galaxy-dev December 2008

galaxy-dev@lists.galaxyproject.org

6 participants
55 discussions

[hg] galaxy 1681: Yet another fix for the deleted histories report.
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d38b593a27b4 changeset: 1681:d38b593a27b4 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 11:05:54 2008 -0500 description: Yet another fix for the deleted histories report. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (12 lines): diff -r e7c679451988 -r d38b593a27b4 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 10:55:42 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 11:05:54 2008 -0500 @@ -93,7 +93,7 @@ if not hda.dataset.purged: dataset_count += 1 try: - disk_space += dataset.file_size + disk_space += hda.dataset.file_size except: pass history_count += 1

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[hg] galaxy 1680: Fix for deleted histories report in the system...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/e7c679451988 changeset: 1680:e7c679451988 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 10:55:42 2008 -0500 description: Fix for deleted histories report in the system controller. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (14 lines): diff -r 48f3b242c75e -r e7c679451988 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 09:53:32 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 10:55:42 2008 -0500 @@ -89,8 +89,8 @@ histories = h.query().filter( where ).options( eagerload( 'datasets' ) ) for history in histories: - for dataset in history.datasets: - if not dataset.purged: + for hda in history.datasets: + if not hda.dataset.purged: dataset_count += 1 try: disk_space += dataset.file_size

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[hg] galaxy 1679: Add security to reports app, fixes reports.
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/48f3b242c75e changeset: 1679:48f3b242c75e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 09:53:32 2008 -0500 description: Add security to reports app, fixes reports. 1 file(s) affected in this change: lib/galaxy/webapps/reports/app.py diffs (18 lines): diff -r c0efda325046 -r 48f3b242c75e lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py Thu Dec 18 16:35:26 2008 -0500 +++ b/lib/galaxy/webapps/reports/app.py Fri Dec 19 09:53:32 2008 -0500 @@ -1,5 +1,6 @@ import sys, config import galaxy.model +from galaxy.web import security class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -19,5 +20,7 @@ db_url, self.config.database_engine_options, create_tables = True ) + # Security helper + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) def shutdown( self ): pass

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[hg] galaxy 1677: Pass in a session cookie name when building th...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d86bacb600db changeset: 1677:d86bacb600db user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Dec 18 09:32:43 2008 -0500 description: Pass in a session cookie name when building the app - this enables the Galaxy session to use a different cookie from the Galaxy reports session. Also add exception handling to decoding the session key so server errors won't result from attempting to retrieve an invalid session key from the db. 3 file(s) affected in this change: lib/galaxy/web/buildapp.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/buildapp.py diffs (160 lines): diff -r b83da0b74595 -r d86bacb600db lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/web/buildapp.py Thu Dec 18 09:32:43 2008 -0500 @@ -55,7 +55,7 @@ app = UniverseApplication( global_conf = global_conf, **kwargs ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.web.framework.WebApplication( app ) + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) add_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) diff -r b83da0b74595 -r d86bacb600db lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Dec 18 09:32:43 2008 -0500 @@ -77,9 +77,9 @@ return FormBuilder( *args, **kwargs ) class WebApplication( base.WebApplication ): - def __init__( self, galaxy_app ): + def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) - self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self ) ) + self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) # Mako support self.mako_template_lookup = mako.lookup.TemplateLookup( directories = [ galaxy_app.config.template_path ] , @@ -101,7 +101,7 @@ Encapsulates web transaction specific state for the Universe application (specifically the user's "cookie" session and history) """ - def __init__( self, environ, app, webapp ): + def __init__( self, environ, app, webapp, session_cookie ): self.app = app self.webapp = webapp self.security = webapp.security @@ -118,7 +118,7 @@ # and such). self.workflow_building_mode = False # Always have a valid galaxy session - self.__ensure_valid_session() + self.__ensure_valid_session( session_cookie ) @property def sa_session( self ): """ @@ -148,7 +148,7 @@ event.session_id = self.galaxy_session.id event.flush() def get_cookie( self, name='galaxysession' ): - """Convienience method for getting the galaxysession cookie""" + """Convenience method for getting a session cookie""" try: # If we've changed the cookie during the request return the new value if name in self.response.cookies: @@ -158,7 +158,7 @@ except: return None def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): - """Convienience method for setting the galaxysession cookie""" + """Convenience method for setting a session cookie""" # The galaxysession cookie value must be a high entropy 128 bit random number encrypted # using a server secret key. Any other value is invalid and could pose security issues. self.response.cookies[name] = value @@ -172,7 +172,7 @@ # if not self.__galaxy_session: # self.__ensure_valid_session() # return self.__galaxy_session - def __ensure_valid_session( self ): + def __ensure_valid_session( self, session_cookie ): """ Ensure that a valid Galaxy session exists and is available as trans.session (part of initialization) @@ -182,7 +182,7 @@ """ sa_session = self.sa_session # Try to load an existing session - secure_id = self.get_cookie( name='galaxysession' ) + secure_id = self.get_cookie( name=session_cookie ) galaxy_session = None prev_galaxy_session = None user_for_new_session = None @@ -193,11 +193,17 @@ if secure_id: # Decode the cookie value to get the session_key session_key = self.security.decode_session_key( secure_id ) - # Retrieve the galaxy_session id via the unique session_key - galaxy_session = self.app.model.GalaxySession.filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, - self.app.model.GalaxySession.table.c.is_valid==True ) ).first() - # If remote user is in use it can invalidate the session, so we need to - # to check some things now. + try: + # Make sure we have a valid UTF-8 string + session_key = session_key.encode( 'utf8' ) + except UnicodeDecodeError: + # We'll end up creating a new galaxy_session + session_key = None + if session_key: + # Retrieve the galaxy_session id via the unique session_key + galaxy_session = self.app.model.GalaxySession.filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, + self.app.model.GalaxySession.table.c.is_valid==True ) ).first() + # If remote user is in use it can invalidate the session, so we need to to check some things now. if self.app.config.use_remote_user: assert "HTTP_REMOTE_USER" in self.environ, \ "use_remote_user is set but no HTTP_REMOTE_USER variable" @@ -232,7 +238,7 @@ galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) galaxy_session_requires_flush = True self.galaxy_session = galaxy_session - self.__update_session_cookie() + self.__update_session_cookie( name=session_cookie ) else: self.galaxy_session = galaxy_session # Do we need to flush the session? @@ -279,11 +285,11 @@ user.external = True #self.log_event( "Automatically created account '%s'", user.email ) return user - def __update_session_cookie( self ): + def __update_session_cookie( self, name='galaxysession' ): """ - Update the 'galaxysession' cookie to match the current session. + Update the session cookie to match the current session. """ - self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name='galaxysession' ) + self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name=name ) def handle_user_login( self, user ): """ @@ -304,7 +310,8 @@ self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) else: self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) - self.__update_session_cookie() + # This method is not called from the Galaxy reports, so the cookie will always be galaxysession + self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): """ Logout the current user: @@ -315,7 +322,8 @@ prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session, None ) self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) - self.__update_session_cookie() + # This method is not called from the Galaxy reports, so the cookie will always be galaxysession + self.__update_session_cookie( name='galaxysession' ) def get_galaxy_session( self ): """ diff -r b83da0b74595 -r d86bacb600db lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/webapps/reports/buildapp.py Thu Dec 18 09:32:43 2008 -0500 @@ -52,7 +52,7 @@ app = UniverseApplication( global_conf = global_conf, **kwargs ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.web.framework.WebApplication( app ) + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxyreportssession' ) add_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/:controller/:action', controller="root", action='index' )

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[hg] galaxy 1678: Enhance the tool panel, now supports following...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c0efda325046 changeset: 1678:c0efda325046 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Dec 18 16:35:26 2008 -0500 description: Enhance the tool panel, now supports following tags: <toolbox> <tool file="data_source/upload.xml"/> # tools outside sections <label text="Basic Tools" id="basic_tools" /> # labels outside sections <workflow id="529fd61ab1c6cc36" /> # workflows outside sections <section name="Get Data" id="getext"> # sections <tool file="data_source/biomart.xml" /> # tools inside sections <label text="In Section" id="in_section" /> # labels inside sections <workflow id="adb5f5c93f827949" /> # workflows inside sections </section> </toolbox> 16 file(s) affected in this change: lib/galaxy/app.py lib/galaxy/config.py lib/galaxy/tools/__init__.py lib/galaxy/web/controllers/workflow.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/config.py reports_wsgi.ini.sample static/june_2007_style/blue/tool_menu.css static/june_2007_style/make_style.py static/june_2007_style/tool_menu.css.tmpl templates/admin_main.mako templates/root/tool_menu.mako templates/workflow/editor.mako test/functional/test_toolbox.py tool_conf.xml.sample universe_wsgi.ini.sample diffs (891 lines): diff -r d86bacb600db -r c0efda325046 lib/galaxy/app.py --- a/lib/galaxy/app.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/app.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,6 +1,7 @@ import sys, os, atexit from galaxy import config, jobs, util, tools, web +from galaxy.web import security import galaxy.model import galaxy.model.mapping import galaxy.datatypes.registry @@ -26,6 +27,8 @@ db_url, self.config.database_engine_options, create_tables = True ) + # Security helper + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Initialize the tools self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self ) #Load datatype converters diff -r d86bacb600db -r c0efda325046 lib/galaxy/config.py --- a/lib/galaxy/config.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/config.py Thu Dec 18 16:35:26 2008 -0500 @@ -35,9 +35,6 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) - # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini - # or the framework's __ensure_valid_session method will throw exceptions when switching between - # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) diff -r d86bacb600db -r c0efda325046 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Dec 18 16:35:26 2008 -0500 @@ -42,8 +42,8 @@ individual tool config files. """ self.tools_by_id = {} - self.tools_and_sections_by_id = {} - self.sections = [] + self.workflows_by_id = {} + self.tool_panel = odict() self.tool_root_dir = tool_root_dir self.app = app try: @@ -54,24 +54,68 @@ def init_tools( self, config_filename ): """ Read the configuration file and load each tool. + The following tags are currently supported: + <toolbox> + <tool file="data_source/upload.xml"/> # tools outside sections + <label text="Basic Tools" id="basic_tools" /> # labels outside sections + <workflow id="529fd61ab1c6cc36" /> # workflows outside sections + <section name="Get Data" id="getext"> # sections + <tool file="data_source/biomart.xml" /> # tools inside sections + <label text="In Section" id="in_section" /> # labels inside sections + <workflow id="adb5f5c93f827949" /> # workflows inside sections + </section> + </toolbox> """ + def load_tool( elem, panel_dict ): + try: + path = elem.get( "file" ) + tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) + self.tools_by_id[ tool.id ] = tool + key = 'tool_' + tool.id + panel_dict[ key ] = tool + log.debug( "Loaded tool: %s %s" % ( tool.id, tool.version ) ) + except: + log.exception( "error reading tool from path: %s" % path ) + def load_workflow( elem, panel_dict ): + try: + # TODO: should id be encoded? + workflow_id = elem.get( 'id' ) + workflow = self.load_workflow( workflow_id ) + self.workflows_by_id[ workflow_id ] = workflow + key = 'workflow_' + workflow_id + panel_dict[ key ] = workflow + log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) + except: + log.exception( "error loading workflow: %s" % workflow_id ) + def load_label( elem, panel_dict ): + label = ToolSectionLabel( elem ) + key = 'label_' + label.id + panel_dict[ key ] = label + def load_section( elem, panel_dict ): + section = ToolSection( elem ) + log.debug( "Loading section: %s" % section.name ) + for section_elem in elem: + if section_elem.tag == 'tool': + load_tool( section_elem, section.elems ) + elif section_elem.tag == 'workflow': + load_workflow( section_elem, section.elems ) + elif section_elem.tag == 'label': + load_label( section_elem, section.elems ) + key = 'section_' + section.id + panel_dict[ key ] = section + log.info("parsing the tool configuration") tree = util.parse_xml( config_filename ) root = tree.getroot() - for elem in root.findall("section"): - section = ToolSection(elem) - log.debug( "Loading tools in section: %s" % section.name ) - for tool in elem.findall("tool"): - try: - path = tool.get("file") - tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) - log.debug( "Loaded tool: %s %s" %( tool.id, tool.version ) ) - self.tools_by_id[tool.id] = tool - self.tools_and_sections_by_id[tool.id] = tool, section - section.tools.append(tool) - except Exception, exc: - log.exception( "error reading tool from path: %s" % path ) - self.sections.append(section) + for elem in root: + if elem.tag == 'tool': + load_tool( elem, self.tool_panel ) + elif elem.tag == 'workflow': + load_workflow( elem, self.tool_panel ) + elif elem.tag == 'section' : + load_section( elem, self.tool_panel ) + elif elem.tag == 'label': + load_label( elem, self.tool_panel ) def load_tool( self, config_file ): """ @@ -94,28 +138,36 @@ def reload( self, tool_id ): """ - Attempt to reload the tool identified by 'tool_id', if successfull + Attempt to reload the tool identified by 'tool_id', if successful replace the old tool. """ - if tool_id not in self.tools_and_sections_by_id: + if tool_id not in self.tools_by_id: raise ToolNotFoundException( "No tool with id %s" % tool_id ) - old_tool, section = self.tools_and_sections_by_id[ tool_id ] + old_tool = self.tools_by_id[ tool_id ] new_tool = self.load_tool( old_tool.config_file ) + # Replace old_tool with new_tool in self.tool_panel + tool_key = 'tool_' + tool_id + for key, val in self.tool_panel.items(): + if key == tool_key: + self.tool_panel[ key ] = new_tool + break + elif key.startswith( 'section' ): + section = val + for section_key, section_val in section.elems.items(): + if section_key == tool_key: + self.tool_panel[ key ].elems[ section_key ] = new_tool + break + self.tools_by_id[ tool_id ] = new_tool log.debug( "Reloaded tool %s %s" %( old_tool.id, old_tool.version ) ) - # Is there a potential sync problem here? This should be roughly - # atomic. Too many indexes for tools... - section.tools[ section.tools.index( old_tool ) ] = new_tool - self.tools_by_id[ tool_id ] = new_tool - self.tools_and_sections_by_id[ tool_id ] = new_tool, section - - def itertools( self ): + + def load_workflow( self, workflow_id ): """ - Iterate over all the tools in the toolbox (ordered by section but - without grouping). + Return an instance of 'Workflow' identified by `id`, + which is encoded in the tool panel. """ - for section in self.sections: - for tool in section.tools: - yield tool + id = self.app.security.decode_id( workflow_id ) + stored = self.app.model.StoredWorkflow.get( id ) + return stored.latest_workflow class ToolSection( object ): """ @@ -126,7 +178,17 @@ self.name = elem.get( "name" ) self.id = elem.get( "id" ) self.version = elem.get( "version" ) - self.tools = [] + self.elems = odict() + +class ToolSectionLabel( object ): + """ + A label for a set of tools that can be displayed above groups of tools + and sections in the user interface + """ + def __init__( self, elem ): + self.text = elem.get( "text" ) + self.id = elem.get( "id" ) + self.version = elem.get( "version" ) class DefaultToolState( object ): """ diff -r d86bacb600db -r c0efda325046 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Thu Dec 18 16:35:26 2008 -0500 @@ -439,13 +439,14 @@ ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose - def run( self, trans, id, **kwargs ): + def run( self, trans, id, check_user=True, **kwargs ): stored = get_stored_workflow( trans, id, check_ownership=False ) - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + if check_user: + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps diff -r d86bacb600db -r c0efda325046 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Dec 18 16:35:26 2008 -0500 @@ -86,8 +86,7 @@ module_directory = galaxy_app.config.template_cache, collection_size = 500 ) # Security helper - from galaxy.web import security - self.security = security.SecurityHelper( id_secret = galaxy_app.config.id_secret ) + self.security = galaxy_app.security def handle_controller_exception( self, e, trans, **kwargs ): if isinstance( e, MessageException ): return trans.show_message( e.message, e.type ) diff -r d86bacb600db -r c0efda325046 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/webapps/reports/config.py Thu Dec 18 16:35:26 2008 -0500 @@ -25,9 +25,6 @@ # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) - # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini - # or the framework's __ensure_valid_session method will throw exceptions when switching between - # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) diff -r d86bacb600db -r c0efda325046 reports_wsgi.ini.sample --- a/reports_wsgi.ini.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/reports_wsgi.ini.sample Thu Dec 18 16:35:26 2008 -0500 @@ -37,7 +37,6 @@ session_secret = changethisinproduction # Galaxy session security -# The value of id_secret MUST be the same as the value of id_secret in universe_wsgi.ini id_secret = changethisinproductiontoo # Configuration for debugging middleware diff -r d86bacb600db -r c0efda325046 static/june_2007_style/blue/tool_menu.css --- a/static/june_2007_style/blue/tool_menu.css Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/blue/tool_menu.css Thu Dec 18 16:35:26 2008 -0500 @@ -35,6 +35,13 @@ font-weight: bold; } +div.toolPanelLabel +{ + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; +} + div.toolTitle { padding-top: 5px; @@ -44,3 +51,10 @@ display: list-item; list-style: square outside; } + + +div.toolTitleNoSection +{ + padding-bottom: 0px; + font-weight: bold; +} diff -r d86bacb600db -r c0efda325046 static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/make_style.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,12 +1,17 @@ #!/usr/bin/env python -import sys +import sys, string, os.path +from galaxy import eggs +import pkg_resources +pkg_resources.require( "Cheetah" ) + from Cheetah.Template import Template -import string from subprocess import Popen, PIPE -import os.path assert sys.version_info[:2] >= ( 2, 4 ) + +# To create a new style ( this is an example ): +# python make_style.py blue_colors.ini blue def run( cmd ): return Popen( cmd, stdout=PIPE).communicate()[0] diff -r d86bacb600db -r c0efda325046 static/june_2007_style/tool_menu.css.tmpl --- a/static/june_2007_style/tool_menu.css.tmpl Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/tool_menu.css.tmpl Thu Dec 18 16:35:26 2008 -0500 @@ -35,6 +35,13 @@ font-weight: bold; } +div.toolPanelLabel +{ + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; +} + div.toolTitle { padding-top: 5px; @@ -44,3 +51,10 @@ display: list-item; list-style: square outside; } + + +div.toolTitleNoSection +{ + padding-bottom: 0px; + font-weight: bold; +} diff -r d86bacb600db -r c0efda325046 templates/admin_main.mako --- a/templates/admin_main.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/admin_main.mako Thu Dec 18 16:35:26 2008 -0500 @@ -2,32 +2,38 @@ <%def name="title()">Galaxy Administration</%def> <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> - <tr> - <td> - <h3 align="center">Galaxy Administration</h3> - %if msg: - <p class="ok_bgr">${msg}</p> - %endif - </td> - </tr> - <tr> - <td> - <form method="post" action="admin"> - <p>Admin password: <input type="password" name="passwd" size="8"></p> - <p> - Reload tool: - <select name="tool_id"> - %for i, section in enumerate( toolbox.sections ): - <optgroup label="${section.name}"> - %for t in section.tools: - <option value="${t.id}">${t.name}</option> - %endfor - %endfor - </select> - <button name="action" value="tool_reload">Reload</button> - </p> - </form> - </td> - </tr> + <tr> + <td> + <h3 align="center">Galaxy Administration</h3> + %if msg: + <p class="ok_bgr">${msg}</p> + %endif + </td> + </tr> + <tr> + <td> + <form method="post" action="admin"> + <p>Admin password: <input type="password" name="passwd" size="8"></p> + <p> + Reload tool: + <select name="tool_id"> + %for key, val in toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + <option value="${val.id}">${val.name}</option> + %elif key.startswith( 'section' ): + <optgroup label="${val.name}"> + <% section = val %> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + <option value="${section_val.id}">${section_val.name}</option> + %endif + %endfor + %endif + %endfor + </select> + <button name="action" value="tool_reload">Reload</button> + </p> + </form> + </td> + </tr> </table> - diff -r d86bacb600db -r c0efda325046 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/root/tool_menu.mako Thu Dec 18 16:35:26 2008 -0500 @@ -1,113 +1,148 @@ +## Render a tool +<%def name="render_tool( tool, section )"> + %if not tool.hidden: + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + <% + if tool.input_required: + link = h.url_for( controller='tool_runner', tool_id=tool.id ) + else: + link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) + %> + ## FIXME: This doesn't look right + ## %if "[[" in tool.description and "]]" in tool.description: + ## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" ) + %if tool.name: + <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.name}</a> ${tool.description} + %else: + <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a> + %endif + </div> + %endif +</%def> + +## Render a workflow +<%def name="render_workflow( key, workflow, section )"> + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + <% encoded_id = key.lstrip( 'workflow_' ) %> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="galaxy_main"}">${workflow.name}</a> + </div> +</%def> + +## Render a label +<%def name="render_label( label )"> + <div class="toolSectionPad"></div> + <div class="toolPanelLabel" id="title_${label.id}"> + <span>${label.text}</span> + </div> + <div class="toolSectionPad"></div> +</%def> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> + <head> + <title>Galaxy Tools</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /> -<head> -<title>Galaxy Tools</title> -<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /> + <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> -<script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> + <script type="text/javascript"> + var q = jQuery.noConflict(); + q(document).ready(function() { + q( "div.toolSectionBody" ).hide(); + q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) + var last_expanded = null; + q( "div.toolSectionTitle" ).each( function() { + var body = q(this).next( "div.toolSectionBody" ); + q(this).click( function() { + if ( body.is( ":hidden" ) ) { + if ( last_expanded ) last_expanded.slideUp( "fast" ); + last_expanded = body; + body.slideDown( "fast" ); + } + else { + body.slideUp( "fast" ); + last_expanded = null; + } + return false; + }); + }); + q( "a[@minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) ); + } + }); + }); + </script> + </head> -<script type="text/javascript"> - var q = jQuery.noConflict(); - q(document).ready(function() { - q( "div.toolSectionBody" ).hide(); - q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) - var last_expanded = null; - q( "div.toolSectionTitle" ).each( function() { - var body = q(this).next( "div.toolSectionBody" ); - q(this).click( function() { - if ( body.is( ":hidden" ) ) { - if ( last_expanded ) last_expanded.slideUp( "fast" ); - last_expanded = body; - body.slideDown( "fast" ); - } - else { - body.slideUp( "fast" ); - last_expanded = null; - } - return false; - }); - }); - q( "a[@minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) ); - } - }); - }); -</script> + <body class="toolMenuPage"> + <div class="toolMenu"> + <div class="toolSectionList"> + %for key, val in toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + ${render_tool( val, False )} + <div class="toolSectionPad"></div> + %elif key.startswith( 'workflow' ): + ${render_workflow( key, val, False )} + %elif key.startswith( 'section' ): + <% section = val %> + <div class="toolSectionTitle" id="title_${section.id}"> + <span>${section.name}</span> + </div> + <div id="${section.id}" class="toolSectionBody"> + <div class="toolSectionBg"> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + ${render_tool( section_val, True )} + %elif section_key.startswith( 'workflow' ): + ${render_workflow( section_key, section_val, True )} + %elif section_key.startswith( 'label' ): + ${render_label( section_val )} + %endif + %endfor + </div> + </div> + <div class="toolSectionPad"></div> + %elif key.startswith( 'label' ): + ${render_label( val )} + %endif + %endfor -</head> + ## Link to workflow management. The location of this may change, but eventually + ## at least some workflows will appear here (the user should be able to + ## configure which of their stored workflows appear in the tools menu). -<body class="toolMenuPage"> - -<div class="toolMenu"> - -<div class="toolSectionList"> -%for i, section in enumerate( toolbox.sections ): - %if i > 0: - <div class="toolSectionPad"></div> - %endif - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for tool in section.tools: - %if not tool.hidden: - <div class="toolTitle"> - <% - if tool.input_required: - link = h.url_for( controller='tool_runner', tool_id=tool.id ) - else: - link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) - %> - ## FIXME: This doesn't look right - ## %if "[[" in tool.description and "]]" in tool.description: - ## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" ) - %if tool.name: - <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.name}</a> ${tool.description} - %else: - <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a> - %endif + <div class="toolSectionPad"></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle" id="title_XXinternalXXworkflow"> + <span>Workflow <i>(beta)</i></span> + </div> + <div id="XXinternalXXworkflow" class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows + </div> + %if t.user: + %for m in t.user.stored_workflow_menu_entries: + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + </div> + %endfor + %endif + </div> + </div> </div> - %endif - %endfor - </div> - </div> -%endfor - -## Link to workflow management. The location of this may change, but eventually -## at least some workflows will appear here (the user should be able to -## configure which of their stored workflows appear in the tools menu). - -<div class="toolSectionPad"></div> -<div class="toolSectionPad"></div> -<div class="toolSectionTitle" id="title_XXinternalXXworkflow"> - <span>Workflow <i>(beta)</i></span> -</div> -<div id="XXinternalXXworkflow" class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows </div> - %if t.user: - %for m in t.user.stored_workflow_menu_entries: - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> - </div> - %endfor - %endif - </div> -</div> - -</div> - -</div> - -<div style="height: 20px"></div> - -</body> - -</html> \ No newline at end of file + <div style="height: 20px"></div> + </body> +</html> diff -r d86bacb600db -r c0efda325046 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/workflow/editor.mako Thu Dec 18 16:35:26 2008 -0500 @@ -344,6 +344,11 @@ padding-bottom: 0px; font-weight: bold; } + div.toolPanelLabel { + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; + } div.toolMenuGroupHeader { font-weight: bold; padding-top: 0.5em; @@ -353,7 +358,6 @@ border-bottom: dotted #333 1px; margin-bottom: 0.5em; } - div.toolTitle { padding-top: 5px; padding-bottom: 5px; @@ -361,6 +365,10 @@ margin-right: 10px; display: list-item; list-style: square outside; + } + div.toolTitleNoSection { + padding-bottom: 0px; + font-weight: bold; } div.toolTitleDisabled { padding-top: 5px; @@ -371,6 +379,11 @@ list-style: square outside; font-style: italic; color: gray; + } + div.toolTitleNoSectionDisabled { + padding-bottom: 0px; + font-style: italic; + color: gray; } div.toolFormRow { position: relative; @@ -467,6 +480,50 @@ </style> </%def> +## Render a tool in the tool panel +<%def name="render_tool( tool, section )"> + %if not tool.hidden: + %if tool.is_workflow_compatible: + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + %if "[[" in tool.description and "]]" in tool.description: + ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} + %elif tool.name: + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} + %else: + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + %endif + </div> + %else: + %if section: + <div class="toolTitleDisabled"> + %else: + <div class="toolTitleNoSectionDisabled"> + %endif + %if "[[" in tool.description and "]]" in tool.description: + ${tool.description.replace( '[[', '' % tool.id ).replace( "]]", "" )} + %elif tool.name: + ${tool.name} ${tool.description} + %else: + ${tool.description} + %endif + </div> + %endif + %endif +</%def> + +## Render a label in the tool panel +<%def name="render_label( label )"> + <div class="toolSectionPad"></div> + <div class="toolPanelLabel" id="title_${label.id}"> + <span>${label.text}</span> + </div> + <div class="toolSectionPad"></div> +</%def> + <div id="overlay"> ## Need a table here for centering in IE6 <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"><tr><td> @@ -501,43 +558,30 @@ <div class="unified-panel-body" style="overflow: auto;"> <div class="toolMenu"> <div class="toolSectionList"> - %for i, section in enumerate( app.toolbox.sections ): - %if i > 0: - <div class="toolSectionPad"></div> - %endif - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for tool in section.tools: - %if not tool.hidden: - %if tool.is_workflow_compatible: - <div class="toolTitle "> - %if "[[" in tool.description and "]]" in tool.description: - ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} - %elif tool.name: - <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} - %else: - <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + %for key, val in app.toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + ${render_tool( val, False )} + %elif key.startswith( 'section' ): + <% section = val %> + <div class="toolSectionTitle" id="title_${section.id}"> + <span>${section.name}</span> + </div> + <div id="${section.id}" class="toolSectionBody"> + <div class="toolSectionBg"> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + ${render_tool( section_val, True )} + %elif section_key.startswith( 'label' ): + ${render_label( section_val )} %endif - </div> - %else: - <div class="toolTitleDisabled"> - %if "[[" in tool.description and "]]" in tool.description: - ${tool.description.replace( '[[', '' % tool.id ).replace( "]]", "" )} - %elif tool.name: - ${tool.name} ${tool.description} - %else: - ${tool.description} - %endif - </div> - %endif - %endif - %endfor - </div> - </div> - %endfor + %endfor + </div> + </div> + <div class="toolSectionPad"></div> + %elif key.startswith( 'label' ): + ${render_label( val )} + %endif + %endfor </div> <div> </div> <div class="toolMenuGroupHeader">Workflow control</div> diff -r d86bacb600db -r c0efda325046 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Thu Dec 18 09:32:43 2008 -0500 +++ b/test/functional/test_toolbox.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,5 +1,4 @@ -import sys -import new +import sys, new from galaxy.tools.parameters import grouping from galaxy.tools.parameters import basic from base.twilltestcase import TwillTestCase @@ -9,6 +8,7 @@ class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" def do_it( self ): + print "###self.testdef: ", self.testdef # If the test generation had an error, raise if self.testdef.error: if self.testdef.exception: @@ -126,10 +126,10 @@ return # Push all the toolbox tests to module level G = globals() - for i, section in enumerate( toolbox.sections ): - for j, tool in enumerate( section.tools ): - if tool.tests: - for k, testdef in enumerate( tool.tests ): - name = "%s > %s > %s" % ( section.name, tool.name, testdef.name ) - testcase = get_testcase( testdef, name ) - G[ 'testcase_%d_%d_%d' % ( i, j, k ) ] = testcase + for i, tool_id in enumerate( toolbox.tools_by_id ): + tool = toolbox.tools_by_id[ tool_id ] + if tool.tests: + for j, testdef in enumerate( tool.tests ): + name = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) + testcase = get_testcase( testdef, name ) + G[ 'testcase_%d_%d' % ( i, j ) ] = testcase diff -r d86bacb600db -r c0efda325046 tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/tool_conf.xml.sample Thu Dec 18 16:35:26 2008 -0500 @@ -2,7 +2,6 @@ <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> - <tool file="data_source/access_libraries.xml" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> diff -r d86bacb600db -r c0efda325046 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/universe_wsgi.ini.sample Thu Dec 18 16:35:26 2008 -0500 @@ -73,7 +73,6 @@ session_secret = changethisinproduction # Galaxy session security -# The value of id_secret MUST be the same as the value of id_secret in reports_wsgi.ini id_secret = changethisinproductiontoo # Use user provided in an upstream server's $REMOTE_USER variable

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[hg] galaxy 1674: Enhancing incorrect_Gops_job script to output ...
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/006bfb42e335 changeset: 1674:006bfb42e335 user: guru date: Wed Dec 17 11:01:57 2008 -0500 description: Enhancing incorrect_Gops_job script to output only those jobs whose output has changed since the BitSetSafeReaderWrapper was fixed. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (45 lines): diff -r f61f2128c692 -r 006bfb42e335 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Tue Dec 16 17:30:19 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:01:57 2008 -0500 @@ -5,7 +5,7 @@ """ from galaxy import eggs -import sys, os, ConfigParser +import sys, os, ConfigParser, tempfile import galaxy.app import galaxy.model.mapping import pkg_resources @@ -62,6 +62,23 @@ history = app.model.History.get( hda.history_id ) print "# ------> processing history id %s" % str( history.id ) if history.user_id: + cmd_line = str( job.command_line ) + new_output = tempfile.NamedTemporaryFile('w') + if (sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1' + ) + ): + new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:])) + job_output = cmd_line.split()[4] + else: + new_cmd_line = " ".join(map(str,cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[4:])) + job_output = cmd_line.split()[3] + os.system(new_cmd_line) + diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output)) + if diff_status == 0: + continue + print "# --------> Outputs differ" user = app.model.User.get( history.user_id ) jobs[ job.id ] = {} jobs[ job.id ][ 'hda_id' ] = hda.id @@ -77,7 +94,7 @@ print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" for jid in jobs: - print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ + print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \ ( str( jid ), str( jobs[ jid ][ 'hda_id' ] ), jobs[ jid ][ 'hda_name' ],

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[hg] galaxy 1675: Fix for a minor bug in my previous commit.
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3a9c9da987a2 changeset: 1675:3a9c9da987a2 user: guru date: Wed Dec 17 11:25:35 2008 -0500 description: Fix for a minor bug in my previous commit. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (16 lines): diff -r 006bfb42e335 -r 3a9c9da987a2 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:01:57 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:25:35 2008 -0500 @@ -64,11 +64,7 @@ if history.user_id: cmd_line = str( job.command_line ) new_output = tempfile.NamedTemporaryFile('w') - if (sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', - app.model.Job.table.c.tool_id == 'gops_subtract_1', - app.model.Job.table.c.tool_id == 'gops_coverage_1' - ) - ): + if job.tool_id in ['gops_intersect_1','gops_subtract_1','gops_coverage_1']: new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:])) job_output = cmd_line.split()[4] else:

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[hg] galaxy 1676: speed enhancement for incorrect_gops_jobs script.
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b83da0b74595 changeset: 1676:b83da0b74595 user: guru date: Wed Dec 17 12:13:38 2008 -0500 description: speed enhancement for incorrect_gops_jobs script. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (30 lines): diff -r 3a9c9da987a2 -r b83da0b74595 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:25:35 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 12:13:38 2008 -0500 @@ -42,13 +42,19 @@ try: for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time.between( '2008-05-23', '2008-11-29' ), app.model.Job.table.c.state == 'ok', - sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', - app.model.Job.table.c.tool_id == 'gops_subtract_1', - app.model.Job.table.c.tool_id == 'gops_merge_1', - app.model.Job.table.c.tool_id == 'gops_coverage_1', - app.model.Job.table.c.tool_id == 'gops_complement_1', - ), - sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) ) + sa.or_( + sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1', + ), + sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) ) + ), + sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_complement_1', + app.model.Job.table.c.tool_id == 'gops_merge_1', + ), + sa.not_( app.model.Job.table.c.command_line.like( '%-1 1,2,3%' ) ) + ) + ) ) ).all(): print "# processing job id %s" % str( job.id )

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[hg] galaxy 1673: Allow workflows to recognize "data_meta" filte...
by Greg Von Kuster 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f61f2128c692 changeset: 1673:f61f2128c692 user: James Taylor <james(a)jamestaylor.org> date: Tue Dec 16 17:30:19 2008 -0500 description: Allow workflows to recognize "data_meta" filters in dynamic options as forcing runtime validation. 2 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py lib/galaxy/tools/parameters/dynamic_options.py diffs (59 lines): diff -r 79d9195e5899 -r f61f2128c692 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Dec 16 14:31:00 2008 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Tue Dec 16 17:30:19 2008 -0500 @@ -495,7 +495,7 @@ # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. if self.is_dynamic and trans.workflow_building_mode \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): assert isinstance( value, UnvalidatedValue ) value = value.value if self.multiple: @@ -519,7 +519,7 @@ # HACK: trans may be None here if doing late validation, this is # treated the same as not being in workflow mode if self.is_dynamic and ( trans and trans.workflow_building_mode ) \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): if self.multiple: value = value.split( "\n" ) return UnvalidatedValue( value ) @@ -560,7 +560,7 @@ def get_initial_value( self, trans, context ): # More working around dynamic options for workflow if self.is_dynamic and trans.workflow_building_mode \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): # Really the best we can do? return UnvalidatedValue( None ) options = list( self.get_options( trans, context ) ) diff -r 79d9195e5899 -r f61f2128c692 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Tue Dec 16 14:31:00 2008 -0500 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Tue Dec 16 17:30:19 2008 -0500 @@ -78,6 +78,7 @@ Filter.__init__( self, d_option, elem ) self.ref_name = elem.get( "ref", None ) assert self.ref_name is not None, "Required 'ref' attribute missing from filter" + d_option.has_dataset_dependencies = True self.key = elem.get( "key", None ) assert self.key is not None, "Required 'key' attribute missing from filter" self.column = elem.get( "column", None ) @@ -290,6 +291,9 @@ self.file_fields = None self.largest_index = 0 self.dataset_ref_name = None + # True if the options generation depends on one or more other parameters + # that are dataset inputs + self.has_dataset_dependencies = False self.validators = [] self.converter_safe = True @@ -320,6 +324,7 @@ self.file_fields = self.parse_file_fields( open( data_file ) ) elif dataset_file is not None: self.dataset_ref_name = dataset_file + self.has_dataset_dependencies = True self.converter_safe = False elif from_parameter is not None: transform_lines = elem.get( 'transform_lines', None )

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[hg] galaxy 1672: Update bx-python to r459
by Nate Coraor 16 Dec '08

16 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/79d9195e5899 changeset: 1672:79d9195e5899 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Dec 16 14:31:00 2008 -0500 description: Update bx-python to r459 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 87f793e3dce5 -r 79d9195e5899 eggs.ini --- a/eggs.ini Tue Dec 16 10:04:30 2008 -0500 +++ b/eggs.ini Tue Dec 16 14:31:00 2008 -0500 @@ -55,12 +55,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r458 +bx_python = _dev_r459 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r458.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r459.tar.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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galaxy-dev December 2008