Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

1 files changed, 187 insertions, 26 deletions

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 29e1313..b664799 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -1,11 +1,16 @@
 (define-module (gn packages ratspub)
   #:use-module ((guix licenses) #:prefix license:)
+  #: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 (gn packages bioinformatics)
+  #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
+  #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gn packages web))
@@ -13,19 +18,27 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.1")
+    (version "0.3.1")
     (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"))))
+              (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
+                "1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin (substitute* "server.py"
+                         ;; Keep the service running on port 4200
+                         (("4201") "4200")
+                         ;; Backport to python-keras-2.2.4
+                         (("learning_rate") "lr") )
+                       #t))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f ; no test suite
+     `(#:tests? #f  ; no test suite
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -34,12 +47,24 @@
            (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))
@@ -51,31 +76,58 @@
          (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"))))
-                 `("PYTHONPATH" ":" prefix (,path))))
+                `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+                                      ,(dirname (which "dirname"))
+                                      ,(dirname (which "grep"))
+                                      ,(dirname (which "sed"))))
+                `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
-     `(("edirect" ,edirect-gn)
+     `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
-       ("python-flask" ,python-flask)
-       ("python-nltk" ,python-nltk)))
+       ("python-bcrypt" ,python-bcrypt)
+       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+       ("python-keras" ,python-keras-for-ratspub)
+       ("python-nltk" ,python-nltk)
+       ("tensorflow" ,tensorflow)))
     (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)    ; empty output
+       ))
     (home-page "http://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
     (description
@@ -86,4 +138,113 @@ 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 license:expat)))
+
+;; 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 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")
+               )
+             #t))
+         (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))
+             #t))
+         (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"))
+               )
+             #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 "/main.py")
+                `("PYTHONPATH" ":" prefix (,path))))
+             #t)))))
+    (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)))