March 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Add GATK tools to tool_conf.xml.main.
by Bitbucket 16 Mar '12

16 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7bb305f17ba7/ changeset: 7bb305f17ba7 user: dan date: 2012-03-16 16:30:21 summary: Add GATK tools to tool_conf.xml.main. affected #: 1 file diff -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -390,6 +390,39 @@ <tool file="samtools/samtools_flagstat.xml" /><tool file="samtools/samtools_rmdup.xml" /></section> + <section name="NGS: GATK Tools (beta)" id="gatk"> + <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <tool file="gatk/depth_of_coverage.xml" /> + <tool file="gatk/print_reads.xml" /> + + <label text="Realignment" id="gatk_realignment" /> + <tool file="gatk/realigner_target_creator.xml" /> + <tool file="gatk/indel_realigner.xml" /> + + <label text="Base Recalibration" id="gatk_recalibration" /> + <tool file="gatk/count_covariates.xml" /> + <tool file="gatk/table_recalibration.xml" /> + <tool file="gatk/analyze_covariates.xml" /> + + <label text="Genotyping" id="gatk_genotyping" /> + <tool file="gatk/unified_genotyper.xml" /> + + <label text="Annotation" id="gatk_annotation" /> + <tool file="gatk/variant_annotator.xml" /> + + <label text="Filtration" id="gatk_filtration" /> + <tool file="gatk/variant_filtration.xml" /> + <tool file="gatk/variant_select.xml" /> + + <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <tool file="gatk/variant_recalibrator.xml" /> + <tool file="gatk/variant_apply_recalibration.xml" /> + + <label text="Variant Utilities" id="gatk_variant_utilities"/> + <tool file="gatk/variants_validate.xml" /> + <tool file="gatk/variant_eval.xml" /> + <tool file="gatk/variant_combine.xml" /> + </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> 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: natefoo: Change the hardcoding of UCSC servers to a config file option, and remove the dependence on ucsc_display_sites, so any display server can be allowed. If you've modified your remoteuser.py, beware the merge.
by Bitbucket 16 Mar '12

16 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7d021b926344/ changeset: 7d021b926344 user: natefoo date: 2012-03-16 16:16:49 summary: Change the hardcoding of UCSC servers to a config file option, and remove the dependence on ucsc_display_sites, so any display server can be allowed. If you've modified your remoteuser.py, beware the merge. affected #: 3 files diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -183,9 +183,9 @@ # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.web.framework.middleware.remoteuser import RemoteUser - app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), - ucsc_display_sites=conf.get( 'ucsc_display_sites', [] ), - admin_users=conf.get( 'admin_users', '' ).split( ',' ) ) + app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ), + display_servers = util.listify( conf.get( 'display_servers', '' ) ), + admin_users = conf.get( 'admin_users', '' ).split( ',' ) ) log.debug( "Enabling 'remote user' middleware" ) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -35,42 +35,22 @@ </html> """ -UCSC_MAIN_SERVERS = ( - 'hgw1.cse.ucsc.edu', - 'hgw2.cse.ucsc.edu', - 'hgw3.cse.ucsc.edu', - 'hgw4.cse.ucsc.edu', - 'hgw5.cse.ucsc.edu', - 'hgw6.cse.ucsc.edu', - 'hgw7.cse.ucsc.edu', - 'hgw8.cse.ucsc.edu', -) -UCSC_ARCHAEA_SERVERS = ( - 'lowepub.cse.ucsc.edu', -) - class RemoteUser( object ): - def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): + def __init__( self, app, maildomain=None, display_servers=None, admin_users=None ): self.app = app self.maildomain = maildomain - self.allow_ucsc_main = False - self.allow_ucsc_archaea = False - self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: - self.allow_ucsc_main = True - if 'archaea' in ucsc_display_sites: - self.allow_ucsc_archaea = True + self.display_servers = display_servers or [] + self.admin_users = admin_users or [] def __call__( self, environ, start_response ): - # Allow through UCSC if the UCSC display links are enabled - if ( self.allow_ucsc_main or self.allow_ucsc_archaea ) and environ.has_key( 'REMOTE_ADDR' ): + # Allow display servers + if self.display_servers and environ.has_key( 'REMOTE_ADDR' ): try: host = socket.gethostbyaddr( environ[ 'REMOTE_ADDR' ] )[0] except( socket.error, socket.herror, socket.gaierror, socket.timeout ): # in the event of a lookup failure, deny access host = None - if ( self.allow_ucsc_main and host in UCSC_MAIN_SERVERS ) or \ - ( self.allow_ucsc_archaea and host in UCSC_ARCHAEA_SERVERS ): - environ[ 'HTTP_REMOTE_USER' ] = 'ucsc_browser_display(a)example.org' + if host in self.display_servers: + environ[ 'HTTP_REMOTE_USER' ] = 'remote_display_server@%s' % ( self.maildomain or 'example.org' ) return self.app( environ, start_response ) # Apache sets REMOTE_USER to the string '(null)' when using the # Rewrite* method for passing REMOTE_USER and a user is diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -210,6 +210,20 @@ # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + # -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. use_nglims = False 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: greg: More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/143abc931cdb/ changeset: 143abc931cdb user: greg date: 2012-03-15 19:12:59 summary: More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed. affected #: 4 files diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -18,8 +18,7 @@ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config - # Get the local non-shed related tool panel config (the default name is tool_conf.xml). If the user has more than 1 - # non-shed tool panel config it could cause problems. + # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -46,11 +46,11 @@ # New installations will not be missing tools, so we don't need to worry about them. missing_tool_configs = [] else: - tool_panel_config = get_non_shed_tool_panel_config( app ) - if tool_panel_config is None: + tool_panel_configs = get_non_shed_tool_panel_configs( app ) + if tool_panel_configs: + missing_tool_configs = check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ) + else: missing_tool_configs = [] - else: - missing_tool_configs = check_for_missing_tools( tool_panel_config, latest_tool_migration_script_number ) config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) @@ -62,13 +62,19 @@ if return_code != 0: raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) elif missing_tool_configs: + if len( tool_panel_configs ) == 1: + plural = '' + tool_panel_config_file_names = tool_panel_configs[ 0 ] + else: + plural = 's' + tool_panel_config_file_names = ', '.join( tool_panel_configs ) msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file named %s.\n\n" % tool_panel_config + msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' @@ -84,7 +90,7 @@ msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file named %s, but only after the installation process finishes.\n\n" % tool_panel_config + msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) for i, missing_tool_config in enumerate( missing_tool_configs ): msg += "%s\n" % missing_tool_config # Should we do the following? diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -39,8 +39,9 @@ if name in migrated_tool_configs: missing_tool_configs.append( name ) return missing_tool_configs -def get_non_shed_tool_panel_config( app ): - # Get the non-shed related tool panel config value from the Galaxy config - the default is tool_conf.xml. +def get_non_shed_tool_panel_configs( app ): + # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. + config_filenames = [] for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> @@ -48,9 +49,8 @@ root = tree.getroot() tool_path = root.get( 'tool_path', None ) if tool_path is None: - # There will be a problem here if the user has defined 2 non-shed related configs. - return config_filename - return None + config_filenames.append( config_filename ) + return config_filenames class MigrateToolsApplication( object ): """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" def __init__( self, tools_migration_config ): diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 scripts/migrate_tools/migrate_tools.py --- a/scripts/migrate_tools/migrate_tools.py +++ b/scripts/migrate_tools/migrate_tools.py @@ -20,12 +20,14 @@ app = MigrateToolsApplication( sys.argv[ 1 ] ) non_shed_tool_confs = app.install_manager.proprietary_tool_confs -msg = "\nThe installation process is finished. You should now remove entries for the installed tools from " if len( non_shed_tool_confs ) == 1: - msg += "your file named %s and start your Galaxy server." % non_shed_tool_conf + plural = '' + file_names = non_shed_tool_confs[ 0 ] else: + plural = 's' file_names = ', '.join( non_shed_tool_confs ) - msg += "your files named %s, and start your Galaxy server." % file_names +msg = "\nThe installation process is finished. You should now remove entries for the installed tools from your file%s named\n" % plural +msg += "%s and start your Galaxy server.\n" % file_names print msg app.shutdown() sys.exit( 0 ) 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: jgoecks: Ensure reference track does not scroll.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d332e63b5367/ changeset: d332e63b5367 user: jgoecks date: 2012-03-15 18:28:47 summary: Ensure reference track does not scroll. affected #: 1 file diff -r 3b9be709d138197d8076f1d5790187c124e98955 -r d332e63b5367ed035dcaf6ee3aafed566200b617 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4238,7 +4238,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack, resize: false }, {}); + TiledTrack.call(this, view, { content_div: view.top_labeltrack, resize: false }, {}); view.reference_track = this; this.left_offset = 200; 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: greg: Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b9be709d138/ changeset: 3b9be709d138 user: greg date: 2012-03-15 16:47:46 summary: Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger. affected #: 3 files diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -6,6 +6,7 @@ from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * +from galaxy.util.odict import odict log = logging.getLogger( __name__ ) class InstallManager( object ): @@ -19,7 +20,7 @@ self.migrated_tools_config = migrated_tools_config # Get the local non-shed related tool panel config (the default name is tool_conf.xml). If the user has more than 1 # non-shed tool panel config it could cause problems. - self.proprietary_tool_conf = self.non_shed_tool_panel_config + self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. tree = util.parse_xml( migrated_tools_config ) @@ -50,10 +51,11 @@ tool = self.toolbox.load_tool( full_path ) return generate_tool_guid( repository_clone_url, tool ) def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): - # Parse self.proprietary_tool_conf (the default is tool_conf.xml) and generate a list of Elements that are either ToolSection elements - # or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml file for the installed tools. + # Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are + # either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml + # file for the installed tools. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) - # Parse the XML and load the file attributes for later checking against self.proprietary_tool_conf. + # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. migrated_tool_configs = [] tree = util.parse_xml( tools_xml_file_path ) root = tree.getroot() @@ -61,30 +63,31 @@ if elem.tag == 'repository': for tool_elem in elem: migrated_tool_configs.append( tool_elem.get( 'file' ) ) - # Parse self.proprietary_tool_conf and generate the list of tool panel Elements that contain them. + # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them. tool_panel_elems = [] - tree = util.parse_xml( self.proprietary_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - # Tools outside of sections. - file_path = elem.get( 'file', None ) - if file_path: - path, name = os.path.split( file_path ) - if name in migrated_tool_configs: - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) - elif elem.tag == 'section': - # Tools contained in a section. - for section_elem in elem: - if section_elem.tag == 'tool': - file_path = section_elem.get( 'file', None ) - if file_path: - path, name = os.path.split( file_path ) - if name in migrated_tool_configs: - # Append the section, not the tool. - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) + for proprietary_tool_conf in self.proprietary_tool_confs: + tree = util.parse_xml( proprietary_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + # Tools outside of sections. + file_path = elem.get( 'file', None ) + if file_path: + path, name = os.path.split( file_path ) + if name in migrated_tool_configs: + if elem not in tool_panel_elems: + tool_panel_elems.append( elem ) + elif elem.tag == 'section': + # Tools contained in a section. + for section_elem in elem: + if section_elem.tag == 'tool': + file_path = section_elem.get( 'file', None ) + if file_path: + path, name = os.path.split( file_path ) + if name in migrated_tool_configs: + # Append the section, not the tool. + if elem not in tool_panel_elems: + tool_panel_elems.append( elem ) return tool_panel_elems def get_containing_tool_sections( self, tool_config ): """ @@ -122,7 +125,7 @@ # updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. # The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places # in the tool panel. - tool_panel_dict_for_display = {} + tool_panel_dict_for_display = odict() for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) @@ -264,8 +267,9 @@ print "Error cloning repository '", name, "': ", str( tmp_stderr.read() ) tmp_stderr.close() @property - def non_shed_tool_panel_config( self ): - # Get the non-shed related tool panel config value from the Galaxy config - the default is tool_conf.xml. + def non_shed_tool_panel_configs( self ): + # Get the non-shed related tool panel config file names from the Galaxy config - the default is tool_conf.xml. + config_filenames = [] for config_filename in self.app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> @@ -274,8 +278,8 @@ tool_path = root.get( 'tool_path', None ) if tool_path is None: # There will be a problem here if the user has defined 2 non-shed related configs. - return config_filename - return None + config_filenames.append( config_filename ) + return config_filenames def __get_url_from_tool_shed( self, tool_shed ): # The value of tool_shed is something like: toolshed.g2.bx.psu.edu # We need the URL to this tool shed, which is something like: diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -70,6 +70,7 @@ self.config = galaxy.config.Configuration( **galaxy_config_dict ) if self.config.database_connection is None: self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + self.config.update_integrated_tool_panel = True self.object_store = build_object_store_from_config( self.config ) # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 scripts/migrate_tools/migrate_tools.py --- a/scripts/migrate_tools/migrate_tools.py +++ b/scripts/migrate_tools/migrate_tools.py @@ -19,8 +19,13 @@ from galaxy.tool_shed.migrate.common import * app = MigrateToolsApplication( sys.argv[ 1 ] ) -non_shed_tool_conf = app.install_manager.proprietary_tool_conf -print "\nThe installation process is finished. You should now remove entries for the installed tools from" -print "your file named %s and start your Galaxy server." % non_shed_tool_conf +non_shed_tool_confs = app.install_manager.proprietary_tool_confs +msg = "\nThe installation process is finished. You should now remove entries for the installed tools from " +if len( non_shed_tool_confs ) == 1: + msg += "your file named %s and start your Galaxy server." % non_shed_tool_conf +else: + file_names = ', '.join( non_shed_tool_confs ) + msg += "your files named %s, and start your Galaxy server." % file_names +print msg app.shutdown() sys.exit( 0 ) 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: greg: Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file.
by Bitbucket 14 Mar '12

14 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aafbc71077ec/ changeset: aafbc71077ec user: greg date: 2012-03-14 22:21:03 summary: Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file. affected #: 4 files diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -70,6 +70,7 @@ self.hours_between_check = 12 except: self.hours_between_check = 12 + self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -75,10 +75,12 @@ if self.integrated_tool_panel_config_has_contents: # Load self.tool_panel based on the order in self.integrated_tool_panel. self.load_tool_panel() - # Always write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. - # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel - # config files, adding or removing locally developed tools or workflows. - self.write_integrated_tool_panel_config_file() + if app.config.update_integrated_tool_panel: + # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. + # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel + # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel + # will be False when things like functional tests are the caller. + self.write_integrated_tool_panel_config_file() def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -430,7 +430,6 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) - # Render the list view return self.repository_metadata_list_grid( trans, **kwd ) @web.expose @web.require_admin @@ -504,7 +503,7 @@ else: del kwd[ 'operation' ] elif operation == 'delete': - return self.mark_repository_deleted( trans, **kwd ) + return self.delete_repository( trans, **kwd ) elif operation == "undelete": return self.undelete_repository( trans, **kwd ) # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change @@ -528,12 +527,13 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin - def mark_repository_deleted( self, trans, **kwd ): + def delete_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: + # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify( id ) count = 0 deleted_repositories = "" @@ -564,6 +564,7 @@ status = params.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: + # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify( id ) count = 0 undeleted_repositories = "" diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -167,6 +167,7 @@ file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, + update_integrated_tool_panel = False, tool_config_file = tool_config_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, 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 Bitbucket 13 Mar '12

13 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/287d56ffaf6e/ changeset: 287d56ffaf6e user: jgoecks date: 2012-03-13 22:15:46 summary: Trackster: prevent resizing of label and reference tracks. affected #: 1 file diff -r 7fe7059a78a37323dc3e8efb832f5831be625dd8 -r 287d56ffaf6e7d8f5130469d427e65a9a68c6fb1 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3161,7 +3161,9 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); if (this.container) { this.container.content_div.append(this.container_div); - this.add_resize_handle(); + if ( !("resize" in obj_dict) || obj_dict.resize ) { + this.add_resize_handle(); + } } }; @@ -3920,8 +3922,7 @@ var LabelTrack = function (view, container) { var obj_dict = { - todo: "label", - todo: false + resize: false }; Track.call(this, view, container, obj_dict); this.container_div.addClass( "label-track" ); @@ -4237,7 +4238,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack, resize: false }, {}); view.reference_track = this; this.left_offset = 200; https://bitbucket.org/galaxy/galaxy-central/changeset/3b1f0bb99b43/ changeset: 3b1f0bb99b43 user: jgoecks date: 2012-03-13 22:22:56 summary: Trackster: make reference track compatible with changeset 8e9d2b492c4c. affected #: 1 file diff -r 287d56ffaf6e7d8f5130469d427e65a9a68c6fb1 -r 3b1f0bb99b43924b869cfc0df626738f18d968fc static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4281,6 +4281,14 @@ return new Tile(track, tile_index, resolution, canvas, seq); } this.content_div.css("height", "0px"); + }, + /** + * If there is a tile with sequence data, set content div so that data is visible. + */ + after_show_tile: function(tile) { + if (tile) { + this.content_div.css("height", "12px"); + } } }); 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: greg: When uploading a tarball to a tool shed repository, eliminate as many undesired directories (.svn, .git, .hg, .cvs) and files (hgrc, .hg_archival.txt, .DS_Store) as possible from the archive before committing the contents to the repository.
by Bitbucket 13 Mar '12

13 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7fe7059a78a3/ changeset: 7fe7059a78a3 user: greg date: 2012-03-13 21:25:15 summary: When uploading a tarball to a tool shed repository, eliminate as many undesired directories (.svn, .git, .hg, .cvs) and files (hgrc, .hg_archival.txt, .DS_Store) as possible from the archive before committing the contents to the repository. affected #: 1 file diff -r 48b64ce958b4ed9ec28639c1057adc67f70ae016 -r 7fe7059a78a37323dc3e8efb832f5831be625dd8 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -8,6 +8,8 @@ log = logging.getLogger( __name__ ) +undesirable_dirs = [ '.hg', '.svn', '.git', '.cvs' ] +undesirable_files = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" CHUNK_SIZE = 2**20 # 1Mb @@ -92,14 +94,14 @@ tar = None istar = False if istar: - ok, message, files_to_remove, content_alert_str = self.upload_tar( trans, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = self.upload_tar( trans, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert ) else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) @@ -150,6 +152,9 @@ else: uncompress_str = ' ' message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) + if istar and ( undesirable_dirs_removed or undesirable_files_removed ): + items_removed = undesirable_dirs_removed + undesirable_files_removed + message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive." % items_removed if istar and remove_repo_files_not_in_tar and files_to_remove: if upload_point is not None: message += " %d files were removed from the repository relative to the selected upload point '%s'." % ( len( files_to_remove ), upload_point ) @@ -206,7 +211,21 @@ full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) else: full_path = os.path.abspath( repo_dir ) - filenames_in_archive = [ tarinfo_obj.name for tarinfo_obj in tar.getmembers() ] + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + filenames_in_archive = [] + for tarinfo_obj in tar.getmembers(): + ok = os.path.basename( tarinfo_obj.name ) not in undesirable_files + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in undesirable_dirs: + undesirable_dirs_removed += 1 + ok = False + break + else: + undesirable_files_removed += 1 + if ok: + filenames_in_archive.append( tarinfo_obj.name ) filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ] # Extract the uploaded tar to the load_point within the repository hierarchy. tar.extractall( path=full_path ) @@ -216,14 +235,15 @@ # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. for root, dirs, files in os.walk( full_path ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + for undesirable_dir in undesirable_dirs: + if undesirable_dir in dirs: + dirs.remove( undesirable_dir ) + undesirable_dirs_removed += 1 + for undesirable_file in undesirable_files: + if undesirable_file in files: + files.remove( undesirable_file ) + undesirable_files_removed += 1 for name in files: full_name = os.path.join( root, name ) if full_name not in filenames_in_archive: @@ -286,7 +306,7 @@ # See if the content of the change set was valid. admin_only = len( repository.downloadable_revisions ) != 1 handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) - return True, '', files_to_remove, content_alert_str + return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for rerunning a tool where the correct id / version are available.
by Bitbucket 12 Mar '12

12 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/48b64ce958b4/ changeset: 48b64ce958b4 user: greg date: 2012-03-12 20:30:37 summary: Fix for rerunning a tool where the correct id / version are available. affected #: 1 file diff -r b199460443afeb3023f1c160f23b2215ba42add4 -r 48b64ce958b4ed9ec28639c1057adc67f70ae016 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -246,9 +246,15 @@ if tool_id in self.tools_by_id: tool = self.tools_by_id[ tool_id ] if tool_version and tool.version == tool_version: - return tool + if get_all_versions: + return [ tool ] + else: + return tool else: - return tool + if get_all_versions: + return [ tool ] + else: + return tool tv = self.__get_tool_version( tool_id ) if tv: tool_version_ids = tv.get_version_ids( self.app ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Check potential tool config files to ensure they are text before attempting to load them in tool shed repositories, and a fix handling for tools contained in a repository that don't peoperly load into Galaxy because they are missing a required entry in the tool_data_table.conf file.
by Bitbucket 12 Mar '12

12 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b199460443af/ changeset: b199460443af user: greg date: 2012-03-12 18:51:07 summary: Check potential tool config files to ensure they are text before attempting to load them in tool shed repositories, and a fix handling for tools contained in a repository that don't peoperly load into Galaxy because they are missing a required entry in the tool_data_table.conf file. affected #: 6 files diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -63,7 +63,7 @@ raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) elif missing_tool_configs: msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refer to tools that are configured to load into the tool panel for\n" + msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2,6 +2,7 @@ from datetime import date, datetime, timedelta from time import strftime from galaxy import util +from galaxy.datatypes.checkers import * from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch from galaxy.model.orm import * @@ -11,6 +12,7 @@ from elementtree.ElementTree import Element, SubElement log = logging.getLogger( __name__ ) + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have @@ -320,14 +322,15 @@ # Find all tool configs. if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - try: - tool = toolbox.load_tool( full_path ) - except Exception, e: - tool = None - if tool is not None: - tool_config = os.path.join( root, name ) - guid = generate_tool_guid( repository_clone_url, tool ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + tool = toolbox.load_tool( full_path ) + except Exception, e: + tool = None + if tool is not None: + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -642,10 +645,14 @@ repository_tools_tups = [] if 'tools' in metadata_dict: for tool_dict in metadata_dict[ 'tools' ]: - relative_path = tool_dict[ 'tool_config' ] - guid = tool_dict[ 'guid' ] - tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) - repository_tools_tups.append( ( relative_path, guid, tool ) ) + relative_path = tool_dict.get( 'tool_config', None ) + guid = tool_dict.get( 'guid', None ) + if relative_path and guid: + tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) + else: + tool = None + if tool: + repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups def get_tool_panel_config_tool_path_install_dir( app, repository ): # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the @@ -745,6 +752,7 @@ missing_data_table_entry = True break if missing_data_table_entry: + sample_file = None # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository. for sample_file in sample_files: head, tail = os.path.split( sample_file ) @@ -753,10 +761,10 @@ error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file ) if error: # TODO: Do more here than logging an exception. - log.debug( exception_msg ) + log.debug( correction_msg ) # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) - repository_tools_tups[ index ] = ( tup_path, repository_tool ) + repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): """Inspect each tool to see if it has any input parameters that are dynamically generated select lists that depend on a .loc file.""" @@ -781,6 +789,46 @@ repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups +def handle_sample_tool_data_table_conf_file( app, filename ): + """ + Parse the incoming filename and add new entries to the in-memory + app.tool_data_tables dictionary as well as appending them to the + shed's tool_data_table_conf.xml file on disk. + """ + error = False + message = '' + try: + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename ) + except Exception, e: + message = str( e ) + error = True + if not error: + # Add an entry to the end of the tool_data_table_conf.xml file. + tdt_config = "%s/tool_data_table_conf.xml" % app.config.root + if os.path.exists( tdt_config ): + # Make a backup of the file since we're going to be changing it. + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date ) + shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) ) + # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file. + fh = tempfile.NamedTemporaryFile( 'wb' ) + tmp_filename = fh.name + fh.close() + new_tdt_config = open( tmp_filename, 'wb' ) + for i, line in enumerate( open( tdt_config, 'rb' ) ): + if line.find( '</tables>' ) >= 0: + for new_table_elem in new_table_elems: + new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) + new_tdt_config.write( '</tables>\n' ) + else: + new_tdt_config.write( line ) + new_tdt_config.close() + shutil.move( tmp_filename, os.path.abspath( tdt_config ) ) + else: + message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." + error = True + return error, message def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ): """ Inspect each tool to see if it includes a "requirement" that refers to a fabric diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2464,46 +2464,6 @@ id = trans.security.decode_id( id ) quota = trans.sa_session.query( trans.model.Quota ).get( id ) return quota -def handle_sample_tool_data_table_conf_file( app, filename ): - """ - Parse the incoming filename and add new entries to the in-memory - app.tool_data_tables dictionary as well as appending them to the - shed's tool_data_table_conf.xml file on disk. - """ - error = False - message = '' - try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename ) - except Exception, e: - message = str( e ) - error = True - if not error: - # Add an entry to the end of the tool_data_table_conf.xml file. - tdt_config = "%s/tool_data_table_conf.xml" % app.config.root - if os.path.exists( tdt_config ): - # Make a backup of the file since we're going to be changing it. - today = date.today() - backup_date = today.strftime( "%Y_%m_%d" ) - tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date ) - shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) ) - # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file. - fh = tempfile.NamedTemporaryFile( 'wb' ) - tmp_filename = fh.name - fh.close() - new_tdt_config = open( tmp_filename, 'wb' ) - for i, line in enumerate( open( tdt_config, 'rb' ) ): - if line.find( '</tables>' ) >= 0: - for new_table_elem in new_table_elems: - new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) - new_tdt_config.write( '</tables>\n' ) - else: - new_tdt_config.write( line ) - new_tdt_config.close() - shutil.move( tmp_filename, os.path.abspath( tdt_config ) ) - else: - message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." - error = True - return error, message def tool_shed_encode( val ): if isinstance( val, dict ): value = simplejson.dumps( val ) diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,10 +1,12 @@ import os, string, socket, logging, simplejson, binascii from time import strftime from datetime import * +from galaxy.datatypes.checkers import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_loc_file, generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -314,19 +316,21 @@ # Find all tool configs. if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - try: - tool = load_tool( trans, full_path ) - valid = True - except Exception, e: - valid = False - invalid_files.append( ( name, str( e ) ) ) - if valid and tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - tool_config = os.path.join( root, name ) - repository_clone_url = generate_clone_url( trans, id ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + tool = load_tool( trans, full_path ) + valid = True + except Exception, e: + valid = False + invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -381,22 +385,24 @@ fh = open( tmp_filename, 'w' ) fh.write( fctx.data() ) fh.close() - try: - tool = load_tool( trans, tmp_filename ) - valid = True - except Exception, e: - invalid_files.append( ( filename, str( e ) ) ) - valid = False - if valid and tool is not None: - # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename - # here is the relative path to the config file within the change set context, something - # like filtering.xml, but when the change set was the repository tip, the value was - # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break - # anything, but may result in a bit of confusion when maintaining the code / data over time. - # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository - # tip, we do not have to handle any .loc.sample files since they would have been handled previously. - repository_clone_url = generate_clone_url( trans, id ) - metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ] + or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ): + try: + tool = load_tool( trans, tmp_filename ) + valid = True + except Exception, e: + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository + # tip, we do not have to handle any .loc.sample files since they would have been handled previously. + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) try: os.unlink( tmp_filename ) except: diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -856,13 +856,15 @@ fh = open( tmp_filename, 'w' ) fh.write( fctx.data() ) fh.close() - try: - tool = load_tool( trans, tmp_filename ) - valid = True - except: - valid = False - if valid and tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ] + or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ): + try: + tool = load_tool( trans, tmp_filename ) + valid = True + except: + valid = False + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) try: os.unlink( tmp_filename ) except: diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,6 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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