Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78d290c9fbf26adc0a4621174502e50047bbd843 https://github.com/galaxyproject/galaxy/commit/78d290c9fbf26adc0a4621174502e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh
Log Message: ----------- Do not install py2-ipaddress under Python 3
Commit: 662682c14818dfbc52579e96ff4aae4a8e047070 https://github.com/galaxyproject/galaxy/commit/662682c14818dfbc52579e96ff4aa... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths: M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py
Log Message: ----------- unicodify bytestrings from uwsgi.opt
Fix the 2 following tracebacks:
``` added lib/ to pythonpath. Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 180, in uwsgi_app return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy") File "lib/galaxy/web/framework/webapp.py", line 968, in build_native_uwsgi_app app_kwds = get_app_kwds(config_section) File "lib/galaxy/web/stack/__init__.py", line 434, in get_app_kwds return application_stack_class().get_app_kwds(config_section, app_name=app_name) File "lib/galaxy/web/stack/__init__.py", line 260, in get_app_kwds has_ini_config = has_ini_config or (config_file and has_ext(config_file, "ini", aliases=True, ignore="sample")) File "lib/galaxy/util/path/__init__.py", line 290, in has_ext root, _ext = __splitext_ignore(path, ignore=ignore) File "lib/galaxy/util/path/__init__.py", line 387, in __splitext_ignore root, ext = __splitext_no_sep(path) File "lib/galaxy/util/path/__init__.py", line 381, in __splitext_no_sep return (path.rsplit(extsep, 1) + [''])[0:2] TypeError: a bytes-like object is required, not 'str' unable to load app 0 (mountpoint='') (callable not found or import error) ```
``` galaxy.queue_worker INFO 2018-06-03 02:12:51,186 [p:2150,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1 Traceback (most recent call last): File "lib/galaxy/web/stack/__init__.py", line 456, in _do_uwsgi_postfork f(*args, **kwargs) File "lib/galaxy/webapps/galaxy/buildapp.py", line 190, in postfork_setup app.application_stack.log_startup() File "lib/galaxy/web/stack/__init__.py", line 351, in log_startup for s in UWSGIApplicationStack._serving_on(): File "lib/galaxy/web/stack/__init__.py", line 237, in _serving_on yield UWSGIApplicationStack._socket_opt_to_str(opt, val) File "lib/galaxy/web/stack/__init__.py", line 208, in _socket_opt_to_str if val.startswith('='): TypeError: startswith first arg must be bytes or a tuple of bytes, not str ```
Commit: e81931cd753e4c85e624d80e3901c97d6064f9e1 https://github.com/galaxyproject/galaxy/commit/e81931cd753e4c85e624d80e3901c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Fix loading of tools under Python 3
Tools containing a text parameter fail with a traceback like: ``` [pid: 2433|app: 0|req: 15/28] 127.0.0.1 () {42 vars in 905 bytes} [Sun Jun 3 02:24:59 2018] GET /api/tools/addValue/build?version=1.0.0&__identifer=nv6x1qdhzxo&tool_version=1.0.0 => generated 71 bytes in 58 msecs (HTTP/1.1 500) 3 headers in 143 bytes (1 switches on core 1) galaxy.web.framework.decorators ERROR 2018-06-03 02:25:01,999 [p:2433,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 281, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 113, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 1913, in to_json 'state_inputs' : params_to_strings(self.inputs, state_inputs, self.app), File "lib/galaxy/tools/parameters/__init__.py", line 207, in params_to_strings rval[key] = value if nested else str(dumps(value)) File "/usr/lib/python3.5/json/__init__.py", line 230, in dumps return _default_encoder.encode(obj) File "/usr/lib/python3.5/json/encoder.py", line 198, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python3.5/json/encoder.py", line 256, in iterencode return _iterencode(o, 0) File "/usr/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError: b'c1,c2' is not JSON serializable ```
Commit: b08455ecab5fa068b7f8b93fe08c9c552c8c25a0 https://github.com/galaxyproject/galaxy/commit/b08455ecab5fa068b7f8b93fe08c9... Author: John Chilton jmchilton@gmail.com Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Merge pull request #6265 from nsoranzo/python3
Python3 fixes
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