gn: python3-genenetwork2: Inherit from genenetwork2

* gn/packages/genenetwork.scm (python3-genenetwork2): Rewrite package
definiton to inherit from genenetwork2 package.

1 files changed, 75 insertions, 116 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 8a76327..30f941b 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -43,7 +43,8 @@
   #:use-module (gn packages python)
   #:use-module (gn packages python24)
   #:use-module (gn packages statistics)
-  #:use-module (gn packages web))
+  #:use-module (gn packages web)
+  #:use-module (srfi srfi-1))
 
 
 
@@ -446,120 +447,79 @@ implemented, light on server resource usage, and fairly speedy.")
     (license license:agpl3+))))
 
 (define-public python3-genenetwork2
-  (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")
-        (S specification->package))
-  (package
-    (name "python3-genenetwork2")
-    (version (string-append "2.11-guix-" (string-take commit 7) ))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
-                   ;; (url "https://github.com/genenetwork/genenetwork2_diet.git")
-                   (commit commit)))
-             (file-name (string-append name "-" version))
-             (sha256
-              (base32
-               "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
-    (propagated-inputs
-     `(;; propagated for development purposes
-       ("python" ,python) ;; probably superfluous
-       ("coreutils" ,coreutils)
-       ("git" ,git)
-       ("vim" ,vim)
-       ("which" ,which)
-       ("grep" ,grep)
-       ("r" ,r)
-       ("r-ctl" ,r-ctl)
-       ; ("r-phewas" ,r-phewas)
-       ("r-qtl" ,r-qtl)
-       ("r-wgcna" ,r-wgcna)
-       ("redis" ,redis)
-       ("mariadb" ,mariadb)
-       ("gemma" ,gemma-gn2)
-       ("gemma-wrapper" ,gemma-wrapper)
-       ("plink-ng-gn" ,plink-ng-gn)
-       ("rust-qtlreaper" ,rust-qtlreaper)
-       ("nginx" ,nginx)
-       ("python-twint" ,python-twint)
-       ("python-flask" ,python-flask)
-       ("gunicorn" ,gunicorn)
-       ("python-pillow" ,python-pillow)
-       ;; ("python2-pil1" ,python2-pil1-gn)
-       ("python2-piddle-gn" ,python2-piddle-gn) ; DEPRECATED
-       ("python-cssselect" ,python-cssselect)
-       ("python-elasticsearch" ,python-elasticsearch)
-       ("python-htmlgen" ,python-htmlgen)
-       ("python-jinja2" ,python-jinja2)
-       ("python-sqlalchemy" ,python-sqlalchemy)
-       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
-       ("python-setuptools" ,python-setuptools)
-       ("python-scipy" ,python-scipy)
-       ("python-lxml" ,python-lxml)
-       ("python-mechanize" ,python-mechanize)
-       ("python-mysqlclient" ,python-mysqlclient)
-       ("python2-numarray" ,python2-numarray) ; DEPRECATED
-       ("python-numpy" ,python-numpy)
-       ("python-pandas" ,python-pandas)
-       ("python-parameterized" ,python-parameterized)
-       ("python-passlib" ,python-passlib)
-       ("python-redis" ,python-redis)
-       ("python-requests" ,python-requests)
-       ("python2-rpy2" ,python2-rpy2) ; TODO
-       ("python-simplejson" ,python-simplejson)
-       ("python-pyyaml" ,python-pyyaml)
-       ("python-unittest2" ,python-unittest2)
-       ("python-xlsxwriter" ,python-xlsxwriter)
-       ;; All the external js dependencies
-       ("javascript-cytoscape" ,javascript-cytoscape)
-       ("javascript-panzoom" ,javascript-cytoscape-panzoom)
-       ("javascript-qtip" ,javascript-cytoscape-qtip)
-       ("javascript-chroma" ,javascript-chroma)
-       ("javascript-d3-tip" ,javascript-d3-tip)
-       ("javascript-jscolor" ,javascript-jscolor)
-       ("javascript-colorbox" ,javascript-colorbox)
-       ("javascript-jszip" ,javascript-jszip)
-       ("js-jstat" ,js-jstat)
-       ("js-md5" ,js-md5)
-       ("js-parsley" ,js-parsley)
-       ("javascript-plotly" ,javascript-plotly)
-       ("javascript-typeahead" ,javascript-typeahead)
-       ("js-underscore" ,js-underscore)
-       ("js-smart-time-ago" ,js-smart-time-ago)
-       ("javascript-nouislider" ,javascript-nouislider)
-       ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser)
-       ("javascript-datatables" ,javascript-datatables)
-       ("javascript-datatables-scroller" ,javascript-datatables-scroller)
-       ("javascript-datatables-buttons" ,javascript-datatables-buttons)
-       ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap)
-       ("javascript-datatables-plugins" ,javascript-datatables-plugins)
-       ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder)
-       ("javascript-datatables-col-resize" ,javascript-datatables-col-resize)
-       ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles)
-       ("javascript-shapiro-wilk" ,javascript-shapiro-wilk)
-       ("javascript-underscore-string" ,javascript-underscore-string)
-       ("javascript-qtip2" ,javascript-qtip2)
-       ("javascript-d3js" ,javascript-d3js)
-       ("javascript-nvd3" ,javascript-nvd3)
-       ("javascript-bootstrap" ,javascript-bootstrap)
-       ("javascript-jquery" ,javascript-jquery)
-       ("javascript-zxcvbn-async" ,javascript-zxcvbn-async)
-       ("javascript-jquery-ui" ,javascript-jquery-ui)
-       ("javascript-jquery-cookie" ,javascript-jquery-cookie)
-       ))
-    (inputs
-     `(("javascript-colorbox" ,(package-source javascript-colorbox))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
+  (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
+    (package
+      (inherit genenetwork2)
+      (name "python3-genenetwork2")
+      (version (string-append "3.11-guix-" (string-take commit 7) ))
+      (propagated-inputs
+       `(,@(fold alist-delete (package-propagated-inputs genenetwork2)
+                 '("python-2"
+                   "python2-coverage"
+                   "python2-flask"
+                   "python2-gunicorn-gn"
+                   "python2-cssselect"
+                   "python2-elasticsearch"
+                   "python2-htmlgen-gn"
+                   "python2-jinja2"
+                   "python2-sqlalchemy"
+                   "python2-flask-sqlalchemy"
+                   "python2-setuptools"
+                   "python2-scipy"
+                   "python2-lxml"
+                   "python2-mechanize"
+                   "python2-mock"
+                   "python2-mysqlclient"
+                   "python2-nose"
+                   "python2-numarray"
+                   "python2-numpy"
+                   "python2-pandas"
+                   "python2-parallel"
+                   "python2-parameterized"
+                   "python2-passlib"
+                   "python2-redis"
+                   "python2-requests"
+                   "python2-simplejson"
+                   "python2-pyyaml"
+                   "python-unittest2"
+                   "python2-xlsxwriter"
+                   "python2-qtlreaper"))
+         ("python-pillow" ,python-pillow)
+         ("python-coverage" ,python-coverage)
+         ("python-flask" ,python-flask)
+         ("gunicorn" ,gunicorn)
+         ("python-cssselect" ,python-cssselect)
+         ("python-elasticsearch" ,python-elasticsearch)
+         ("python-htmlgen" ,python-htmlgen)
+         ("python-jinja2" ,python-jinja2)
+         ("python-sqlalchemy" ,python-sqlalchemy)
+         ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+         ("python-setuptools" ,python-setuptools)
+         ("python-scipy" ,python-scipy)
+         ("python-lxml" ,python-lxml)
+         ("python-mechanize" ,python-mechanize)
+         ("python-mysqlclient" ,python-mysqlclient)
+         ("python-numpy" ,python-numpy)
+         ("python-pandas" ,python-pandas)
+         ("python-mock" ,python-mock)
+         ("python-parameterized" ,python-parameterized)
+         ("python-passlib" ,python-passlib)
+         ("python-redis" ,python-redis)
+         ("python-requests" ,python-requests)
+         ("python-simplejson" ,python-simplejson)
+         ("python-pyyaml" ,python-pyyaml)
+         ("python-unittest2" ,python-unittest2)
+         ("python-xlsxwriter" ,python-xlsxwriter)))
+      (arguments
+       `(#:python ,python-3
+         #:phases
          (modify-phases %standard-phases
            (delete 'reset-gzip-timestamps)
            (add-after 'unpack 'fix-paths-scripts
              (lambda _
                (substitute* "bin/genenetwork2"
                  (("/usr/bin/env") (which "env"))
-                 (("python ") (string-append (which "python2") " "))
+                 (("python ") (string-append (which "python") " "))
                  (("readlink") (which "readlink"))
                  (("dirname") (which "dirname"))
                  (("basename") (which "basename"))
@@ -581,18 +541,17 @@ implemented, light on server resource usage, and fairly speedy.")
                  #t)))
            (add-before 'install 'fix-paths
              (lambda* (#:key inputs #:allow-other-keys)
-               (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
-                      (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")))
+               (let* (
+                      (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
+                      (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+                      )
                  (substitute* '("etc/default_settings.py")
                    (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
                    (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
                    )
                  ))))
-       #:tests? #f))   ; no 'setup.py test'
-    (home-page "http://genenetwork.org/")
-    (synopsis "Full genenetwork services")
-    (description "Genenetwork installation sumo.")
-    (license license:agpl3+))))
+         #:tests? #f)) ; no 'setup.py test'
+      )))
 
 ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
 ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x