May 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 May '13

29 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a6f688dade80/ Changeset: a6f688dade80 Branch: next-stable User: natefoo Date: 2013-05-29 19:55:08 Summary: Make PBKDF2 password hashing conditional, enable by default. Affected #: 3 files diff -r 886a722b0aef6560320c1ddf7382e6207731f49f -r a6f688dade808b0e16903fbb50186ad9656c0d1c lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -62,7 +62,8 @@ self.config.database_engine_options, database_query_profiling_proxy = self.config.database_query_profiling_proxy, object_store = self.object_store, - trace_logger=self.trace_logger ) + trace_logger=self.trace_logger, + use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) # Manage installed tool shed repositories. self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager( self ) # Create an empty datatypes registry. diff -r 886a722b0aef6560320c1ddf7382e6207731f49f -r a6f688dade808b0e16903fbb50186ad9656c0d1c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -62,6 +62,7 @@ class User( object, APIItem ): + use_pbkdf2 = True """ Data for a Galaxy user or admin and relations to their histories, credentials, and roles. @@ -87,7 +88,10 @@ """ Set user password to the digest of `cleartext`. """ - self.password = galaxy.security.passwords.hash_password( cleartext ) + if User.use_pbkdf2: + self.password = galaxy.security.passwords.hash_password( cleartext ) + else: + self.password = new_secure_hash( text_type=cleartext ) def check_password( self, cleartext ): """ diff -r 886a722b0aef6560320c1ddf7382e6207731f49f -r a6f688dade808b0e16903fbb50186ad9656c0d1c lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -2008,12 +2008,14 @@ # Let this go, it could possibly work with db's we don't support log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) -def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None ): +def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True ): """Connect mappings to the database""" # Connect dataset to the file path model.Dataset.file_path = file_path # Connect dataset to object store model.Dataset.object_store = object_store + # Use PBKDF2 password hashing? + model.User.use_pbkdf2 = use_pbkdf2 # Load the appropriate db module load_egg_for_url( url ) # Should we use the logging proxy? https://bitbucket.org/galaxy/galaxy-central/commits/e3455a092882/ Changeset: e3455a092882 User: natefoo Date: 2013-05-29 19:55:22 Summary: merge next-stable. Affected #: 3 files diff -r 35ac562e7e81f232b99c2c377d415b6aeab538cb -r e3455a0928824b8ef0fb8f9337e3b0a1d194d2ed lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -62,7 +62,8 @@ self.config.database_engine_options, database_query_profiling_proxy = self.config.database_query_profiling_proxy, object_store = self.object_store, - trace_logger=self.trace_logger ) + trace_logger=self.trace_logger, + use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) # Manage installed tool shed repositories. self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager( self ) # Create an empty datatypes registry. diff -r 35ac562e7e81f232b99c2c377d415b6aeab538cb -r e3455a0928824b8ef0fb8f9337e3b0a1d194d2ed lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -62,6 +62,7 @@ class User( object, APIItem ): + use_pbkdf2 = True """ Data for a Galaxy user or admin and relations to their histories, credentials, and roles. @@ -87,7 +88,10 @@ """ Set user password to the digest of `cleartext`. """ - self.password = galaxy.security.passwords.hash_password( cleartext ) + if User.use_pbkdf2: + self.password = galaxy.security.passwords.hash_password( cleartext ) + else: + self.password = new_secure_hash( text_type=cleartext ) def check_password( self, cleartext ): """ diff -r 35ac562e7e81f232b99c2c377d415b6aeab538cb -r e3455a0928824b8ef0fb8f9337e3b0a1d194d2ed lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -2008,12 +2008,14 @@ # Let this go, it could possibly work with db's we don't support log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) -def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None ): +def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True ): """Connect mappings to the database""" # Connect dataset to the file path model.Dataset.file_path = file_path # Connect dataset to object store model.Dataset.object_store = object_store + # Use PBKDF2 password hashing? + model.User.use_pbkdf2 = use_pbkdf2 # Load the appropriate db module load_egg_for_url( url ) # Should we use the logging proxy? 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 29 May '13

29 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/886a722b0aef/ Changeset: 886a722b0aef Branch: next-stable User: Dave Bouvier Date: 2013-05-29 19:26:38 Summary: Fix for set_environment appearing in multiple action sections. Fix for interpolating multiple environment variables in set_environment actions. Affected #: 2 files diff -r 8c69611137c19dd59d9e6f7cc339484213a88b18 -r 886a722b0aef6560320c1ddf7382e6207731f49f lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -22,7 +22,6 @@ log = logging.getLogger( __name__ ) -CMD_SEPARATOR = '__CMD_SEP__' INSTALLATION_LOG = 'INSTALLATION.log' VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' @@ -51,21 +50,90 @@ return output.return_code def handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): + """ + This method works with with a combination of three tool dependency definition tag sets, which are defined in the tool_dependencies.xml file in the + order discussed here. The example for this discussion is the tool_dependencies.xml file contained in the osra repository, which is available at: + + http://testtoolshed.g2.bx.psu.edu/view/bgruening/osra + + The first tag set defines a complex repository dependency like this. This tag set ensures that changeset revision XXX of the repository named + package_graphicsmagick_1_3 owned by YYY in the tool shed ZZZ has been previously installed. + + <tool_dependency> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" prior_installation_required="True" toolshed="ZZZ" /> + </package> + ... + + * By the way, there is an env.sh file associated with version 1.3.18 of the graphicsmagick package which looks something like this (we'll reference + this file later in this discussion. + ---- + GRAPHICSMAGICK_ROOT_DIR=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick; + export GRAPHICSMAGICK_ROOT_DIR + ---- + + The second tag set defines a specific package dependency that has been previously installed (guaranteed by the tag set discussed above) and compiled, + where the compiled dependency is needed by the tool dependency currently being installed (osra version 2.0.0 in this case) and complied in order for + it's installation and compilation to succeed. This tag set is contained within the <package name="osra" version="2.0.0"> tag set, which implies that + version 2.0.0 of the osra package requires version 1.3.18 of the graphicsmagick package in order to successfully compile. When this tag set is handled, + one of the effects is that the env.sh file associated with graphicsmagick version 1.3.18 is "sourced", which undoubtedly sets or alters certain environment + variables (e.g. PATH, PYTHONPATH, etc). + +  + <action type="set_environment_for_install"> + <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" toolshed="ZZZ"> + <package name="graphicsmagick" version="1.3.18" /> + </repository> + </action> + + The third tag set enables discovery of the same required package dependency discussed above for correctly compiling the osra version 2.0.0 package, but + in this case the package can be discovered at tool execution time. Using the $ENV[] option as shown in this example, the value of the environment + variable named GRAPHICSMAGICK_ROOT_DIR (which was set in the environment using the second tag set described above) will be used to automatically alter + the env.sh file associated with the osra version 2.0.0 tool dependency when it is installed into Galaxy. * Refer to where we discussed the env.sh file + for version 1.3.18 of the graphicsmagick package above. + + <action type="set_environment"> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> +  + <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> + </action> + + The above tag will produce an env.sh file for version 2.0.0 of the osra package when it it installed into Galaxy that looks something like this. Notice + that the path to the gmagick binary is included here since it expands the defined $ENV[GRAPHICSMAGICK_ROOT_DIR] value in the above tag set. + + ---- + LD_LIBRARY_PATH=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick/lib/:$LD_LIBRARY_PATH; + export LD_LIBRARY_PATH + LD_LIBRARY_PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/potrace/build/lib/:$LD_LIBRARY_PATH; + export LD_LIBRARY_PATH + PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/bin:$PATH; + export PATH + OSRA_DATA_FILES=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/share; + export OSRA_DATA_FILES + ---- + """ env_var_value = env_var_dict[ 'value' ] + # env_var_value is the text of an environment variable tag like this: <environment_variable action="prepend_to" name="LD_LIBRARY_PATH"> + # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/ if '$ENV[' in env_var_value and ']' in env_var_value: # Pull out the name of the environment variable to populate. inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0] to_replace = '$ENV[%s]' % inherited_env_var_name - # Build a command line that outputs CMD_SEPARATOR + environment variable value + CMD_SEPARATOR. - set_prior_environment_commands.extend( [ "echo '%s'" % CMD_SEPARATOR, 'echo $%s' % inherited_env_var_name, "echo '%s'" % CMD_SEPARATOR ] ) + # Build a command line that outputs VARIABLE_NAME: <the value of the variable>. + set_prior_environment_commands.append( 'echo "%s: $%s"' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) - # And extract anything between the two instances of CMD_SEPARATOR. - environment_variable_value = command_return.split( CMD_SEPARATOR )[1].split( CMD_SEPARATOR )[0].strip( '\n' ) - if environment_variable_value: - log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, environment_variable_value ) - env_var_value = env_var_value.replace( to_replace, environment_variable_value ) + # And extract anything labeled with the name of the environment variable we're populating here. + if '%s: ' % inherited_env_var_name in command_return: + environment_variable_value = command_return.split( '\n' ) + for line in environment_variable_value: + if line.startswith( inherited_env_var_name ): + inherited_env_var_value = line.replace( '%s: ' % inherited_env_var_name, '' ) + log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, inherited_env_var_value ) + env_var_value = env_var_value.replace( to_replace, inherited_env_var_value ) else: # If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on. log.error( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name ) diff -r 8c69611137c19dd59d9e6f7cc339484213a88b18 -r 886a722b0aef6560320c1ddf7382e6207731f49f lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -339,6 +339,7 @@ actions_dict[ 'package_name' ] = package_name actions = [] all_env_shell_file_paths = [] + env_var_dicts = [] # Make sure to skip all comments, since they are now included in the XML tree. for action_elem in actions_elem.findall( 'action' ): action_dict = {} @@ -389,7 +390,6 @@ # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> - env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_dict = common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) https://bitbucket.org/galaxy/galaxy-central/commits/35ac562e7e81/ Changeset: 35ac562e7e81 User: Dave Bouvier Date: 2013-05-29 19:27:48 Summary: Merge with next-stable. Affected #: 2 files diff -r 964071e63ee3173e35f245d193e3cb8252fabc7c -r 35ac562e7e81f232b99c2c377d415b6aeab538cb lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -22,7 +22,6 @@ log = logging.getLogger( __name__ ) -CMD_SEPARATOR = '__CMD_SEP__' INSTALLATION_LOG = 'INSTALLATION.log' VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' @@ -94,7 +93,7 @@ for version 1.3.18 of the graphicsmagick package above. <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[$GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable><environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable><environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> @@ -102,7 +101,7 @@ </action> The above tag will produce an env.sh file for version 2.0.0 of the osra package when it it installed into Galaxy that looks something like this. Notice - that the path to the gmagick binary is included here since it expands the defined $ENV[$GRAPHICSMAGICK_ROOT_DIR] value in the above tag set. + that the path to the gmagick binary is included here since it expands the defined $ENV[GRAPHICSMAGICK_ROOT_DIR] value in the above tag set. ---- LD_LIBRARY_PATH=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick/lib/:$LD_LIBRARY_PATH; @@ -116,20 +115,25 @@ ---- """ env_var_value = env_var_dict[ 'value' ] + # env_var_value is the text of an environment variable tag like this: <environment_variable action="prepend_to" name="LD_LIBRARY_PATH"> + # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/ if '$ENV[' in env_var_value and ']' in env_var_value: # Pull out the name of the environment variable to populate. inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0] to_replace = '$ENV[%s]' % inherited_env_var_name - # Build a command line that outputs CMD_SEPARATOR + environment variable value + CMD_SEPARATOR. - set_prior_environment_commands.extend( [ "echo '%s'" % CMD_SEPARATOR, 'echo $%s' % inherited_env_var_name, "echo '%s'" % CMD_SEPARATOR ] ) + # Build a command line that outputs VARIABLE_NAME: <the value of the variable>. + set_prior_environment_commands.append( 'echo "%s: $%s"' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) - # And extract anything between the two instances of CMD_SEPARATOR. - environment_variable_value = command_return.split( CMD_SEPARATOR )[1].split( CMD_SEPARATOR )[0].strip( '\n' ) - if environment_variable_value: - log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, environment_variable_value ) - env_var_value = env_var_value.replace( to_replace, environment_variable_value ) + # And extract anything labeled with the name of the environment variable we're populating here. + if '%s: ' % inherited_env_var_name in command_return: + environment_variable_value = command_return.split( '\n' ) + for line in environment_variable_value: + if line.startswith( inherited_env_var_name ): + inherited_env_var_value = line.replace( '%s: ' % inherited_env_var_name, '' ) + log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, inherited_env_var_value ) + env_var_value = env_var_value.replace( to_replace, inherited_env_var_value ) else: # If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on. log.error( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name ) diff -r 964071e63ee3173e35f245d193e3cb8252fabc7c -r 35ac562e7e81f232b99c2c377d415b6aeab538cb lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -339,6 +339,7 @@ actions_dict[ 'package_name' ] = package_name actions = [] all_env_shell_file_paths = [] + env_var_dicts = [] # Make sure to skip all comments, since they are now included in the XML tree. for action_elem in actions_elem.findall( 'action' ): action_dict = {} @@ -389,7 +390,6 @@ # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> - env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_dict = common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge with next-stable
by commits-noreply＠bitbucket.org 28 May '13

28 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/964071e63ee3/ Changeset: 964071e63ee3 User: dannon Date: 2013-05-28 23:25:11 Summary: Merge with next-stable 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 28 May '13

28 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a9a6e51304c/ Changeset: 1a9a6e51304c User: dannon Date: 2013-05-28 23:23:17 Summary: Bugfix for standard dataset upload Affected #: 1 file diff -r 79889b1c7da331afc80e2fa64e9d568a9c559cbe -r 1a9a6e51304c95d79322d17c9583afbaf305b25b lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -209,13 +209,12 @@ trans.sa_session.add( dp ) trans.sa_session.flush() return ldda + def new_upload( trans, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None ): if library_bunch: return __new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state ) - elif history: + else: return __new_history_upload( trans, uploaded_dataset, history=history, state=state ) - else: - raise Exception("new_upload must be called with empty values for library_bunch and history") def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset_upload_inputs, library_bunch=None, history=None ): uploaded_datasets = [] https://bitbucket.org/galaxy/galaxy-central/commits/8c69611137c1/ Changeset: 8c69611137c1 Branch: next-stable User: dannon Date: 2013-05-28 23:23:17 Summary: Bugfix for standard dataset upload Affected #: 1 file diff -r 6b4b91d27c3316960ae0e65bfb7c87371831be41 -r 8c69611137c19dd59d9e6f7cc339484213a88b18 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -209,13 +209,12 @@ trans.sa_session.add( dp ) trans.sa_session.flush() return ldda + def new_upload( trans, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None ): if library_bunch: return __new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state ) - elif history: + else: return __new_history_upload( trans, uploaded_dataset, history=history, state=state ) - else: - raise Exception("new_upload must be called with empty values for library_bunch and history") def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset_upload_inputs, library_bunch=None, history=None ): uploaded_datasets = [] 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 28 May '13

28 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7395e351ec85/ Changeset: 7395e351ec85 User: jgoecks Date: 2013-05-26 21:05:31 Summary: Trackster: whitespace additions between functions. Affected #: 1 file diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 7395e351ec8564c8c38c38ffcef79a57d02ec836 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1137,9 +1137,11 @@ // FIXME: need to use this approach to enable inheritance of DrawableCollection functions. extend( TracksterView.prototype, DrawableCollection.prototype, { + changed: function() { this.has_changes = true; }, + /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.drawables.length === 0) { @@ -1149,6 +1151,7 @@ this.intro_div.hide(); } }, + /** * Triggers navigate events as needed. If there is a delay, * then event is triggered only after navigation has stopped. @@ -1171,6 +1174,7 @@ view.trigger("navigate", new_chrom + ":" + new_low + "-" + new_high); } }, + update_location: function(low, high) { this.location_span.text( commatize(low) + ' - ' + commatize(high) ); this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) ); @@ -1182,6 +1186,7 @@ this.trigger_navigate(chrom, view.low, view.high, true); } }, + /** * Load chrom data for the view. Returns a jQuery Deferred. */ @@ -1230,6 +1235,7 @@ return chrom_data; }, + change_chrom: function(chrom, low, high) { var view = this; // If chrom data is still loading, wait for it. @@ -1365,6 +1371,7 @@ var chrom = view.chrom_select.val(); this.trigger_navigate(chrom, view.low, view.high, true); }, + /** * Add a drawable to the view. */ @@ -1374,11 +1381,13 @@ this.changed(); this.update_intro_div(); }, + add_label_track: function (label_track) { label_track.view = this; label_track.init(); this.label_tracks.push(label_track); }, + /** * Remove drawable from the view. */ @@ -1392,11 +1401,13 @@ }); } }, + reset: function() { this.low = this.max_low; this.high = this.max_high; this.viewport_container.find(".yaxislabel").remove(); }, + /** * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. */ @@ -1439,6 +1450,7 @@ this.requested_redraw = true; } }, + /** * Redraws view and tracks. * NOTE: this method should never be called directly; request_redraw() should be used so @@ -1503,6 +1515,7 @@ this.label_tracks[i]._draw(); } }, + zoom_in: function (point, container) { if (this.max_high === 0 || this.high - this.low <= this.min_separation) { return; @@ -1518,6 +1531,7 @@ this.changed(); this.request_redraw(); }, + zoom_out: function () { if (this.max_high === 0) { return; @@ -1530,10 +1544,12 @@ this.changed(); this.request_redraw(); }, + resize_window: function() { this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.request_redraw(); }, + /** Show a Drawable in the overview. */ set_overview: function(drawable) { if (this.overview_drawable) { @@ -1561,6 +1577,7 @@ view.overview_drawable.request_draw(); this.changed(); }, + view /** Close and reset overview. */ reset_overview: function() { // Update UI. https://bitbucket.org/galaxy/galaxy-central/commits/79889b1c7da3/ Changeset: 79889b1c7da3 User: jgoecks Date: 2013-05-28 21:22:58 Summary: Automated merge Affected #: 1 file diff -r c3199d306781ce61ce121a2c34c846310dac74c7 -r 79889b1c7da331afc80e2fa64e9d568a9c559cbe static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1137,9 +1137,11 @@ // FIXME: need to use this approach to enable inheritance of DrawableCollection functions. extend( TracksterView.prototype, DrawableCollection.prototype, { + changed: function() { this.has_changes = true; }, + /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.drawables.length === 0) { @@ -1149,6 +1151,7 @@ this.intro_div.hide(); } }, + /** * Triggers navigate events as needed. If there is a delay, * then event is triggered only after navigation has stopped. @@ -1171,6 +1174,7 @@ view.trigger("navigate", new_chrom + ":" + new_low + "-" + new_high); } }, + update_location: function(low, high) { this.location_span.text( commatize(low) + ' - ' + commatize(high) ); this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) ); @@ -1182,6 +1186,7 @@ this.trigger_navigate(chrom, view.low, view.high, true); } }, + /** * Load chrom data for the view. Returns a jQuery Deferred. */ @@ -1230,6 +1235,7 @@ return chrom_data; }, + change_chrom: function(chrom, low, high) { var view = this; // If chrom data is still loading, wait for it. @@ -1365,6 +1371,7 @@ var chrom = view.chrom_select.val(); this.trigger_navigate(chrom, view.low, view.high, true); }, + /** * Add a drawable to the view. */ @@ -1374,11 +1381,13 @@ this.changed(); this.update_intro_div(); }, + add_label_track: function (label_track) { label_track.view = this; label_track.init(); this.label_tracks.push(label_track); }, + /** * Remove drawable from the view. */ @@ -1392,11 +1401,13 @@ }); } }, + reset: function() { this.low = this.max_low; this.high = this.max_high; this.viewport_container.find(".yaxislabel").remove(); }, + /** * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. */ @@ -1439,6 +1450,7 @@ this.requested_redraw = true; } }, + /** * Redraws view and tracks. * NOTE: this method should never be called directly; request_redraw() should be used so @@ -1503,6 +1515,7 @@ this.label_tracks[i]._draw(); } }, + zoom_in: function (point, container) { if (this.max_high === 0 || this.high - this.low <= this.min_separation) { return; @@ -1518,6 +1531,7 @@ this.changed(); this.request_redraw(); }, + zoom_out: function () { if (this.max_high === 0) { return; @@ -1530,10 +1544,12 @@ this.changed(); this.request_redraw(); }, + resize_window: function() { this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.request_redraw(); }, + /** Show a Drawable in the overview. */ set_overview: function(drawable) { if (this.overview_drawable) { @@ -1561,6 +1577,7 @@ view.overview_drawable.request_draw(); this.changed(); }, + view /** Close and reset overview. */ reset_overview: function() { // Update UI. 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 28 May '13

28 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b4b91d27c33/ Changeset: 6b4b91d27c33 Branch: next-stable User: Dave Bouvier Date: 2013-05-28 20:49:19 Summary: Explicitly filter by tag name actions when building the actions dict for tool dependency installation. Affected #: 1 file diff -r 412b9edb65ec78b029cae0969956b194c16ac053 -r 6b4b91d27c3316960ae0e65bfb7c87371831be41 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -339,7 +339,8 @@ actions_dict[ 'package_name' ] = package_name actions = [] all_env_shell_file_paths = [] - for action_elem in actions_elem: + # Make sure to skip all comments, since they are now included in the XML tree. + for action_elem in actions_elem.findall( 'action' ): action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) if action_type == 'shell_command': https://bitbucket.org/galaxy/galaxy-central/commits/c3199d306781/ Changeset: c3199d306781 User: Dave Bouvier Date: 2013-05-28 20:51:18 Summary: Merge with next-stable. Affected #: 1 file diff -r 79d036fbc175dc9e8eeb3c3a8e57352ded1fbbbf -r c3199d306781ce61ce121a2c34c846310dac74c7 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -339,7 +339,8 @@ actions_dict[ 'package_name' ] = package_name actions = [] all_env_shell_file_paths = [] - for action_elem in actions_elem: + # Make sure to skip all comments, since they are now included in the XML tree. + for action_elem in actions_elem.findall( 'action' ): action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) if action_type == 'shell_command': 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 28 May '13

28 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/412b9edb65ec/ Changeset: 412b9edb65ec Branch: next-stable User: jmchilton Date: 2013-05-26 22:15:19 Summary: Fix job splitting to rewrite references in config files in addition to command-line. Affected #: 1 file diff -r 69f70d84619de8024e8de7ef5669bda6dfaffce8 -r 412b9edb65ec78b029cae0969956b194c16ac053 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1573,6 +1573,12 @@ self.sa_session.flush() # Build any required config files config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + for config_filename in config_filenames: + config_contents = open(config_filename, "r").read() + for k, v in fnames.iteritems(): + config_contents = config_contents.replace(k, v) + open(config_filename, "w").write(config_contents) + # FIXME: Build the param file (might return None, DEPRECATED) param_filename = self.tool.build_param_file( param_dict, self.working_directory ) # Build the job's command line https://bitbucket.org/galaxy/galaxy-central/commits/79d036fbc175/ Changeset: 79d036fbc175 User: dannon Date: 2013-05-28 20:44:29 Summary: Merge PR169 to next-stable 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 28 May '13

28 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4294c2a836fe/ Changeset: 4294c2a836fe User: jmchilton Date: 2013-05-26 22:15:19 Summary: Fix job splitting to rewrite references in config files in addition to command-line. Affected #: 1 file diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 4294c2a836fea78d50e65c29fc85bb047b095fd3 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1573,6 +1573,12 @@ self.sa_session.flush() # Build any required config files config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + for config_filename in config_filenames: + config_contents = open(config_filename, "r").read() + for k, v in fnames.iteritems(): + config_contents = config_contents.replace(k, v) + open(config_filename, "w").write(config_contents) + # FIXME: Build the param file (might return None, DEPRECATED) param_filename = self.tool.build_param_file( param_dict, self.working_directory ) # Build the job's command line https://bitbucket.org/galaxy/galaxy-central/commits/f3e6cf36517e/ Changeset: f3e6cf36517e User: dannon Date: 2013-05-28 20:43:12 Summary: Merged in jmchilton/galaxy-central-api-history-uploads (pull request #169) Fix job splitting to rewrite references in config files in addition to command-line. Affected #: 1 file diff -r a3f91ab1dc83c242ef284627df58f19ee95c0b12 -r f3e6cf36517e7db7b507fc1b15af7a43ad4a84f5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1573,6 +1573,12 @@ self.sa_session.flush() # Build any required config files config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + for config_filename in config_filenames: + config_contents = open(config_filename, "r").read() + for k, v in fnames.iteritems(): + config_contents = config_contents.replace(k, v) + open(config_filename, "w").write(config_contents) + # FIXME: Build the param file (might return None, DEPRECATED) param_filename = self.tool.build_param_file( param_dict, self.working_directory ) # Build the job's command line 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: Merge
by commits-noreply＠bitbucket.org 28 May '13

28 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3f91ab1dc83/ Changeset: a3f91ab1dc83 User: dannon Date: 2013-05-28 20:30:49 Summary: Merge 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: jmchilton: Fix API uploads (must have broken with API/Web transaction unification).
by commits-noreply＠bitbucket.org 28 May '13

28 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/69f70d84619d/ Changeset: 69f70d84619d Branch: next-stable User: jmchilton Date: 2013-05-26 22:10:43 Summary: Fix API uploads (must have broken with API/Web transaction unification). Affected #: 3 files diff -r 4df405e7a2aff50c4ef83806c55d01448227cc5d -r 69f70d84619de8024e8de7ef5669bda6dfaffce8 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py +++ b/lib/galaxy/tools/actions/upload.py @@ -16,7 +16,7 @@ incoming = upload_common.persist_uploads( incoming ) # We can pass an empty string as the cntrller here since it is used to check whether we # are in an admin view, and this tool is currently not used there. - uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs ) + uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if not uploaded_datasets: @@ -24,4 +24,4 @@ json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] - return upload_common.create_job( trans, incoming, tool, json_file_path, data_list ) + return upload_common.create_job( trans, incoming, tool, json_file_path, data_list, history=history ) diff -r 4df405e7a2aff50c4ef83806c55d01448227cc5d -r 69f70d84619de8024e8de7ef5669bda6dfaffce8 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -107,11 +107,13 @@ data.state = data.states.ERROR data.info = 'No file contents were available.' -def new_history_upload( trans, uploaded_dataset, state=None ): +def __new_history_upload( trans, uploaded_dataset, history=None, state=None ): + if not history: + history = trans.history hda = trans.app.model.HistoryDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type, dbkey = uploaded_dataset.dbkey, - history = trans.history, + history = history, create_dataset = True, sa_session = trans.sa_session ) if state: @@ -120,12 +122,13 @@ hda.state = hda.states.QUEUED trans.sa_session.add( hda ) trans.sa_session.flush() - trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) - permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) + history.add_dataset( hda, genome_build=uploaded_dataset.dbkey ) + permissions = trans.app.security_agent.history_get_default_permissions( history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) trans.sa_session.flush() return hda -def new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state=None ): + +def __new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state=None ): current_user_roles = trans.get_current_user_roles() if not ( ( trans.user_is_admin() and cntrller in [ 'library_admin', 'api' ] ) or trans.app.security_agent.can_add_library_item( current_user_roles, library_bunch.folder ) ): # This doesn't have to be pretty - the only time this should happen is if someone's being malicious. @@ -206,19 +209,22 @@ trans.sa_session.add( dp ) trans.sa_session.flush() return ldda -def new_upload( trans, cntrller, uploaded_dataset, library_bunch=None, state=None ): +def new_upload( trans, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None ): if library_bunch: - return new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state ) + return __new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state ) + elif history: + return __new_history_upload( trans, uploaded_dataset, history=history, state=state ) else: - return new_history_upload( trans, uploaded_dataset, state ) -def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset_upload_inputs, library_bunch=None ): + raise Exception("new_upload must be called with empty values for library_bunch and history") + +def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset_upload_inputs, library_bunch=None, history=None ): uploaded_datasets = [] for dataset_upload_input in dataset_upload_inputs: uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) for uploaded_dataset in uploaded_datasets: data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name ) if not data: - data = new_upload( trans, cntrller, uploaded_dataset, library_bunch ) + data = new_upload( trans, cntrller, uploaded_dataset, library_bunch=library_bunch, history=history ) else: data.extension = uploaded_dataset.file_type data.dbkey = uploaded_dataset.dbkey @@ -246,7 +252,9 @@ trans.sa_session.add( info_association ) trans.sa_session.flush() else: - trans.history.genome_build = uploaded_dataset.dbkey + if not history: + history = trans.history + history.genome_build = uploaded_dataset.dbkey uploaded_dataset.data = data return uploaded_datasets def create_paramfile( trans, uploaded_datasets ): @@ -320,7 +328,7 @@ if trans.app.config.external_chown_script: _chown( json_file_path ) return json_file_path -def create_job( trans, params, tool, json_file_path, data_list, folder=None ): +def create_job( trans, params, tool, json_file_path, data_list, folder=None, history=None ): """ Create the upload job. """ @@ -333,7 +341,9 @@ if folder: job.library_folder_id = folder.id else: - job.history_id = trans.history.id + if not history: + history = trans.history + job.history_id = history.id job.tool_id = tool.id job.tool_version = tool.version job.state = job.states.UPLOAD diff -r 4df405e7a2aff50c4ef83806c55d01448227cc5d -r 69f70d84619de8024e8de7ef5669bda6dfaffce8 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -78,7 +78,6 @@ if history_id: target_history = trans.sa_session.query(trans.app.model.History).get( trans.security.decode_id(history_id)) - trans.galaxy_session.current_history = target_history else: target_history = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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