1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9cad38925c8d/
Changeset: 9cad38925c8d
User: jmchilton
Date: 2014-10-07 01:25:30+00:00
Summary: Update master API key handling in tests for d7dd1f9.
Now aware of anyone actually overriding this with GALAXY_TEST_MASTER_API_KEY so not maintaining backward compatibility with respect to that environment variable.
Affected #: 1 file
diff -r d7dd1f92d5b8e35ed9530fc5f0494e160ff8c4da -r 9cad38925c8da6221a1ce9817d382421c6627ecd test/base/api_util.py
--- a/test/base/api_util.py
+++ b/test/base/api_util.py
@@ -9,7 +9,11 @@
configured as a master API key and should be able to create additional
users and keys.
"""
- return os.environ.get( "GALAXY_TEST_MASTER_API_KEY", DEFAULT_GALAXY_MASTER_API_KEY )
+ for key in ["GALAXY_CONFIG_MASTER_API_KEY", "GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY"]:
+ value = os.environ.get(key, None)
+ if value:
+ return value
+ return DEFAULT_GALAXY_MASTER_API_KEY
def get_user_api_key():
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f92d5b8/
Changeset: d7dd1f92d5b8
User: jmchilton
Date: 2014-10-07 00:56:58+00:00
Summary: Make functional tests to respect GALAXY_CONFIG_ environment variables.
Functional tests don't work without the tweak to imports in cloudlaunch - not sure if that has always been a problem and I am just running the tests in a different Galaxy instance or if the earlier import of util caused the problem.
Regardless I guess we shoud update to a version of bioblend that doesn't require simplejson.
Affected #: 2 files
diff -r 594b48fe90b7b17ed22f5c597837022d8204db47 -r d7dd1f92d5b8e35ed9530fc5f0494e160ff8c4da lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -17,6 +17,7 @@
eggs.require('PyYAML')
eggs.require('boto')
+eggs.require('simplejson')
eggs.require('bioblend')
from boto.exception import EC2ResponseError
diff -r 594b48fe90b7b17ed22f5c597837022d8204db47 -r d7dd1f92d5b8e35ed9530fc5f0494e160ff8c4da scripts/functional_tests.py
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -16,6 +16,7 @@
from base.tool_shed_util import parse_tool_panel_config
from galaxy import eggs
+from galaxy.util.properties import load_app_properties
eggs.require( "nose" )
eggs.require( "NoseHTML" )
@@ -401,6 +402,9 @@
kwargs[ 'global_conf' ] = get_webapp_global_conf()
kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file
kwargs[ 'config_file' ] = galaxy_config_file
+ kwargs = load_app_properties(
+ kwds=kwargs
+ )
# Build the Universe Application
app = UniverseApplication( **kwargs )
database_contexts.galaxy_context = app.model.context
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e98b33105381/
Changeset: e98b33105381
Branch: stable
User: natefoo
Date: 2014-10-06 19:31:09+00:00
Summary: Added tag latest_2014.10.06 for changeset 2092948937ac
Affected #: 1 file
diff -r 3b3cd242b4b7cd20b9c868c393c455524b31b87c -r e98b33105381ac94f590edee1859ab550d328833 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,3 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
+2092948937ac30ef82f71463a235c66d34987088 latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8f372abd1912/
Changeset: 8f372abd1912
Branch: next-stable
User: dan
Date: 2014-10-06 15:49:09+00:00
Summary: Remove deprecation warnings from util.json methods.
Affected #: 1 file
diff -r 054d8af08f098c76b9b64eb5d60835956abc8ae1 -r 8f372abd19124a95fa79f0eeb7da497dc88682f5 lib/galaxy/util/json.py
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -17,12 +17,10 @@
def to_json_string(*args, **kwargs):
- log.warning("Using deprecated function to_json_string.")
return json.dumps(*args, **kwargs)
def from_json_string(*args, **kwargs):
- log.warning("Using deprecated function from_json_string.")
return json.loads(*args, **kwargs)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/594b48fe90b7/
Changeset: 594b48fe90b7
User: dan
Date: 2014-10-06 15:49:09+00:00
Summary: Remove deprecation warnings from util.json methods.
Affected #: 1 file
diff -r ae1a6cb7f4aae2ee7746fdee01d83d96cff5a0a2 -r 594b48fe90b7b17ed22f5c597837022d8204db47 lib/galaxy/util/json.py
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -17,12 +17,10 @@
def to_json_string(*args, **kwargs):
- log.warning("Using deprecated function to_json_string.")
return json.dumps(*args, **kwargs)
def from_json_string(*args, **kwargs):
- log.warning("Using deprecated function from_json_string.")
return json.loads(*args, **kwargs)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ae1a6cb7f4aa/
Changeset: ae1a6cb7f4aa
User: jmchilton
Date: 2014-10-06 13:24:53+00:00
Summary: Eliminate Galaxy dependencies from lib/galaxy/tools/loader.py.
Should allow for reuse in command-line tools that operate on Galaxy tools. Updates for targetting Python 2.6+.
Affected #: 1 file
diff -r 8f746975db66785dcec2ef16f943052d767b01d4 -r ae1a6cb7f4aae2ee7746fdee01d83d96cff5a0a2 lib/galaxy/tools/loader.py
--- a/lib/galaxy/tools/loader.py
+++ b/lib/galaxy/tools/loader.py
@@ -1,10 +1,8 @@
-from __future__ import with_statement
+from xml.etree import ElementTree, ElementInclude
from copy import deepcopy
import os
-from galaxy.util import parse_xml
-
def load_tool(path):
"""
@@ -16,7 +14,7 @@
_import_macros(root, path)
# Expand xml macros
- macro_dict = _macros_of_type(root, 'xml', lambda el: list(el.getchildren()))
+ macro_dict = _macros_of_type(root, 'xml', lambda el: list(el))
_expand_macros([root], macro_dict)
# Expand tokens
@@ -42,7 +40,7 @@
""" Load raw (no macro expansion) tree representation of tool represented
at the specified path.
"""
- tree = parse_xml(path)
+ tree = _parse_xml(path)
return tree
@@ -54,7 +52,7 @@
def _import_macros(root, path):
tool_dir = os.path.dirname(path)
macros_el = _macros_el(root)
- if macros_el:
+ if macros_el is not None:
macro_els = _load_macros(macros_el, tool_dir)
_xml_set_children(macros_el, macro_els)
@@ -66,7 +64,7 @@
def _macros_of_type(root, type, el_func):
macros_el = root.find('macros')
macro_dict = {}
- if macros_el:
+ if macros_el is not None:
macro_els = macros_el.findall('macro')
macro_dict = dict([(macro_el.get("name"), el_func(macro_el)) \
for macro_el in macro_els \
@@ -88,7 +86,7 @@
new_value = _expand_tokens_str(value, tokens)
if not (new_value is value):
element.attrib[key] = new_value
- _expand_tokens(list(element.getchildren()), tokens)
+ _expand_tokens(list(element), tokens)
def _expand_tokens_str(str, tokens):
@@ -129,7 +127,7 @@
def _expand_yield_statements(macro_def, expand_el):
yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
- expand_el_children = expand_el.getchildren()
+ expand_el_children = list(expand_el)
macro_def_parent_map = \
dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p)
@@ -151,7 +149,7 @@
macro_els = []
# attribute typed macro
- if macros_el:
+ if macros_el is not None:
macro_els = macros_el.findall("macro")
for macro in macro_els:
if 'type' not in macro.attrib:
@@ -163,7 +161,7 @@
typed_tag = ['template', 'xml', 'token']
for tag in typed_tag:
macro_els = []
- if macros_el:
+ if macros_el is not None:
macro_els = macros_el.findall(tag)
for macro_el in macro_els:
macro_el.attrib['type'] = tag
@@ -188,7 +186,7 @@
def _imported_macro_paths_from_el(macros_el):
imported_macro_paths = []
macro_import_els = []
- if macros_el:
+ if macros_el is not None:
macro_import_els = macros_el.findall("import")
for macro_import_el in macro_import_els:
raw_import_path = macro_import_el.text
@@ -199,13 +197,13 @@
def _load_macro_file(path, tool_dir):
- tree = parse_xml(path)
+ tree = _parse_xml(path)
root = tree.getroot()
return _load_macros(root, tool_dir)
def _xml_set_children(element, new_children):
- for old_child in element.getchildren():
+ for old_child in element:
element.remove(old_child)
for i, new_child in enumerate(new_children):
element.insert(i, new_child)
@@ -216,7 +214,7 @@
parent_el = parent_map[query]
matching_index = -1
#for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation
- for index, el in enumerate(parent_el.getchildren()):
+ for index, el in enumerate(list(parent_el)):
if el == query:
matching_index = index
break
@@ -226,3 +224,10 @@
current_index += 1
parent_el.insert(current_index, deepcopy(target))
parent_el.remove(query)
+
+
+def _parse_xml(fname):
+ tree = ElementTree.parse(fname)
+ root = tree.getroot()
+ ElementInclude.include(root)
+ return tree
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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