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commit/galaxy-central: carlfeberhard: History: allow admin to use display_structured w/ id, add display_structured link in history/view, allow switching to a history from history/view
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b526afe822e5/ Changeset: b526afe822e5 User: carlfeberhard Date: 2014-04-29 18:34:07 Summary: History: allow admin to use display_structured w/ id, add display_structured link in history/view, allow switching to a history from history/view Affected #: 2 files diff -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded -r b526afe822e53ce530fabe94dff683818a33b29a lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -456,7 +456,10 @@ eagerload_all( 'active_datasets.children' ) ).get( id ) assert history - assert history.user and ( history.user.id == trans.user.id ) or ( history.id == trans.history.id ) + #TODO: formalize to trans.show_error + assert ( history.user and ( history.user.id == trans.user.id ) + or ( history.id == trans.history.id ) + or ( trans.user_is_admin() ) ) # Resolve jobs and workflow invocations for the datasets in the history # items is filled with items (hdas, jobs, or workflows) that go at the # top level diff -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded -r b526afe822e53ce530fabe94dff683818a33b29a templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -72,24 +72,37 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"><% + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history[ 'id' ], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history[ 'id' ] ) + + structure_url = h.url_for( controller='history', action='display_structured', id=history[ 'id' ] ) + + switch_to_url = h.url_for( controller='history', action='switch_to_history', hist_id=history[ 'id' ] ) + show_deleted = context.get( 'show_deleted', None ) show_hidden = context.get( 'show_hidden', None ) user_is_owner_json = 'true' if user_is_owner else 'false' show_deleted_json = h.to_json_string( show_deleted ) show_hidden_json = h.to_json_string( show_hidden ) - - imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) - imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) %><div id="header" class="clear"> - <div id="history-view-controls" class="pull-right"> - %if not user_is_owner and not history[ 'purged' ]: - <button id="import" class="btn btn-default"></button> - %endif - <button id="toggle-deleted" class="btn btn-default"></button> - <button id="toggle-hidden" class="btn btn-default"></button> + <div id="history-view-controls"> + <div class="pull-left"> + %if not history[ 'purged' ]: + %if user_is_owner: + <button id="switch" class="btn btn-default">${ _( 'Switch to this history' ) }</button> + %else: + <button id="import" class="btn btn-default"></button> + %endif + <a id="structure" href="${ structure_url }" class="btn btn-default">${ _( 'Show structure' ) }</a> + %endif + </div> + <div class="pull-right"> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button> + </div></div></div> @@ -120,6 +133,18 @@ ] }); + $( '#switch' ).click( function( ev ){ + ##HACK:ity hack hack + ##TODO: remove when out of iframe + var hpanel = Galaxy.currHistoryPanel + || ( top.Galaxy && top.Galaxy.currHistoryPanel )? top.Galaxy.currHistoryPanel : null; + if( hpanel ){ + hpanel.switchToHistory( "${ history[ 'id' ] }" ); + } else { + window.location = "${ switch_to_url }"; + } + }); + $( '#import' ).modeButton({ switchModesOnClick : false, initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", @@ -149,11 +174,7 @@ baseUrl : "${h.url_for( '/static/scripts' )}" })([ 'mvc/user/user-model', panelToUse.location, 'utils/localization' ], function( user, panelMod, _l ){ $(function(){ - window._l = _l; setUpBehaviors(); - if( !Galaxy.currUser ){ - Galaxy.currUser = new user.User( ${h.to_json_string( get_user_json() )} ); - } var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. 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: dan: Fix for setting environment paths when using setup_virutalenv.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78a2fa5ee8b8/ Changeset: 78a2fa5ee8b8 User: dan Date: 2014-04-29 18:13:01 Summary: Fix for setting environment paths when using setup_virutalenv. Affected #: 1 file diff -r 9469c1d11af520686d6c0e934146dbdab05995a8 -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1158,20 +1158,15 @@ full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) return_code = install_environment.handle_command( app, tool_dependency, install_dir, full_setup_command ) if return_code: + log.error( "Failed to do setup_virtualenv install, exit code='%s'", return_code ) + # would it be better to try to set env variables anway, instead of returning here? return tool_dependency, None, None - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - site_packages_command = \ - r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % \ - os.path.join( venv_directory, "bin", "python" ) - output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - return tool_dependency, None, None - if not os.path.exists( output.stdout ): - log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) - return tool_dependency, None, None - env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout ) + site_packages_directory, site_packages_directory_list = self.__get_site_packages_directory( install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ) env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) + if site_packages_directory is None: + log.error( "virtualenv's site-packages directory '%s' does not exist", site_packages_directory_list ) + else: + env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=site_packages_directory ) # The caller should check the status of the returned tool_dependency since this function does nothing # with the return_code. return_code = env_file_builder.return_code @@ -1203,6 +1198,34 @@ action_dict[ 'python' ] = action_elem.get( 'python', 'python' ) return action_dict + def __get_site_packages_directory( self, install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ): + lib_dir = os.path.join( venv_directory, "lib" ) + rval = os.path.join( lib_dir, python_cmd, 'site-packages' ) + site_packages_directory_list = [ rval ] + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + for ( dirpath, dirnames, filenames ) in os.walk( lib_dir ): + for dirname in dirnames: + rval = os.path.join( lib_dir, dirname, 'site-packages' ) + site_packages_directory_list.append( rval ) + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + break + # fall back to python call to get site packages + # FIXME: This is probably more robust?, but there is currently an issue with handling the output.stdout + # preventing the entire path from being included (it gets truncated) + # Use raw strings so that python won't automatically unescape the quotes before passing the command + # to subprocess.Popen. + for site_packages_command in [ r"""%s -c 'import site; site.getsitepackages()[0]'""" % \ + os.path.join( venv_directory, "bin", "python" ), + r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" % \ + os.path.join( venv_directory, "bin", "python" ) ]: + output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) + site_packages_directory_list.append( output.stdout ) + if not output.return_code and os.path.exists( output.stdout ): + return ( output.stdout, site_packages_directory_list ) + return ( None, site_packages_directory_list ) + class ShellCommand( RecipeStep ): def __init__( self ): 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: carlfeberhard: D'oh: fix to ef8ef4ff2e15
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9469c1d11af5/ Changeset: 9469c1d11af5 User: carlfeberhard Date: 2014-04-29 17:41:22 Summary: D'oh: fix to ef8ef4ff2e15 Affected #: 1 file diff -r ef8ef4ff2e1505660871f49b1cfd680f3e5552da -r 9469c1d11af520686d6c0e934146dbdab05995a8 templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -243,7 +243,7 @@ <span class="light">${ _( 'Library' ) + ':' }</span><span class="bold"><a href="${ h.url_for( controller='library', action='list' ) + '#folders/F' + folder_id }"> - ${ library.name } + ${ folder.name } </a></span></div> 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: carlfeberhard: History, structured: wrap copied HDA's in info about library/history they were copied from
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef8ef4ff2e15/ Changeset: ef8ef4ff2e15 User: carlfeberhard Date: 2014-04-29 17:38:20 Summary: History, structured: wrap copied HDA's in info about library/history they were copied from Affected #: 1 file diff -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef -r ef8ef4ff2e1505660871f49b1cfd680f3e5552da templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -9,7 +9,7 @@ body { padding: 5px; } - body > .workflow, body > .toolForm { + body > .workflow, body > .toolForm, body > .copied-from { /*width : 80%;*/ margin-bottom : 8px; /*margin-left : auto;*/ @@ -95,6 +95,18 @@ float: right; } + .copied-from { + border: 1px solid lightgrey; + border-width: 1px 1px 0px 1px; + } + .copied-from .header { + border-bottom: 1px solid lightgrey; + padding: 5px; + } + .copied-from .header .bold, .copied-from .header a { + color: #888; + } + .dataset.hda { min-height : 37px; border-width: 0px 0px 1px 0px; @@ -113,6 +125,7 @@ </style></%def> +## ---------------------------------------------------------------------------- <%def name="javascripts()"><% self.js_app = 'display-structured' @@ -174,12 +187,72 @@ %></%def> -<%def name="render_item_hda( hda, children )"> +## ---------------------------------------------------------------------------- hda +<%def name="render_item_hda( hda, children )"> ## render hdas as a id'd stub for js to fill later + + %if hda.copied_from_history_dataset_association: + ${ render_hda_copied_from_history( hda, children ) } + + %elif hda.copied_from_library_dataset_dataset_association: + ${ render_hda_copied_from_library( hda, children ) } + + %else: <% id = trans.security.encode_id( hda.id ) %><div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + %endif </%def> +<%def name="render_hda_copied_from_history( hda, children )"> +## wrap an hda in info about the history from where it was copied + <% id = trans.security.encode_id( hda.id ) %> + <% history_id = trans.security.encode_id( hda.copied_from_history_dataset_association.history_id ) %> + <div class="copied-from copied-from-history"> + <div class="header"> + <div class="copied-from-dataset"> + <span class="light">${ _( 'Copied from history dataset' ) + ':' }</span> + <span class="bold">${ hda.copied_from_history_dataset_association.name }</span> + </div> + <div class="copied-from-source"> + <span class="light">${ _( 'History' ) + ':' }</span> + <span class="bold"> + <a href="${ h.url_for( controller='history', action='view', id=history_id ) }"> + ${ hda.copied_from_history_dataset_association.history.name } + </a> + </span> + </div> + </div> + <div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + </div> +</%def> + +<%def name="render_hda_copied_from_library( hda, children )"> +## wrap an hda in info about the library from where it was copied + <% id = trans.security.encode_id( hda.id ) %> + <% + folder = hda.copied_from_library_dataset_dataset_association.library_dataset.folder + folder_id = 'F' + trans.security.encode_id( folder.id ) + %> + <div class="copied-from copied-from-library"> + <div class="header"> + <div class="copied-from-dataset"> + <span class="light">${ _( 'Copied from library dataset' ) + ':' }</span> + <span class="bold">${ hda.copied_from_library_dataset_dataset_association.name }</span> + </div> + <div class="copied-from-source"> + <span class="light">${ _( 'Library' ) + ':' }</span> + <span class="bold"> + <a href="${ h.url_for( controller='library', action='list' ) + '#folders/F' + folder_id }"> + ${ library.name } + </a> + </span> + </div> + </div> + <div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + </div> +</%def> + +## ---------------------------------------------------------------------------- job (and output hdas) <%def name="render_item_job( job, children )"> ## render a job (as a toolForm) and its children (hdas) <div class="tool toolForm"> @@ -220,6 +293,7 @@ </div></%def> +## ---------------------------------------------------------------------------- workflow (w/ jobs, hdas) <%def name="render_item_wf( wf, children )"> ## render a workflow and its children (jobs/toolForms) <div class="workflow"> @@ -235,7 +309,7 @@ </div></%def> -## ---------------------------------------------------------------------------- +## ---------------------------------------------------------------------------- body ## render all items from a dictionary prov. by history/display_structured %for entity, children in items: ${render_item( entity, children )} 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: carlfeberhard: Fix to 197878e: properly namespace def and use in grid_async
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/828286e70c05/ Changeset: 828286e70c05 User: carlfeberhard Date: 2014-04-29 16:07:40 Summary: Fix to 197878e: properly namespace def and use in grid_async Affected #: 2 files diff -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -73,13 +73,13 @@ // load grid viewer require(['mvc/grid/grid-view'], function(GridView) { $(function() { - gridView = new GridView( ${ h.to_json_string( self.grid_config() ) } ); + gridView = new GridView( ${ h.to_json_string( self.get_grid_config() ) } ); }); }); </script></%def> -<%def name="grid_config( embedded=False, insert=None )"> +<%def name="get_grid_config( embedded=False, insert=None )"> ## generates dictionary <% self.grid_config = { diff -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef templates/grid_base_async.mako --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,4 +1,4 @@ <%namespace name="grid_base" file="./grid_base.mako" import="*" /> ${init()} -${h.to_json_string( grid_base.grid_config )} \ No newline at end of file +${h.to_json_string( grid_base.get_grid_config() )} 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: greg: Fix for determining the list of all repository dependency dictionaries when installing a repository into Galaxy that has a deep dependency hierarchy.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5846eb77fc8e/ Changeset: 5846eb77fc8e User: greg Date: 2014-04-29 15:34:58 Summary: Fix for determining the list of all repository dependency dictionaries when installing a repository into Galaxy that has a deep dependency hierarchy. Affected #: 1 file diff -r e3808d426ef2387a25aa79cbba397a6ec2f0d8f5 -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -464,7 +464,15 @@ all_required_repo_info_dict[ k ] = v if required_repo_info_dicts: for required_repo_info_dict in required_repo_info_dicts: - if required_repo_info_dict not in all_repo_info_dicts: + # Each required_repo_info_dict has a single entry, and all_repo_info_dicts is a list + # of dictionaries, each of which has a single entry. We'll check keys here rather than + # the entire dictionary because a dictionary entry in all_repo_info_dicts will include + # lists of discovered repository dependencies, but these lists will be empty in the + # required_repo_info_dict since dependency discovery has not yet been performed for these + # dictionaries. + required_repo_infor_dict_key = required_repo_info_dict.keys()[ 0 ] + all_repo_info_dicts_keys = [ d.keys()[ 0 ] for d in all_repo_info_dicts ] + if required_repo_infor_dict_key not in all_repo_info_dicts_keys: all_repo_info_dicts.append( required_repo_info_dict ) all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict 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: greg: Handle changing http protocols in the tool shed registry's password_manager_for_url() function.
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3808d426ef2/ Changeset: e3808d426ef2 User: greg Date: 2014-04-28 21:58:48 Summary: Handle changing http protocols in the tool shed registry's password_manager_for_url() function. Affected #: 1 file diff -r 04befb2eb25baa347a3f440ed22045d01e75ebc7 -r e3808d426ef2387a25aa79cbba397a6ec2f0d8f5 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -2,6 +2,7 @@ import sys import urllib2 from galaxy.util.odict import odict +from tool_shed.util import common_util from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -39,13 +40,17 @@ def password_manager_for_url( self, url ): """ - If the tool shed is using external auth, the client to the tool shed must authenticate to that as well. This provides access to the - urllib2.HTTPPasswordMgrWithdefaultRealm() object for the url passed in. + If the tool shed is using external auth, the client to the tool shed must authenticate to that + as well. This provides access to the urllib2.HTTPPasswordMgrWithdefaultRealm() object for the + url passed in. - Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at some stage... + Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at + some stage... """ + url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( url ) for shed_name, shed_url in self.tool_sheds.items(): - if shed_url.find( url ) >= 0: + shed_url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( shed_url ) + if shed_url_sans_protocol.find( url_sans_protocol ) >= 0: return self.tool_sheds_auth[ shed_name ] log.debug( "Invalid url '%s' received by tool shed registry's password_manager_for_url method." % str( url ) ) return None 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: 3 new changesets
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31d00b1b6a9f/ Changeset: 31d00b1b6a9f User: dan Date: 2014-04-28 21:35:47 Summary: For setup_virtualenv: allow specifying to not use requirements file for pip install. Empirically, calling pip install PACKAGE may work better than using a requirements file with some package combinations. Specify a specific log file for pip to use during installation. Affected #: 1 file diff -r ef1ed48f60a5d6592d148ec55ff2f50dc3587035 -r 31d00b1b6a9f7ed88a74f03569b686e15558d196 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1139,7 +1139,22 @@ # POSIXLY_CORRECT forces shell commands . and source to have the same # and well defined behavior in bash/zsh. activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) - install_command = "python '%s' install -r '%s'" % ( os.path.join( venv_directory, "bin", "pip" ), requirements_path ) + if action_dict[ 'use_requirements_file' ]: + install_command = "python '%s' install -r '%s' --log '%s'" % ( os.path.join( venv_directory, "bin", "pip" ), requirements_path, os.path.join( install_dir, 'pip_install.log' ) ) + else: + install_command = '' + with open( requirements_path, "rb" ) as f: + while True: + line = f.readline() + if not line: + break + line = line.strip() + if line: + line_install_command = "python '%s' install %s --log '%s'" % ( os.path.join( venv_directory, "bin", "pip" ), line, os.path.join( install_dir, 'pip_install_%s.log' % ( line ) ) ) + if not install_command: + install_command = line_install_command + else: + install_command = "%s && %s" % ( install_command, line_install_command ) full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) return_code = install_environment.handle_command( app, tool_dependency, install_dir, full_setup_command ) if return_code: @@ -1183,6 +1198,7 @@ # <action type="setup_virtualenv">pyyaml==3.2.0 # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. + action_dict[ 'use_requirements_file' ] = asbool( action_elem.get( 'use_requirements_file', True ) ) action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) action_dict[ 'python' ] = action_elem.get( 'python', 'python' ) return action_dict https://bitbucket.org/galaxy/galaxy-central/commits/dd2f7cb5e0b1/ Changeset: dd2f7cb5e0b1 User: dan Date: 2014-04-28 21:39:55 Summary: merge default Affected #: 3 files diff -r 31d00b1b6a9f7ed88a74f03569b686e15558d196 -r dd2f7cb5e0b14f6410b3bf6c7262f25783e144e8 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -40,7 +40,8 @@ # Setup the database engine and ORM config_file = kwargs.get( 'global_conf', {} ).get( '__file__', None ) - self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file ) + check_migrate_tools = self.config.check_migrate_tools + self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) # Manage installed tool shed repositories. from tool_shed.galaxy_install import installed_repository_manager diff -r 31d00b1b6a9f7ed88a74f03569b686e15558d196 -r dd2f7cb5e0b14f6410b3bf6c7262f25783e144e8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -4,8 +4,12 @@ # absolute_import needed for tool_shed package. from __future__ import absolute_import -import sys, os, tempfile, re -import logging, logging.config +import os +import re +import sys +import tempfile +import logging +import logging.config import ConfigParser from datetime import timedelta from galaxy.web.formatting import expand_pretty_datetime_format @@ -23,11 +27,14 @@ path = os.path.join( root, path ) return path + class ConfigurationError( Exception ): pass + class Configuration( object ): deprecated_options = ( 'database_file', ) + def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) @@ -87,6 +94,9 @@ self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have + # been migrated from the Galaxy code distribution to the Tool Shed. + self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) self.shed_tool_data_path = kwargs.get( "shed_tool_data_path", None ) if self.shed_tool_data_path: self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root ) @@ -397,13 +407,16 @@ return rval except ConfigParser.NoSectionError: return {} + def get( self, key, default ): return self.config_dict.get( key, default ) + def get_bool( self, key, default ): if key in self.config_dict: return string_as_bool( self.config_dict[key] ) else: return default + def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] # Check that required directories exist @@ -488,7 +501,6 @@ rval[ key ] = value return rval - def configure_logging( config ): """ Allow some basic logging configuration to be read from ini file. diff -r 31d00b1b6a9f7ed88a74f03569b686e15558d196 -r dd2f7cb5e0b14f6410b3bf6c7262f25783e144e8 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -136,6 +136,13 @@ # Tools can be locally developed or installed from Galaxy tool sheds. #tool_config_file = tool_conf.xml,shed_tool_conf.xml +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. #tool_path = tools https://bitbucket.org/galaxy/galaxy-central/commits/04befb2eb25b/ Changeset: 04befb2eb25b User: dan Date: 2014-04-28 21:40:15 Summary: merge default Affected #: 1 file diff -r dd2f7cb5e0b14f6410b3bf6c7262f25783e144e8 -r 04befb2eb25baa347a3f440ed22045d01e75ebc7 test/functional/api/test_tools.py --- a/test/functional/api/test_tools.py +++ b/test/functional/api/test_tools.py @@ -1,6 +1,4 @@ # Test tools API. -from itertools import chain - from base import api from operator import itemgetter from .helpers import DatasetPopulator @@ -13,22 +11,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) def test_index( self ): - index = self._get( "tools" ) - tools_index = index.json() - # In panels by default, so flatten out sections... - tools = list( chain( *map( itemgetter( "elems" ), tools_index ) ) ) - tool_ids = map( itemgetter( "id" ), tools ) + tool_ids = self.__tool_ids() assert "upload1" in tool_ids - assert "cat1" in tool_ids def test_no_panel_index( self ): - index = self._get( "tools", data=dict(in_panel="false") ) + index = self._get( "tools", data=dict( in_panel="false" ) ) tools_index = index.json() # No need to flatten out sections, with in_panel=False, only tools are # returned. tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids - assert "cat1" in tool_ids def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() @@ -58,6 +50,7 @@ self.assertEquals( result_content, table ) def test_run_cat1( self ): + self.__skip_without_tool( "cat1" ) # Run simple non-upload tool with an input data parameter. history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -72,6 +65,7 @@ self.assertEqual( output1_content.strip(), "Cat1Test" ) def test_run_cat1_with_two_inputs( self ): + self.__skip_without_tool( "cat1" ) # Run tool with an multiple data parameter and grouping (repeat) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -118,6 +112,25 @@ self._assert_status_code_is( display_response, 200 ) return display_response.content + def __tool_ids( self ): + index = self._get( "tools" ) + tools_index = index.json() + # In panels by default, so flatten out sections... + tools = [] + for tool_or_section in tools_index: + if "elems" in tool_or_section: + tools.extend( tool_or_section[ "elems" ] ) + else: + tools.append( tool_or_section ) + + tool_ids = map( itemgetter( "id" ), tools ) + return tool_ids + + def __skip_without_tool( self, tool_id ): + from nose.plugins.skip import SkipTest + if tool_id not in self.__tool_ids( ): + raise SkipTest( ) + def dataset_to_param( dataset ): return dict( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Tools API Improvements.
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d88d8b71662/ Changeset: 5d88d8b71662 User: jmchilton Date: 2014-04-28 21:38:45 Summary: Tools API Improvements. Ablity to require tool for API test. Fix test_index for tool panels containing tools outside a section. Affected #: 1 file diff -r a3b4e0950ae60007af2efcc257a78be6dbe7ca7a -r 5d88d8b716623e06dcc2dbca442c5f52c0a43389 test/functional/api/test_tools.py --- a/test/functional/api/test_tools.py +++ b/test/functional/api/test_tools.py @@ -1,6 +1,4 @@ # Test tools API. -from itertools import chain - from base import api from operator import itemgetter from .helpers import DatasetPopulator @@ -13,22 +11,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) def test_index( self ): - index = self._get( "tools" ) - tools_index = index.json() - # In panels by default, so flatten out sections... - tools = list( chain( *map( itemgetter( "elems" ), tools_index ) ) ) - tool_ids = map( itemgetter( "id" ), tools ) + tool_ids = self.__tool_ids() assert "upload1" in tool_ids - assert "cat1" in tool_ids def test_no_panel_index( self ): - index = self._get( "tools", data=dict(in_panel="false") ) + index = self._get( "tools", data=dict( in_panel="false" ) ) tools_index = index.json() # No need to flatten out sections, with in_panel=False, only tools are # returned. tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids - assert "cat1" in tool_ids def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() @@ -58,6 +50,7 @@ self.assertEquals( result_content, table ) def test_run_cat1( self ): + self.__skip_without_tool( "cat1" ) # Run simple non-upload tool with an input data parameter. history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -72,6 +65,7 @@ self.assertEqual( output1_content.strip(), "Cat1Test" ) def test_run_cat1_with_two_inputs( self ): + self.__skip_without_tool( "cat1" ) # Run tool with an multiple data parameter and grouping (repeat) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -118,6 +112,25 @@ self._assert_status_code_is( display_response, 200 ) return display_response.content + def __tool_ids( self ): + index = self._get( "tools" ) + tools_index = index.json() + # In panels by default, so flatten out sections... + tools = [] + for tool_or_section in tools_index: + if "elems" in tool_or_section: + tools.extend( tool_or_section[ "elems" ] ) + else: + tools.append( tool_or_section ) + + tool_ids = map( itemgetter( "id" ), tools ) + return tool_ids + + def __skip_without_tool( self, tool_id ): + from nose.plugins.skip import SkipTest + if tool_id not in self.__tool_ids( ): + raise SkipTest( ) + def dataset_to_param( dataset ): return dict( 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: greg: Make checking for for migrated tools when starting the Galaxy server a config setting that defaults to True. This setting should generally be False only for development Galaxy environments that are often set up from scratch (with new db, etc) and migrated tools are not needed in the Galaxy tool panel. In those cases where this setting is False, starting a fresh Galaxy instance (with no checking for migrated tools) will be much faster.
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3b4e0950ae6/ Changeset: a3b4e0950ae6 User: greg Date: 2014-04-28 21:35:41 Summary: Make checking for for migrated tools when starting the Galaxy server a config setting that defaults to True. This setting should generally be False only for development Galaxy environments that are often set up from scratch (with new db, etc) and migrated tools are not needed in the Galaxy tool panel. In those cases where this setting is False, starting a fresh Galaxy instance (with no checking for migrated tools) will be much faster. Affected #: 3 files diff -r ef1ed48f60a5d6592d148ec55ff2f50dc3587035 -r a3b4e0950ae60007af2efcc257a78be6dbe7ca7a lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -40,7 +40,8 @@ # Setup the database engine and ORM config_file = kwargs.get( 'global_conf', {} ).get( '__file__', None ) - self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file ) + check_migrate_tools = self.config.check_migrate_tools + self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) # Manage installed tool shed repositories. from tool_shed.galaxy_install import installed_repository_manager diff -r ef1ed48f60a5d6592d148ec55ff2f50dc3587035 -r a3b4e0950ae60007af2efcc257a78be6dbe7ca7a lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -4,8 +4,12 @@ # absolute_import needed for tool_shed package. from __future__ import absolute_import -import sys, os, tempfile, re -import logging, logging.config +import os +import re +import sys +import tempfile +import logging +import logging.config import ConfigParser from datetime import timedelta from galaxy.web.formatting import expand_pretty_datetime_format @@ -23,11 +27,14 @@ path = os.path.join( root, path ) return path + class ConfigurationError( Exception ): pass + class Configuration( object ): deprecated_options = ( 'database_file', ) + def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) @@ -87,6 +94,9 @@ self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have + # been migrated from the Galaxy code distribution to the Tool Shed. + self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) self.shed_tool_data_path = kwargs.get( "shed_tool_data_path", None ) if self.shed_tool_data_path: self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root ) @@ -397,13 +407,16 @@ return rval except ConfigParser.NoSectionError: return {} + def get( self, key, default ): return self.config_dict.get( key, default ) + def get_bool( self, key, default ): if key in self.config_dict: return string_as_bool( self.config_dict[key] ) else: return default + def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] # Check that required directories exist @@ -488,7 +501,6 @@ rval[ key ] = value return rval - def configure_logging( config ): """ Allow some basic logging configuration to be read from ini file. diff -r ef1ed48f60a5d6592d148ec55ff2f50dc3587035 -r a3b4e0950ae60007af2efcc257a78be6dbe7ca7a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -136,6 +136,13 @@ # Tools can be locally developed or installed from Galaxy tool sheds. #tool_config_file = tool_conf.xml,shed_tool_conf.xml +# Enable / disable checking if any tools defined in the above non-shed tool_config_files +# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool +# Shed. This setting should generally be set to False only for development Galaxy environments +# that are often rebuilt from scratch where migrated tools do not need to be available in the +# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +#check_migrate_tools = True + # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. #tool_path = tools 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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