)
       ("jquery" ,web-jquery)
       ;("js-popper" ,js-popper)    ; empty output
       ))
    (home-page "https://github.com/noderboarder/hrdp-project")
    (synopsis "")
    (description "")
    (license license:expat)))

(define-public genecup
  (package
    (name "genecup")
    (version "1.8")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                     (url "https://github.com/hakangunturkun/GeneCup")
                     (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32 "0clnlnj6cl816yj3nalh1h6hsvnh3sjq2g84x1kmj1zkqkw184ri"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #f  ; no test suite
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         ;; Change the port for running the service.
         (add-after 'unpack 'use-different-port
           (lambda _
             (substitute* "server.py"
               (("4200") "4204"))))
         (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"))))))
         (add-after 'unpack 'extract-pubmed-archive
           (lambda _
             (invoke "gzip" "-d" "minipubmed.tgz")
             (invoke "tar" "xvf" "minipubmed.tar")))
         (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)
       ("gzip" ,gzip)
       ("tar" ,tar)
       ("python-bcrypt" ,python-bcrypt)
       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
       ("python-keras" ,python-keras-no-tests)
       ("python-nltk" ,python-nltk)
       ("python-pandas" ,python-pandas)
       ("python-regex" ,python-regex)
       ("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 "http://genecup.org")
    (synopsis "Using PubMed to find out how a gene contributes to addiction")
    (description "GeneCup automatically extracts information from PubMed and
@url{https://www.ebi.ac.uk/gwas/, @acronym{NHGRI-EBI GWAS, European
Bioinformatics Institute Genome-Wide Association Studies}} catalog on the
relationship of any gene with a custom list of keywords hierarchically organized
into an ontology.  The users create an ontology by identifying categories of
concepts and a list of keywords for each concept.")
    (license license:expat)))

(define genecup-master
  (package
    (inherit genecup)
    (name "genecup-master")
    (version "HEAD-of-master-branch")
    (source
      (git-checkout
        (url "https://git.genenetwork.org/genecup")
        (branch "master")))))

(define-public genecup-with-tensorflow-native
  (package
    (inherit
      (use-corrected-inputs genecup))
    (name "genecup-with-tensorflow-native")))

(define-public genecup-latest-with-tensorflow-native
  (package
    (inherit
      (use-corrected-inputs genecup-master))
    (name "genecup-latest-with-tensorflow-native")))