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

commit/galaxy-central: guerler: Charts: Fix jqplot bar axis
by commits-noreply＠bitbucket.org 18 Jun '14

18 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/385c4b53694e/ Changeset: 385c4b53694e User: guerler Date: 2014-06-18 12:42:11 Summary: Charts: Fix jqplot bar axis Affected #: 4 files diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -20,7 +20,12 @@ makeConfig : function(groups, plot_config){ $.extend(true, plot_config, { seriesDefaults: { - renderer : $.jqplot.BarRenderer + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 + } } }); } diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -16,8 +16,8 @@ showLine : true, // whether to render the line segments or not. rendererOptions: { shadowDepth : 0, - //barDirection : 'horizontal', - barWidth : 1 + barWidth : 3, + barPadding : 3 }, markerRenderer : $.jqplot.MarkerRenderer, markerOptions: { @@ -56,7 +56,6 @@ angle : chart.settings.get('use_panels') === 'true' ? 0 : -30, showGridline : chart.settings.get('x_axis_grid') === 'true' }, - tickInterval : 1, pad : 0 }, yaxis: { diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 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 @@ -134,7 +134,7 @@ formatter : function(formatter) { if (formatter) { plot_config.axes[id + 'axis'].tickOptions.formatter = function(format, value) { - return formatter(value); + return formatter(value); }; } } diff -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 -r 385c4b53694eb1838c0f2487b38b4e798b16c522 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 @@ -361,6 +361,9 @@ // add handler svg.call(d3zoom).on('dblclick.zoom', unzoomed); + + // return + return d3zoom; }; // return 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: jmchilton: Fix typo in b267ce103960.
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45963b149ddb/ Changeset: 45963b149ddb User: jmchilton Date: 2014-06-18 00:22:55 Summary: Fix typo in b267ce103960. Affected #: 1 file diff -r b267ce1039608f0c8fbbd42f148a372871668c22 -r 45963b149ddb39de0e62617a49e0af59e7f2fc06 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -6,7 +6,7 @@ GALAXY_SLOTS="$SLURM_NTASKS" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" -elif [ -n "$PBS_NCPUS" ] then +elif [ -n "$PBS_NCPUS" ]; then GALAXY_SLOTS="$PBS_NCPUS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` 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: jmchilton: Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots.
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b267ce103960/ Changeset: b267ce103960 User: jmchilton Date: 2014-06-17 22:10:58 Summary: Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots. Affected #: 1 file diff -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 -r b267ce1039608f0c8fbbd42f148a372871668c22 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -6,6 +6,8 @@ GALAXY_SLOTS="$SLURM_NTASKS" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" +elif [ -n "$PBS_NCPUS" ] then + GALAXY_SLOTS="$PBS_NCPUS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` elif [ -n "$LSB_DJOB_NUMPROC" ]; then 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: Eliminate the use of the repository_util.py module for Galaxy installs from the Tool Shed.
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6294a65d863a/ Changeset: 6294a65d863a User: greg Date: 2014-06-17 20:38:02 Summary: Eliminate the use of the repository_util.py module for Galaxy installs from the Tool Shed. Affected #: 16 files diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -19,6 +19,7 @@ from galaxy.jobs import metrics as job_metrics from galaxy.web.base import pluginframework from galaxy.queue_worker import GalaxyQueueWorker +from tool_shed.galaxy_install import update_repository_manager import logging log = logging.getLogger( __name__ ) @@ -80,12 +81,8 @@ # Load Data Manager self.data_managers = DataManagers( self ) - # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. - if self.config.get_bool( 'enable_tool_shed_check', False ): - from tool_shed.galaxy_install import update_repository_manager - self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self ) - else: - self.update_repository_manager = None + # Load the update repository manager. + self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self ) # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications() # Load datatype display applications defined in local datatypes_conf.xml @@ -159,8 +156,7 @@ self.object_store.shutdown() if self.heartbeat: self.heartbeat.shutdown() - if self.update_repository_manager is not None: - self.update_repository_manager.shutdown() + self.update_repository_manager.shutdown() if self.control_worker: self.control_worker.shutdown() try: diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -105,7 +105,6 @@ self.shed_tool_data_path = self.tool_data_path self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ] self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) - self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -24,11 +24,11 @@ from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util from tool_shed.util import xml_util -from tool_shed.galaxy_install import repository_util from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids @@ -114,7 +114,8 @@ # repository dependencies and tool dependencies will be current. Only allow selecting a different section # in the tool panel if the repository was uninstalled and it contained tools that should be displayed in # the tool panel. - changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( trans.app, repository ) + changeset_revision_dict = \ + trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev( repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_changeset_revision and current_ctx_rev: @@ -588,11 +589,10 @@ updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) else: updated_metadata = None - repository = repository_util.update_repository_record( trans.app, - repository=repository, - updated_metadata_dict=updated_metadata, - updated_changeset_revision=updating_to_changeset_revision, - updated_ctx_rev=updating_to_ctx_rev ) + repository = trans.app.update_repository_manager.update_repository_record( repository=repository, + updated_metadata_dict=updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) if install_tool_dependencies: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, repository, @@ -657,7 +657,7 @@ def manage_repositories( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tsridslist = repository_util.get_tool_shed_repository_ids( **kwd ) + tsridslist = common_util.get_tool_shed_repository_ids( **kwd ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if not tsridslist: @@ -941,7 +941,7 @@ @web.expose @web.require_admin def monitor_repository_installation( self, trans, **kwd ): - tsridslist = repository_util.get_tool_shed_repository_ids( **kwd ) + tsridslist = common_util.get_tool_shed_repository_ids( **kwd ) if not tsridslist: tsridslist = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False ) kwd[ 'tool_shed_repository_ids' ] = tsridslist @@ -1062,11 +1062,10 @@ decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) # Now that the user has decided whether they will handle dependencies, we can update # the repository to the latest revision. - repository = repository_util.update_repository_record( trans.app, - repository=repository, - updated_metadata_dict=decoded_updated_metadata, - updated_changeset_revision=updating_to_changeset_revision, - updated_ctx_rev=updating_to_ctx_rev ) + repository = trans.app.update_repository_manager.update_repository_record( repository=repository, + updated_metadata_dict=decoded_updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) @@ -1081,7 +1080,7 @@ tool_path=tool_path, tool_shed_url=tool_shed_url ) created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ - repository_util.handle_tool_shed_repositories( trans.app, installation_dict, using_api=False ) + irm.handle_tool_shed_repositories( installation_dict, using_api=False ) if created_or_updated_tool_shed_repositories: installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, filtered_repo_info_dicts=filtered_repo_info_dicts, @@ -1367,16 +1366,17 @@ tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None - repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = \ + repository_maintenance_util.create_repo_info_dict( app=trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) if repo_info_dict not in repo_info_dicts: repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. @@ -1581,16 +1581,17 @@ repository_dependencies = \ repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) - repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - ctx_rev=tool_shed_repository.ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = \ + repository_maintenance_util.create_repo_info_dict( app=trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, @@ -2024,11 +2025,10 @@ return self.install_tool_dependencies_with_update( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. - repository = repository_util.update_repository_record( trans.app, - repository=repository, - updated_metadata_dict=metadata_dict, - updated_changeset_revision=latest_changeset_revision, - updated_ctx_rev=latest_ctx_rev ) + repository = trans.app.update_repository_manager.update_repository_record( repository=repository, + updated_metadata_dict=metadata_dict, + updated_changeset_revision=latest_changeset_revision, + updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ ( name, latest_changeset_revision ) else: diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,3 +1,4 @@ +import json import logging import os import tarfile @@ -6,13 +7,11 @@ from galaxy import eggs from galaxy import util from galaxy import web -from galaxy.util import json from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc -from tool_shed.galaxy_install import repository_util from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util @@ -192,7 +191,10 @@ includes_tools_for_display_in_tool_panel, \ has_repository_dependencies, \ has_repository_dependencies_only_if_compiling_contained_td = \ - repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision ) + repository_maintenance_util.get_repo_info_dict( trans.app, + trans.user, + encoded_repository_id, + changeset_revision ) return repository_dict, repository_metadata_dict, repo_info_dict else: log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \ @@ -465,7 +467,7 @@ results = handle_repository( trans, repository, results ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time - return json.to_json_string( results, sort_keys=True, indent=4 ) + return json.dumps( results, sort_keys=True, indent=4 ) @web.expose_api def reset_metadata_on_repository( self, trans, payload, **kwd ): @@ -504,7 +506,7 @@ results = handle_repository( trans, start_time, repository ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time - return json.to_json_string( results, sort_keys=True, indent=4 ) + return json.dumps( results, sort_keys=True, indent=4 ) @web.expose_api_anonymous def show( self, trans, id, **kwd ): diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -31,7 +31,7 @@ from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util -from tool_shed.galaxy_install import repository_util +from tool_shed.galaxy_install import install_manager from galaxy.webapps.tool_shed.util import ratings_util import galaxy.tools import tool_shed.grids.repository_grids as repository_grids @@ -1761,7 +1761,7 @@ repository_id, changeset_revision = tup repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \ cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \ - repository_util.get_repo_info_dict( trans, repository_id, changeset_revision ) + repository_maintenance_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision ) if cur_has_repository_dependencies and not has_repository_dependencies: has_repository_dependencies = True if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td: @@ -1881,7 +1881,7 @@ """ repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) if not repository_metadata: @@ -1892,16 +1892,16 @@ after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) + repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) includes_data_managers = False includes_datatypes = False includes_tools = False diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -20,14 +20,17 @@ from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import container_util +from tool_shed.util import data_manager_util +from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install import repository_util from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager @@ -488,6 +491,136 @@ repo_info_dicts = [ repo_info_dict ] return repository_revision_dict, repo_info_dicts + def handle_repository_contents( self, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, + tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ): + """ + Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy + (never the tool shed) when an administrator is installing a new repository or reinstalling an uninstalled repository. + """ + install_model = self.app.install_model + shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) + metadata_dict, invalid_file_tups = \ + metadata_util.generate_metadata_for_changeset_revision( app=self.app, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + tool_shed_repository.metadata = metadata_dict + # Update the tool_shed_repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) + if tool_shed_status_dict: + tool_shed_repository.tool_shed_status = tool_shed_status_dict + install_model.context.add( tool_shed_repository ) + install_model.context.flush() + if 'tool_dependencies' in metadata_dict and not reinstalling: + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, + tool_shed_repository, + relative_install_dir, + set_status=True ) + if 'sample_files' in metadata_dict: + sample_files = metadata_dict.get( 'sample_files', [] ) + tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_data_table_conf_filename, tool_data_table_elems = \ + tool_util.install_tool_data_tables( self.app, tool_shed_repository, tool_index_sample_files ) + if tool_data_table_elems: + self.app.tool_data_tables.add_new_entries_from_config_file( tool_data_table_conf_filename, + None, + self.app.config.shed_tool_data_table_config, + persist=True ) + if 'tools' in metadata_dict: + tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + sample_files = metadata_dict.get( 'sample_files', [] ) + tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + sample_files_copied = [ str( s ) for s in tool_index_sample_files ] + repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict ) + if repository_tools_tups: + # Handle missing data table entries for tool parameters that are dynamically generated select lists. + repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, + relative_install_dir, + tool_path, + repository_tools_tups ) + # Handle missing index files for tool parameters that are dynamically generated select lists. + repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app, + tool_path, + sample_files, + repository_tools_tups, + sample_files_copied ) + # Copy remaining sample files included in the repository to the ~/tool-data directory of the + # local Galaxy instance. + tool_util.copy_sample_files( self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) + tool_util.add_to_tool_panel( app=self.app, + repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) + if 'data_manager' in metadata_dict: + new_data_managers = data_manager_util.install_data_managers( self.app, + self.app.config.shed_data_manager_config_file, + metadata_dict, + shed_config_dict, + relative_install_dir, + tool_shed_repository, + repository_tools_tups ) + if 'datatypes' in metadata_dict: + tool_shed_repository.status = install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES + if not tool_shed_repository.includes_datatypes: + tool_shed_repository.includes_datatypes = True + install_model.context.add( tool_shed_repository ) + install_model.context.flush() + files_dir = relative_install_dir + if shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) + # Load data types required by tools. + converter_path, display_path = \ + datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, files_dir, override=False ) + if converter_path or display_path: + # Create a dictionary of tool shed repository related information. + repository_dict = \ + datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + name=tool_shed_repository.name, + owner=tool_shed_repository.owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) + if converter_path: + # Load proprietary datatype converters + self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict ) + if display_path: + # Load proprietary datatype display applications + self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) + + def handle_tool_shed_repositories( self, installation_dict, using_api=False ): + # The following installation_dict entries are all required. + install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] + new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ] + no_changes_checked = installation_dict[ 'no_changes_checked' ] + repo_info_dicts = installation_dict[ 'repo_info_dicts' ] + tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ] + tool_path = installation_dict[ 'tool_path' ] + tool_shed_url = installation_dict[ 'tool_shed_url' ] + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ + repository_dependency_util.create_repository_dependency_objects( app=self.app, + tool_path=tool_path, + tool_shed_url=tool_shed_url, + repo_info_dicts=repo_info_dicts, + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts + def initiate_repository_installation( self, installation_dict ): install_model = self.app.install_model # The following installation_dict entries are all required. @@ -699,9 +832,9 @@ cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: if reinstalling: - # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated. - changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( self.app, - tool_shed_repository ) + # Since we're reinstalling the repository we need to find the latest changeset revision to + # which it can be updated. + changeset_revision_dict = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev( tool_shed_repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: @@ -711,15 +844,14 @@ create=False ) hg_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) hg_util.update_repository( repo, ctx_rev=current_ctx_rev ) - repository_util.handle_repository_contents( self.app, - tool_shed_repository=tool_shed_repository, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - tool_shed=tool_shed_repository.tool_shed, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - reinstalling=reinstalling ) + self.handle_repository_contents( tool_shed_repository=tool_shed_repository, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + tool_shed=tool_shed_repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + reinstalling=reinstalling ) install_model.context.refresh( tool_shed_repository ) metadata = tool_shed_repository.metadata if 'tools' in metadata: diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -4,13 +4,13 @@ log = logging.getLogger( __name__ ) from tool_shed.galaxy_install import install_manager -from tool_shed.galaxy_install import repository_util from tool_shed.util import common_install_util from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import shed_util_common as suc from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -123,16 +123,16 @@ new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None - repo_info_dict = repository_util.create_repo_info_dict( app=self.app, - repository_clone_url=repository_clone_url, - changeset_revision=repository.changeset_revision, - ctx_rev=repository.ctx_rev, - repository_owner=repository.owner, - repository_name=repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app, + repository_clone_url=repository_clone_url, + changeset_revision=repository.changeset_revision, + ctx_rev=repository.ctx_rev, + repository_owner=repository.owner, + repository_name=repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) return repo_info_dict, tool_panel_section_key def repair_tool_shed_repository( self, repository, repo_info_dict ): diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ /dev/null @@ -1,382 +0,0 @@ -import logging -import os -from galaxy import util -from galaxy import web -import tool_shed.util.shed_util_common as suc -from tool_shed.util import common_util -from tool_shed.util import data_manager_util -from tool_shed.util import datatype_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import repository_dependency_util -from tool_shed.util import metadata_util -from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util - -log = logging.getLogger( __name__ ) - -def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, - repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): - """ - Return a dictionary that includes all of the information needed to install a repository into a local - Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined - for the repository, as well as the defined tool dependencies. - - This method is called from Galaxy under four scenarios: - 1. During the tool shed repository installation process via the tool shed's get_repository_information() - method. In this case both the received repository and repository_metadata will be objects, but - tool_dependencies and repository_dependencies will be None. - 2. When getting updates for an install repository where the updates include newly defined repository - dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() - method is the caller, and both the received repository and repository_metadata will be objects, but - tool_dependencies and repository_dependencies will be None. - 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no - updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies - and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes - definitions for them. - 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates - available. In this case, this method is reached via the tool shed's get_updated_repository_information() - method, and both repository and repository_metadata will be objects but tool_dependencies and - repository_dependencies will be None. - """ - repo_info_dict = {} - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - if app.name == 'tool_shed': - # We're in the tool shed. - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, - app.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) - # Get a dictionary of all repositories upon which the contents of the received repository depends. - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=tool_shed_url, - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None, - circular_repository_dependencies=None ) - tool_dependencies = metadata.get( 'tool_dependencies', {} ) - if tool_dependencies: - new_tool_dependencies = {} - for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key in [ 'set_environment' ]: - new_set_environment_dict_list = [] - for set_environment_dict in requirements_dict: - set_environment_dict[ 'repository_name' ] = repository_name - set_environment_dict[ 'repository_owner' ] = repository_owner - set_environment_dict[ 'changeset_revision' ] = changeset_revision - new_set_environment_dict_list.append( set_environment_dict ) - new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list - else: - requirements_dict[ 'repository_name' ] = repository_name - requirements_dict[ 'repository_owner' ] = repository_owner - requirements_dict[ 'changeset_revision' ] = changeset_revision - new_tool_dependencies[ dependency_key ] = requirements_dict - tool_dependencies = new_tool_dependencies - # Cast unicode to string, with the exception of description, since it is free text and can contain special characters. - repo_info_dict[ str( repository.name ) ] = ( repository.description, - str( repository_clone_url ), - str( changeset_revision ), - str( ctx_rev ), - str( repository_owner ), - repository_dependencies, - tool_dependencies ) - return repo_info_dict - -def get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ): - """ - Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received list of tsr_ids - and whose associated repository must be installed prior to the repository associated with the tsr_id key. - """ - # Initialize the dictionary. - prior_install_required_dict = {} - for tsr_id in tsr_ids: - prior_install_required_dict[ tsr_id ] = [] - # Inspect the repository dependencies for each repository about to be installed and populate the dictionary. - for repo_info_dict in repo_info_dicts: - repository, repository_dependencies = suc.get_repository_and_repository_dependencies_from_repo_info_dict( trans.app, repo_info_dict ) - if repository: - encoded_repository_id = trans.security.encode_id( repository.id ) - if encoded_repository_id in tsr_ids: - # We've located the database table record for one of the repositories we're about to install, so find out if it has any repository - # dependencies that require prior installation. - prior_install_ids = suc.get_repository_ids_requiring_prior_import_or_install( trans.app, tsr_ids, repository_dependencies ) - prior_install_required_dict[ encoded_repository_id ] = prior_install_ids - return prior_install_required_dict - -def get_repo_info_dict( trans, repository_id, changeset_revision ): - repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, - repository_id, - changeset_revision ) - if not repository_metadata: - # The received changeset_revision is no longer installable, so get the next changeset_revision - # in the repository's changelog. This generally occurs only with repositories of type - # repository_suite_definition or tool_dependency_definition. - next_downloadable_changeset_revision = \ - suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision ) - if next_downloadable_changeset_revision: - repository_metadata = \ - suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, next_downloadable_changeset_revision ) - if repository_metadata: - # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption - # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the - # returned repo_info_dict. - metadata = repository_metadata.metadata - if 'tools' in metadata: - includes_tools = True - else: - includes_tools = False - includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel - repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) - repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) - has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ - suc.get_repository_dependency_types( repository_dependencies ) - if 'tool_dependencies' in metadata: - includes_tool_dependencies = True - else: - includes_tool_dependencies = False - else: - # Here's where we may have to handle enhancements to the callers. See above comment. - includes_tools = False - has_repository_dependencies = False - has_repository_dependencies_only_if_compiling_contained_td = False - includes_tool_dependencies = False - includes_tools_for_display_in_tool_panel = False - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) - return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ - has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td - -def get_tool_shed_repository_ids( as_string=False, **kwd ): - tsrid = kwd.get( 'tool_shed_repository_id', None ) - tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) ) - if not tsridslist: - tsridslist = util.listify( kwd.get( 'id', None ) ) - if tsridslist: - if tsrid and tsrid not in tsridslist: - tsridslist.append( tsrid ) - if as_string: - return ','.join( tsridslist ) - return tsridslist - else: - tsridslist = util.listify( kwd.get( 'ordered_tsr_ids', None ) ) - if as_string: - return ','.join( tsridslist ) - return tsridslist - if as_string: - '' - return [] - -def get_update_to_changeset_revision_and_ctx_rev( app, repository ): - """Return the changeset revision hash to which the repository can be updated.""" - changeset_revision_dict = {} - tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) ) - params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), - str( repository.owner ), - str( repository.installed_changeset_revision ) ) - url = common_util.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev%s' % params ) - try: - encoded_update_dict = common_util.tool_shed_get( app, tool_shed_url, url ) - if encoded_update_dict: - update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) - includes_data_managers = update_dict.get( 'includes_data_managers', False ) - includes_datatypes = update_dict.get( 'includes_datatypes', False ) - includes_tools = update_dict.get( 'includes_tools', False ) - includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False ) - includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) - includes_workflows = update_dict.get( 'includes_workflows', False ) - has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) - changeset_revision = update_dict.get( 'changeset_revision', None ) - ctx_rev = update_dict.get( 'ctx_rev', None ) - changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers - changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes - changeset_revision_dict[ 'includes_tools' ] = includes_tools - changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel - changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies - changeset_revision_dict[ 'includes_workflows' ] = includes_workflows - changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies - changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td - changeset_revision_dict[ 'changeset_revision' ] = changeset_revision - changeset_revision_dict[ 'ctx_rev' ] = ctx_rev - except Exception, e: - log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) - changeset_revision_dict[ 'includes_data_managers' ] = False - changeset_revision_dict[ 'includes_datatypes' ] = False - changeset_revision_dict[ 'includes_tools' ] = False - changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False - changeset_revision_dict[ 'includes_tool_dependencies' ] = False - changeset_revision_dict[ 'includes_workflows' ] = False - changeset_revision_dict[ 'has_repository_dependencies' ] = False - changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False - changeset_revision_dict[ 'changeset_revision' ] = None - changeset_revision_dict[ 'ctx_rev' ] = None - return changeset_revision_dict - -def handle_repository_contents( app, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, - tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ): - """ - Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy - (never the tool shed) when an administrator is installing a new repository or reinstalling an uninstalled repository. - """ - install_model = app.install_model - shed_config_dict = app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = \ - metadata_util.generate_metadata_for_changeset_revision( app=app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict - # Update the tool_shed_repository.tool_shed_status column in the database. - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, tool_shed_repository ) - if tool_shed_status_dict: - tool_shed_repository.tool_shed_status = tool_shed_status_dict - install_model.context.add( tool_shed_repository ) - install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: - tool_dependencies = tool_dependency_util.create_tool_dependency_objects( app, - tool_shed_repository, - relative_install_dir, - set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) - tool_data_table_conf_filename, tool_data_table_elems = \ - tool_util.install_tool_data_tables( app, tool_shed_repository, tool_index_sample_files ) - if tool_data_table_elems: - app.tool_data_tables.add_new_entries_from_config_file( tool_data_table_conf_filename, - None, - app.config.shed_tool_data_table_config, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) - tool_util.copy_sample_files( app, tool_index_sample_files, tool_path=tool_path ) - sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = suc.get_repository_tools_tups( app, metadata_dict ) - if repository_tools_tups: - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = tool_util.handle_missing_data_table_entry( app, - relative_install_dir, - tool_path, - repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = \ - tool_util.handle_missing_index_file( app, - tool_path, - sample_files, - repository_tools_tups, - sample_files_copied ) - # Copy remaining sample files included in the repository to the ~/tool-data directory of the - # local Galaxy instance. - tool_util.copy_sample_files( app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - tool_util.add_to_tool_panel( app=app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) - if 'data_manager' in metadata_dict: - new_data_managers = data_manager_util.install_data_managers( app, - app.config.shed_data_manager_config_file, - metadata_dict, - shed_config_dict, - relative_install_dir, - tool_shed_repository, - repository_tools_tups ) - if 'datatypes' in metadata_dict: - tool_shed_repository.status = install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES - if not tool_shed_repository.includes_datatypes: - tool_shed_repository.includes_datatypes = True - install_model.context.add( tool_shed_repository ) - install_model.context.flush() - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) - datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) - # Load data types required by tools. - converter_path, display_path = \ - datatype_util.alter_config_and_load_prorietary_datatypes( app, datatypes_config, files_dir, override=False ) - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = \ - datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - if converter_path: - # Load proprietary datatype converters - app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=repository_dict ) - if display_path: - # Load proprietary datatype display applications - app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - -def handle_tool_shed_repositories( app, installation_dict, using_api=False ): - # The following installation_dict entries are all required. - install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] - new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ] - no_changes_checked = installation_dict[ 'no_changes_checked' ] - repo_info_dicts = installation_dict[ 'repo_info_dicts' ] - tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ] - tool_path = installation_dict[ 'tool_path' ] - tool_shed_url = installation_dict[ 'tool_shed_url' ] - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ - repository_dependency_util.create_repository_dependency_objects( app=app, - tool_path=tool_path, - tool_shed_url=tool_shed_url, - repo_info_dicts=repo_info_dicts, - install_repository_dependencies=install_repository_dependencies, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts - -def update_repository_record( app, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): - """ - Update a tool_shed_repository database record with new information retrieved from the - Tool Shed. This happens when updating an installed repository to a new changeset revision. - """ - repository.metadata = updated_metadata_dict - # Update the repository.changeset_revision column in the database. - repository.changeset_revision = updated_changeset_revision - repository.ctx_rev = updated_ctx_rev - # Update the repository.tool_shed_status column in the database. - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, repository ) - if tool_shed_status_dict: - repository.tool_shed_status = tool_shed_status_dict - else: - repository.tool_shed_status = None - app.install_model.context.add( repository ) - app.install_model.context.flush() - app.install_model.context.refresh( repository ) - return repository diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -111,11 +111,11 @@ created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name, changeset_revision, repository_dependencies_dict ) - # Order the repositories for proper installation. This process is similar to the process used when installing tool - # shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/ - # repository_util), but does not handle managing tool panel sections and other components since repository dependency - # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository - # dependency that contains a tool. + # Order the repositories for proper installation. This process is similar to the + # process used when installing tool shed repositories, but does not handle managing + # tool panel sections and other components since repository dependency definitions + # contained in tool shed repositories with migrated tools must never define a relationship + # to a repository dependency that contains a tool. ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories, repository_dependencies_dict ) @@ -585,11 +585,10 @@ in the list of repositories about to be installed, then they are not considered. Repository dependency definitions that contain circular dependencies should not result in an infinite loop, but obviously prior installation will not be handled for one or more of the repositories that require prior installation. This - process is similar to the process used when installing tool shed repositories (i.e., the - order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not - handle managing tool panel sections and other components since repository dependency definitions contained - in tool shed repositories with migrated tools must never define a relationship to a repository dependency - that contains a tool. + process is similar to the process used when installing tool shed repositories, but does not handle managing + tool panel sections and other components since repository dependency definitions contained in tool shed + repositories with migrated tools must never define a relationship to a repository dependency that contains + a tool. """ ordered_tool_shed_repositories = [] ordered_tsr_ids = [] diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/galaxy_install/update_repository_manager.py --- a/lib/tool_shed/galaxy_install/update_repository_manager.py +++ b/lib/tool_shed/galaxy_install/update_repository_manager.py @@ -4,6 +4,8 @@ import logging import threading import tool_shed.util.shed_util_common as suc +from tool_shed.util import common_util +from tool_shed.util import encoding_util log = logging.getLogger( __name__ ) @@ -20,6 +22,52 @@ self.restarter.start() self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) + def get_update_to_changeset_revision_and_ctx_rev( self, repository ): + """Return the changeset revision hash to which the repository can be updated.""" + changeset_revision_dict = {} + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, str( repository.tool_shed ) ) + params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), + str( repository.owner ), + str( repository.installed_changeset_revision ) ) + url = common_util.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev%s' % params ) + try: + encoded_update_dict = common_util.tool_shed_get( self.app, tool_shed_url, url ) + if encoded_update_dict: + update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) + includes_data_managers = update_dict.get( 'includes_data_managers', False ) + includes_datatypes = update_dict.get( 'includes_datatypes', False ) + includes_tools = update_dict.get( 'includes_tools', False ) + includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) + includes_workflows = update_dict.get( 'includes_workflows', False ) + has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) + has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + changeset_revision = update_dict.get( 'changeset_revision', None ) + ctx_rev = update_dict.get( 'ctx_rev', None ) + changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers + changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes + changeset_revision_dict[ 'includes_tools' ] = includes_tools + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel + changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies + changeset_revision_dict[ 'includes_workflows' ] = includes_workflows + changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td + changeset_revision_dict[ 'changeset_revision' ] = changeset_revision + changeset_revision_dict[ 'ctx_rev' ] = ctx_rev + except Exception, e: + log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) + changeset_revision_dict[ 'includes_data_managers' ] = False + changeset_revision_dict[ 'includes_datatypes' ] = False + changeset_revision_dict[ 'includes_tools' ] = False + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False + changeset_revision_dict[ 'includes_tool_dependencies' ] = False + changeset_revision_dict[ 'includes_workflows' ] = False + changeset_revision_dict[ 'has_repository_dependencies' ] = False + changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False + changeset_revision_dict[ 'changeset_revision' ] = None + changeset_revision_dict[ 'ctx_rev' ] = None + return changeset_revision_dict + def __restarter( self ): log.info( 'Update repository manager restarter starting up...' ) while self.running: @@ -48,6 +96,26 @@ self.running = False self.sleeper.wake() + def update_repository_record( self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): + """ + Update a tool_shed_repository database record with new information retrieved from the + Tool Shed. This happens when updating an installed repository to a new changeset revision. + """ + repository.metadata = updated_metadata_dict + # Update the repository.changeset_revision column in the database. + repository.changeset_revision = updated_changeset_revision + repository.ctx_rev = updated_ctx_rev + # Update the repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository ) + if tool_shed_status_dict: + repository.tool_shed_status = tool_shed_status_dict + else: + repository.tool_shed_status = None + self.app.install_model.context.add( repository ) + self.app.install_model.context.flush() + self.app.install_model.context.refresh( repository ) + return repository + class Sleeper( object ): """ diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 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 @@ -1,12 +1,11 @@ import copy +import json import logging import os import urllib import urllib2 from galaxy import util from galaxy import web -from galaxy.util import json -from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util from tool_shed.util import container_util @@ -15,7 +14,6 @@ from tool_shed.util import datatype_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util -from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -452,7 +450,7 @@ response = urllib2.urlopen( request ).read() if response: try: - required_repo_info_dict = json.from_json_string( response ) + required_repo_info_dict = json.loads( response ) except Exception, e: log.exception( e ) return all_repo_info_dicts diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -1,7 +1,8 @@ +import json import logging import os import urllib2 -from galaxy.util import json +from galaxy import util from galaxy.util.odict import odict from galaxy.web import url_for from tool_shed.util import encoding_util @@ -109,12 +110,12 @@ tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) ) return url_join( tool_shed_url, 'repos', str( repository.owner ), str( repository.name ) ) -def generate_clone_url_for_repository_in_tool_shed( trans, repository ): +def generate_clone_url_for_repository_in_tool_shed( user, repository ): """Generate the URL for cloning a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) - if trans and trans.user: + if user: protocol, base = base_url.split( '://' ) - username = '%s@' % trans.user.username + username = '%s@' % user.username return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) @@ -156,7 +157,7 @@ print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) if tool_shed_accessible: if len( raw_text ) > 2: - encoded_text = json.from_json_string( raw_text ) + encoded_text = json.loads( raw_text ) repository_dependencies_dict = encoding_util.tool_shed_decode( encoded_text ) return tool_shed_accessible, repository_dependencies_dict @@ -194,6 +195,27 @@ tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type ) ) return tool_shed_accessible, tool_dependencies +def get_tool_shed_repository_ids( as_string=False, **kwd ): + tsrid = kwd.get( 'tool_shed_repository_id', None ) + tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) ) + if not tsridslist: + tsridslist = util.listify( kwd.get( 'id', None ) ) + if tsridslist is not None: + if tsrid is not None and tsrid not in tsridslist: + tsridslist.append( tsrid ) + if as_string: + return ','.join( tsridslist ) + return tsridslist + else: + tsridslist = util.listify( kwd.get( 'ordered_tsr_ids', None ) ) + if tsridslist is not None: + if as_string: + return ','.join( tsridslist ) + return tsridslist + if as_string: + '' + return [] + def get_tool_shed_url_from_tool_shed_registry( app, tool_shed ): """ The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -256,7 +256,7 @@ repo_info_dict = {} # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ), + common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ), str( changeset_revision ), str( ctx.rev() ), str( repository.user.username ), diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1776,7 +1776,7 @@ log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. changeset_revisions = [] @@ -1955,7 +1955,7 @@ message = '' status = 'done' encoded_id = trans.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -3,9 +3,12 @@ import os import re import tool_shed.util.shed_util_common as suc +from tool_shed.util import common_util from tool_shed.util import hg_util from tool_shed.util import import_util +from tool_shed.util import repository_dependency_util from galaxy import util +from galaxy import web from galaxy.web.form_builder import build_select_field from galaxy.webapps.tool_shed.model import directory_hash_id @@ -53,6 +56,79 @@ fp.write( 'hgext.purge=' ) fp.close() +def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, + repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): + """ + Return a dictionary that includes all of the information needed to install a repository into a local + Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined + for the repository, as well as the defined tool dependencies. + + This method is called from Galaxy under four scenarios: + 1. During the tool shed repository installation process via the tool shed's get_repository_information() + method. In this case both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 2. When getting updates for an install repository where the updates include newly defined repository + dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() + method is the caller, and both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no + updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies + and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes + definitions for them. + 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates + available. In this case, this method is reached via the tool shed's get_updated_repository_information() + method, and both repository and repository_metadata will be objects but tool_dependencies and + repository_dependencies will be None. + """ + repo_info_dict = {} + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + if app.name == 'tool_shed': + # We're in the tool shed. + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + app.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + # Get a dictionary of all repositories upon which the contents of the received repository depends. + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=tool_shed_url, + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) + tool_dependencies = metadata.get( 'tool_dependencies', {} ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies + # Cast unicode to string, with the exception of description, since it is free text and can contain special characters. + repo_info_dict[ str( repository.name ) ] = ( repository.description, + str( repository_clone_url ), + str( changeset_revision ), + str( ctx_rev ), + str( repository_owner ), + repository_dependencies, + tool_dependencies ) + return repo_info_dict + def create_repository( trans, name, type, description, long_description, user_id, category_ids=[] ): # Add the repository record to the database. repository = trans.app.model.Repository( name=name, @@ -182,6 +258,62 @@ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) return import_results_tups +def get_repo_info_dict( app, user, repository_id, changeset_revision ): + repository = suc.get_repository_in_tool_shed( app, repository_id ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + repository_id, + changeset_revision ) + if not repository_metadata: + # The received changeset_revision is no longer installable, so get the next changeset_revision + # in the repository's changelog. This generally occurs only with repositories of type + # repository_suite_definition or tool_dependency_definition. + next_downloadable_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + if next_downloadable_changeset_revision: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + repository_id, + next_downloadable_changeset_revision ) + if repository_metadata: + # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption + # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the + # returned repo_info_dict. + metadata = repository_metadata.metadata + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True + else: + includes_tool_dependencies = False + else: + # Here's where we may have to handle enhancements to the callers. See above comment. + includes_tools = False + has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False + includes_tool_dependencies = False + includes_tools_for_display_in_tool_panel = False + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) + repo_info_dict = create_repo_info_dict( app=app, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) + return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td + def get_repository_admin_role_name( repository_name, repository_owner ): return '%s_%s_admin' % ( str( repository_name ), str( repository_owner ) ) diff -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb -r 6294a65d863a4875a9e096ca5e81c3f30e8b0bb6 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -216,7 +216,7 @@ <%def name="render_clone_str( repository )"><% from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed - clone_str = generate_clone_url_for_repository_in_tool_shed( trans, repository ) + clone_str = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) %> hg clone <a href="${clone_str}">${clone_str}</a></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager.
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95937a7e51f2/ Changeset: 95937a7e51f2 User: greg Date: 2014-06-17 17:24:33 Summary: For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager. Affected #: 4 files diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -82,10 +82,10 @@ self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): - from tool_shed.galaxy_install import update_manager - self.update_manager = update_manager.UpdateManager( self ) + from tool_shed.galaxy_install import update_repository_manager + self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self ) else: - self.update_manager = None + self.update_repository_manager = None # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications() # Load datatype display applications defined in local datatypes_conf.xml @@ -159,8 +159,8 @@ self.object_store.shutdown() if self.heartbeat: self.heartbeat.shutdown() - if self.update_manager: - self.update_manager.shutdown() + if self.update_repository_manager is not None: + self.update_repository_manager.shutdown() if self.control_worker: self.control_worker.shutdown() try: diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -887,7 +887,7 @@ """Handle a request from a local Galaxy instance.""" message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. + # If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url. galaxy_url = common_util.handle_galaxy_url( trans, **kwd ) name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_manager.py --- a/lib/tool_shed/galaxy_install/update_manager.py +++ /dev/null @@ -1,67 +0,0 @@ -""" -Determine if installed tool shed repositories have updates available in their respective tool sheds. -""" -import logging -import threading -from galaxy.util import string_as_bool -import tool_shed.util.shed_util_common as suc -from tool_shed.util import common_util -from galaxy.model.orm import and_ - -log = logging.getLogger( __name__ ) - - -class UpdateManager( object ): - - def __init__( self, app ): - self.app = app - self.context = self.app.install_model.context - # Ideally only one Galaxy server process should be able to check for repository updates. - self.running = True - self.sleeper = Sleeper() - self.restarter = threading.Thread( target=self.__restarter ) - self.restarter.start() - self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) - - def __restarter( self ): - log.info( 'Update manager restarter starting up...' ) - while self.running: - # Make a call to the tool shed for each installed repository to get the latest status information in the tool shed for the - # repository. This information includes items like newer installable repository revisions, current revision updates, whether - # the repository revision is the latest installable revision, and whether the repository has been deprecated in the tool shed. - for repository in self.context.query( self.app.install_model.ToolShedRepository ) \ - .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ): - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository ) - if tool_shed_status_dict: - if tool_shed_status_dict != repository.tool_shed_status: - repository.tool_shed_status = tool_shed_status_dict - self.context.flush() - else: - # The received tool_shed_status_dict is an empty dictionary, so coerce to None. - tool_shed_status_dict = None - if tool_shed_status_dict != repository.tool_shed_status: - repository.tool_shed_status = tool_shed_status_dict - self.context.flush() - self.sleeper.sleep( self.seconds_to_sleep ) - log.info( 'Update manager restarter shutting down...' ) - - def shutdown( self ): - self.running = False - self.sleeper.wake() - - -class Sleeper( object ): - """Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method is called (from a different thread).""" - - def __init__( self ): - self.condition = threading.Condition() - - def sleep( self, seconds ): - self.condition.acquire() - self.condition.wait( seconds ) - self.condition.release() - - def wake( self ): - self.condition.acquire() - self.condition.notify() - self.condition.release() diff -r fa69b6d3cafdc18e2531cfd015676223f33cee67 -r 95937a7e51f20da0ebf0853f9385286d2c70c4eb lib/tool_shed/galaxy_install/update_repository_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/update_repository_manager.py @@ -0,0 +1,69 @@ +""" +Determine if installed tool shed repositories have updates available in their respective tool sheds. +""" +import logging +import threading +import tool_shed.util.shed_util_common as suc + +log = logging.getLogger( __name__ ) + + +class UpdateRepositoryManager( object ): + + def __init__( self, app ): + self.app = app + self.context = self.app.install_model.context + # Ideally only one Galaxy server process should be able to check for repository updates. + self.running = True + self.sleeper = Sleeper() + self.restarter = threading.Thread( target=self.__restarter ) + self.restarter.start() + self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) + + def __restarter( self ): + log.info( 'Update repository manager restarter starting up...' ) + while self.running: + # Make a call to the Tool Shed for each installed repository to get the latest + # status information in the Tool Shed for the repository. This information includes + # items like newer installable repository revisions, current revision updates, whether + # the repository revision is the latest installable revision, and whether the repository + # has been deprecated in the Tool Shed. + for repository in self.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ): + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository ) + if tool_shed_status_dict: + if tool_shed_status_dict != repository.tool_shed_status: + repository.tool_shed_status = tool_shed_status_dict + self.context.flush() + else: + # The received tool_shed_status_dict is an empty dictionary, so coerce to None. + tool_shed_status_dict = None + if tool_shed_status_dict != repository.tool_shed_status: + repository.tool_shed_status = tool_shed_status_dict + self.context.flush() + self.sleeper.sleep( self.seconds_to_sleep ) + log.info( 'Update repository manager restarter shutting down...' ) + + def shutdown( self ): + self.running = False + self.sleeper.wake() + + +class Sleeper( object ): + """ + Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method + is called (from a different thread). + """ + + def __init__( self ): + self.condition = threading.Condition() + + def sleep( self, seconds ): + self.condition.acquire() + self.condition.wait( seconds ) + self.condition.release() + + def wake( self ): + self.condition.acquire() + self.condition.notify() + self.condition.release() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Instantiate the Tool Shed's various tool dependency recipe classes with app so it doesn't have to be passed to functions.
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fa69b6d3cafd/ Changeset: fa69b6d3cafd User: greg Date: 2014-06-17 17:00:49 Summary: Instantiate the Tool Shed's various tool dependency recipe classes with app so it doesn't have to be passed to functions. Affected #: 7 files diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -58,9 +58,10 @@ actions = actions_dict.get( 'actions', None ) filtered_actions = [] env_file_builder = EnvFileBuilder( install_dir ) - install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir, + install_environment = InstallEnvironment( app=self.app, + tool_shed_repository_install_dir=tool_shed_repository_install_dir, install_dir=install_dir ) - step_manager = StepManager() + step_manager = StepManager( self.app ) if actions: with install_environment.make_tmp_dir() as work_dir: with lcd( work_dir ): @@ -76,8 +77,7 @@ # tool_dependency status in this stage because it should not have been changed based on a # download. tool_dependency, filtered_actions, dir = \ - step_manager.execute_step( app=self.app, - tool_dependency=tool_dependency, + step_manager.execute_step( tool_dependency=tool_dependency, package_name=package_name, actions=actions, action_type=action_type, @@ -102,8 +102,7 @@ with lcd( current_dir ): action_type, action_dict = action_tup tool_dependency, tmp_filtered_actions, tmp_dir = \ - step_manager.execute_step( app=self.app, - tool_dependency=tool_dependency, + step_manager.execute_step( tool_dependency=tool_dependency, package_name=package_name, actions=actions, action_type=action_type, @@ -154,7 +153,7 @@ """ attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] installed_packages = [] - tag_manager = TagManager() + tag_manager = TagManager( self.app ) # Parse the tool_dependencies.xml config. tree, error_message = xml_util.parse_xml( tool_dependencies_config ) if tree is None: @@ -192,8 +191,7 @@ # If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will # handle everything - no additional installation is necessary. tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( self.app, - tool_shed_repository, + tag_manager.process_tag_set( tool_shed_repository, tool_dependency, elem, name, @@ -250,9 +248,9 @@ elems = [ action_elem ] else: elems = [] - step_manager = StepManager() + step_manager = StepManager( self.app ) tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( tool_shed_repository ) - install_environment = InstallEnvironment( tool_shed_repository_install_dir, install_dir ) + install_environment = InstallEnvironment( self.app, tool_shed_repository_install_dir, install_dir ) for action_elem in elems: # Make sure to skip all comments, since they are now included in the XML tree. if action_elem.tag != 'action': @@ -260,8 +258,7 @@ action_dict = {} action_type = action_elem.get( 'type', None ) if action_type is not None: - action_dict = step_manager.prepare_step( app=self.app, - tool_dependency=tool_dependency, + action_dict = step_manager.prepare_step( tool_dependency=tool_dependency, action_type=action_type, action_elem=action_elem, action_dict=action_dict, @@ -287,7 +284,7 @@ Install a tool dependency package defined by the XML element elem. The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. """ - tag_manager = TagManager() + tag_manager = TagManager( self.app ) # The value of package_name should match the value of the "package" type in the tool config's # <requirements> tag set, but it's not required. package_name = elem.get( 'name', None ) @@ -300,8 +297,7 @@ if tool_dependency is not None: for package_elem in elem: tool_dependency, proceed_with_install, actions_elem_tuples = \ - tag_manager.process_tag_set( self.app, - tool_shed_repository, + tag_manager.process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py @@ -17,7 +17,7 @@ return_code = self.file_append( env_entry, env_file, make_executable=make_executable ) self.return_code = self.return_code or return_code return self.return_code - + @staticmethod def create_or_update_env_shell_file( install_dir, env_var_dict ): env_var_action = env_var_dict[ 'action' ] diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py @@ -35,12 +35,13 @@ """Object describing the environment built up as part of the process of building and installing a package.""" - def __init__( self, tool_shed_repository_install_dir, install_dir ): + def __init__( self, app, tool_shed_repository_install_dir, install_dir ): """ The value of the received tool_shed_repository_install_dir is the root installation directory of the repository containing the tool dependency, and the value of the received install_dir is the root installation directory of the tool dependency. """ + self.app = app self.env_shell_file_paths = [] self.install_dir = install_dir self.tool_shed_repository_install_dir = tool_shed_repository_install_dir @@ -122,9 +123,9 @@ log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) ) return env_vars - def handle_command( self, app, tool_dependency, cmd, return_output=False ): + def handle_command( self, tool_dependency, cmd, return_output=False ): """Handle a command and log the results.""" - context = app.install_model.context + context = self.app.install_model.context command = str( cmd ) output = self.handle_complex_command( command ) self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) ) @@ -137,7 +138,7 @@ print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) if output.return_code not in [ 0 ]: - tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency.status = self.app.install_model.ToolDependency.installation_status.ERROR if stderr: tool_dependency.error_message = unicodify( stderr ) elif stdout: diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -9,18 +9,18 @@ class StepManager( object ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.step_handlers_by_type = self.load_step_handlers() def get_step_handler_by_type( self, type ): return self.step_handlers_by_type.get( type, None ) - def execute_step( self, app, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions, + def execute_step( self, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): if actions: step_handler = self.get_step_handler_by_type( action_type ) - tool_dependency, filtered_actions, dir = step_handler.execute_step( app=app, - tool_dependency=tool_dependency, + tool_dependency, filtered_actions, dir = step_handler.execute_step( tool_dependency=tool_dependency, package_name=package_name, actions=actions, action_dict=action_dict, @@ -35,39 +35,38 @@ return tool_dependency, filtered_actions, dir def load_step_handlers( self ): - step_handlers_by_type = dict( assert_directory_executable=step_handler.AssertDirectoryExecutable(), - assert_directory_exists=step_handler.AssertDirectoryExists(), - assert_file_executable=step_handler.AssertFileExecutable(), - assert_file_exists=step_handler.AssertFileExists(), - autoconf=step_handler.Autoconf(), - change_directory=step_handler.ChangeDirectory(), - chmod=step_handler.Chmod(), - download_binary=step_handler.DownloadBinary(), - download_by_url=step_handler.DownloadByUrl(), - download_file=step_handler.DownloadFile(), - make_directory=step_handler.MakeDirectory(), - make_install=step_handler.MakeInstall(), - move_directory_files=step_handler.MoveDirectoryFiles(), - move_file=step_handler.MoveFile(), - set_environment=step_handler.SetEnvironment(), - set_environment_for_install=step_handler.SetEnvironmentForInstall(), - setup_perl_environment=step_handler.SetupPerlEnvironment(), - setup_r_environment=step_handler.SetupREnvironment(), - setup_ruby_environment=step_handler.SetupRubyEnvironment(), - setup_virtualenv=step_handler.SetupVirtualEnv(), - shell_command=step_handler.ShellCommand(), - template_command=step_handler.TemplateCommand() ) + step_handlers_by_type = dict( assert_directory_executable=step_handler.AssertDirectoryExecutable( self.app ), + assert_directory_exists=step_handler.AssertDirectoryExists( self.app ), + assert_file_executable=step_handler.AssertFileExecutable( self.app ), + assert_file_exists=step_handler.AssertFileExists( self.app ), + autoconf=step_handler.Autoconf( self.app ), + change_directory=step_handler.ChangeDirectory( self.app ), + chmod=step_handler.Chmod( self.app ), + download_binary=step_handler.DownloadBinary( self.app ), + download_by_url=step_handler.DownloadByUrl( self.app ), + download_file=step_handler.DownloadFile( self.app ), + make_directory=step_handler.MakeDirectory( self.app ), + make_install=step_handler.MakeInstall( self.app ), + move_directory_files=step_handler.MoveDirectoryFiles( self.app ), + move_file=step_handler.MoveFile( self.app ), + set_environment=step_handler.SetEnvironment( self.app ), + set_environment_for_install=step_handler.SetEnvironmentForInstall( self.app ), + setup_perl_environment=step_handler.SetupPerlEnvironment( self.app ), + setup_r_environment=step_handler.SetupREnvironment( self.app ), + setup_ruby_environment=step_handler.SetupRubyEnvironment( self.app ), + setup_virtualenv=step_handler.SetupVirtualEnv( self.app ), + shell_command=step_handler.ShellCommand( self.app ), + template_command=step_handler.TemplateCommand( self.app ) ) return step_handlers_by_type - def prepare_step( self, app, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download ): """ Prepare the recipe step for later execution. This generally alters the received action_dict with new information needed during this step's execution. """ if action_elem is not None: step_handler = self.get_step_handler_by_type( action_type ) - action_dict = step_handler.prepare_step( app=app, - tool_dependency=tool_dependency, + action_dict = step_handler.prepare_step( tool_dependency=tool_dependency, action_elem=action_elem, action_dict=action_dict, install_environment=install_environment, @@ -76,18 +75,18 @@ class TagManager( object ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag_handlers = self.load_tag_handlers() def get_tag_handler_by_tag( self, tag ): return self.tag_handlers.get( tag, None ) - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): tag_handler = self.get_tag_handler_by_tag( package_elem.tag ) tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_handler.process_tag_set( app, - tool_shed_repository, + tag_handler.process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, @@ -97,10 +96,10 @@ return tool_dependency, proceed_with_install, action_elem_tuples def load_tag_handlers( self ): - tag_handlers = dict( environment_variable=tag_handler.SetEnvironment(), - install=tag_handler.Install(), - package=tag_handler.Package(), - readme=tag_handler.ReadMe(), - repository=tag_handler.Repository(), - set_environment=tag_handler.SetEnvironment() ) + tag_handlers = dict( environment_variable=tag_handler.SetEnvironment( self.app ), + install=tag_handler.Install( self.app ), + package=tag_handler.Package( self.app ), + readme=tag_handler.ReadMe( self.app ), + repository=tag_handler.Repository( self.app ), + set_environment=tag_handler.SetEnvironment( self.app ) ) return tag_handlers diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 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 @@ -180,17 +180,18 @@ class RecipeStep( object ): """Abstract class that defines a standard format for handling recipe steps when installing packages.""" - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): raise "Unimplemented Method" - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): raise "Unimplemented Method" class AssertDirectoryExecutable( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'assert_directory_executable' def assert_directory_executable( self, full_path ): @@ -209,7 +210,7 @@ return True return False - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Make sure a symbolic link or directory on disk exists and is executable, but is not a file. @@ -221,16 +222,16 @@ else: full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) if not self.assert_directory_executable( full_path=full_path ): - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a directory or is not executable by the owner.' % str( full_path ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency, status=status, error_message=error_message, remove_from_disk=False ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action> if action_elem.text: action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -239,7 +240,8 @@ class AssertDirectoryExists( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'assert_directory_exists' def assert_directory_exists( self, full_path ): @@ -254,7 +256,7 @@ return True return False - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Make sure a a symbolic link or directory on disk exists, but is not a file. Since this @@ -266,16 +268,16 @@ else: full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) if not self.assert_directory_exists( full_path=full_path ): - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a directory or does not exist.' % str( full_path ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency, status=status, error_message=error_message, remove_from_disk=False ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="make_directory">$INSTALL_DIR/mira</action> if action_elem.text: action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -284,7 +286,8 @@ class AssertFileExecutable( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'assert_file_executable' def assert_file_executable( self, full_path ): @@ -303,7 +306,7 @@ return True return False - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Make sure a symbolic link or file on disk exists and is executable, but is not a directory. @@ -315,16 +318,16 @@ else: full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) if not self.assert_file_executable( full_path=full_path ): - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a file or is not executable by the owner.' % str( full_path ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency, status=status, error_message=error_message, remove_from_disk=False ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action> if action_elem.text: action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -333,7 +336,8 @@ class AssertFileExists( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'assert_file_exists' def assert_file_exists( self, full_path ): @@ -349,7 +353,7 @@ return True return False - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Make sure a symbolic link or file on disk exists, but is not a directory. Since this @@ -361,16 +365,16 @@ else: full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) if not self.assert_file_exists( full_path=full_path ): - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a file or does not exist.' % str( full_path ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency, status=status, error_message=error_message, remove_from_disk=False ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="assert_on_path">$INSTALL_DIR/mira/my_file</action> if action_elem.text: action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -379,10 +383,11 @@ class Autoconf( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'autoconf' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Handle configure, make and make install in a shell, allowing for configuration options. Since this @@ -396,15 +401,14 @@ else: pre_cmd = './configure --prefix=$INSTALL_DIR %s && make && make install' % configure_opts cmd = install_environment.build_command( basic_util.evaluate_template( pre_cmd, install_environment ) ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) # The caller should check the status of the returned tool_dependency since this function # does nothing with the return_code. return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # Handle configure, make and make install allow providing configuration options if action_elem.text: configure_opts = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -414,10 +418,11 @@ class ChangeDirectory( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'change_directory' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Change the working directory in a shell. Since this class is not used in the initial download stage, @@ -436,7 +441,7 @@ dir = current_dir return tool_dependency, None, dir - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="change_directory">PHYLIP-3.6b</action> if action_elem.text: action_dict[ 'directory' ] = action_elem.text @@ -445,10 +450,11 @@ class Chmod( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'chmod' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Change the mode setting for certain files in the installation environment. Since this class is not @@ -462,7 +468,7 @@ log.debug( 'Invalid file %s specified, ignoring %s action.', target_file, action_type ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # Change the read, write, and execute bits on a file. # <action type="chmod"> # <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file> @@ -492,7 +498,8 @@ class DownloadBinary( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'download_binary' def download_binary( self, url, work_dir ): @@ -510,7 +517,7 @@ filtered_actions.append( action ) return filtered_actions - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Download a binary file. If the value of initial_download is True, the recipe steps will be @@ -561,7 +568,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): platform_info_dict = tool_dependency_util.get_platform_info_dict() platform_info_dict[ 'name' ] = str( tool_dependency.name ) platform_info_dict[ 'version' ] = str( tool_dependency.version ) @@ -584,10 +591,11 @@ class DownloadByUrl( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'download_by_url' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Download a file via HTTP. If the value of initial_download is True, the recipe steps will be @@ -622,7 +630,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="download_by_url"> # http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1… # </action> @@ -638,10 +646,11 @@ class DownloadFile( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'download_file' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Download a file. If the value of initial_download is True, the recipe steps will be @@ -667,7 +676,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> if action_elem.text: action_dict[ 'url' ] = action_elem.text @@ -680,10 +689,11 @@ class MakeDirectory( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'make_directory' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Make a directory on disk. Since this class is not used in the initial download stage, no recipe step @@ -700,7 +710,7 @@ if not os.path.exists( full_path ): os.makedirs( full_path ) - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: action_dict[ 'full_path' ] = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -709,10 +719,11 @@ class MakeInstall( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'make_install' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Execute a make_install command in a shell. Since this class is not used in the initial download stage, @@ -722,15 +733,14 @@ with settings( warn_only=True ): make_opts = action_dict.get( 'make_opts', '' ) cmd = install_environment.build_command( 'make %s && make install' % make_opts ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) # The caller should check the status of the returned tool_dependency since this function # does nothing with the return_code. return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # make; make install; allow providing make options if action_elem.text: make_opts = basic_util.evaluate_template( action_elem.text, install_environment ) @@ -740,10 +750,11 @@ class MoveDirectoryFiles( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'move_directory_files' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Move a directory of files. Since this class is not used in the initial download stage, no recipe step @@ -774,7 +785,7 @@ for source_file, destination_file in regular_files: shutil.move( source_file, destination_file ) - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="move_directory_files"> # <source_directory>bin</source_directory> # <destination_directory>$INSTALL_DIR/bin</destination_directory> @@ -788,10 +799,11 @@ class MoveFile( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'move_file' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Move a file on disk. Since this class is not used in the initial download stage, no recipe step @@ -803,7 +815,7 @@ rename_to=action_dict[ 'rename_to' ] ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="move_file" rename_to="new_file_name"> # <source>misc/some_file</source> # <destination>$INSTALL_DIR/bin</destination> @@ -816,10 +828,11 @@ class SetEnvironment( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'set_environment' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Configure an install environment. Since this class is not used in the initial download stage, @@ -831,8 +844,7 @@ env_var_dicts = action_dict.get( 'environment_variable', [] ) for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = self.handle_environment_variables( app=app, - install_environment=install_environment, + env_var_dict = self.handle_environment_variables( install_environment=install_environment, tool_dependency=tool_dependency, env_var_dict=env_var_dict, set_prior_environment_commands=cmds ) @@ -842,7 +854,7 @@ return_code = env_file_builder.return_code return tool_dependency, None, None - def handle_environment_variables( self, app, install_environment, tool_dependency, env_var_dict, + def handle_environment_variables( self, install_environment, tool_dependency, env_var_dict, set_prior_environment_commands ): """ This method works with with a combination of three tool dependency definition tag sets, which are defined @@ -925,8 +937,7 @@ set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - command_return = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + command_return = install_environment.handle_command( tool_dependency=tool_dependency, cmd=command, return_output=True ) # And extract anything labeled with the name of the environment variable we're populating here. @@ -944,7 +955,7 @@ env_var_dict[ 'value' ] = env_var_value return env_var_dict - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # This function is only called for set environment actions as defined above, not within a <set_environment> tool # dependency type. Here is an example of the tag set this function does handle: # <action type="set_environment"> @@ -955,7 +966,7 @@ # <action type="set_environment"> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> # </action> - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': @@ -971,10 +982,11 @@ class SetEnvironmentForInstall( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'set_environment_for_install' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Configure an environment for compiling a package. Since this class is not used in the initial @@ -989,7 +1001,7 @@ install_environment.add_env_shell_file_paths( env_shell_file_paths ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="set_environment_for_install"> # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> # <package name="numpy" version="1.7.1" /> @@ -1002,7 +1014,7 @@ # the current tool dependency package. See the package_matplotlib_1_2 repository in the test tool # shed for a real-world example. all_env_shell_file_paths = [] - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) for env_elem in action_elem: if env_elem.tag == 'repository': env_shell_file_paths = env_manager.get_env_shell_file_paths( env_elem ) @@ -1014,10 +1026,11 @@ class SetupPerlEnvironment( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'setup_purl_environment' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Initialize the environment for installing Perl packages. The class is called during the initial @@ -1076,8 +1089,7 @@ return tool_dependency, None, None with lcd( tmp_work_dir ): cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) if return_code: @@ -1089,8 +1101,7 @@ # cpanm should be installed with the parent perl distribution, otherwise this will not work. cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( perl_package ) cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) if return_code: @@ -1115,7 +1126,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # setup a Perl environment. # <action type="setup_perl_environment"> # <repository name="package_perl_5_18" owner="bgruening"> @@ -1129,7 +1140,7 @@ # with each repository. This will potentially update the value of the 'env_shell_file_paths' entry # in action_dict. all_env_shell_file_paths = [] - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, action_elem, action_dict ) @@ -1149,10 +1160,11 @@ class SetupREnvironment( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'setup_r_environment' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Initialize the environment for installing R packages. The class is called during the initial @@ -1198,8 +1210,7 @@ Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % \ ( str( tarball_name ) ) cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) if return_code: @@ -1219,7 +1230,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # setup an R environment. # <action type="setup_r_environment"> # <repository name="package_r_3_0_1" owner="bgruening"> @@ -1232,7 +1243,7 @@ # associated with each repository. This will potentially update the value of the # 'env_shell_file_paths' entry in action_dict. all_env_shell_file_paths = [] - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, action_elem, action_dict ) @@ -1247,10 +1258,11 @@ class SetupRubyEnvironment( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'setup_ruby_environment' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Initialize the environment for installing Ruby packages. The class is called during the initial @@ -1313,8 +1325,7 @@ cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s''' % ( gem ) cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) if return_code: @@ -1338,7 +1349,7 @@ return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # setup a Ruby environment. # <action type="setup_ruby_environment"> # <repository name="package_ruby_2_0" owner="bgruening"> @@ -1353,7 +1364,7 @@ # associated with each repository. This will potentially update the value of the # 'env_shell_file_paths' entry in action_dict. all_env_shell_file_paths = [] - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, action_elem, action_dict ) @@ -1381,10 +1392,11 @@ class SetupVirtualEnv( Download, RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'setup_virtualenv' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Initialize a virtual environment for installing packages. If initial_download is True, the recipe @@ -1395,8 +1407,8 @@ # This class is not currently used during stage 1 of the installation process, so filter_actions # are not affected, and dir is not set. Enhancements can easily be made to this function if this # class is needed in stage 1. - venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) - if not self.install_virtualenv( app, install_environment, venv_src_directory ): + venv_src_directory = os.path.abspath( os.path.join( self.app.config.tool_dependency_dir, '__virtualenv_src' ) ) + if not self.install_virtualenv( install_environment, venv_src_directory ): log.debug( 'Unable to install virtualenv' ) return tool_dependency, None, None requirements = action_dict[ 'requirements' ] @@ -1438,8 +1450,7 @@ 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=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=full_setup_command, return_output=False ) if return_code: @@ -1448,7 +1459,7 @@ return tool_dependency, None, None site_packages_directory, site_packages_directory_list = \ self.__get_site_packages_directory( install_environment, - app, + self.app, tool_dependency, python_cmd, venv_directory ) @@ -1462,7 +1473,7 @@ return_code = env_file_builder.return_code return tool_dependency, None, None - def install_virtualenv( self, app, install_environment, venv_dir ): + def install_virtualenv( self, install_environment, venv_dir ): if not os.path.exists( venv_dir ): with install_environment.make_tmp_dir() as work_dir: downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1] @@ -1476,7 +1487,7 @@ shutil.move( full_path_to_dir, venv_dir ) return True - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="setup_virtualenv" /> ## Install requirements from file requirements.txt of downloaded bundle - or - # <action type="setup_virtualenv">tools/requirements.txt</action> @@ -1511,8 +1522,7 @@ 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=app, - tool_dependency=tool_dependency, + output = install_environment.handle_command( tool_dependency=tool_dependency, cmd=site_packages_command, return_output=True ) site_packages_directory_list.append( output.stdout ) @@ -1522,10 +1532,11 @@ class ShellCommand( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'shell_command' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Execute a command in a shell. If the value of initial_download is True, the recipe steps will @@ -1546,15 +1557,14 @@ with settings( warn_only=True ): # The caller should check the status of the returned tool_dependency since this function # does nothing with return_code. - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) if initial_download: return tool_dependency, filtered_actions, dir return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # <action type="shell_command">make</action> action_elem_text = basic_util.evaluate_template( action_elem.text, install_environment ) if action_elem_text: @@ -1564,10 +1574,11 @@ class TemplateCommand( RecipeStep ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.type = 'template_command' - def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False ): """ Execute a template command in a shell. If the value of initial_download is True, the recipe steps @@ -1586,13 +1597,12 @@ cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars ) # The caller should check the status of the returned tool_dependency since this function # does nothing with return_code. - return_code = install_environment.handle_command( app=app, - tool_dependency=tool_dependency, + return_code = install_environment.handle_command( tool_dependency=tool_dependency, cmd=cmd, return_output=False ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): # Default to Cheetah as it's the first template language supported. language = action_elem.get( 'language', 'cheetah' ).lower() if language == 'cheetah': diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -20,24 +20,25 @@ class RecipeTag( object ): """Abstract class that defines a standard format for handling recipe tags when installing packages.""" - def process_tag_set( app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): raise "Unimplemented Method" class Install( RecipeTag ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag = 'install' - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): # <install version="1.0"> # Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository. actions_elem_tuples = [] proceed_with_install = False install_dir = \ - tool_dependency_util.get_tool_dependency_install_dir( app=app, + tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, repository_changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -57,7 +58,7 @@ else: # Notice that we'll throw away the following tool_dependency if it can be installed. tool_dependency, proceed_with_install = \ - tool_dependency_util.sync_database_with_file_system( app, + tool_dependency_util.sync_database_with_file_system( self.app, tool_shed_repository, package_name, package_version, @@ -71,9 +72,9 @@ proceed_with_install = True if proceed_with_install: package_install_version = package_elem.get( 'version', '1.0' ) - status = app.install_model.ToolDependency.installation_status.INSTALLING + status = self.app.install_model.ToolDependency.installation_status.INSTALLING tool_dependency = \ - tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_dependency_util.create_or_update_tool_dependency( app=self.app, tool_shed_repository=tool_shed_repository, name=package_name, version=package_version, @@ -95,7 +96,7 @@ error_message += 'tag set.' # Since there was an installation error, update the tool dependency status to Error. # The remove_installation_path option must be left False here. - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) @@ -106,29 +107,30 @@ class Package( RecipeTag ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag = 'package' - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): action_elem_tuples = [] proceed_with_install = False # Only install the tool_dependency if it is not already installed and it is associated with a database # record in the received tool_dependencies. if package_name and package_version: - dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies() + dependencies_ignored = not self.app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: attr_tups_of_dependencies_for_install = [] log.debug( "Skipping installation of tool dependency package %s because tool shed dependency resolver not enabled." % \ str( package_name ) ) # Tool dependency resolves have been configured and they do not include the tool shed. Do not install package. - if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY: + if self.app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY: ## TODO: Do something here such as marking it installed or configured externally. pass tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.ERROR, + status=self.app.install_model.ToolDependency.installation_status.ERROR, error_message=None, remove_from_disk=False ) else: @@ -142,10 +144,11 @@ class ReadMe( RecipeTag ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag = 'readme' - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): # Nothing to be done. action_elem_tuples = [] @@ -155,12 +158,13 @@ class Repository( RecipeTag ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag = 'repository' - def create_temporary_tool_dependencies_config( self, app, tool_shed_url, name, owner, changeset_revision ): + def create_temporary_tool_dependencies_config( self, tool_shed_url, name, owner, changeset_revision ): """Make a call to the tool shed to get the required repository's tool_dependencies.xml file.""" - tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url ) + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed_url ) if tool_shed_url is None or name is None or owner is None or changeset_revision is None: message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the " message += "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \ @@ -169,7 +173,7 @@ params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) url = common_util.url_join( tool_shed_url, 'repository/get_tool_dependencies_config_contents%s' % params ) - text = common_util.tool_shed_get( app, tool_shed_url, url ) + text = common_util.tool_shed_get( self.app, tool_shed_url, url ) if text: # Write the contents to a temporary file on disk so it can be reloaded and parsed. fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-cttdc" ) @@ -185,7 +189,7 @@ raise Exception( message ) return None - def create_tool_dependency_with_initialized_env_sh_file( self, app, dependent_install_dir, tool_shed_repository, + def create_tool_dependency_with_initialized_env_sh_file( self, dependent_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): """ Create or get a tool_dependency record that is defined by the received package_name and package_version. @@ -215,7 +219,7 @@ # Check the database to see if we have a record for the required tool dependency (we may not which is ok). If we # find a record, we need to see if it is in an error state and if so handle it appropriately. required_tool_dependency = \ - tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + tool_dependency_util.get_tool_dependency_by_name_version_type_repository( self.app, required_repository, required_td_package_name, required_td_package_version, @@ -223,29 +227,29 @@ if required_td_package_name == package_name and required_td_package_version == package_version: # Get or create a database tool_dependency record with which the installed package on disk will be associated. tool_dependency = \ - tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_dependency_util.create_or_update_tool_dependency( app=self.app, tool_shed_repository=tool_shed_repository, name=package_name, version=package_version, type='package', - status=app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + status=self.app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, set_status=True ) # Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in # the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh # file currently exists.. required_tool_dependency_env_file_path = \ - tool_dependency_util.get_required_repository_package_env_sh_path( app, + tool_dependency_util.get_required_repository_package_env_sh_path( self.app, package_name, package_version, required_repository ) - env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( app ) ) + env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( self.app ) ) env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: error_message = 'Error defining env.sh file for package %s, return_code: %s' % \ ( str( package_name ), str( return_code ) ) tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) @@ -253,47 +257,47 @@ error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \ ( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) ) tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) else: tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.INSTALLED ) + status=self.app.install_model.ToolDependency.installation_status.INSTALLED ) tool_dependencies.append( tool_dependency ) return tool_dependencies - def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, app, tool_shed_url, name, owner, changeset_revision ): - sa_session = app.install_model.context + def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, tool_shed_url, name, owner, changeset_revision ): + sa_session = self.app.install_model.context # The protocol is not stored, but the port is if it exists. tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) - tool_shed_repository = sa_session.query( app.install_model.ToolShedRepository ) \ - .filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, - app.install_model.ToolShedRepository.table.c.name == name, - app.install_model.ToolShedRepository.table.c.owner == owner, - app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \ + .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, + self.app.install_model.ToolShedRepository.table.c.name == name, + self.app.install_model.ToolShedRepository.table.c.owner == owner, + self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() if tool_shed_repository: return tool_shed_repository # The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file, # so call the tool shed to get all appropriate newer changeset revisions. - text = suc.get_updated_changeset_revisions_from_tool_shed( app, tool_shed_url, name, owner, changeset_revision ) + text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, tool_shed_url, name, owner, changeset_revision ) if text: changeset_revisions = listify( text ) for changeset_revision in changeset_revisions: - tool_shed_repository = sa_session.query( app.install_model.ToolShedRepository ) \ - .filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, - app.install_model.ToolShedRepository.table.c.name == name, - app.install_model.ToolShedRepository.table.c.owner == owner, - app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \ + .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, + self.app.install_model.ToolShedRepository.table.c.name == name, + self.app.install_model.ToolShedRepository.table.c.owner == owner, + self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() if tool_shed_repository: return tool_shed_repository return None - def handle_complex_repository_dependency_for_package( self, app, elem, package_name, package_version, tool_shed_repository, + def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository, from_tool_migration_manager=False ): """ Inspect the repository defined by a complex repository dependency definition and take certain steps to @@ -310,8 +314,7 @@ required_repository_owner = elem.attrib[ 'owner' ] default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ] required_repository = \ - self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, - tool_shed, + self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( tool_shed, required_repository_name, required_repository_owner, default_required_repository_changeset_revision ) @@ -320,7 +323,7 @@ required_repository_changeset_revision = required_repository.installed_changeset_revision # Define the installation directory for the required tool dependency package in the required repository. required_repository_package_install_dir = \ - tool_dependency_util.get_tool_dependency_install_dir( app=app, + tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=required_repository_name, repository_owner=required_repository_owner, repository_changeset_revision=required_repository_changeset_revision, @@ -330,7 +333,7 @@ # Define this dependent repository's tool dependency installation directory that will contain # the env.sh file with a path to the required repository's installed tool dependency package. dependent_install_dir = \ - tool_dependency_util.get_tool_dependency_install_dir( app=app, + tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, repository_changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -350,7 +353,7 @@ else: # Notice that we'll throw away the following tool_dependency if it can be installed. tool_dependency, can_install_tool_dependency = \ - tool_dependency_util.sync_database_with_file_system( app, + tool_dependency_util.sync_database_with_file_system( self.app, tool_shed_repository, package_name, package_version, @@ -370,7 +373,7 @@ if required_repository.is_deactivated_or_installed: if not os.path.exists( required_repository_package_install_dir ): print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) - repo_files_dir = required_repository.repo_files_directory( app ) + repo_files_dir = required_repository.repo_files_directory( self.app ) tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) if tool_dependencies_config: config_to_use = tool_dependencies_config @@ -381,7 +384,7 @@ else: # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision # should be updated if it's not current. - text = suc.get_updated_changeset_revisions_from_tool_shed( app=app, + text = suc.get_updated_changeset_revisions_from_tool_shed( app=self.app, tool_shed_url=tool_shed, name=required_repository_name, owner=required_repository_owner, @@ -391,15 +394,13 @@ # The list of changeset revisions is in reverse order, so the newest will be first. required_repository_changeset_revision = updated_changeset_revisions[ 0 ] # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. - tmp_filename = self.create_temporary_tool_dependencies_config( app, - tool_shed, + tmp_filename = self.create_temporary_tool_dependencies_config( tool_shed, required_repository_name, required_repository_owner, required_repository_changeset_revision ) config_to_use = tmp_filename handled_tool_dependencies = \ - self.create_tool_dependency_with_initialized_env_sh_file( app=app, - dependent_install_dir=dependent_install_dir, + self.create_tool_dependency_with_initialized_env_sh_file( dependent_install_dir=dependent_install_dir, tool_shed_repository=tool_shed_repository, required_repository=required_repository, package_name=package_name, @@ -412,19 +413,18 @@ raise Exception( message ) return handled_tool_dependencies - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): # We have a complex repository dependency definition. action_elem_tuples = [] proceed_with_install = False - rd_tool_dependencies = self.handle_complex_repository_dependency_for_package( app, - package_elem, + rd_tool_dependencies = self.handle_complex_repository_dependency_for_package( package_elem, package_name, package_version, tool_shed_repository, from_tool_migration_manager=from_tool_migration_manager ) for rd_tool_dependency in rd_tool_dependencies: - if rd_tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR: + if rd_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: # We'll log the error here, but continue installing packages since some may not require this dependency. print "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message ) return tool_dependency, proceed_with_install, action_elem_tuples @@ -441,10 +441,11 @@ class SetEnvironment( RecipeTag ): - def __init__( self ): + def __init__( self, app ): + self.app = app self.tag = 'set_environment' - def process_tag_set( self, app, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): # We need to handle two tag sets for package_elem here, this: # <set_environment version="1.0"> @@ -459,21 +460,21 @@ else: attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependency_db_records ] try: - tool_dependencies = self.set_environment( app, package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) + tool_dependencies = self.set_environment( package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) except Exception, e: error_message = "Error setting environment for tool dependency: %s" % str( e ) log.debug( error_message ) for tool_dependency in tool_dependencies: - if tool_dependency and tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR: + if tool_dependency and tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: # Since there was an installation error, update the tool dependency status to Error. The # remove_installation_path option must be left False here. - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) return tool_dependency, proceed_with_install, action_elem_tuples - def set_environment( self, app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): + def set_environment( self, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): """ Create a ToolDependency to set an environment variable. This is different from the process used to set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml @@ -497,10 +498,10 @@ # <set_environment version="1.0"> # <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" /> # </set_environment> - env_manager = EnvManager( app ) + env_manager = EnvManager( self.app ) tool_dependencies = [] env_var_version = elem.get( 'version', '1.0' ) - tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( app ) ) + tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( self.app ) ) if elem.tag == 'environment_variable': # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> elems = [ elem ] @@ -520,23 +521,24 @@ attr_tup = ( env_var_name, None, 'set_environment' ) if attr_tup in attr_tups_of_dependencies_for_install: install_dir = \ - tool_dependency_util.get_tool_dependency_install_dir( app=app, + tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, repository_changeset_revision=tool_shed_repository.installed_changeset_revision, tool_dependency_type='set_environment', tool_dependency_name=env_var_name, tool_dependency_version=None ) - install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir, + install_environment = InstallEnvironment( app=self.app, + tool_shed_repository_install_dir=tool_shed_repository_install_dir, install_dir=install_dir ) env_var_dict = env_manager.create_env_var_dict( elem=env_var_elem, install_environment=install_environment ) if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) - status = app.install_model.ToolDependency.installation_status.INSTALLING + status = self.app.install_model.ToolDependency.installation_status.INSTALLING tool_dependency = \ - tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_dependency_util.create_or_update_tool_dependency( app=self.app, tool_shed_repository=tool_shed_repository, name=env_var_name, version=None, @@ -551,19 +553,19 @@ error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ ( str( tool_dependency.name ), str( return_code ) ) log.debug( error_message ) - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, status=status, error_message=error_message, remove_from_disk=False ) else: - if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR, - app.install_model.ToolDependency.installation_status.INSTALLED ]: - status = app.install_model.ToolDependency.installation_status.INSTALLED + if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR, + self.app.install_model.ToolDependency.installation_status.INSTALLED ]: + status = self.app.install_model.ToolDependency.installation_status.INSTALLED tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, status=status, error_message=None, @@ -572,9 +574,9 @@ ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) else: error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' - status = app.install_model.ToolDependency.installation_status.ERROR + status = self.app.install_model.ToolDependency.installation_status.ERROR tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, status=status, error_message=error_message, diff -r ac9a4a915fdef0fb425e7146637d551066844af7 -r fa69b6d3cafdc18e2531cfd015676223f33cee67 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 @@ -17,8 +17,6 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager - log = logging.getLogger( __name__ ) def activate_repository( app, repository ): 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: Minor fixes, hide tooltip, patch nvd3 library
by commits-noreply＠bitbucket.org 17 Jun '14

17 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac9a4a915fde/ Changeset: ac9a4a915fde User: guerler Date: 2014-06-17 14:36:47 Summary: Charts: Minor fixes, hide tooltip, patch nvd3 library Affected #: 5 files diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var 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options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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i=n.pos[0]+(r.offsetLeft||0),o=n.pos[1]+(r.offsetTop||0),f=s.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?u:a).tickFormat()(t.y()(n.point,n.pointIndex)),c=N(n.series.key,f,l,n,B);e.tooltip.show([i,o],c,n.value<0?"n":"s",null,r)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),r.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),r.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),D.on("tooltipHide",function(){T&&e.tooltip.cleanup()}),B.dispatch=D,B.legend=c,B.lines=t,B.lines2=n,B.bars=r,B.bars2=i,B.xAxis=s,B.x2Axis=o,B.y1Axis=u,B.y2Axis=a,B.y3Axis=f,B.y4Axis=l,d3.rebind(B,t,"defined","size","clipVoronoi","interpolate"),B.options=e.utils.optionsFunc.bind(B),B.x=function(e){return arguments.length?(y=e,t.x(e),r.x(e),B):y},B.y=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,o=$("<svg/>");o.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var u="",a=0;t.find("svg").each(function(){var e=$(this),t=$('<g transform="translate('+a+', 0)">');t.append(e.clone().find("g").first()),o.append(t),a+=i});var u=s.serializeToString(o[0]);window.location.href="data:none/none;base64,"+btoa(u)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}return{createPNG:t,createSVG:s}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG or SVG file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file-o",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{jqplot_bar:p,nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,jqplot_line:d,jqplot_scatter:v,jqplot_boxplot:m,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -21,15 +21,6 @@ $.extend(true, plot_config, { seriesDefaults: { renderer : $.jqplot.BarRenderer - }, - axes: { - xaxis: { - pad : 1.2 - }, - - yaxis: { - pad : 1.2 - } } }); } diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -11,27 +11,13 @@ seriesColors: d3.scale.category20().range(), seriesDefaults: { renderer : $.jqplot.LineRenderer, - //lineWidth : 1, // Width of the line in pixels. + //lineWidth : 1, // width of the line in pixels. shadow : false, // show shadow or not. showLine : true, // whether to render the line segments or not. - - // Show point labels to the right ('e'ast) of each bar. - // edgeTolerance of -15 allows labels flow outside the grid - // up to 15 pixels. If they flow out more than that, they - // will be hidden. - //pointLabels : { show: true, location: 'e', edgeTolerance: -15 }, - // Rotate the bar shadow as if bar is lit from top right. - //shadowAngle : 135, - // Here's where we tell the chart it is oriented horizontally. rendererOptions: { shadowDepth : 0, //barDirection : 'horizontal', - //barPadding : 5, - //barMargin : 2, - //barWidth : Math.max(0.5 / chart.groups.length, 2), - barWidth : 10, - //fillToZero : true, - //stackedValue : true + barWidth : 1 }, markerRenderer : $.jqplot.MarkerRenderer, markerOptions: { @@ -43,9 +29,9 @@ shadow : false, // wether to draw shadow on marker or not. shadowAngle : 45, // angle of the shadow. Clockwise from x axis. shadowOffset : 1, // offset from the line of the shadow, - shadowDepth : 3, // Number of strokes to make when drawing shadow. Each stroke + shadowDepth : 3, // number of strokes to make when drawing shadow. Each stroke // offset by shadowOffset from the last. - shadowAlpha : 0.07 // Opacity of the shadow + shadowAlpha : 0.07 // opacity of the shadow } }, @@ -104,7 +90,7 @@ series: [] }; - // Show the legend and put it outside the grid + // show the legend and put it outside the grid if (chart.settings.get('show_legend') == 'true') { plot_config.legend = { renderer : $.jqplot.EnhancedLegendRenderer, diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -65,7 +65,7 @@ this._makeTickFormat('y'); // add tooltip - this.tooltip = d3.select('.charts-viewport').append('div') + this.tooltip = d3.select('.charts-viewport-container').append('div') .attr('class', 'charts-tooltip') .style(this.options.style) .style('opacity', 0); @@ -210,12 +210,16 @@ self.tooltip.style('opacity', 0.9); self.tooltip .html(self._templateTooltip(d)) .style('left', (d3.event.pageX) + 'px') - .style('top', (d3.event.pageY - 28) + 'px'); + .style('top', (d3.event.pageY - 20) + 'px'); }) .on('mouseout', function(d) { self.tooltip.style('opacity', 0); }); + // initially hide tooltips + this.tooltip.style('opacity', 0); + + // exit boxes.exit().remove(); }, diff -r 45df9d2018e1c452478549b933476937595bf6a4 -r ac9a4a915fdef0fb425e7146637d551066844af7 config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js --- a/config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js +++ b/config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js @@ -11104,10 +11104,10 @@ var pX = getX(point,pointIndex); var pY = getY(point,pointIndex); - return [x(pX)+ Math.random() * 1e-7, - y(pY)+ Math.random() * 1e-7, + return [x(pX), + y(pY), groupIndex, - pointIndex, point]; //temp hack to add noise untill I think of a better way so there are no duplicates + pointIndex, point]; }) .filter(function(pointArray, pointIndex) { return pointActive(pointArray[4], pointIndex); // Issue #237.. move filter to after map, so pointIndex is correct! @@ -11158,6 +11158,18 @@ [width + 10,-10] ]); + // delete duplicates from vertices - essential assumption for d3.geom.voronoi + var epsilon = 1e-6; // d3 uses 1e-6 to determine equivalence. + vertices = vertices.sort(function(a,b){return ((a[0] - b[0]) || (a[1] - b[1]))}); + for (var i = 0; i < vertices.length - 1; ) { + if ((Math.abs(vertices[i][0] - vertices[i+1][0]) < epsilon) && + (Math.abs(vertices[i][1] - vertices[i+1][1]) < epsilon)) { + vertices.splice(i+1, 1); + } else { + i++; + } + } + var voronoi = d3.geom.voronoi(vertices).map(function(d, i) { return { 'data': bounds.clip(d), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Update LWR client and synchronized modules through LWR changeset 148132f.
by commits-noreply＠bitbucket.org 16 Jun '14

16 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45df9d2018e1/ Changeset: 45df9d2018e1 User: jmchilton Date: 2014-06-17 06:14:59 Summary: Update LWR client and synchronized modules through LWR changeset 148132f. Mostly style fixes but also adds ability to configure LWR file staging actions with YAML instead of JSON. Affected #: 6 files diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -11,6 +11,7 @@ from re import escape import galaxy.util from galaxy.util.bunch import Bunch +from .config_util import read_file from .util import directory_files from .util import unique_path_prefix from .transport import get_file @@ -160,7 +161,7 @@ def __client_to_config(self, client): action_config_path = client.action_config_path if action_config_path: - config = load(open(action_config_path, 'rb')) + config = read_file(action_config_path) else: config = dict() config["default_action"] = client.default_file_action @@ -434,7 +435,7 @@ elif value is REQUIRED_ACTION_KWD: message_template = "action_type %s requires key word argument %s" message = message_template % (action_type, key) - raise Exception( message ) + raise Exception(message) self.action_type = action_type self.action_kwds = action_kwds path_types_str = config.get('path_types', "*defaults*") diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -73,7 +73,8 @@ except (IOError, socket.error), exc: # In testing, errno is None log.warning('Got %s, will retry: %s', exc.__class__.__name__, exc) - heartbeat_thread.join() + if heartbeat_thread: + heartbeat_thread.join() def heartbeat(self, connection): log.debug('AMQP heartbeat thread alive') diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/config_util.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/config_util.py @@ -0,0 +1,80 @@ +""" Generic interface for reading YAML/INI/JSON config files into nested dictionaries. +""" + +try: + from galaxy import eggs + eggs.require('PyYAML') +except Exception: + # If not in Galaxy, ignore this. + pass +try: + import yaml +except ImportError: + yaml = None +try: + from ConfigParser import ConfigParser +except ImportError: + from configparser import ConfigParser +import json + + +CONFIG_TYPE_JSON = "json" +CONFIG_TYPE_YAML = "yaml" +CONFIG_TYPE_INI = "ini" + +DEFAULT_CONFIG_TYPE = CONFIG_TYPE_YAML + +JSON_EXTS = [".json"] +YAML_EXTS = [".yaml", ".yml"] +INI_EXTS = [".ini"] + +EXT_MAP = { + CONFIG_TYPE_JSON: JSON_EXTS, + CONFIG_TYPE_YAML: YAML_EXTS, + CONFIG_TYPE_INI: INI_EXTS, +} + + +def read_file(path, type=None, default_type=DEFAULT_CONFIG_TYPE): + if path is None: + raise ValueError("Undefined path supplied.") + + config_type = __find_type(path, type, default_type) + return EXT_READERS[config_type](path) + + +def __find_type(path, explicit_type, default_type): + if explicit_type: + return explicit_type + + for config_type, config_exts in EXT_MAP.items(): + for ext in config_exts: + if path.endswith(ext): + return config_type + + return default_type + + +def __read_yaml(path): + if yaml is None: + raise ImportError("Attempting to read YAML configuration file - but PyYAML dependency unavailable.") + + with open(path, "rb") as f: + return yaml.load(f) + + +def __read_ini(path): + config = ConfigParser() + config.read(path) + return config._sections + + +def __read_json(path): + with open(path, "rb") as f: + return json.load(f) + +EXT_READERS = { + CONFIG_TYPE_JSON: __read_json, + CONFIG_TYPE_YAML: __read_yaml, + CONFIG_TYPE_INI: __read_ini, +} diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/transport/curl.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/curl.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/curl.py @@ -10,7 +10,7 @@ PYCURL_UNAVAILABLE_MESSAGE = \ - "You are attempting to use the Pycurl version of the LWR client by pycurl is unavailable." + "You are attempting to use the Pycurl version of the LWR client but pycurl is unavailable." class PycurlTransport(object): diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -135,7 +135,7 @@ message_template = "Cannot compute new path for file %s, does not start with %s." message = message_template % (posix_path, old_base) raise Exception(message) - stripped_path = posix_path[ len(old_base): ] + stripped_path = posix_path[len(old_base):] while stripped_path.startswith("/"): stripped_path = stripped_path[1:] path_parts = stripped_path.split(self.separator) diff -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc -r 45df9d2018e1c452478549b933476937595bf6a4 lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -1,4 +1,4 @@ -# A simple CLI runner for slurm that can be used when running Galaxy from a +# A simple CLI runner for slurm that can be used when running Galaxy from a # non-submit host and using a Slurm cluster. try: @@ -22,6 +22,7 @@ 'partition': '-p' } + class Slurm(BaseJobExec): def __init__(self, **params): @@ -31,8 +32,8 @@ def job_script_kwargs(self, ofile, efile, job_name): scriptargs = {'-o': ofile, - '-e': efile, - '-J': job_name} + '-e': efile, + '-J': job_name} # Map arguments using argmap. for k, v in self.params.items(): @@ -66,7 +67,7 @@ def parse_status(self, status, job_ids): # Get status for each job, skipping header. rval = {} - for line in status.splitlines()[ 1: ]: + for line in status.splitlines()[1:]: id, state = line.split() if id in job_ids: # map job states to Galaxy job states. @@ -75,7 +76,7 @@ def parse_single_status(self, status, job_id): status = status.splitlines() - if len( status ) > 1: + if len(status) > 1: # Job still on cluster and has state. id, state = status[1].split() return self._get_job_state(state) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Rename install_manage.IntallManager to be install_manager.InstallToolDependencyManager and add a new class to the same module named InstallRepositoryManager and move appropriate utility functions into it. Add a new repair_repository_manager.RepairRepositoryManager class and move appropriate utility functions into it. Change a log of utility functions that took trans to now take app.
by commits-noreply＠bitbucket.org 16 Jun '14

16 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a428afbc235/ Changeset: 0a428afbc235 User: greg Date: 2014-06-16 22:57:24 Summary: Rename install_manage.IntallManager to be install_manager.InstallToolDependencyManager and add a new class to the same module named InstallRepositoryManager and move appropriate utility functions into it. Add a new repair_repository_manager.RepairRepositoryManager class and move appropriate utility functions into it. Change a log of utility functions that took trans to now take app. Affected #: 18 files diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -10,7 +10,8 @@ from galaxy.util import json from galaxy.web.base.controller import BaseAPIController -from tool_shed.galaxy_install import repository_util +from tool_shed.galaxy_install.install_manager import InstallRepositoryManager +from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util @@ -235,7 +236,13 @@ # Get the information about the repository to be installed from the payload. tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) self.__ensure_can_install_repos( trans ) - installed_tool_shed_repositories = repository_util.install( trans.app, tool_shed_url, name, owner, changeset_revision, payload ) + install_repository_manager = InstallRepositoryManager( trans.app ) + installed_tool_shed_repositories = install_repository_manager.install( trans.app, + tool_shed_url, + name, + owner, + changeset_revision, + payload ) def to_dict( tool_shed_repository ): tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) @@ -341,8 +348,13 @@ # Get the information about the repository to be installed from the payload. tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) tool_shed_repositories = [] - tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) - repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, + tool_shed_url, + name, + owner, + changeset_revision ) + rrm = RepairRepositoryManager( trans.app ) + repair_dict = rrm.get_repair_dict( tool_shed_repository ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) if ordered_tsr_ids and ordered_repo_info_dicts: @@ -350,9 +362,8 @@ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) repo_info_dict = ordered_repo_info_dicts[ index ] # TODO: handle errors in repair_dict. - repair_dict = repository_util.repair_tool_shed_repository( trans, - repository, - encoding_util.tool_shed_encode( repo_info_dict ) ) + repair_dict = rrm.repair_tool_shed_repository( repository, + encoding_util.tool_shed_encode( repo_info_dict ) ) repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans, repository ) ) repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -29,6 +29,8 @@ from tool_shed.util import workflow_util from tool_shed.util import xml_util from tool_shed.galaxy_install import repository_util +from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids log = logging.getLogger( __name__ ) @@ -473,12 +475,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) - installed_tool_dependencies = \ - common_install_util.install_specified_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) + itdm = install_manager.InstallToolDependencyManager( trans.app ) + installed_tool_dependencies = itdm.install_specified_tool_dependencies( tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) @@ -587,7 +588,7 @@ updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) else: updated_metadata = None - repository = repository_util.update_repository_record( trans, + repository = repository_util.update_repository_record( trans.app, repository=repository, updated_metadata_dict=updated_metadata, updated_changeset_revision=updating_to_changeset_revision, @@ -635,17 +636,17 @@ # There must be a one-to-one mapping between items in the 3 lists: tool_shed_repositories, tool_panel_section_keys, repo_info_dicts. tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] ) repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) + irm = install_manager.InstallRepositoryManager( trans.app ) for index, tool_shed_repository in enumerate( tool_shed_repositories ): repo_info_dict = repo_info_dicts[ index ] tool_panel_section_key = tool_panel_section_keys[ index ] - repository_util.install_tool_shed_repository( trans.app, - tool_shed_repository, - repo_info_dict, - tool_panel_section_key, - shed_tool_conf, - tool_path, - install_tool_dependencies, - reinstalling=reinstalling ) + irm.install_tool_shed_repository( tool_shed_repository, + repo_info_dict, + tool_panel_section_key, + shed_tool_conf, + tool_path, + install_tool_dependencies, + reinstalling=reinstalling ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', @@ -688,6 +689,7 @@ kwd[ 'message' ] = 'All selected tool shed repositories are already uninstalled.' kwd[ 'status' ] = 'error' elif operation == "install": + irm = install_manager.InstallRepositoryManager( trans.app ) reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) ) encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) @@ -701,10 +703,9 @@ # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the # required order. ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ - repository_util.order_components_for_installation( trans.app, - tsr_ids, - repo_info_dicts, - tool_panel_section_keys=tool_panel_section_keys ) + irm.order_components_for_installation( tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) for tsr_id in ordered_tsr_ids: repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .get( trans.security.decode_id( tsr_id ) ) @@ -712,10 +713,10 @@ trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) repo_info_dict, tool_panel_section_key = \ - repository_util.get_repository_components_for_installation( tsr_id, - ordered_tsr_ids, - ordered_repo_info_dicts, - ordered_tool_panel_section_keys ) + irm.get_repository_components_for_installation( tsr_id, + ordered_tsr_ids, + ordered_repo_info_dicts, + ordered_tool_panel_section_keys ) filtered_repo_info_dicts.append( repo_info_dict ) filtered_tool_panel_section_keys.append( tool_panel_section_key ) if repositories_for_installation: @@ -1050,6 +1051,7 @@ includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] + irm = install_manager.InstallRepositoryManager( trans.app ) if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ): if updating: @@ -1060,7 +1062,7 @@ decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) # Now that the user has decided whether they will handle dependencies, we can update # the repository to the latest revision. - repository = repository_util.update_repository_record( trans, + repository = repository_util.update_repository_record( trans.app, repository=repository, updated_metadata_dict=decoded_updated_metadata, updated_changeset_revision=updating_to_changeset_revision, @@ -1098,7 +1100,7 @@ tool_path=tool_path, tool_shed_url=tool_shed_url ) encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ - repository_util.initiate_repository_installation( trans.app, installation_dict ) + irm.initiate_repository_installation( installation_dict ) return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', encoded_kwd=encoded_kwd, query=query, @@ -1139,7 +1141,7 @@ missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) - readme_files_dict = readme_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) + readme_files_dict = readme_util.get_readme_files_dict_for_display( trans.app, tool_shed_url, repo_info_dict ) # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in @@ -1150,15 +1152,14 @@ # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate. containers_dict = \ - repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - updating=updating ) + irm.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. containers_dicts = [] @@ -1185,18 +1186,17 @@ name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) containers_dict = \ - repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=None, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - updating=updating ) + irm.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=None, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) containers_dicts.append( containers_dict ) # Merge all containers into a single container. - containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts ) + containers_dict = irm.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1271,7 +1271,8 @@ repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) if repository: if kwd.get( 'purge_repository', False ): - purge_status, purge_message = repository_util.purge_repository( trans.app, repository ) + irm = install_manager.InstallRepositoryManager( trans.app ) + purge_status, purge_message = irm.purge_repository( trans.app, repository ) if purge_status == 'ok': new_kwd[ 'status' ] = "done" else: @@ -1358,7 +1359,7 @@ # Entering this else block occurs only if the tool_shed_repository does not include any valid tools. if install_repository_dependencies: repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, + repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) else: repository_dependencies = None @@ -1366,7 +1367,7 @@ tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None - repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.changeset_revision, ctx_rev=ctx_rev, @@ -1443,6 +1444,7 @@ message=message, status=status ) ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + rrm = RepairRepositoryManager( trans.app ) if kwd.get( 'repair_repository_button', False ): encoded_repair_dict = kwd.get( 'repair_dict', None ) if encoded_repair_dict: @@ -1450,7 +1452,7 @@ else: repair_dict = None if not repair_dict: - repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + repair_dict = rrm.get_repair_dict( tool_shed_repository ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) if ordered_tsr_ids and ordered_repo_info_dicts: @@ -1458,9 +1460,9 @@ for tsr_id in ordered_tsr_ids: repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) repositories_for_repair.append( repository ) - return self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) + return self.repair_tool_shed_repositories( trans, rrm, repositories_for_repair, ordered_repo_info_dicts ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) - repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + repair_dict = rrm.get_repair_dict( tool_shed_repository ) encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) @@ -1473,14 +1475,13 @@ @web.expose @web.require_admin - def repair_tool_shed_repositories( self, trans, tool_shed_repositories, repo_info_dicts, **kwd ): + def repair_tool_shed_repositories( self, trans, repair_repository_manager, tool_shed_repositories, repo_info_dicts, **kwd ): """Repair specified tool shed repositories.""" # The received lists of tool_shed_repositories and repo_info_dicts are ordered. for index, tool_shed_repository in enumerate( tool_shed_repositories ): repo_info_dict = repo_info_dicts[ index ] - repair_dict = repository_util.repair_tool_shed_repository( trans, - tool_shed_repository, - encoding_util.tool_shed_encode( repo_info_dict ) ) + repair_dict = repair_repository_manager.repair_tool_shed_repository( tool_shed_repository, + encoding_util.tool_shed_encode( repo_info_dict ) ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', @@ -1578,9 +1579,9 @@ readme_files_dict = json.from_json_string( raw_text ) tool_dependencies = metadata.get( 'tool_dependencies', None ) repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, + repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) - repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, ctx_rev=tool_shed_repository.ctx_rev, @@ -1643,19 +1644,19 @@ original_section_name = '' tool_panel_section_select_field = None shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) + irm = install_manager.InstallRepositoryManager( trans.app ) containers_dict = \ - repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - updating=False ) + irm.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=False ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. - containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + containers_dict = irm.merge_missing_repository_dependencies_to_installed_container( containers_dict ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. @@ -1748,13 +1749,13 @@ """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): - repository_util.set_repository_attributes( trans.app, - repository, - status=trans.install_model.ToolShedRepository.installation_status.NEW, - error_message=None, - deleted=False, - uninstalled=False, - remove_from_disk=True ) + suc.set_repository_attributes( trans.app, + repository, + status=trans.install_model.ToolShedRepository.installation_status.NEW, + error_message=None, + deleted=False, + uninstalled=False, + remove_from_disk=True ) new_kwd = {} new_kwd[ 'message' ] = "You can now attempt to install the repository named <b>%s</b> again." % str( repository.name ) new_kwd[ 'status' ] = "done" @@ -1908,7 +1909,7 @@ repo_path=repo_files_dir, create=False ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) - repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) + hg_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) hg_util.update_repository( repo, latest_ctx_rev ) # Remove old Data Manager entries if repository.includes_data_managers: @@ -2023,7 +2024,7 @@ return self.install_tool_dependencies_with_update( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. - repository = repository_util.update_repository_record( trans, + repository = repository_util.update_repository_record( trans.app, repository=repository, updated_metadata_dict=metadata_dict, updated_changeset_revision=latest_changeset_revision, diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -723,7 +723,10 @@ # Update repository files for browsing. hg_util.update_repository( repo ) changeset_revision = repository.tip( trans.app ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=True ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, + id, + changeset_revision, + metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, @@ -970,7 +973,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans.app, id ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, id, repository.tip( trans.app ), metadata_only=True ) @@ -1106,7 +1109,7 @@ if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, repository_id, changeset_revision, metadata_only=True ) @@ -1195,7 +1198,7 @@ metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -1206,7 +1209,7 @@ # Only display repository dependencies if they exist. exclude = [ 'datatypes', 'invalid_repository_dependencies', 'invalid_tool_dependencies', 'invalid_tools', 'readme_files', 'tool_dependencies', 'tools', 'tool_test_results', 'workflows', 'data_manager' ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, repository, changeset_revision, repository_dependencies, @@ -1691,7 +1694,7 @@ if repository_metadata: metadata = repository_metadata.metadata if metadata: - return readme_util.build_readme_files_dict( trans, + return readme_util.build_readme_files_dict( trans.app, repository, changeset_revision, repository_metadata.metadata ) @@ -1720,7 +1723,7 @@ metadata = repository_metadata.metadata if metadata: repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -1889,7 +1892,7 @@ after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, ctx_rev=str( ctx.rev() ), @@ -1921,7 +1924,7 @@ break if 'workflows' in metadata: includes_workflows = True - readme_files_dict = readme_util.build_readme_files_dict( trans, repository, changeset_revision, metadata ) + readme_files_dict = readme_util.build_readme_files_dict( trans.app, repository, changeset_revision, metadata ) # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies. has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -2349,7 +2352,7 @@ metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -2389,7 +2392,7 @@ skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans.app ) selected_categories = [ rca.category_id for rca in repository.categories ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, repository, changeset_revision, repository_dependencies, @@ -2547,7 +2550,7 @@ # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=toolshed_base_url, @@ -2581,7 +2584,11 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, + repository, + changeset_revision, + repository_dependencies, + repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, @@ -2661,7 +2668,7 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, id, changeset_revision, metadata_only=True ) @@ -2770,7 +2777,7 @@ status = "error" repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) changeset_revision = repository.tip( trans.app ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, id, changeset_revision, metadata_only=True ) @@ -2941,7 +2948,7 @@ repository = None if repository: repository_id = trans.security.encode_id( repository.id ) - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, repository_id, changeset_revision ) if not repository_metadata: @@ -2950,7 +2957,7 @@ upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if upper_bound_changeset_revision: changeset_revision = upper_bound_changeset_revision - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, repository_id, changeset_revision ) if repository_metadata: @@ -3098,7 +3105,7 @@ 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, id, repository.tip( trans.app ), metadata_only=True ) @@ -3142,7 +3149,10 @@ diffs.append( basic_util.to_html_string( diff ) ) modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean - metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, + id, + ctx_str, + metadata_only=True ) # For rendering the prev button. if ctx_parent: ctx_parent_date = hg_util.get_readable_ctx_date( ctx_parent ) @@ -3243,7 +3253,7 @@ metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -3265,7 +3275,7 @@ else: message += malicious_error status = 'error' - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, repository, changeset_revision, repository_dependencies, diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -1,8 +1,12 @@ +import json import logging import os import sys +import tempfile +import threading import traceback +from galaxy import exceptions from galaxy import eggs eggs.require( 'paramiko' ) @@ -11,8 +15,19 @@ from fabric.api import lcd +from galaxy.model.orm import or_ + +from tool_shed.util import basic_util +from tool_shed.util import common_util +from tool_shed.util import container_util +from tool_shed.util import encoding_util +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util +from tool_shed.util import xml_util +from tool_shed.galaxy_install import repository_util from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager @@ -20,22 +35,24 @@ log = logging.getLogger( __name__ ) -INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', - 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] - -class InstallManager( object ): +class InstallToolDependencyManager( object ): + + def __init__( self, app ): + self.app = app + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', + 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] def format_traceback( self ): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) - def get_tool_shed_repository_install_dir( self, app, tool_shed_repository ): - return os.path.abspath( tool_shed_repository.repo_files_directory( app ) ) + def get_tool_shed_repository_install_dir( self, tool_shed_repository ): + return os.path.abspath( tool_shed_repository.repo_files_directory( self.app ) ) - def install_and_build_package( self, app, tool_shed_repository, tool_dependency, actions_dict ): + def install_and_build_package( self, tool_shed_repository, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" - tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( tool_shed_repository ) install_dir = actions_dict[ 'install_dir' ] package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) @@ -53,13 +70,13 @@ # the filtered actions being used in the next stage below. The installation directory (i.e., dir) # is also defined in this stage and is used in the next stage below when defining current_dir. action_type, action_dict = actions[ 0 ] - if action_type in INSTALL_ACTIONS: + if action_type in self.INSTALL_ACTIONS: # Some of the parameters passed here are needed only by a subset of the step handler classes, # but to allow for a standard method signature we'll pass them along. We don't check the # tool_dependency status in this stage because it should not have been changed based on a # download. tool_dependency, filtered_actions, dir = \ - step_manager.execute_step( app=app, + step_manager.execute_step( app=self.app, tool_dependency=tool_dependency, package_name=package_name, actions=actions, @@ -85,7 +102,7 @@ with lcd( current_dir ): action_type, action_dict = action_tup tool_dependency, tmp_filtered_actions, tmp_dir = \ - step_manager.execute_step( app=app, + step_manager.execute_step( app=self.app, tool_dependency=tool_dependency, package_name=package_name, actions=actions, @@ -97,7 +114,7 @@ work_dir=work_dir, current_dir=current_dir, initial_download=False ) - if tool_dependency.status in [ app.install_model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR ]: # If the tool_dependency status is in an error state, return it with no additional # processing. return tool_dependency @@ -108,31 +125,115 @@ dir = tmp_dir return tool_dependency - def install_and_build_package_via_fabric( self, app, tool_shed_repository, tool_dependency, actions_dict ): - sa_session = app.install_model.context + def install_and_build_package_via_fabric( self, tool_shed_repository, tool_dependency, actions_dict ): + sa_session = self.app.install_model.context try: # There is currently only one fabric method. - tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict ) + tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) except Exception, e: log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) ) # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must # be left False here. error_message = '%s\n%s' % ( self.format_traceback(), str( e ) ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) - tool_dependency = tool_dependency_util.mark_tool_dependency_installed( app, tool_dependency ) + tool_dependency = self.mark_tool_dependency_installed( tool_dependency ) return tool_dependency - def install_via_fabric( self, app, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None, + def install_specified_tool_dependencies( self, tool_shed_repository, tool_dependencies_config, tool_dependencies, + from_tool_migration_manager=False ): + """ + Follow the recipe in the received tool_dependencies_config to install specified packages for + repository tools. The received list of tool_dependencies are the database records for those + dependencies defined in the tool_dependencies_config that are to be installed. This list may + be a subset of the set of dependencies defined in the tool_dependencies_config. This allows + for filtering out dependencies that have not been checked for installation on the 'Manage tool + dependencies' page for an installed Tool Shed repository. + """ + attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] + installed_packages = [] + tag_manager = TagManager() + # Parse the tool_dependencies.xml config. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + log.debug( "The received tool_dependencies.xml file is likely invalid: %s" % str( error_message ) ) + return installed_packages + root = tree.getroot() + elems = [] + for elem in root: + if elem.tag == 'set_environment': + version = elem.get( 'version', '1.0' ) + if version != '1.0': + raise Exception( 'The <set_environment> tag must have a version attribute with value 1.0' ) + for sub_elem in elem: + elems.append( sub_elem ) + else: + elems.append( elem ) + for elem in elems: + name = elem.get( 'name', None ) + version = elem.get( 'version', None ) + type = elem.get( 'type', None ) + if type is None: + if elem.tag in [ 'environment_variable', 'set_environment' ]: + type = 'set_environment' + else: + type = 'package' + if ( name and type == 'set_environment' ) or ( name and version ): + # elem is a package set_environment tag set. + attr_tup = ( name, version, type ) + try: + index = attr_tups_of_dependencies_for_install.index( attr_tup ) + except Exception, e: + index = None + if index is not None: + tool_dependency = tool_dependencies[ index ] + # If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will + # handle everything - no additional installation is necessary. + tool_dependency, proceed_with_install, action_elem_tuples = \ + tag_manager.process_tag_set( self.app, + tool_shed_repository, + tool_dependency, + elem, + name, + version, + from_tool_migration_manager=from_tool_migration_manager, + tool_dependency_db_records=tool_dependencies ) + if ( tool_dependency.type == 'package' and proceed_with_install ): + try: + tool_dependency = self.install_package( elem, + tool_shed_repository, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=from_tool_migration_manager ) + except Exception, e: + error_message = "Error installing tool dependency %s version %s: %s" % \ + ( str( name ), str( version ), str( e ) ) + log.exception( error_message ) + if tool_dependency: + # Since there was an installation error, update the tool dependency status to Error. The + # remove_installation_path option must be left False here. + tool_dependency = \ + tool_dependency_util.handle_tool_dependency_installation_error( self.app, + tool_dependency, + error_message, + remove_installation_path=False ) + if tool_dependency and tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.INSTALLED, + self.app.install_model.ToolDependency.installation_status.ERROR ]: + installed_packages.append( tool_dependency ) + if self.app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + self.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + return installed_packages + + def install_via_fabric( self, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ): """ Parse a tool_dependency.xml file's <actions> tag set to gather information for installation using self.install_and_build_package(). The use of fabric is being eliminated, so some of these functions may need to be renamed at some point. """ - sa_session = app.install_model.context + sa_session = self.app.install_model.context if not os.path.exists( install_dir ): os.makedirs( install_dir ) actions_dict = dict( install_dir=install_dir ) @@ -150,7 +251,7 @@ else: elems = [] step_manager = StepManager() - tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + tool_shed_repository_install_dir = self.get_tool_shed_repository_install_dir( tool_shed_repository ) install_environment = InstallEnvironment( tool_shed_repository_install_dir, install_dir ) for action_elem in elems: # Make sure to skip all comments, since they are now included in the XML tree. @@ -159,7 +260,7 @@ action_dict = {} action_type = action_elem.get( 'type', None ) if action_type is not None: - action_dict = step_manager.prepare_step( app=app, + action_dict = step_manager.prepare_step( app=self.app, tool_dependency=tool_dependency, action_type=action_type, action_elem=action_elem, @@ -178,10 +279,10 @@ # TODO: this is not yet supported or functional, but when it is handle it using the fabric api. raise Exception( 'Tool dependency installation using proprietary fabric scripts is not yet supported.' ) else: - tool_dependency = self.install_and_build_package_via_fabric( app, tool_shed_repository, tool_dependency, actions_dict ) + tool_dependency = self.install_and_build_package_via_fabric( tool_shed_repository, tool_dependency, actions_dict ) return tool_dependency - def install_package( self, app, elem, tool_shed_repository, tool_dependencies=None, from_tool_migration_manager=False ): + def install_package( self, elem, tool_shed_repository, tool_dependencies=None, from_tool_migration_manager=False ): """ Install a tool dependency package defined by the XML element elem. The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. @@ -199,7 +300,7 @@ if tool_dependency is not None: for package_elem in elem: tool_dependency, proceed_with_install, actions_elem_tuples = \ - tag_manager.process_tag_set( app, + tag_manager.process_tag_set( self.app, tool_shed_repository, tool_dependency, package_elem, @@ -211,7 +312,7 @@ # Get the installation directory for tool dependencies that will be installed for the received # tool_shed_repository. install_dir = \ - tool_dependency_util.get_tool_dependency_install_dir( app=app, + tool_dependency_util.get_tool_dependency_install_dir( app=self.app, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, repository_changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -244,14 +345,13 @@ if binary_installed: continue # No platform-specific <actions> recipe has yet resulted in a successful installation. - tool_dependency = self.install_via_fabric( app, - tool_shed_repository, + tool_dependency = self.install_via_fabric( tool_shed_repository, tool_dependency, install_dir, package_name=package_name, actions_elem=actions_elem, action_elem=None ) - if tool_dependency.status == app.install_model.ToolDependency.installation_status.INSTALLED: + if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: # If an <actions> tag was found that matches the current platform, and # self.install_via_fabric() did not result in an error state, set binary_installed # to True in order to skip any remaining platform-specific <actions> tags. @@ -266,17 +366,18 @@ # We've reached an <actions> tag that defines the recipe for installing and compiling from # source. If binary installation failed, we proceed with the recipe. if not binary_installed: - installation_directory = tool_dependency.installation_directory( app ) + installation_directory = tool_dependency.installation_directory( self.app ) if os.path.exists( installation_directory ): # Delete contents of installation directory if attempt at binary installation failed. installation_directory_contents = os.listdir( installation_directory ) if installation_directory_contents: - removed, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) + removed, error_message = tool_dependency_util.remove_tool_dependency( self.app, + tool_dependency ) if removed: can_install_from_source = True else: log.debug( 'Error removing old files from installation directory %s: %s' % \ - ( str( tool_dependency.installation_directory( app ), str( error_message ) ) ) ) + ( str( installation_directory, str( error_message ) ) ) ) else: can_install_from_source = True else: @@ -286,20 +387,18 @@ # tag set that defines the recipe to install and compile from source. log.debug( 'Proceeding with install and compile recipe for tool dependency %s.' % \ str( tool_dependency.name ) ) - tool_dependency = self.install_via_fabric( app, - tool_shed_repository, + tool_dependency = self.install_via_fabric( tool_shed_repository, tool_dependency, install_dir, package_name=package_name, actions_elem=actions_elem, action_elem=None ) if actions_elem.tag == 'action' and \ - tool_dependency.status != app.install_model.ToolDependency.installation_status.ERROR: + tool_dependency.status != self.app.install_model.ToolDependency.installation_status.ERROR: # If the tool dependency is not in an error state, perform any final actions that have been # defined within the actions_group tag set, but outside of an <actions> tag, which defines # the recipe for installing and compiling from source. - tool_dependency = self.install_via_fabric( app, - tool_shed_repository, + tool_dependency = self.install_via_fabric( tool_shed_repository, tool_dependency, install_dir, package_name=package_name, @@ -309,14 +408,603 @@ # Checks for "os" and "architecture" attributes are not made for any <actions> tag sets outside of # an <actions_group> tag set. If the attributes are defined, they will be ignored. All <actions> tags # outside of an <actions_group> tag set will always be processed. - tool_dependency = self.install_via_fabric( app, - tool_shed_repository, + tool_dependency = self.install_via_fabric( tool_shed_repository, tool_dependency, install_dir, package_name=package_name, actions_elem=actions_elems, action_elem=None ) - if tool_dependency.status != app.install_model.ToolDependency.installation_status.ERROR: + if tool_dependency.status != self.app.install_model.ToolDependency.installation_status.ERROR: log.debug( 'Tool dependency %s version %s has been installed in %s.' % \ ( str( package_name ), str( package_version ), str( install_dir ) ) ) return tool_dependency + + def mark_tool_dependency_installed( self, tool_dependency ): + if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR, + self.app.install_model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), + str( tool_dependency.status ), + str( self.app.install_model.ToolDependency.installation_status.INSTALLED ) ) ) + status = self.app.install_model.ToolDependency.installation_status.INSTALLED + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, + tool_dependency=tool_dependency, + status=status, + error_message=None, + remove_from_disk=False ) + return tool_dependency + + +class InstallRepositoryManager( object ): + + def __init__( self, app ): + self.app = app + + def get_repository_components_for_installation( self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, + tool_panel_section_keys ): + """ + The received encoded_tsr_ids, repo_info_dicts, and tool_panel_section_keys are 3 lists that + contain associated elements at each location in the list. This method will return the elements + from repo_info_dicts and tool_panel_section_keys associated with the received encoded_tsr_id + by determining its location in the received encoded_tsr_ids list. + """ + for index, tsr_id in enumerate( encoded_tsr_ids ): + if tsr_id == encoded_tsr_id: + repo_info_dict = repo_info_dicts[ index ] + tool_panel_section_key = tool_panel_section_keys[ index ] + return repo_info_dict, tool_panel_section_key + return None, None + + def __get_install_info_from_tool_shed( self, tool_shed_url, name, owner, changeset_revision ): + params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) + url = common_util.url_join( tool_shed_url, + 'api/repositories/get_repository_revision_install_info%s' % params ) + try: + raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url ) + except Exception, e: + message = "Error attempting to retrieve installation information from tool shed " + message += "%s for revision %s of repository %s owned by %s: %s" % \ + ( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) ) + log.warn( message ) + raise exceptions.InternalServerError( message ) + if raw_text: + # If successful, the response from get_repository_revision_install_info will be 3 + # dictionaries, a dictionary defining the Repository, a dictionary defining the + # Repository revision (RepositoryMetadata), and a dictionary including the additional + # information required to install the repository. + items = json.loads( raw_text ) + repository_revision_dict = items[ 1 ] + repo_info_dict = items[ 2 ] + else: + message = "Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s: %s" % \ + ( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) ) + log.warn( message ) + raise exceptions.InternalServerError( message ) + # Make sure the tool shed returned everything we need for installing the repository. + if not repository_revision_dict or not repo_info_dict: + invalid_parameter_message = "No information is available for the requested repository revision.\n" + invalid_parameter_message += "One or more of the following parameter values is likely invalid:\n" + invalid_parameter_message += "tool_shed_url: %s\n" % str( tool_shed_url ) + invalid_parameter_message += "name: %s\n" % str( name ) + invalid_parameter_message += "owner: %s\n" % str( owner ) + invalid_parameter_message += "changeset_revision: %s\n" % str( changeset_revision ) + raise exceptions.RequestParameterInvalidException( invalid_parameter_message ) + repo_info_dicts = [ repo_info_dict ] + return repository_revision_dict, repo_info_dicts + + def initiate_repository_installation( self, installation_dict ): + install_model = self.app.install_model + # The following installation_dict entries are all required. + created_or_updated_tool_shed_repositories = installation_dict[ 'created_or_updated_tool_shed_repositories' ] + filtered_repo_info_dicts = installation_dict[ 'filtered_repo_info_dicts' ] + has_repository_dependencies = installation_dict[ 'has_repository_dependencies' ] + includes_tool_dependencies = installation_dict[ 'includes_tool_dependencies' ] + includes_tools = installation_dict[ 'includes_tools' ] + includes_tools_for_display_in_tool_panel = installation_dict[ 'includes_tools_for_display_in_tool_panel' ] + install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] + install_tool_dependencies = installation_dict[ 'install_tool_dependencies' ] + message = installation_dict[ 'message' ] + new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ] + shed_tool_conf = installation_dict[ 'shed_tool_conf' ] + status = installation_dict[ 'status' ] + tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ] + tool_panel_section_keys = installation_dict[ 'tool_panel_section_keys' ] + tool_path = installation_dict[ 'tool_path' ] + tool_shed_url = installation_dict[ 'tool_shed_url' ] + # Handle contained tools. + if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): + tool_panel_section_key, tool_section = \ + tool_util.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + else: + tool_panel_section_key = None + tool_section = None + encoded_repository_ids = [ self.app.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + new_kwd = dict( includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, + has_repository_dependencies=has_repository_dependencies, + install_repository_dependencies=install_repository_dependencies, + includes_tool_dependencies=includes_tool_dependencies, + install_tool_dependencies=install_tool_dependencies, + message=message, + repo_info_dicts=filtered_repo_info_dicts, + shed_tool_conf=shed_tool_conf, + status=status, + tool_path=tool_path, + tool_panel_section_keys=tool_panel_section_keys, + tool_shed_repository_ids=encoded_repository_ids, + tool_shed_url=tool_shed_url ) + encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) + tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] + tool_shed_repositories = [] + for tsr_id in tsr_ids: + tsr = install_model.context.query( install_model.ToolShedRepository ).get( tsr_id ) + tool_shed_repositories.append( tsr ) + clause_list = [] + for tsr_id in tsr_ids: + clause_list.append( install_model.ToolShedRepository.table.c.id == tsr_id ) + query = install_model.context.query( install_model.ToolShedRepository ).filter( or_( *clause_list ) ) + return encoded_kwd, query, tool_shed_repositories, encoded_repository_ids + + def install( self, tool_shed_url, name, owner, changeset_revision, install_options ): + # Get all of the information necessary for installing the repository from the specified tool shed. + repository_revision_dict, repo_info_dicts = self.__get_install_info_from_tool_shed( tool_shed_url, + name, + owner, + changeset_revision ) + installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict, + repo_info_dicts, + install_options ) + return installed_tool_shed_repositories + + def __install_repositories( self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options ): + # Keep track of all repositories that are installed - there may be more than one if repository dependencies are installed. + installed_tool_shed_repositories = [] + try: + has_repository_dependencies = repository_revision_dict[ 'has_repository_dependencies' ] + except: + raise exceptions.InternalServerError( "Tool shed response missing required parameter 'has_repository_dependencies'." ) + try: + includes_tools = repository_revision_dict[ 'includes_tools' ] + except: + raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tools'." ) + try: + includes_tool_dependencies = repository_revision_dict[ 'includes_tool_dependencies' ] + except: + raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tool_dependencies'." ) + try: + includes_tools_for_display_in_tool_panel = repository_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] + except: + raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tools_for_display_in_tool_panel'." ) + # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information. + install_repository_dependencies = install_options.get( 'install_repository_dependencies', False ) + install_tool_dependencies = install_options.get( 'install_tool_dependencies', False ) + if install_tool_dependencies: + if self.app.config.tool_dependency_dir is None: + no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set " + no_tool_dependency_dir_message += "the value of your 'tool_dependency_dir' setting in your Galaxy " + no_tool_dependency_dir_message += "configuration file (universe_wsgi.ini) and restart your Galaxy server. " + raise exceptions.ConfigDoesNotAllowException( no_tool_dependency_dir_message ) + new_tool_panel_section_label = install_options.get( 'new_tool_panel_section_label', '' ) + shed_tool_conf = install_options.get( 'shed_tool_conf', None ) + if shed_tool_conf: + # Get the tool_path setting. + index, shed_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + tool_path = shed_conf_dict[ 'tool_path' ] + else: + # Pick a semi-random shed-related tool panel configuration file and get the tool_path setting. + for shed_config_dict in self.app.toolbox.shed_tool_confs: + # Don't use migrated_tools_conf.xml. + if shed_config_dict[ 'config_filename' ] != self.app.config.migrated_tools_config: + break + shed_tool_conf = shed_config_dict[ 'config_filename' ] + tool_path = shed_config_dict[ 'tool_path' ] + if not shed_tool_conf: + raise exceptions.RequestParameterMissingException( "Missing required parameter 'shed_tool_conf'." ) + tool_panel_section_id = install_options.get( 'tool_panel_section_id', '' ) + if tool_panel_section_id not in [ None, '' ]: + if tool_panel_section_id not in self.app.toolbox.tool_panel: + fixed_tool_panel_section_id = 'section_%s' % tool_panel_section_id + if fixed_tool_panel_section_id in self.app.toolbox.tool_panel: + tool_panel_section_id = fixed_tool_panel_section_id + else: + tool_panel_section_id = '' + else: + tool_panel_section_id = '' + # Build the dictionary of information necessary for creating tool_shed_repository database records + # for each repository being installed. + installation_dict = dict( install_repository_dependencies=install_repository_dependencies, + new_tool_panel_section_label=new_tool_panel_section_label, + no_changes_checked=False, + repo_info_dicts=repo_info_dicts, + tool_panel_section_id=tool_panel_section_id, + tool_path=tool_path, + tool_shed_url=tool_shed_url ) + # Create the tool_shed_repository database records and gather additional information for repository installation. + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ + self.handle_tool_shed_repositories( installation_dict, using_api=True ) + if created_or_updated_tool_shed_repositories: + # Build the dictionary of information necessary for installing the repositories. + installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, + filtered_repo_info_dicts=filtered_repo_info_dicts, + has_repository_dependencies=has_repository_dependencies, + includes_tool_dependencies=includes_tool_dependencies, + includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, + install_repository_dependencies=install_repository_dependencies, + install_tool_dependencies=install_tool_dependencies, + message='', + new_tool_panel_section_label=new_tool_panel_section_label, + shed_tool_conf=shed_tool_conf, + status='done', + tool_panel_section_id=tool_panel_section_id, + tool_panel_section_keys=tool_panel_section_keys, + tool_path=tool_path, + tool_shed_url=tool_shed_url ) + # Prepare the repositories for installation. Even though this method receives a single combination + # of tool_shed_url, name, owner and changeset_revision, there may be multiple repositories for installation + # at this point because repository dependencies may have added additional repositories for installation + # along with the single specified repository. + encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ + initiate_repository_installation( self.app, installation_dict ) + # Some repositories may have repository dependencies that are required to be installed before the + # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in + # the required order. + tsr_ids = [ self.app.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ] + ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ + self.order_components_for_installation( tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) + # Install the repositories, keeping track of each one for later display. + for index, tsr_id in enumerate( ordered_tsr_ids ): + install_model = self.app.install_model + tool_shed_repository = install_model.context.query( install_model.ToolShedRepository ) \ + .get( self.app.security.decode_id( tsr_id ) ) + if tool_shed_repository.status in [ install_model.ToolShedRepository.installation_status.NEW, + install_model.ToolShedRepository.installation_status.UNINSTALLED ]: + repo_info_dict = ordered_repo_info_dicts[ index ] + tool_panel_section_key = ordered_tool_panel_section_keys[ index ] + self.install_tool_shed_repository( tool_shed_repository, + repo_info_dict, + tool_panel_section_key, + shed_tool_conf, + tool_path, + install_tool_dependencies, + reinstalling=False ) + installed_tool_shed_repositories.append( tool_shed_repository ) + else: + # We're attempting to install more than 1 repository, and all of them have already been installed. + raise exceptions.RequestParameterInvalidException( 'All repositories that you are attempting to install have been previously installed.' ) + return installed_tool_shed_repositories + + def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, + install_tool_dependencies, reinstalling=False ): + install_model = self.app.install_model + if tool_panel_section_key: + try: + tool_section = self.app.toolbox.tool_panel[ tool_panel_section_key ] + except KeyError: + log.debug( 'Invalid tool_panel_section_key "%s" specified. Tools will be loaded outside of sections in the tool panel.', + str( tool_panel_section_key ) ) + tool_section = None + else: + tool_section = None + if isinstance( repo_info_dict, basestring ): + repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) + # Clone each repository to the configured location. + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + install_model.ToolShedRepository.installation_status.CLONING ) + repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, + tool_shed_repository.installed_changeset_revision ) + relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name ) + install_dir = os.path.join( tool_path, relative_install_dir ) + cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + if cloned_ok: + if reinstalling: + # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated. + changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( self.app, + tool_shed_repository ) + current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) + current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) + if current_ctx_rev != ctx_rev: + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=os.path.abspath( install_dir ), + create=False ) + hg_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) + hg_util.update_repository( repo, ctx_rev=current_ctx_rev ) + repository_util.handle_repository_contents( self.app, + tool_shed_repository=tool_shed_repository, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + tool_shed=tool_shed_repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + reinstalling=reinstalling ) + install_model.context.refresh( tool_shed_repository ) + metadata = tool_shed_repository.metadata + if 'tools' in metadata: + # Get the tool_versions from the tool shed for each tool in the installed change set. + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, str( tool_shed_repository.tool_shed ) ) + params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( tool_shed_repository.name ), + str( tool_shed_repository.owner ), + str( tool_shed_repository.changeset_revision ) ) + url = common_util.url_join( tool_shed_url, + '/repository/get_tool_versions%s' % params ) + text = common_util.tool_shed_get( self.app, tool_shed_url, url ) + if text: + tool_version_dicts = json.loads( text ) + tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) + else: + if not error_message: + error_message = "" + error_message += "Version information for the tools included in the <b>%s</b> repository is missing. " % tool_shed_repository.name + error_message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " + error_message += "from the installed repository's <b>Repository Actions</b> menu. " + if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itsr" ) + # Install tool dependencies. + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + # Get the tool_dependencies.xml file from the repository. + tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', install_dir ) + itdm = InstallToolDependencyManager( self.app ) + installed_tool_dependencies = itdm.install_specified_tool_dependencies( tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) + basic_util.remove_dir( work_dir ) + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + install_model.ToolShedRepository.installation_status.INSTALLED ) + if self.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + self.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + else: + # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. + suc.set_repository_attributes( self.app, + tool_shed_repository, + status=install_model.ToolShedRepository.installation_status.ERROR, + error_message=error_message, + deleted=False, + uninstalled=False, + remove_from_disk=True ) + + def merge_containers_dicts_for_new_install( self, containers_dicts ): + """ + When installing one or more tool shed repositories for the first time, the received list of + containers_dicts contains a containers_dict for each repository being installed. Since the + repositories are being installed for the first time, all entries are None except the repository + dependencies and tool dependencies. The entries for missing dependencies are all None since + they have previously been merged into the installed dependencies. This method will merge the + dependencies entries into a single container and return it for display. + """ + new_containers_dict = dict( readme_files=None, + datatypes=None, + missing_repository_dependencies=None, + repository_dependencies=None, + missing_tool_dependencies=None, + tool_dependencies=None, + invalid_tools=None, + valid_tools=None, + workflows=None ) + if containers_dicts: + lock = threading.Lock() + lock.acquire( True ) + try: + repository_dependencies_root_folder = None + tool_dependencies_root_folder = None + # Use a unique folder id (hopefully the following is). + folder_id = 867 + for old_container_dict in containers_dicts: + # Merge repository_dependencies. + old_container_repository_dependencies_root = old_container_dict[ 'repository_dependencies' ] + if old_container_repository_dependencies_root: + if repository_dependencies_root_folder is None: + repository_dependencies_root_folder = container_util.Folder( id=folder_id, + key='root', + label='root', + parent=None ) + folder_id += 1 + repository_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Repository dependencies', + parent=repository_dependencies_root_folder ) + folder_id += 1 + # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder. + old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[ 0 ] + # Change the folder id so it won't confict with others being merged. + old_container_repository_dependencies_folder.id = folder_id + folder_id += 1 + repository_components_tuple = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + name = components_list[ 1 ] + # Generate the label by retrieving the repository name. + old_container_repository_dependencies_folder.label = str( name ) + repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) + # Merge tool_dependencies. + old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] + if old_container_tool_dependencies_root: + if tool_dependencies_root_folder is None: + tool_dependencies_root_folder = container_util.Folder( id=folder_id, + key='root', + label='root', + parent=None ) + folder_id += 1 + tool_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Tool dependencies', + parent=tool_dependencies_root_folder ) + folder_id += 1 + else: + td_list = [ td.listify for td in tool_dependencies_folder.tool_dependencies ] + # The old_container_tool_dependencies_root will be a root folder containing a single sub_folder. + old_container_tool_dependencies_folder = old_container_tool_dependencies_root.folders[ 0 ] + for td in old_container_tool_dependencies_folder.tool_dependencies: + if td.listify not in td_list: + tool_dependencies_folder.tool_dependencies.append( td ) + if repository_dependencies_root_folder: + repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + new_containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + if tool_dependencies_root_folder: + tool_dependencies_root_folder.folders.append( tool_dependencies_folder ) + new_containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + except Exception, e: + log.debug( "Exception in merge_containers_dicts_for_new_install: %s" % str( e ) ) + finally: + lock.release() + return new_containers_dict + + def merge_missing_repository_dependencies_to_installed_container( self, containers_dict ): + """Merge the list of missing repository dependencies into the list of installed repository dependencies.""" + missing_rd_container_root = containers_dict.get( 'missing_repository_dependencies', None ) + if missing_rd_container_root: + # The missing_rd_container_root will be a root folder containing a single sub_folder. + missing_rd_container = missing_rd_container_root.folders[ 0 ] + installed_rd_container_root = containers_dict.get( 'repository_dependencies', None ) + # The installed_rd_container_root will be a root folder containing a single sub_folder. + if installed_rd_container_root: + installed_rd_container = installed_rd_container_root.folders[ 0 ] + installed_rd_container.label = 'Repository dependencies' + for index, rd in enumerate( missing_rd_container.repository_dependencies ): + # Skip the header row. + if index == 0: + continue + installed_rd_container.repository_dependencies.append( rd ) + installed_rd_container_root.folders = [ installed_rd_container ] + containers_dict[ 'repository_dependencies' ] = installed_rd_container_root + else: + # Change the folder label from 'Missing repository dependencies' to be 'Repository dependencies' for display. + root_container = containers_dict[ 'missing_repository_dependencies' ] + for sub_container in root_container.folders: + # There should only be 1 sub-folder. + sub_container.label = 'Repository dependencies' + containers_dict[ 'repository_dependencies' ] = root_container + containers_dict[ 'missing_repository_dependencies' ] = None + return containers_dict + + def merge_missing_tool_dependencies_to_installed_container( self, containers_dict ): + """ Merge the list of missing tool dependencies into the list of installed tool dependencies.""" + missing_td_container_root = containers_dict.get( 'missing_tool_dependencies', None ) + if missing_td_container_root: + # The missing_td_container_root will be a root folder containing a single sub_folder. + missing_td_container = missing_td_container_root.folders[ 0 ] + installed_td_container_root = containers_dict.get( 'tool_dependencies', None ) + # The installed_td_container_root will be a root folder containing a single sub_folder. + if installed_td_container_root: + installed_td_container = installed_td_container_root.folders[ 0 ] + installed_td_container.label = 'Tool dependencies' + for index, td in enumerate( missing_td_container.tool_dependencies ): + # Skip the header row. + if index == 0: + continue + installed_td_container.tool_dependencies.append( td ) + installed_td_container_root.folders = [ installed_td_container ] + containers_dict[ 'tool_dependencies' ] = installed_td_container_root + else: + # Change the folder label from 'Missing tool dependencies' to be 'Tool dependencies' for display. + root_container = containers_dict[ 'missing_tool_dependencies' ] + for sub_container in root_container.folders: + # There should only be 1 subfolder. + sub_container.label = 'Tool dependencies' + containers_dict[ 'tool_dependencies' ] = root_container + containers_dict[ 'missing_tool_dependencies' ] = None + return containers_dict + + def order_components_for_installation( self, tsr_ids, repo_info_dicts, tool_panel_section_keys ): + """ + Some repositories may have repository dependencies that are required to be installed + before the dependent repository. This method will inspect the list of repositories + about to be installed and make sure to order them appropriately. For each repository + about to be installed, if required repositories are not contained in the list of repositories + about to be installed, then they are not considered. Repository dependency definitions + that contain circular dependencies should not result in an infinite loop, but obviously + prior installation will not be handled for one or more of the repositories that require + prior installation. + """ + ordered_tsr_ids = [] + ordered_repo_info_dicts = [] + ordered_tool_panel_section_keys = [] + # Create a dictionary whose keys are the received tsr_ids and whose values are a list of + # tsr_ids, each of which is contained in the received list of tsr_ids and whose associated + # repository must be installed prior to the repository associated with the tsr_id key. + prior_install_required_dict = suc.get_prior_import_or_install_required_dict( self.app, + tsr_ids, + repo_info_dicts ) + processed_tsr_ids = [] + while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ): + tsr_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_install_required_dict, + processed_tsr_ids ) + processed_tsr_ids.append( tsr_id ) + # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists. + if tsr_id not in ordered_tsr_ids: + prior_install_required_ids = prior_install_required_dict[ tsr_id ] + for prior_install_required_id in prior_install_required_ids: + if prior_install_required_id not in ordered_tsr_ids: + # Install the associated repository dependency first. + prior_repo_info_dict, prior_tool_panel_section_key = \ + self.get_repository_components_for_installation( prior_install_required_id, + tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) + ordered_tsr_ids.append( prior_install_required_id ) + ordered_repo_info_dicts.append( prior_repo_info_dict ) + ordered_tool_panel_section_keys.append( prior_tool_panel_section_key ) + repo_info_dict, tool_panel_section_key = \ + self.get_repository_components_for_installation( tsr_id, + tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) + ordered_tsr_ids.append( tsr_id ) + ordered_repo_info_dicts.append( repo_info_dict ) + ordered_tool_panel_section_keys.append( tool_panel_section_key ) + return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys + + def populate_containers_dict_for_new_install( self, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies, + updating=False ): + """ + Return the populated containers for a repository being installed for the first time or for an installed repository + that is being updated and the updates include newly defined repository (and possibly tool) dependencies. + """ + installed_tool_dependencies, missing_tool_dependencies = \ + tool_dependency_util.populate_tool_dependencies_dicts( app=self.app, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository_installed_tool_dependencies=installed_tool_dependencies, + repository_missing_tool_dependencies=missing_tool_dependencies, + required_repo_info_dicts=None ) + # Most of the repository contents are set to None since we don't yet know what they are. + containers_dict = \ + container_util.build_repository_containers_for_galaxy( app=self.app, + repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) + if not updating: + # If we installing a new repository and not updaing an installed repository, we can merge + # the missing_repository_dependencies container contents to the installed_repository_dependencies + # container. When updating an installed repository, merging will result in losing newly defined + # dependencies included in the updates. + containers_dict = self.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. + containers_dict = self.merge_missing_tool_dependencies_to_installed_container( containers_dict ) + return containers_dict diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -289,6 +289,117 @@ if installed_repository_dict[ 'display_path' ]: datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + def purge_repository( self, app, repository ): + """Purge a repository with status New (a white ghost) from the database.""" + sa_session = self.app.model.context.current + status = 'ok' + message = '' + purged_tool_versions = 0 + purged_tool_dependencies = 0 + purged_required_repositories = 0 + purged_orphan_repository_repository_dependency_association_records = 0 + purged_orphan_repository_dependency_records = 0 + if repository.is_new: + # Purge this repository's associated tool versions. + if repository.tool_versions: + for tool_version in repository.tool_versions: + try: + tool_version_association = tool_version.parent_tool_association + sa_session.delete( tool_version_association ) + sa_session.flush() + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + tool_version_association = tool_version.child_tool_association + sa_session.delete( tool_version_association ) + sa_session.flush() + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + sa_session.delete( tool_version ) + sa_session.flush() + purged_tool_versions += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge this repository's associated tool dependencies. + if repository.tool_dependencies: + for tool_dependency in repository.tool_dependencies: + try: + sa_session.delete( tool_dependency ) + sa_session.flush() + purged_tool_dependencies += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge tool_dependencies for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge this repository's associated required repositories. + if repository.required_repositories: + for rrda in repository.required_repositories: + try: + sa_session.delete( rrda ) + sa_session.flush() + purged_required_repositories += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge required_repositories for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge any "orphan" repository_dependency records associated with the repository, but not with any + # repository_repository_dependency_association records. + for orphan_repository_dependency in \ + sa_session.query( self.app.install_model.RepositoryDependency ) \ + .filter( self.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ): + # Purge any repository_repository_dependency_association records whose repository_dependency_id is + # the id of the orphan repository_dependency record. + for orphan_rrda in \ + sa_session.query( self.app.install_model.RepositoryRepositoryDependencyAssociation ) \ + .filter( self.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ): + try: + sa_session.delete( orphan_rrda ) + sa_session.flush() + purged_orphan_repository_repository_dependency_association_records += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge repository_repository_dependency_association records associated with ' + message += 'an orphan repository_dependency record for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + try: + sa_session.delete( orphan_repository_dependency ) + sa_session.flush() + purged_orphan_repository_dependency_records += 1 + except Exception, e: + status = 'error' + message = 'Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s.' % \ + ( str( repository.name ), str( repository.status ), str( e ) ) + return status, message + # Purge the repository. + sa_session.delete( repository ) + sa_session.flush() + message = 'The repository named <b>%s</b> with status <b>%s</b> has been purged.<br/>' % \ + ( str( repository.name ), str( repository.status ) ) + message += 'Total associated tool_version records purged: %d<br/>' % purged_tool_versions + message += 'Total associated tool_dependency records purged: %d<br/>' % purged_tool_dependencies + message += 'Total associated repository_repository_dependency_association records purged: %d<br/>' % purged_required_repositories + message += 'Total associated orphan repository_repository_dependency_association records purged: %d<br/>' % \ + purged_orphan_repository_repository_dependency_association_records + message += 'Total associated orphan repository_dependency records purged: %d<br/>' % purged_orphan_repository_dependency_records + else: + status = 'error' + message = 'A repository must have the status <b>New</b> in order to be purged. This repository has ' + message += ' the status %s.' % str( repository.status ) + return status, message + def remove_entry_from_installed_repository_dependencies_of_installed_repositories( self, repository ): """ Remove an entry from self.installed_repository_dependencies_of_installed_repositories. A side-effect of this method diff -r 7f506e778275715639d8f5d37041712be9662b39 -r 0a428afbc23538b6f8d0a8d9dcc29b9a576c1ddc lib/tool_shed/galaxy_install/repair_repository_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -0,0 +1,216 @@ +import logging +import os + +log = logging.getLogger( __name__ ) + +from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install import repository_util + +from tool_shed.util import common_install_util +from tool_shed.util import common_util +from tool_shed.util import container_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import repository_dependency_util +from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util + +class RepairRepositoryManager(): + + def __init__( self, app ): + self.app = app + + def get_installed_repositories_from_repository_dependencies( self, repository_dependencies_dict ): + installed_repositories = [] + if repository_dependencies_dict and isinstance( repository_dependencies_dict, dict ): + for rd_key, rd_vals in repository_dependencies_dict.items(): + if rd_key in [ 'root_key', 'description' ]: + continue + # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635f…' + # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] + repository_components_tuple = container_util.get_components_from_key( rd_key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] + installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app, + tool_shed, + name, + owner, + changeset_revision ) + if installed_repository not in installed_repositories: + installed_repositories.append( installed_repository ) + for rd_val in rd_vals: + tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] + installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app, + tool_shed, + name, + owner, + changeset_revision ) + if installed_repository not in installed_repositories: + installed_repositories.append( installed_repository ) + return installed_repositories + + def get_repair_dict( self, repository ): + """ + Inspect the installed repository dependency hierarchy for a specified repository + and attempt to make sure they are all properly installed as well as each repository's + tool dependencies. This method is called only from Galaxy when attempting to correct + issues with an installed repository that has installation problems somewhere in its + dependency hierarchy. + """ + tsr_ids = [] + repo_info_dicts = [] + tool_panel_section_keys = [] + repair_dict = {} + irm = install_manager.InstallRepositoryManager( self.app ) + # Get a dictionary of all repositories upon which the contents of the current repository_metadata + #record depend. + repository_dependencies_dict = \ + repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( self.app, repository ) + if repository_dependencies_dict: + # Generate the list of installed repositories from the information contained in the + # repository_dependencies dictionary. + installed_repositories = self.get_installed_repositories_from_repository_dependencies( repository_dependencies_dict ) + # Some repositories may have repository dependencies that are required to be installed before + # the dependent repository, so we'll order the list of tsr_ids to ensure all repositories are + # repaired in the required order. + for installed_repository in installed_repositories: + tsr_ids.append( self.app.security.encode_id( installed_repository.id ) ) + repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( installed_repository ) + tool_panel_section_keys.append( tool_panel_section_key ) + repo_info_dicts.append( repo_info_dict ) + else: + # The received repository has no repository dependencies. + tsr_ids.append( self.app.security.encode_id( repository.id ) ) + repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( repository ) + tool_panel_section_keys.append( tool_panel_section_key ) + repo_info_dicts.append( repo_info_dict ) + ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ + irm.order_components_for_installation( tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) + repair_dict[ 'ordered_tsr_ids' ] = ordered_tsr_ids + repair_dict[ 'ordered_repo_info_dicts' ] = ordered_repo_info_dicts + repair_dict[ 'ordered_tool_panel_section_keys' ] = ordered_tool_panel_section_keys + return repair_dict + + def get_repo_info_dict_for_repair( self, repository ): + tool_panel_section_key = None + repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( self.app, repository ) + metadata = repository.metadata + if metadata: + tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_panel_section_dict = metadata.get( 'tool_panel_section', None ) + if tool_panel_section_dict: + # The repository must be in the uninstalled state. The structure of tool_panel_section_dict is: + # {<tool guid> : + # [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]} + # Here is an example: + # {"localhost:9009/repos/test/filter/Filter1/1.1.0": + # [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]} + # Currently all tools contained within an installed tool shed repository must be loaded into the same + # section in the tool panel, so we can get the section id of the first guid in the tool_panel_section_dict. + # In the future, we'll have to handle different sections per guid. + guid = tool_panel_section_dict.keys()[ 0 ] + section_dicts = tool_panel_section_dict[ guid ] + section_dict = section_dicts[ 0 ] + tool_panel_section_id = section_dict[ 'id' ] + tool_panel_section_name = section_dict[ 'name' ] + if tool_panel_section_id: + tool_panel_section_key, tool_panel_section = \ + tool_util.get_or_create_tool_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=tool_panel_section_name ) + else: + tool_dependencies = None + repo_info_dict = repository_util.create_repo_info_dict( app=self.app, + repository_clone_url=repository_clone_url, + changeset_revision=repository.changeset_revision, + ctx_rev=repository.ctx_rev, + repository_owner=repository.owner, + repository_name=repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) + return repo_info_dict, tool_panel_section_key + + def repair_tool_shed_repository( self, repository, repo_info_dict ): + + def add_repair_dict_entry( repository_name, error_message ): + if repository_name in repair_dict: + repair_dict[ repository_name ].append( error_message ) + else: + repair_dict[ repository_name ] = [ error_message ] + return repair_dict + + metadata = repository.metadata + repair_dict = {} + if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]: + try: + common_install_util.activate_repository( self.app, repository ) + except Exception, e: + error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) ) + log.debug( error_message ) + repair_dict [ repository.name ] = error_message + elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]: + shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) + # Reset the repository attributes to the New state for installation. + if metadata: + tool_section, tool_panel_section_key = \ + tool_util.handle_tool_panel_selection( self.app.toolbox, + metadata, + no_changes_checked=True, + tool_panel_section_id=None, + new_tool_panel_section_label=None ) + else: + # The tools will be loaded outside of any sections in the tool panel. + tool_panel_section_key = None + suc.set_repository_attributes( self.app, + repository, + status=self.app.install_model.ToolShedRepository.installation_status.NEW, + error_message=None, + deleted=False, + uninstalled=False, + remove_from_disk=True ) + irm = install_manager.InstallRepositoryManager( self.app ) + irm.install_tool_shed_repository( repository, + repo_info_dict, + tool_panel_section_key, + shed_tool_conf, + tool_path, + install_tool_dependencies=True, + reinstalling=True ) + if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.ERROR ]: + repair_dict = add_repair_dict_entry( repository.name, repository.error_message ) + else: + # We have an installed tool shed repository, so handle tool dependencies if necessary. + if repository.missing_tool_dependencies and metadata and 'tool_dependencies' in metadata: + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itdep" ) + # Reset missing tool dependencies. + for tool_dependency in repository.missing_tool_dependencies: + if tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR, + self.app.install_model.ToolDependency.installation_status.INSTALLING ]: + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( self.app, + tool_dependency=tool_dependency, + status=self.app.install_model.ToolDependency.installation_status.UNINSTALLED, + error_message=None, + remove_from_disk=True ) + # Install tool dependencies. + suc.update_tool_shed_repository_status( self.app, + repository, + self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + # Get the tool_dependencies.xml file from the repository. + tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( self.app ) ) + itdm = install_manager.InstallToolDependencyManager( self.app ) + installed_tool_dependencies = itdm.install_specified_tool_dependencies( tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) + for installed_tool_dependency in installed_tool_dependencies: + if installed_tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR ]: + repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) + basic_util.remove_dir( work_dir ) + suc.update_tool_shed_repository_status( self.app, repository, self.app.install_model.ToolShedRepository.installation_status.INSTALLED ) + return repair_dict \ No newline at end of file This diff is so big that we needed to truncate the remainder. 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 16 Jun '14

16 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0c0517794198/ Changeset: 0c0517794198 User: jmchilton Date: 2014-06-16 20:08:37 Summary: Redo 74826a5: Attempt fix of UI problems when collections & datasets in same history have same id. Approach outlined by Carl, introduces separation between Backbone model id and underlying Galaxy id. Backbone id now includes type in the id. Lots of switching around which id is used where - probably introduces some bugs if I failed to update which id is to be used or switched to wrong one. Affected #: 6 files diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ b/static/scripts/mvc/collection/dataset-collection-base.js @@ -144,7 +144,7 @@ contentView.$el.children( '.dataset-body' ).replaceWith( contentView._render_body() ); contentView.$el.children( '.dataset-body' ).slideDown( contentView.fxSpeed, function(){ contentView.expanded = true; - contentView.trigger( 'body-expanded', contentView.model.get( 'id' ) ); + contentView.trigger( 'body-expanded', contentView.model ); }); } // TODO: Fetch more details like HDA view... @@ -158,7 +158,7 @@ var hdaView = this; this.$el.children( '.dataset-body' ).slideUp( hdaView.fxSpeed, function(){ hdaView.expanded = false; - hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); + hdaView.trigger( 'body-collapsed', hdaView.model.id ); }); }, diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -319,7 +319,7 @@ title : "Data Viewer: " + self.model.get('name'), type : "other", content : function(parent_elt) { - var new_dataset = new dataset.TabularDataset({id: self.model.id}); + var new_dataset = new dataset.TabularDataset({id: self.model.get('id')}); $.when(new_dataset.fetch()).then(function() { dataset.createTabularDatasetChunkedView({ model: new_dataset, @@ -568,7 +568,7 @@ hdaView.$el.children( '.dataset-body' ).replaceWith( hdaView._render_body() ); hdaView.$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){ hdaView.expanded = true; - hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); + hdaView.trigger( 'body-expanded', hdaView.model ); }); //hdaView.render( false ).$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){ @@ -595,7 +595,7 @@ var hdaView = this; this.$el.children( '.dataset-body' ).slideUp( hdaView.fxSpeed, function(){ hdaView.expanded = false; - hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); + hdaView.trigger( 'body-collapsed', hdaView.model.id ); }); }, diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -12,9 +12,22 @@ * @constructs */ var HistoryContent = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( { + idAttribute : 'type_id', /** fetch location of this HDA's history in the api */ urlRoot: galaxy_config.root + 'api/histories/', + + constructor : function( attrs, options ){ + attrs.type_id = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); + Backbone.Model.apply( this, arguments ); + }, + + initialize : function( attrs, options ){ + // assumes type won't change + this.on( 'change:id', this._createTypeId ); + //TODO: not sure this covers all the bases... + }, + /** full url spec. for this HDA */ url : function(){ return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get('history_content_type') + 's/' + this.get( 'id' ); @@ -138,10 +151,19 @@ term = term.replace( /"/g, '' ); return model.matches( term ); }); - } + }, + + _createTypeId : function(){ + this.set( 'type_id', TypeIdModel.typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ) ); + }, } ); +/** create a type + id string for use in mixed collections */ +HistoryContent.typeIdStr = function _typeId( type, id ){ + return [ type, id ].join( '-' ); +}; + //============================================================================== /** @class (HDA) model for a Galaxy dataset * related to a history. @@ -228,7 +250,7 @@ initialize : function( data ){ this.log( this + '.initialize', this.attributes ); this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - + //!! this state is not in trans.app.model.Dataset.states - set it here - if( !this.get( 'accessible' ) ){ this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); @@ -482,7 +504,7 @@ * @returns array of encoded ids */ ids : function(){ - return this.map( function( hda ){ return hda.id; }); + return this.map( function( hda ){ return hda.get('id'); }); }, /** Get hdas that are not ready @@ -614,7 +636,9 @@ // see Backbone.Collection.set and _prepareModel var collection = this; models = _.map( models, function( model ){ - var existing = collection.get( model.id ); + var attrs = model.attributes || model; // Handle raw json or Backbone model. + var typeId = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); + var existing = collection.get( typeId ); if( !existing ){ return model; } // merge the models _BEFORE_ calling the superclass version @@ -643,7 +667,7 @@ this.chain().each( function( hda ) { // TODO: Handle duplicate names. var name = hda.attributes.name; - var id = hda.id; + var id = hda.get('id'); var content_type = hda.attributes.history_content_type; if( content_type == "dataset" ) { if( full_collection_type != "list" ) { diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -236,7 +236,7 @@ // for symmetry, not actually used by backend of consumed // by frontend. data[ "dataset_collection_details" ] = hdcaDetailIds.join( ',' ); - } + } return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data }); } diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -273,7 +273,7 @@ * @param {HistoryDatasetAssociation} hda */ _createContentView : function( hda ){ - var hdaId = hda.get( 'id' ), + var hdaId = hda.id, historyContentType = hda.get( 'history_content_type' ), hdaView = null; @@ -328,7 +328,7 @@ // only } else { - var id = hdaView.model.get( 'id' ); + var id = hdaView.model.id; historyView.lastSelectedViewId = id; //console.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); selectedIds = [ id ]; @@ -340,7 +340,7 @@ }); hdaView.on( 'de-selected', function( hdaView, event ){ //console.debug( 'de-selected', event ); - var id = hdaView.model.get( 'id' ); + var id = hdaView.model.id; historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); //console.debug( 'de-selected', historyView.selectedHdaIds ); }); diff -r 1b2fdf69104d821fa3a52e04321d5795d6f4c6d0 -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -18,9 +18,9 @@ //TODO: add scroll position? }, /** add an hda id to the hash of expanded hdas */ - addExpandedHda : function( id ){ + addExpandedHda : function( model ){ var key = 'expandedHdas'; - this.save( key, _.extend( this.get( key ), _.object([ id ], [ true ]) ) ); + this.save( key, _.extend( this.get( key ), _.object([ model.id ], [ model.get( 'id' ) ]) ) ); }, /** remove an hda id from the hash of expanded hdas */ removeExpandedHda : function( id ){ @@ -264,7 +264,7 @@ var hdaDetailIds = function( historyData ){ // will be called to get hda ids that need details from the api //TODO: non-visible HDAs are getting details loaded... either stop loading them at all or filter ids thru isVisible - return _.keys( HistoryPrefs.get( historyData.id ).get( 'expandedHdas' ) ); + return _.values( HistoryPrefs.get( historyData.id ).get( 'expandedHdas' ) ); }; return this.loadHistory( historyId, attributes, historyFn, hdaFn, hdaDetailIds ); }, @@ -591,7 +591,7 @@ if( visibleHdas.length ){ visibleHdas.each( function( hda ){ // render it (NOTE: reverse order, newest on top (prepend)) - var hdaId = hda.get( 'id' ), + var hdaId = hda.id, hdaView = panel._createContentView( hda ); newHdaViews[ hdaId ] = hdaView; // persist selection @@ -610,7 +610,7 @@ * @param {HistoryDatasetAssociation} hda */ _createContentView : function( hda ){ - var hdaId = hda.get( 'id' ), + var hdaId = hda.id, historyContentType = hda.get( "history_content_type" ), hdaView = null; if( historyContentType === "dataset" ){ @@ -646,8 +646,8 @@ panel.errorHandler( model, xhr, options, msg ); }); // maintain a list of hdas whose bodies are expanded - hdaView.on( 'body-expanded', function( id ){ - panel.storage.addExpandedHda( id ); + hdaView.on( 'body-expanded', function( model ){ + panel.storage.addExpandedHda( model ); }); hdaView.on( 'body-collapsed', function( id ){ panel.storage.removeExpandedHda( id ); https://bitbucket.org/galaxy/galaxy-central/commits/7f506e778275/ Changeset: 7f506e778275 User: jmchilton Date: 2014-06-16 20:09:54 Summary: Pack scripts. Affected #: 5 files diff -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 -r 7f506e778275715639d8f5d37041712be9662b39 static/scripts/packed/mvc/collection/dataset-collection-base.js --- a/static/scripts/packed/mvc/collection/dataset-collection-base.js +++ b/static/scripts/packed/mvc/collection/dataset-collection-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(b,a){var c=a.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(d){if(d.logger){this.logger=this.model.logger=d.logger}this.log(this+".initialize:",d);this.selectable=d.selectable||false;this.selected=d.selected||false;this.expanded=d.expanded||false},render:function(e){var d=this._buildNewRender();this._queueNewRender(d,e);return this},templateSkeleton:function(){return['<div class="dataset hda">','<div class="dataset-warnings">',"<% if ( deleted ) { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</div>","<% } %>","<% if ( ! visible ) { %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%= hid %></span> ','<span class="dataset-name"><%= name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("")},templateBody:function(){return['<div class="dataset-body">','<div class="dataset-summary">',"A dataset collection.","</div>"].join("")},_buildNewRender:function(){var d=$(_.template(this.templateSkeleton(),this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);return d},_render_titleButtons:function(){return[]},_render_body:function(){var e=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),d=this["_render_body_"+this.model.get("state")];if(_.isFunction(d)){e=d.call(this)}this._setUpBehaviors(e);if(this.expanded){e.show()}return e},_setUpBehaviors:function(d){d=d||this.$el;make_popup_menus(d);d.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var d=this;function e(){d.$el.children(".dataset-body").replaceWith(d._render_body());d.$el.children(".dataset-body").slideDown(d.fxSpeed,function(){d.expanded=true;d.trigger("body-expanded",d.model.get("id"))})}e()},collapseBody:function(){var d=this;this.$el.children(".dataset-body").slideUp(d.fxSpeed,function(){d.expanded=false;d.trigger("body-collapsed",d.model.get("id"))})},_render_body_ok:function(){var d=$(_.template(this.templateBody(),this.model.toJSON()));if(this.model.get("deleted")){return d}return d}});return{DatasetCollectionBaseView:c}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(b,a){var c=a.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(d){if(d.logger){this.logger=this.model.logger=d.logger}this.log(this+".initialize:",d);this.selectable=d.selectable||false;this.selected=d.selected||false;this.expanded=d.expanded||false},render:function(e){var d=this._buildNewRender();this._queueNewRender(d,e);return this},templateSkeleton:function(){return['<div class="dataset hda">','<div class="dataset-warnings">',"<% if ( deleted ) { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</div>","<% } %>","<% if ( ! visible ) { %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%= hid %></span> ','<span class="dataset-name"><%= name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("")},templateBody:function(){return['<div class="dataset-body">','<div class="dataset-summary">',"A dataset collection.","</div>"].join("")},_buildNewRender:function(){var d=$(_.template(this.templateSkeleton(),this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);return d},_render_titleButtons:function(){return[]},_render_body:function(){var e=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),d=this["_render_body_"+this.model.get("state")];if(_.isFunction(d)){e=d.call(this)}this._setUpBehaviors(e);if(this.expanded){e.show()}return e},_setUpBehaviors:function(d){d=d||this.$el;make_popup_menus(d);d.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var d=this;function e(){d.$el.children(".dataset-body").replaceWith(d._render_body());d.$el.children(".dataset-body").slideDown(d.fxSpeed,function(){d.expanded=true;d.trigger("body-expanded",d.model)})}e()},collapseBody:function(){var d=this;this.$el.children(".dataset-body").slideUp(d.fxSpeed,function(){d.expanded=false;d.trigger("body-collapsed",d.model.id)})},_render_body_ok:function(){var d=$(_.template(this.templateBody(),this.model.toJSON()));if(this.model.get("deleted")){return d}return d}});return{DatasetCollectionBaseView:c}}); \ No newline at end of file diff -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 -r 7f506e778275715639d8f5d37041712be9662b39 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","mvc/data","utils/localization"],function(e,b,g,d){var h=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",fxSpeed:"fast",_queueNewRender:function(j,k){k=(k===undefined)?(true):(k);var i=this;if(k){$(i).queue(function(l){this.$el.fadeOut(i.fxSpeed,l)})}$(i).queue(function(l){this.$el.empty().attr("class",i.className).addClass("state-"+i.model.get("state")).append(j.children());if(this.selectable){this.showSelector(0)}l()});if(k){$(i).queue(function(l){this.$el.fadeIn(i.fxSpeed,l)})}$(i).queue(function(l){this.trigger("rendered",i);if(this.model.inReadyState()){this.trigger("rendered:ready",i)}if(this.draggable){this.draggableOn()}l()})},toggleBodyVisibility:function(l,j){var i=32,k=13;if(l&&(l.type==="keydown")&&!(l.keyCode===i||l.keyCode===k)){return true}var m=this.$el.find(".dataset-body");j=(j===undefined)?(!m.is(":visible")):(j);if(j){this.expandBody()}else{this.collapseBody()}return false},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(i){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,i);this.selected=true}return false},deselect:function(i){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,i);this.selected=false}return false},toggleSelect:function(i){if(this.selected){this.deselect(i)}else{this.select(i)}}});var c=h.extend({className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+".initialize:",i);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=i.linkTarget||"_blank";this.selectable=i.selectable||false;this.selected=i.selected||false;this.expanded=i.expanded||false;this.draggable=i.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(j,i){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(j){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var i=this._buildNewRender();this._queueNewRender(i,j);return this},_buildNewRender:function(){var i=$(c.templates.skeleton(this.model.toJSON()));i.find(".dataset-primary-actions").append(this._render_titleButtons());i.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(i);return i},_setUpBehaviors:function(i){i=i||this.$el;make_popup_menus(i);i.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===e.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===e.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var j={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){j.disabled=true;j.title=d("Cannot display datasets removed from disk")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=d("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=d("This dataset is not yet viewable")}else{j.title=d("View data");j.href=this.urls.display;var i=this;j.onclick=function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+i.model.get("name"),type:"other",content:function(l){var m=new g.TabularDataset({id:i.model.id});$.when(m.fetch()).then(function(){g.createTabularDatasetChunkedView({model:m,parent_elt:l,embedded:true,height:"100%"})})}});k.preventDefault()}}}}}j.faIcon="fa-eye";return faIconButton(j)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var j=this.urls,k=this.model.get("meta_files");if(_.isEmpty(k)){return $(['<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var l="dataset-"+this.model.get("id")+"-popup",i=['<div popupmenu="'+l+'">','<a href="'+j.download+'">',d("Download dataset"),"</a>","<a>"+d("Additional files")+"</a>",_.map(k,function(m){return['<a class="action-button" href="',j.meta_download+m.file_type,'">',d("Download")," ",m.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+l+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(i)},_render_showParamsButton:function(){return faIconButton({title:d("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var j=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),i=this["_render_body_"+this.model.get("state")];if(_.isFunction(i)){j=i.call(this)}this._setUpBehaviors(j);if(this.expanded){j.show()}return j},_render_stateBodyHelper:function(i,l){l=l||[];var j=this,k=$(c.templates.body(_.extend(this.model.toJSON(),{body:i})));k.find(".dataset-actions .left").append(_.map(l,function(m){return m.call(j)}));return k},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+d("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+d("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+d("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+d("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+d("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+d("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+d("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+d('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var i=['<span class="help-text">',d("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){i="<div>"+this.model.get("misc_blurb")+"</div>"+i}return this._render_stateBodyHelper(i,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+d("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var i=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(d("An error occurred setting the metadata for this dataset"))),j=this._render_body_ok();j.prepend(i);return j},_render_body_ok:function(){var i=this,k=$(c.templates.body(this.model.toJSON())),j=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);k.find(".dataset-actions .left").append(_.map(j,function(l){return l.call(i)}));if(this.model.isDeletedOrPurged()){return k}return k},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var i=this;function j(){i.$el.children(".dataset-body").replaceWith(i._render_body());i.$el.children(".dataset-body").slideDown(i.fxSpeed,function(){i.expanded=true;i.trigger("body-expanded",i.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(k){i.urls=i.model.urls();j()})}else{j()}},collapseBody:function(){var i=this;this.$el.children(".dataset-body").slideUp(i.fxSpeed,function(){i.expanded=false;i.trigger("body-collapsed",i.model.get("id"))})},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var i=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);i.addEventListener("dragstart",this.dragStartHandler,false);i.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var i=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);i.removeEventListener("dragstart",this.dragStartHandler,false);i.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(i){this.trigger("dragstart",this);i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(i){this.trigger("dragend",this);return false},remove:function(j){var i=this;this.$el.fadeOut(i.fxSpeed,function(){i.$el.remove();i.off();if(j){j()}})},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+i+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',d("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',d("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',d("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var f=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',d("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',d("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));c.templates={skeleton:function(i){return a({_l:d,hda:i})},body:function(i){return f({_l:d,hda:i})}};return{HistoryContentBaseView:h,HDABaseView:c}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc","mvc/data","utils/localization"],function(e,b,g,d){var h=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",fxSpeed:"fast",_queueNewRender:function(j,k){k=(k===undefined)?(true):(k);var i=this;if(k){$(i).queue(function(l){this.$el.fadeOut(i.fxSpeed,l)})}$(i).queue(function(l){this.$el.empty().attr("class",i.className).addClass("state-"+i.model.get("state")).append(j.children());if(this.selectable){this.showSelector(0)}l()});if(k){$(i).queue(function(l){this.$el.fadeIn(i.fxSpeed,l)})}$(i).queue(function(l){this.trigger("rendered",i);if(this.model.inReadyState()){this.trigger("rendered:ready",i)}if(this.draggable){this.draggableOn()}l()})},toggleBodyVisibility:function(l,j){var i=32,k=13;if(l&&(l.type==="keydown")&&!(l.keyCode===i||l.keyCode===k)){return true}var m=this.$el.find(".dataset-body");j=(j===undefined)?(!m.is(":visible")):(j);if(j){this.expandBody()}else{this.collapseBody()}return false},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(i){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,i);this.selected=true}return false},deselect:function(i){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,i);this.selected=false}return false},toggleSelect:function(i){if(this.selected){this.deselect(i)}else{this.select(i)}}});var c=h.extend({className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+".initialize:",i);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=i.linkTarget||"_blank";this.selectable=i.selectable||false;this.selected=i.selected||false;this.expanded=i.expanded||false;this.draggable=i.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(j,i){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(j){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var i=this._buildNewRender();this._queueNewRender(i,j);return this},_buildNewRender:function(){var i=$(c.templates.skeleton(this.model.toJSON()));i.find(".dataset-primary-actions").append(this._render_titleButtons());i.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(i);return i},_setUpBehaviors:function(i){i=i||this.$el;make_popup_menus(i);i.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===e.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===e.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var j={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){j.disabled=true;j.title=d("Cannot display datasets removed from disk")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=d("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=d("This dataset is not yet viewable")}else{j.title=d("View data");j.href=this.urls.display;var i=this;j.onclick=function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+i.model.get("name"),type:"other",content:function(l){var m=new g.TabularDataset({id:i.model.get("id")});$.when(m.fetch()).then(function(){g.createTabularDatasetChunkedView({model:m,parent_elt:l,embedded:true,height:"100%"})})}});k.preventDefault()}}}}}j.faIcon="fa-eye";return faIconButton(j)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var j=this.urls,k=this.model.get("meta_files");if(_.isEmpty(k)){return $(['<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var l="dataset-"+this.model.get("id")+"-popup",i=['<div popupmenu="'+l+'">','<a href="'+j.download+'">',d("Download dataset"),"</a>","<a>"+d("Additional files")+"</a>",_.map(k,function(m){return['<a class="action-button" href="',j.meta_download+m.file_type,'">',d("Download")," ",m.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+l+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(i)},_render_showParamsButton:function(){return faIconButton({title:d("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var j=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),i=this["_render_body_"+this.model.get("state")];if(_.isFunction(i)){j=i.call(this)}this._setUpBehaviors(j);if(this.expanded){j.show()}return j},_render_stateBodyHelper:function(i,l){l=l||[];var j=this,k=$(c.templates.body(_.extend(this.model.toJSON(),{body:i})));k.find(".dataset-actions .left").append(_.map(l,function(m){return m.call(j)}));return k},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+d("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+d("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+d("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+d("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+d("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+d("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+d("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+d('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var i=['<span class="help-text">',d("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){i="<div>"+this.model.get("misc_blurb")+"</div>"+i}return this._render_stateBodyHelper(i,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+d("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var i=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(d("An error occurred setting the metadata for this dataset"))),j=this._render_body_ok();j.prepend(i);return j},_render_body_ok:function(){var i=this,k=$(c.templates.body(this.model.toJSON())),j=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);k.find(".dataset-actions .left").append(_.map(j,function(l){return l.call(i)}));if(this.model.isDeletedOrPurged()){return k}return k},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var i=this;function j(){i.$el.children(".dataset-body").replaceWith(i._render_body());i.$el.children(".dataset-body").slideDown(i.fxSpeed,function(){i.expanded=true;i.trigger("body-expanded",i.model)})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(k){i.urls=i.model.urls();j()})}else{j()}},collapseBody:function(){var i=this;this.$el.children(".dataset-body").slideUp(i.fxSpeed,function(){i.expanded=false;i.trigger("body-collapsed",i.model.id)})},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var i=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);i.addEventListener("dragstart",this.dragStartHandler,false);i.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var i=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);i.removeEventListener("dragstart",this.dragStartHandler,false);i.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(i){this.trigger("dragstart",this);i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(i){this.trigger("dragend",this);return false},remove:function(j){var i=this;this.$el.fadeOut(i.fxSpeed,function(){i.$el.remove();i.off();if(j){j()}})},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+i+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',d("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',d("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',d("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var f=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',d("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',d("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));c.templates={skeleton:function(i){return a({_l:d,hda:i})},body:function(i){return f({_l:d,hda:i})}};return{HistoryContentBaseView:h,HDABaseView:c}}); \ No newline at end of file diff -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 -r 7f506e778275715639d8f5d37041712be9662b39 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},isVisible:function(n,o){var m=true;if((!n)&&(this.get("deleted")||this.get("purged"))){m=false}if((!o)&&(!this.get("visible"))){m=false}return m},searchAttribute:function(o,m){var n=this.get(o);if(!m||(n===undefined||n===null)){return false}if(_.isArray(n)){return this._searchArrayAttribute(n,m)}return(n.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)},_searchArrayAttribute:function(n,m){m=m.toLowerCase();return _.any(n,function(o){return(o.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)})},search:function(m){var n=this;return _.filter(this.searchAttributes,function(o){return n.searchAttribute(o,m)})},matches:function(n){var p="=",m=n.split(p);if(m.length>=2){var o=m[0];o=this.searchAliases[o]||o;return this.searchAttribute(o,m[1])}return !!this.search(n).length},matchesAll:function(n){var m=this;n=n.match(/(".*"|\w*=".*"|\S*)/g).filter(function(o){return !!o});return _.all(n,function(o){o=o.replace(/"/g,"");return m.matches(o)})}});var l=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var n=this.get("id");if(!n){return{}}var m={purge:galaxy_config.root+"datasets/"+n+"/purge_async",display:galaxy_config.root+"datasets/"+n+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+n+"/edit",download:galaxy_config.root+"datasets/"+n+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+n,rerun:galaxy_config.root+"tool_runner/rerun?id="+n,show_params:galaxy_config.root+"datasets/"+n+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+n,set:galaxy_config.root+"dataset/annotate_async?id="+n},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+n+"&metadata_name="};return m},initialize:function(m){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",l.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(n,m){this.log(this+" has changed state:",n,m);if(this.inReadyState()){this.trigger("state:ready",n,m,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var m=_.contains(l.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||m)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},purge:function g(m){if(this.get("purged")){return jQuery.when()}m=m||{};m.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var n=this,o=jQuery.ajax(m);o.done(function(r,p,q){n.set({deleted:true,purged:true})});o.fail(function(t,p,s){var q=c("Unable to purge dataset");var r=("Removal of datasets by users is not allowed in this Galaxy instance");if(t.responseJSON&&t.responseJSON.error){q=t.responseJSON.error}else{if(t.responseText.indexOf(r)!==-1){q=r}}t.responseText=q;n.trigger("error",n,t,m,c(q),{error:q})});return o},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var m=this.get("id")||"";if(this.get("name")){m=this.get("hid")+' :"'+this.get("name")+'",'+m}return"HDA("+m+")"}});l.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};l.READY_STATES=[l.STATES.OK,l.STATES.EMPTY,l.STATES.PAUSED,l.STATES.FAILED_METADATA,l.STATES.NOT_VIEWABLE,l.STATES.DISCARDED,l.STATES.ERROR];l.NOT_READY_STATES=[l.STATES.UPLOAD,l.STATES.QUEUED,l.STATES.RUNNING,l.STATES.SETTING_METADATA,l.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(n,m){if(n.history_content_type=="dataset"){return new l(n,m)}else{if(n.history_content_type=="dataset_collection"){return new j(n,m)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(n,m){m=m||{};this.historyId=m.historyId},ids:function(){return this.map(function(m){return m.id})},notReady:function(){return this.filter(function(m){return !m.inReadyState()})},running:function(){var m=[];this.each(function(n){if(!n.inReadyState()){m.push(n.get("id"))}});return m},getByHid:function(m){return _.first(this.filter(function(n){return n.get("hid")===m}))},getVisible:function(m,p,o){o=o||[];var n=new b(this.filter(function(q){return q.isVisible(m,p)}));_.each(o,function(q){if(!_.isFunction(q)){return}n=new b(n.filter(q))});return n},haveDetails:function(){return this.all(function(m){return m.hasDetails()})},fetchAllDetails:function(n){n=n||{};var m={details:"all"};n.data=(n.data)?(_.extend(n.data,m)):(m);return this.fetch(n)},ajaxQueue:function(p,o){var n=jQuery.Deferred(),m=this.length,r=[];if(!m){n.resolve([]);return n}var q=this.chain().reverse().map(function(t,s){return function(){var u=p.call(t,o);u.done(function(v){n.notify({curr:s,total:m,response:v,model:t})});u.always(function(v){r.push(v);if(q.length){q.shift()()}else{n.resolve(r)}})}}).value();q.shift()();return n},matches:function(m){return this.filter(function(n){return n.matches(m)})},set:function(o,m){var n=this;o=_.map(o,function(q){var r=n.get(q.id);if(!r){return q}var p=r.toJSON();_.extend(p,q);return p});Backbone.Collection.prototype.set.call(this,o,m)},promoteToHistoryDatasetCollection:function k(r,p,n){n=n||{};n.url=this.url();n.type="POST";var t=p;var q=[],m=null;if(p=="list"){this.chain().each(function(w){var u=w.attributes.name;var x=w.id;var v=w.attributes.history_content_type;if(v=="dataset"){if(t!="list"){console.log("Invalid collection type")}q.push({name:u,src:"hda",id:x})}else{if(t=="list"){t="list:"+w.attributes.collection_type}else{if(t!="list:"+w.attributes.collection_type){console.log("Invalid collection type")}}q.push({name:u,src:"hdca",id:x})}});m="New Dataset List"}else{if(p=="paired"){var o=this.ids();if(o.length!=2){}q.push({name:"forward",src:"hda",id:o[0]});q.push({name:"reverse",src:"hda",id:o[1]});m="New Dataset Pair"}}n.data={type:"dataset_collection",name:m,collection_type:t,element_identifiers:JSON.stringify(q),};var s=jQuery.ajax(n);s.done(function(w,u,v){r.refresh()});s.fail(function(w,u,v){if(w.responseJSON&&w.responseJSON.error){error=w.responseJSON.error}else{error=w.responseJSON}w.responseText=error});return s},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var j=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:l,HDACollection:b}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({idAttribute:"type_id",urlRoot:galaxy_config.root+"api/histories/",constructor:function(o,n){o.type_id=a.typeIdStr(o.history_content_type,o.id);Backbone.Model.apply(this,arguments)},initialize:function(o,n){this.on("change:id",this._createTypeId)},url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},isVisible:function(o,p){var n=true;if((!o)&&(this.get("deleted")||this.get("purged"))){n=false}if((!p)&&(!this.get("visible"))){n=false}return n},searchAttribute:function(p,n){var o=this.get(p);if(!n||(o===undefined||o===null)){return false}if(_.isArray(o)){return this._searchArrayAttribute(o,n)}return(o.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)},_searchArrayAttribute:function(o,n){n=n.toLowerCase();return _.any(o,function(p){return(p.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)})},search:function(n){var o=this;return _.filter(this.searchAttributes,function(p){return o.searchAttribute(p,n)})},matches:function(o){var q="=",n=o.split(q);if(n.length>=2){var p=n[0];p=this.searchAliases[p]||p;return this.searchAttribute(p,n[1])}return !!this.search(o).length},matchesAll:function(o){var n=this;o=o.match(/(".*"|\w*=".*"|\S*)/g).filter(function(p){return !!p});return _.all(o,function(p){p=p.replace(/"/g,"");return n.matches(p)})},_createTypeId:function(){this.set("type_id",TypeIdModel.typeIdStr(this.get("history_content_type"),this.get("id")))},});a.typeIdStr=function h(n,o){return[n,o].join("-")};var m=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var o=this.get("id");if(!o){return{}}var n={purge:galaxy_config.root+"datasets/"+o+"/purge_async",display:galaxy_config.root+"datasets/"+o+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+o+"/edit",download:galaxy_config.root+"datasets/"+o+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+o,rerun:galaxy_config.root+"tool_runner/rerun?id="+o,show_params:galaxy_config.root+"datasets/"+o+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+o,set:galaxy_config.root+"dataset/annotate_async?id="+o},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+o+"&metadata_name="};return n},initialize:function(n){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",m.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(o,n){this.log(this+" has changed state:",o,n);if(this.inReadyState()){this.trigger("state:ready",o,n,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var n=_.contains(m.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||n)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},purge:function g(n){if(this.get("purged")){return jQuery.when()}n=n||{};n.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var o=this,p=jQuery.ajax(n);p.done(function(s,q,r){o.set({deleted:true,purged:true})});p.fail(function(u,q,t){var r=c("Unable to purge dataset");var s=("Removal of datasets by users is not allowed in this Galaxy instance");if(u.responseJSON&&u.responseJSON.error){r=u.responseJSON.error}else{if(u.responseText.indexOf(s)!==-1){r=s}}u.responseText=r;o.trigger("error",o,u,n,c(r),{error:r})});return p},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var n=this.get("id")||"";if(this.get("name")){n=this.get("hid")+' :"'+this.get("name")+'",'+n}return"HDA("+n+")"}});m.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};m.READY_STATES=[m.STATES.OK,m.STATES.EMPTY,m.STATES.PAUSED,m.STATES.FAILED_METADATA,m.STATES.NOT_VIEWABLE,m.STATES.DISCARDED,m.STATES.ERROR];m.NOT_READY_STATES=[m.STATES.UPLOAD,m.STATES.QUEUED,m.STATES.RUNNING,m.STATES.SETTING_METADATA,m.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(o,n){if(o.history_content_type=="dataset"){return new m(o,n)}else{if(o.history_content_type=="dataset_collection"){return new k(o,n)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(o,n){n=n||{};this.historyId=n.historyId},ids:function(){return this.map(function(n){return n.get("id")})},notReady:function(){return this.filter(function(n){return !n.inReadyState()})},running:function(){var n=[];this.each(function(o){if(!o.inReadyState()){n.push(o.get("id"))}});return n},getByHid:function(n){return _.first(this.filter(function(o){return o.get("hid")===n}))},getVisible:function(n,q,p){p=p||[];var o=new b(this.filter(function(r){return r.isVisible(n,q)}));_.each(p,function(r){if(!_.isFunction(r)){return}o=new b(o.filter(r))});return o},haveDetails:function(){return this.all(function(n){return n.hasDetails()})},fetchAllDetails:function(o){o=o||{};var n={details:"all"};o.data=(o.data)?(_.extend(o.data,n)):(n);return this.fetch(o)},ajaxQueue:function(q,p){var o=jQuery.Deferred(),n=this.length,s=[];if(!n){o.resolve([]);return o}var r=this.chain().reverse().map(function(u,t){return function(){var v=q.call(u,p);v.done(function(w){o.notify({curr:t,total:n,response:w,model:u})});v.always(function(w){s.push(w);if(r.length){r.shift()()}else{o.resolve(s)}})}}).value();r.shift()();return o},matches:function(n){return this.filter(function(o){return o.matches(n)})},set:function(p,n){var o=this;p=_.map(p,function(s){var r=s.attributes||s;var t=a.typeIdStr(r.history_content_type,r.id);var u=o.get(t);if(!u){return s}var q=u.toJSON();_.extend(q,s);return q});Backbone.Collection.prototype.set.call(this,p,n)},promoteToHistoryDatasetCollection:function l(s,q,o){o=o||{};o.url=this.url();o.type="POST";var u=q;var r=[],n=null;if(q=="list"){this.chain().each(function(x){var v=x.attributes.name;var y=x.get("id");var w=x.attributes.history_content_type;if(w=="dataset"){if(u!="list"){console.log("Invalid collection type")}r.push({name:v,src:"hda",id:y})}else{if(u=="list"){u="list:"+x.attributes.collection_type}else{if(u!="list:"+x.attributes.collection_type){console.log("Invalid collection type")}}r.push({name:v,src:"hdca",id:y})}});n="New Dataset List"}else{if(q=="paired"){var p=this.ids();if(p.length!=2){}r.push({name:"forward",src:"hda",id:p[0]});r.push({name:"reverse",src:"hda",id:p[1]});n="New Dataset Pair"}}o.data={type:"dataset_collection",name:n,collection_type:u,element_identifiers:JSON.stringify(r),};var t=jQuery.ajax(o);t.done(function(x,v,w){s.refresh()});t.fail(function(x,v,w){if(x.responseJSON&&x.responseJSON.error){error=x.responseJSON.error}else{error=x.responseJSON}x.responseText=error});return t},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var k=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:m,HDACollection:b}}); \ No newline at end of file diff -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 -r 7f506e778275715639d8f5d37041712be9662b39 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.get("id"),l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.get("id");i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.get("id");i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.id,l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.id;i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.id;i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file diff -r 0c0517794198ec32fedc0bb022fe375e9f2e11e7 -r 7f506e778275715639d8f5d37041712be9662b39 static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/collection/dataset-collection-base","mvc/dataset/hda-base","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(g,k,b,a,f,d){var i=f.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(n){var m="expandedHdas";this.save(m,_.extend(this.get(m),_.object([n],[true])))},removeExpandedHda:function(n){var m="expandedHdas";this.save(m,_.omit(this.get(m),n))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function e(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(f.LoggableMixin).extend({HDAViewClass:b.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){console.error(o,r,n,q,p);if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(p,t,o,s,r){var n=Galaxy.currUser,m={message:this._bePolite(s),details:{user:(n instanceof a.User)?(n.toJSON()):(n+""),source:(p instanceof Backbone.Model)?(p.toJSON()):(p+""),xhr:t,options:(t)?(_.omit(o,"xhr")):(o)}};_.extend(m.details,r||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var q=t.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(u){return u.split(": ")});m.details.xhr.responseHeaders=_.object(q)}return m},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.keys(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=g.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new g.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addContentView,this);this.model.on("error error:hdas",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.get("id"),s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(n){var m=n.get("id"),p=n.get("history_content_type"),o=null;if(p==="dataset"){o=new this.HDAViewClass({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}else{o=new k.DatasetCollectionBaseView({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}this._setUpHdaListeners(o);return o},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("body-expanded",function(o){m.storage.addExpandedHda(o)});n.on("body-collapsed",function(o){m.storage.removeExpandedHda(o)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},hdaViewRange:function(p,o){if(p===o){return[p]}var m=this,n=false,q=[];this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters).each(function(r){if(n){q.push(m.hdaViews[r.id]);if(r===p.model||r===o.model){n=false}}else{if(r===p.model||r===o.model){n=true;q.push(m.hdaViews[r.id])}}});return q},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.hdas.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.hdas.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.hdas.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/collection/dataset-collection-base","mvc/dataset/hda-base","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(g,k,b,a,f,d){var i=f.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(m){var n="expandedHdas";this.save(n,_.extend(this.get(n),_.object([m.id],[m.get("id")])))},removeExpandedHda:function(n){var m="expandedHdas";this.save(m,_.omit(this.get(m),n))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function e(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(f.LoggableMixin).extend({HDAViewClass:b.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){console.error(o,r,n,q,p);if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(p,t,o,s,r){var n=Galaxy.currUser,m={message:this._bePolite(s),details:{user:(n instanceof a.User)?(n.toJSON()):(n+""),source:(p instanceof Backbone.Model)?(p.toJSON()):(p+""),xhr:t,options:(t)?(_.omit(o,"xhr")):(o)}};_.extend(m.details,r||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var q=t.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(u){return u.split(": ")});m.details.xhr.responseHeaders=_.object(q)}return m},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.values(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=g.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new g.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addContentView,this);this.model.on("error error:hdas",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.id,s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(n){var m=n.id,p=n.get("history_content_type"),o=null;if(p==="dataset"){o=new this.HDAViewClass({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}else{o=new k.DatasetCollectionBaseView({model:n,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[m],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}this._setUpHdaListeners(o);return o},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("body-expanded",function(o){m.storage.addExpandedHda(o)});n.on("body-collapsed",function(o){m.storage.removeExpandedHda(o)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},hdaViewRange:function(p,o){if(p===o){return[p]}var m=this,n=false,q=[];this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters).each(function(r){if(n){q.push(m.hdaViews[r.id]);if(r===p.model||r===o.model){n=false}}else{if(r===p.model||r===o.model){n=true;q.push(m.hdaViews[r.id])}}});return q},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.hdas.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.hdas.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.hdas.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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