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commit/galaxy-central: dannon: Close branch setup_python_env
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e4038ef670b/ Changeset: 7e4038ef670b Branch: setup_python_env User: dannon Date: 2014-07-09 17:35:51 Summary: Close branch setup_python_env Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b424e9c2e57/ Changeset: 7b424e9c2e57 Branch: setup_python_env User: Bjoern Gruening Date: 2014-06-29 20:19:03 Summary: Add new install_python_environment installation tag to the Tool Shed. It can be used like the following example: <action type="setup_python_environment"><repository name="package_python_2_7" owner="iuc"><package name="python" version="2.7" /></repository><package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.8.tar.gz</package><package>kMer-0.2.0.tar.gz</package></action> Currently, you can specify one URL to a tarball or a name to a locally shiped tarball. Important: The underlying easy_install will skip all dependencies. The Tool Author need to specify every dependency explicitly. Test repository can be found on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/bgruening/test_repository_setup_pyt… https://testtoolshed.g2.bx.psu.edu/view/bgruening/test_repository_setup_pyt… Affected #: 4 files diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7b424e9c2e57ec12eca26f35c8f4259bbcc55cdb lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -44,7 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', + 'setup_perl_environment', 'setup_python_environment', 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7b424e9c2e57ec12eca26f35c8f4259bbcc55cdb lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py @@ -124,7 +124,7 @@ Parse an XML tag set to discover all child repository dependency tags and define the path to an env.sh file associated with the repository (this requires the repository dependency to be in an installed state). The received action_dict will be updated with these discovered paths and returned to the caller. This method handles tool dependency definition - tag sets <setup_r_environment>, <setup_ruby_environment> and <setup_perl_environment>. + tag sets <setup_r_environment>, <setup_ruby_environment>, <setup_python_environment> and <setup_perl_environment>. """ # An example elem is: # <action type="setup_perl_environment"> diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7b424e9c2e57ec12eca26f35c8f4259bbcc55cdb lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -54,6 +54,7 @@ setup_perl_environment=step_handler.SetupPerlEnvironment( self.app ), setup_r_environment=step_handler.SetupREnvironment( self.app ), setup_ruby_environment=step_handler.SetupRubyEnvironment( self.app ), + setup_python_environment=step_handler.SetupPythonEnvironment( self.app ), setup_virtualenv=step_handler.SetupVirtualEnv( self.app ), shell_command=step_handler.ShellCommand( self.app ), template_command=step_handler.TemplateCommand( self.app ) ) diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7b424e9c2e57ec12eca26f35c8f4259bbcc55cdb lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1390,6 +1390,140 @@ return action_dict +class SetupPythonEnvironment( Download, RecipeStep ): + + def __init__( self, app ): + self.app = app + self.type = 'setup_python_environment' + + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, current_dir=None, initial_download=False ): + """ + Initialize the environment for installing Python packages. The class is called during the initial + download stage when installing packages, so the value of initial_download will generally be True. + However, the parameter value allows this class to also be used in the second stage of the installation, + although it may never be necessary. If initial_download is True, the recipe steps will be filtered + and returned and the installation directory (i.e., dir) will be defined and returned. If we're not + in the initial download stage, these actions will not occur, and None values will be returned for them. + + Warning: easy_install is configured that it will not be install any dependency, the tool developer needs + to specify every dependency explicitly + """ + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + dir = None + if initial_download: + filtered_actions = actions[ 1: ] + env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) + log.debug( '\n%s\n' % env_shell_file_paths ) + if env_shell_file_paths is None: + log.debug( 'Missing Python environment, make sure your specified Python installation exists.' ) + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + else: + install_environment.add_env_shell_file_paths( env_shell_file_paths ) + log.debug( 'Handling setup_python_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ + ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) + dir = os.path.curdir + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): + with settings( warn_only=True ): + python_package_tups = action_dict.get( 'python_package_tups', [] ) + for python_package_tup in python_package_tups: + package, package_version = python_package_tup + package_path = os.path.join( install_environment.tool_shed_repository_install_dir, package ) + if os.path.isfile( package_path ): + # we assume a local shipped python package + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_path ) + elif package.find( '://' ) != -1: + # We assume a URL to a python package. + url = package + package_name = url.split( '/' )[ -1 ] + self.url_download( work_dir, package_name, url, extract=False ) + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_name ) + else: + pass + # pypi can be implemented or for > python3.4 we can use the build-in system + cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) + return_code = install_environment.handle_command( tool_dependency=tool_dependency, + cmd=cmd, + return_output=False ) + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + # Pull in python dependencies (runtime). + env_file_builder.handle_action_shell_file_paths( action_dict ) + env_file_builder.append_line( name="PYTHONPATH", + action="prepend_to", + value= os.path.join( install_environment.install_dir, 'lib', 'python') ) + env_file_builder.append_line( name="PATH", + action="prepend_to", + value=os.path.join( install_environment.install_dir, 'bin' ) ) + return_code = env_file_builder.return_code + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + # setup a Python environment. + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + # Discover all child repository dependency tags and define the path to an env.sh file + # associated with each repository. This will potentially update the value of the + # 'env_shell_file_paths' entry in action_dict. + all_env_shell_file_paths = [] + env_manager = EnvManager( self.app ) + action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, + action_elem, + action_dict ) + python_package_tups = [] + for env_elem in action_elem: + if env_elem.tag == 'package': + #A valid package definitions can be: + # pysam.tar.gz -> locally shipped tarball + # ftp://ftp.gruening.de/pysam.tar.gz -> online tarball + python_token = env_elem.text.strip().split( '=' ) + if len( python_token ) == 2: + # version string + package_name = python_token[ 0 ] + package_version = python_token[ 1 ] + python_package_tups.append( ( package_name, package_version ) ) + else: + # package name for pypi.org without version number + package = env_elem.text.strip() + python_package_tups.append( ( package, None ) ) + if python_package_tups: + action_dict[ 'python_package_tups' ] = python_package_tups + return action_dict + + + class SetupVirtualEnv( Download, RecipeStep ): def __init__( self, app ): https://bitbucket.org/galaxy/galaxy-central/commits/4411a021a9fa/ Changeset: 4411a021a9fa User: dannon Date: 2014-07-09 17:35:51 Summary: Merged in BjoernGruening/galaxy-central-bgruening/setup_python_env (pull request #431) Add new install_python_environment installation tag to the Tool Shed. Affected #: 4 files diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -44,7 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', + 'setup_perl_environment', 'setup_python_environment', 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py @@ -124,7 +124,7 @@ Parse an XML tag set to discover all child repository dependency tags and define the path to an env.sh file associated with the repository (this requires the repository dependency to be in an installed state). The received action_dict will be updated with these discovered paths and returned to the caller. This method handles tool dependency definition - tag sets <setup_r_environment>, <setup_ruby_environment> and <setup_perl_environment>. + tag sets <setup_r_environment>, <setup_ruby_environment>, <setup_python_environment> and <setup_perl_environment>. """ # An example elem is: # <action type="setup_perl_environment"> diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -54,6 +54,7 @@ setup_perl_environment=step_handler.SetupPerlEnvironment( self.app ), setup_r_environment=step_handler.SetupREnvironment( self.app ), setup_ruby_environment=step_handler.SetupRubyEnvironment( self.app ), + setup_python_environment=step_handler.SetupPythonEnvironment( self.app ), setup_virtualenv=step_handler.SetupVirtualEnv( self.app ), shell_command=step_handler.ShellCommand( self.app ), template_command=step_handler.TemplateCommand( self.app ) ) diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1390,6 +1390,140 @@ return action_dict +class SetupPythonEnvironment( Download, RecipeStep ): + + def __init__( self, app ): + self.app = app + self.type = 'setup_python_environment' + + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, current_dir=None, initial_download=False ): + """ + Initialize the environment for installing Python packages. The class is called during the initial + download stage when installing packages, so the value of initial_download will generally be True. + However, the parameter value allows this class to also be used in the second stage of the installation, + although it may never be necessary. If initial_download is True, the recipe steps will be filtered + and returned and the installation directory (i.e., dir) will be defined and returned. If we're not + in the initial download stage, these actions will not occur, and None values will be returned for them. + + Warning: easy_install is configured that it will not be install any dependency, the tool developer needs + to specify every dependency explicitly + """ + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + dir = None + if initial_download: + filtered_actions = actions[ 1: ] + env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) + log.debug( '\n%s\n' % env_shell_file_paths ) + if env_shell_file_paths is None: + log.debug( 'Missing Python environment, make sure your specified Python installation exists.' ) + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + else: + install_environment.add_env_shell_file_paths( env_shell_file_paths ) + log.debug( 'Handling setup_python_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ + ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) + dir = os.path.curdir + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): + with settings( warn_only=True ): + python_package_tups = action_dict.get( 'python_package_tups', [] ) + for python_package_tup in python_package_tups: + package, package_version = python_package_tup + package_path = os.path.join( install_environment.tool_shed_repository_install_dir, package ) + if os.path.isfile( package_path ): + # we assume a local shipped python package + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_path ) + elif package.find( '://' ) != -1: + # We assume a URL to a python package. + url = package + package_name = url.split( '/' )[ -1 ] + self.url_download( work_dir, package_name, url, extract=False ) + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_name ) + else: + pass + # pypi can be implemented or for > python3.4 we can use the build-in system + cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) + return_code = install_environment.handle_command( tool_dependency=tool_dependency, + cmd=cmd, + return_output=False ) + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + # Pull in python dependencies (runtime). + env_file_builder.handle_action_shell_file_paths( action_dict ) + env_file_builder.append_line( name="PYTHONPATH", + action="prepend_to", + value= os.path.join( install_environment.install_dir, 'lib', 'python') ) + env_file_builder.append_line( name="PATH", + action="prepend_to", + value=os.path.join( install_environment.install_dir, 'bin' ) ) + return_code = env_file_builder.return_code + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + # setup a Python environment. + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + # Discover all child repository dependency tags and define the path to an env.sh file + # associated with each repository. This will potentially update the value of the + # 'env_shell_file_paths' entry in action_dict. + all_env_shell_file_paths = [] + env_manager = EnvManager( self.app ) + action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, + action_elem, + action_dict ) + python_package_tups = [] + for env_elem in action_elem: + if env_elem.tag == 'package': + #A valid package definitions can be: + # pysam.tar.gz -> locally shipped tarball + # ftp://ftp.gruening.de/pysam.tar.gz -> online tarball + python_token = env_elem.text.strip().split( '=' ) + if len( python_token ) == 2: + # version string + package_name = python_token[ 0 ] + package_version = python_token[ 1 ] + python_package_tups.append( ( package_name, package_version ) ) + else: + # package name for pypi.org without version number + package = env_elem.text.strip() + python_package_tups.append( ( package, None ) ) + if python_package_tups: + action_dict[ 'python_package_tups' ] = python_package_tups + return action_dict + + + class SetupVirtualEnv( Download, RecipeStep ): def __init__( self, app ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in BjoernGruening/galaxy-central-bgruening/setup_python_env (pull request #431)
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4411a021a9fa/ Changeset: 4411a021a9fa User: dannon Date: 2014-07-09 17:35:51 Summary: Merged in BjoernGruening/galaxy-central-bgruening/setup_python_env (pull request #431) Add new install_python_environment installation tag to the Tool Shed. Affected #: 4 files diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -44,7 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', + 'setup_perl_environment', 'setup_python_environment', 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py @@ -124,7 +124,7 @@ Parse an XML tag set to discover all child repository dependency tags and define the path to an env.sh file associated with the repository (this requires the repository dependency to be in an installed state). The received action_dict will be updated with these discovered paths and returned to the caller. This method handles tool dependency definition - tag sets <setup_r_environment>, <setup_ruby_environment> and <setup_perl_environment>. + tag sets <setup_r_environment>, <setup_ruby_environment>, <setup_python_environment> and <setup_perl_environment>. """ # An example elem is: # <action type="setup_perl_environment"> diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -54,6 +54,7 @@ setup_perl_environment=step_handler.SetupPerlEnvironment( self.app ), setup_r_environment=step_handler.SetupREnvironment( self.app ), setup_ruby_environment=step_handler.SetupRubyEnvironment( self.app ), + setup_python_environment=step_handler.SetupPythonEnvironment( self.app ), setup_virtualenv=step_handler.SetupVirtualEnv( self.app ), shell_command=step_handler.ShellCommand( self.app ), template_command=step_handler.TemplateCommand( self.app ) ) diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 4411a021a9fad918cef26e00adf6f49e247fb0bd lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1390,6 +1390,140 @@ return action_dict +class SetupPythonEnvironment( Download, RecipeStep ): + + def __init__( self, app ): + self.app = app + self.type = 'setup_python_environment' + + def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, current_dir=None, initial_download=False ): + """ + Initialize the environment for installing Python packages. The class is called during the initial + download stage when installing packages, so the value of initial_download will generally be True. + However, the parameter value allows this class to also be used in the second stage of the installation, + although it may never be necessary. If initial_download is True, the recipe steps will be filtered + and returned and the installation directory (i.e., dir) will be defined and returned. If we're not + in the initial download stage, these actions will not occur, and None values will be returned for them. + + Warning: easy_install is configured that it will not be install any dependency, the tool developer needs + to specify every dependency explicitly + """ + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + dir = None + if initial_download: + filtered_actions = actions[ 1: ] + env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) + log.debug( '\n%s\n' % env_shell_file_paths ) + if env_shell_file_paths is None: + log.debug( 'Missing Python environment, make sure your specified Python installation exists.' ) + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + else: + install_environment.add_env_shell_file_paths( env_shell_file_paths ) + log.debug( 'Handling setup_python_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ + ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) + dir = os.path.curdir + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): + with settings( warn_only=True ): + python_package_tups = action_dict.get( 'python_package_tups', [] ) + for python_package_tup in python_package_tups: + package, package_version = python_package_tup + package_path = os.path.join( install_environment.tool_shed_repository_install_dir, package ) + if os.path.isfile( package_path ): + # we assume a local shipped python package + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_path ) + elif package.find( '://' ) != -1: + # We assume a URL to a python package. + url = package + package_name = url.split( '/' )[ -1 ] + self.url_download( work_dir, package_name, url, extract=False ) + + cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH; + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR; + easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s + ''' % ( package_name ) + else: + pass + # pypi can be implemented or for > python3.4 we can use the build-in system + cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) ) + return_code = install_environment.handle_command( tool_dependency=tool_dependency, + cmd=cmd, + return_output=False ) + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + # Pull in python dependencies (runtime). + env_file_builder.handle_action_shell_file_paths( action_dict ) + env_file_builder.append_line( name="PYTHONPATH", + action="prepend_to", + value= os.path.join( install_environment.install_dir, 'lib', 'python') ) + env_file_builder.append_line( name="PATH", + action="prepend_to", + value=os.path.join( install_environment.install_dir, 'bin' ) ) + return_code = env_file_builder.return_code + if return_code: + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + if initial_download: + return tool_dependency, filtered_actions, dir + return tool_dependency, None, None + + def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + # setup a Python environment. + # <action type="setup_python_environment"> + # <repository name="package_python_2_7" owner="bgruening"> + # <package name="python" version="2.7" /> + # </repository> + #  + # <package>pysam.tar.gz</package> + # <package>http://url-to-some-python-package.de/pysam.tar.gz</package> + # </action> + # Discover all child repository dependency tags and define the path to an env.sh file + # associated with each repository. This will potentially update the value of the + # 'env_shell_file_paths' entry in action_dict. + all_env_shell_file_paths = [] + env_manager = EnvManager( self.app ) + action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_shell_file_paths, + action_elem, + action_dict ) + python_package_tups = [] + for env_elem in action_elem: + if env_elem.tag == 'package': + #A valid package definitions can be: + # pysam.tar.gz -> locally shipped tarball + # ftp://ftp.gruening.de/pysam.tar.gz -> online tarball + python_token = env_elem.text.strip().split( '=' ) + if len( python_token ) == 2: + # version string + package_name = python_token[ 0 ] + package_version = python_token[ 1 ] + python_package_tups.append( ( package_name, package_version ) ) + else: + # package name for pypi.org without version number + package = env_elem.text.strip() + python_package_tups.append( ( package, None ) ) + if python_package_tups: + action_dict[ 'python_package_tups' ] = python_package_tups + return action_dict + + + class SetupVirtualEnv( Download, RecipeStep ): def __init__( self, app ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: fix track name reversion for Backbone view.
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1d5fcd5bec6/ Changeset: d1d5fcd5bec6 User: jgoecks Date: 2014-07-09 16:59:21 Summary: Trackster: fix track name reversion for Backbone view. Affected #: 1 file diff -r f7000698a92dd293b24563249cc50f7016b8ffcb -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -332,7 +332,6 @@ revert_name: function() { if (this.old_name) { this.config.set_value('name', this.old_name); - this.name_div.text(this.old_name); } }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/120cd61c88ef/ Changeset: 120cd61c88ef User: jgoecks Date: 2014-07-09 16:39:05 Summary: Trackster: fixes for drawing groups from recent Backbone refactoring. Affected #: 2 files diff -r e9cef9ca217f8801f7efd72e913424c1cd0ded38 -r 120cd61c88efa535d3abb599fad933837ab4cec0 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -225,7 +225,8 @@ // unless flag set, create header. if (obj_dict.header !== false) { var header_view = new viz_views.TrackHeaderView({ - model: this + model: this, + id: this.id }); this.header_div = header_view.$el; @@ -552,6 +553,10 @@ // Set up filters. this.filters_manager = new filters_mod.FiltersManager(this); this.header_div.after(this.filters_manager.parent_div); + + // HACK: add div to clear floating elements. + this.filters_manager.parent_div.after( $("<div style='clear: both'/>") ); + // For saving drawables' filter managers when group-level filtering is done: this.saved_filters_managers = []; @@ -591,7 +596,7 @@ { name: "filters_icon", title: "Filters", - css_class: "filters-icon", + css_class: "ui-slider-050", on_click_fn: function(group) { // TODO: update Tooltip text. if (group.filters_manager.visible()) { diff -r e9cef9ca217f8801f7efd72e913424c1cd0ded38 -r 120cd61c88efa535d3abb599fad933837ab4cec0 static/scripts/viz/viz_views.js --- a/static/scripts/viz/viz_views.js +++ b/static/scripts/viz/viz_views.js @@ -20,14 +20,12 @@ // Icons container. this.action_icons = {}; this.render_action_icons(); - - this.$el.append( $("<div style='clear: both'/>") ); - + // Suppress double clicks in header so that they do not impact viz under header. this.$el.dblclick( function(e) { e.stopPropagation(); } ); // Needed for floating elts in header. - $("<div style='clear: both'/>").appendTo(this.container_div); + this.$el.append( $("<div style='clear: both'/>") ); }, update_name: function() { @@ -41,7 +39,7 @@ self.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); }); - + // Set up behavior for modes popup. this.set_display_modes(this.model.display_modes); }, https://bitbucket.org/galaxy/galaxy-central/commits/b894ebecb393/ Changeset: b894ebecb393 User: jgoecks Date: 2014-07-09 16:51:15 Summary: Trackster: replace jQuery if/show/hide statements with simpler toggle. Affected #: 1 file diff -r 120cd61c88efa535d3abb599fad933837ab4cec0 -r b894ebecb393fe5f7cfe7717b0b8c3bb8a29201f static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -647,9 +647,7 @@ this.action_icons.filters_icon.hide(); } else if (num_drawables === 1) { - if (this.drawables[0] instanceof CompositeTrack) { - this.action_icons.composite_icon.show(); - } + this.action_icons.composite_icon.toggle(this.drawables[0] instanceof CompositeTrack); this.action_icons.filters_icon.hide(); } else { // There are 2 or more tracks. @@ -738,12 +736,7 @@ } // Show/hide icon based on filter availability. - if (this.filters_manager.filters.length > 0) { - this.action_icons.filters_icon.show(); - } - else { - this.action_icons.filters_icon.hide(); - } + this.action_icons.filters_icon.toggle(this.filters_manager.filters.length > 0); } else { this.action_icons.filters_icon.hide(); @@ -1134,12 +1127,7 @@ /** Add or remove intro div depending on view state. */ update_intro_div: function() { - if (this.drawables.length === 0) { - this.intro_div.show(); - } - else { - this.intro_div.hide(); - } + this.intro_div.toggle(this.drawables.length === 0); }, /** @@ -1716,12 +1704,7 @@ * Show or hide tool depending on tool visibility state. */ set_visible: function() { - if (this.model.is_visible()) { - this.$el.show(); - } - else { - this.$el.hide(); - } + this.$el.toggle(this.model.is_visible()); }, /** @@ -2691,24 +2674,13 @@ // // Show/hide filter icon. // - if (track.filters_available) { - track.action_icons.filters_icon.show(); - } - else { - track.action_icons.filters_icon.hide(); - } + track.action_icons.filters_icon.toggle(track.filters_available); // // Show/hide tool icons. // - if (track.tool) { - track.action_icons.tools_icon.show(); - track.action_icons.param_space_viz_icon.show(); - } - else { - track.action_icons.tools_icon.hide(); - track.action_icons.param_space_viz_icon.hide(); - } + track.action_icons.tools_icon.toggle(track.tool !== null); + track.action_icons.param_space_viz_icon.toggle(track.tool !== null); }, /** @@ -3834,12 +3806,7 @@ break; } } - if (!all_slotted) { - this.action_icons.show_more_rows_icon.show(); - } - else { - this.action_icons.show_more_rows_icon.hide(); - } + this.action_icons.show_more_rows_icon.toggle(!all_slotted); } else { this.action_icons.show_more_rows_icon.hide(); https://bitbucket.org/galaxy/galaxy-central/commits/f7000698a92d/ Changeset: f7000698a92d User: jgoecks Date: 2014-07-09 16:54:52 Summary: Automated merge Affected #: 1 file diff -r b894ebecb393fe5f7cfe7717b0b8c3bb8a29201f -r f7000698a92dd293b24563249cc50f7016b8ffcb lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -201,7 +201,7 @@ delete( self, trans, id, **kwd ) * DELETE /api/histories/{id} delete the history with the given ``id`` - .. note:: Currently does not stop any active jobs in the history. + .. note:: Stops all active jobs in the history if purge is set. :type id: str :param id: the encoded id of the history to delete Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: hackdna: Update comments related to stopping jobs when history is deleted using the API.
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b921f6dbfe1/ Changeset: 0b921f6dbfe1 User: hackdna Date: 2014-07-09 16:32:51 Summary: Update comments related to stopping jobs when history is deleted using the API. Affected #: 1 file diff -r e9cef9ca217f8801f7efd72e913424c1cd0ded38 -r 0b921f6dbfe1a02fcd2f153914cfbbb4aa179654 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -201,7 +201,7 @@ delete( self, trans, id, **kwd ) * DELETE /api/histories/{id} delete the history with the given ``id`` - .. note:: Currently does not stop any active jobs in the history. + .. note:: Stops all active jobs in the history if purge is set. :type id: str :param id: the encoded id of the history to delete Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Close branch fix_to_data_library_display
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f270ddf6db10/ Changeset: f270ddf6db10 Branch: fix_to_data_library_display User: dannon Date: 2014-07-09 02:57:29 Summary: Close branch fix_to_data_library_display Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in christopherbare/galaxy-central/fix_to_data_library_display (pull request #428)
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9cef9ca217f/ Changeset: e9cef9ca217f User: dannon Date: 2014-07-09 02:57:29 Summary: Merged in christopherbare/galaxy-central/fix_to_data_library_display (pull request #428) use galaxy.util.json rather than json from the python libraries Affected #: 1 file diff -r f53d750acf557eeb84fa62c4151074c5fe5b7039 -r e9cef9ca217f8801f7efd72e913424c1cd0ded38 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -10,7 +10,6 @@ import collections import errno import grp -import json import logging import os import pickle @@ -24,6 +23,8 @@ import tempfile import threading +from galaxy.util import json + from email.MIMEText import MIMEText from os.path import relpath @@ -312,8 +313,8 @@ def pretty_print_json(json_data, is_json_string=False): if is_json_string: - json_data = json.loads(json_data) - return json.dumps(json_data, sort_keys=True, indent=4 * ' ') + json_data = json.from_json_string(json_data) + return json.to_json_string(json_data, sort_keys=True, indent=4) # characters that are valid valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/06f3cbf62ab8/ Changeset: 06f3cbf62ab8 Branch: fix_to_data_library_display User: christopherbare Date: 2014-06-28 21:55:15 Summary: use galaxy.util.json rather than json from the python libraries Affected #: 1 file diff -r 2577b386dbbe421e80c816abf7683359ab64fe1f -r 06f3cbf62ab84a2a411d0253e72f0d977c5c34a8 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -10,7 +10,6 @@ import collections import errno import grp -import json import logging import os import pickle @@ -24,6 +23,9 @@ import tempfile import threading +# note: this imports galaxy.util.json +import json + from email.MIMEText import MIMEText from os.path import relpath @@ -312,8 +314,8 @@ def pretty_print_json(json_data, is_json_string=False): if is_json_string: - json_data = json.loads(json_data) - return json.dumps(json_data, sort_keys=True, indent=4 * ' ') + json_data = json.from_json_string(json_data) + return json.to_json_string(json_data, sort_keys=True, indent=4) # characters that are valid valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") https://bitbucket.org/galaxy/galaxy-central/commits/92d1f4f2e873/ Changeset: 92d1f4f2e873 Branch: fix_to_data_library_display User: christopherbare Date: 2014-06-30 04:47:47 Summary: changed import to explicitly import galaxy.util.json based on code review Affected #: 1 file diff -r 06f3cbf62ab84a2a411d0253e72f0d977c5c34a8 -r 92d1f4f2e873eb6cfe9e25419c3bf5cc2917a9c6 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -23,8 +23,7 @@ import tempfile import threading -# note: this imports galaxy.util.json -import json +from galaxy.util import json from email.MIMEText import MIMEText https://bitbucket.org/galaxy/galaxy-central/commits/e9cef9ca217f/ Changeset: e9cef9ca217f User: dannon Date: 2014-07-09 02:57:29 Summary: Merged in christopherbare/galaxy-central/fix_to_data_library_display (pull request #428) use galaxy.util.json rather than json from the python libraries Affected #: 1 file diff -r f53d750acf557eeb84fa62c4151074c5fe5b7039 -r e9cef9ca217f8801f7efd72e913424c1cd0ded38 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -10,7 +10,6 @@ import collections import errno import grp -import json import logging import os import pickle @@ -24,6 +23,8 @@ import tempfile import threading +from galaxy.util import json + from email.MIMEText import MIMEText from os.path import relpath @@ -312,8 +313,8 @@ def pretty_print_json(json_data, is_json_string=False): if is_json_string: - json_data = json.loads(json_data) - return json.dumps(json_data, sort_keys=True, indent=4 * ' ') + json_data = json.from_json_string(json_data) + return json.to_json_string(json_data, sort_keys=True, indent=4) # characters that are valid valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 08 Jul '14

08 Jul '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a89cb141be4e/ Changeset: a89cb141be4e User: jgoecks Date: 2014-07-08 22:16:36 Summary: Trackster: add Backbone view for track header. Affected #: 1 file diff -r 558e521c3934f3b02c0fa31a8b93803d08aabf22 -r a89cb141be4e7e138f436e0dabd9efa96a6a25ab static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -177,6 +177,30 @@ return Math.round(num * val) / val; } + +/** + * View for track/group header. + */ +var TrackHeaderView = Backbone.View.extend({ + className: 'track-header', + + initialize: function() { + // Watch and update name changes. + this.model.config.get('name').on('change:value', this.update_name, this); + this.render(); + }, + + render: function() { + this.$el.append($("<div/>").addClass(this.model.drag_handle_class)); + this.$el.append($("<div/>").addClass("track-name") + .text(this.model.config.get_value('name'))); + }, + + update_name: function() { + this.$el.find('.track-name').text(this.model.config.get_value('name')); + } +}); + /** * Drawables hierarchy: * @@ -327,7 +351,6 @@ set_name: function(new_name) { this.old_name = this.config.get_value('name'); this.config.set_value('name', new_name); - this.name_div.text(new_name); }, /** @@ -659,10 +682,10 @@ }, build_header_div: function() { - var header_div = $("<div/>").addClass("track-header"); - header_div.append($("<div/>").addClass(this.drag_handle_class)); - this.name_div = $("<div/>").addClass("track-name").text(this.config.get_value('name')).appendTo(header_div); - return header_div; + var header_view = new TrackHeaderView({ + model: this + }); + return header_view.$el; }, hide_contents: function () { @@ -2325,11 +2348,10 @@ }, build_header_div: function() { - var header_div = $("<div class='track-header'/>"); - if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); } - this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.config.get_value('name')) - .attr( "id", this.config.get_value('name').replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); - return header_div; + var header_view = new TrackHeaderView({ + model: this + }); + return header_view.$el; }, /** https://bitbucket.org/galaxy/galaxy-central/commits/4ed4088326ec/ Changeset: 4ed4088326ec User: jgoecks Date: 2014-07-08 22:36:23 Summary: Trackster: clean up logic for creating track headers. Affected #: 2 files diff -r a89cb141be4e7e138f436e0dabd9efa96a6a25ab -r 4ed4088326ec129519ee11f71b308c9e329ad3bd static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -243,9 +243,16 @@ // Build Drawable HTML and behaviors. this.container_div = this.build_container_div(); - this.header_div = this.build_header_div(); - - if (this.header_div) { + this.header_div = null; + + // Use opt-out policy on header creation because this is the more frequent approach: + // unless flag set, create header. + if (obj_dict.header !== false) { + var header_view = new TrackHeaderView({ + model: this + }); + + this.header_div = header_view.$el; this.container_div.append(this.header_div); // Icons container. @@ -384,11 +391,6 @@ build_container_div: function() {}, /** - * Build drawable's header div. - */ - build_header_div: function() {}, - - /** * Add an action icon to this object. Appends icon unless prepend flag is specified. */ add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { @@ -681,13 +683,6 @@ return container_div; }, - build_header_div: function() { - var header_view = new TrackHeaderView({ - model: this - }); - return header_view.$el; - }, - hide_contents: function () { this.tiles_div.hide(); }, @@ -2347,13 +2342,6 @@ return $("<div/>").addClass('track').attr("id", "track_" + this.id); }, - build_header_div: function() { - var header_view = new TrackHeaderView({ - model: this - }); - return header_view.$el; - }, - /** * Set track's dataset. */ @@ -3348,15 +3336,13 @@ }); var LabelTrack = function (view, container) { - var obj_dict = { - resize: false - }; - Track.call(this, view, container, obj_dict); + Track.call(this, view, container, { + resize: false, + header: false + }); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { - build_header_div: function() {}, - init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -3618,7 +3604,7 @@ * Displays reference genome data. */ var ReferenceTrack = function (view) { - TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false }); + TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false, header: false }); // Use offset to ensure that bases at tile edges are drawn. this.left_offset = view.canvas_manager.char_width_px; @@ -3636,8 +3622,6 @@ { key: 'height', type: 'int', default_value: 13, hidden: true } ] ), - build_header_div: function() {}, - init: function() { this.data_manager.clear(); // Enable by default because there should always be data when drawing track. diff -r a89cb141be4e7e138f436e0dabd9efa96a6a25ab -r 4ed4088326ec129519ee11f71b308c9e329ad3bd static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -225,7 +225,7 @@ // Create view. var self = this, - view = new tracks.TracksterView(view_config); + view = new tracks.TracksterView(_.extend(view_config, {header: false})); view.editor = true; $.when( view.load_chroms_deferred ).then(function(chrom_info) { // Viewport config. https://bitbucket.org/galaxy/galaxy-central/commits/28470b4c9f5f/ Changeset: 28470b4c9f5f User: jgoecks Date: 2014-07-08 23:10:58 Summary: Trackster: move icon rendering into Backbone view. Affected #: 1 file diff -r 4ed4088326ec129519ee11f71b308c9e329ad3bd -r 28470b4c9f5ffc52bdad71c24c754af615cd283c static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -194,10 +194,82 @@ this.$el.append($("<div/>").addClass(this.model.drag_handle_class)); this.$el.append($("<div/>").addClass("track-name") .text(this.model.config.get_value('name'))); + + // Icons container. + this.action_icons = {}; + this.render_action_icons(); + + this.$el.append( $("<div style='clear: both'/>") ); + + // Suppress double clicks in header so that they do not impact viz under header. + this.$el.dblclick( function(e) { e.stopPropagation(); } ); + + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); }, update_name: function() { this.$el.find('.track-name').text(this.model.config.get_value('name')); + }, + + render_action_icons: function() { + var self = this; + this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.$el); + _.each(this.model.action_icons_def, function(icon_dict) { + self.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, + icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); + }); + + // Set up behavior for modes popup. + this.set_display_modes(this.model.display_modes); + }, + + /** + * Add an action icon to this object. Appends icon unless prepend flag is specified. + */ + add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { + var self = this; + this.action_icons[name] = $("<a/>").attr("title", title) + .addClass("icon-button").addClass(css_class).tooltip() + .click( function() { on_click_fn(self.model); } ) + .appendTo(this.icons_div); + if (hide) { + this.action_icons[name].hide(); + } + }, + + /** + * Set track's modes and update mode icon popup. + */ + set_display_modes: function(new_modes, init_mode) { + if (!new_modes) { return; } + + // HACK: move this out of view and into track. + + // Set modes, init mode. + this.model.display_modes = new_modes; + this.model.mode = (init_mode || this.model.config.get_value('mode') || this.model.display_modes[0]); + + this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); + + // Setup popup menu for changing modes. + var self = this, + track = this.model, + mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { + track.change_mode(mode); + // HACK: the popup menu messes with the track's hover event, so manually show/hide + // icons div for now. + //self.icons_div.show(); + //track.container_div.mouseleave(function() { track.icons_div.hide(); } ); + }; + }(mode); + } + + make_popupmenu(this.action_icons.mode_icon, mode_mapping); } }); @@ -254,24 +326,13 @@ this.header_div = header_view.$el; this.container_div.append(this.header_div); - - // Icons container. - this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.header_div); - this.build_action_icons(this.action_icons_def); - - this.header_div.append( $("<div style='clear: both'/>") ); - - // Suppress double clicks in header so that they do not impact viz. - this.header_div.dblclick( function(e) { e.stopPropagation(); } ); - + // Show icons when users is hovering over track. - var drawable = this; + var icons_div = header_view.icons_div; + this.action_icons = header_view.action_icons; this.container_div.hover( - function() { drawable.icons_div.show(); }, function() { drawable.icons_div.hide(); } + function() { icons_div.show(); }, function() { icons_div.hide(); } ); - - // Needed for floating elts in header. - $("<div style='clear: both'/>").appendTo(this.container_div); } }; @@ -389,33 +450,6 @@ * Build drawable's container div; this is the parent div for all drawable's elements. */ build_container_div: function() {}, - - /** - * Add an action icon to this object. Appends icon unless prepend flag is specified. - */ - add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { - var drawable = this; - this.action_icons[name] = $("<a/>").attr("title", title) - .addClass("icon-button").addClass(css_class).tooltip() - .click( function() { on_click_fn(drawable); } ) - .appendTo(this.icons_div); - if (hide) { - this.action_icons[name].hide(); - } - }, - - /** - * Build drawable's icons div from object's icons_dict. - */ - build_action_icons: function(action_icons_def) { - // Create icons. - var icon_dict; - for (var i = 0; i < action_icons_def.length; i++) { - icon_dict = action_icons_def[i]; - this.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, - icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); - } - }, /** * Update icons. @@ -2395,46 +2429,6 @@ }, /** - * Set track's modes and update mode icon popup. - */ - set_display_modes: function(new_modes, init_mode) { - // Set modes, init mode. - this.display_modes = new_modes; - this.mode = (init_mode ? init_mode : - (this.config && this.config.get_value('mode') ? - this.config.get_value('mode') : this.display_modes[0]) - ); - - this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); - - // Setup popup menu for changing modes. - var track = this, - mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { - track.change_mode(mode); - // HACK: the popup menu messes with the track's hover event, so manually show/hide - // icons div for now. - track.icons_div.show(); - track.container_div.mouseleave(function() { track.icons_div.hide(); } ); }; - }(mode); - } - - make_popupmenu(this.action_icons.mode_icon, mode_mapping); - }, - - build_action_icons: function() { - Drawable.prototype.build_action_icons.call(this, this.action_icons_def); - - // Set up behavior for modes popup. - if (this.display_modes !== undefined) { - this.set_display_modes(this.display_modes); - } - }, - - /** * Hide any elements that are part of the tracks contents area. Should * remove as approprite, the track will be redrawn by show_contents. */ https://bitbucket.org/galaxy/galaxy-central/commits/f53d750acf55/ Changeset: f53d750acf55 User: jgoecks Date: 2014-07-08 23:26:29 Summary: Client-side viz framework: create viz_views.js for visualization view objects and add TrackHeaderView to viz_views. Affected #: 2 files diff -r 28470b4c9f5ffc52bdad71c24c754af615cd283c -r f53d750acf557eeb84fa62c4151074c5fe5b7039 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ -define( ["libs/underscore", "viz/visualization", "viz/trackster/util", +define( ["libs/underscore", "viz/visualization", "viz/viz_views", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters", "mvc/data", "mvc/tools", "utils/config" ], - function(_, visualization, util, slotting, painters, filters_mod, data, tools_mod, config_mod) { + function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod) { var extend = _.extend; @@ -177,102 +177,6 @@ return Math.round(num * val) / val; } - -/** - * View for track/group header. - */ -var TrackHeaderView = Backbone.View.extend({ - className: 'track-header', - - initialize: function() { - // Watch and update name changes. - this.model.config.get('name').on('change:value', this.update_name, this); - this.render(); - }, - - render: function() { - this.$el.append($("<div/>").addClass(this.model.drag_handle_class)); - this.$el.append($("<div/>").addClass("track-name") - .text(this.model.config.get_value('name'))); - - // Icons container. - this.action_icons = {}; - this.render_action_icons(); - - this.$el.append( $("<div style='clear: both'/>") ); - - // Suppress double clicks in header so that they do not impact viz under header. - this.$el.dblclick( function(e) { e.stopPropagation(); } ); - - // Needed for floating elts in header. - $("<div style='clear: both'/>").appendTo(this.container_div); - }, - - update_name: function() { - this.$el.find('.track-name').text(this.model.config.get_value('name')); - }, - - render_action_icons: function() { - var self = this; - this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.$el); - _.each(this.model.action_icons_def, function(icon_dict) { - self.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, - icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); - }); - - // Set up behavior for modes popup. - this.set_display_modes(this.model.display_modes); - }, - - /** - * Add an action icon to this object. Appends icon unless prepend flag is specified. - */ - add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { - var self = this; - this.action_icons[name] = $("<a/>").attr("title", title) - .addClass("icon-button").addClass(css_class).tooltip() - .click( function() { on_click_fn(self.model); } ) - .appendTo(this.icons_div); - if (hide) { - this.action_icons[name].hide(); - } - }, - - /** - * Set track's modes and update mode icon popup. - */ - set_display_modes: function(new_modes, init_mode) { - if (!new_modes) { return; } - - // HACK: move this out of view and into track. - - // Set modes, init mode. - this.model.display_modes = new_modes; - this.model.mode = (init_mode || this.model.config.get_value('mode') || this.model.display_modes[0]); - - this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); - - // Setup popup menu for changing modes. - var self = this, - track = this.model, - mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { - track.change_mode(mode); - // HACK: the popup menu messes with the track's hover event, so manually show/hide - // icons div for now. - //self.icons_div.show(); - //track.container_div.mouseleave(function() { track.icons_div.hide(); } ); - }; - }(mode); - } - - make_popupmenu(this.action_icons.mode_icon, mode_mapping); - } -}); - /** * Drawables hierarchy: * @@ -320,7 +224,7 @@ // Use opt-out policy on header creation because this is the more frequent approach: // unless flag set, create header. if (obj_dict.header !== false) { - var header_view = new TrackHeaderView({ + var header_view = new viz_views.TrackHeaderView({ model: this }); diff -r 28470b4c9f5ffc52bdad71c24c754af615cd283c -r f53d750acf557eeb84fa62c4151074c5fe5b7039 static/scripts/viz/viz_views.js --- /dev/null +++ b/static/scripts/viz/viz_views.js @@ -0,0 +1,102 @@ +define( ["libs/underscore"], function(_) { + +/** + * View for track/group header. + */ +var TrackHeaderView = Backbone.View.extend({ + className: 'track-header', + + initialize: function() { + // Watch and update name changes. + this.model.config.get('name').on('change:value', this.update_name, this); + this.render(); + }, + + render: function() { + this.$el.append($("<div/>").addClass(this.model.drag_handle_class)); + this.$el.append($("<div/>").addClass("track-name") + .text(this.model.config.get_value('name'))); + + // Icons container. + this.action_icons = {}; + this.render_action_icons(); + + this.$el.append( $("<div style='clear: both'/>") ); + + // Suppress double clicks in header so that they do not impact viz under header. + this.$el.dblclick( function(e) { e.stopPropagation(); } ); + + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); + }, + + update_name: function() { + this.$el.find('.track-name').text(this.model.config.get_value('name')); + }, + + render_action_icons: function() { + var self = this; + this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.$el); + _.each(this.model.action_icons_def, function(icon_dict) { + self.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, + icon_dict.on_click_fn, icon_dict.prepend, icon_dict.hide); + }); + + // Set up behavior for modes popup. + this.set_display_modes(this.model.display_modes); + }, + + /** + * Add an action icon to this object. Appends icon unless prepend flag is specified. + */ + add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { + var self = this; + this.action_icons[name] = $("<a/>").attr("title", title) + .addClass("icon-button").addClass(css_class).tooltip() + .click( function() { on_click_fn(self.model); } ) + .appendTo(this.icons_div); + if (hide) { + this.action_icons[name].hide(); + } + }, + + /** + * Set track's modes and update mode icon popup. + */ + set_display_modes: function(new_modes, init_mode) { + if (!new_modes) { return; } + + // HACK: move this out of view and into track. + + // Set modes, init mode. + this.model.display_modes = new_modes; + this.model.mode = (init_mode || this.model.config.get_value('mode') || this.model.display_modes[0]); + + this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); + + // Setup popup menu for changing modes. + var self = this, + track = this.model, + mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { + track.change_mode(mode); + // HACK: the popup menu messes with the track's hover event, so manually show/hide + // icons div for now. + //self.icons_div.show(); + //track.container_div.mouseleave(function() { track.icons_div.hide(); } ); + }; + }(mode); + } + + make_popupmenu(this.action_icons.mode_icon, mode_mapping); + } +}); + +return { + TrackHeaderView: TrackHeaderView +}; + +}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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