updates

3 files changed, 69 insertions, 24 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 7b1650a..98be132 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -849,7 +849,8 @@ written in C")
                    ;; Where GN1 is located:
                    (("/gnshare/gn") out)
                    ;; Where the database is located:
-                   (("tux01") "localhost"))
+                   (("tux01.uthsc.edu") "localhost"))
+                   ;(("tux01.uthsc.edu") "lily.uthsc.edu"))
                  ;; This directory is expected to be writable
                  (symlink "/tmp" "web/tmp")
                  #t)))
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index 6f27e22..51f4fe9 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -5,6 +5,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system python)
+  #:use-module (gn packages databases)
   #:use-module (gn packages python)
   #:use-module (gn packages statistics)
   #:use-module (past packages python)
@@ -13,6 +14,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tls)
   #:use-module (srfi srfi-1))
 
 (define (default-python2.4)
@@ -397,45 +399,82 @@ clusters (computers connected via network).")
     (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))
+        (method url-fetch)
+        (uri (pypi-uri "MySQL-python" version ".zip"))
         (sha256
          (base32
-          "193h09afkmz9nw2jlwfdikx1xj9sybswd2705k8jy48h1ks6fnbj"))))
+          "0x0c2jg0bb3pp84njaqiic050qkyd7ymwhfvhipnimg58yv40441"))
+        ;(patches
+        ;  (list
+        ;    (origin
+        ;      (method url-fetch)
+        ;      (uri "https://sources.debian.org/data/main/p/python-mysqldb/1.2.3-2.1/debian/patches/03_converters_set2str.patch")
+        ;      (file-name "mysqlclient-converters_set2str.patch")
+        ;      (sha256
+        ;       (base32
+        ;        "0xkbfscy6kqc84lij1ml7d8vxf5xqi99vx5ha75cg8yyx6cvv34i")))
+        ;    (origin
+        ;      (method url-fetch)
+        ;      (uri "https://github.com/PyMySQL/mysqlclient-python/commit/d663649f851794dffa84010db6290e693d4baab8.patch")
+        ;      (file-name "mysqlclient-mariadb-10.2-compat.patch")
+        ;      (sha256
+        ;       (base32
+        ;        "0pz2r8l7299yhl58w0zp0kplg1h9zi3qv9ynpcidxm8mf8884284")))
+        ;    ))
+        ))
     (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-after 'unpack 'work-with-newer-mysql
+         ;  (lambda _
+         ;    (substitute* '("_mysql.c"
+         ;                   "MySQLdb/connections.py")
+         ;      (("unix_socket") "socket"))
+             ;; ProgrammingError: (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near '%s' at line 1")
+             ;(substitute* "MySQLdb/cursors.py"
+             ;  (("query % tuple.*")
+             ;   "query = query.encode(db.unicode_literal.charset)\n"))
+         ;    #t))
          (add-before 'check 'pre-check
            (lambda _
+             ;; All of these tests require a running mysql server.
+             ;; When they are all deleted there are no tests.
+             (delete-file "tests/test_MySQLdb_dbapi20.py") ; 35 tests, 54 errors
+             (delete-file "tests/test_MySQLdb_capabilities.py") ; 20 tests, 20 errors
+             (delete-file "tests/test_MySQLdb_nonstandard.py") ; 14 tests, 6 errors
+             (mkdir-p "/tmp/mysqld")
              (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"
+                         datadir = /tmp/mysqld~@
+                         port = 3306~@
+                         user = nixbld~@
+                         #character-set-server = utf8mb4~@
+                         socket = /tmp/mysqld/mysql.sock~%")))
+             (setenv "TESTDB" "/tmp/my.cnf")
+             ;(system "mysqld --defaults-file=/tmp/my.cnf --initialize &") ; mariadb
+             ;(system (string-append (assoc-ref %build-inputs "mysql") "/libexec/mysqld --defaults-file=/tmp/my.cnf &")) ; mysql-5.0
+             (system "mysqld --defaults-file=/tmp/my.cnf &") ; mysql-5.5
+             (sleep 5)
+             (system "mysqladmin -S /tmp/mysqld/mysql.sock variables")
+             ;(invoke "mysqladmin" "-S" "/tmp/mysqld/mysql.sock" "variables")
+             (system "mysql -S /tmp/mysqld/mysql.sock -e 'create database mysqldb_test charset utf8;'")
+             ;(invoke "mysql" "-S" "/tmp/mysqld/mysql.sock"
              ;        "-e" "'create database mysqldb_test charset utf8;'")
-             #t)))
-       #:tests? #f))    ; TODO: Run the test suite
+             #t))
+         )
+       #:tests? #t))    ; TODO: Run the test suite
     (native-inputs
-     `(("mariadb" ,mariadb "dev")
-       ("mariadb:bin" ,mariadb)
+     `(("mysql" ,mysql-5.5)
        ("python-nose" ,python24-nose)
-       ("python-setuptools" ,python24-setuptools)))
+       ("python-setuptools" ,python24-setuptools)
+       ("unzip" ,unzip)))
     (inputs
-     `(("zlib" ,zlib)))
+     `(("openssl" ,openssl-1.0)
+       ("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
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 73194fb..0926921 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -165,7 +165,12 @@ interaction networks.")
                             "/R-" version ".tar.gz"))
         (sha256
          (base32
-          "1mjmq95s5nrwppbzic6lzanjq65j3sxg85l1q09c0fxdin7s70y5"))))
+          "1mjmq95s5nrwppbzic6lzanjq65j3sxg85l1q09c0fxdin7s70y5"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin
+            (delete-file "NEWS.pdf")
+            #t))))
     (arguments
      (substitute-keyword-arguments (package-arguments r-minimal)
        ((#:tests? _ #t) #t)