commit/galaxy-central: jmchilton: API endpoint for reloading tool data tables (from Bjoern).
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/bcaffc4a0a61/
Changeset: bcaffc4a0a61
User: jmchilton
Date: 2015-02-03 17:44:39+00:00
Summary: API endpoint for reloading tool data tables (from Bjoern).
The endpoint isn't "RESTful" IMO - but it does match what we are doing for tools - so it is consistent which is more important.
Affected #: 2 files
diff -r 944074958b72d49757455a07a503024e631d15a6 -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 lib/galaxy/webapps/galaxy/api/tool_data.py
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -28,6 +28,19 @@
@web.require_admin
@expose_api
+ def reload( self, trans, id, **kwd ):
+ """
+ GET /api/tool_data/{id}/reload
+
+ Reloads a tool_data table.
+ """
+ decoded_tool_data_id = id
+ data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
+ return data_table.reload_from_files()
+
+
+ @web.require_admin
+ @expose_api
def delete( self, trans, id, **kwd ):
"""
DELETE /api/tool_data/{id}
diff -r 944074958b72d49757455a07a503024e631d15a6 -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -174,6 +174,7 @@
webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' )
webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" )
webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" )
+ webapp.mapper.connect( '/api/tool_data/{id:.+?}/reload', action='reload', controller="tool_data" )
webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/')
webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' )
webapp.mapper.resource( 'request', 'requests', path_prefix='/api' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Small cleanup to lib/galaxy/tools/evaluation.py.
by commits-noreply＠bitbucket.org
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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commit/galaxy-central: jmchilton: Drop test that is failing due to improved HDA accessibility consistency.
by commits-noreply＠bitbucket.org
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 )
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commit/galaxy-central: jmchilton: Expose $__tool_directory__ to tools.
by commits-noreply＠bitbucket.org
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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commit/galaxy-central: carlfeberhard: Browser tests: remove starting slash from workflow return url comparisons
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/eb26a9648323/
Changeset: eb26a9648323
User: carlfeberhard
Date: 2015-02-03 14:00:51+00:00
Summary: Browser tests: remove starting slash from workflow return url comparisons
Affected #: 1 file
diff -r adcb595753b02cc9757a8f36a34898d4ea2233e7 -r eb26a96483238cd353c3fc1bdce9699382dfadb6 test/casperjs/api-workflow-tests.js
--- a/test/casperjs/api-workflow-tests.js
+++ b/test/casperjs/api-workflow-tests.js
@@ -55,7 +55,7 @@
"uploaded workflow defaults to un-published: " + returned.published );
this.test.assert( utils.isArray( returned.tags ) && returned.tags.length === 0,
"upload returned an empty tag array: " + this.jsonStr( returned.tags ) );
- this.test.assert( returned.url === '/' + utils.format( this.api.workflows.urlTpls.show, returned.id ),
+ this.test.assert( returned.url === utils.format( this.api.workflows.urlTpls.show, returned.id ),
"url matches the show url: " + returned.url );
@@ -79,7 +79,7 @@
"workflow is un-published: " + firstWorkflow.published );
this.test.assert( utils.isArray( firstWorkflow.tags ) && firstWorkflow.tags.length === 0,
"tag array is empty: " + this.jsonStr( firstWorkflow.tags ) );
- this.test.assert( firstWorkflow.url === '/' + utils.format( this.api.workflows.urlTpls.show, firstWorkflow.id ),
+ this.test.assert( firstWorkflow.url === utils.format( this.api.workflows.urlTpls.show, firstWorkflow.id ),
"url matches the show url: " + firstWorkflow.url );
@@ -99,7 +99,7 @@
"workflow is un-published: " + workflowShow.published );
this.test.assert( utils.isArray( workflowShow.tags ) && workflowShow.tags.length === 0,
"tag array is empty: " + this.jsonStr( workflowShow.tags ) );
- this.test.assert( workflowShow.url === '/' + utils.format( this.api.workflows.urlTpls.show, workflowShow.id ),
+ this.test.assert( workflowShow.url === utils.format( this.api.workflows.urlTpls.show, workflowShow.id ),
"url matches the show url: " + workflowShow.url );
this.test.comment( 'inputs from show should be an object (and, in this case, empty)' );
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Update tag latest_2015.01.13 for changeset 5e4060f5ac7a
by commits-noreply＠bitbucket.org
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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commit/galaxy-central: carlfeberhard: 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)
by commits-noreply＠bitbucket.org
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 )
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commit/galaxy-central: carlfeberhard: API, folders & folder_contents: use _future_expose_api on NotImplemented routes
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/147c8b343d4a/
Changeset: 147c8b343d4a
User: carlfeberhard
Date: 2015-02-02 23:01:44+00:00
Summary: API, folders & folder_contents: use _future_expose_api on NotImplemented routes
Affected #: 3 files
diff -r 1d57664c6d9c4875e5c818220fa8199cf3967de0 -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e lib/galaxy/webapps/galaxy/api/folder_contents.py
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -315,14 +315,14 @@
else:
raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) )
- @web.expose_api
+ @expose_api
def show( self, trans, id, library_id, **kwd ):
"""
GET /api/folders/{encoded_folder_id}/
"""
raise exceptions.NotImplemented( 'Showing the library folder content is not implemented here.' )
- @web.expose_api
+ @expose_api
def update( self, trans, id, library_id, payload, **kwd ):
"""
PUT /api/folders/{encoded_folder_id}/contents
diff -r 1d57664c6d9c4875e5c818220fa8199cf3967de0 -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -20,7 +20,7 @@
super( FoldersController, self ).__init__( app )
self.folder_manager = folders.FolderManager()
- @web.expose_api
+ @expose_api
def index( self, trans, **kwd ):
"""
*GET /api/folders/
@@ -29,7 +29,7 @@
"""
raise exceptions.NotImplemented( 'Listing all accessible library folders is not implemented.' )
- @web.expose_api
+ @expose_api
def show( self, trans, id, **kwd ):
"""
show( self, trans, id, **kwd )
@@ -255,7 +255,7 @@
folder_dict = self.folder_manager.get_folder_dict( trans, folder )
return folder_dict
- @web.expose_api
+ @expose_api
def update( self, trans, id, library_id, payload, **kwd ):
"""
PUT /api/folders/{encoded_folder_id}
diff -r 1d57664c6d9c4875e5c818220fa8199cf3967de0 -r 147c8b343d4ae09d4ae71d424037e45f06bd8e9e lib/galaxy/webapps/galaxy/api/library_contents.py
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -436,7 +436,7 @@
except exceptions.httpexceptions.HTTPException:
raise
except Exception, exc:
- log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s',
+ log.exception( 'library_contents API, delete: uncaught exception: %s, %s\n%s',
id, str( kwd ), str( exc ) )
trans.response.status = 500
rval.update({ 'error': str( exc ) })
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