June 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a1755cd7fa0/ Changeset: 6a1755cd7fa0 User: jmchilton Date: 2014-06-11 22:16:05 Summary: Introduce unit(-ish) tests for routes. Allows testing both how URLs are going to map to controllers and actions as well as testing what paths will be produced by url_for. Requires some refactoring of Galaxy framework classes and buildapp to allow stubbing out actual instantiation of controllers, etc.... Affected #: 3 files diff -r f07db0284a42d88a1c88f280c9c22757a671deec -r 6a1755cd7fa0115142e1c277db4129e6e2add217 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -454,7 +454,8 @@ for key in dir( module ): T = getattr( module, key ) if inspect.isclass( T ) and T is not BaseUIController and issubclass( T, BaseUIController ): - self.add_ui_controller( name, T( app ) ) + controller = self._instantiate_controller( T, app ) + self.add_ui_controller( name, controller ) def add_api_controllers( self, package_name, app ): """ @@ -480,7 +481,14 @@ if inspect.isclass( T ) and not key.startswith("Base") and issubclass( T, BaseAPIController ): # By default use module_name, but allow controller to override name controller_name = getattr( T, "controller_name", name ) - self.add_api_controller( controller_name, T( app ) ) + controller = self._instantiate_controller( T, app ) + self.add_api_controller( controller_name, controller ) + + def _instantiate_controller( self, T, app ): + """ Extension point, allow apps to contstruct controllers differently, + really just used to stub out actual controllers for routes testing. + """ + return T( app ) class GalaxyWebTransaction( base.DefaultWebTransaction ): diff -r f07db0284a42d88a1c88f280c9c22757a671deec -r 6a1755cd7fa0115142e1c277db4129e6e2add217 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -70,10 +70,38 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # ================ - # ===== API ===== - # ================ + # TODO: Refactor above routes into external method to allow testing in + # isolation as well. + populate_api_routes( webapp, app ) + # ==== Done + # Indicate that all configuration settings have been provided + webapp.finalize_config() + + # Wrap the webapp in some useful middleware + if kwargs.get( 'middleware', True ): + webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) + if asbool( kwargs.get( 'static_enabled', True ) ): + webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) + #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) + if asbool(kwargs.get('pack_scripts', False)): + pack_scripts() + # Close any pooled database connections before forking + try: + galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() + except: + pass + # Close any pooled database connections before forking + try: + galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() + except: + pass + + # Return + return webapp + + +def populate_api_routes( webapp, app ): webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) valid_history_contents_types = [ @@ -350,32 +378,6 @@ controller="metrics", action="create", conditions=dict( method=["POST"] ) ) - # ==== Done - # Indicate that all configuration settings have been provided - webapp.finalize_config() - - # Wrap the webapp in some useful middleware - if kwargs.get( 'middleware', True ): - webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) - #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) - if asbool(kwargs.get('pack_scripts', False)): - pack_scripts() - # Close any pooled database connections before forking - try: - galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() - except: - pass - # Close any pooled database connections before forking - try: - galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() - except: - pass - - # Return - return webapp - def pack_scripts(): from glob import glob from subprocess import call diff -r f07db0284a42d88a1c88f280c9c22757a671deec -r 6a1755cd7fa0115142e1c277db4129e6e2add217 test/unit/test_routes.py --- /dev/null +++ b/test/unit/test_routes.py @@ -0,0 +1,81 @@ +#import routes + +# Unused but adds some stuff to routes.Mapper. +from galaxy.web.framework import WebApplication +from galaxy.webapps.galaxy import buildapp as galaxy_buildapp + +from galaxy.web import url_for +from galaxy.util.bunch import Bunch + + +class TestWebapp( WebApplication ): + + def _instantiate_controller( self, type, app ): + # Stub out all actual controllers - just want to test routes. + return object() + + def assert_maps( self, url, method="GET", **parts ): + map_result = self.mapper.match( url, environ={"REQUEST_METHOD": method } ) + for key, expected_value in parts.iteritems(): + actual_value = map_result[ key ] + if actual_value != expected_value: + message = "Problem mapping route [%s], part %s expected value [%s] but obtained [%s]" + raise AssertionError(message % ( url, key, expected_value, actual_value ) ) + + +def test_galaxy_routes( ): + test_config = Bunch( template_path="/tmp", template_cache="/tmp" ) + app = Bunch( config=test_config, security=object(), trace_logger=None ) + test_webapp = TestWebapp( app ) + + galaxy_buildapp.populate_api_routes( test_webapp, app ) + + assert_url_is( url_for( "api_key_retrieval" ), "/api/authenticate/baseauth" ) + + # Test previously problematic tool ids with slashes. + test_webapp.assert_maps( + "/api/tools/testtoolshed.g2.bx.psu.edu/devteam/tool1", + controller="tools", + id="testtoolshed.g2.bx.psu.edu/devteam/tool1" + ) + + test_webapp.assert_maps( + "/api/datatypes/sniffers", + controller="datatypes", + action="sniffers" + ) + + test_webapp.assert_maps( + "/api/histories/123/contents/456", + controller="history_contents", + action="show" + ) + + test_webapp.assert_maps( + "/api/histories/123/contents/456", + method="PUT", + controller="history_contents", + action="update", + ) + + # Test differeniating datasets and datasets collections + # in history contents. + test_webapp.assert_maps( + "/api/histories/123/contents/datasets/456", + method="PUT", + controller="history_contents", + action="update", + type="dataset" + ) + + test_webapp.assert_maps( + "/api/histories/123/contents/dataset_collections/456", + method="PUT", + controller="history_contents", + action="update", + type="dataset_collection" + ) + + +def assert_url_is( actual, expected ): + assert actual == expected, "Expected URL [%s] but obtained [%s]" % ( expected, actual ) https://bitbucket.org/galaxy/galaxy-central/commits/651c1ed8e4d3/ Changeset: 651c1ed8e4d3 User: jmchilton Date: 2014-06-11 22:16:05 Summary: Rework type-differentiated history contents routes. url_for now can produce the routes I build by hand in say bioblend and the GUI. Affected #: 4 files diff -r 6a1755cd7fa0115142e1c277db4129e6e2add217 -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -70,7 +70,7 @@ encoded_id = security.encode_id( dataset_colleciton_instance.id ) if isinstance( parent, model.History ): encoded_history_id = security.encode_id( parent.id ) - dict_value[ 'url' ] = web.url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) + dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) elif isinstance( parent, model.LibraryFolder ): encoded_library_id = security.encode_id( parent.library.id ) encoded_folder_id = security.encode_id( parent.id ) diff -r 6a1755cd7fa0115142e1c277db4129e6e2add217 -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), + 'url' : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): diff -r 6a1755cd7fa0115142e1c277db4129e6e2add217 -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -108,15 +108,16 @@ 'dataset', 'dataset_collection', ] - # This must come before history contents below. + # Accesss HDA details via histories/:history_id/contents/datasets/:hda_id - webapp.mapper.resource( "typed_content", + webapp.mapper.resource( "content_typed", "{type:%s}s" % "|".join( valid_history_contents_types ), - name_prefix="history_content_", + name_prefix="history_", controller='history_contents', path_prefix='/api/histories/:history_id/contents', parent_resources=dict( member_name='history', collection_name='histories' ), ) + # Legacy access to HDA details via histories/:history_id/contents/:hda_id webapp.mapper.resource( 'content', 'contents', diff -r 6a1755cd7fa0115142e1c277db4129e6e2add217 -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 test/unit/test_routes.py --- a/test/unit/test_routes.py +++ b/test/unit/test_routes.py @@ -76,6 +76,16 @@ type="dataset_collection" ) + assert_url_is( + url_for( "history_content", history_id="123", id="456" ), + "/api/histories/123/contents/456" + ) + + assert_url_is( + url_for( "history_content_typed", history_id="123", id="456", type="dataset" ), + "/api/histories/123/contents/datasets/456" + ) + def assert_url_is( actual, expected ): assert actual == expected, "Expected URL [%s] but obtained [%s]" % ( expected, actual ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Fix the 3xx redirect handler in the tool shed's API methods to correctly handle PUT requests.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f07db0284a42/ Changeset: f07db0284a42 User: davebgx Date: 2014-06-11 22:05:46 Summary: Fix the 3xx redirect handler in the tool shed's API methods to correctly handle PUT requests. Affected #: 1 file diff -r 5b67e047172f5fc1ddd0971533b4b3eb37153116 -r f07db0284a42d88a1c88f280c9c22757a671deec lib/tool_shed/scripts/api/common.py --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -13,22 +13,36 @@ class HTTPRedirectWithDataHandler( urllib2.HTTPRedirectHandler ): + + def __init__( self, method ): + ''' + Upon first inspection, it would seem that this shouldn't be necessary, but for some reason + not having a constructor explicitly set the request method breaks PUT requests. + ''' + self.valid_methods = [ 'GET', 'HEAD', 'POST', 'PUT', 'DELETE' ] + self.redirect_codes = [ '301', '302', '303', '307' ] + self.method = method - def redirect_request( self, request, fp, code, msg, headers, newurl ): + def redirect_request( self, request, fp, code, msg, headers, new_url ): request_method = request.get_method() - if ( code in ( 301, 302, 303, 307 ) and request_method in ( "GET", "HEAD", "POST", "PUT", "DELETE" ) ): - newurl = newurl.replace( ' ', '%20' ) - return urllib2.Request( newurl, - data=request.data, - headers=request.headers, - origin_req_host=request.get_origin_req_host(), - unverifiable=True ) + if str( code ) in self.redirect_codes and request_method in self.valid_methods: + new_url = new_url.replace( ' ', '%20' ) + request = urllib2.Request( new_url, + data=request.data, + headers=request.headers, + origin_req_host=request.get_origin_req_host(), + unverifiable=True ) + if self.method in self.valid_methods: + if request.get_method() != self.method: + request.get_method = lambda: self.method + return request else: - urllib2.HTTPRedirectHandler.redirect_request( request, fp, code, msg, headers, newurl ) + urllib2.HTTPRedirectHandler.redirect_request( request, fp, code, msg, headers, new_url ) def build_request_with_data( url, data, api_key, method ): """Build a request with the received method.""" - opener = urllib2.build_opener( HTTPRedirectWithDataHandler ) + http_redirect_with_data_handler = HTTPRedirectWithDataHandler( method=method ) + opener = urllib2.build_opener( http_redirect_with_data_handler ) urllib2.install_opener( opener ) url = make_url( url, api_key=api_key, args=None ) request = urllib2.Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d2c1d24c4f0/ Changeset: 1d2c1d24c4f0 User: davebgx Date: 2014-06-11 20:53:06 Summary: Merge stable. Affected #: 8 files diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_push = False - if not is_deprecated and not is_new and not is_malicious: + if not is_deprecated and not is_new and not changeset_is_malicious: can_download = True else: can_download = False diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/browse_repository.mako --- a/templates/webapps/tool_shed/repository/browse_repository.mako +++ b/templates/webapps/tool_shed/repository/browse_repository.mako @@ -31,7 +31,7 @@ can_browse_contents = not is_new %> -${render_tool_shed_repository_actions( repository, changeset_revision=changeset_revision )} +${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/contact_owner.mako --- a/templates/webapps/tool_shed/repository/contact_owner.mako +++ b/templates/webapps/tool_shed/repository/contact_owner.mako @@ -11,7 +11,7 @@ %><%inherit file="${inherit(context)}"/> -${render_tool_shed_repository_actions( repository )} +${render_tool_shed_repository_actions( repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/export_repository.mako --- a/templates/webapps/tool_shed/repository/export_repository.mako +++ b/templates/webapps/tool_shed/repository/export_repository.mako @@ -23,7 +23,7 @@ ${container_javascripts()} </%def> -${render_tool_shed_repository_actions( repository, changeset_revision=changeset_revision )} +${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/view_changelog.mako --- a/templates/webapps/tool_shed/repository/view_changelog.mako +++ b/templates/webapps/tool_shed/repository/view_changelog.mako @@ -29,7 +29,7 @@ ${h.js( "libs/jquery/jquery.rating" )} </%def> -${render_tool_shed_repository_actions( repository=repository )} +${render_tool_shed_repository_actions( repository=repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/view_changeset.mako --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -29,7 +29,7 @@ ${h.js( "libs/jquery/jquery.rating" )} </%def> -${render_tool_shed_repository_actions( repository=repository )} +${render_tool_shed_repository_actions( repository=repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -61,7 +61,7 @@ </%def> %if trans.webapp.name == 'tool_shed': - ${render_tool_shed_repository_actions( repository=repository, changeset_revision=changeset_revision )} + ${render_tool_shed_repository_actions( repository=repository, metadata=metadata, changeset_revision=changeset_revision )} %else: ${render_galaxy_repository_actions( repository=repository )} %endif diff -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f -r 1d2c1d24c4f02b809c49f358a22971f6285c3f1a templates/webapps/tool_shed/repository/view_tool_metadata.mako --- a/templates/webapps/tool_shed/repository/view_tool_metadata.mako +++ b/templates/webapps/tool_shed/repository/view_tool_metadata.mako @@ -22,7 +22,7 @@ <%inherit file="${inherit(context)}"/> %if render_repository_actions_for == 'tool_shed': - ${render_tool_shed_repository_actions( repository=repository, changeset_revision=changeset_revision )} + ${render_tool_shed_repository_actions( repository=repository, metadata=metadata, changeset_revision=changeset_revision )} %else: ${render_galaxy_repository_actions( repository=repository )} %endif https://bitbucket.org/galaxy/galaxy-central/commits/5b67e047172f/ Changeset: 5b67e047172f User: davebgx Date: 2014-06-11 21:08:05 Summary: Merge stable. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Fix for pull request 413 that did not take into account refactoring that had been committed to -default.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0af48b3c8f33/ Changeset: 0af48b3c8f33 Branch: stable User: davebgx Date: 2014-06-11 21:01:25 Summary: Fix for pull request 413 that did not take into account refactoring that had been committed to -default. Affected #: 1 file diff -r dd3e833aa8724283200b1bf44e44fc93a5441b52 -r 0af48b3c8f33fbe0f05e775f98a14761804c7ac5 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_push = False - if not is_deprecated and not is_new and not changeset_is_malicious: + if not is_deprecated and not is_new and not is_malicious: can_download = True else: can_download = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Fix for displaying repository actions under certain conditions.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd3e833aa872/ Changeset: dd3e833aa872 Branch: stable User: davebgx Date: 2014-06-11 20:48:59 Summary: Fix for displaying repository actions under certain conditions. Affected #: 8 files diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_push = False - if not is_deprecated and not is_new and not is_malicious: + if not is_deprecated and not is_new and not changeset_is_malicious: can_download = True else: can_download = False diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/browse_repository.mako --- a/templates/webapps/tool_shed/repository/browse_repository.mako +++ b/templates/webapps/tool_shed/repository/browse_repository.mako @@ -31,7 +31,7 @@ can_browse_contents = not is_new %> -${render_tool_shed_repository_actions( repository, changeset_revision=changeset_revision )} +${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/contact_owner.mako --- a/templates/webapps/tool_shed/repository/contact_owner.mako +++ b/templates/webapps/tool_shed/repository/contact_owner.mako @@ -11,7 +11,7 @@ %><%inherit file="${inherit(context)}"/> -${render_tool_shed_repository_actions( repository )} +${render_tool_shed_repository_actions( repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/export_repository.mako --- a/templates/webapps/tool_shed/repository/export_repository.mako +++ b/templates/webapps/tool_shed/repository/export_repository.mako @@ -23,7 +23,7 @@ ${container_javascripts()} </%def> -${render_tool_shed_repository_actions( repository, changeset_revision=changeset_revision )} +${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/view_changelog.mako --- a/templates/webapps/tool_shed/repository/view_changelog.mako +++ b/templates/webapps/tool_shed/repository/view_changelog.mako @@ -29,7 +29,7 @@ ${h.js( "libs/jquery/jquery.rating" )} </%def> -${render_tool_shed_repository_actions( repository=repository )} +${render_tool_shed_repository_actions( repository=repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/view_changeset.mako --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -29,7 +29,7 @@ ${h.js( "libs/jquery/jquery.rating" )} </%def> -${render_tool_shed_repository_actions( repository=repository )} +${render_tool_shed_repository_actions( repository=repository, metadata=metadata )} %if message: ${render_msg( message, status )} diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -61,7 +61,7 @@ </%def> %if trans.webapp.name == 'tool_shed': - ${render_tool_shed_repository_actions( repository=repository, changeset_revision=changeset_revision )} + ${render_tool_shed_repository_actions( repository=repository, metadata=metadata, changeset_revision=changeset_revision )} %else: ${render_galaxy_repository_actions( repository=repository )} %endif diff -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 -r dd3e833aa8724283200b1bf44e44fc93a5441b52 templates/webapps/tool_shed/repository/view_tool_metadata.mako --- a/templates/webapps/tool_shed/repository/view_tool_metadata.mako +++ b/templates/webapps/tool_shed/repository/view_tool_metadata.mako @@ -22,7 +22,7 @@ <%inherit file="${inherit(context)}"/> %if render_repository_actions_for == 'tool_shed': - ${render_tool_shed_repository_actions( repository=repository, changeset_revision=changeset_revision )} + ${render_tool_shed_repository_actions( repository=repository, metadata=metadata, changeset_revision=changeset_revision )} %else: ${render_galaxy_repository_actions( repository=repository )} %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Merge stable.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/61d72d2b2e6e/ Changeset: 61d72d2b2e6e User: davebgx Date: 2014-06-11 20:21:12 Summary: Merge stable. Affected #: 1 file diff -r ecc4feed8db4fa8bf880904406ac59bba75950e4 -r 61d72d2b2e6e0afb60057b7a753b7506c56f4e1f templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_push = False - if not is_deprecated and not is_new and ( not changeset_is_malicious or can_push ): + if not is_deprecated and not is_new and not is_malicious: can_download = True else: can_download = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Display the repository export action for users who are not the repository owner.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/426de9e7912b/ Changeset: 426de9e7912b Branch: stable User: davebgx Date: 2014-06-11 20:17:13 Summary: Display the repository export action for users who are not the repository owner. Affected #: 1 file diff -r ef56567006a42ecfaee303b22f4f379a759c03b8 -r 426de9e7912bed1db4548acfe64e2ca86f9cdf99 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_push = False - if not is_deprecated and not is_new and ( not is_malicious or can_push ): + if not is_deprecated and not is_new and not is_malicious: can_download = True else: can_download = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Unify multi-panel viewing
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ecc4feed8db4/ Changeset: ecc4feed8db4 User: guerler Date: 2014-06-11 19:57:13 Summary: Charts: Unify multi-panel viewing Affected #: 9 files diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -211,6 +211,22 @@ value : 'false' } ] + }, + use_panels : { + title : 'Use multi-panels', + info : 'Would you like to separate your data into individual panels?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] } } }; diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -26,17 +26,17 @@ var plot = new Tools.panelHelper({ app : this.app, process_id : this.options.process_id, - canvas : this.options.canvas, + canvas_list : this.options.canvas_list, chart : this.options.chart, request_dictionary : this.options.request_dictionary, - render : function(groups, canvas) { - return self.render(groups, canvas) + render : function(canvas_id, groups) { + return self.render(canvas_id, groups) } }); }, // draw all data into a single canvas - render: function(groups, el_canvas) { + render: function(canvas_id, groups) { // get parameters var chart = this.options.chart; var makeCategories = this.options.makeCategories; @@ -45,13 +45,10 @@ // create configuration var plot_config = configmaker(chart); - var plot_data = [] - + var plot_data = []; + // draw plot try { - // canvas - var canvas = el_canvas[0]; - // make custom categories call this._makeAxes(plot_config, groups, chart.settings); @@ -72,11 +69,15 @@ return false; } - // Draw graph with default options, overwriting with passed options + // draw graph with default options, overwriting with passed options function drawGraph (opts) { - el_canvas.empty(); + var canvas = $('#' + canvas_id); + if(canvas.length == 0) { + return; + } + canvas.empty(); var plot_cnf = _.extend(_.clone(plot_config), opts || {}); - return plot = $.jqplot('canvas', plot_data, plot_cnf); + return plot = $.jqplot(canvas_id, plot_data, plot_cnf); } // draw plot @@ -84,7 +85,7 @@ // catch window resize event var self = this; - $(window).resize(function () { + $(window).on('resize', function () { drawGraph(); }); diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -17,17 +17,17 @@ var plot = Tools.panelHelper({ app : this.app, process_id : this.options.process_id, - canvas : this.options.canvas, + canvas_list : this.options.canvas_list, chart : this.options.chart, request_dictionary : this.options.request_dictionary, - render : function(groups, canvas) { - return self.render(groups, canvas) + render : function(canvas_id, groups) { + return self.render(canvas_id, groups) } }); }, // render - render : function(groups, canvas) { + render : function(canvas_id, groups) { var chart = this.options.chart; var type = this.options.type; var makeConfig = this.options.makeConfig; @@ -67,7 +67,11 @@ d3chart.yAxis.showMaxMin(chart.definition.showmaxmin); // draw chart - canvas.datum(groups) + if ($('#' + canvas_id).length == 0) { + return; + } + var canvas = d3.select('#' + canvas_id); + canvas.datum(groups) .call(d3chart); // add zoom/pan handler diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js @@ -11,19 +11,17 @@ }, // render - draw : function(process_id, chart, request_dictionary) - { - // request data + draw : function(process_id, chart, request_dictionary) { + // setup handler var self = this; - this.app.datasets.request(request_dictionary, function() { - + request_dictionary.success = function() { // loop through data groups for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; // draw group - self._draw_group(chart, group, self.options.canvas[group_index]); + self._draw_group(chart, group, self.options.canvas_list[group_index]); } // set chart state @@ -31,12 +29,18 @@ // unregister process chart.deferred.done(process_id); - }); + } + + // request data + this.app.datasets.request(request_dictionary); }, // draw group - _draw_group: function(chart, group, canvas) { + _draw_group: function(chart, group, canvas_id) { try { + // get canvas + var canvas = d3.select('#' + canvas_id); + // add title var title = canvas.append('text'); diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -12,7 +12,7 @@ var chart = options.chart; var request_dictionary = options.request_dictionary; var render = options.render; - var canvas = options.canvas; + var canvas_list = options.canvas_list; var app = options.app; // get request size from chart @@ -22,17 +22,12 @@ request_dictionary.success = function() { try { // check if this chart has multiple panels - if (!chart.definition.use_panels && chart.settings.get('use_panels') !== 'true') { - // draw all groups into a single panel - if (render(request_dictionary.groups, canvas[0])) { - chart.state('ok', 'Chart drawn.'); - } - } else { + if (chart.definition.use_panels || chart.settings.get('use_panels') === 'true') { // draw groups in separate panels var valid = true; for (var group_index in request_dictionary.groups) { var group = request_dictionary.groups[group_index]; - if (!render([group], canvas[group_index])) { + if (!render(canvas_list[group_index], [group])) { valid = false; break; } @@ -40,6 +35,11 @@ if (valid) { chart.state('ok', 'Multi-panel chart drawn.'); } + } else { + // draw all groups into a single panel + if (render(canvas_list[0], request_dictionary.groups)) { + chart.state('ok', 'Chart drawn.'); + } } // unregister process @@ -58,7 +58,9 @@ // add progress request_dictionary.progress = function(percentage) { - chart.state('wait', 'Loading data...' + percentage + '%'); + if (chart.get('state') == 'wait') { + chart.state('wait', 'Loading data...' + percentage + '%'); + } }; // request data diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/views/types.js --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -34,7 +34,7 @@ // construct chart type subset selection buttons this.library = new Ui.RadioButton({ - data : [ { label: 'Few (<1k)', value: 'small' }, + data : [ { label: 'Few (<500)', value: 'small' }, { label: 'Some (<10k)', value: 'medium' }, { label: 'Many (>10k)', value: 'large' }], onchange: function(value) { diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -107,20 +107,16 @@ // create requested canvas elements for (var i = 0; i < n; i++) { // create element - var canvas_el = $(this._templateContainer(tag, parseInt(100 / n))); + var container_el = $(this._templateContainer(tag, parseInt(100 / n))); // add to view - this.$el.append(canvas_el); + this.$el.append(container_el); // add to list - this.container_list[i] = canvas_el; + this.container_list[i] = container_el; // add a separate list for canvas elements - if (tag == 'svg') { - this.canvas_list[i] = d3.select(canvas_el.find('#canvas')[0]); - } else { - this.canvas_list[i] = canvas_el.find('#canvas'); - } + this.canvas_list[i] = container_el.find('.charts-viewport-canvas').attr('id'); } }, @@ -167,8 +163,8 @@ // create chart view var self = this; require(['plugin/charts/' + this.app.chartPath(chart_type) + '/wrapper'], function(ChartView) { - // create chart - var view = new ChartView(self.app, {canvas : self.canvas_list}); + // create chart and parse list of dom ids + var view = new ChartView(self.app, {canvas_list : self.canvas_list}); // request data if (self.chart_definition.execute) { @@ -284,7 +280,7 @@ _templateContainer: function(tag, width) { return '<div class="charts-viewport-container" style="width:' + width + '%;">' + '<div id="menu"/>' + - '<' + tag + ' id="canvas" class="charts-viewport-canvas">' + + '<' + tag + ' id="' + Utils.uuid() + '" class="charts-viewport-canvas">' + '</div>'; } diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}if(q==200){o&&o(response)}else{k&&k(response)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return(new Date().getTime()).toString(36)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file +define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}if(q==200){o&&o(response)}else{k&&k(response)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file diff -r 26dd63d984585f13369bf04c503eca01f874ece7 -r ecc4feed8db4fa8bf880904406ac59bba75950e4 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -113,7 +113,7 @@ // unique ide function uuid(){ - return (new Date().getTime()).toString(36); + return 'x' + Math.random().toString(36).substring(2, 9); }; // wrap Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Modify url_for in history_contents.py.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26dd63d98458/ Changeset: 26dd63d98458 User: jmchilton Date: 2014-06-11 19:37:24 Summary: Modify url_for in history_contents.py. No clue why - but this randomly fails on main. Will keep looking into it - but it wasn't really giving the pretty URL I wanted anyway (though it was working and this still works due to backward compatbility on this route). Affected #: 1 file diff -r 56f88d255425410b07c09ac5fcd2168f3f19fa1c -r 26dd63d984585f13369bf04c503eca01f874ece7 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: History Contents API: Import url_for from galaxy.web like the other controllers, instead of galaxy.web.base.controller.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56f88d255425/ Changeset: 56f88d255425 User: dannon Date: 2014-06-11 18:24:05 Summary: History Contents API: Import url_for from galaxy.web like the other controllers, instead of galaxy.web.base.controller. Affected #: 1 file diff -r 6b6c0b985ef35056b773197354afe83b07d88afa -r 56f88d255425410b07c09ac5fcd2168f3f19fa1c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -7,6 +7,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import url_for from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin @@ -18,7 +19,6 @@ from galaxy.dataset_collections.util import api_payload_to_create_params from galaxy.dataset_collections.util import dictify_dataset_collection_instance -from galaxy.web.base.controller import url_for from galaxy.managers import histories from galaxy.managers import hdas Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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