Branch: refs/heads/master
Home: https://github.com/galaxyproject/ansible-galaxy
Commit: 7ed9bbfd1b3351f1f300843183898db54f07038c
https://github.com/galaxyproject/ansible-galaxy/commit/7ed9bbfd1b3351f1f300…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-01-29 (Thu, 29 Jan 2015)
Changed paths:
M defaults/main.yml
M tasks/clone.yml
A tasks/download.yml
M tasks/main.yml
A tasks/virtualenv.yml
Log Message:
-----------
Implement option to download Galaxy (instead of cloning it).
Until we have debs this is... a... way to get Galaxy without the whole history for throw away machines like Docker - where keeping the size of the image small is more important than being able to update the Galaxy found inside.
Commit: 47c4fd6714f70a69a4cd04acec45569c0613f512
https://github.com/galaxyproject/ansible-galaxy/commit/47c4fd6714f70a69a4cd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-02-03 (Tue, 03 Feb 2015)
Changed paths:
M defaults/main.yml
M tasks/clone.yml
A tasks/download.yml
M tasks/main.yml
A tasks/virtualenv.yml
Log Message:
-----------
Merge pull request #3 from jmchilton/download_option
Implement option to download Galaxy (instead of cloning it).
Compare: https://github.com/galaxyproject/ansible-galaxy/compare/c9559f7d9c4c...47c4…
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/944074958b72/
Changeset: 944074958b72
User: jmchilton
Date: 2015-02-03 17:22:57+00:00
Summary: Small cleanup to lib/galaxy/tools/evaluation.py.
Eliminate the absolute path call outside the compute_environment - since we wouldn't want to take the absolute path on a *nix box for a Windows path and because it is already being absolute-itized inside of the the ComputeEnviornment abstraction.
Eliminate TODO comment that has already been TODONE.
Affected #: 1 file
diff -r 99a7a07c6ffba2948b2e1197a3a33554f60126ba -r 944074958b72d49757455a07a503024e631d15a6 lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -353,8 +353,7 @@
# More convienent access to app.config.new_file_path; we don't need to
# wrap a string, but this method of generating additional datasets
# should be considered DEPRECATED
- # TODO: path munging for cluster/dataset server relocatability
- param_dict['__new_file_path__'] = os.path.abspath(self.compute_environment.new_file_path())
+ param_dict['__new_file_path__'] = self.compute_environment.new_file_path()
# The following points to location (xxx.loc) files which are pointers
# to locally cached data
param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
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/99a7a07c6ffb/
Changeset: 99a7a07c6ffb
User: jmchilton
Date: 2015-02-03 17:20:41+00:00
Summary: Drop test that is failing due to improved HDA accessibility consistency.
Affected #: 1 file
diff -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 -r 99a7a07c6ffba2948b2e1197a3a33554f60126ba test/api/test_dataset_collections.py
--- a/test/api/test_dataset_collections.py
+++ b/test/api/test_dataset_collections.py
@@ -105,7 +105,9 @@
)
create_response = self._post( "dataset_collections", payload )
- self._assert_status_code_is( create_response, 403 )
+ # TODO: re-enable once there is a way to restrict access
+ # to this dataset via the API.
+ #self._assert_status_code_is( create_response, 403 )
def test_enforces_unique_names( self ):
element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id )
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/ddbe0d12bc86/
Changeset: ddbe0d12bc86
User: jmchilton
Date: 2015-02-03 15:29:34+00:00
Summary: Expose $__tool_directory__ to tools.
Repeatedly one wants to do things like create symbolic links and then call a helper script - the 'interpreter' tag doesn't allow shell commands before calling a helper script so they could not be used in this fashion. The previous pattern for doing this was then to use the ToolShed only 'set_environment' requirement tag. These were onerous to setup and the resulting tools were no longer portable to non-ToolShed installed contexts - I believe this variant is more robust and elegant.
More information https://trello.com/c/0pgF5PBQ and here https://trello.com/c/XK5SqE1i.
Affected #: 5 files
diff -r eb26a96483238cd353c3fc1bdce9699382dfadb6 -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1783,7 +1783,11 @@
@abstractmethod
def new_file_path( self ):
- """ Location to dump new files for this job on remote server. """
+ """ Absolute path to dump new files for this job on compute server. """
+
+ @abstractmethod
+ def tool_directory( self ):
+ """ Absolute path to tool files for this job on compute server. """
@abstractmethod
def version_path( self ):
@@ -1836,6 +1840,9 @@
def version_path( self ):
return self.job_wrapper.get_version_string_path()
+ def tool_directory( self ):
+ return os.path.abspath(self.job_wrapper.tool.tool_dir)
+
class NoopQueue( object ):
"""
diff -r eb26a96483238cd353c3fc1bdce9699382dfadb6 -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 lib/galaxy/jobs/runners/pulsar.py
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -708,3 +708,6 @@
def unstructured_path_rewriter( self ):
return self.rewriter
+
+ def tool_directory( self ):
+ return self._tool_dir
diff -r eb26a96483238cd353c3fc1bdce9699382dfadb6 -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -345,6 +345,7 @@
if table_name in self.app.tool_data_tables:
return self.app.tool_data_tables[ table_name ].get_entry( query_attr, query_val, return_attr )
+ param_dict['__tool_directory__'] = self.compute_environment.tool_directory()
param_dict['__get_data_table_entry__'] = get_data_table_entry
# We add access to app here, this allows access to app.config, etc
diff -r eb26a96483238cd353c3fc1bdce9699382dfadb6 -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 test/functional/tools/samples_tool_conf.xml
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -32,6 +32,7 @@
<tool file="validation_repeat.xml" /><tool file="identifier_single.xml" /><tool file="identifier_multiple.xml" />
+ <tool file="tool_directory.xml" /><tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" />
diff -r eb26a96483238cd353c3fc1bdce9699382dfadb6 -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 test/functional/tools/tool_directory.xml
--- /dev/null
+++ b/test/functional/tools/tool_directory.xml
@@ -0,0 +1,20 @@
+<tool id="tool_directory" name="tool_directory">
+ <command>
+ cp $__tool_directory__/tool_directory.xml output1
+ </command>
+ <inputs>
+ <param type="integer" name="ignored" label="Ignored" value="0" />
+ </inputs>
+ <outputs>
+ <data name="output1" type="xml" from_work_dir="output1" />
+ </outputs>
+ <tests>
+ <test>
+ <output name="output1">
+ <assert_contents>
+ <has_text text="QUINE" />
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+</tool>
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/097bbb3b7d32/
Changeset: 097bbb3b7d32
Branch: stable
User: natefoo
Date: 2015-02-03 14:00:27+00:00
Summary: Update tag latest_2015.01.13 for changeset 5e4060f5ac7a
Affected #: 1 file
diff -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -22,4 +22,4 @@
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06
2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
-fd75aaee91cf3e8a0916689dfea72e0c752c447c latest_2015.01.13
+5e4060f5ac7a3c11d4681bc80f94c620df9d0479 latest_2015.01.13
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/adcb595753b0/
Changeset: adcb595753b0
User: carlfeberhard
Date: 2015-02-02 23:57:54+00:00
Summary: Fix to 8e5b9ca: implement _future_expose_api_anonymous_and_sessionless to allow endpoints to be access without user or session (fixes access to api/authenticate)
Affected #: 3 files
diff -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e -r adcb595753b02cc9757a8f36a34898d4ea2233e7 lib/galaxy/web/__init__.py
--- a/lib/galaxy/web/__init__.py
+++ b/lib/galaxy/web/__init__.py
@@ -18,6 +18,7 @@
from framework.decorators import _future_expose_api_anonymous
from framework.decorators import _future_expose_api_raw
from framework.decorators import _future_expose_api_raw_anonymous
+from framework.decorators import _future_expose_api_anonymous_and_sessionless
from framework.formbuilder import form
from framework.formbuilder import FormBuilder
diff -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e -r adcb595753b02cc9757a8f36a34898d4ea2233e7 lib/galaxy/web/framework/decorators.py
--- a/lib/galaxy/web/framework/decorators.py
+++ b/lib/galaxy/web/framework/decorators.py
@@ -196,7 +196,7 @@
# ----------------------------------------------------------------------------- (new) api decorators
# TODO: rename as expose_api and make default.
-def _future_expose_api( func, to_json=True, user_required=True ):
+def _future_expose_api( func, to_json=True, user_required=True, user_or_session_required=True ):
"""
Expose this function via the API.
"""
@@ -206,10 +206,11 @@
# TODO: Document this branch, when can this happen,
# I don't understand it.
return __api_error_response( trans, err_msg=trans.error_message )
+
# error if user required and anon
# error if anon and no session
if ( ( trans.anonymous and user_required )
- or ( trans.anonymous and not trans.galaxy_session ) ):
+ or ( trans.anonymous and user_or_session_required and not trans.galaxy_session ) ):
error_code = error_codes.USER_NO_API_KEY
# Use error codes default error message.
err_msg = "API authentication required for this request"
@@ -325,17 +326,20 @@
return dumps( error_dict )
-# TODO: rename as expose_api and make default.
def _future_expose_api_anonymous( func, to_json=True ):
"""
Expose this function via the API but don't require a set user.
"""
return _future_expose_api( func, to_json=to_json, user_required=False )
+def _future_expose_api_anonymous_and_sessionless( func, to_json=True ):
+ """
+ Expose this function via the API but don't require a user or a galaxy_session.
+ """
+ return _future_expose_api( func, to_json=to_json, user_required=False, user_or_session_required=False )
def _future_expose_api_raw( func ):
return _future_expose_api( func, to_json=False, user_required=True )
-
def _future_expose_api_raw_anonymous( func ):
return _future_expose_api( func, to_json=False, user_required=False )
diff -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e -r adcb595753b02cc9757a8f36a34898d4ea2233e7 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -14,7 +14,7 @@
from base64 import b64decode
from urllib import unquote
-from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
from galaxy.managers import api_keys
from galaxy import exceptions
from galaxy.web.base.controller import BaseAPIController
@@ -29,7 +29,7 @@
super( AuthenticationController, self ).__init__( app )
self.api_keys_manager = api_keys.ApiKeyManager( app )
- @expose_api_anonymous
+ @expose_api_anonymous_and_sessionless
def get_api_key( self, trans, **kwd ):
"""
def get_api_key( self, trans, **kwd )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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