A running genenetwork

4 files changed, 92 insertions, 24 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 214f040..36975bd 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -694,10 +694,9 @@ written in C")
          (base32
           "1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi"))))
       (build-system gnu-build-system)
-      (propagated-inputs
+      (native-inputs
        `(("ghostscript" ,ghostscript)
          ("graphviz" ,graphviz-2.26)
-         ("httpd" ,httpd22-mod-python-24)
          ("python24" ,python-2.4)
          ("python-piddle" ,python24-piddle)
          ("wget" ,wget)))
@@ -708,8 +707,9 @@ written in C")
            (delete 'configure)
            (delete 'build)
            (add-after 'patch-generated-file-shebangs 'patch-more-files
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((piddle (assoc-ref inputs "python-piddle")))
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((piddle (assoc-ref inputs "python-piddle"))
+                     (out    (assoc-ref outputs "out")))
                  (substitute* "web/webqtl/networkGraph/networkGraphUtils.py"
                    (("/usr/local/bin/neato") (which "neato"))
                    (("/usr/local/bin/circo") (which "circo"))
@@ -730,6 +730,7 @@ written in C")
                    (("/usr/bin/python") (which "python"))
                    (("/usr/bin/env python") (which "python")))
                  (substitute* "web/webqtl/base/webqtlConfigLocal.py"
+                   (("/gnshare/gn") out)
                    (("PythonPath.*")
                     (string-append "PythonPath = '" (which "python") "'\n"))
                    (("PIDDLE_FONT_PATH.*/lib")
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index bae5304..916c33c 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -3,10 +3,12 @@
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system python)
   #:use-module (gn packages python)
   #:use-module (past packages python)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages python-xyz)
   #:use-module (srfi srfi-1))
@@ -435,3 +437,60 @@ clusters (computers connected via network).")
     (synopsis "")
     (description "")
     (license license:bsd-3)))
+
+(define-public python24-mysqlclient
+  (package
+    (name "python24-mysqlclient")
+    (version "1.2.5")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/PyMySQL/mysqlclient-python")
+               (commit "MySQLdb-1.2.5")))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32
+          "193h09afkmz9nw2jlwfdikx1xj9sybswd2705k8jy48h1ks6fnbj"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2.4
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'dont-create-release-file
+           (lambda _
+             (substitute* "setup_common.py"
+               (("MySQLdb/release.py")
+                (string-append (getcwd) "/release.py")))
+             #t))
+         (add-before 'check 'pre-check
+           (lambda _
+             (call-with-output-file "/tmp/my.cnf"
+               (lambda (p)
+                 (format p
+                         "[mysqld]~@
+                         datadir=/tmp~@
+                         socket=/tmp/mysql.sock~%")))
+             (system* "mysqld" "--defaults-file=/tmp/my.cnf" "--bootstrap")
+             ;(invoke "mysql" "-S" "/tmp/mysql.sock"
+             ;        "-e" "'create database mysqldb_test charset utf8;'")
+             #t)))
+       #:tests? #f))    ; TODO: Run the test suite
+    (native-inputs
+     `(("mariadb" ,mariadb "dev")
+       ("mariadb:bin" ,mariadb)
+       ("python-nose" ,python24-nose)
+       ("python-setuptools" ,python24-setuptools)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "http://mysql-python.sourceforge.net/")
+    (synopsis "Python interface to MySQL")
+    (description "MySQLdb is an interface to the popular MySQL database server
+for Python.  The design goals are:
+@itemize
+@item with Python database API version 2.0
+@item Thread-safety
+@item Thread-friendliness (threads will not block each other)
+@item Compatibility with MySQL-3.23 and later
+@end itemize")
+    (license license:gpl2+)))
diff --git a/gn/packages/web.scm b/gn/packages/web.scm
index a6ce42f..a9ec973 100644
--- a/gn/packages/web.scm
+++ b/gn/packages/web.scm
@@ -370,10 +370,6 @@ connections and other data between hits and access to Apache internals.")
                 (lambda _
                   ;; Make sure we're in the correct folder
                   (chdir "../mod_python-3.3.1")
-                  ;; We can't import cPickle because we don't wrap with Python.
-                  (substitute* (find-files "." "\\.py$")
-                    (("import cPickle")
-                     "try:\n    import cPickle\nexcept:\n    import pickle as cPickle"))
                   #t))
               (add-after 'change-directory 'bootstrap-mod-python
                 (lambda* (#:key inputs #:allow-other-keys)
@@ -383,12 +379,15 @@ connections and other data between hits and access to Apache internals.")
                          (tcl-version ,(version-major+minor (package-version tcl))))
                     (substitute* "configure.in"
                       (("PY_LIBS=.*")
-                       (string-append "PY_LIBS=-L" python "/lib/python" py-version "\n"))
-                      (("PY_LDFLAGS=.*")
-                       (string-append "PY_LDFLAGS=\"-lpython" py-version
+                       (string-append "PY_LIBS=\"" python
+                                      "/lib/libpython" py-version ".so "
+                                      " -lpthread -ldl  -lutil -lm" ; LIB[SMC]
+                                      " -lpython" py-version
                                       " -lreadline -lssl -lcrypto"
                                       " -ltk" tcl-version " -ltcl" tcl-version
                                       " -lgdbm -ltirpc -lnsl -lz\"\n"))
+                      (("PY_LDFLAGS=.*")
+                       (string-append "PY_LDFLAGS=\"-Wl,-rpath=" python "/lib -Wl,-rpath=" python "/lib/python" py-version "/lib-dynload\"\n"))
                       (("PY_INCLUDES=.*")
                        (string-append "PY_INCLUDES=-I" python "/include/python" py-version "\n")))
                     (invoke "autoreconf" "-vfi"))))
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index bf09270..8f5bfc4 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -9,12 +9,6 @@
 (use-service-modules web)
 (use-package-modules python)
 
-(define %python-path
-  "/lib/python2.4/site-packages")
-
-(define %mod-python-path
-  (file-append httpd22-mod-python-24 %python-path))
-
 (define %default-httpd22-modules
   (map (match-lambda
          ((name file)
@@ -85,7 +79,10 @@
                    python24-qtlreaper
                    python24-htmlgen-GN1
                    python24-json-GN1
+                   python24-mysqlclient ; MySQLdb
+                   python24-numarray
                    python24-piddle
+                   python24-pp-GN1
                    python24-pyx-GN1
                    python24-pyxlwriter
                    python24-svg-GN1
@@ -97,13 +94,13 @@
                              (config
                                (httpd-config-file
                                  (server-name "www.genenetwork.org")
-                                 ;; Defaults to httpd, largely irrelevant.
+                                 ;; Defaults to httpd, should be same as 'package' above.
                                  (server-root httpd22-mod-python-24)
                                  (user "nobody")
                                  (group "root")
+                                 ;; Only while debugging
                                  (pid-file "/tmp/httpd-genenetwork1")
                                  (error-log "/tmp/httpd-genenetwork1-error-log")
-                                 (document-root (file-append genenetwork1 "/web"))
                                  (listen '("8042"))
                                  (modules (cons*
                                             (httpd-module
@@ -111,20 +108,32 @@
                                               (file "modules/mod_python.so"))
                                             %default-httpd22-modules))
                                  (extra-config (list "\
-TypesConfig etc/httpd/mime.types
+TypesConfig " httpd22-mod-python-24 "/etc/httpd/mime.types
 DefaultType application/octet-stream
-#DocumentRoot MUST NOT be in the PythonPath
-PythonPath \"['/run/current-system/profile/lib/python2.4', '" httpd22-mod-python-24 "/lib/python2.4/site-packages']\"
+# DocumentRoot MUST NOT be in the PythonPath. Because genenetwork1 must be in PythonPath we leave the document-root keyword above unset.
+PythonPath \"['/run/current-system/profile/lib/python2.4', '/run/current-system/profile/lib/python2.4/site-packages', '" httpd22-mod-python-24 "/lib/python2.4/site-packages', '" genenetwork1 "/web/webqtl']\"
+# same as 'listen' above
+NameVirtualHost *:8042
+<VirtualHost *:8042>
+  DocumentRoot "genenetwork1 "/web
+</VirtualHost>
 <Directory " genenetwork1 "/web/webqtl>
+  PythonOption session FileSession
+  #what is the difference between these two?
   #AddHandler mod_python .py
   SetHandler python-program
+  #publisher has more debug information
+  PythonHandler " genenetwork1 "/web/webqtl/main.py
   #PythonHandler mod_python.publisher
-  PythonHandler mod_python.cgihandler
-  #PythonAutoReload Off
+  #PythonHandler mod_python.cgihandler
   # only while debugging:
   PythonDebug On
 </Directory>
+# only while debugging:
 <Location /mpinfo>
   SetHandler python-program
   PythonHandler mod_python.testhandler
 </Location>")))))))))
+
+;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genenetwork.scm --network
+;; xdg-open http://localhost:8042