diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 2 | ||||
| -rw-r--r-- | gn/packages/python24.scm | 94 |
2 files changed, 32 insertions, 64 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 09e683f..3507064 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -774,7 +774,7 @@ written in C") ;; Where GN1 is located: (("/gnshare/gn") out) ;; Where the database is located: - (("tux01.uthsc.edu") "localhost")) + (("tux01") "localhost")) ;(("tux01.uthsc.edu") "lily.uthsc.edu")) ;; This directory is expected to be writable (symlink "/tmp" "web/tmp") diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index 51f4fe9..8edb1be 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -393,85 +393,53 @@ clusters (computers connected via network).") (description "") (license license:bsd-3))) +;; 1.2.3 exactly. There was an API change between 1.2.3 and 1.2.5. +;; https://stackoverflow.com/questions/21740359/python-mysqldb-typeerror-not-all-arguments-converted-during-string-formatting/53563287#53563287 (define-public python24-mysqlclient (package (name "python24-mysqlclient") - (version "1.2.5") + (version "1.2.3") (source (origin (method url-fetch) - (uri (pypi-uri "MySQL-python" version ".zip")) + (uri (pypi-uri "MySQL-python" version)) (sha256 (base32 - "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"))) - ; )) - )) + "0vkyg9dmj29hzk7fy77f42p7bfj28skyzsjsjry4wqr3z6xnzrkx")))) (build-system python-build-system) (arguments `(#:python ,python-2.4 #:phases (modify-phases %standard-phases - ;(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/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? #t)) ; TODO: Run the test suite + (lambda* (#:key inputs tests? #:allow-other-keys) + (if tests? + (begin + (mkdir-p "/tmp/mysqld") + (call-with-output-file "/tmp/my.cnf" + (lambda (p) + (format p + "[mysqld]~@ + datadir = /tmp/mysqld~@ + port = 3306~@ + user = nixbld~@ + #character-set-server = utf8mb4~@ + socket = /tmp/mysqld/mysql.sock~%"))) + (setenv "TESTDB" "/tmp/my.cnf") + ;; mysql-5.0 puts mysqld in libexec + (setenv "PATH" (string-append (getenv "PATH") ":" + (assoc-ref inputs "mysql") "/libexec")) + (system "mysqld --defaults-file=/tmp/my.cnf &") + (sleep 5) + (invoke "mysqladmin" "-S" "/tmp/mysqld/mysql.sock" "variables") + (invoke "mysql" "-S" "/tmp/mysqld/mysql.sock" + "-e" "'create database mysqldb_test charset utf8;'")) + #t)))) + #:tests? #f)) ; TODO: Run the test suite (native-inputs - `(("mysql" ,mysql-5.5) + `(("mysql" ,mysql-5.0) ; Best supported version according to the README. ("python-nose" ,python24-nose) - ("python-setuptools" ,python24-setuptools) - ("unzip" ,unzip))) + ("python-setuptools" ,python24-setuptools))) (inputs `(("openssl" ,openssl-1.0) ("zlib" ,zlib))) |