galaxy-commits July 2014

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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/5a5f22a64812/ Changeset: 5a5f22a64812 User: jgoecks Date: 2014-07-09 17:46:31 Summary: Trackster: truncate long track names. Affected #: 2 files diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -22,6 +22,7 @@ .group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px} .group{min-height:20px;border-top:1px solid #888;border-bottom:1px solid #888}.group>.track-header{position:relative;float:left} .track-header{height:16px;position:absolute;z-index:2;background-color:rgba(1,1,1,0.1);border-radius:5px;padding:0px 2px;text-align:left;margin:2px;}.track-header:hover{background-color:#DDDDDD} +.track-header .track-name{max-width:200px;white-space:nowrap;overflow:hidden;text-overflow:ellipsis} .track-header .menubutton{margin-left:0px} .track-name{float:left;margin-top:2px} .tiles{background:url('../images/tracks/diag_bg.gif');position:relative;overflow:hidden} diff -r d1d5fcd5bec6d4d48908f6da58a31ca9242e694e -r 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -200,6 +200,14 @@ background-color: #DDDDDD; } + // Truncate long track names. + .track-name { + max-width: 200px; + white-space: nowrap; + overflow: hidden; + text-overflow: ellipsis; + } + .menubutton { margin-left: 0px; } https://bitbucket.org/galaxy/galaxy-central/commits/cbe3fe407093/ Changeset: cbe3fe407093 User: jgoecks Date: 2014-07-09 17:46:51 Summary: Automated merge Affected #: 4 files diff -r 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 -r cbe3fe407093b0161469e1de662623d1d13bf532 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 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 -r cbe3fe407093b0161469e1de662623d1d13bf532 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 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 -r cbe3fe407093b0161469e1de662623d1d13bf532 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 5a5f22a6481261d44ac2b4c308dbbfa87c93a457 -r cbe3fe407093b0161469e1de662623d1d13bf532 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 @@ -8,6 +8,7 @@ import time import urllib2 import zipfile +import hashlib from galaxy.util import asbool from galaxy.util.template import fill_template @@ -139,10 +140,29 @@ class Download( object ): def url_download( self, install_dir, downloaded_file_name, download_url, extract=True ): + """ + The given download_url can have an extension like #md5# or #sha256#. + This indicates a checksum which will be chekced after download. + If the checksum does not match an exception is thrown. + + https://pypi.python.org/packages/source/k/khmer/khmer-1.0.tar.gz#md5#b60639… + """ + file_path = os.path.join( install_dir, downloaded_file_name ) src = None dst = None + checksum = None + sha256 = False + md5 = False # Set a timer so we don't sit here forever. + + if '#md5#' in download_url: + md5 = True + download_url, checksum = download_url.split('#md5#') + elif '#sha256#' in download_url: + sha256 = True + download_url, checksum = download_url.split('#sha256#') + start_time = time.time() try: src = urllib2.urlopen( download_url ) @@ -166,6 +186,18 @@ src.close() if dst: dst.close() + + try: + if sha256: + downloaded_checksum = hashlib.sha256(open(file_path, 'rb').read()).hexdigest() + elif md5: + downloaded_checksum = hashlib.md5(open(file_path, 'rb').read()).hexdigest() + + if checksum and downloaded_checksum != checksum: + raise Exception( 'Given checksum does not match with the one from the downloaded file (%s).' % (downloaded_checksum) ) + except Exception, e: + raise + if extract: if tarfile.is_tarfile( file_path ) or ( zipfile.is_zipfile( file_path ) and not file_path.endswith( '.jar' ) ): archive = CompressedFile( file_path ) @@ -174,6 +206,7 @@ extraction_path = os.path.abspath( install_dir ) else: extraction_path = os.path.abspath( install_dir ) + return extraction_path @@ -1390,6 +1423,139 @@ 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 ) + 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: dannon: Close branch tool_shed_checksum
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ed443abea720/ Changeset: ed443abea720 Branch: tool_shed_checksum User: dannon Date: 2014-07-09 17:39:45 Summary: Close branch tool_shed_checksum 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: 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/d1572a4a0f52/ Changeset: d1572a4a0f52 Branch: tool_shed_checksum User: Bjoern Gruening Date: 2014-06-29 21:35:02 Summary: With that PR the Tool Shed will be able to get checksums from the Tool Developer. These checksums will be verified after download and in case of an mismatch an error is thrown. Currently, md5 and sha256 checksums are supported. Example: <package>https://pypi.python.org/packages/source/k/khmer/khmer-1.0.tar.gz#md5=b60639…</package> Affected #: 1 file diff -r 7b424e9c2e57ec12eca26f35c8f4259bbcc55cdb -r d1572a4a0f529fb20f2c7036eb7dfed19563ac89 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 @@ -8,6 +8,7 @@ import time import urllib2 import zipfile +import hashlib from galaxy.util import asbool from galaxy.util.template import fill_template @@ -139,10 +140,29 @@ class Download( object ): def url_download( self, install_dir, downloaded_file_name, download_url, extract=True ): + """ + The given download_url can have an extension like #md5# or #sha256#. + This indicates a checksum which will be chekced after download. + If the checksum does not match an exception is thrown. + + https://pypi.python.org/packages/source/k/khmer/khmer-1.0.tar.gz#md5#b60639… + """ + file_path = os.path.join( install_dir, downloaded_file_name ) src = None dst = None + checksum = None + sha256 = False + md5 = False # Set a timer so we don't sit here forever. + + if '#md5#' in download_url: + md5 = True + dowonload_url, checksum = download_url.split('#md5#') + elif '#sha256#' in download_url: + sha256 = True + download_url, checksum = download_url.split('#sha256#') + start_time = time.time() try: src = urllib2.urlopen( download_url ) @@ -166,6 +186,18 @@ src.close() if dst: dst.close() + + try: + if sha256: + downloaded_checksum = hashlib.sha256(open(file_path, 'rb').read()).hexdigest() + elif md5: + downloaded_checksum = hashlib.md5(open(file_path, 'rb').read()).hexdigest() + + if checksum and downloaded_checksum != checksum: + raise Exception( 'Given checksum does not match with the one from the downloaded file (%s).' % (downloaded_checksum) ) + except Exception, e: + raise + if extract: if tarfile.is_tarfile( file_path ) or ( zipfile.is_zipfile( file_path ) and not file_path.endswith( '.jar' ) ): archive = CompressedFile( file_path ) @@ -174,6 +206,7 @@ extraction_path = os.path.abspath( install_dir ) else: extraction_path = os.path.abspath( install_dir ) + return extraction_path @@ -1421,7 +1454,6 @@ 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: https://bitbucket.org/galaxy/galaxy-central/commits/848a727a1141/ Changeset: 848a727a1141 Branch: tool_shed_checksum User: BjoernGruening Date: 2014-06-29 22:34:56 Summary: spelling fix Affected #: 1 file diff -r d1572a4a0f529fb20f2c7036eb7dfed19563ac89 -r 848a727a1141aa65a0cce41f9c046ff3296bb504 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 @@ -158,7 +158,7 @@ if '#md5#' in download_url: md5 = True - dowonload_url, checksum = download_url.split('#md5#') + download_url, checksum = download_url.split('#md5#') elif '#sha256#' in download_url: sha256 = True download_url, checksum = download_url.split('#sha256#') https://bitbucket.org/galaxy/galaxy-central/commits/b86bab7dad7d/ Changeset: b86bab7dad7d User: dannon Date: 2014-07-09 17:39:45 Summary: Merged in BjoernGruening/galaxy-central-bgruening/tool_shed_checksum (pull request #432) Implement Tool Shed checksums Affected #: 1 file diff -r 4411a021a9fad918cef26e00adf6f49e247fb0bd -r b86bab7dad7d744c57f6eebe9f5b390ad083a8f6 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 @@ -8,6 +8,7 @@ import time import urllib2 import zipfile +import hashlib from galaxy.util import asbool from galaxy.util.template import fill_template @@ -139,10 +140,29 @@ class Download( object ): def url_download( self, install_dir, downloaded_file_name, download_url, extract=True ): + """ + The given download_url can have an extension like #md5# or #sha256#. + This indicates a checksum which will be chekced after download. + If the checksum does not match an exception is thrown. + + https://pypi.python.org/packages/source/k/khmer/khmer-1.0.tar.gz#md5#b60639… + """ + file_path = os.path.join( install_dir, downloaded_file_name ) src = None dst = None + checksum = None + sha256 = False + md5 = False # Set a timer so we don't sit here forever. + + if '#md5#' in download_url: + md5 = True + download_url, checksum = download_url.split('#md5#') + elif '#sha256#' in download_url: + sha256 = True + download_url, checksum = download_url.split('#sha256#') + start_time = time.time() try: src = urllib2.urlopen( download_url ) @@ -166,6 +186,18 @@ src.close() if dst: dst.close() + + try: + if sha256: + downloaded_checksum = hashlib.sha256(open(file_path, 'rb').read()).hexdigest() + elif md5: + downloaded_checksum = hashlib.md5(open(file_path, 'rb').read()).hexdigest() + + if checksum and downloaded_checksum != checksum: + raise Exception( 'Given checksum does not match with the one from the downloaded file (%s).' % (downloaded_checksum) ) + except Exception, e: + raise + if extract: if tarfile.is_tarfile( file_path ) or ( zipfile.is_zipfile( file_path ) and not file_path.endswith( '.jar' ) ): archive = CompressedFile( file_path ) @@ -174,6 +206,7 @@ extraction_path = os.path.abspath( install_dir ) else: extraction_path = os.path.abspath( install_dir ) + return extraction_path @@ -1421,7 +1454,6 @@ 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: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merged in BjoernGruening/galaxy-central-bgruening/tool_shed_checksum (pull request #432)
by commits-noreply＠bitbucket.org 09 Jul '14

09 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b86bab7dad7d/ Changeset: b86bab7dad7d User: dannon Date: 2014-07-09 17:39:45 Summary: Merged in BjoernGruening/galaxy-central-bgruening/tool_shed_checksum (pull request #432) Implement Tool Shed checksums Affected #: 1 file diff -r 4411a021a9fad918cef26e00adf6f49e247fb0bd -r b86bab7dad7d744c57f6eebe9f5b390ad083a8f6 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 @@ -8,6 +8,7 @@ import time import urllib2 import zipfile +import hashlib from galaxy.util import asbool from galaxy.util.template import fill_template @@ -139,10 +140,29 @@ class Download( object ): def url_download( self, install_dir, downloaded_file_name, download_url, extract=True ): + """ + The given download_url can have an extension like #md5# or #sha256#. + This indicates a checksum which will be chekced after download. + If the checksum does not match an exception is thrown. + + https://pypi.python.org/packages/source/k/khmer/khmer-1.0.tar.gz#md5#b60639… + """ + file_path = os.path.join( install_dir, downloaded_file_name ) src = None dst = None + checksum = None + sha256 = False + md5 = False # Set a timer so we don't sit here forever. + + if '#md5#' in download_url: + md5 = True + download_url, checksum = download_url.split('#md5#') + elif '#sha256#' in download_url: + sha256 = True + download_url, checksum = download_url.split('#sha256#') + start_time = time.time() try: src = urllib2.urlopen( download_url ) @@ -166,6 +186,18 @@ src.close() if dst: dst.close() + + try: + if sha256: + downloaded_checksum = hashlib.sha256(open(file_path, 'rb').read()).hexdigest() + elif md5: + downloaded_checksum = hashlib.md5(open(file_path, 'rb').read()).hexdigest() + + if checksum and downloaded_checksum != checksum: + raise Exception( 'Given checksum does not match with the one from the downloaded file (%s).' % (downloaded_checksum) ) + except Exception, e: + raise + if extract: if tarfile.is_tarfile( file_path ) or ( zipfile.is_zipfile( file_path ) and not file_path.endswith( '.jar' ) ): archive = CompressedFile( file_path ) @@ -174,6 +206,7 @@ extraction_path = os.path.abspath( install_dir ) else: extraction_path = os.path.abspath( install_dir ) + return extraction_path @@ -1421,7 +1454,6 @@ 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: 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 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. 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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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