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[galaxyproject/usegalaxy-playbook] 827e17: Update Test. And integrated_tool_panel.xml has cha...
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 827e17cca73c7e6fa9f5e95d79d2b84746fde0c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/827e17cca73c7e6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/group_vars/all.yml Log Message: ----------- Update Test. And integrated_tool_panel.xml has changed again...

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commit/galaxy-central: 13 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

13 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6e7085ce60/ Changeset: 0a6e7085ce60 User: dan Date: 2015-02-26 22:16:55+00:00 Summary: Allow TabularToolDataTable to be loaded from a url instead of a path. Affected #: 1 file diff -r 71596d6f10285ebb23d2a257eda3b70cb04ff655 -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -14,6 +14,8 @@ import hashlib from glob import glob +from tempfile import NamedTemporaryFile +from urllib2 import urlopen from galaxy import util from galaxy.util.odict import odict @@ -279,7 +281,22 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) + tmp_file = None + filename = file_element.get( 'path', None ) + if filename is None: + # Handle URLs as files + filename = file_element.get( 'url', None ) + if filename: + tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name ) + try: + tmp_file.write( urlopen( filename ).read() ) + except Exception, e: + log.error( 'Error loading Data Table URL "%s": %s', filename, e ) + continue + log.debug( 'Loading Data Table URL "%s" as filename "%s".', filename, tmp_file.name ) + filename = tmp_file.name + tmp_file.flush() + filename = file_path = expand_here_template( filename, here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -325,6 +342,9 @@ config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) + # Remove URL tmp file + if tmp_file is not None: + tmp_file.close() def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) https://bitbucket.org/galaxy/galaxy-central/commits/b6fe31e55f48/ Changeset: b6fe31e55f48 User: dannon Date: 2015-02-27 00:59:26+00:00 Summary: Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit. Affected #: 2 files diff -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -1,5 +1,7 @@ +import config import sys -import config +import time + import galaxy.model from galaxy.web import security @@ -26,6 +28,8 @@ self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. + self.server_starttime = int(time.time()) def shutdown( self ): pass diff -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -1,17 +1,18 @@ import config import sys +import time +import galaxy.datatypes.registry +import galaxy.quota +import galaxy.tools.data +import galaxy.webapps.tool_shed.model from galaxy import tools -import galaxy.tools.data -import galaxy.quota -import galaxy.datatypes.registry -import galaxy.webapps.tool_shed.model +from galaxy.managers.tags import CommunityTagManager from galaxy.openid.providers import OpenIDProviders from galaxy.util.dbkeys import GenomeBuilds from galaxy.web import security -from galaxy.managers.tags import CommunityTagManager -from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager import tool_shed.repository_registry import tool_shed.repository_types.registry +from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager class UniverseApplication( object ): @@ -70,6 +71,8 @@ self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir # Initialize the repository registry. self.repository_registry = tool_shed.repository_registry.Registry( self ) + # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. + self.server_starttime = int(time.time()) print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config def shutdown( self ): https://bitbucket.org/galaxy/galaxy-central/commits/eed154f337fc/ Changeset: eed154f337fc User: dannon Date: 2015-02-27 01:13:48+00:00 Summary: Fix reports webapp under default database broken in ba825fc5 Affected #: 1 file diff -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b -r eed154f337fc090168956bcbec92491d0a5d75c9 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -25,7 +25,10 @@ db_url, self.config.database_engine_options, create_tables=True ) - self.targets_mysql = 'mysql' in self.config.database_connection + if not self.config.database_connection: + self.targets_mysql = False + else: + self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. https://bitbucket.org/galaxy/galaxy-central/commits/4e30957ab121/ Changeset: 4e30957ab121 User: jmchilton Date: 2015-02-27 03:36:14+00:00 Summary: Fix incorrect usage of __all__ not containing strings... ...for plugin_config.py plugins. Affected #: 12 files diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/core.py --- a/lib/galaxy/jobs/metrics/instrumenters/core.py +++ b/lib/galaxy/jobs/metrics/instrumenters/core.py @@ -82,4 +82,4 @@ pass return value -__all__ = [ CorePlugin ] +__all__ = [ 'CorePlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py --- a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py @@ -59,4 +59,4 @@ def __instrument_cpuinfo_path( self, job_directory ): return self._instrument_file_path( job_directory, "cpuinfo" ) -__all__ = [ CpuInfoPlugin ] +__all__ = [ 'CpuInfoPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/env.py --- a/lib/galaxy/jobs/metrics/instrumenters/env.py +++ b/lib/galaxy/jobs/metrics/instrumenters/env.py @@ -68,4 +68,4 @@ def __env_file( self, job_directory ): return self._instrument_file_path( job_directory, "vars" ) -__all__ = [ EnvPlugin ] +__all__ = [ 'EnvPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/meminfo.py --- a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py @@ -56,4 +56,4 @@ def __instrument_meminfo_path( self, job_directory ): return self._instrument_file_path( job_directory, "meminfo" ) -__all__ = [ MemInfoPlugin ] +__all__ = [ 'MemInfoPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/uname.py --- a/lib/galaxy/jobs/metrics/instrumenters/uname.py +++ b/lib/galaxy/jobs/metrics/instrumenters/uname.py @@ -31,4 +31,4 @@ return self._instrument_file_path( job_directory, "uname" ) -__all__ = [ UnamePlugin ] +__all__ = [ 'UnamePlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py --- a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py @@ -147,4 +147,4 @@ return base -__all__ = [HomebrewToolShedDependencyResolver] +__all__ = ['HomebrewToolShedDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/galaxy_packages.py --- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py +++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py @@ -71,4 +71,4 @@ commands = 'PACKAGE_BASE=%s; export PACKAGE_BASE; . %s' % ( base_path, self.script ) return commands -__all__ = [GalaxyPackageDependencyResolver, GalaxyPackageDependency] +__all__ = ['GalaxyPackageDependencyResolver', 'GalaxyPackageDependency'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/homebrew.py --- a/lib/galaxy/tools/deps/resolvers/homebrew.py +++ b/lib/galaxy/tools/deps/resolvers/homebrew.py @@ -53,4 +53,4 @@ return str( value ).lower() == "true" -__all__ = [HomebrewDependencyResolver] +__all__ = ['HomebrewDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/modules.py --- a/lib/galaxy/tools/deps/resolvers/modules.py +++ b/lib/galaxy/tools/deps/resolvers/modules.py @@ -153,4 +153,4 @@ def _string_as_bool( value ): return str( value ).lower() == "true" -__all__ = [ModuleDependencyResolver] +__all__ = ['ModuleDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/tool_shed_packages.py --- a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py @@ -56,4 +56,4 @@ return INDETERMINATE_DEPENDENCY -__all__ = [ToolShedPackageDependencyResolver] +__all__ = ['ToolShedPackageDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/util/plugin_config.py --- a/lib/galaxy/util/plugin_config.py +++ b/lib/galaxy/util/plugin_config.py @@ -25,6 +25,10 @@ # FIXME: this is not how one is suppose to use __all__ why did you do # this past John? for clazz in getattr( plugin_module, "__all__", [] ): + try: + clazz = getattr( plugin_module, clazz ) + except TypeError: + clazz = clazz plugin_type = getattr( clazz, plugin_type_identifier, None ) if plugin_type: plugin_dict[ plugin_type ] = clazz diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/workflow/schedulers/core.py --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -43,4 +43,4 @@ workflow_invocation=workflow_invocation, ) -__all__ = [ CoreWorkflowSchedulingPlugin ] +__all__ = [ 'CoreWorkflowSchedulingPlugin' ] https://bitbucket.org/galaxy/galaxy-central/commits/e8c37fd94209/ Changeset: e8c37fd94209 User: jmchilton Date: 2015-02-27 05:29:07+00:00 Summary: Update pulsar client and related modules. Affected #: 24 files diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/cli.py --- a/lib/galaxy/jobs/metrics/collectl/cli.py +++ b/lib/galaxy/jobs/metrics/collectl/cli.py @@ -12,7 +12,8 @@ class CollectlCli( object ): - """ Abstraction over (some of) the command-line arguments of collectl. + """ + Abstraction over (some of) the command-line arguments of collectl. Ideally this will be useful for building up command line arguments for remote execution as well as runnning directly on local host. @@ -20,33 +21,43 @@ collectl CLI - logic more directly related to the Galaxy job metric plugin plugin should be placed in other modules. - Keyword Arguments: - collectl_path: Path to collectl executable (defaults to collectl - i.e. - search the PATH). + **Keyword Arguments:** - playback_path (defaults to None): If this is None collectl will run in - record mode, else it will playback specified file. + ``collectl_path`` + Path to collectl executable (defaults to collectl - i.e. + search the PATH). - Playback Mode Options: - - sep : Separator used in playback mode (set to 9 to produce tsv) - (defaults to None). + ``playback_path`` (defaults to ``None``) + If this is ``None``, collectl will run in + record mode, else it will playback specified file. - Record Mode Options (some of these may work in playback mode also): + **Playback Mode Options:** - destination_path: Location of path files to write to (defaults to None - and collectl will just use cwd). Really this is just to prefix - - collectl will append hostname and datetime to file. - interval: Setup polling interval (secs) for most subsystems (defaults - to None and when unspecified collectl will use default of 1 second). - interval2: Setup polling interval (secs) for process information - (defaults to None and when unspecified collectl will use default to - 60 seconds). - interval3: Setup polling interval (secs) for environment information - (defaults to None and when unspecified collectl will use default to - 300 seconds). - procfilt: Optional argument to procfilt. (defaults to None). - flush : Optional flush interval (defaults to None). + ``sep`` + Separator used in playback mode (set to 9 to produce tsv) + (defaults to None). + + **Record Mode Options** (some of these may work in playback mode also) + + ``destination_path`` + Location of path files to write to (defaults to None + and collectl will just use cwd). Really this is just to prefix - + collectl will append hostname and datetime to file. + ``interval`` + Setup polling interval (secs) for most subsystems (defaults + to None and when unspecified collectl will use default of 1 second). + ``interval2`` + Setup polling interval (secs) for process information + (defaults to None and when unspecified collectl will use default to + 60 seconds). + ``interval3`` + Setup polling interval (secs) for environment information + (defaults to None and when unspecified collectl will use default to + 300 seconds). + ``procfilt`` + Optional argument to procfilt. (defaults to None). + ``flush`` + Optional flush interval (defaults to None). """ def __init__( self, **kwargs ): @@ -125,4 +136,4 @@ if return_code: raise Exception( "Problem running collectl command." ) -__all__ = [ CollectlCli ] +__all__ = [ 'CollectlCli' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/processes.py --- a/lib/galaxy/jobs/metrics/collectl/processes.py +++ b/lib/galaxy/jobs/metrics/collectl/processes.py @@ -26,7 +26,7 @@ # # Process data dumped one row per process per interval. -#http://collectl.sourceforge.net/Data-detail.html +# http://collectl.sourceforge.net/Data-detail.html PROCESS_COLUMNS = [ "#Date", # Date of interval - e.g. 20140322 "Time", # Time of interval - 12:18:58 @@ -36,7 +36,7 @@ "PPID", # Parent PID of process. "THRD", # Thread??? "S", # Process state - S - Sleeping, D - Uninterruptable Sleep, R - Running, Z - Zombie or T - Stopped/Traced - ## Memory options - http://ewx.livejournal.com/579283.html + # Memory options - http://ewx.livejournal.com/579283.html "VmSize", "VmLck", "VmRSS", @@ -93,7 +93,7 @@ statistics = DEFAULT_STATISTICS statistics = util.listify( statistics ) - statistics = map( __tuplize_statistic, statistics ) + statistics = map( _tuplize_statistic, statistics ) # Check for validity... for statistic in statistics: if statistic[ 0 ] not in STATISTIC_TYPES: @@ -109,10 +109,10 @@ with tempfile.NamedTemporaryFile( ) as tmp_tsv: collectl_playback_cli.run( stdout=tmp_tsv ) with open( tmp_tsv.name, "r" ) as tsv_file: - return __read_process_statistics( tsv_file, pid, statistics ) + return _read_process_statistics( tsv_file, pid, statistics ) -def __read_process_statistics( tsv_file, pid, statistics ): +def _read_process_statistics( tsv_file, pid, statistics ): process_summarizer = CollectlProcessSummarizer( pid, statistics ) current_interval = None @@ -167,7 +167,7 @@ to_num = float else: to_num = long - + interval_stat = sum( to_num( r[ column_index ] ) for r in rows ) self.tree_statistics[ column_name ].track( interval_stat ) @@ -228,7 +228,7 @@ ability to filter out just rows corresponding to the process tree corresponding to a given pid. """ - + def __init__( self ): self.rows = [] @@ -242,11 +242,11 @@ self.rows.append( row ) -def __tuplize_statistic( statistic ): +def _tuplize_statistic( statistic ): if not isinstance( statistic, tuple ): statistic_split = statistic.split( "_", 1 ) statistic = ( statistic_split[ 0 ].lower(), statistic_split[ 1 ] ) return statistic -__all__ = [ generate_process_statistics ] +__all__ = [ 'generate_process_statistics' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/subsystems.py --- a/lib/galaxy/jobs/metrics/collectl/subsystems.py +++ b/lib/galaxy/jobs/metrics/collectl/subsystems.py @@ -69,4 +69,4 @@ """ return SUBSYSTEM_DICT[ name ] -__all__ = [ get_subsystem ] +__all__ = [ 'get_subsystem' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/instrumenters/collectl.py --- a/lib/galaxy/jobs/metrics/instrumenters/collectl.py +++ b/lib/galaxy/jobs/metrics/instrumenters/collectl.py @@ -211,4 +211,4 @@ return "" -__all__ = [ CollectlPlugin ] +__all__ = [ 'CollectlPlugin' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -7,4 +7,4 @@ from .kill import kill_pid -__all__ = [kill_pid, Bunch] +__all__ = ['kill_pid', 'Bunch'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/__init__.py --- a/lib/galaxy/jobs/runners/util/cli/__init__.py +++ b/lib/galaxy/jobs/runners/util/cli/__init__.py @@ -6,6 +6,9 @@ DEFAULT_SHELL_PLUGIN = 'LocalShell' +ERROR_MESSAGE_NO_JOB_PLUGIN = "No job plugin parameter found, cannot create CLI job interface" +ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN = "Failed to find job_plugin of type %s, available types include %s" + class CliInterface(object): """ @@ -53,8 +56,14 @@ return shell def get_job_interface(self, job_params): - job_plugin = job_params['plugin'] - job_interface = self.cli_job_interfaces[job_plugin](**job_params) + job_plugin = job_params.get('plugin', None) + if not job_plugin: + raise ValueError(ERROR_MESSAGE_NO_JOB_PLUGIN) + job_plugin_class = self.cli_job_interfaces.get(job_plugin, None) + if not job_plugin_class: + raise ValueError(ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN % (job_plugin, self.cli_job_interfaces.keys())) + job_interface = job_plugin_class(**job_params) + return job_interface diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/factory.py --- a/lib/galaxy/jobs/runners/util/cli/factory.py +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -12,7 +12,11 @@ code_dir = '.' +def build_cli_interface(): + return CliInterface(code_dir=code_dir) + + def get_shell(params): - cli_interface = CliInterface(code_dir=code_dir) + cli_interface = build_cli_interface() shell_params, _ = split_params(params) return cli_interface.get_shell_plugin(shell_params) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce 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 @@ -1,6 +1,10 @@ # A simple CLI runner for slurm that can be used when running Galaxy from a # non-submit host and using a Slurm cluster. +from ..job import BaseJobExec + +from logging import getLogger + try: from galaxy.model import Job job_states = Job.states @@ -9,11 +13,6 @@ from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed") -from ..job import BaseJobExec - -__all__ = ('Slurm',) - -from logging import getLogger log = getLogger(__name__) argmap = { @@ -94,3 +93,6 @@ }.get(state) except KeyError: raise KeyError("Failed to map slurm status code [%s] to job state." % state) + + +__all__ = ('Slurm',) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/job/torque.py --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -1,3 +1,4 @@ +from logging import getLogger try: import xml.etree.cElementTree as et except: @@ -13,10 +14,10 @@ from ..job import BaseJobExec -__all__ = ('Torque',) +log = getLogger(__name__) -from logging import getLogger -log = getLogger(__name__) +ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s' + argmap = {'destination': '-q', 'Execution_Time': '-a', @@ -58,8 +59,8 @@ if not k.startswith('-'): k = argmap[k] pbsargs[k] = v - except: - log.warning('Unrecognized long argument passed to Torque CLI plugin: %s' % k) + except KeyError: + log.warning(ERROR_MESSAGE_UNRECOGNIZED_ARG % k) template_pbsargs = '' for k, v in pbsargs.items(): template_pbsargs += '#PBS %s %s\n' % (k, v) @@ -118,3 +119,6 @@ }.get(state) except KeyError: raise KeyError("Failed to map torque status code [%s] to job state." % state) + + +__all__ = ('Torque',) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/shell/local.py --- a/lib/galaxy/jobs/runners/util/cli/shell/local.py +++ b/lib/galaxy/jobs/runners/util/cli/shell/local.py @@ -24,7 +24,7 @@ True >>> exec_result.stdout.strip() == u'Hello World' True - >>> exec_result = exec_python("import time; time.sleep(90)", timeout=3, timeout_check_interval=1) + >>> exec_result = exec_python("import time; time.sleep(90)", timeout=1, timeout_check_interval=.1) >>> exec_result.stdout == u'' True >>> exec_result.stderr == 'Execution timed out' diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/__init__.py --- a/lib/pulsar/client/__init__.py +++ b/lib/pulsar/client/__init__.py @@ -1,6 +1,6 @@ """ pulsar client -====== +================= This module contains logic for interfacing with an external Pulsar server. @@ -50,13 +50,13 @@ from .path_mapper import PathMapper __all__ = [ - build_client_manager, - OutputNotFoundException, - url_to_destination_params, - finish_job, - submit_job, - ClientJobDescription, - PulsarOutputs, - ClientOutputs, - PathMapper, + 'build_client_manager', + 'OutputNotFoundException', + 'url_to_destination_params', + 'finish_job', + 'submit_job', + 'ClientJobDescription', + 'PulsarOutputs', + 'ClientOutputs', + 'PathMapper', ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/action_mapper.py --- a/lib/pulsar/client/action_mapper.py +++ b/lib/pulsar/client/action_mapper.py @@ -1,5 +1,6 @@ from json import load from os import makedirs +from os import unlink from os.path import exists from os.path import abspath from os.path import dirname @@ -16,6 +17,9 @@ from .util import unique_path_prefix from .transport import get_file from .transport import post_file +from .transport import rsync_get_file, scp_get_file +from .transport import rsync_post_file, scp_post_file +import tempfile DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? @@ -130,6 +134,7 @@ if config is None: config = self.__client_to_config(client) self.default_action = config.get("default_action", "transfer") + self.ssh_key = config.get("ssh_key", None) self.mappers = mappers_from_dicts(config.get("paths", [])) self.files_endpoint = config.get("files_endpoint", None) @@ -155,6 +160,7 @@ return dict( default_action=self.default_action, files_endpoint=self.files_endpoint, + ssh_key=self.ssh_key, paths=map(lambda m: m.to_dict(), self.mappers) ) @@ -166,6 +172,8 @@ config = dict() config["default_action"] = client.default_file_action config["files_endpoint"] = client.files_endpoint + if hasattr(client, 'ssh_key'): + config["ssh_key"] = client.ssh_key return config def __load_action_config(self, path): @@ -209,6 +217,9 @@ # TODO: URL encode path. url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) action.url = url + elif action.action_type in ["remote_rsync_transfer", "remote_scp_transfer"]: + # Required, so no check for presence + action.ssh_key = self.ssh_key REQUIRED_ACTION_KWD = object() @@ -375,6 +386,95 @@ post_file(self.url, pulsar_path) +class PubkeyAuthenticatedTransferAction(BaseAction): + """Base class for file transfers requiring an SSH public/private key + """ + action_spec = dict( + ssh_user=REQUIRED_ACTION_KWD, + ssh_host=REQUIRED_ACTION_KWD, + ssh_port=REQUIRED_ACTION_KWD, + ) + action_type = "remote_pubkey_transfer" + staging = STAGING_ACTION_REMOTE + ssh_key = None + + def __init__(self, path, file_lister=None, url=None, ssh_user=None, + ssh_host=None, ssh_port=None, ssh_key=None): + super(PubkeyAuthenticatedTransferAction, self).__init__(path, file_lister=file_lister) + self.url = url + self.ssh_user = ssh_user + self.ssh_host = ssh_host + self.ssh_port = ssh_port + self.ssh_key = ssh_key + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type, url=self.url, + ssh_user=self.ssh_user, ssh_host=self.ssh_host, + ssh_port=self.ssh_port) + + def serialize_ssh_key(self): + f = tempfile.NamedTemporaryFile(delete=False) + if self.ssh_key is not None: + f.write(self.ssh_key) + else: + raise Exception("SSH_KEY not available") + return f.name + + def cleanup_ssh_key(self, keyfile): + if exists(keyfile): + unlink(keyfile) + + +class RsyncTransferAction(PubkeyAuthenticatedTransferAction): + action_type = "remote_rsync_transfer" + + @classmethod + def from_dict(cls, action_dict): + return RsyncTransferAction(path=action_dict["path"], + url=action_dict["url"], + ssh_user=action_dict["ssh_user"], + ssh_host=action_dict["ssh_host"], + ssh_port=action_dict["ssh_port"], + ssh_key=action_dict["ssh_key"]) + + def write_to_path(self, path): + key_file = self.serialize_ssh_key() + rsync_get_file(self.path, path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + def write_from_path(self, pulsar_path): + key_file = self.serialize_ssh_key() + rsync_post_file(pulsar_path, self.path, self.ssh_user, + self.ssh_host, self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + +class ScpTransferAction(PubkeyAuthenticatedTransferAction): + action_type = "remote_scp_transfer" + + @classmethod + def from_dict(cls, action_dict): + return ScpTransferAction(path=action_dict["path"], + url=action_dict["url"], + ssh_user=action_dict["ssh_user"], + ssh_host=action_dict["ssh_host"], + ssh_port=action_dict["ssh_port"], + ssh_key=action_dict["ssh_key"]) + + def write_to_path(self, path): + key_file = self.serialize_ssh_key() + scp_get_file(self.path, path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + def write_from_path(self, pulsar_path): + key_file = self.serialize_ssh_key() + scp_post_file(pulsar_path, self.path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + class MessageAction(object): """ Sort of pseudo action describing "files" store in memory and transferred via message (HTTP, Python-call, MQ, etc...) @@ -408,7 +508,7 @@ open(path, "w").write(self.contents) -DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction] +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction, RsyncTransferAction, ScpTransferAction] def from_dict(action_dict): @@ -517,10 +617,10 @@ def mappers_from_dicts(mapper_def_list): - return map(lambda m: __mappper_from_dict(m), mapper_def_list) + return map(lambda m: _mappper_from_dict(m), mapper_def_list) -def __mappper_from_dict(mapper_dict): +def _mappper_from_dict(mapper_dict): map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) return MAPPER_CLASS_DICT[map_type](mapper_dict) @@ -554,14 +654,16 @@ CopyAction, RemoteCopyAction, RemoteTransferAction, + RsyncTransferAction, + ScpTransferAction, ] actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) __all__ = [ - FileActionMapper, - path_type, - from_dict, - MessageAction, - RemoteTransferAction, # For testing + 'FileActionMapper', + 'path_type', + 'from_dict', + 'MessageAction', + 'RemoteTransferAction', # For testing ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/amqp_exchange.py --- a/lib/pulsar/client/amqp_exchange.py +++ b/lib/pulsar/client/amqp_exchange.py @@ -1,13 +1,16 @@ +import copy +import uuid +import socket +import logging +import threading +from time import sleep + try: import kombu from kombu import pools except ImportError: kombu = None -import socket -import logging -import threading -from time import sleep log = logging.getLogger(__name__) @@ -101,24 +104,45 @@ log.debug('AMQP heartbeat thread exiting') def publish(self, name, payload): + # Consider optionally disabling if throughput becomes main concern. + transaction_uuid = uuid.uuid1() key = self.__queue_name(name) - log.debug("Begin publishing to key %s" % key) + publish_log_prefix = self.__publish_log_prefex(transaction_uuid) + log.debug("%sBegin publishing to key %s", publish_log_prefix, key) with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: - log.debug("Have producer for publishing to key %s" % key) + log.debug("%sHave producer for publishing to key %s", publish_log_prefix, key) + publish_kwds = self.__prepare_publish_kwds(publish_log_prefix) producer.publish( payload, serializer='json', exchange=self.__exchange, declare=[self.__exchange], routing_key=key, - **self.__publish_kwds + **publish_kwds ) - log.debug("Published to key %s" % key) + log.debug("%sPublished to key %s", publish_log_prefix, key) - def __publish_errback(self, exc, interval): - log.error("Connection error while publishing: %r", exc, exc_info=1) - log.info("Retrying in %s seconds", interval) + def __prepare_publish_kwds(self, publish_log_prefix): + if "retry_policy" in self.__publish_kwds: + publish_kwds = copy.deepcopy(self.__publish_kwds) + + def errback(exc, interval): + return self.__publish_errback(exc, interval, publish_log_prefix) + publish_kwds["retry_policy"]["errback"] = errback + else: + publish_kwds = self.__publish_kwds + return publish_kwds + + def __publish_errback(self, exc, interval, publish_log_prefix=""): + log.error("%sConnection error while publishing: %r", publish_log_prefix, exc, exc_info=1) + log.info("%sRetrying in %s seconds", publish_log_prefix, interval) + + def __publish_log_prefex(self, transaction_uuid=None): + prefix = "" + if transaction_uuid: + prefix = "[publish:%s] " % str(transaction_uuid) + return prefix def connection(self, connection_string, **kwargs): if "ssl" not in kwargs: diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/client.py --- a/lib/pulsar/client/client.py +++ b/lib/pulsar/client/client.py @@ -41,6 +41,12 @@ ) else: job_directory = None + + if "ssh_key" in (destination_params or {}): + self.ssh_key = destination_params["ssh_key"] + else: + self.ssh_key = None + self.env = destination_params.get("env", []) self.files_endpoint = destination_params.get("files_endpoint", None) self.job_directory = job_directory @@ -271,6 +277,7 @@ launch_params['env'] = env if remote_staging: launch_params['remote_staging'] = remote_staging + launch_params['remote_staging']['ssh_key'] = self.ssh_key if job_config and self.setup_handler.local: # Setup not yet called, job properties were inferred from # destination arguments. Hence, must have Pulsar setup job diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/manager.py --- a/lib/pulsar/client/manager.py +++ b/lib/pulsar/client/manager.py @@ -220,4 +220,8 @@ int_val = int(val) return int_val -__all__ = [ClientManager, ObjectStoreClientManager, HttpPulsarInterface] +__all__ = [ + 'ClientManager', + 'ObjectStoreClientManager', + 'HttpPulsarInterface' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/path_mapper.py --- a/lib/pulsar/client/path_mapper.py +++ b/lib/pulsar/client/path_mapper.py @@ -95,4 +95,4 @@ message = "PathMapper cannot handle path type %s" % dataset_path_type raise Exception(message) -__all__ = [PathMapper] +__all__ = ['PathMapper'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/setup_handler.py --- a/lib/pulsar/client/setup_handler.py +++ b/lib/pulsar/client/setup_handler.py @@ -82,6 +82,7 @@ unstructured_files_directory = job_directory.unstructured_files_directory() sep = system_properties.get("sep", os.sep) job_config = { + "job_directory": job_directory.path, "working_directory": working_directory, "outputs_directory": outputs_directory, "configs_directory": configs_directory, @@ -100,4 +101,4 @@ return job_config -__all__ = [build_job_config, build] +__all__ = ['build_job_config', 'build'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/staging/down.py --- a/lib/pulsar/client/staging/down.py +++ b/lib/pulsar/client/staging/down.py @@ -152,4 +152,4 @@ except Exception: log.warn("Failed to cleanup remote Pulsar job") -__all__ = [finish_job] +__all__ = ['finish_job'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/staging/up.py --- a/lib/pulsar/client/staging/up.py +++ b/lib/pulsar/client/staging/up.py @@ -349,14 +349,18 @@ local_action = action.staging_action_local if local_action: response = self.client.put_file(path, type, name=name, contents=contents) - get_path = lambda: response['path'] + + def get_path(): + return response['path'] else: job_directory = self.client.job_directory assert job_directory, "job directory required for action %s" % action if not name: name = basename(path) self.__add_remote_staging_input(action, name, type) - get_path = lambda: job_directory.calculate_path(name, type) + + def get_path(): + return job_directory.calculate_path(name, type) register = self.rewrite_paths or type == 'tool' # Even if inputs not rewritten, tool must be. if register: self.register_rewrite(path, get_path(), type, force=True) @@ -417,4 +421,4 @@ input.close() -__all__ = [submit_job] +__all__ = ['submit_job'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/__init__.py --- a/lib/pulsar/client/transport/__init__.py +++ b/lib/pulsar/client/transport/__init__.py @@ -2,26 +2,8 @@ from .curl import PycurlTransport import os - -def get_transport(transport_type=None, os_module=os): - transport_type = __get_transport_type(transport_type, os_module) - if transport_type == 'urllib': - transport = Urllib2Transport() - else: - transport = PycurlTransport() - return transport - - -def __get_transport_type(transport_type, os_module): - if not transport_type: - use_curl = os_module.getenv('PULSAR_CURL_TRANSPORT', "0") - # If PULSAR_CURL_TRANSPORT is unset or set to 0, use default, - # else use curl. - if use_curl.isdigit() and not int(use_curl): - transport_type = 'urllib' - else: - transport_type = 'curl' - return transport_type +from .ssh import rsync_get_file, scp_get_file +from .ssh import rsync_post_file, scp_post_file from .curl import curl_available from .requests import requests_multipart_post_available @@ -35,4 +17,33 @@ from .poster import get_file from .poster import post_file -__all__ = [get_transport, get_file, post_file] + +def get_transport(transport_type=None, os_module=os): + transport_type = _get_transport_type(transport_type, os_module) + if transport_type == 'urllib': + transport = Urllib2Transport() + else: + transport = PycurlTransport() + return transport + + +def _get_transport_type(transport_type, os_module): + if not transport_type: + use_curl = os_module.getenv('PULSAR_CURL_TRANSPORT', "0") + # If PULSAR_CURL_TRANSPORT is unset or set to 0, use default, + # else use curl. + if use_curl.isdigit() and not int(use_curl): + transport_type = 'urllib' + else: + transport_type = 'curl' + return transport_type + +__all__ = [ + 'get_transport', + 'get_file', + 'post_file', + 'rsync_get_file', + 'rsync_post_file', + 'scp_get_file', + 'scp_post_file' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/curl.py --- a/lib/pulsar/client/transport/curl.py +++ b/lib/pulsar/client/transport/curl.py @@ -2,32 +2,37 @@ from cStringIO import StringIO except ImportError: from io import StringIO -curl_available = True + try: - from pycurl import Curl + from pycurl import Curl, HTTP_CODE + curl_available = True except ImportError: curl_available = False -from os.path import getsize + +import os.path PYCURL_UNAVAILABLE_MESSAGE = \ "You are attempting to use the Pycurl version of the Pulsar client but pycurl is unavailable." +NO_SUCH_FILE_MESSAGE = "Attempt to post file %s to URL %s, but file does not exist." +POST_FAILED_MESSAGE = "Failed to post_file properly for url %s, remote server returned status code of %s." +GET_FAILED_MESSAGE = "Failed to get_file properly for url %s, remote server returned status code of %s." + class PycurlTransport(object): def execute(self, url, method=None, data=None, input_path=None, output_path=None): buf = _open_output(output_path) try: - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + c = _new_curl_object_for_url(url) c.setopt(c.WRITEFUNCTION, buf.write) if method: c.setopt(c.CUSTOMREQUEST, method) if input_path: c.setopt(c.UPLOAD, 1) c.setopt(c.READFUNCTION, open(input_path, 'rb').read) - filesize = getsize(input_path) + filesize = os.path.getsize(input_path) c.setopt(c.INFILESIZE, filesize) if data: c.setopt(c.POST, 1) @@ -42,19 +47,30 @@ def post_file(url, path): - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + if not os.path.exists(path): + # pycurl doesn't always produce a great exception for this, + # wrap it in a better one. + message = NO_SUCH_FILE_MESSAGE % (path, url) + raise Exception(message) + c = _new_curl_object_for_url(url) c.setopt(c.HTTPPOST, [("file", (c.FORM_FILE, path.encode('ascii')))]) c.perform() + status_code = c.getinfo(HTTP_CODE) + if int(status_code) != 200: + message = POST_FAILED_MESSAGE % (url, status_code) + raise Exception(message) def get_file(url, path): buf = _open_output(path) try: - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + c = _new_curl_object_for_url(url) c.setopt(c.WRITEFUNCTION, buf.write) c.perform() + status_code = c.getinfo(HTTP_CODE) + if int(status_code) != 200: + message = GET_FAILED_MESSAGE % (url, status_code) + raise Exception(message) finally: buf.close() @@ -63,10 +79,20 @@ return open(output_path, 'wb') if output_path else StringIO() +def _new_curl_object_for_url(url): + c = _new_curl_object() + c.setopt(c.URL, url.encode('ascii')) + return c + + def _new_curl_object(): try: return Curl() except NameError: raise ImportError(PYCURL_UNAVAILABLE_MESSAGE) -___all__ = [PycurlTransport, post_file, get_file] +__all__ = [ + 'PycurlTransport', + 'post_file', + 'get_file' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/poster.py --- a/lib/pulsar/client/transport/poster.py +++ b/lib/pulsar/client/transport/poster.py @@ -1,4 +1,7 @@ from __future__ import absolute_import + +import logging + try: from urllib2 import urlopen except ImportError: @@ -20,7 +23,6 @@ POSTER_UNAVAILABLE_MESSAGE = "Pulsar configured to use poster module - but it is unavailable. Please install poster." -import logging log = logging.getLogger(__name__) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/requests.py --- a/lib/pulsar/client/transport/requests.py +++ b/lib/pulsar/client/transport/requests.py @@ -1,4 +1,7 @@ from __future__ import absolute_import + +import logging + try: from galaxy import eggs eggs.require("requests") @@ -9,18 +12,18 @@ import requests except ImportError: requests = None -requests_multipart_post_available = False + try: import requests_toolbelt requests_multipart_post_available = True except ImportError: + requests_multipart_post_available = False requests_toolbelt = None REQUESTS_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests module - but it is unavailable. Please install requests." REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests_toolbelt module - but it is unavailable. Please install requests_toolbelt." -import logging log = logging.getLogger(__name__) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/ssh.py --- /dev/null +++ b/lib/pulsar/client/transport/ssh.py @@ -0,0 +1,64 @@ +import subprocess +SSH_OPTIONS = ('-o', 'StrictHostKeyChecking=no', '-o', 'PreferredAuthentications=publickey', '-o', 'PubkeyAuthentication=yes') + + +def rsync_get_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'rsync', + '-e', + 'ssh -i %s -p %s %s' % (key, port, ' '.join(SSH_OPTIONS)), + '%s@%s:%s' % (user, host, uri_from), + uri_to, + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("Rsync exited with code %s" % exit_code) + + +def rsync_post_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'rsync', + '-e', + 'ssh -i %s -p %s %s' % (key, port, ' '.join(SSH_OPTIONS)), + uri_from, + '%s@%s:%s' % (user, host, uri_to), + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("Rsync exited with code %s" % exit_code) + + +def scp_get_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'scp', + '-P', str(port), + '-i', key, + SSH_OPTIONS, + '%s@%s:%s' % (user, host, uri_from), + uri_to, + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("scp exited with code %s" % exit_code) + + +def scp_post_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'scp', + '-P', str(port), + '-i', key, + SSH_OPTIONS, + uri_from, + '%s@%s:%s' % (user, host, uri_to), + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("scp exited with code %s" % exit_code) + + +___all__ = [ + 'rsync_post_file', + 'rsync_get_file', + 'scp_post_file', + 'scp_get_file' +] https://bitbucket.org/galaxy/galaxy-central/commits/e630e74d5571/ Changeset: e630e74d5571 User: guerler Date: 2015-02-27 06:30:48+00:00 Summary: ToolForm: Show initial validation errors on re-run Affected #: 3 files diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/eb6b7fb7a91c/ Changeset: eb6b7fb7a91c User: guerler Date: 2015-02-27 06:35:38+00:00 Summary: ToolForm/Collections: Re-introduce parameter expansion Affected #: 4 files diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2366,7 +2366,7 @@ else: value, error = check_param(trans, input, default_value, context) except Exception, err: - log.error('Checking parameter failed. %s', str(err)) + log.error('Checking parameter %s failed. %s', input.name, str(err)) pass return [value, error] @@ -2482,6 +2482,11 @@ else: state[k] = jsonify(state[k]) + # expand incoming parameters (parameters might trigger multiple tool executions, + # here we select the first execution only in order to resolve dynamic parameters) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] + # do param translation here, used by datasource tools if self.input_translator: self.input_translator.translate( params ) diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var h=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k);f.deferred.done(i)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/46feb8f33ba9/ Changeset: 46feb8f33ba9 User: guerler Date: 2015-02-27 06:49:53+00:00 Summary: Parameters: Prevent uncaught exception on unavailable datasets in column validation Affected #: 1 file diff -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1340,6 +1340,10 @@ datasets = util.listify( referent ) for dataset in datasets: if dataset: + # Check if metadata is available + if not hasattr(dataset, 'metadata'): + return True + # Check if the dataset does not have the expected metadata for columns if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready https://bitbucket.org/galaxy/galaxy-central/commits/448272e06e42/ Changeset: 448272e06e42 User: guerler Date: 2015-02-27 06:57:39+00:00 Summary: ToolForm/Ui: Limit selection to available options Affected #: 3 files diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/94298235c5c4/ Changeset: 94298235c5c4 User: guerler Date: 2015-02-27 06:59:43+00:00 Summary: Parameters: Fix deleted datasets validation message Affected #: 1 file diff -r 448272e06e42db47dec46a3a0dae58f9ca265160 -r 94298235c5c4df5f53bbfc5f7bb742837781001c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2021,7 +2021,7 @@ for v in values: if v: if v.deleted: - raise ValueError( "The previously selected dataset has been previously deleted" ) + raise ValueError( "The previously selected dataset has been deleted." ) if hasattr( v, "dataset" ) and v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) if not self.multiple: https://bitbucket.org/galaxy/galaxy-central/commits/81c09bf641da/ Changeset: 81c09bf641da User: guerler Date: 2015-02-27 09:26:15+00:00 Summary: Parameters: Set hidden attribute for hidden dataset parameter Affected #: 1 file diff -r 94298235c5c4df5f53bbfc5f7bb742837781001c -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2425,6 +2425,7 @@ DataToolParameter.__init__( self, tool, elem ) self.value = "None" self.type = "hidden_data" + self.hidden = True def get_initial_value( self, trans, context, history=None ): return None https://bitbucket.org/galaxy/galaxy-central/commits/b11c4470b151/ Changeset: b11c4470b151 User: guerler Date: 2015-02-27 09:36:20+00:00 Summary: ToolForm/Ui: Restrict available option requirement to single select fields Affected #: 3 files diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)||this.options.multiple){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/6bd6c350296c/ Changeset: 6bd6c350296c User: carlfeberhard Date: 2015-02-27 15:03:47+00:00 Summary: Fix display_structure by using serializer; fix structure by removing extra decode_id Affected #: 2 files diff -r b11c4470b151100c14f1a2abfb8047ac16b26f30 -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -543,8 +543,10 @@ def structure( self, trans, id=None, **kwargs ): """ """ - id = self.decode_id( id ) if id else trans.history.id - history_to_view = self.history_manager.get_accessible( trans, id, trans.user ) + unencoded_history_id = trans.history.id + if id: + unencoded_history_id = self.decode_id( id ) + history_to_view = self.history_manager.get_accessible( trans, unencoded_history_id, trans.user ) history_data = self.history_manager._get_history_data( trans, history_to_view ) history_dictionary = history_data[ 'history' ] @@ -552,7 +554,7 @@ jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == trans.user ) - .filter( trans.app.model.Job.history_id == self.decode_id( id ) ) ).all() + .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) tools = {} diff -r b11c4470b151100c14f1a2abfb8047ac16b26f30 -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -128,13 +128,15 @@ ## ---------------------------------------------------------------------------- <%def name="javascripts()"><% + from galaxy.managers import hdas + hda_serializer = hdas.HDASerializer( trans.app ) self.js_app = 'display-structured' controller = trans.webapp.controllers[ 'history' ] hda_dicts = [] id_hda_dict_map = {} for hda in history.active_datasets: - hda_dict = controller.get_hda_dict( trans, hda ) + hda_dict = hda_serializer.serialize_to_view( trans, hda, 'detailed' ) id_hda_dict_map[ hda_dict[ 'id' ] ] = hda_dict hda_dicts.append( hda_dict ) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 7c39ef: Update Test and Main, update datatypes_conf.xml fo...
by GitHub 26 Feb '15

26 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c39efb81374ba5ff8c37d2e6069cb04b69518fd https://github.com/galaxyproject/usegalaxy-playbook/commit/7c39efb81374ba5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-26 (Thu, 26 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M stage/group_vars/all.yml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Test and Main, update datatypes_conf.xml for both, fetch mutable configs.

1 0

commit/galaxy-central: 14 new changesets
by commits-noreply＠bitbucket.org 26 Feb '15

26 Feb '15

14 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3fb019e8e64/ Changeset: a3fb019e8e64 Branch: release_15.03 User: guerler Date: 2015-02-23 22:56:38+00:00 Summary: Allow text selection in tool form Affected #: 2 files diff -r 9dcc6d00e76eae06705d79ec7d276202494ad545 -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1410,7 +1410,7 @@ .upload-header .header-selection{width:200px;min-width:200px;font-size:11px;padding-right:10px} .upload-header .select2-choice{max-height:20px;line-height:18px;background:transparent;text-align:center;font-weight:normal}.upload-header .select2-choice .select2-arrow b{background-position:0 -3px} .upload-top{height:5%;text-align:center}.upload-top .upload-info{margin-top:0px;font-weight:normal;text-align:center} -.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} +.no-highlight,.ui-button-icon{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .no-padding{padding:0px !important} .ui-margin-top{padding-top:5px !important} .ui-margin-bottom{margin-bottom:5px !important} @@ -1434,7 +1434,7 @@ .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-table-form-info{clear:both !important} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} -.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} +.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} .ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-limited .portlet-header .portlet-title .icon,.ui-portlet-narrow .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} .ui-portlet .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-limited .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-narrow .portlet-header .portlet-operations .ui-button-icon{margin-left:5px} .ui-portlet .portlet-content,.ui-portlet-limited .portlet-content,.ui-portlet-narrow .portlet-content{height:inherit;padding-left:10px;padding-right:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-limited .portlet-content .content,.ui-portlet-narrow .portlet-content .content{padding:0px;height:100%;width:100%} diff -r 9dcc6d00e76eae06705d79ec7d276202494ad545 -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -182,7 +182,6 @@ // portlets .ui-portlet { - &:extend(.no-highlight); border: solid @form-border 1px; border-radius: @border-radius-base; https://bitbucket.org/galaxy/galaxy-central/commits/aaa07e311e79/ Changeset: aaa07e311e79 Branch: release_15.03 User: guerler Date: 2015-02-23 23:04:02+00:00 Summary: Fix job ids in success message Affected #: 3 files diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/a67681113778/ Changeset: a67681113778 Branch: release_15.03 User: guerler Date: 2015-02-24 23:37:52+00:00 Summary: Show error message on server error Affected #: 3 files diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){return this.error(c)}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/27c9c0c6b072/ Changeset: 27c9c0c6b072 Branch: release_15.03 User: guerler Date: 2015-02-25 00:08:36+00:00 Summary: Charts: Rebuild and update charts Affected #: 4 files diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 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) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // 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.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e)},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function i(t,r,s){s=s||[];for(o in r){var u=r[o],a=u.options.length>0,f=s.slice(0),l=$("<div/>");if(a){var c=e.uuid(),h=$('<span id="button-'+c+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),p=$('<div id="subgroup-'+c+'" style="display: none; margin-left: 25px;"/>');f.push(c);var d=$("<div/>");d.append(h),d.append(n._templateOption({label:u.name,value:u.value})),l.append(d),i(p,u.options,f),l.append(p)}else l.append(n._templateOption({label:u.name,value:u.value})),n.header_index[u.value]=f;t.append(l)}}var n=this;this.header_index={},this.header_list=[];var s=$("<div/>");i(s,t);for(var o in this.header_index)this.header_list=_.uniq(this.header_list.concat(this.header_index[o]));for(var o in this.header_list)r(s,this.header_list[o]);return s},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<label>"+e.info+"</label>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",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 legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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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 arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=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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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return 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 e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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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class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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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Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -189,7 +189,7 @@ if (valid) { // add to selection columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'label' : 'Column: ' + (parseInt(key) + 1), 'value' : key }); } diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -115,7 +115,7 @@ }); // append portlet - this.portlet.append(this.message.$el); + this.portlet.append(this.message.$el.addClass('ui-margin-top')); this.portlet.append(this.viewport_view.$el); // set element diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -12,6 +12,7 @@ ## install shared libraries ${h.js( 'libs/jquery/jquery', + 'libs/jquery/select2', 'libs/bootstrap', 'libs/require', 'libs/underscore', https://bitbucket.org/galaxy/galaxy-central/commits/03993b5418ab/ Changeset: 03993b5418ab Branch: release_15.03 User: guerler Date: 2015-02-25 00:41:30+00:00 Summary: Charts: Fix missing data message Affected #: 2 files diff -r 27c9c0c6b072e138c59323a163757f123fa87445 -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$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 t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$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,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div 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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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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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Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium 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/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/jqplot/histogram_discrete/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:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 27c9c0c6b072e138c59323a163757f123fa87445 -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -295,7 +295,7 @@ return; } for (var key in chart_def.columns) { - if (group.attributes[key] === '__undefined__') { + if (group.attributes[key] === '__null__') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); valid = false; https://bitbucket.org/galaxy/galaxy-central/commits/462142655af2/ Changeset: 462142655af2 Branch: release_15.03 User: guerler Date: 2015-02-25 01:31:43+00:00 Summary: ToolForm: Enable collection for multiple data parameter Affected #: 3 files diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/81a68eaf2ebd/ Changeset: 81a68eaf2ebd Branch: release_15.03 User: dannon Date: 2015-02-25 14:14:59+00:00 Summary: Fix returning encoded None library folder parent ids in library_contents API; thanks to nsoranzo Affected #: 1 file diff -r 462142655af2a768ca01afac78b67ee8eb4f3b79 -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -128,7 +128,8 @@ content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) rval = content.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) rval[ 'id' ] = 'F' + str( rval[ 'id' ] ) - rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) + if rval[ 'parent_id' ] is not None: # This can happen for root folders. + rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] ) else: content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) https://bitbucket.org/galaxy/galaxy-central/commits/79bf433cb5fe/ Changeset: 79bf433cb5fe Branch: release_15.03 User: guerler Date: 2015-02-26 06:05:27+00:00 Summary: Collections: Enable the batch mode execution for nested collections (without adding a new button) Affected #: 4 files diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2364,24 +2364,6 @@ return True # TODO def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): - d = super( DataCollectionToolParameter, self ).to_dict( trans ) - if other_values is None: - # No need to produce lists of datasets for history. - return d - - dataset_matcher = DatasetMatcher( trans, self, None, other_values ) - history = trans.history - - for hdca in self.match_collections( trans, history, dataset_matcher ): - pass - - for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - pass - - return d - - def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): # create dictionary and fill default parameters d = super( DataCollectionToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions @@ -2414,7 +2396,8 @@ 'id_uncoded' : hdca.id, 'hid' : hdca.hid, 'name' : hdca.name, - 'src' : 'hdca' + 'src' : 'hdca', + 'map_over_type' : subcollection_type }) # sort both lists diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/7cb17705d749/ Changeset: 7cb17705d749 Branch: release_15.03 User: guerler Date: 2015-02-26 16:12:45+00:00 Summary: Remove collection expansion Affected #: 1 file diff -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 -r 7cb17705d74906d937ef71e070b1a759fb04653e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,8 +2299,6 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) - expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) - params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/ee8e400d704f/ Changeset: ee8e400d704f Branch: release_15.03 User: dannon Date: 2015-02-26 17:40:26+00:00 Summary: Fix cache-busting under require.js. Affected #: 13 files diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -2,10 +2,11 @@ Provides factory methods to assemble the Galaxy web application """ -import sys +import atexit +import time import os import os.path -import atexit +import sys from paste import httpexceptions import pkg_resources @@ -114,6 +115,8 @@ except: pass + app.server_starttime = int(time.time()) # used for cachebusting + if not app.config.is_uwsgi: postfork_setup() diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -79,7 +79,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -89,7 +89,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -13,7 +13,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(['mvc/data'], function(data) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -12,7 +12,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/data' ], function( data ) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -97,7 +97,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -49,7 +49,8 @@ hdaJSON = ${h.dumps( hda_dicts )}; require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -48,7 +48,8 @@ $embeddedHistory = $( thisScript ).prev(); require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -177,7 +177,8 @@ baseUrl : "${h.url_for( '/static/scripts' )}", paths : { 'jquery' : 'libs/jquery/jquery' - } + }, + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -9,7 +9,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/underscore": { exports: "_" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["mvc/tools"], function(tools_mod) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -58,7 +58,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require( ["viz/trackster"], function(trackster) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -147,7 +147,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -116,7 +116,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/6a1e3bd62bab/ Changeset: 6a1e3bd62bab Branch: release_15.03 User: dannon Date: 2015-02-26 17:47:50+00:00 Summary: Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. Affected #: 2 files diff -r ee8e400d704f066ef61dc01c3df406931a13efac -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys import os +import time from galaxy import config, jobs import galaxy.model import galaxy.security @@ -147,6 +148,7 @@ self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self ) self.model.engine.dispose() + self.server_starttime = int(time.time()) # used for cachebusting def setup_control_queue(self): self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), diff -r ee8e400d704f066ef61dc01c3df406931a13efac -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -3,7 +3,6 @@ """ import atexit -import time import os import os.path import sys @@ -115,8 +114,6 @@ except: pass - app.server_starttime = int(time.time()) # used for cachebusting - if not app.config.is_uwsgi: postfork_setup() https://bitbucket.org/galaxy/galaxy-central/commits/12b292368631/ Changeset: 12b292368631 Branch: release_15.03 User: jmchilton Date: 2015-02-26 17:48:28+00:00 Summary: Bugfix: serializing "None" for UUIDs for older workflows. Prevents workflows from being saved :(. Affected #: 1 file diff -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed -r 12b2923686314fb1482ef1fa7b67b39161bf0c98 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -346,7 +346,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation_str, 'post_job_actions': {}, - 'uuid': str(step.uuid), + 'uuid': str(step.uuid) if step.uuid else None, 'label': step.label or None, 'workflow_outputs': [] } https://bitbucket.org/galaxy/galaxy-central/commits/322022d07ed5/ Changeset: 322022d07ed5 Branch: release_15.03 User: dannon Date: 2015-02-26 19:07:35+00:00 Summary: Attempt at a fix for get('') in tools/params/basic.py Affected #: 1 file diff -r 12b2923686314fb1482ef1fa7b67b39161bf0c98 -r 322022d07ed5216ab7b6d0de5d727f39fef59212 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1977,7 +1977,7 @@ return None if not value and not self.optional: raise ValueError( "History does not include a dataset of the required format / build" ) - if value in [None, "None"]: + if value in [None, "None", '']: return None if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] https://bitbucket.org/galaxy/galaxy-central/commits/b046e38c21d1/ Changeset: b046e38c21d1 Branch: release_15.03 User: carlfeberhard Date: 2015-02-26 19:15:47+00:00 Summary: Fix visualization controller to use security.decode_id in grids Affected #: 1 file diff -r 322022d07ed5216ab7b6d0de5d727f39fef59212 -r b046e38c21d140d9fdbba80fc1861cd6cf4e8352 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -128,7 +128,7 @@ class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==self.decode_id(history_id) ) + return query.filter( model.History.id==trans.security.decode_id(history_id) ) class HistoryDatasetsSelectionGrid( grids.Grid ): # Grid definition. @@ -157,7 +157,7 @@ Current item for grid is the history being queried. This is a bit of hack since current_item typically means the current item in the grid. """ - return trans.sa_session.query( model.History ).get( self.decode_id( kwargs[ 'f-history' ] ) ) + return trans.sa_session.query( model.History ).get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) def apply_query_filter( self, trans, query, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 17 new changesets
by commits-noreply＠bitbucket.org 26 Feb '15

26 Feb '15

17 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/79a7008a2140/ Changeset: 79a7008a2140 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Show error message on server error Affected #: 3 files diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){return this.error(c)}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/924245fea397/ Changeset: 924245fea397 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Charts: Rebuild and update charts Affected #: 4 files diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 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) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // 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.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e)},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function i(t,r,s){s=s||[];for(o in r){var u=r[o],a=u.options.length>0,f=s.slice(0),l=$("<div/>");if(a){var c=e.uuid(),h=$('<span id="button-'+c+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),p=$('<div id="subgroup-'+c+'" style="display: none; margin-left: 25px;"/>');f.push(c);var d=$("<div/>");d.append(h),d.append(n._templateOption({label:u.name,value:u.value})),l.append(d),i(p,u.options,f),l.append(p)}else l.append(n._templateOption({label:u.name,value:u.value})),n.header_index[u.value]=f;t.append(l)}}var n=this;this.header_index={},this.header_list=[];var s=$("<div/>");i(s,t);for(var o in this.header_index)this.header_list=_.uniq(this.header_list.concat(this.header_index[o]));for(var o in this.header_list)r(s,this.header_list[o]);return s},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<label>"+e.info+"</label>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",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 legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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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 arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=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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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return 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 e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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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class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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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u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -189,7 +189,7 @@ if (valid) { // add to selection columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'label' : 'Column: ' + (parseInt(key) + 1), 'value' : key }); } diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -115,7 +115,7 @@ }); // append portlet - this.portlet.append(this.message.$el); + this.portlet.append(this.message.$el.addClass('ui-margin-top')); this.portlet.append(this.viewport_view.$el); // set element diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -12,6 +12,7 @@ ## install shared libraries ${h.js( 'libs/jquery/jquery', + 'libs/jquery/select2', 'libs/bootstrap', 'libs/require', 'libs/underscore', https://bitbucket.org/galaxy/galaxy-central/commits/1ec20f0f8da0/ Changeset: 1ec20f0f8da0 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Charts: Fix missing data message Affected #: 2 files diff -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 -r 1ec20f0f8da089f06ea73fc45970b76c914216fd config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$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 t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$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,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div 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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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=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+'"/>'}}),f=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},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.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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"||a==="zero")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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){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=this.app.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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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){window.location.href="data:none/none;base64,"+btoa(a(e).string)}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){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.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(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$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",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.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$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){this.app.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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={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.app.deferred.done(l)}};this.app.datasets.request(c)},_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=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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(e,{title:"Configuration",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","mvc/ui/ui-misc"],function(e,t){return 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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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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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Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium 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/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/jqplot/histogram_discrete/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:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 -r 1ec20f0f8da089f06ea73fc45970b76c914216fd config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -295,7 +295,7 @@ return; } for (var key in chart_def.columns) { - if (group.attributes[key] === '__undefined__') { + if (group.attributes[key] === '__null__') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); valid = false; https://bitbucket.org/galaxy/galaxy-central/commits/a9779a00f055/ Changeset: a9779a00f055 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: ToolForm: Enable collection for multiple data parameter Affected #: 3 files diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/ebaf186a2db8/ Changeset: ebaf186a2db8 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix two incorrect (undefined) references and misc cleanup in installed_repository_manager.py Affected #: 1 file diff -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 -r ebaf186a2db8eeb73885a9154294d9ab29a71e9e 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 @@ -103,12 +103,12 @@ # Hack to add repository.name here, which is actually the root of the installed repository data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) - new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - repository.metadata, - repository.get_shed_config_dict( self.app ), - data_manager_relative_install_dir, - repository, - repository_tools_tups ) + dmh.install_data_managers( self.app.config.shed_data_manager_config_file, + repository.metadata, + repository.get_shed_config_dict( self.app ), + data_manager_relative_install_dir, + repository, + repository_tools_tups ) self.install_model.context.add( repository ) self.install_model.context.flush() if repository.includes_datatypes: @@ -400,14 +400,8 @@ installed_repository_dependencies = {} missing_rd_tups = [] installed_rd_tups = [] - description, \ - repository_clone_url, \ - changeset_revision, \ - ctx_rev, \ - repository_owner, \ - repository_dependencies, \ - tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) + ( description, repository_clone_url, changeset_revision, ctx_rev, + repository_owner, repository_dependencies, tool_dependencies ) = suc.get_repo_info_tuple_contents( repo_info_tuple ) if repository_dependencies: description = repository_dependencies[ 'description' ] root_key = repository_dependencies[ 'root_key' ] @@ -460,7 +454,7 @@ prior_installation_required, only_if_compiling_contained_td, None, - 'Never installed' ] + 'Never installed' ] if not util.asbool( only_if_compiling_contained_td ): # A repository dependency that is not installed will not be considered missing if its value for # only_if_compiling_contained_td is True - see above... @@ -564,10 +558,10 @@ continue if required_repository_tup not in dependency_tups: dependency_tups.append( required_repository_tup ) - return get_repository_dependency_tups_for_installed_repository( required_repository, - dependency_tups=dependency_tups ) + return self.get_repository_dependency_tups_for_installed_repository( required_repository, + dependency_tups=dependency_tups ) return dependency_tups - + def get_repository_tuple_for_installed_repository_manager( self, repository ): return ( str( repository.tool_shed ), str( repository.name ), @@ -611,10 +605,10 @@ contents = open( env_shell_file_path, 'r' ).read() except Exception, e: contents = None - log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ - ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) + log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % + ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) if contents is not None and contents.find( required_env_shell_file_path ) >= 0: - td_tuple = get_tool_dependency_tuple_for_installed_repository_manager( td ) + td_tuple = self.get_tool_dependency_tuple_for_installed_repository_manager( td ) runtime_dependent_tool_dependency_tups.append( td_tuple ) return runtime_dependent_tool_dependency_tups @@ -672,8 +666,7 @@ # Remove this tool_dependency from all values in # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - for td_tup, installed_runtime_dependent_tool_dependency_tups in \ - self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): + for ( td_tup, installed_runtime_dependent_tool_dependency_tups ) in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups: # Remove the tool_dependency from the list. installed_runtime_dependent_tool_dependency_tups.remove( tool_dependency_tup ) @@ -684,7 +677,7 @@ altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies. self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) - # Remove the entry for this tool_dependency from + # Remove the entry for this tool_dependency from # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories. @@ -864,7 +857,7 @@ 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 ) + message += ' the status %s.' % str( repository.status ) return status, message def remove_entry_from_installed_repository_dependencies_of_installed_repositories( self, repository ): @@ -884,7 +877,7 @@ debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \ ( r_installed_changeset_revision, r_name, r_owner ) debug_msg += "in installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) + log.debug( debug_msg ) v_tups.remove( repository_tup ) altered_installed_dependent_repositories_of_installed_repositories[ r_tup ] = v_tups self.installed_dependent_repositories_of_installed_repositories = \ @@ -957,7 +950,7 @@ if cleaned_repository_dependency_tool_shed == cleaned_tool_shed and \ repository_dependency.name == name and \ repository_dependency.owner == owner and \ - ( repository_dependency.installed_changeset_revision == changeset_revision or \ + ( repository_dependency.installed_changeset_revision == changeset_revision or repository_dependency.changeset_revision == changeset_revision ): return True return False @@ -970,9 +963,9 @@ # This method is called only from Galaxy when rendering repository dependencies # for an installed tool shed repository. # TODO: Do we need to check more than changeset_revision here? - required_repository_tup = [ required_repository.tool_shed, \ - required_repository.name, \ - required_repository.owner, \ + required_repository_tup = [ required_repository.tool_shed, + required_repository.name, + required_repository.owner, required_repository.changeset_revision ] for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: partial_tup = tup[ 0:4 ] @@ -1009,12 +1002,12 @@ pulled by a Galaxy administrator when getting updates to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is:: - + {"name": "bwa", "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", "type": "package", "version": "0.6.2"} - + The new_dependencies_dict is the dictionary generated by the metadata_util.generate_tool_dependency_metadata method. """ new_tool_dependency = None @@ -1046,12 +1039,12 @@ break if new_dependency_name and new_dependency_type and new_dependency_version: # Update all attributes of the tool_dependency record in the database. - log.debug( "Updating version %s of tool dependency %s %s to have new version %s and type %s." % \ - ( str( tool_dependency.version ), - str( tool_dependency.type ), - str( tool_dependency.name ), - str( new_dependency_version ), - str( new_dependency_type ) ) ) + log.debug( "Updating version %s of tool dependency %s %s to have new version %s and type %s." + % ( str( tool_dependency.version ), + str( tool_dependency.type ), + str( tool_dependency.name ), + str( new_dependency_version ), + str( new_dependency_type ) ) ) tool_dependency.type = new_dependency_type tool_dependency.version = new_dependency_version tool_dependency.status = self.app.install_model.ToolDependency.installation_status.UNINSTALLED @@ -1062,8 +1055,8 @@ else: # We have no new tool dependency definition based on a matching dependency name, so remove # the existing tool dependency record from the database. - log.debug( "Deleting version %s of tool dependency %s %s from the database since it is no longer defined." % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) ) + log.debug( "Deleting version %s of tool dependency %s %s from the database since it is no longer defined." + % ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) ) context.delete( tool_dependency ) context.flush() return new_tool_dependency https://bitbucket.org/galaxy/galaxy-central/commits/067a4072a9a0/ Changeset: 067a4072a9a0 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Cleanup in galaxy.web.framework.base, correct bug where encoding didn't exist and would blow up if (not that this ever happened afaik) we attempted to stream back a nested iterable. Affected #: 1 file diff -r ebaf186a2db8eeb73885a9154294d9ab29a71e9e -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -2,7 +2,7 @@ A simple WSGI application/framework. """ -import cgi # For FieldStorage +import cgi # For FieldStorage import logging import os.path import socket @@ -67,7 +67,7 @@ # FIXME: The following two options are deprecated and should be # removed. Consult the Routes documentation. self.mapper.minimization = True - #self.mapper.explicit = False + # self.mapper.explicit = False self.transaction_factory = DefaultWebTransaction # Set if trace logging is enabled self.trace_logger = None @@ -79,12 +79,12 @@ method use `add_route`. """ log.debug( "Enabling '%s' controller, class: %s", - controller_name, controller.__class__.__name__ ) + controller_name, controller.__class__.__name__ ) self.controllers[ controller_name ] = controller def add_api_controller( self, controller_name, controller ): log.debug( "Enabling '%s' API controller, class: %s", - controller_name, controller.__class__.__name__ ) + controller_name, controller.__class__.__name__ ) self.api_controllers[ controller_name ] = controller def add_route( self, route, **kwargs ): @@ -148,7 +148,7 @@ else: environ[ 'is_api_request' ] = False controllers = self.controllers - if map == None: + if map is None: raise httpexceptions.HTTPNotFound( "No route for " + path_info ) self.trace( path_info=path_info, map=map ) # Setup routes @@ -239,11 +239,13 @@ associated object (provides property style access to keys in the WSGI environment) """ - def __init__( self, key, default = '' ): + def __init__( self, key, default='' ): self.key = key self.default = default - def __get__( self, obj, type = None ): - if obj is None: return self + + def __get__( self, obj, type=None ): + if obj is None: + return self return obj.environ.get( self.key, self.default ) @@ -254,8 +256,10 @@ """ def __init__( self, func ): self.func = func - def __get__(self, obj, type = None ): - if obj is None: return self + + def __get__(self, obj, type=None ): + if obj is None: + return self value = self.func( obj ) setattr( obj, self.func.func_name, value ) return value @@ -273,6 +277,7 @@ self.environ = environ self.request = Request( environ ) self.response = Response() + @lazy_property def session( self ): """ @@ -291,11 +296,14 @@ # but for performance reasons it's way better to use Paste's tempfile than to # create a new one and copy. import tempfile + + class FieldStorage( cgi.FieldStorage ): def make_file(self, binary=None): return tempfile.NamedTemporaryFile() + def read_lines(self): - # Always make a new file + # Always make a new file self.file = self.make_file() self.__file = None if self.outerboundary: @@ -313,45 +321,58 @@ """ Create a new request wrapping the WSGI environment `environ` """ - ## self.environ = environ + # self.environ = environ webob.Request.__init__( self, environ, charset='utf-8', decode_param_names=False ) # Properties that are computed and cached on first use + @lazy_property def remote_host( self ): try: return socket.gethostbyname( self.remote_addr ) except socket.error: return self.remote_addr + @lazy_property def remote_hostname( self ): try: return socket.gethostbyaddr( self.remote_addr )[0] except socket.error: return self.remote_addr + @lazy_property def cookies( self ): return get_cookies( self.environ ) + @lazy_property def base( self ): return ( self.scheme + "://" + self.host ) - ## @lazy_property - ## def params( self ): - ## return parse_formvars( self.environ ) + + # @lazy_property + # def params( self ): + # return parse_formvars( self.environ ) + @lazy_property def path( self ): return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] + @lazy_property def browser_url( self ): return self.base + self.path + # Descriptors that map properties to the associated environment - ## scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' ) - ## remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' ) + + # scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' ) + # remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' ) + remote_port = WSGIEnvironmentProperty( 'REMOTE_PORT' ) - ## method = WSGIEnvironmentProperty( 'REQUEST_METHOD' ) - ## script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' ) + + # method = WSGIEnvironmentProperty( 'REQUEST_METHOD' ) + # script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' ) + protocol = WSGIEnvironmentProperty( 'SERVER_PROTOCOL' ) - ## query_string = WSGIEnvironmentProperty( 'QUERY_STRING' ) - ## path_info = WSGIEnvironmentProperty( 'PATH_INFO' ) + + # query_string = WSGIEnvironmentProperty( 'QUERY_STRING' ) + # path_info = WSGIEnvironmentProperty( 'PATH_INFO' ) class Response( object ): @@ -406,7 +427,8 @@ # ---- Utilities ------------------------------------------------------------ -CHUNK_SIZE = 2**16 +CHUNK_SIZE = 2 ** 16 + def send_file( start_response, trans, body ): # If configured use X-Accel-Redirect header for nginx @@ -426,6 +448,7 @@ trans.response.wsgi_headeritems() ) return body + def iterate_file( file ): """ Progressively return chunks from `file`. @@ -436,13 +459,14 @@ break yield chunk + def flatten( seq ): """ Flatten a possible nested set of iterables """ for x in seq: if isinstance( x, ( types.GeneratorType, list, tuple ) ): - for y in flatten( x, encoding ): + for y in flatten( x ): yield y else: yield x https://bitbucket.org/galaxy/galaxy-central/commits/7dd485f6027a/ Changeset: 7dd485f6027a User: martenson Date: 2015-02-26 19:32:48+00:00 Summary: Revert "create library root folder with '/' as default name" This reverts commit 9dfa83bf0f2abd1c2182da9edef1bb0996d7d757. Affected #: 2 files diff -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 lib/galaxy/managers/libraries.py --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -54,7 +54,7 @@ raise exceptions.ItemAccessibilityException( 'Only administrators can create libraries.' ) else: library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) - root_folder = trans.app.model.LibraryFolder( name='/', description='' ) + root_folder = trans.app.model.LibraryFolder( name=name, description='' ) library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() diff -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -85,13 +85,12 @@ raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) - root_encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) - root_name = library.root_folder.name + encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) # appending root folder - rval.append( dict( id=root_encoded_id, + rval.append( dict( id=encoded_id, type='folder', - name=root_name, - url=url_for( 'library_content', library_id=library_id, id=root_encoded_id ) ) ) + name='/', + url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) library.root_folder.api_path = '' # appending all other items in the library recursively for content in traverse( library.root_folder ): https://bitbucket.org/galaxy/galaxy-central/commits/6af59c8cc870/ Changeset: 6af59c8cc870 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix bug in scramble exception, incorrect reference to source_path Affected #: 1 file diff -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 -r 6af59c8cc8702d937ced0829db7df5206c615b63 lib/galaxy/eggs/scramble.py --- a/lib/galaxy/eggs/scramble.py +++ b/lib/galaxy/eggs/scramble.py @@ -134,7 +134,7 @@ elif zipfile.is_zipfile( self.source_path ): self.unpack_zip() else: - raise Exception( "%s(): Unknown archive file type for %s" % ( sys._getframe().f_code.co_name, source_path ) ) + raise Exception( "%s(): Unknown archive file type for %s" % ( sys._getframe().f_code.co_name, self.source_path ) ) log.warning( "%s(): Unpacked to:" % sys._getframe().f_code.co_name ) log.warning( " %s" % self.buildpath ) def unpack_zip( self ): https://bitbucket.org/galaxy/galaxy-central/commits/8252c18ebf34/ Changeset: 8252c18ebf34 User: jmchilton Date: 2015-02-26 19:32:48+00:00 Summary: Add test case demonstrating data params don't need namespace... ... unlike other parameters. Is this a bug? Has been this way for at least three releases it seems. https://github.com/galaxyproject/tools-devteam/commit/c01b354711d982f61f1fd… Affected #: 2 files diff -r 6af59c8cc8702d937ced0829db7df5206c615b63 -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -27,6 +27,7 @@ <tool file="column_param.xml" /><tool file="column_multi_param.xml" /><tool file="special_params.xml" /> + <tool file="top_level_data.xml" /><tool file="validation_default.xml" /><tool file="validation_sanitizer.xml" /><tool file="validation_repeat.xml" /> diff -r 6af59c8cc8702d937ced0829db7df5206c615b63 -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 test/functional/tools/tol_level_data.xml --- /dev/null +++ b/test/functional/tools/tol_level_data.xml @@ -0,0 +1,34 @@ +<tool id="top_level_data" name="top_level_data" version="0.1.0"> + <command> + cat '${f1}' >> $out1; + echo '${library.f2}' >> $out2;  + </command> + <inputs> + <conditional name="library"> + <param name="type" type="select" label="Parameter Settings"> + <option value="no">Use defaults</option> + <option value="yes">Full parameter list</option> + </param> + <when value="yes"> + <param name="f1" type="data" format="txt" label="Data 1" /> + <param name="f2" type="text" label="Text 1" /> + </when> + <when value="no"> + <param name="f1" type="data" format="txt" label="Data 1" /> + <param name="f2" type="text" label="TExt 1" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out1" /> + <data format="txt" name="out2" /> + </outputs> + <tests> + <test> + <param name="f1" value="simple_line.txt" /> + <param name="f2" value="This is a line of text." /> + <output name="out1" file="simple_line.txt" /> + <output name="out2" file="simple_line.txt" /> + </test> + </tests> +</tool> https://bitbucket.org/galaxy/galaxy-central/commits/1e6f3918b2d6/ Changeset: 1e6f3918b2d6 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Collections: Enable the batch mode execution for nested collections (without adding a new button) Affected #: 4 files diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2369,24 +2369,6 @@ return True # TODO def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): - d = super( DataCollectionToolParameter, self ).to_dict( trans ) - if other_values is None: - # No need to produce lists of datasets for history. - return d - - dataset_matcher = DatasetMatcher( trans, self, None, other_values ) - history = trans.history - - for hdca in self.match_collections( trans, history, dataset_matcher ): - pass - - for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - pass - - return d - - def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): # create dictionary and fill default parameters d = super( DataCollectionToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions @@ -2419,7 +2401,8 @@ 'id_uncoded' : hdca.id, 'hid' : hdca.hid, 'name' : hdca.name, - 'src' : 'hdca' + 'src' : 'hdca', + 'map_over_type' : subcollection_type }) # sort both lists diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9111c6aed248/ Changeset: 9111c6aed248 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Remove collection expansion Affected #: 1 file diff -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 -r 9111c6aed248e894112d0ace01446c89b72a208e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,8 +2299,6 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) - expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) - params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/743840286044/ Changeset: 743840286044 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix cache-busting under require.js. Affected #: 13 files diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -2,10 +2,11 @@ Provides factory methods to assemble the Galaxy web application """ -import sys +import atexit +import time import os import os.path -import atexit +import sys from paste import httpexceptions import pkg_resources @@ -114,6 +115,8 @@ except: pass + app.server_starttime = int(time.time()) # used for cachebusting + if not app.config.is_uwsgi: postfork_setup() diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -79,7 +79,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -89,7 +89,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -13,7 +13,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(['mvc/data'], function(data) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -12,7 +12,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/data' ], function( data ) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -97,7 +97,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -49,7 +49,8 @@ hdaJSON = ${h.dumps( hda_dicts )}; require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -48,7 +48,8 @@ $embeddedHistory = $( thisScript ).prev(); require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -177,7 +177,8 @@ baseUrl : "${h.url_for( '/static/scripts' )}", paths : { 'jquery' : 'libs/jquery/jquery' - } + }, + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -9,7 +9,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/underscore": { exports: "_" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["mvc/tools"], function(tools_mod) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -58,7 +58,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require( ["viz/trackster"], function(trackster) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -147,7 +147,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -116,7 +116,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/714deef6027b/ Changeset: 714deef6027b User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. Affected #: 2 files diff -r 743840286044c18aaef85ac6400b78a196e5c0bb -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys import os +import time from galaxy import config, jobs import galaxy.model import galaxy.security @@ -147,6 +148,7 @@ self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self ) self.model.engine.dispose() + self.server_starttime = int(time.time()) # used for cachebusting def setup_control_queue(self): self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), diff -r 743840286044c18aaef85ac6400b78a196e5c0bb -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -3,7 +3,6 @@ """ import atexit -import time import os import os.path import sys @@ -115,8 +114,6 @@ except: pass - app.server_starttime = int(time.time()) # used for cachebusting - if not app.config.is_uwsgi: postfork_setup() https://bitbucket.org/galaxy/galaxy-central/commits/3765ae2904ff/ Changeset: 3765ae2904ff User: jmchilton Date: 2015-02-26 19:32:48+00:00 Summary: Bugfix: serializing "None" for UUIDs for older workflows. Prevents workflows from being saved :(. Affected #: 1 file diff -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -346,7 +346,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation_str, 'post_job_actions': {}, - 'uuid': str(step.uuid), + 'uuid': str(step.uuid) if step.uuid else None, 'label': step.label or None, 'workflow_outputs': [] } https://bitbucket.org/galaxy/galaxy-central/commits/5f8bb3b239c0/ Changeset: 5f8bb3b239c0 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Remove unnecessary casting to int of what's already an int that got left in w/ modifications to cache busting. Affected #: 12 files diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -80,7 +80,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); </script> diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -90,7 +90,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); </script> diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -14,7 +14,7 @@ shim: { "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(['mvc/data'], function(data) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -13,7 +13,7 @@ shim: { "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require([ 'mvc/data' ], function( data ) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -98,7 +98,7 @@ "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -50,7 +50,7 @@ require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -49,7 +49,7 @@ require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -178,7 +178,7 @@ paths : { 'jquery' : 'libs/jquery/jquery' }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -10,7 +10,7 @@ shim: { "libs/underscore": { exports: "_" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["mvc/tools"], function(tools_mod) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -59,7 +59,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require( ["viz/trackster"], function(trackster) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -148,7 +148,7 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -117,7 +117,7 @@ "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/cecbf657cd9f/ Changeset: cecbf657cd9f User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Attempt at a fix for get('') in tools/params/basic.py Affected #: 1 file diff -r 5f8bb3b239c06e00f5e661d638316baf5546974f -r cecbf657cd9f9a9ba3684c1d847a1c51a3a7e06a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1982,7 +1982,7 @@ return None if not value and not self.optional: raise ValueError( "History does not include a dataset of the required format / build" ) - if value in [None, "None"]: + if value in [None, "None", '']: return None if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] https://bitbucket.org/galaxy/galaxy-central/commits/71596d6f1028/ Changeset: 71596d6f1028 User: carlfeberhard Date: 2015-02-26 19:32:48+00:00 Summary: Fix visualization controller to use security.decode_id in grids Affected #: 1 file diff -r cecbf657cd9f9a9ba3684c1d847a1c51a3a7e06a -r 71596d6f10285ebb23d2a257eda3b70cb04ff655 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -128,7 +128,7 @@ class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==self.decode_id(history_id) ) + return query.filter( model.History.id==trans.security.decode_id(history_id) ) class HistoryDatasetsSelectionGrid( grids.Grid ): # Grid definition. @@ -157,7 +157,7 @@ Current item for grid is the history being queried. This is a bit of hack since current_item typically means the current item in the grid. """ - return trans.sa_session.query( model.History ).get( self.decode_id( kwargs[ 'f-history' ] ) ) + return trans.sa_session.query( model.History ).get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) def apply_query_filter( self, trans, query, **kwargs ): 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.

1 0

[galaxyproject/usegalaxy-playbook] 7bd1a2: Turns out XML parsers can't parse invalid XML.
by GitHub 26 Feb '15

26 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7bd1a20f612babbebec8c088281f83487d08c652 https://github.com/galaxyproject/usegalaxy-playbook/commit/7bd1a20f612babbe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-26 (Thu, 26 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Turns out XML parsers can't parse invalid XML.

1 0

[galaxyproject/usegalaxy-playbook] 52cd35: Increase NVC memory to 16GB on Test.
by GitHub 26 Feb '15

26 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 52cd351e8b2324ff11d8e54937f8f8dde4fe6374 https://github.com/galaxyproject/usegalaxy-playbook/commit/52cd351e8b2324ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-26 (Thu, 26 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase NVC memory to 16GB on Test.

1 0

[galaxyproject/usegalaxy-playbook] 87c37a: Update Test and Main
by GitHub 25 Feb '15

25 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 87c37a944d5425daee366dd712461a4b9f2e6f06 https://github.com/galaxyproject/usegalaxy-playbook/commit/87c37a944d5425da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-25 (Wed, 25 Feb 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main

1 0

commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 25 Feb '15

25 Feb '15

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b0255200ef92/ Changeset: b0255200ef92 Branch: release_15.03 User: carlfeberhard Date: 2015-02-24 22:20:10+00:00 Summary: Fix to layering of dropdown buttons and menus Affected #: 3 files diff -r 4a42638e8cd45652db9dc1f1eed54be6aa2c20b1 -r b0255200ef921a6de641b303ef486ac56c0d8740 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2030,8 +2030,8 @@ .list-panel .controls .list-actions:after{clear:both} .list-panel .controls .list-actions:before,.list-panel .controls .list-actions:after{content:" ";display:table;} .list-panel .controls .list-actions:after{clear:both} -.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%;z-index:inherit} -.list-panel .controls .list-actions .list-action-menu{float:right}.list-panel .controls .list-actions .list-action-menu .dropdown-menu{z-index:inherit} +.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%} +.list-panel .controls .list-actions .list-action-menu{float:right} .list-panel .list-items .list-item:not(:last-child){border-bottom-width:0px} .list-panel .empty-message{display:none;margin:0px} .list-item .details .list-panel{margin-top:8px;border-radius:3px;background:white;padding:4px}.list-item .details .list-panel .list-items{border:1px solid #bfbfbf;border-radius:3px}.list-item .details .list-panel .list-items .list-item:first-child{border-top-width:0px;border-radius:3px 3px 0px 0px} @@ -2138,9 +2138,10 @@ .multi-panel-history .control-column.control-column-right{text-align:right} .multi-panel-history .outer-middle{overflow:auto} .multi-panel-history .middle{min-width:100%;margin:0px 0px 0px 0px;background-color:white;padding:8px} -.multi-panel-history .history-column{width:312px;margin:0 8px 0 0}.multi-panel-history .history-column:first-child{position:fixed;z-index:2}.multi-panel-history .history-column:first-child .history-panel{border:1px solid black;box-shadow:4px 4px 4px rgba(96,96,96,0.3)} +.multi-panel-history .history-column{width:312px;margin:0 8px 0 0}.multi-panel-history .history-column:first-child{position:fixed;z-index:10}.multi-panel-history .history-column:first-child .history-panel{border:1px solid black;box-shadow:4px 4px 4px rgba(96,96,96,0.3)} .multi-panel-history .history-column:nth-child(2){margin-left:320px} .multi-panel-history .history-column:last-child{margin-right:0px} +.multi-panel-history .history-column .dropdown-menu{z-index:inherit} .multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} .multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px} .multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px} diff -r 4a42638e8cd45652db9dc1f1eed54be6aa2c20b1 -r b0255200ef921a6de641b303ef486ac56c0d8740 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -744,7 +744,7 @@ // current history &:first-child { position: fixed; - z-index : 2; + z-index : 10; // visually differentiate the current history .history-panel { @@ -759,6 +759,9 @@ &:last-child { margin-right: 0px; } + .dropdown-menu { + z-index: inherit; + } .panel-controls { width: 100%; diff -r 4a42638e8cd45652db9dc1f1eed54be6aa2c20b1 -r b0255200ef921a6de641b303ef486ac56c0d8740 static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -167,13 +167,9 @@ padding-top: 2px; padding-bottom: 2px; font-size: 90%; - z-index: inherit; } .list-action-menu { float: right; - .dropdown-menu { - z-index: inherit; - } } } } https://bitbucket.org/galaxy/galaxy-central/commits/a83c0d80639e/ Changeset: a83c0d80639e Branch: release_15.03 User: dannon Date: 2015-02-24 23:55:50+00:00 Summary: More tweaks to mutable capabilities, adding back in a copy and stripping pickle from MutationList Affected #: 1 file diff -r b0255200ef921a6de641b303ef486ac56c0d8740 -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,4 +1,5 @@ import binascii +import copy import json import logging import uuid @@ -62,6 +63,12 @@ else: return self.impl + def copy_value( self, value ): + return copy.deepcopy( value ) + + def compare_values( self, x, y ): + return ( x == y ) + class MutationObj(Mutable): """ @@ -196,12 +203,6 @@ list.remove(self, value) self.changed() - def __getstate__(self): - return list(self) - - def __setstate__(self, state): - self.update(state) - MutationObj.associate_with(JSONType) https://bitbucket.org/galaxy/galaxy-central/commits/48012dc829bb/ Changeset: 48012dc829bb Branch: release_15.03 User: jmchilton Date: 2015-02-18 16:34:23+00:00 Summary: Tool diagnostic API endpoints. It is easy to get Galaxy's database and shed tool files out of sync and the results are bad. I don't think this is new but I may have made it worse this cycle by trying to slowly walk back Galaxy's use of the database to track lineages (e.g. https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a1…) New API endpoints include: /api/configuration/dynamic_tool_confs /api/configuration/tool_lineages /api/<tool_id>/diagnostics Affected #: 6 files diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/tools/toolbox/lineages/interface.py --- a/lib/galaxy/tools/toolbox/lineages/interface.py +++ b/lib/galaxy/tools/toolbox/lineages/interface.py @@ -40,3 +40,9 @@ externally). """ return self.version is None + + def to_dict(self): + return dict( + id=self.id, + version=self.version, + ) diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/tools/toolbox/lineages/stock.py --- a/lib/galaxy/tools/toolbox/lineages/stock.py +++ b/lib/galaxy/tools/toolbox/lineages/stock.py @@ -38,6 +38,13 @@ # method for comparing tool versions. return sorted( versions, key=_to_loose_version ) + def to_dict(self): + return dict( + tool_id=self.tool_id, + tool_versions=list(self.tool_versions), + lineage_type='stock', + ) + def _to_loose_version( tool_lineage_version ): version = str( tool_lineage_version.version ) diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/tools/toolbox/lineages/tool_shed.py --- a/lib/galaxy/tools/toolbox/lineages/tool_shed.py +++ b/lib/galaxy/tools/toolbox/lineages/tool_shed.py @@ -8,9 +8,11 @@ """ Representation of tool lineage derived from tool shed repository installations. """ - def __init__(self, app, tool_version): + def __init__(self, app, tool_version, tool_shed_repository=None): self.app = app self.tool_version_id = tool_version.id + # Only used for logging + self._tool_shed_repository = tool_shed_repository @staticmethod def from_tool( app, tool, tool_shed_repository ): @@ -36,6 +38,16 @@ def get_versions( self, reverse=False ): return map( ToolLineageVersion.from_guid, self.get_version_ids( reverse=reverse ) ) + def to_dict(self): + tool_shed_repository = self._tool_shed_repository + rval = dict( + tool_version_id=self.tool_version_id, + tool_versions=map(lambda v: v.to_dict(), self.get_versions()), + tool_shed_repository=tool_shed_repository if tool_shed_repository is not None else None, + lineage_type='tool_shed', + ) + return rval + def get_install_tool_version( app, tool_id ): return app.install_model.context.query( diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -4,6 +4,8 @@ """ from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import require_admin from galaxy.web.base.controller import BaseAPIController from galaxy.managers import base @@ -33,6 +35,13 @@ @expose_api_anonymous def version( self, trans, **kwds ): + """ + GET /api/version + Return a description of the major version of Galaxy (e.g. 15.03). + + :rtype: dict + :returns: dictionary with major version keyed on 'version_major' + """ return {"version_major": self.app.config.version_major } def get_config_dict( self, trans, return_admin=False, view=None, keys=None, default_view='all' ): @@ -52,6 +61,29 @@ view=view, keys=keys, default_view=default_view ) return serialized + @expose_api + @require_admin + def dynamic_tool_confs(self, trans): + confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True) + return map(_tool_conf_to_dict, confs) + + @expose_api + @require_admin + def tool_lineages(self, trans): + rval = [] + for id, tool in self.app.toolbox.tools(): + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + + entry = dict( + id=id, + lineage=lineage_dict + ) + rval.append(entry) + return rval + #TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports? class ConfigSerializer( base.ModelSerializer ): @@ -122,3 +154,10 @@ 'allow_user_creation' : _defaults_to( False ), 'allow_user_deletion' : _defaults_to( False ), }) + + +def _tool_conf_to_dict(conf): + return dict( + config_filename=conf['config_filename'], + tool_path=conf['tool_path'], + ) diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -94,6 +94,36 @@ message, status = trans.app.toolbox.reload_tool_by_id( tool_id ) return { status: message } + @_future_expose_api + @web.require_admin + def diagnostics( self, trans, id, **kwd ): + """ + GET /api/tools/{tool_id}/diagnostics + Return diagnostic information to help debug panel + and dependency related problems. + """ + to_dict = lambda x: x.to_dict() + tool = self._get_tool( id, user=trans.user ) + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + tool_shed_dependencies = tool.installed_tool_dependencies + if tool_shed_dependencies: + tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies) + else: + tool_shed_dependencies_dict = None + tool = self._get_tool( id, user=trans.user ) + return { + "tool_id": tool.id, + "tool_version": tool.version, + "dependency_shell_commands": tool.build_dependency_shell_commands(), + "lineage": lineage_dict, + "requirements": map(to_dict, tool.requirements), + "installed_tool_shed_dependencies": tool_shed_dependencies_dict, + "tool_dir": tool.tool_dir, + } + @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): tool = self._get_tool( id, user=trans.user ) diff -r a83c0d80639eb92228ead6a47e3b6a26c2f1b94e -r 48012dc829bb437e7bcb7c6507d91647a32a26ef lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -210,6 +210,7 @@ webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/reload', action='reload', controller="tools" ) + webapp.mapper.connect( '/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" ) @@ -221,6 +222,18 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) + webapp.mapper.connect( + 'dynamic_tool_confs', + '/api/configuration/dynamic_tool_confs', + controller="configuration", + action="dynamic_tool_confs" + ) + webapp.mapper.connect( + 'tool_lineages', + '/api/configuration/tool_lineages', + controller="configuration", + action="tool_lineages" + ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) webapp.mapper.connect( "configuration_version", "/api/version", controller="configuration", https://bitbucket.org/galaxy/galaxy-central/commits/e0916bcf81bb/ Changeset: e0916bcf81bb Branch: release_15.03 User: jmchilton Date: 2015-02-24 00:52:17+00:00 Summary: Improved tool diagnostics API. Affected #: 1 file diff -r 48012dc829bb437e7bcb7c6507d91647a32a26ef -r e0916bcf81bb3a27e31c919e7cc5d2ee6b987a28 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -102,6 +102,7 @@ Return diagnostic information to help debug panel and dependency related problems. """ + # TODO: Move this into tool. to_dict = lambda x: x.to_dict() tool = self._get_tool( id, user=trans.user ) if hasattr( tool, 'lineage' ): @@ -113,7 +114,6 @@ tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies) else: tool_shed_dependencies_dict = None - tool = self._get_tool( id, user=trans.user ) return { "tool_id": tool.id, "tool_version": tool.version, @@ -122,6 +122,11 @@ "requirements": map(to_dict, tool.requirements), "installed_tool_shed_dependencies": tool_shed_dependencies_dict, "tool_dir": tool.tool_dir, + "tool_shed": tool.tool_shed, + "repository_name": tool.repository_name, + "repository_owner": tool.repository_owner, + "installed_changeset_revision": None, + "guid": tool.guid, } @_future_expose_api_anonymous https://bitbucket.org/galaxy/galaxy-central/commits/4de6535bd780/ Changeset: 4de6535bd780 Branch: release_15.03 User: jmchilton Date: 2015-02-25 14:10:17+00:00 Summary: Expand out meta parameters when validating for tool.to_json(). Bring this code closer inline with what handle_input() does and should solve the problem with column validation of parameters that are being 'batched'. See https://trello.com/c/8NweTvLh and comment on https://github.com/galaxyproject/galaxy/commit/d57088409c7b23e55ead4c9f2fad…. Affected #: 1 file diff -r e0916bcf81bb3a27e31c919e7cc5d2ee6b987a28 -r 4de6535bd78019ce34511f4f4ee2784f74963396 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,6 +2299,8 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/9dcc6d00e76e/ Changeset: 9dcc6d00e76e Branch: release_15.03 User: dan Date: 2015-02-25 17:07:39+00:00 Summary: Fix for ToolShed not having config.shed_tool_data_path Affected #: 1 file diff -r 4de6535bd78019ce34511f4f4ee2784f74963396 -r 9dcc6d00e76eae06705d79ec7d276202494ad545 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -137,6 +137,10 @@ self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) @property + def shed_tool_data_path( self ): + return self.tool_data_path + + @property def sentry_dsn_public( self ): """ Sentry URL with private key removed for use in client side scripts, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 17 new changesets
by commits-noreply＠bitbucket.org 25 Feb '15

25 Feb '15

17 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d381771a18cf/ Changeset: d381771a18cf User: dannon Date: 2015-02-25 13:22:54+00:00 Summary: Cleanup in api/library contents and folders, associated folder manager. Affected #: 3 files diff -r 658833a7988fe335a5aaaac9709f9e6dfed4a7b2 -r d381771a18cfd6e7d8ecf7563041675a26af0ccd lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -2,9 +2,7 @@ Manager and Serializer for Library Folders. """ -import galaxy.web from galaxy import exceptions -from galaxy.model import orm import logging log = logging.getLogger( __name__ ) @@ -156,7 +154,7 @@ def get_current_roles( self, trans, folder ): """ - Find all roles currently connected to relevant permissions + Find all roles currently connected to relevant permissions on the folder. :param folder: the model object @@ -165,7 +163,7 @@ :returns: dict of current roles for all available permission types :rtype: dictionary """ - # Omit duplicated roles by converting to set + # Omit duplicated roles by converting to set modify_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) manage_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) add_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) @@ -173,7 +171,9 @@ modify_folder_role_list = [ ( modify_role.name, trans.security.encode_id( modify_role.id ) ) for modify_role in modify_roles ] manage_folder_role_list = [ ( manage_role.name, trans.security.encode_id( manage_role.id ) ) for manage_role in manage_roles ] add_library_item_role_list = [ ( add_role.name, trans.security.encode_id( add_role.id ) ) for add_role in add_roles ] - return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list ) + return dict( modify_folder_role_list=modify_folder_role_list, + manage_folder_role_list=manage_folder_role_list, + add_library_item_role_list=add_library_item_role_list ) def can_add_item( self, trans, folder ): """ diff -r 658833a7988fe335a5aaaac9709f9e6dfed4a7b2 -r d381771a18cfd6e7d8ecf7563041675a26af0ccd lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -2,7 +2,6 @@ API operations on library folders. """ from galaxy import util -from galaxy import web from galaxy import exceptions from galaxy.managers import folders from galaxy.web import _future_expose_api as expose_api @@ -82,7 +81,7 @@ parent_folder = self.folder_manager.get( trans, decoded_parent_folder_id ) new_folder = self.folder_manager.create( trans, parent_folder.id, name, description ) return self.folder_manager.get_folder_dict( trans, new_folder ) - + @expose_api def get_permissions( self, trans, encoded_folder_id, **kwd ): """ @@ -141,18 +140,18 @@ *POST /api/folders/{encoded_folder_id}/permissions :param encoded_folder_id: the encoded id of the folder to set the permissions of - :type encoded_folder_id: an encoded id string + :type encoded_folder_id: an encoded id string :param action: (required) describes what action should be performed available actions: set_permissions - :type action: string + :type action: string :param add_ids[]: list of Role.id defining roles that should have add item permission on the folder - :type add_ids[]: string or list + :type add_ids[]: string or list :param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder - :type manage_ids[]: string or list + :type manage_ids[]: string or list :param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder - :type modify_ids[]: string or list + :type modify_ids[]: string or list :rtype: dictionary :returns: dict of current roles for all available permission types. @@ -189,8 +188,8 @@ else: invalid_add_roles_names.append( role_id ) if len( invalid_add_roles_names ) > 0: - log.warning( "The following roles could not be added to the add library item permission: " + str( invalid_add_roles_names ) ) - + log.warning( "The following roles could not be added to the add library item permission: " + str( invalid_add_roles_names ) ) + # MANAGE FOLDER ROLES valid_manage_roles = [] invalid_manage_roles_names = [] @@ -203,8 +202,8 @@ else: invalid_manage_roles_names.append( role_id ) if len( invalid_manage_roles_names ) > 0: - log.warning( "The following roles could not be added to the manage folder permission: " + str( invalid_manage_roles_names ) ) - + log.warning( "The following roles could not be added to the manage folder permission: " + str( invalid_manage_roles_names ) ) + # MODIFY FOLDER ROLES valid_modify_roles = [] invalid_modify_roles_names = [] @@ -217,16 +216,16 @@ else: invalid_modify_roles_names.append( role_id ) if len( invalid_modify_roles_names ) > 0: - log.warning( "The following roles could not be added to the modify folder permission: " + str( invalid_modify_roles_names ) ) + log.warning( "The following roles could not be added to the modify folder permission: " + str( invalid_modify_roles_names ) ) - permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ADD : valid_add_roles } - permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE : valid_manage_roles } ) - permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } ) + permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ADD: valid_add_roles } + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE: valid_manage_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles } ) trans.app.security_agent.set_all_library_permissions( trans, folder, permissions ) else: - raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' - 'Allowed values are: "set_permissions"' ) + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' + 'Allowed values are: "set_permissions"' ) return self.folder_manager.get_current_roles( trans, folder ) @expose_api @@ -256,7 +255,7 @@ return folder_dict @expose_api - def update( self, trans, id, library_id, payload, **kwd ): + def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id} @@ -269,7 +268,7 @@ Method loads the role from the DB based on the given role name. :param role_name: name of the role to load from the DB - :type role_name: string + :type role_name: string :rtype: Role :returns: the loaded Role object diff -r 658833a7988fe335a5aaaac9709f9e6dfed4a7b2 -r d381771a18cfd6e7d8ecf7563041675a26af0ccd lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -212,8 +212,8 @@ if create_type == 'file' and from_hda_id: return self._copy_hda_to_library_folder( trans, from_hda_id, library_id, real_folder_id, ldda_message ) - #check for extended metadata, store it and pop it out of the param - #otherwise sanitize_param will have a fit + # check for extended metadata, store it and pop it out of the param + # otherwise sanitize_param will have a fit ex_meta_payload = payload.pop('extended_metadata', None) # Now create the desired content object, either file or folder. @@ -280,8 +280,8 @@ for path, value in self._scan_json_block(a, prefix + "[%d]" % (i)): yield path, value else: - #BUG: Everything is cast to string, which can lead to false positives - #for cross type comparisions, ie "True" == True + # BUG: Everything is cast to string, which can lead to false positives + # for cross type comparisions, ie "True" == True yield prefix, ("%s" % (meta)).encode("utf8", errors='replace') def _copy_hda_to_library_folder( self, trans, from_hda_id, library_id, folder_id, ldda_message='' ): @@ -293,15 +293,15 @@ in its payload. """ log.debug( '_copy_hda_to_library_folder: %s' % ( str(( from_hda_id, library_id, folder_id, ldda_message )) ) ) - #PRECONDITION: folder_id has already been altered to remove the folder prefix ('F') - #TODO: allow name and other, editable ldda attrs? + # PRECONDITION: folder_id has already been altered to remove the folder prefix ('F') + # TODO: allow name and other, editable ldda attrs? if ldda_message: ldda_message = util.sanitize_html.sanitize_html( ldda_message, 'utf-8' ) rval = {} try: # check permissions on (all three?) resources: hda, library, folder - #TODO: do we really need the library?? + # TODO: do we really need the library?? from_hda_id = self.decode_id( from_hda_id ) hda = self.hda_manager.get_owned( trans, from_hda_id, trans.user ) hda = self.hda_manager.error_if_uploading( trans, hda ) @@ -319,7 +319,7 @@ rval = trans.security.encode_dict_ids( ldda_dict ) except Exception, exc: - #TODO: grrr... + # TODO: grrr... if 'not accessible to the current user' in str( exc ): trans.response.status = 403 return { 'error': str( exc ) } @@ -411,7 +411,7 @@ trans.sa_session.add( ld ) trans.sa_session.flush() - #TODO: had to change this up a bit from Dataset.user_can_purge + # TODO: had to change this up a bit from Dataset.user_can_purge dataset = ld.library_dataset_dataset_association.dataset no_history_assoc = len( dataset.history_associations ) == len( dataset.purged_history_associations ) no_library_assoc = dataset.library_associations == [ ld.library_dataset_dataset_association ] https://bitbucket.org/galaxy/galaxy-central/commits/132692a47ba3/ Changeset: 132692a47ba3 User: dannon Date: 2015-02-25 13:26:11+00:00 Summary: Avoid referring to galaxy.exceptions as exceptions, overriding stdlib exceptions. Be explicit in using them. Affected #: 1 file diff -r d381771a18cfd6e7d8ecf7563041675a26af0ccd -r 132692a47ba3bd421fb59e8338fed627ea240e98 lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -2,8 +2,7 @@ Manager and Serializer for Library Folders. """ -from galaxy import exceptions - +import galaxy.exceptions import logging log = logging.getLogger( __name__ ) @@ -30,12 +29,12 @@ """ try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() - except MultipleResultsFound: - raise exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) - except NoResultFound: - raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) + except galaxy.exceptions.MultipleResultsFound: + raise galaxy.exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) + except galaxy.exceptions.NoResultFound: + raise galaxy.exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) except Exception, e: - raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) + raise galaxy.exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) folder = self.secure( trans, folder, check_manageable, check_accessible ) return folder @@ -72,10 +71,10 @@ :raises: AuthenticationRequired, InsufficientPermissionsException """ if not trans.user: - raise exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' ) + raise galaxy.exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' ) current_user_roles = trans.get_current_user_roles() if not trans.app.security_agent.can_manage_library_item( current_user_roles, folder ): - raise exceptions.InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' ) + raise galaxy.exceptions.InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' ) else: return folder @@ -123,7 +122,7 @@ parent_folder = self.get( trans, parent_folder_id ) current_user_roles = trans.get_current_user_roles() if not ( trans.user_is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, parent_folder ) ): - raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to create folders under given folder.' ) + raise galaxy.exceptions.InsufficientPermissionsException( 'You do not have proper permission to create folders under given folder.' ) new_folder = trans.app.model.LibraryFolder( name=new_folder_name, description=new_folder_description ) # We are associating the last used genome build with folders, so we will always # initialize a new folder with the first dbkey in genome builds list which is currently @@ -195,7 +194,7 @@ if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] else: - raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) + raise galaxy.exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) return cut_id def decode_folder_id( self, trans, encoded_folder_id ): @@ -205,7 +204,7 @@ try: decoded_id = trans.security.decode_id( encoded_folder_id ) except ValueError: - raise exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_folder_id ) ) ) + raise galaxy.exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_folder_id ) ) ) return decoded_id def cut_and_decode( self, trans, encoded_folder_id ): https://bitbucket.org/galaxy/galaxy-central/commits/fe7ae6f22b95/ Changeset: fe7ae6f22b95 User: dannon Date: 2015-02-25 13:59:34+00:00 Summary: In web.security.encode_id, raise MalformedId exception when attempting to encode None. This will likely throw errors in other parts of the codebase, but those will need to be fixed instead of silently using what is actually a broken identifier. Affected #: 1 file diff -r 132692a47ba3bd421fb59e8338fed627ea240e98 -r fe7ae6f22b95756515da5ada8442b270bfb387e0 lib/galaxy/web/security/__init__.py --- a/lib/galaxy/web/security/__init__.py +++ b/lib/galaxy/web/security/__init__.py @@ -6,6 +6,8 @@ import pkg_resources pkg_resources.require( "pycrypto" ) +import galaxy.exceptions + from Crypto.Cipher import Blowfish from Crypto.Util.randpool import RandomPool from Crypto.Util import number @@ -45,6 +47,8 @@ self.id_ciphers_for_kind = _cipher_cache( per_kind_id_secret_base ) def encode_id( self, obj_id, kind=None ): + if obj_id is None: + raise galaxy.exceptions.MalformedId("Attempted to encode None id") id_cipher = self.__id_cipher( kind ) # Convert to string s = str( obj_id ) https://bitbucket.org/galaxy/galaxy-central/commits/0565f566e550/ Changeset: 0565f566e550 User: jmchilton Date: 2015-02-25 14:10:17+00:00 Summary: Expand out meta parameters when validating for tool.to_json(). Bring this code closer inline with what handle_input() does and should solve the problem with column validation of parameters that are being 'batched'. See https://trello.com/c/8NweTvLh and comment on https://github.com/galaxyproject/galaxy/commit/d57088409c7b23e55ead4c9f2fad…. Affected #: 1 file diff -r fe7ae6f22b95756515da5ada8442b270bfb387e0 -r 0565f566e5509d16863a7d8b76908cc7079decf4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,6 +2299,8 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/771789ce8753/ Changeset: 771789ce8753 User: dannon Date: 2015-02-25 14:14:59+00:00 Summary: Fix returning encoded None library folder parent ids in library_contents API; thanks to nsoranzo Affected #: 1 file diff -r 0565f566e5509d16863a7d8b76908cc7079decf4 -r 771789ce8753017b8aef602419d502ce597214a1 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -128,7 +128,8 @@ content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) rval = content.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) rval[ 'id' ] = 'F' + str( rval[ 'id' ] ) - rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) + if rval[ 'parent_id' ] is not None: # This can happen for root folders. + rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] ) else: content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) https://bitbucket.org/galaxy/galaxy-central/commits/1876ae3314d3/ Changeset: 1876ae3314d3 User: jmchilton Date: 2015-02-25 14:12:44+00:00 Summary: Handle column references on data_collection parameters... ... in column parameter's need_late_validation. There may be other places that need to be updated to get this working fully. Affected #: 1 file diff -r 771789ce8753017b8aef602419d502ce597214a1 -r 1876ae3314d3b2da4ce91ee457c5fbafc2649d03 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1332,7 +1332,12 @@ if self.data_ref not in context: return False # Get the selected dataset if selected - datasets = util.listify( context[ self.data_ref ] ) + referent = context[ self.data_ref ] + if getattr( referent, 'history_content_type', None ) == "dataset_collection": + # TODO: also check datasets have been populated. + referent = referent.collection.dataset_instances + + datasets = util.listify( referent ) for dataset in datasets: if dataset: # Check if the dataset does not have the expected metadata for columns https://bitbucket.org/galaxy/galaxy-central/commits/9653a478480a/ Changeset: 9653a478480a User: dannon Date: 2015-02-25 14:22:56+00:00 Summary: Fix undefined variable 'flus_needed' in toolshed admin controller. Affected #: 1 file diff -r 1876ae3314d3b2da4ce91ee457c5fbafc2649d03 -r 9653a478480aebcfd3221e6249787a5c37fc814d lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -250,7 +250,7 @@ flush_needed = True if original_category_description != new_description: category.description = new_description - if not flus_needed: + if not flush_needed: flush_needed = True if flush_needed: trans.sa_session.add( category ) https://bitbucket.org/galaxy/galaxy-central/commits/51638aef252a/ Changeset: 51638aef252a User: dannon Date: 2015-02-25 14:23:50+00:00 Summary: Fix another undefined variable 'tran' in toolshed admin controller. Affected #: 1 file diff -r 9653a478480aebcfd3221e6249787a5c37fc814d -r 51638aef252a51a3296ac7a1300f2bd12123a870 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -88,7 +88,7 @@ changeset_revision_str = 'changeset_revision_' if k.startswith( changeset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) - repository = suc.get_repository_in_tool_shed( tran.apps, repository_id ) + repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', https://bitbucket.org/galaxy/galaxy-central/commits/bc6b7f12f0aa/ Changeset: bc6b7f12f0aa User: dannon Date: 2015-02-25 14:29:23+00:00 Summary: Cleanup and pep8 in galaxy admin controller prior to new dev. Affected #: 1 file diff -r 51638aef252a51a3296ac7a1300f2bd12123a870 -r bc6b7f12f0aa2afcc36e81bfb43c60a28ad79b28 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -25,23 +25,17 @@ class UserListGrid( grids.Grid ): - class EmailColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): return user.email - class UserNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): if user.username: return user.username return 'not set' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.purged: return "purged" @@ -49,47 +43,35 @@ return "deleted" return "" - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.groups: return len( user.groups ) return 0 - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.roles: return len( user.roles ) return 0 - class ExternalColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.external: return 'yes' return 'no' - class LastLoginColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' - class TimeCreatedColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): return user.create_time.strftime('%x') - class ActivatedColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): if user.active: return 'Y' @@ -99,7 +81,7 @@ # Grid definition title = "Users" model_class = model.User - template='/admin/user/grid.mako' + template = '/admin/user/grid.mako' default_sort_key = "email" columns = [ EmailColumn( "Email", @@ -158,46 +140,33 @@ class RoleListGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): return role.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): if role.description: return role.description return '' - class TypeColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): return role.type - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): if role.deleted: return "deleted" return "" - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): if role.groups: return len( role.groups ) return 0 - class UsersColumn( grids.GridColumn ): - - def get_value( self, trans, grid, role ): if role.users: return len( role.users ) @@ -206,7 +175,7 @@ # Grid definition title = "Roles" model_class = model.Role - template='/admin/dataset_security/role/grid.mako' + template = '/admin/dataset_security/role/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -270,31 +239,23 @@ class GroupListGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, group ): return group.name - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): if group.deleted: return "deleted" return "" - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): if group.roles: return len( group.roles ) return 0 - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): if group.members: return len( group.members ) @@ -303,7 +264,7 @@ # Grid definition title = "Groups" model_class = model.Group - template='/admin/dataset_security/group/grid.mako' + template = '/admin/dataset_security/group/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -351,31 +312,24 @@ preserve_state = False use_paging = True + class QuotaListGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, quota ): return quota.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, quota ): if quota.description: return quota.description return '' - class AmountColumn( grids.TextColumn ): - def get_value( self, trans, grid, quota ): return quota.operation + quota.display_amount - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, quota ): if quota.deleted: return "deleted" @@ -383,17 +337,13 @@ return "<strong>default for %s users</strong>" % quota.default[0].type return "" - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, quota ): if quota.users: return len( quota.users ) return 0 - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, quota ): if quota.groups: return len( quota.groups ) @@ -402,7 +352,7 @@ # Grid definition title = "Quotas" model_class = model.Quota - template='/admin/quota/grid.mako' + template = '/admin/quota/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -417,10 +367,10 @@ attach_popup=False, filterable="advanced" ), AmountColumn( "Amount", - key='amount', - model_class=model.Quota, - attach_popup=False, - filterable="advanced" ), + key='amount', + model_class=model.Quota, + attach_popup=False, + filterable="advanced" ), UsersColumn( "Users", attach_popup=False ), GroupsColumn( "Groups", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), @@ -483,9 +433,7 @@ class ToolVersionListGrid( grids.Grid ): - class ToolIdColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_version ): toolbox = trans.app.toolbox if toolbox.has_tool( tool_version.tool_id, exact=True ): @@ -494,9 +442,7 @@ return '<div class="count-box state-color-ok">%s%s</a></div>' % ( link_str, tool_version.tool_id ) return tool_version.tool_id - class ToolVersionsColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_version ): tool_ids_str = '' toolbox = trans.app.toolbox @@ -508,10 +454,11 @@ else: tool_ids_str += '%s<br/>' % tool_id return tool_ids_str + # Grid definition title = "Tool versions" model_class = install_model.ToolVersion - template='/admin/tool_version/grid.mako' + template = '/admin/tool_version/grid.mako' default_sort_key = "tool_id" columns = [ ToolIdColumn( "Tool id", @@ -531,7 +478,7 @@ num_rows_per_page = 50 preserve_state = False use_paging = True - + def build_initial_query( self, trans, **kwd ): return trans.install_model.context.query( self.model_class ) @@ -899,10 +846,11 @@ kwargs={'display_application_ids': kwd.get( 'id' )} ) reloaded, failed = trans.app.datatypes_registry.reload_display_applications( kwd.get( 'id' ) ) if not reloaded and failed: - return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").' % ( len( failed ), '", "'.join( failed ) ) ) + return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").' + % ( len( failed ), '", "'.join( failed ) ) ) if failed: return trans.show_warn_message( 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' - % ( len( reloaded ), '", "'.join( reloaded ), len( failed ), '", "'.join( failed ) ) ) + % ( len( reloaded ), '", "'.join( reloaded ), len( failed ), '", "'.join( failed ) ) ) if not reloaded: return trans.show_warn_message( 'You need to request at least one display application to reload.' ) return trans.show_ok_message( 'Reloaded %i requested display applications ("%s").' % ( len( reloaded ), '", "'.join( reloaded ) ) ) https://bitbucket.org/galaxy/galaxy-central/commits/390042b7f036/ Changeset: 390042b7f036 User: dannon Date: 2015-02-25 14:34:42+00:00 Summary: Update queries/filters in galaxy admin controller to use sqlalchemy constructs for True, False, testing for None. Affected #: 1 file diff -r bc6b7f12f0aa2afcc36e81bfb43c60a28ad79b28 -r 390042b7f0365ff1650e5a56ac4ee869952d5ad4 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -2,6 +2,8 @@ import logging import os +from sqlalchemy.sql import expression + import galaxy.queue_worker import galaxy.util from galaxy import model @@ -540,14 +542,14 @@ new_in_users = [] new_in_groups = [] for user in trans.sa_session.query( trans.app.model.User ) \ - .filter( trans.app.model.User.table.c.deleted==False ) \ + .filter( trans.app.model.User.table.c.deleted == expression.false() ) \ .order_by( trans.app.model.User.table.c.email ): if user.id in in_users: new_in_users.append( ( user.id, user.email ) ) else: params.out_users.append( ( user.id, user.email ) ) for group in trans.sa_session.query( trans.app.model.Group ) \ - .filter( trans.app.model.Group.table.c.deleted==False ) \ + .filter( trans.app.model.Group.table.c.deleted == expression.false() ) \ .order_by( trans.app.model.Group.table.c.name ): if group.id in in_groups: new_in_groups.append( ( group.id, group.name ) ) @@ -592,14 +594,14 @@ in_groups = [] out_groups = [] for user in trans.sa_session.query( trans.app.model.User ) \ - .filter( trans.app.model.User.table.c.deleted==False ) \ + .filter( trans.app.model.User.table.c.deleted == expression.false() ) \ .order_by( trans.app.model.User.table.c.email ): if user in [ x.user for x in quota.users ]: in_users.append( ( user.id, user.email ) ) else: out_users.append( ( user.id, user.email ) ) for group in trans.sa_session.query( trans.app.model.Group ) \ - .filter( trans.app.model.Group.table.c.deleted==False ) \ + .filter( trans.app.model.Group.table.c.deleted == expression.false()) \ .order_by( trans.app.model.Group.table.c.name ): if group in [ x.group for x in quota.groups ]: in_groups.append( ( group.id, group.name ) ) @@ -722,7 +724,7 @@ webapp=params.webapp, message=sanitize_text( str( e ) ), status='error' ) ) - if do_op == True or ( do_op != False and params.get( do_op, False ) ): + if do_op is True or ( do_op is not False and params.get( do_op, False ) ): try: message = op_method( quota, params ) return None, trans.response.send_redirect( web.url_for( controller='admin', https://bitbucket.org/galaxy/galaxy-central/commits/592c5347b33b/ Changeset: 592c5347b33b User: peterjc Date: 2015-02-25 19:37:56+00:00 Summary: Suppress filenames in SAM merge using egrep Based on fix suggested by Roberto Alonso (at CIPF) on the mailing list, see: https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-February/021589.h… Affected #: 1 file diff -r 390042b7f0365ff1650e5a56ac4ee869952d5ad4 -r 592c5347b33b4fe52244ba5077a20dd6b757278c lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -480,7 +480,7 @@ if result != 0: raise Exception('Result %s from %s' % (result, cmd)) if len(split_files) > 1: - cmd = 'egrep -v "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file ) + cmd = 'egrep -v -h "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file ) result = os.system(cmd) if result != 0: raise Exception('Result %s from %s' % (result, cmd)) https://bitbucket.org/galaxy/galaxy-central/commits/86f24f45ccdf/ Changeset: 86f24f45ccdf User: martenson Date: 2015-02-25 14:56:37+00:00 Summary: fix missing sqlalchemy imports and add documentation to folder manager Affected #: 1 file diff -r 592c5347b33b4fe52244ba5077a20dd6b757278c -r 86f24f45ccdfdc8769dff0272cabb57c6ce52171 lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -3,6 +3,8 @@ """ import galaxy.exceptions +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound import logging log = logging.getLogger( __name__ ) @@ -19,19 +21,21 @@ :param decoded_folder_id: decoded folder id :type decoded_folder_id: int - :param check_manageable: flag whether the check that user can manage item - :type check_manageable: bool + :param check_manageable: flag whether the check that user can manage item + :type check_manageable: bool :param check_accessible: flag whether to check that user can access item :type check_accessible: bool :returns: the requested folder :rtype: LibraryFolder + + :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError """ try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() - except galaxy.exceptions.MultipleResultsFound: + except MultipleResultsFound: raise galaxy.exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) - except galaxy.exceptions.NoResultFound: + except NoResultFound: raise galaxy.exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) except Exception, e: raise galaxy.exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) @@ -139,6 +143,14 @@ """ Mark given folder deleted/undeleted based on the flag. + :param folder: the model object + :type folder: LibraryFolder + :param undelete: flag whether to delete (when False) or undelete + :type undelete: Bool + + :returns: the folder + :rtype: LibraryFolder + :raises: ItemAccessibilityException """ if not trans.user_is_admin(): @@ -190,6 +202,14 @@ def cut_the_prefix( self, encoded_folder_id ): """ Remove the prefix from the encoded folder id. + + :param encoded_folder_id: encoded id of the Folder object with 'F' prepended + :type encoded_folder_id: string + + :returns: encoded Folder id without the 'F' prefix + :rtype: string + + :raises: MalformedId """ if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] @@ -200,6 +220,14 @@ def decode_folder_id( self, trans, encoded_folder_id ): """ Decode the folder id given that it has already lost the prefixed 'F'. + + :param encoded_folder_id: encoded id of the Folder object + :type encoded_folder_id: string + + :returns: decoded Folder id + :rtype: int + + :raises: MalformedId """ try: decoded_id = trans.security.decode_id( encoded_folder_id ) @@ -210,5 +238,11 @@ def cut_and_decode( self, trans, encoded_folder_id ): """ Cuts the folder prefix (the prepended 'F') and returns the decoded id. + + :param encoded_folder_id: encoded id of the Folder object + :type encoded_folder_id: string + + :returns: decoded Folder id + :rtype: int """ return self.decode_folder_id( trans, self.cut_the_prefix( encoded_folder_id ) ) https://bitbucket.org/galaxy/galaxy-central/commits/e6941d81339e/ Changeset: e6941d81339e User: martenson Date: 2015-02-25 15:52:35+00:00 Summary: create library root folder with '/' as default name fix for showing actual name of root folder when calling GET /api/libraries/{library_id}/contents Affected #: 2 files diff -r 86f24f45ccdfdc8769dff0272cabb57c6ce52171 -r e6941d81339e1bf706fa8f137e14b0cbb701a77a lib/galaxy/managers/libraries.py --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -54,7 +54,7 @@ raise exceptions.ItemAccessibilityException( 'Only administrators can create libraries.' ) else: library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) - root_folder = trans.app.model.LibraryFolder( name=name, description='' ) + root_folder = trans.app.model.LibraryFolder( name='/', description='' ) library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() diff -r 86f24f45ccdfdc8769dff0272cabb57c6ce52171 -r e6941d81339e1bf706fa8f137e14b0cbb701a77a lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -85,12 +85,13 @@ raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) - encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) + root_encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) + root_name = library.root_folder.name # appending root folder - rval.append( dict( id=encoded_id, + rval.append( dict( id=root_encoded_id, type='folder', - name='/', - url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) + name=root_name, + url=url_for( 'library_content', library_id=library_id, id=root_encoded_id ) ) ) library.root_folder.api_path = '' # appending all other items in the library recursively for content in traverse( library.root_folder ): https://bitbucket.org/galaxy/galaxy-central/commits/6ff3bb74e727/ Changeset: 6ff3bb74e727 User: dannon Date: 2015-02-25 16:48:01+00:00 Summary: Initial commit of recalculating user disk usage from the admin interface (user grid). Affected #: 1 file diff -r e6941d81339e1bf706fa8f137e14b0cbb701a77a -r 6ff3bb74e727ab565f486cae42ca579159e48465 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -1,17 +1,16 @@ import imp import logging import os - from sqlalchemy.sql import expression import galaxy.queue_worker import galaxy.util from galaxy import model -from galaxy.model import tool_shed_install as install_model from galaxy import web from galaxy.actions.admin import AdminActions from galaxy.exceptions import MessageException -from galaxy.util import sanitize_text +from galaxy.model import tool_shed_install as install_model +from galaxy.util import nice_size, sanitize_text from galaxy.util.odict import odict from galaxy.web import url_for from galaxy.web.base.controller import BaseUIController, UsesQuotaMixin @@ -124,7 +123,11 @@ condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False, - url_args=dict( webapp="galaxy", action="reset_user_password" ) ) + url_args=dict( webapp="galaxy", action="reset_user_password" ) ), + grids.GridOperation( "Recalculate Disk Usage", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( webapp="galaxy", action="recalculate_user_disk_usage" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -856,3 +859,69 @@ if not reloaded: return trans.show_warn_message( 'You need to request at least one display application to reload.' ) return trans.show_ok_message( 'Reloaded %i requested display applications ("%s").' % ( len( reloaded ), '", "'.join( reloaded ) ) ) + + @web.expose + @web.require_admin + def recalculate_user_disk_usage( self, trans, **kwd ): + user_id = kwd.get( 'id', None ) + user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) + if not user: + return trans.show_error_message( "User not found for id (%s)" % sanitize_text( str( user_id ) ) ) + engine = None + if trans.app.config.database_connection: + engine = trans.app.config.database_connection.split(':')[0] + if engine not in ( 'postgres', 'postgresql' ): + done = False + while not done: + current = user.get_disk_usage() + new = user.calculate_disk_usage() + trans.sa_session.refresh( user ) + # make sure usage didn't change while calculating, set done + if user.get_disk_usage() == current: + done = True + if new not in (current, None): + user.set_disk_usage( new ) + trans.sa_session.add( user ) + trans.sa_session.flush() + else: + # We can use the lightning fast pgcalc! + current = user.get_disk_usage() + new = pgcalc( self.sa_session, user.id ) + # yes, still a small race condition between here and the flush + if new in ( current, None ): + message = 'Usage is unchanged at %s.' % nice_size( current ) + else: + message = 'Usage has changed by %s to %s.' % ( nice_size( new - current ), nice_size( current ) ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message=sanitize_text( message ), + status='info' ) ) + + +def pgcalc( sa_session, id, dryrun=False ): + """ + Utility method for quickly recalculating user disk usage in postgres. + TODO: Move this elsewhere and update scripts/set_user_disk_usage.py + """ + sql = """ + UPDATE galaxy_user + SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) + FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id + FROM history_dataset_association hda + JOIN history h ON h.id = hda.history_id + JOIN dataset d ON hda.dataset_id = d.id + WHERE h.user_id = :id + AND h.purged = false + AND hda.purged = false + AND d.purged = false + AND d.id NOT IN (SELECT dataset_id + FROM library_dataset_dataset_association) + ) sizes) + WHERE id = :id + RETURNING disk_usage; + """ + r = sa_session.execute(sql, {'id': id}) + new = r.fetchone()[0] + if dryrun: + sa_session.rollback() + return new https://bitbucket.org/galaxy/galaxy-central/commits/970982d0841d/ Changeset: 970982d0841d User: dan Date: 2015-02-25 17:07:39+00:00 Summary: Fix for ToolShed not having config.shed_tool_data_path Affected #: 1 file diff -r 6ff3bb74e727ab565f486cae42ca579159e48465 -r 970982d0841d3b1717ae0263f303cfed6305c46f lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -137,6 +137,10 @@ self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) @property + def shed_tool_data_path( self ): + return self.tool_data_path + + @property def sentry_dsn_public( self ): """ Sentry URL with private key removed for use in client side scripts, https://bitbucket.org/galaxy/galaxy-central/commits/7ef30f55b759/ Changeset: 7ef30f55b759 User: dannon Date: 2015-02-25 17:52:47+00:00 Summary: Refactoring of set_user_disk_usage and admin controller disk usage to use the same pgcalc Affected #: 3 files diff -r 970982d0841d3b1717ae0263f303cfed6305c46f -r 7ef30f55b759ef1bbd53cd1113887f3637fc4e96 lib/galaxy/model/util.py --- /dev/null +++ b/lib/galaxy/model/util.py @@ -0,0 +1,36 @@ +""" +Utility helpers related to the model +""" + + +def pgcalc( sa_session, id, dryrun=False ): + """ + Utility method for quickly recalculating user disk usage in postgres. + + TODO: Move this elsewhere and update scripts/set_user_disk_usage.py + + TODO: Check against the recently updated versions of sqlalchemy if this + 'special' postgresql version is even necessary. + """ + sql = """ + UPDATE galaxy_user + SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) + FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id + FROM history_dataset_association hda + JOIN history h ON h.id = hda.history_id + JOIN dataset d ON hda.dataset_id = d.id + WHERE h.user_id = :id + AND h.purged = false + AND hda.purged = false + AND d.purged = false + AND d.id NOT IN (SELECT dataset_id + FROM library_dataset_dataset_association) + ) sizes) + WHERE id = :id + RETURNING disk_usage; + """ + r = sa_session.execute(sql, {'id': id}) + new = r.fetchone()[0] + if dryrun: + sa_session.rollback() + return new diff -r 970982d0841d3b1717ae0263f303cfed6305c46f -r 7ef30f55b759ef1bbd53cd1113887f3637fc4e96 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -10,6 +10,7 @@ from galaxy.actions.admin import AdminActions from galaxy.exceptions import MessageException from galaxy.model import tool_shed_install as install_model +from galaxy.model.util import pgcalc from galaxy.util import nice_size, sanitize_text from galaxy.util.odict import odict from galaxy.web import url_for @@ -896,32 +897,3 @@ action='users', message=sanitize_text( message ), status='info' ) ) - - -def pgcalc( sa_session, id, dryrun=False ): - """ - Utility method for quickly recalculating user disk usage in postgres. - TODO: Move this elsewhere and update scripts/set_user_disk_usage.py - """ - sql = """ - UPDATE galaxy_user - SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id - FROM history_dataset_association hda - JOIN history h ON h.id = hda.history_id - JOIN dataset d ON hda.dataset_id = d.id - WHERE h.user_id = :id - AND h.purged = false - AND hda.purged = false - AND d.purged = false - AND d.id NOT IN (SELECT dataset_id - FROM library_dataset_dataset_association) - ) sizes) - WHERE id = :id - RETURNING disk_usage; - """ - r = sa_session.execute(sql, {'id': id}) - new = r.fetchone()[0] - if dryrun: - sa_session.rollback() - return new diff -r 970982d0841d3b1717ae0263f303cfed6305c46f -r 7ef30f55b759ef1bbd53cd1113887f3637fc4e96 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -1,9 +1,22 @@ #!/usr/bin/env python -import os, sys +import os +import sys + from ConfigParser import ConfigParser from optparse import OptionParser +sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) + +from galaxy import eggs +import pkg_resources + +import galaxy.config +from galaxy.model.util import pgcalc +from galaxy.util import nice_size +from galaxy.objectstore import build_object_store_from_config + + default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'config/galaxy.ini') ) parser = OptionParser() @@ -13,6 +26,7 @@ parser.add_option( '--dry-run', dest='dryrun', help='Dry run (show changes but do not save to database)', action='store_true', default=False ) ( options, args ) = parser.parse_args() + def init(): options.config = os.path.abspath( options.config ) @@ -21,19 +35,8 @@ if options.email == 'all': options.email = None - sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) - - from galaxy import eggs - import pkg_resources - - import galaxy.config - from galaxy.objectstore import build_object_store_from_config - - # lazy - globals()['nice_size'] = __import__( 'galaxy.util', globals(), locals(), ( 'nice_size', ) ).nice_size - - config_parser = ConfigParser( dict( here = os.getcwd(), - database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) ) + config_parser = ConfigParser( dict( here=os.getcwd(), + database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) ) config_parser.read( options.config ) config_dict = {} @@ -45,31 +48,10 @@ from galaxy.model import mapping - return mapping.init( config.file_path, config.database_connection, create_tables = False, object_store = object_store ), object_store, config.database_connection.split(':')[0] + return (mapping.init( config.file_path, config.database_connection, create_tables=False, object_store=object_store ), + object_store, + config.database_connection.split(':')[0]) -def pgcalc( sa_session, id ): - sql = """ - UPDATE galaxy_user - SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id - FROM history_dataset_association hda - JOIN history h ON h.id = hda.history_id - JOIN dataset d ON hda.dataset_id = d.id - WHERE h.user_id = :id - AND h.purged = false - AND hda.purged = false - AND d.purged = false - AND d.id NOT IN (SELECT dataset_id - FROM library_dataset_dataset_association) - ) sizes) - WHERE id = :id - RETURNING disk_usage; - """ - r = sa_session.execute(sql, {'id':id}) - new = r.fetchone()[0] - if options.dryrun: - sa_session.rollback() - return new def quotacheck( sa_session, users, engine ): sa_session.refresh( user ) @@ -83,7 +65,7 @@ print 'usage changed while calculating, trying again...' return quotacheck( sa_session, user, engine ) else: - new = pgcalc( sa_session, user.id ) + new = pgcalc( sa_session, user.id, dryrun=options.dryrun ) # yes, still a small race condition between here and the flush print 'old usage:', nice_size( current ), 'change:', if new in ( current, None ): https://bitbucket.org/galaxy/galaxy-central/commits/51264e606805/ Changeset: 51264e606805 User: dannon Date: 2015-02-25 17:54:43+00:00 Summary: Remove finished TODO. Affected #: 1 file diff -r 7ef30f55b759ef1bbd53cd1113887f3637fc4e96 -r 51264e606805464d65d032b06d80021d1bf2800e lib/galaxy/model/util.py --- a/lib/galaxy/model/util.py +++ b/lib/galaxy/model/util.py @@ -7,8 +7,6 @@ """ Utility method for quickly recalculating user disk usage in postgres. - TODO: Move this elsewhere and update scripts/set_user_disk_usage.py - TODO: Check against the recently updated versions of sqlalchemy if this 'special' postgresql version is even necessary. """ 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.

1 0

[galaxyproject/usegalaxy-playbook] 1d0a9a: Update test to 658833a7988fe335a5aaaac9709f9e6dfed...
by GitHub 25 Feb '15

25 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d0a9a2d58d4d1dfcfbbbbd08a9053c8e0bd8107 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d0a9a2d58d4d1df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-02-25 (Wed, 25 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/all.yml Log Message: ----------- Update test to 658833a7988fe335a5aaaac9709f9e6dfed4a7b2

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 25 Feb '15

25 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1177b255f17d/ Changeset: 1177b255f17d User: martenson Date: 2015-02-23 22:42:17+00:00 Summary: add API endpoint to create TS repository Affected #: 3 files diff -r a12fc23ff13785d2c2ef7d223dca100ef334ea87 -r 1177b255f17d80190849fc64a5ce9bd88bbe7fd7 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 @@ -10,8 +10,10 @@ from galaxy import util from galaxy import web +from galaxy import exceptions from galaxy.datatypes import checkers from galaxy.model.orm import and_ +from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago @@ -31,6 +33,7 @@ from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util + log = logging.getLogger( __name__ ) @@ -577,13 +580,72 @@ id=trans.security.encode_id( repository.id ) ) return repository_dict + @expose_api + def create( self, trans, payload, **kwd ): + """ + create( self, trans, payload, **kwd ) + * POST /api/repositories: + Creates a new repository. + Only ``name`` and ``synopsis`` parameters are required. + + :param payload: dictionary structure containing:: + 'name': new repo's name (required) + 'synopsis': new repo's synopsis (required) + 'description': new repo's description (optional) + 'remote_repository_url': new repo's remote repo (optional) + 'homepage_url': new repo's homepage url (optional) + 'category_ids[]': list of existing encoded TS category ids + the new repo should be associated with (optional) + 'type': new repo's type, defaults to ``unrestricted`` (optional) + + :type payload: dict + + :returns: detailed repository information + :rtype: dict + + :raises: RequestParameterMissingException + """ + params = util.Params( payload ) + name = util.restore_text( params.get( 'name', None ) ) + if not name: + raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." ) + synopsis = util.restore_text( params.get( 'synopsis', None ) ) + if not synopsis: + raise exceptions.RequestParameterMissingException( "Missing required parameter 'synopsis'." ) + + description = util.restore_text( params.get( 'description', '' ) ) + remote_repository_url = util.restore_text( params.get( 'remote_repository_url', '' ) ) + homepage_url = util.restore_text( params.get( 'homepage_url', '' ) ) + category_ids = util.listify( params.get( 'category_ids[]', '' ) ) + selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] + + repo_type = kwd.get( 'type', rt_util.UNRESTRICTED ) + if repo_type not in rt_util.types: + raise exceptions.RequestParameterInvalidException( 'This repository type is not valid' ) + + invalid_message = repository_util.validate_repository_name( trans.app, name, trans.user ) + if invalid_message: + raise exceptions.RequestParameterInvalidException( invalid_message ) + + repo, message = repository_util.create_repository( app=trans.app, + name=name, + type=repo_type, + description=synopsis, + long_description=description, + user_id = trans.user.id, + category_ids=category_ids, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url ) + + return repo.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) ) + @web.expose_api def create_changeset_revision( self, trans, id, payload, **kwd ): """ POST /api/repositories/{encoded_repository_id}/changeset_revision Create a new tool shed repository commit - leaving PUT on parent - resource open for updating meta-attirbutes of the repository (and + resource open for updating meta-attributes of the repository (and Galaxy doesn't allow PUT multipart data anyway https://trello.com/c/CQwmCeG6) diff -r a12fc23ff13785d2c2ef7d223dca100ef334ea87 -r 1177b255f17d80190849fc64a5ce9bd88bbe7fd7 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -129,6 +129,11 @@ controller='repositories', action='create_changeset_revision', conditions=dict( method=[ "POST" ] ) ) + webapp.mapper.connect( 'create_repository', + '/api/repositories', + controller='repositories', + action='create', + conditions=dict( method=[ "POST" ] ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r a12fc23ff13785d2c2ef7d223dca100ef334ea87 -r 1177b255f17d80190849fc64a5ce9bd88bbe7fd7 lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -313,8 +313,11 @@ return associations_dict def validate_repository_name( app, name, user ): - # Repository names must be unique for each user, must be at least four characters - # in length and must contain only lower-case letters, numbers, and the '_' character. + """ + Validate whether the given name qualifies as a new TS repo name. + Repository names must be unique for each user, must be at least two characters + in length and must contain only lower-case letters, numbers, and the '_' character. + """ if name in [ 'None', None, '' ]: return 'Enter the required repository name.' if name in [ 'repos' ]: @@ -322,13 +325,13 @@ check_existing = suc.get_repository_by_name_and_owner( app, name, user.username ) if check_existing is not None: if check_existing.deleted: - return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name + return 'You own a deleted repository named <b>%s</b>, please choose a different name.' % escape( name ) else: - return "You already have a repository named <b>%s</b>, so choose a different name." % name + return "You already own a repository named <b>%s</b>, please choose a different name." % escape( name ) if len( name ) < 2: return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( name ) ): - return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." + return "Repository names must contain only lower-case letters, numbers and underscore." return '' https://bitbucket.org/galaxy/galaxy-central/commits/05d1b7925348/ Changeset: 05d1b7925348 User: jmchilton Date: 2015-02-24 20:37:45+00:00 Summary: Fix tool shed-y workflowing for ce1f85a0f09689e86fce1839390a5a00a730321f. Affected #: 1 file diff -r 1177b255f17d80190849fc64a5ce9bd88bbe7fd7 -r 05d1b792534806bd064865d813edcff012dbf81f lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -6,10 +6,10 @@ import galaxy.tools import galaxy.tools.parameters -import galaxy.webapps.galaxy.controllers.workflow from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html from galaxy.workflow.render import WorkflowCanvas +from galaxy.workflow.steps import attach_ordered_steps from galaxy.workflow.modules import module_types from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory @@ -312,7 +312,7 @@ step.input_connections.append( conn ) del step.temp_input_connections # Order the steps if possible. - galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps ) + attach_ordered_steps( workflow, steps ) # Return the in-memory Workflow object for display or later persistence to the Galaxy database. return workflow, missing_tool_tups https://bitbucket.org/galaxy/galaxy-central/commits/20bf9ebc1cd1/ Changeset: 20bf9ebc1cd1 User: carlfeberhard Date: 2015-02-24 22:20:10+00:00 Summary: Fix to layering of dropdown buttons and menus Affected #: 3 files diff -r 05d1b792534806bd064865d813edcff012dbf81f -r 20bf9ebc1cd143d29bb651caf1994f1d9c2db05a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2030,8 +2030,8 @@ .list-panel .controls .list-actions:after{clear:both} .list-panel .controls .list-actions:before,.list-panel .controls .list-actions:after{content:" ";display:table;} .list-panel .controls .list-actions:after{clear:both} -.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%;z-index:inherit} -.list-panel .controls .list-actions .list-action-menu{float:right}.list-panel .controls .list-actions .list-action-menu .dropdown-menu{z-index:inherit} +.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%} +.list-panel .controls .list-actions .list-action-menu{float:right} .list-panel .list-items .list-item:not(:last-child){border-bottom-width:0px} .list-panel .empty-message{display:none;margin:0px} .list-item .details .list-panel{margin-top:8px;border-radius:3px;background:white;padding:4px}.list-item .details .list-panel .list-items{border:1px solid #bfbfbf;border-radius:3px}.list-item .details .list-panel .list-items .list-item:first-child{border-top-width:0px;border-radius:3px 3px 0px 0px} @@ -2138,9 +2138,10 @@ .multi-panel-history .control-column.control-column-right{text-align:right} .multi-panel-history .outer-middle{overflow:auto} .multi-panel-history .middle{min-width:100%;margin:0px 0px 0px 0px;background-color:white;padding:8px} -.multi-panel-history .history-column{width:312px;margin:0 8px 0 0}.multi-panel-history .history-column:first-child{position:fixed;z-index:2}.multi-panel-history .history-column:first-child .history-panel{border:1px solid black;box-shadow:4px 4px 4px rgba(96,96,96,0.3)} +.multi-panel-history .history-column{width:312px;margin:0 8px 0 0}.multi-panel-history .history-column:first-child{position:fixed;z-index:10}.multi-panel-history .history-column:first-child .history-panel{border:1px solid black;box-shadow:4px 4px 4px rgba(96,96,96,0.3)} .multi-panel-history .history-column:nth-child(2){margin-left:320px} .multi-panel-history .history-column:last-child{margin-right:0px} +.multi-panel-history .history-column .dropdown-menu{z-index:inherit} .multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} .multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px} .multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px} diff -r 05d1b792534806bd064865d813edcff012dbf81f -r 20bf9ebc1cd143d29bb651caf1994f1d9c2db05a static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -744,7 +744,7 @@ // current history &:first-child { position: fixed; - z-index : 2; + z-index : 10; // visually differentiate the current history .history-panel { @@ -759,6 +759,9 @@ &:last-child { margin-right: 0px; } + .dropdown-menu { + z-index: inherit; + } .panel-controls { width: 100%; diff -r 05d1b792534806bd064865d813edcff012dbf81f -r 20bf9ebc1cd143d29bb651caf1994f1d9c2db05a static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -167,13 +167,9 @@ padding-top: 2px; padding-bottom: 2px; font-size: 90%; - z-index: inherit; } .list-action-menu { float: right; - .dropdown-menu { - z-index: inherit; - } } } } https://bitbucket.org/galaxy/galaxy-central/commits/658833a7988f/ Changeset: 658833a7988f User: dannon Date: 2015-02-24 23:55:50+00:00 Summary: More tweaks to mutable capabilities, adding back in a copy and stripping pickle from MutationList Affected #: 1 file diff -r 20bf9ebc1cd143d29bb651caf1994f1d9c2db05a -r 658833a7988fe335a5aaaac9709f9e6dfed4a7b2 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,4 +1,5 @@ import binascii +import copy import json import logging import uuid @@ -62,6 +63,12 @@ else: return self.impl + def copy_value( self, value ): + return copy.deepcopy( value ) + + def compare_values( self, x, y ): + return ( x == y ) + class MutationObj(Mutable): """ @@ -196,12 +203,6 @@ list.remove(self, value) self.changed() - def __getstate__(self): - return list(self) - - def __setstate__(self, state): - self.update(state) - MutationObj.associate_with(JSONType) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] f65108: Fetch modified integrated_tool_panel.xml from Main
by GitHub 24 Feb '15

24 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f65108118e2fa0f18274944b21084b1234937889 https://github.com/galaxyproject/usegalaxy-playbook/commit/f65108118e2fa0f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Fetch modified integrated_tool_panel.xml from Main Commit: cf4260106a86f13850876a14db8976fbf1c719d9 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf4260106a86f138… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Switch Test/Main to use a slurm-drmaa compiled without optimization, to assist with tracking down the pthread deadlock. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/eb8faf9d51a1...…

1 0

[galaxyproject/usegalaxy-playbook] eb8faf: Unfortunately, metadata failure is still considere...
by GitHub 24 Feb '15

24 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eb8faf9d51a1b7cffa7f75bdf5b9bc4d5495f05b https://github.com/galaxyproject/usegalaxy-playbook/commit/eb8faf9d51a1b7cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Unfortunately, metadata failure is still considered a job "success", and the jobdir is removed. So, set Test to never remove jobdirs while we debug metadata failures.

1 0

[galaxyproject/usegalaxy-playbook] bf3597: Update Test
by GitHub 24 Feb '15

24 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf3597a0e5a22b66969f58b22cf08ce5c507bcbb https://github.com/galaxyproject/usegalaxy-playbook/commit/bf3597a0e5a22b66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Feb '15

24 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99fef2a32e19/ Changeset: 99fef2a32e19 Branch: release_15.03 User: dan Date: 2015-02-24 17:02:42+00:00 Summary: Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. Affected #: 2 files diff -r d1c3d84a7e06553cf948fcbd8c00b45bebcfb059 -r 99fef2a32e19ce5a8cf6137c1da2dbd9ddbb0536 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -217,6 +217,10 @@ # https://wiki.galaxyproject.org/Admin/DataIntegration #tool_data_path = tool-data +# Directory where Tool Data Table related files will be placed +# when installed from a ToolShed. Defaults to tool_data_path +#shed_tool_data_path = tool-data + # File containing old-style genome builds #builds_file_path = tool-data/shared/ucsc/builds.txt diff -r d1c3d84a7e06553cf948fcbd8c00b45bebcfb059 -r 99fef2a32e19ce5a8cf6137c1da2dbd9ddbb0536 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -103,7 +103,7 @@ try: new_table_elems, message = self.app.tool_data_tables \ .add_new_entries_from_config_file( config_filename=filename, - tool_data_path=self.app.config.tool_data_path, + tool_data_path=self.app.config.shed_tool_data_path, shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=persist ) if message: https://bitbucket.org/galaxy/galaxy-central/commits/4a42638e8cd4/ Changeset: 4a42638e8cd4 Branch: release_15.03 User: dannon Date: 2015-02-24 19:50:02+00:00 Summary: Apply custom_types bugfixes from dev branch to release. Affected #: 1 file diff -r 99fef2a32e19ce5a8cf6137c1da2dbd9ddbb0536 -r 4a42638e8cd45652db9dc1f1eed54be6aa2c20b1 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,25 +1,23 @@ -from sqlalchemy.types import * +import binascii +import json +import logging +import uuid -import json -import pickle -import copy -import uuid -import binascii -from galaxy.util.bunch import Bunch +from galaxy import eggs +eggs.require("SQLAlchemy") +import sqlalchemy + from galaxy.util.aliaspickler import AliasPickleModule +from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator +from sqlalchemy.ext.mutable import Mutable -# For monkeypatching BIGINT -import sqlalchemy.dialects.sqlite -import sqlalchemy.dialects.postgresql -import sqlalchemy.dialects.mysql - -import logging log = logging.getLogger( __name__ ) # Default JSON encoder and decoder json_encoder = json.JSONEncoder( sort_keys=True ) json_decoder = json.JSONDecoder( ) + def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue @@ -31,39 +29,32 @@ return binascii.unhexlify( value[2:] ) else: return value - except Exception, ex: + except Exception: return value -class JSONType( TypeDecorator ): + +class JSONType(sqlalchemy.types.TypeDecorator): """ - Defines a JSONType for SQLAlchemy. Takes a primitive as input and - JSONifies it. This should replace PickleType throughout Galaxy. + Represents an immutable structure as a json-encoded string. + + If default is, for example, a dict, then a NULL value in the + database will be exposed as an empty dict. """ + + # TODO: Figure out why this is a large binary, and provide a migratino to + # something like sqlalchemy.String, or even better, when applicable, native + # sqlalchemy.dialects.postgresql.JSON impl = LargeBinary - def process_bind_param( self, value, dialect ): - if value is None: - return None - return json_encoder.encode( value ) + def process_bind_param(self, value, dialect): + if value is not None: + value = json_encoder.encode(value) + return value - def process_result_value( self, value, dialect ): + def process_result_value(self, value, dialect): if value is not None: - try: - return json_decoder.decode( str( _sniffnfix_pg9_hex( value ) ) ) - except Exception, e: - log.error( 'Failed to decode JSON (%s): %s', value, e ) - return None - - def copy_value( self, value ): - # return json_decoder.decode( json_encoder.encode( value ) ) - return copy.deepcopy( value ) - - def compare_values( self, x, y ): - # return json_encoder.encode( x ) == json_encoder.encode( y ) - return ( x == y ) - - def is_mutable( self ): - return True + value = json_decoder.decode( str( _sniffnfix_pg9_hex( value ) ) ) + return value def load_dialect_impl(self, dialect): if dialect.name == "mysql": @@ -72,10 +63,153 @@ return self.impl +class MutationObj(Mutable): + """ + Mutable JSONType for SQLAlchemy from original gist: + https://gist.github.com/dbarnett/1730610 + + Using minor changes from this fork of the gist: + https://gist.github.com/miracle2k/52a031cced285ba9b8cd + + And other minor changes to make it work for us. + """ + @classmethod + def coerce(cls, key, value): + if isinstance(value, dict) and not isinstance(value, MutationDict): + return MutationDict.coerce(key, value) + if isinstance(value, list) and not isinstance(value, MutationList): + return MutationList.coerce(key, value) + return value + + @classmethod + def _listen_on_attribute(cls, attribute, coerce, parent_cls): + key = attribute.key + if parent_cls is not attribute.class_: + return + + # rely on "propagate" here + parent_cls = attribute.class_ + + def load(state, *args): + val = state.dict.get(key, None) + if coerce: + val = cls.coerce(key, val) + state.dict[key] = val + if isinstance(val, cls): + val._parents[state.obj()] = key + + def set(target, value, oldvalue, initiator): + if not isinstance(value, cls): + value = cls.coerce(key, value) + if isinstance(value, cls): + value._parents[target.obj()] = key + if isinstance(oldvalue, cls): + oldvalue._parents.pop(target.obj(), None) + return value + + def pickle(state, state_dict): + val = state.dict.get(key, None) + if isinstance(val, cls): + if 'ext.mutable.values' not in state_dict: + state_dict['ext.mutable.values'] = [] + state_dict['ext.mutable.values'].append(val) + + def unpickle(state, state_dict): + if 'ext.mutable.values' in state_dict: + for val in state_dict['ext.mutable.values']: + val._parents[state.obj()] = key + + sqlalchemy.event.listen(parent_cls, 'load', load, raw=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'refresh', load, raw=True, propagate=True) + sqlalchemy.event.listen(attribute, 'set', set, raw=True, retval=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'pickle', pickle, raw=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'unpickle', unpickle, raw=True, propagate=True) + + +class MutationDict(MutationObj, dict): + @classmethod + def coerce(cls, key, value): + """Convert plain dictionary to MutationDict""" + self = MutationDict((k, MutationObj.coerce(key, v)) for (k, v) in value.items()) + self._key = key + return self + + def __setitem__(self, key, value): + if hasattr(self, '_key'): + value = MutationObj.coerce(self._key, value) + dict.__setitem__(self, key, value) + self.changed() + + def __delitem__(self, key): + dict.__delitem__(self, key) + self.changed() + + def __getstate__(self): + return dict(self) + + def __setstate__(self, state): + self.update(state) + + +class MutationList(MutationObj, list): + @classmethod + def coerce(cls, key, value): + """Convert plain list to MutationList""" + self = MutationList((MutationObj.coerce(key, v) for v in value)) + self._key = key + return self + + def __setitem__(self, idx, value): + list.__setitem__(self, idx, MutationObj.coerce(self._key, value)) + self.changed() + + def __setslice__(self, start, stop, values): + list.__setslice__(self, start, stop, (MutationObj.coerce(self._key, v) for v in values)) + self.changed() + + def __delitem__(self, idx): + list.__delitem__(self, idx) + self.changed() + + def __delslice__(self, start, stop): + list.__delslice__(self, start, stop) + self.changed() + + def append(self, value): + list.append(self, MutationObj.coerce(self._key, value)) + self.changed() + + def insert(self, idx, value): + list.insert(self, idx, MutationObj.coerce(self._key, value)) + self.changed() + + def extend(self, values): + list.extend(self, (MutationObj.coerce(self._key, v) for v in values)) + self.changed() + + def pop(self, *args, **kw): + value = list.pop(self, *args, **kw) + self.changed() + return value + + def remove(self, value): + list.remove(self, value) + self.changed() + + def __getstate__(self): + return list(self) + + def __setstate__(self, state): + self.update(state) + + +MutationObj.associate_with(JSONType) + metadata_pickler = AliasPickleModule( { - ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) + ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) + class MetadataType( JSONType ): """ Backward compatible metadata type. Can read pickles or JSON, but always @@ -96,6 +230,7 @@ ret = None return ret + class UUIDType(TypeDecorator): """ Platform-independent UUID type. @@ -129,31 +264,9 @@ class TrimmedString( TypeDecorator ): impl = String + def process_bind_param( self, value, dialect ): """Automatically truncate string values""" if self.impl.length and value is not None: value = value[0:self.impl.length] return value - - -#class BigInteger( Integer ): - #""" - #A type for bigger ``int`` integers. - - #Typically generates a ``BIGINT`` in DDL, and otherwise acts like - #a normal :class:`Integer` on the Python side. - - #""" - -#class BIGINT( BigInteger ): - #"""The SQL BIGINT type.""" - -#class SLBigInteger( BigInteger ): - #def get_col_spec( self ): - #return "BIGINT" - -#sqlalchemy.dialects.sqlite.SLBigInteger = SLBigInteger -#sqlalchemy.dialects.sqlite.colspecs[BigInteger] = SLBigInteger -#sqlalchemy.dialects.sqlite.ischema_names['BIGINT'] = SLBigInteger -#sqlalchemy.dialects.postgres.colspecs[BigInteger] = sqlalchemy.dialects.postgres.PGBigInteger -#sqlalchemy.dialects.mysql.colspecs[BigInteger] = sqlalchemy.dialects.mysql.MSBigInteger Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 24 Feb '15

24 Feb '15

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/59cd12ceafc4/ Changeset: 59cd12ceafc4 User: dannon Date: 2015-02-24 16:38:18+00:00 Summary: Cleanup of comments, doc of customtypes. Affected #: 1 file diff -r 476c79d7b00a5edde57847ca1882d7e7781030b6 -r 59cd12ceafc4628e05600be46939124d4ca59c08 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -33,15 +33,6 @@ return value -# Mutable JSONType for SQLAlchemy from original gist: -# https://gist.github.com/dbarnett/1730610 -# -# Also using minor changes from this fork of the gist: -# https://gist.github.com/miracle2k/52a031cced285ba9b8cd -# -# And other minor changes to make it work for us. - - class JSONType(sqlalchemy.types.TypeDecorator): """Represents an immutable structure as a json-encoded string. @@ -69,6 +60,15 @@ class MutationObj(Mutable): + """ + Mutable JSONType for SQLAlchemy from original gist: + https://gist.github.com/dbarnett/1730610 + + Using minor changes from this fork of the gist: + https://gist.github.com/miracle2k/52a031cced285ba9b8cd + + And other minor changes to make it work for us. + """ @classmethod def coerce(cls, key, value): if isinstance(value, dict) and not isinstance(value, MutationDict): @@ -192,13 +192,6 @@ MutationObj.associate_with(JSONType) -"""A type to encode/decode JSON on the fly - -sqltype is the string type for the underlying DB column:: - - Column(JSON) -""" - metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) https://bitbucket.org/galaxy/galaxy-central/commits/834b3e714755/ Changeset: 834b3e714755 User: dan Date: 2015-02-24 16:50:58+00:00 Summary: Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. Affected #: 2 files diff -r 59cd12ceafc4628e05600be46939124d4ca59c08 -r 834b3e71475518902f071d4066d69e707f752730 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -217,6 +217,10 @@ # https://wiki.galaxyproject.org/Admin/DataIntegration #tool_data_path = tool-data +# Directory where Tool Data Table related files will be placed +# when installed from a ToolShed. Defaults to tool_data_path +#shed_tool_data_path = tool-data + # File containing old-style genome builds #builds_file_path = tool-data/shared/ucsc/builds.txt diff -r 59cd12ceafc4628e05600be46939124d4ca59c08 -r 834b3e71475518902f071d4066d69e707f752730 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -103,7 +103,7 @@ try: new_table_elems, message = self.app.tool_data_tables \ .add_new_entries_from_config_file( config_filename=filename, - tool_data_path=self.app.config.tool_data_path, + tool_data_path=self.app.config.shed_tool_data_path, shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=persist ) if message: https://bitbucket.org/galaxy/galaxy-central/commits/b154ff11d2ea/ Changeset: b154ff11d2ea User: jmchilton Date: 2015-02-24 17:01:35+00:00 Summary: Fix unit tests for dde2fc9572be6d909e22dda510520639db5260bf. Thanks to @ dannon for the bug report. Affected #: 1 file diff -r 834b3e71475518902f071d4066d69e707f752730 -r b154ff11d2ea00d6978da97ee60bb1013f4f7f4e test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -21,6 +21,7 @@ job_config_file=os.path.join( self.temp_directory, "job_conf.xml" ), use_tasked_jobs=False, job_resource_params_file="/tmp/fake_absent_path", + config_dict={}, ) self.__write_config_from( SIMPLE_JOB_CONF ) self.app = bunch.Bunch( config=self.config, job_metrics=MockJobMetrics() ) https://bitbucket.org/galaxy/galaxy-central/commits/64b4a5b00522/ Changeset: 64b4a5b00522 User: dannon Date: 2015-02-24 18:47:29+00:00 Summary: Fix for JSONType getstate/setstate with pickle (exhibited error during uploading of a file). Affected #: 1 file diff -r b154ff11d2ea00d6978da97ee60bb1013f4f7f4e -r 64b4a5b005224c5639482de4eda52adcfa25df10 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -143,6 +143,12 @@ dict.__delitem__(self, key) self.changed() + def __getstate__(self): + return dict(self) + + def __setstate__(self, state): + self.update(state) + class MutationList(MutationObj, list): @classmethod https://bitbucket.org/galaxy/galaxy-central/commits/9f3d45b2e032/ Changeset: 9f3d45b2e032 User: dannon Date: 2015-02-24 18:56:19+00:00 Summary: Add getstate/setstate for pickling to the MutationList as well, though I'm not sure we use this anywhere. Future-proofing. Affected #: 1 file diff -r 64b4a5b005224c5639482de4eda52adcfa25df10 -r 9f3d45b2e032b7d208c1e7e021ab3460795272fe lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -195,6 +195,12 @@ list.remove(self, value) self.changed() + def __getstate__(self): + return list(self) + + def __setstate__(self, state): + self.update(state) + MutationObj.associate_with(JSONType) https://bitbucket.org/galaxy/galaxy-central/commits/a12fc23ff137/ Changeset: a12fc23ff137 User: dannon Date: 2015-02-24 19:18:24+00:00 Summary: Commentary in custom_types w/ a TODO. Remove irrelevant comments about OrderedDict, since we're not relying on that. Affected #: 1 file diff -r 9f3d45b2e032b7d208c1e7e021ab3460795272fe -r a12fc23ff13785d2c2ef7d223dca100ef334ea87 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -34,12 +34,16 @@ class JSONType(sqlalchemy.types.TypeDecorator): - """Represents an immutable structure as a json-encoded string. + """ + Represents an immutable structure as a json-encoded string. If default is, for example, a dict, then a NULL value in the database will be exposed as an empty dict. """ + # TODO: Figure out why this is a large binary, and provide a migratino to + # something like sqlalchemy.String, or even better, when applicable, native + # sqlalchemy.dialects.postgresql.JSON impl = LargeBinary def process_bind_param(self, value, dialect): @@ -131,9 +135,6 @@ return self def __setitem__(self, key, value): - # Due to the way OrderedDict works, this is called during __init__. - # At this time we don't have a key set, but what is more, the value - # being set has already been coerced. So special case this and skip. if hasattr(self, '_key'): value = MutationObj.coerce(self._key, value) dict.__setitem__(self, key, value) 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.

1 0

[galaxyproject/usegalaxy-playbook] 7a7a4e: update mutable confs
by GitHub 24 Feb '15

24 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7a7a4e4d8ef3b238d8ef93d00c77372fef237c04 https://github.com/galaxyproject/usegalaxy-playbook/commit/7a7a4e4d8ef3b238… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update mutable confs

1 0

[galaxyproject/usegalaxy-playbook] f84180: Update test to 476c79d7b00a5edde57847ca1882d7e7781...
by GitHub 24 Feb '15

24 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f841803b0b0a3b0b8dd8d2bb4f42845be982f341 https://github.com/galaxyproject/usegalaxy-playbook/commit/f841803b0b0a3b0b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-02-24 (Tue, 24 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M stage/group_vars/all.yml Log Message: ----------- Update test to 476c79d7b00a5edde57847ca1882d7e7781030b6

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Feb '15

24 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/525b1fc16a58/ Changeset: 525b1fc16a58 Branch: release_15.03 User: jmchilton Date: 2015-02-22 05:32:46+00:00 Summary: Fix for watching tools on some more interesting file systems. Affected #: 3 files diff -r 33fd43f7590f17ed611ce07178cae8c2b70525d0 -r 525b1fc16a587e91d60cdc4f9152f8e881b7e7de config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -176,11 +176,15 @@ # install from in the admin interface (.sample used if default does not exist). #tool_sheds_config_file = config/tool_sheds_conf.xml -# Enable monitoring of tools and tool directories listed in any tool config file -# specified in tool_config_file option. If changes are found, tools are -# automatically reloaded. -# Watchdog ( https://pypi.python.org/pypi/watchdog ) must be installed and -# available to Galaxy to use this option. +# Set to True to Enable monitoring of tools and tool directories +# listed in any tool config file specified in tool_config_file option. +# If changes are found, tools are automatically reloaded. Watchdog ( +# https://pypi.python.org/pypi/watchdog ) must be installed and +# available to Galaxy to use this option. Other options include 'auto' +# which will attempt to watch tools if the watchdog library is available +# but won't fail to load Galaxy if it is not and 'polling' which will use +# a less efficient monitoring scheme that may work in wider range of scenarios +# then the watchdog default montiory. #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates diff -r 33fd43f7590f17ed611ce07178cae8c2b70525d0 -r 525b1fc16a587e91d60cdc4f9152f8e881b7e7de lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -272,7 +272,7 @@ self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) - self.watch_tools = string_as_bool( kwargs.get( 'watch_tools', False ) ) + self.watch_tools = kwargs.get( 'watch_tools', 'false' ) # On can mildly speed up Galaxy startup time by disabling index of help, # not needed on production systems but useful if running many functional tests. self.index_tool_help = string_as_bool( kwargs.get( "index_tool_help", True ) ) diff -r 33fd43f7590f17ed611ce07178cae8c2b70525d0 -r 525b1fc16a587e91d60cdc4f9152f8e881b7e7de lib/galaxy/tools/toolbox/watcher.py --- a/lib/galaxy/tools/toolbox/watcher.py +++ b/lib/galaxy/tools/toolbox/watcher.py @@ -2,9 +2,11 @@ try: from watchdog.events import FileSystemEventHandler from watchdog.observers import Observer + from watchdog.observers.polling import PollingObserver can_watch = True except ImportError: FileSystemEventHandler = object + PollingObserver = object can_watch = False import logging @@ -12,23 +14,34 @@ def get_watcher(toolbox, config): - watch_tools = getattr(config, "watch_tools", False) - if watch_tools: + watch_tools_val = str( getattr(config, "watch_tools", False) ).lower() + if watch_tools_val in ( 'true', 'yes', 'on' ): return ToolWatcher(toolbox) + elif watch_tools_val == "auto": + try: + return ToolWatcher(toolbox) + except Exception: + log.info("Failed to load ToolWatcher (watchdog is likely unavailable) - proceeding without tool monitoring.") + return NullWatcher() + elif watch_tools_val == "polling": + log.info("Using less ineffecient polling toolbox watcher.") + return ToolWatcher(toolbox, observer_class=PollingObserver) else: return NullWatcher() class ToolWatcher(object): - def __init__(self, toolbox): + def __init__(self, toolbox, observer_class=None): if not can_watch: raise Exception("Watchdog library unavailble, cannot watch tools.") + if observer_class is None: + observer_class = Observer self.toolbox = toolbox self.tool_file_ids = {} self.tool_dir_callbacks = {} self.monitored_dirs = {} - self.observer = Observer() + self.observer = observer_class() self.event_handler = ToolFileEventHandler(self) self.start() https://bitbucket.org/galaxy/galaxy-central/commits/d1c3d84a7e06/ Changeset: d1c3d84a7e06 Branch: release_15.03 User: jmchilton Date: 2015-02-24 04:09:19+00:00 Summary: Comment out broken liftOver tests. liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF) If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either. Only option left, admittedly a crappy one, is to comment out the tests. Affected #: 1 file diff -r 525b1fc16a587e91d60cdc4f9152f8e881b7e7de -r d1c3d84a7e06553cf948fcbd8c00b45bebcfb059 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml +++ b/tools/extract/liftOver_wrapper.xml @@ -62,6 +62,7 @@ <requirement type="package">ucsc_tools</requirement></requirements><tests> + </tests><help> .. class:: warningmark 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.

1 0

commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 24 Feb '15

24 Feb '15

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9ef633f09b00/ Changeset: 9ef633f09b00 User: guerler Date: 2015-02-23 22:56:38+00:00 Summary: Allow text selection in tool form Affected #: 2 files diff -r b18fce698ca0b29aaca7733cf9ba95b65c56ca48 -r 9ef633f09b006774c402120fced862cf6b8effed static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1410,7 +1410,7 @@ .upload-header .header-selection{width:200px;min-width:200px;font-size:11px;padding-right:10px} .upload-header .select2-choice{max-height:20px;line-height:18px;background:transparent;text-align:center;font-weight:normal}.upload-header .select2-choice .select2-arrow b{background-position:0 -3px} .upload-top{height:5%;text-align:center}.upload-top .upload-info{margin-top:0px;font-weight:normal;text-align:center} -.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} +.no-highlight,.ui-button-icon{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .no-padding{padding:0px !important} .ui-margin-top{padding-top:5px !important} .ui-margin-bottom{margin-bottom:5px !important} @@ -1434,7 +1434,7 @@ .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-table-form-info{clear:both !important} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} -.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} +.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} .ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-limited .portlet-header .portlet-title .icon,.ui-portlet-narrow .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} .ui-portlet .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-limited .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-narrow .portlet-header .portlet-operations .ui-button-icon{margin-left:5px} .ui-portlet .portlet-content,.ui-portlet-limited .portlet-content,.ui-portlet-narrow .portlet-content{height:inherit;padding-left:10px;padding-right:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-limited .portlet-content .content,.ui-portlet-narrow .portlet-content .content{padding:0px;height:100%;width:100%} diff -r b18fce698ca0b29aaca7733cf9ba95b65c56ca48 -r 9ef633f09b006774c402120fced862cf6b8effed static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -182,7 +182,6 @@ // portlets .ui-portlet { - &:extend(.no-highlight); border: solid @form-border 1px; border-radius: @border-radius-base; https://bitbucket.org/galaxy/galaxy-central/commits/0a95eaf36a88/ Changeset: 0a95eaf36a88 User: guerler Date: 2015-02-23 23:04:02+00:00 Summary: Fix job ids in success message Affected #: 3 files diff -r 9ef633f09b006774c402120fced862cf6b8effed -r 0a95eaf36a88e1a18bea59461c906b48a214b943 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r 9ef633f09b006774c402120fced862cf6b8effed -r 0a95eaf36a88e1a18bea59461c906b48a214b943 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r 9ef633f09b006774c402120fced862cf6b8effed -r 0a95eaf36a88e1a18bea59461c906b48a214b943 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/c18c22d74ce2/ Changeset: c18c22d74ce2 User: jmchilton Date: 2015-02-24 00:52:17+00:00 Summary: Improved tool diagnostics API. Affected #: 1 file diff -r 0a95eaf36a88e1a18bea59461c906b48a214b943 -r c18c22d74ce26f484b50baa61eab27bc160f8b43 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -102,6 +102,7 @@ Return diagnostic information to help debug panel and dependency related problems. """ + # TODO: Move this into tool. to_dict = lambda x: x.to_dict() tool = self._get_tool( id, user=trans.user ) if hasattr( tool, 'lineage' ): @@ -113,7 +114,6 @@ tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies) else: tool_shed_dependencies_dict = None - tool = self._get_tool( id, user=trans.user ) return { "tool_id": tool.id, "tool_version": tool.version, @@ -122,6 +122,11 @@ "requirements": map(to_dict, tool.requirements), "installed_tool_shed_dependencies": tool_shed_dependencies_dict, "tool_dir": tool.tool_dir, + "tool_shed": tool.tool_shed, + "repository_name": tool.repository_name, + "repository_owner": tool.repository_owner, + "installed_changeset_revision": None, + "guid": tool.guid, } @_future_expose_api_anonymous https://bitbucket.org/galaxy/galaxy-central/commits/08153b7c614a/ Changeset: 08153b7c614a User: jmchilton Date: 2015-02-22 05:32:46+00:00 Summary: Fix for watching tools on some more interesting file systems. Affected #: 3 files diff -r c18c22d74ce26f484b50baa61eab27bc160f8b43 -r 08153b7c614a26b19ee3130acb0a2a9a1bd6763c config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -176,11 +176,15 @@ # install from in the admin interface (.sample used if default does not exist). #tool_sheds_config_file = config/tool_sheds_conf.xml -# Enable monitoring of tools and tool directories listed in any tool config file -# specified in tool_config_file option. If changes are found, tools are -# automatically reloaded. -# Watchdog ( https://pypi.python.org/pypi/watchdog ) must be installed and -# available to Galaxy to use this option. +# Set to True to Enable monitoring of tools and tool directories +# listed in any tool config file specified in tool_config_file option. +# If changes are found, tools are automatically reloaded. Watchdog ( +# https://pypi.python.org/pypi/watchdog ) must be installed and +# available to Galaxy to use this option. Other options include 'auto' +# which will attempt to watch tools if the watchdog library is available +# but won't fail to load Galaxy if it is not and 'polling' which will use +# a less efficient monitoring scheme that may work in wider range of scenarios +# then the watchdog default montiory. #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates diff -r c18c22d74ce26f484b50baa61eab27bc160f8b43 -r 08153b7c614a26b19ee3130acb0a2a9a1bd6763c lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -272,7 +272,7 @@ self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) - self.watch_tools = string_as_bool( kwargs.get( 'watch_tools', False ) ) + self.watch_tools = kwargs.get( 'watch_tools', 'false' ) # On can mildly speed up Galaxy startup time by disabling index of help, # not needed on production systems but useful if running many functional tests. self.index_tool_help = string_as_bool( kwargs.get( "index_tool_help", True ) ) diff -r c18c22d74ce26f484b50baa61eab27bc160f8b43 -r 08153b7c614a26b19ee3130acb0a2a9a1bd6763c lib/galaxy/tools/toolbox/watcher.py --- a/lib/galaxy/tools/toolbox/watcher.py +++ b/lib/galaxy/tools/toolbox/watcher.py @@ -2,9 +2,11 @@ try: from watchdog.events import FileSystemEventHandler from watchdog.observers import Observer + from watchdog.observers.polling import PollingObserver can_watch = True except ImportError: FileSystemEventHandler = object + PollingObserver = object can_watch = False import logging @@ -12,23 +14,34 @@ def get_watcher(toolbox, config): - watch_tools = getattr(config, "watch_tools", False) - if watch_tools: + watch_tools_val = str( getattr(config, "watch_tools", False) ).lower() + if watch_tools_val in ( 'true', 'yes', 'on' ): return ToolWatcher(toolbox) + elif watch_tools_val == "auto": + try: + return ToolWatcher(toolbox) + except Exception: + log.info("Failed to load ToolWatcher (watchdog is likely unavailable) - proceeding without tool monitoring.") + return NullWatcher() + elif watch_tools_val == "polling": + log.info("Using less ineffecient polling toolbox watcher.") + return ToolWatcher(toolbox, observer_class=PollingObserver) else: return NullWatcher() class ToolWatcher(object): - def __init__(self, toolbox): + def __init__(self, toolbox, observer_class=None): if not can_watch: raise Exception("Watchdog library unavailble, cannot watch tools.") + if observer_class is None: + observer_class = Observer self.toolbox = toolbox self.tool_file_ids = {} self.tool_dir_callbacks = {} self.monitored_dirs = {} - self.observer = Observer() + self.observer = observer_class() self.event_handler = ToolFileEventHandler(self) self.start() https://bitbucket.org/galaxy/galaxy-central/commits/872867495129/ Changeset: 872867495129 User: jmchilton Date: 2015-02-24 01:33:05+00:00 Summary: Allow setting job_conf params via environment variables & galaxy.ini. Affected #: 2 files diff -r 08153b7c614a26b19ee3130acb0a2a9a1bd6763c -r 8728674951297e85894b9e191ceb4d26a85bde4d config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -427,6 +427,15 @@ <param id="nativeSpecification">--mem-per-cpu=512</param><resubmit condition="memory_limit_reached" destination="bigmem" /></destination> +  + <destination id="params_from_environment" runner="slurm"> + <param id="nativeSpecification" from_environ="NATIVE_SPECIFICATION">--time=00:05:00 --nodes=1</param> + <param id="docker_enabled" from_config="use_docker">false</param> + </destination></destinations><resources default="default"> diff -r 08153b7c614a26b19ee3130acb0a2a9a1bd6763c -r 8728674951297e85894b9e191ceb4d26a85bde4d lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -445,7 +445,15 @@ """ rval = {} for param in parent.findall('param'): - rval[param.get('id')] = param.text + key = param.get('id') + param_value = param.text + if 'from_environ' in param.attrib: + environ_var = param.attrib['from_environ'] + param_value = os.environ.get(environ_var, param_value) + elif 'from_config' in param.attrib: + config_val = param.attrib['from_config'] + param_value = self.app.config.config_dict.get(config_val, param_value) + rval[key] = param_value return rval def __get_envs(self, parent): https://bitbucket.org/galaxy/galaxy-central/commits/678bb1ba4d89/ Changeset: 678bb1ba4d89 User: jmchilton Date: 2015-02-24 16:03:42+00:00 Summary: Docfixes - grammar and spelling problems caught by Nicola. Affected #: 2 files diff -r 8728674951297e85894b9e191ceb4d26a85bde4d -r 678bb1ba4d89b3043dd75d6b2d0c36663f693e62 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -176,7 +176,7 @@ # install from in the admin interface (.sample used if default does not exist). #tool_sheds_config_file = config/tool_sheds_conf.xml -# Set to True to Enable monitoring of tools and tool directories +# Set to True to enable monitoring of tools and tool directories # listed in any tool config file specified in tool_config_file option. # If changes are found, tools are automatically reloaded. Watchdog ( # https://pypi.python.org/pypi/watchdog ) must be installed and @@ -184,7 +184,7 @@ # which will attempt to watch tools if the watchdog library is available # but won't fail to load Galaxy if it is not and 'polling' which will use # a less efficient monitoring scheme that may work in wider range of scenarios -# then the watchdog default montiory. +# than the watchdog default. #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates diff -r 8728674951297e85894b9e191ceb4d26a85bde4d -r 678bb1ba4d89b3043dd75d6b2d0c36663f693e62 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -427,9 +427,9 @@ <param id="nativeSpecification">--mem-per-cpu=512</param><resubmit condition="memory_limit_reached" destination="bigmem" /></destination> - <destination id="params_from_environment" runner="slurm"> https://bitbucket.org/galaxy/galaxy-central/commits/476c79d7b00a/ Changeset: 476c79d7b00a User: dannon Date: 2015-02-24 16:30:43+00:00 Summary: Improved Mutable Handling w/ JSONType and MetadataType -- should resolve the outstanding sqlalchemy coerce/list bug Affected #: 1 file diff -r 678bb1ba4d89b3043dd75d6b2d0c36663f693e62 -r 476c79d7b00a5edde57847ca1882d7e7781030b6 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,5 +1,4 @@ import binascii -import copy import json import logging import uuid @@ -34,67 +33,33 @@ return value -class MutableDict(Mutable, dict): - # MutableDict following http://docs.sqlalchemy.org/en/latest/orm/extensions/mutable.html - @classmethod - def coerce(cls, key, value): - "Convert plain dictionaries to MutableDict." +# Mutable JSONType for SQLAlchemy from original gist: +# https://gist.github.com/dbarnett/1730610 +# +# Also using minor changes from this fork of the gist: +# https://gist.github.com/miracle2k/52a031cced285ba9b8cd +# +# And other minor changes to make it work for us. - if not isinstance(value, MutableDict): - if isinstance(value, dict): - return MutableDict(value) - # this call will raise ValueError - return Mutable.coerce(key, value) - else: - return value +class JSONType(sqlalchemy.types.TypeDecorator): + """Represents an immutable structure as a json-encoded string. - def __setitem__(self, key, value): - "Detect dictionary set events and emit change events." + If default is, for example, a dict, then a NULL value in the + database will be exposed as an empty dict. + """ - dict.__setitem__(self, key, value) - self.changed() - - def __delitem__(self, key): - "Detect dictionary del events and emit change events." - - dict.__delitem__(self, key) - self.changed() - - def __getstate__(self): - return dict(self) - - def __setstate__(self, state): - self.update(state) - - -class JSONType( TypeDecorator ): - """ - Defines a JSONType for SQLAlchemy. Takes a primitive as input and - JSONifies it. This should replace PickleType throughout Galaxy. - """ impl = LargeBinary - def process_bind_param( self, value, dialect ): - if value is None: - return None - return json_encoder.encode( value ) + def process_bind_param(self, value, dialect): + if value is not None: + value = json_encoder.encode(value) + return value - def process_result_value( self, value, dialect ): + def process_result_value(self, value, dialect): if value is not None: - try: - return json_decoder.decode( str( _sniffnfix_pg9_hex( value ) ) ) - except Exception, e: - log.error( 'Failed to decode JSON (%s): %s', value, e ) - return None - - def copy_value( self, value ): - # return json_decoder.decode( json_encoder.encode( value ) ) - return copy.deepcopy( value ) - - def compare_values( self, x, y ): - # return json_encoder.encode( x ) == json_encoder.encode( y ) - return ( x == y ) + value = json_decoder.decode( str( _sniffnfix_pg9_hex( value ) ) ) + return value def load_dialect_impl(self, dialect): if dialect.name == "mysql": @@ -103,8 +68,136 @@ return self.impl -MutableDict.associate_with(JSONType) +class MutationObj(Mutable): + @classmethod + def coerce(cls, key, value): + if isinstance(value, dict) and not isinstance(value, MutationDict): + return MutationDict.coerce(key, value) + if isinstance(value, list) and not isinstance(value, MutationList): + return MutationList.coerce(key, value) + return value + @classmethod + def _listen_on_attribute(cls, attribute, coerce, parent_cls): + key = attribute.key + if parent_cls is not attribute.class_: + return + + # rely on "propagate" here + parent_cls = attribute.class_ + + def load(state, *args): + val = state.dict.get(key, None) + if coerce: + val = cls.coerce(key, val) + state.dict[key] = val + if isinstance(val, cls): + val._parents[state.obj()] = key + + def set(target, value, oldvalue, initiator): + if not isinstance(value, cls): + value = cls.coerce(key, value) + if isinstance(value, cls): + value._parents[target.obj()] = key + if isinstance(oldvalue, cls): + oldvalue._parents.pop(target.obj(), None) + return value + + def pickle(state, state_dict): + val = state.dict.get(key, None) + if isinstance(val, cls): + if 'ext.mutable.values' not in state_dict: + state_dict['ext.mutable.values'] = [] + state_dict['ext.mutable.values'].append(val) + + def unpickle(state, state_dict): + if 'ext.mutable.values' in state_dict: + for val in state_dict['ext.mutable.values']: + val._parents[state.obj()] = key + + sqlalchemy.event.listen(parent_cls, 'load', load, raw=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'refresh', load, raw=True, propagate=True) + sqlalchemy.event.listen(attribute, 'set', set, raw=True, retval=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'pickle', pickle, raw=True, propagate=True) + sqlalchemy.event.listen(parent_cls, 'unpickle', unpickle, raw=True, propagate=True) + + +class MutationDict(MutationObj, dict): + @classmethod + def coerce(cls, key, value): + """Convert plain dictionary to MutationDict""" + self = MutationDict((k, MutationObj.coerce(key, v)) for (k, v) in value.items()) + self._key = key + return self + + def __setitem__(self, key, value): + # Due to the way OrderedDict works, this is called during __init__. + # At this time we don't have a key set, but what is more, the value + # being set has already been coerced. So special case this and skip. + if hasattr(self, '_key'): + value = MutationObj.coerce(self._key, value) + dict.__setitem__(self, key, value) + self.changed() + + def __delitem__(self, key): + dict.__delitem__(self, key) + self.changed() + + +class MutationList(MutationObj, list): + @classmethod + def coerce(cls, key, value): + """Convert plain list to MutationList""" + self = MutationList((MutationObj.coerce(key, v) for v in value)) + self._key = key + return self + + def __setitem__(self, idx, value): + list.__setitem__(self, idx, MutationObj.coerce(self._key, value)) + self.changed() + + def __setslice__(self, start, stop, values): + list.__setslice__(self, start, stop, (MutationObj.coerce(self._key, v) for v in values)) + self.changed() + + def __delitem__(self, idx): + list.__delitem__(self, idx) + self.changed() + + def __delslice__(self, start, stop): + list.__delslice__(self, start, stop) + self.changed() + + def append(self, value): + list.append(self, MutationObj.coerce(self._key, value)) + self.changed() + + def insert(self, idx, value): + list.insert(self, idx, MutationObj.coerce(self._key, value)) + self.changed() + + def extend(self, values): + list.extend(self, (MutationObj.coerce(self._key, v) for v in values)) + self.changed() + + def pop(self, *args, **kw): + value = list.pop(self, *args, **kw) + self.changed() + return value + + def remove(self, value): + list.remove(self, value) + self.changed() + + +MutationObj.associate_with(JSONType) + +"""A type to encode/decode JSON on the fly + +sqltype is the string type for the underlying DB column:: + + Column(JSON) +""" metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

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commit/galaxy-central: 8 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

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[galaxyproject/usegalaxy-playbook] 9e3a88: update test
by GitHub 23 Feb '15

23 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9e3a882297981048b076f0f987797ecdd0793e93 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e3a882297981048… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-02-23 (Mon, 23 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da044e190f11/ Changeset: da044e190f11 User: martenson Date: 2015-02-23 15:44:51+00:00 Summary: fix toolshed auth API returning double converted json allow sessionless key retrieval Affected #: 1 file diff -r 67222d8cb3a54c7a3dc28accc8f16ff502fe547b -r da044e190f11d33a8556aa60ff563f1e801abf6d lib/galaxy/webapps/tool_shed/api/authenticate.py --- a/lib/galaxy/webapps/tool_shed/api/authenticate.py +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -13,13 +13,14 @@ from galaxy import web from galaxy.webapps.galaxy.api.authenticate import AuthenticationController +from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless log = logging.getLogger( __name__ ) class ToolShedAuthenticationController( AuthenticationController ): - @web.expose_api_anonymous + @expose_api_raw_anonymous_and_sessionless def get_tool_shed_api_key( self, trans, **kwd ): """ def get_api_key( self, trans, **kwd ) https://bitbucket.org/galaxy/galaxy-central/commits/d06aa2582d93/ Changeset: d06aa2582d93 User: martenson Date: 2015-02-23 15:54:52+00:00 Summary: Return more specific API auth errors Affected #: 1 file diff -r da044e190f11d33a8556aa60ff563f1e801abf6d -r d06aa2582d9353a39fe7e6afccfa34d58464551f lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -45,9 +45,11 @@ user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() - if ( len( user ) is not 1 ): - # DB is inconsistent and we have more users with same email - raise exceptions.ObjectNotFound() + if ( len( user ) == 0 ): + raise exceptions.ObjectNotFound( 'The user does not exist.' ) + elif ( len( user ) > 1 ): + # DB is inconsistent and we have more users with the same email. + raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' ) else: user = user[0] is_valid_user = user.check_password( password ) @@ -55,7 +57,7 @@ key = self.api_keys_manager.get_or_create_api_key( user ) return dict( api_key=key ) else: - raise exceptions.AuthenticationFailed() + raise exceptions.AuthenticationFailed( 'Invalid password.' ) def _decode_baseauth( self, encoded_str ): """ https://bitbucket.org/galaxy/galaxy-central/commits/cc3c4f51d1ea/ Changeset: cc3c4f51d1ea User: jmchilton Date: 2015-02-18 16:34:23+00:00 Summary: Tool diagnostic API endpoints. It is easy to get Galaxy's database and shed tool files out of sync and the results are bad. I don't think this is new but I may have made it worse this cycle by trying to slowly walk back Galaxy's use of the database to track lineages (e.g. https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a1…) New API endpoints include: /api/configuration/dynamic_tool_confs /api/configuration/tool_lineages /api/<tool_id>/diagnostics Affected #: 6 files diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/interface.py --- a/lib/galaxy/tools/toolbox/lineages/interface.py +++ b/lib/galaxy/tools/toolbox/lineages/interface.py @@ -40,3 +40,9 @@ externally). """ return self.version is None + + def to_dict(self): + return dict( + id=self.id, + version=self.version, + ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/stock.py --- a/lib/galaxy/tools/toolbox/lineages/stock.py +++ b/lib/galaxy/tools/toolbox/lineages/stock.py @@ -38,6 +38,13 @@ # method for comparing tool versions. return sorted( versions, key=_to_loose_version ) + def to_dict(self): + return dict( + tool_id=self.tool_id, + tool_versions=list(self.tool_versions), + lineage_type='stock', + ) + def _to_loose_version( tool_lineage_version ): version = str( tool_lineage_version.version ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/tool_shed.py --- a/lib/galaxy/tools/toolbox/lineages/tool_shed.py +++ b/lib/galaxy/tools/toolbox/lineages/tool_shed.py @@ -8,9 +8,11 @@ """ Representation of tool lineage derived from tool shed repository installations. """ - def __init__(self, app, tool_version): + def __init__(self, app, tool_version, tool_shed_repository=None): self.app = app self.tool_version_id = tool_version.id + # Only used for logging + self._tool_shed_repository = tool_shed_repository @staticmethod def from_tool( app, tool, tool_shed_repository ): @@ -36,6 +38,16 @@ def get_versions( self, reverse=False ): return map( ToolLineageVersion.from_guid, self.get_version_ids( reverse=reverse ) ) + def to_dict(self): + tool_shed_repository = self._tool_shed_repository + rval = dict( + tool_version_id=self.tool_version_id, + tool_versions=map(lambda v: v.to_dict(), self.get_versions()), + tool_shed_repository=tool_shed_repository if tool_shed_repository is not None else None, + lineage_type='tool_shed', + ) + return rval + def get_install_tool_version( app, tool_id ): return app.install_model.context.query( diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -4,6 +4,8 @@ """ from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import require_admin from galaxy.web.base.controller import BaseAPIController from galaxy.managers import base @@ -33,6 +35,13 @@ @expose_api_anonymous def version( self, trans, **kwds ): + """ + GET /api/version + Return a description of the major version of Galaxy (e.g. 15.03). + + :rtype: dict + :returns: dictionary with major version keyed on 'version_major' + """ return {"version_major": self.app.config.version_major } def get_config_dict( self, trans, return_admin=False, view=None, keys=None, default_view='all' ): @@ -52,6 +61,29 @@ view=view, keys=keys, default_view=default_view ) return serialized + @expose_api + @require_admin + def dynamic_tool_confs(self, trans): + confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True) + return map(_tool_conf_to_dict, confs) + + @expose_api + @require_admin + def tool_lineages(self, trans): + rval = [] + for id, tool in self.app.toolbox.tools(): + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + + entry = dict( + id=id, + lineage=lineage_dict + ) + rval.append(entry) + return rval + #TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports? class ConfigSerializer( base.ModelSerializer ): @@ -122,3 +154,10 @@ 'allow_user_creation' : _defaults_to( False ), 'allow_user_deletion' : _defaults_to( False ), }) + + +def _tool_conf_to_dict(conf): + return dict( + config_filename=conf['config_filename'], + tool_path=conf['tool_path'], + ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -94,6 +94,36 @@ message, status = trans.app.toolbox.reload_tool_by_id( tool_id ) return { status: message } + @_future_expose_api + @web.require_admin + def diagnostics( self, trans, id, **kwd ): + """ + GET /api/tools/{tool_id}/diagnostics + Return diagnostic information to help debug panel + and dependency related problems. + """ + to_dict = lambda x: x.to_dict() + tool = self._get_tool( id, user=trans.user ) + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + tool_shed_dependencies = tool.installed_tool_dependencies + if tool_shed_dependencies: + tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies) + else: + tool_shed_dependencies_dict = None + tool = self._get_tool( id, user=trans.user ) + return { + "tool_id": tool.id, + "tool_version": tool.version, + "dependency_shell_commands": tool.build_dependency_shell_commands(), + "lineage": lineage_dict, + "requirements": map(to_dict, tool.requirements), + "installed_tool_shed_dependencies": tool_shed_dependencies_dict, + "tool_dir": tool.tool_dir, + } + @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): tool = self._get_tool( id, user=trans.user ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -210,6 +210,7 @@ webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/reload', action='reload', controller="tools" ) + webapp.mapper.connect( '/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" ) @@ -221,6 +222,18 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) + webapp.mapper.connect( + 'dynamic_tool_confs', + '/api/configuration/dynamic_tool_confs', + controller="configuration", + action="dynamic_tool_confs" + ) + webapp.mapper.connect( + 'tool_lineages', + '/api/configuration/tool_lineages', + controller="configuration", + action="tool_lineages" + ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) webapp.mapper.connect( "configuration_version", "/api/version", controller="configuration", 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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