Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

1 files changed, 163 insertions, 88 deletions

diff --git a/gn/packages/web.scm b/gn/packages/web.scm
index 6c426e1..8b041b4 100644
--- a/gn/packages/web.scm
+++ b/gn/packages/web.scm
@@ -2,6 +2,8 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages web)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -14,115 +16,188 @@
 
 (define-public web-jquery
   (package
-   (name "web-jquery")
-   (version "3.2.1")
-   (source
-    (origin
-     (method url-fetch)
-     (uri (string-append "https://github.com/jquery/jquery/archive/" version ".zip"))
-     (file-name (string-append name "-" version))
-     (sha256
-      (base32 "0a8sq7a52bh3a4slf03yfclwsv4iadlzmha4v6kqfby5sd66si18"))))
-   (build-system trivial-build-system)
-   (native-inputs `(("source" ,source)
-                    ("unzip" ,unzip)))
-   (arguments
-    `(#:modules ((guix build utils))
-      #:builder
-      (let* ((out (assoc-ref %outputs "out"))
-             (name "jquery")
-             (targetdir (string-append out "/share/web/" name))
-             )
-        (begin
-          (use-modules (guix build utils))
-          (let ((source (assoc-ref %build-inputs "source"))
-                   (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))
-                )
-            (and
-             (mkdir-p "source")
-             (chdir "source")
-             (zero? (system* unzip source))
-             (mkdir-p targetdir)
-             (copy-recursively "jquery-3.2.1/dist" targetdir)
-
-             ; (copy-recursively source targetdir)
-             ; (file-copy (string-append out "/dist/jquery.slim.min.j") source)
-             ))))))
-   (home-page "http://jquery.com/")
-   (synopsis "JQuery web framework")
-   (description "jQuery.")
-   (license license:expat)))
+    (name "web-jquery")
+    (version "3.4.1") ; May 1, 2019
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/jquery/jquery.git")
+               (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "03pasw49xshwvcaa0iailv43jlyhkwhf19fnwmwlhyn4701kpx1d"))))
+    (build-system trivial-build-system)
+    (arguments
+      `(#:modules ((guix build utils))
+        #:builder
+        (let* ((out (assoc-ref %outputs "out"))
+               (targetdir (string-append out "/share/web/jquery"))
+               (source (assoc-ref %build-inputs "source"))
+               (dist (string-append source "/dist")))
+          (begin
+            (use-modules (guix build utils))
+            (copy-recursively dist targetdir)))))
+    (native-inputs `(("source" ,source)))
+    (home-page "https://jquery.com/")
+    (synopsis "JQuery web framework")
+    (description "jQuery is a fast, small, and feature-rich JavaScript library.
+It makes things like HTML document traversal and manipulation, event handling,
+animation, and Ajax much simpler with an easy-to-use API that works across a
+multitude of browsers.  With a combination of versatility and extensibility,
+jQuery has changed the way that millions of people write JavaScript.")
+    (license license:expat)))
 
 (define-public web-bootstrap
-  (let ((commit "betabeta"))
   (package
     (name "web-bootstrap")
-    (version (string-append "4.0.0" "-" (string-take commit 7)))
+    (version "4.3.1") ; Feb. 13, 2019
     (source
-     (origin
-       (method url-fetch)
-       (uri "https://github.com/twbs/bootstrap/releases/download/v4.0.0-beta/bootstrap-4.0.0-beta-dist.zip")
-       (file-name (string-append name "-" version))
-       (sha256
-        (base32 "0jzi76gm3vyxld5lz1723al8a8skcn9r1ch51sdgzxx32f273bc9"))))
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/twbs/bootstrap.git")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "18g76r53sa2ahcriy7jk5wvxd3s8qc4as87xwqvfkxibdn5ifrxs"))))
     (build-system trivial-build-system)
-    (native-inputs `(("unzip" ,unzip)
-                     ("source" ,source)))
     (arguments
      `(#:modules ((guix build utils))
        #:builder
          (let* ((out (assoc-ref %outputs "out"))
                 (name "bootstrap")
                 (targetdir (string-append out "/share/web/" name))
-                )
+                (source (assoc-ref %build-inputs "source"))
+                (dist (string-append source "/dist")))
            (begin
              (use-modules (guix build utils))
-             (let ((source (assoc-ref %build-inputs "source"))
-                   (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))
-                   )
-               (and
-                (mkdir-p targetdir)
-                (zero? (system* unzip source "-d" targetdir))
-                ))))))
-    (home-page "http://getbootstrap.com/")
+             (copy-recursively dist targetdir)))))
+    (native-inputs `(("source" ,source)))
+    (home-page "https://getbootstrap.com/")
     (synopsis "Bootstrap web framework")
     (description "Bootstrap is an open source toolkit for developing
-with HTML, CSS, and JS. Quickly prototype your ideas or build your
+with HTML, CSS, and JS.  Quickly prototype your ideas or build your
 entire app with our Sass variables and mixins, responsive grid system,
 extensive prebuilt components, and powerful plugins built on jQuery.")
-    (license license:expat))))
+    (license license:expat)))
 
 (define-public web-bootstrap-native
   (let ((commit "2e48d7ee29d4063e3bd2024ff83ddc50a550c4dd"))
+    (package
+      (name "web-bootstrap-native")
+      (version (string-append "4.0.0" "-beta-" (string-take commit 7))) ; Sept, 8, 2017
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/thednp/bootstrap.native.git")
+                       (commit commit)))
+                (file-name (string-append name "-" commit))
+                (sha256
+                 (base32
+                  "1hkyibyfby0mnkavr3xbmr20kb88wy6jw28b206pd236xnp2qkx0"))))
+      (build-system trivial-build-system)
+      (arguments
+       `(#:modules ((guix build utils))
+         #:builder
+         (let* ((out (assoc-ref %outputs "out"))
+                (name "bootstrap-native")
+                (targetdir (string-append out "/share/web/" name))
+                (source (assoc-ref %build-inputs "source")))
+           (begin
+             (use-modules (guix build utils))
+             (copy-recursively source targetdir)))))
+      (native-inputs `(("source" ,source)))
+      (home-page "https://github.com/thednp/bootstrap.native")
+      (synopsis "Bootstrap minimal")
+      (description "Bootstrap native does not use jquery.")
+      (license license:expat))))
+
+(define-public mod-python
+  (let ((commit "902bb8700e2c45ffd96b78e2f1146a3c101be7f5")
+        (revision "1"))
+    (package
+      (name "mod-python")
+      (version (git-version "3.5.0" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/grisha/mod_python.git")
+                 (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+           (base32
+            "0lqlpldw11dml24n05305xzpbjlkay497djjczvgsj5v8djkxcq0"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:tests? #f ; tests require a running apache server
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-source
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out    (assoc-ref outputs "out")))
+                 (substitute* "Makefile.in"
+                   ;; Don't use httpd's prefix
+                   (("LIBEXECDIR=.*") (string-append "LIBEXECDIR=" out "/modules\n")))
+                 (substitute* "scripts/Makefile.in"
+                   (("BINDIR=.*") (string-append "BINDIR=" out "/bin")))
+                 (substitute* "dist/setup.py.in"
+                   ;; we want out modules dir, not httpd's
+                   ;; If we want SYSCONFDIR to be the same as httpd's :
+                   ;; (("@SYSCONFDIR@") (string-append (assoc-ref %build-inputs "httpd") "/etc/httpd"))
+                   (("@LIBEXECDIR@") (string-append out "/modules")))
+                 (substitute* "dist/Makefile.in"
+                   (("\\$\\(DESTDIR\\)") "/")
+                   (("--root") (string-append "--prefix=" out " --root"))))
+               #t)))))
+      (inputs
+       `(("httpd" ,httpd)
+         ("python" ,python-2))) ; does not seem to build with python3.7+
+      (native-inputs `(("flex" ,(@ (gnu packages flex) flex))))
+      (home-page "http://modpython.org/")
+      (synopsis "Apache/Python Integration")
+      (description "Mod_python is an Apache module that embeds the Python
+interpreter within the server.  With mod_python you can write web-based
+applications in Python that will run many times faster than traditional CGI and
+will have access to advanced features such as ability to retain database
+connections and other data between hits and access to Apache internals.")
+      (license license:asl2.0))))
+
+(define-public web-font-awesome
   (package
-    (name "web-bootstrap-native")
-    (version (string-append "4.0.0" "-beta-" (string-take commit 7)))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/thednp/bootstrap.native.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit))
-             (sha256
-              (base32
-               "1hkyibyfby0mnkavr3xbmr20kb88wy6jw28b206pd236xnp2qkx0"))))
+    (name "web-font-awesome")
+    (version "4.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://fontawesome.com/v" version
+                            "/assets/font-awesome-" version ".zip"))
+        (sha256
+         (base32 "0jgn26cr5xhqyxfwqmki0564cid4i4l38cwsddcslr3qkzpmhx2j"))))
     (build-system trivial-build-system)
-    (native-inputs `(("source" ,source)))
     (arguments
-     `(#:modules ((guix build utils))
-       #:builder
-       (let* ((out (assoc-ref %outputs "out"))
-              (name "bootstrap-native")
-              (targetdir (string-append out "/share/web/" name))
-              )
-           (begin
-             (use-modules (guix build utils))
-             (let ((source (assoc-ref %build-inputs "source")))
-               (and
-                    ; (mkdir-p targetdir)
-                    (copy-recursively source targetdir)
-                    ))))))
-    (home-page "https://github.com/thednp/bootstrap.native")
-    (synopsis "Bootstrap minimal")
-    (description "Bootstrap native does not use jquery.")
-    (license license:expat))))
+       `(#:modules ((guix build utils))
+         #:builder
+         (begin
+           (use-modules (guix build utils))
+           (let* ((out (assoc-ref %outputs "out"))
+                  (name "font-awesome")
+                  (unzip (string-append (assoc-ref %build-inputs "unzip")
+                                        "/bin/unzip"))
+                  (targetdir (string-append out "/share/web/" name))
+                  (source (assoc-ref %build-inputs "source")))
+             (invoke unzip source)
+             (copy-recursively (string-append "font-awesome-" ,version)
+                               targetdir)))))
+    (native-inputs
+     `(("source" ,source)
+       ("unzip" ,unzip)))
+    (home-page "https://fontawesome.com/")
+    (synopsis "iconic font designed for use with Twitter Bootstrap")
+    (description "This font contains about 249 various icon glyphs.  Glyphs are
+designed as scalable vector graphics hence display very well at any screen size.
+This font was basically designed to be used with the Twitter bootstrap library
+but can be used in other places also.")
+    (license (list license:cc-by4.0
+                   license:silofl1.1))))