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commit/galaxy-central: dannon: Allow dynamic_options to use $__user_email__ as a filter_value. This would enable tools to use dynamic options defined in a file listing user_specific options for a tool (file paths, etc).
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddc3b1579121/ changeset: ddc3b1579121 user: dannon date: 2013-02-06 03:11:32 summary: Allow dynamic_options to use $__user_email__ as a filter_value. This would enable tools to use dynamic options defined in a file listing user_specific options for a tool (file paths, etc). affected #: 1 file diff -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 -r ddc3b1579121233cec5b4c6717d43c97ddc040bc lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -53,8 +53,14 @@ self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def filter_options( self, options, trans, other_values ): rval = [] + filter_value = self.value + try: + if trans.user.email: + filter_value = filter_value.replace('$__user_email__',trans.user.email) + except: + pass for fields in options: - if ( self.keep and fields[self.column] == self.value ) or ( not self.keep and fields[self.column] != self.value ): + if ( self.keep and fields[self.column] == filter_value ) or ( not self.keep and fields[self.column] != filter_value ): rval.append( fields ) return rval 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: inithello: Bugfixes for tool shed functional test scripts.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ff0b52b5850/ changeset: 6ff0b52b5850 user: inithello date: 2013-02-05 22:05:33 summary: Bugfixes for tool shed functional test scripts. affected #: 3 files diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -127,6 +127,7 @@ def test_0065_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) tip = self.get_repository_tip( repository ) self.check_for_valid_tools( repository ) strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -39,7 +39,7 @@ strings_displayed=[] ) self.upload_file( repository, 'bwa/complex/tool_dependencies.xml', - strings_displayed=[], + strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) def test_0010_create_bwa_base_repository( self ): @@ -148,17 +148,23 @@ commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) self.check_repository_dependency( base_repository, tool_repository ) self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) - def test_0040_update_base_repository( self ): - '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.''' + def test_0040_generate_tool_dependency( self ): + '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem. + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. self.display_manage_repository_page( base_repository, strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ], strings_not_displayed=[ previous_changeset ] ) - diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,7 +1,6 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -import logging -log = logging.getLogger(__name__) + bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -45,7 +44,6 @@ old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) - log.debug( xml_filename ) file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, @@ -182,7 +180,6 @@ old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) - log.debug( xml_filename ) file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add 'log' level for stdio inspection.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b6800bbce75/ changeset: 2b6800bbce75 user: jgoecks date: 2013-02-05 20:28:28 summary: Add 'log' level for stdio inspection. affected #: 1 file diff -r 2b7503087b4c2520bd6d7639d07933f960281792 -r 2b6800bbce751d434c9b22783a47de0ce522e355 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -49,10 +49,16 @@ # that warning < fatal. This is really meant to just be an enum. class StdioErrorLevel( object ): NO_ERROR = 0 - WARNING = 1 - FATAL = 2 - MAX = 2 - descs = {NO_ERROR : 'No error', WARNING : 'Warning', FATAL : 'Fatal error'} + LOG = 1 + WARNING = 2 + FATAL = 3 + MAX = 3 + descs = { + NO_ERROR : 'No error', + LOG: 'Log', + WARNING : 'Warning', + FATAL : 'Fatal error' + } @staticmethod def desc( error_level ): err_msg = "Unknown error" @@ -1377,19 +1383,15 @@ # TODO: This method doesn't have to be part of the Tool class. def parse_error_level( self, err_level ): """ - Return fatal or warning depending on what's in the error level. - This will assume that the error level fatal is returned if it's - unparsable. + Parses error level and returns error level enumeration. If + unparsable, returns 'fatal' """ - # What should the default be? I'm claiming it should be fatal: - # if you went to the trouble to write the rule, then it's - # probably a problem. I think there are easily three substantial - # camps: make it fatal, make it a warning, or, if it's missing, - # just throw an exception and ignore the exit_code element. return_level = StdioErrorLevel.FATAL try: - if ( None != err_level ): - if ( re.search( "warning", err_level, re.IGNORECASE ) ): + if err_level: + if ( re.search( "log", err_level, re.IGNORECASE ) ): + return_level = StdioErrorLevel.LOG + elif ( re.search( "warning", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.WARNING elif ( re.search( "fatal", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.FATAL 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: Tool stdout/err checking: (a) add tool id to error message and (b) add support for specifying 'both' as an alias for searching both stdout and stderr, which matches the documentation.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b7503087b4c/ changeset: 2b7503087b4c user: jgoecks date: 2013-02-05 18:36:59 summary: Tool stdout/err checking: (a) add tool id to error message and (b) add support for specifying 'both' as an alias for searching both stdout and stderr, which matches the documentation. affected #: 1 file diff -r 7b96c5b684d1dbf142a7f9caf7dce76c217d9e09 -r 2b7503087b4c2520bd6d7639d07933f960281792 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1086,7 +1086,7 @@ else: self.trackster_conf = None def parse_inputs( self, root ): - r""" + """ Parse the "<inputs>" element and create appropriate `ToolParameter`s. This implementation supports multiple pages and grouping constructs. """ @@ -1352,14 +1352,17 @@ # and anything to do with "err". If neither stdout nor # stderr were specified, then raise a warning and scan both. for src in src_list: + if re.search( "both", src, re.IGNORECASE ): + regex.stdout_match = True + regex.stderr_match = True if re.search( "out", src, re.IGNORECASE ): regex.stdout_match = True if re.search( "err", src, re.IGNORECASE ): regex.stderr_match = True if (not regex.stdout_match and not regex.stderr_match): - log.warning( "Unable to determine if tool stream " - + "source scanning is output, error, " - + "or both. Defaulting to use both." ) + log.warning( "Tool id %s: unable to determine if tool " + "stream source scanning is output, error, " + "or both. Defaulting to use both." % self.id ) regex.stdout_match = True regex.stderr_match = True self.stdio_regexes.append( regex ) 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: james_taylor: eggs: Update Paste and PasteDeploy
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b96c5b684d1/ changeset: 7b96c5b684d1 user: james_taylor date: 2013-02-05 05:30:32 summary: eggs: Update Paste and PasteDeploy affected #: 1 file diff -r 3720c0455a436c9812d8ccb8577fd042c59b2048 -r 7b96c5b684d1dbf142a7f9caf7dce76c217d9e09 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -46,8 +46,8 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 -Paste = 1.6 -PasteDeploy = 1.3.3 +Paste = 1.7.5.1 +PasteDeploy = 1.5.0 pexpect = 2.4 python_openid = 2.2.5 python_daemon = 1.5.5 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: james_taylor: logging: If sentry is configured attach to the root logger no matter how logging was originally configured
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3720c0455a43/ changeset: 3720c0455a43 user: james_taylor date: 2013-02-05 00:07:04 summary: logging: If sentry is configured attach to the root logger no matter how logging was originally configured affected #: 1 file diff -r 0856c4a75c92c56f54028f72502ce0ceb55b2e11 -r 3720c0455a436c9812d8ccb8577fd042c59b2048 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -401,36 +401,34 @@ """ Allow some basic logging configuration to be read from ini file. """ - # PasteScript will have already configured the logger if the appropriate - # sections were found in the config file, so we do nothing if the - # config has a loggers section, otherwise we do some simple setup - # using the 'log_*' values from the config. - if config.global_conf_parser.has_section( "loggers" ): - return - format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) - level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] - destination = config.get( "log_destination", "stdout" ) - log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) # Get root logger root = logging.getLogger() - # Set level - root.setLevel( level ) - # Turn down paste httpserver logging - if level <= logging.DEBUG: - logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) - # Remove old handlers - for h in root.handlers[:]: - root.removeHandler(h) - # Create handler - if destination == "stdout": - handler = logging.StreamHandler( sys.stdout ) - else: - handler = logging.FileHandler( destination ) - # Create formatter - formatter = logging.Formatter( format ) - # Hook everything up - handler.setFormatter( formatter ) - root.addHandler( handler ) + # PasteScript will have already configured the logger if the + # 'loggers' section was found in the config file, otherwise we do + # some simple setup using the 'log_*' values from the config. + if not config.global_conf_parser.has_section( "loggers" ): + format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) + level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] + destination = config.get( "log_destination", "stdout" ) + log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) + # Set level + root.setLevel( level ) + # Turn down paste httpserver logging + if level <= logging.DEBUG: + logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) + # Remove old handlers + for h in root.handlers[:]: + root.removeHandler(h) + # Create handler + if destination == "stdout": + handler = logging.StreamHandler( sys.stdout ) + else: + handler = logging.FileHandler( destination ) + # Create formatter + formatter = logging.Formatter( format ) + # Hook everything up + handler.setFormatter( formatter ) + root.addHandler( handler ) # If sentry is configured, also log to it if config.sentry_dsn: pkg_resources.require( "raven" ) 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: Uncomment temporary file cleanup block in tool shed functiona tests.
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0856c4a75c92/ changeset: 0856c4a75c92 user: greg date: 2013-02-04 21:22:53 summary: Uncomment temporary file cleanup block in tool shed functiona tests. affected #: 1 file diff -r b6be9c3a2d2df94f4d5236184a4392ec00961743 -r 0856c4a75c92c56f54028f72502ce0ceb55b2e11 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -392,18 +392,18 @@ galaxyapp.shutdown() galaxyapp = None log.info( "Embedded galaxy application stopped" ) -# if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: -# try: -# for dir in [ tool_shed_test_tmp_dir ]: -# if os.path.exists( dir ): -# log.info( "Cleaning up temporary files in %s" % dir ) -# shutil.rmtree( dir ) -# except: -# pass -# if success: -# return 0 -# else: -# return 1 + if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: + try: + for dir in [ tool_shed_test_tmp_dir ]: + if os.path.exists( dir ): + log.info( "Cleaning up temporary files in %s" % dir ) + shutil.rmtree( dir ) + except: + pass + if success: + return 0 + else: + return 1 if __name__ == "__main__": sys.exit( main() ) 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 04 Feb '13

04 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac3195ac1025/ changeset: ac3195ac1025 branch: next-stable user: inithello date: 2013-02-04 20:00:31 summary: Updated BWA's tool_dependencies.xml to no longer rely on a network connection to correctly complete functional tests. affected #: 4 files diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -483,7 +483,10 @@ # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): - return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + temp_path = os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + if not os.path.exists( temp_path ): + os.makedirs( temp_path ) + return temp_path def get_datatypes_count( self ): url = '/admin/view_datatypes_registry' self.visit_galaxy_url( url ) diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -41,8 +42,15 @@ strings_displayed=[] ) if self.repository_is_new( repository ): running_standalone = True + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, - 'bwa/complex/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -171,8 +179,15 @@ base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> diff -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac -r ac3195ac1025f73bcabeeafa66e93b964fbac7b2 test/tool_shed/test_data/bwa/complex/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> https://bitbucket.org/galaxy/galaxy-central/commits/b6be9c3a2d2d/ changeset: b6be9c3a2d2d user: inithello date: 2013-02-04 20:01:50 summary: Merged in changes from next-stable. affected #: 4 files diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -483,7 +483,10 @@ # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): - return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + temp_path = os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + if not os.path.exists( temp_path ): + os.makedirs( temp_path ) + return temp_path def get_datatypes_count( self ): url = '/admin/view_datatypes_registry' self.visit_galaxy_url( url ) diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -41,8 +42,15 @@ strings_displayed=[] ) if self.repository_is_new( repository ): running_standalone = True + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, - 'bwa/complex/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) @@ -171,8 +179,15 @@ base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + log.debug( xml_filename ) + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> diff -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 -r b6be9c3a2d2df94f4d5236184a4392ec00961743 test/tool_shed/test_data/bwa/complex/tool_dependencies.xml --- a/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml +++ b/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml @@ -3,12 +3,7 @@ <package name="bwa" version="0.5.9"><install version="1.0"><actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bwa</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">file://__PATH__/bwa_base.tar</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Refactor tabular chunked display into Backbone and use for displaying tabular data.
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2faf4a9871bb/ changeset: 2faf4a9871bb user: jgoecks date: 2013-02-04 18:37:32 summary: Refactor tabular chunked display into Backbone and use for displaying tabular data. affected #: 3 files diff -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -1,3 +1,4 @@ +// Additional dependencies: jQuery, underscore. define(["libs/backbone/backbone-relational"], function() { /** @@ -46,13 +47,175 @@ urlRoot: galaxy_paths.get('datasets_url') }); +/** + * A tabular dataset. This object extends dataset to provide incremental chunked data. + */ +var TabularDataset = Dataset.extend({ + defaults: _.extend({}, Dataset.prototype.defaults, { + chunk_url: null, + first_data_chunk: null, + chunk_index: -1, + at_eof: false + }), + + initialize: function(options) { + Dataset.prototype.initialize.call(this); + + // If first data chunk is available, next + // chunk is 1. + chunk_index = (this.attributes.first_data_chunk ? 1 : 0); + }, + + /** + * Set first data chunk; useful when initializing on the server side. + */ + set_first_chunk: function(chunk) { + this.attributes.first_data_chunk = chunk; + this.attributes.chunk_index = 1; + }, + + /** + * Returns a jQuery Deferred object that resolves to the next data chunk or null if at EOF. + */ + get_next_chunk: function() { + // If already at end of file, do nothing. + if (this.attributes.at_eof) { + return null; + } + + // Get next chunk. + var self = this, + next_chunk = $.Deferred(); + $.getJSON(this.attributes.chunk_url, { + chunk: self.attributes.chunk_index++ + }).success(function(chunk) { + var rval; + if (chunk.ck_data !== '') { + // Found chunk. + rval = chunk; + } + else { + // At EOF. + self.attributes.at_eof = true; + rval = null; + } + next_chunk.resolve(rval); + }); + + return next_chunk; + } +}); + var DatasetCollection = Backbone.Collection.extend({ model: Dataset }); +/** + * Provides table-based, dynamic view of a tabular dataset. + */ +var TabularDatasetChunkedView = Backbone.View.extend({ + + initialize: function(options) {}, + + render: function() { + // Add loading indicator div. + this.$el.append( $('<div/>').attr('id', 'loading_indicator') ); + + // Add data table and header. + var data_table = $('<table/>').attr({ + id: 'content_table', + cellpadding: 0 + }); + this.$el.append(data_table); + var column_names = this.model.get_metadata('column_names'); + if (column_names) { + data_table.append('<tr><th>' + column_names.join('</th><th>') + '</th></tr>'); + } + + // Add first chunk. + var first_chunk = this.model.get('first_data_chunk'); + if (first_chunk) { + this._renderChunk(first_chunk); + } + + // Show new chunks during scrolling. + var self = this; + $(window).scroll(function() { + if ($(window).scrollTop() === $(document).height() - $(window).height()) { + $.when(self.model.get_next_chunk()).then(function(result) { + if (result) { + self._renderChunk(result); + } + }); + } + }); + $('#loading_indicator').ajaxStart(function(){ + $(this).show(); + }).ajaxStop(function(){ + $(this).hide(); + }); + }, + + // -- Helper functions. -- + + _renderCell: function(cell_contents, index, colspan) { + var column_types = this.model.get_metadata('column_types'); + if (colspan !== undefined) { + return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); + } + else if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + return $('<td>').addClass('stringalign').text(cell_contents); + } + else { + return $('<td>').text(cell_contents); + } + }, + + _renderRow: function(line) { + // Check length of cells to ensure this is a complete row. + var cells = line.split('\t'), + row = $('<tr>'), + num_columns = this.model.get_metadata('columns'); + if (cells.length === num_columns) { + _.each(cells, function(cell_contents, index) { + row.append(this._renderCell(cell_contents, index)); + }, this); + } + else if (cells.length > num_columns) { + // SAM file or like format with optional metadata included. + _.each(cells.slice(0, num_columns - 1), function(cell_contents, index) { + row.append(this._renderCell(cell_contents, index)); + }, this); + row.append(this._renderCell(cells.slice(num_columns - 1).join('\t'), num_columns - 1)); + } + else if (num_columns > 5 && cells.length === num_columns - 1 ) { + // SAM file or like format with optional metadata missing. + _.each(cells, function(cell_contents, index) { + row.append(this._renderCell(cell_contents, index)); + }, this); + row.append($('<td>')); + } + else { + // Comment line, just return the one cell. + row.append(this._renderCell(line, 0, num_columns)); + } + return row; + }, + + _renderChunk: function(chunk) { + var data_table = this.$el.find('table'); + _.each(chunk.ck_data.split('\n'), function(line, index) { + data_table.append(this._renderRow(line)); + }, this); + } +}); + return { Dataset: Dataset, - DatasetCollection: DatasetCollection + TabularDataset: TabularDataset, + DatasetCollection: DatasetCollection, + TabularDatasetChunkedView: TabularDatasetChunkedView }; }); diff -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.RelationalModel.extend({});var b=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var d=new a();_.each(_.keys(this.attributes),function(e){if(e.indexOf("metadata_")===0){var f=e.split("metadata_")[1];d.set(f,this.attributes[e]);delete this.attributes[e]}},this);this.set("metadata",d)},get_metadata:function(d){return this.attributes.metadata.get(d)},urlRoot:galaxy_paths.get("datasets_url")});var c=Backbone.Collection.extend({model:b});return{Dataset:b,DatasetCollection:c}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var b=Backbone.RelationalModel.extend({});var c=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var f=new b();_.each(_.keys(this.attributes),function(g){if(g.indexOf("metadata_")===0){var h=g.split("metadata_")[1];f.set(h,this.attributes[g]);delete this.attributes[g]}},this);this.set("metadata",f)},get_metadata:function(f){return this.attributes.metadata.get(f)},urlRoot:galaxy_paths.get("datasets_url")});var a=c.extend({defaults:_.extend({},c.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(f){c.prototype.initialize.call(this);chunk_index=(this.attributes.first_data_chunk?1:0)},set_first_chunk:function(f){this.attributes.first_data_chunk=f;this.attributes.chunk_index=1},get_next_chunk:function(){if(this.attributes.at_eof){return null}var f=this,g=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:f.attributes.chunk_index++}).success(function(h){var i;if(h.ck_data!==""){i=h}else{f.attributes.at_eof=true;i=null}g.resolve(i)});return g}});var e=Backbone.Collection.extend({model:c});var d=Backbone.View.extend({initialize:function(f){},render:function(){this.$el.append($("<div/>").attr("id","loading_indicator"));var i=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(i);var f=this.model.get_metadata("column_names");if(f){i.append("<tr><th>"+f.join("</th><th>")+"</th></tr>")}var h=this.model.get("first_data_chunk");if(h){this._renderChunk(h)}var g=this;$(window).scroll(function(){if($(window).scrollTop()===$(document).height()-$(window).height()){$.when(g.model.get_next_chunk()).then(function(j){if(j){g._renderChunk(j)}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(h,f,i){var g=this.model.get_metadata("column_types");if(i!==undefined){return $("<td>").attr("colspan",i).addClass("stringalign").text(h)}else{if(g[f]==="str"||g==="list"){return $("<td>").addClass("stringalign").text(h)}else{return $("<td>").text(h)}}},_renderRow:function(f){var g=f.split("\t"),i=$("<tr>"),h=this.model.get_metadata("columns");if(g.length===h){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this)}else{if(g.length>h){_.each(g.slice(0,h-1),function(k,j){i.append(this._renderCell(k,j))},this);i.append(this._renderCell(g.slice(h-1).join("\t"),h-1))}else{if(h>5&&g.length===h-1){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this);i.append($("<td>"))}else{i.append(this._renderCell(f,0,h))}}}return i},_renderChunk:function(f){var g=this.$el.find("table");_.each(f.ck_data.split("\n"),function(h,i){g.append(this._renderRow(h))},this)}});return{Dataset:c,TabularDataset:a,DatasetCollection:e,TabularDatasetChunkedView:d}}); \ No newline at end of file diff -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 -r 2faf4a9871bb58da2b16d1a8929a53c68f951cc0 templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -5,91 +5,31 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js( "libs/require" )} <script type="text/javascript"> - var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var COLUMN_NUMBER = ${column_number}; - var COLUMN_TYPES = ${column_types}; - var COLUMN_NAMES = ${column_names}; + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); - var chunk = ${chunk}; - var current_chunk = 0; + require([ 'mvc/data' ], function(data) { - function renderCell(cell_contents, index, colspan){ - if (colspan !== undefined){ - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); - } - else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){ - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents);; - } - else{ - return $('<td>').text(cell_contents); - } - } - - function renderRow(line){ - /* Check length of cells to ensure this is a complete row. */ - var cells = line.split('\t'); - var row = $('<tr>'); - if (cells.length == COLUMN_NUMBER){ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - } - else if(cells.length > COLUMN_NUMBER){ - /* SAM file or like format with optional metadata included */ - $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1)); - } - else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){ - /* SAM file or like format with optional metadata missing */ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append($('<td>')); - } - else{ - /* Comment line, just return the one cell*/ - row.append(renderCell(line, 0, COLUMN_NUMBER)); - } - return row; - } - - function renderChunk(chunk){ - var table = $('#content_table'); - if (chunk.ck_data == ""){ - current_chunk = -1; - } - else if(chunk.ck_index === current_chunk + 1){ - if (current_chunk === 0 && COLUMN_NAMES){ - table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>'); - } - var lines = chunk.ck_data.split('\n'); - $.each(lines, function(index, line){ - table.append(renderRow(line)); - }); - current_chunk = chunk.ck_index; - } - } - - $(document).ready(function(){ - renderChunk(chunk); - $(window).scroll(function(){ - if ($(window).scrollTop() == $(document).height() - $(window).height()){ - if (current_chunk !== -1){ - $.getJSON(DATASET_URL, - {chunk: current_chunk}, - function(result){renderChunk(result)}); - } - } + // Set up dataset and attributes. + var dataset = new data.TabularDataset( ${h.to_json_string( dataset.get_api_value() )} ); + dataset.set('chunk_url', + "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"); + dataset.set_first_chunk(${chunk}) + + // Set up, render, and add view. + var dataset_view = new data.TabularDatasetChunkedView({ + model: dataset }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show(); - }).ajaxStop(function(){ - $(this).hide(); - }); + dataset_view.render(); + $('body').append(dataset_view.$el); }); </script></%def> @@ -97,7 +37,3 @@ <%def name="stylesheets()"> ${parent.stylesheets()} </%def> - -<div id="loading_indicator" ></div> -<table id="content_table" cellpadding="0"> -</table> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: ensure deleted or purged datasets are considered ready to the updater; pack scripts
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/909868dda881/ changeset: 909868dda881 user: carlfeberhard date: 2013-02-04 18:14:23 summary: history panel: ensure deleted or purged datasets are considered ready to the updater; pack scripts affected #: 3 files diff -r 596b4c29f84256767975caf9770d8c316d97386e -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -130,7 +130,8 @@ //TODO: to list inclusion test //TODO: class level readyStates list return ( - ( state === HistoryDatasetAssociation.STATES.OK ) + this.isDeletedOrPurged() + || ( state === HistoryDatasetAssociation.STATES.OK ) || ( state === HistoryDatasetAssociation.STATES.EMPTY ) || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) diff -r 596b4c29f84256767975caf9770d8c316d97386e -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return 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confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 596b4c29f84256767975caf9770d8c316d97386e -r 909868dda8812fcba2215a6eb77bdbaf71c6dfd0 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return(this.isDeletedOrPurged()||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 04 Feb '13

04 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1ab19b93abbd/ changeset: 1ab19b93abbd branch: next-stable user: inithello date: 2013-02-04 17:51:42 summary: Tool shed functional tests for complex repository dependencies, detection and setting of metadata for invalid repository dependencies. Fixes for detecting and displaying invalid repository dependencies. affected #: 10 files diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1292,8 +1292,8 @@ for repository_elem in root.findall( 'repository' ): current_rd_tups, error_message = handle_repository_elem( app, repository_elem, repository_dependencies_tups ) if error_message: + # Log the problem, but generate metadata for the invalid repository dependencies. log.debug( error_message ) - return metadata_dict, error_message for crdt in current_rd_tups: repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: @@ -1868,10 +1868,12 @@ .first() # We're in the tool shed. user = get_user_by_username( app, owner ) - return sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.name == name, - app.model.Repository.table.c.user_id == user.id ) ) \ - .first() + if user: + return sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + return None def get_repository_dependencies_for_changeset_revision( trans, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): @@ -2284,9 +2286,13 @@ def get_user_by_username( app, username ): """Get a user from the database by username.""" sa_session = app.model.context.current - return sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.username == username ) \ - .one() + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == username ) \ + .one() + return user + except Exception, e: + return None def handle_circular_repository_dependency( repository_key, repository_dependency, circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies ): all_repository_dependencies_root_key = all_repository_dependencies[ 'root_key' ] repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) @@ -2510,6 +2516,11 @@ else: # We're in the tool shed. if tool_shed_is_this_tool_shed( toolshed ): + # Append the repository dependency definition regardless of whether it's valid or not, as Galaxy needs this to + # properly display an error when the repository dependency is invalid at the time of installation. + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in new_rd_tups: + new_rd_tups.append( repository_dependencies_tup ) try: user = sa_session.query( app.model.User ) \ .filter( app.model.User.table.c.username == owner ) \ @@ -2539,9 +2550,6 @@ error_message = "Invalid changeset revision <b>%s</b> defined. Repository dependencies will be ignored." % str( changeset_revision ) log.debug( error_message ) return new_rd_tups, error_message - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) - if repository_dependencies_tup not in new_rd_tups: - new_rd_tups.append( repository_dependencies_tup ) else: # Repository dependencies are currentlhy supported within a single tool shed. error_message = "Invalid tool shed <b>%s</b> defined for repository <b>%s</b>. " % ( toolshed, name ) @@ -3179,7 +3187,7 @@ updating_installed_repository=False, persist=False ) # We'll only display error messages for the repository tip (it may be better to display error messages for each installable changeset revision). - if current_metadata_dict == repository.tip( trans.app ): + if current_changeset_revision == repository.tip( trans.app ): invalid_file_tups.extend( invalid_tups ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -11,8 +11,8 @@ echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" echo "'run_functional_tests.sh -list' for listing all the tool ids" - echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" - echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" + echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" + echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" elif [ $1 = '-id' ]; then python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html elif [ $1 = '-sid' ]; then diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -32,7 +32,7 @@ self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) self.shed_tool_conf = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF' ) # TODO: Figure out a way to alter these attributes during tests. - self.galaxy_tool_dependency_dir = None # os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) + self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} self.home() def add_repository_review_component( self, **kwd ): @@ -450,6 +450,10 @@ dependency_template = string.Template( common.complex_repository_dependency_template ) repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines='\n'.join( dependency_entries ) ) else: + if not description: + description = ' description=""' + else: + description = ' description="%s"' % description template_parser = string.Template( common.new_repository_dependencies_xml ) repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) # Save the generated xml to the specified location. @@ -625,7 +629,8 @@ ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_galaxy_url( url ) return util.listify( repository_ids ) - def install_repositories_from_search_results( self, repositories, strings_displayed=[], strings_not_displayed=[], **kwd ): + def install_repositories_from_search_results( self, repositories, install_tool_dependencies=False, + strings_displayed=[], strings_not_displayed=[], **kwd ): ''' Normally, it would be possible to check the appropriate boxes in the search results, and click the install button. This works in a browser, but Twill manages to lose the 'toolshedgalaxyurl' cookie between one page and the next, so it's necessary to work @@ -640,15 +645,12 @@ form = tc.browser.get_form( 'select_tool_panel_section' ) checkbox = form.find_control( id="install_tool_dependencies" ) checkbox.disabled = False - if 'install_tool_dependencies' in kwd: - install_tool_dependencies = kwd[ 'install_tool_dependencies' ] - del kwd[ 'install_tool_dependencies' ] - else: - install_tool_dependencies = False if install_tool_dependencies: checkbox.selected = True + kwd[ 'install_tool_dependencies' ] = 'True' else: checkbox.selected = False + kwd[ 'install_tool_dependencies' ] = 'False' self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) repository_ids = self.initiate_installation_process() self.wait_for_repository_installation( repository_ids ) @@ -676,8 +678,10 @@ checkbox.disabled = False if install_tool_dependencies: checkbox.selected = True + kwd[ 'install_tool_dependencies' ] = 'True' else: checkbox.selected = False + kwd[ 'install_tool_dependencies' ] = 'False' if 'install_repository_dependencies' in self.last_page(): kwd[ 'install_repository_dependencies' ] = str( install_repository_dependencies ).lower() if 'shed_tool_conf' not in kwd: @@ -688,7 +692,7 @@ self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) else: - self.check_for_strings(strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] ) + self.check_for_strings( strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] ) args = dict( shed_tool_conf=self.shed_tool_conf ) self.submit_form( 1, 'select_shed_tool_panel_config_button', **args ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -60,15 +60,16 @@ commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' ) def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' - name = repository.name - owner = repository.user.username - changeset_revision = self.get_repository_tip( repository ) + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'Invalid tool shed %s defined for repository %s' % ( url, repository.name ) ] + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ] self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -77,16 +78,16 @@ strings_displayed=strings_displayed ) def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): '''Generate and upload a complex repository definition that specifies an invalid repository name.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' - owner = repository.user.username - changeset_revision = self.get_repository_tip( repository ) + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = 'Ignoring repository dependency definition for tool shed %s, name %s, owner %s' % ( url, name, owner ) - strings_displayed += ', changeset revision %s because the name is invalid.' % changeset_revision + strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -95,15 +96,16 @@ strings_displayed=[ strings_displayed ] ) def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): '''Generate and upload a complex repository definition that specifies an invalid owner.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = repository.name + name = tool_repository.name owner = 'invalid_owner!?' - changeset_revision = self.get_repository_tip( repository ) + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'Invalid owner %s defined for repository %s. Repository dependencies will be ignored.' % ( owner, name ) ] + strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ] self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -112,16 +114,16 @@ strings_displayed=strings_displayed ) def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = repository.name - owner = repository.user.username + name = tool_repository.name + owner = tool_repository.user.username changeset_revision = '1234abcd' self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = 'Ignoring repository dependency definition for tool shed %s, name %s, owner %s' % ( url, name, owner ) - strings_displayed += ', changeset revision %s because the changeset revision is invalid.' % changeset_revision + strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -129,13 +131,21 @@ commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.', strings_displayed=[ strings_displayed ] ) def test_0035_generate_complex_repository_dependency( self ): - '''Generate and upload a tool_dependencies.xml file that specifies a repository rather than a tool.''' + '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) - self.create_repository_complex_dependency( base_repository, - self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ), - depends_on=dict( package='bwa', version='0.5.9', repositories=[ tool_repository ] ) ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) + self.upload_file( base_repository, + 'tool_dependencies.xml', + valid_tools_only=True, + filepath=dependency_path, + commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) self.check_repository_dependency( base_repository, tool_repository ) self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) def test_0040_update_base_repository( self ): diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py @@ -0,0 +1,129 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'emboss_datatypes_0110' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss_0110' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +category_name = 'Test 0110 Invalid Repository Dependencies' +category_desc = 'Test 0110 Invalid Repository Dependencies' + +class TestBasicRepositoryDependencies( ShedTwillTestCase ): + '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( name=category_name, description=category_desc ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): + '''Create and populate the emboss_datatypes repository.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): + '''Verify that the emboss_datatypes repository contains datatype entries.''' + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): + '''Create and populate the emboss_5_0110 repository.''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + def test_0025_generate_repository_dependency_with_invalid_url( self ): + '''Generate a repository dependency for emboss 5 with an invalid URL.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = repository.name + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0030_generate_repository_dependency_with_invalid_name( self ): + '''Generate a repository dependency for emboss 5 with an invalid name.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = '!?invalid?!' + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0035_generate_repository_dependency_with_invalid_owner( self ): + '''Generate a repository dependency for emboss 5 with an invalid owner.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = '!?invalid?!' + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ): + '''Generate a repository dependency for emboss 5 with an invalid changeset revision.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = repository.user.username + changeset_revision = '!?invalid?!' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -72,8 +72,8 @@ self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=strings_displayed ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' - strings_displayed=[ 'Never installed', 'can be automatically installed', 'Set the tool_dependency_dir' ] - strings_displayed.extend( [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] ) + strings_displayed=[ 'Never installed', 'dependencies can be automatically handled', 'Handle', 'tool dependencies' ] + strings_displayed.extend( [ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] ) self.install_repository( repository_name, common.test_user_1_name, category_name, diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -1,4 +1,4 @@ -from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os, logging +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util column_repository_name = 'column_maker_1087' @@ -12,8 +12,6 @@ category_name = 'Test 1087 Advanced Circular Dependencies' category_description = 'Test circular dependency features' -log = logging.getLogger( __name__ ) - class TestRepositoryDependencies( ShedTwillTestCase ): '''Test installing a repository, then updating it to include repository dependencies.''' def test_0000_create_or_login_admin_user( self ): @@ -91,7 +89,6 @@ convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) self.check_repository_dependency( column_repository, convert_repository ) - log.debug( [ repository.id for repository in test_db_util.get_all_installed_repositories() ] ) def test_0030_reinstall_column_repository( self ): '''Reinstall column_maker and verify that it now shows repository dependencies.''' installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -0,0 +1,228 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +bwa_base_repository_name = 'bwa_base_repository_0100' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" + +bwa_tool_repository_name = 'bwa_tool_repository_0100' +bwa_tool_repository_description = "BWA Tool" +bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." + +category_name = 'Test 0100 Complex Repository Dependencies' +category_description = 'Test 0100 Complex Repository Dependencies' +running_standalone = False + +class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ): + '''Test features related to installing repositories with complex repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_tool_repository( self ): + '''Create and populate bwa_tool_0100.''' + global running_standalone + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_tool_repository_name, + description=bwa_tool_repository_description, + long_description=bwa_tool_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'bwa/complex/tool_dependencies.xml', + strings_displayed=[], + commit_message='Uploaded tool_dependencies.xml.' ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) + def test_0010_create_bwa_base_repository( self ): + '''Create and populate bwa_base_0100.''' + global running_standalone + if running_standalone: + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_base_repository_name, + description=bwa_base_repository_description, + long_description=bwa_base_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'bwa/complex/bwa_base.tar', + strings_displayed=[], + commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' ) + def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): + '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ] + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid url.', + strings_displayed=strings_displayed ) + def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): + '''Generate and upload a complex repository definition that specifies an invalid repository name.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = 'invalid_repository!?' + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid repository name.', + strings_displayed=[ strings_displayed ] ) + def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): + '''Generate and upload a complex repository definition that specifies an invalid owner.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = tool_repository.name + owner = 'invalid_owner!?' + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ] + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid owner.', + strings_displayed=strings_displayed ) + def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): + '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = '1234abcd' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.', + strings_displayed=[ strings_displayed ] ) + def test_0035_generate_valid_complex_repository_dependency( self ): + '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' + global running_standalone + if running_standalone: + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) + self.upload_file( base_repository, + 'tool_dependencies.xml', + valid_tools_only=True, + filepath=dependency_path, + commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) + self.check_repository_dependency( base_repository, tool_repository ) + self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) + def test_0040_update_tool_repository( self ): + '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.''' + global running_standalone + if running_standalone: + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + previous_changeset = self.get_repository_tip( tool_repository ) + self.upload_file( tool_repository, + 'bwa/complex/readme/tool_dependencies.xml', + strings_displayed=[], + commit_message='Uploaded new tool_dependencies.xml.' ) + # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. + self.display_manage_repository_page( base_repository, + strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ], + strings_not_displayed=[ previous_changeset ] ) + def test_0045_install_base_repository( self ): + '''Verify installation of the repository with complex repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ] + self.install_repository( bwa_base_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=True, + preview_strings_displayed=preview_strings_displayed, + post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ], + includes_tools=True ) + def test_0050_verify_installed_repositories( self ): + '''Verify that the installed repositories are displayed properly.''' + base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + strings_displayed = [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision ] + strings_displayed.extend( [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ] ) + strings_displayed.append( self.url.replace( 'http://', '' ) ) + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] ) + checks = [ ( tool_repository, + [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'Missing tool dependencies' ] ), + ( base_repository, + [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision, tool_repository.name, + tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'Missing tool dependencies' ] ) ] + for repository, strings_displayed, strings_not_displayed in checks: + self.display_installed_repository_manage_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + def test_0055_verify_complex_tool_dependency( self ): + '''Verify that the generated env.sh contains the right data.''' + base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, + 'bwa', + '0.5.9', + base_repository.owner, + base_repository.name, + base_repository.installed_changeset_revision, + 'env.sh' ) + assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path + contents = file( env_sh_path, 'r' ).read() + if tool_repository.installed_changeset_revision not in contents or tool_repository.name not in contents: + raise AssertionError( 'The env.sh file was not correctly generated. Contents: %s' % contents ) + diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- /dev/null +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -0,0 +1,159 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'emboss_datatypes_0110' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss_0110' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +category_name = 'Test 0110 Invalid Repository Dependencies' +category_desc = 'Test 0110 Invalid Repository Dependencies' +running_standalone = False + +class TestBasicRepositoryDependencies( ShedTwillTestCase ): + '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( name=category_name, description=category_desc ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): + '''Create and populate the emboss_datatypes repository.''' + global running_standalone + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): + '''Verify that the emboss_datatypes repository contains datatype entries.''' + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): + '''Create and populate the emboss_5_0110 repository.''' + global running_standalone + if running_standalone: + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + def test_0025_generate_repository_dependency_with_invalid_url( self ): + '''Generate a repository dependency for emboss 5 with an invalid URL.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = repository.name + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0030_generate_repository_dependency_with_invalid_name( self ): + '''Generate a repository dependency for emboss 5 with an invalid name.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = '!?invalid?!' + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid name.', + strings_displayed=strings_displayed ) + def test_0035_generate_repository_dependency_with_invalid_owner( self ): + '''Generate a repository dependency for emboss 5 with an invalid owner.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = '!?invalid?!' + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid owner.', + strings_displayed=strings_displayed ) + def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ): + '''Generate a repository dependency for emboss 5 with an invalid changeset revision.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = repository.user.username + changeset_revision = '!?invalid?!' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid changeset revision.', + strings_displayed=strings_displayed ) + def test_0045_install_repository_with_invalid_repository_dependency( self ): + '''Install the repository and verify that galaxy detects invalid repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + preview_strings_displayed = [ repository.name, self.get_repository_tip( repository ), 'will be ignored' ] + self.install_repository( emboss_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + preview_strings_displayed=preview_strings_displayed, + post_submit_strings_displayed=[ repository.name, repository.name, 'new' ], + includes_tools=True ) + repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) + self.display_installed_repository_manage_page( repository, strings_not_displayed=[ 'Repository dependencies' ] ) diff -r 73bb36c4ee3b34c3ca32ed830b4f91df79b971c5 -r 1ab19b93abbdf10d831dd2b9804a0081d7867fac test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -288,6 +288,7 @@ shed_tool_path = galaxy_shed_tool_path, template_path = "templates", tool_data_path = tool_data_path, + tool_dependency_dir = galaxy_tool_dependency_dir, tool_path = tool_path, tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file = galaxy_tool_sheds_conf_file, @@ -391,18 +392,18 @@ galaxyapp.shutdown() galaxyapp = None log.info( "Embedded galaxy application stopped" ) - if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: - try: - for dir in [ tool_shed_test_tmp_dir ]: - if os.path.exists( dir ): - log.info( "Cleaning up temporary files in %s" % dir ) - shutil.rmtree( dir ) - except: - pass - if success: - return 0 - else: - return 1 +# if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: +# try: +# for dir in [ tool_shed_test_tmp_dir ]: +# if os.path.exists( dir ): +# log.info( "Cleaning up temporary files in %s" % dir ) +# shutil.rmtree( dir ) +# except: +# pass +# if success: +# return 0 +# else: +# return 1 if __name__ == "__main__": sys.exit( main() ) https://bitbucket.org/galaxy/galaxy-central/commits/596b4c29f842/ changeset: 596b4c29f842 user: inithello date: 2013-02-04 17:52:33 summary: Merged in changes from next-stable. affected #: 10 files diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1292,8 +1292,8 @@ for repository_elem in root.findall( 'repository' ): current_rd_tups, error_message = handle_repository_elem( app, repository_elem, repository_dependencies_tups ) if error_message: + # Log the problem, but generate metadata for the invalid repository dependencies. log.debug( error_message ) - return metadata_dict, error_message for crdt in current_rd_tups: repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: @@ -1868,10 +1868,12 @@ .first() # We're in the tool shed. user = get_user_by_username( app, owner ) - return sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.name == name, - app.model.Repository.table.c.user_id == user.id ) ) \ - .first() + if user: + return sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + return None def get_repository_dependencies_for_changeset_revision( trans, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): @@ -2284,9 +2286,13 @@ def get_user_by_username( app, username ): """Get a user from the database by username.""" sa_session = app.model.context.current - return sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.username == username ) \ - .one() + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == username ) \ + .one() + return user + except Exception, e: + return None def handle_circular_repository_dependency( repository_key, repository_dependency, circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies ): all_repository_dependencies_root_key = all_repository_dependencies[ 'root_key' ] repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) @@ -2510,6 +2516,11 @@ else: # We're in the tool shed. if tool_shed_is_this_tool_shed( toolshed ): + # Append the repository dependency definition regardless of whether it's valid or not, as Galaxy needs this to + # properly display an error when the repository dependency is invalid at the time of installation. + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in new_rd_tups: + new_rd_tups.append( repository_dependencies_tup ) try: user = sa_session.query( app.model.User ) \ .filter( app.model.User.table.c.username == owner ) \ @@ -2539,9 +2550,6 @@ error_message = "Invalid changeset revision <b>%s</b> defined. Repository dependencies will be ignored." % str( changeset_revision ) log.debug( error_message ) return new_rd_tups, error_message - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) - if repository_dependencies_tup not in new_rd_tups: - new_rd_tups.append( repository_dependencies_tup ) else: # Repository dependencies are currentlhy supported within a single tool shed. error_message = "Invalid tool shed <b>%s</b> defined for repository <b>%s</b>. " % ( toolshed, name ) @@ -3179,7 +3187,7 @@ updating_installed_repository=False, persist=False ) # We'll only display error messages for the repository tip (it may be better to display error messages for each installable changeset revision). - if current_metadata_dict == repository.tip( trans.app ): + if current_changeset_revision == repository.tip( trans.app ): invalid_file_tups.extend( invalid_tups ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -11,8 +11,8 @@ echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" echo "'run_functional_tests.sh -list' for listing all the tool ids" - echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" - echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" + echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" + echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" elif [ $1 = '-id' ]; then python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html elif [ $1 = '-sid' ]; then diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -32,7 +32,7 @@ self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) self.shed_tool_conf = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF' ) # TODO: Figure out a way to alter these attributes during tests. - self.galaxy_tool_dependency_dir = None # os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) + self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} self.home() def add_repository_review_component( self, **kwd ): @@ -450,6 +450,10 @@ dependency_template = string.Template( common.complex_repository_dependency_template ) repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines='\n'.join( dependency_entries ) ) else: + if not description: + description = ' description=""' + else: + description = ' description="%s"' % description template_parser = string.Template( common.new_repository_dependencies_xml ) repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) # Save the generated xml to the specified location. @@ -625,7 +629,8 @@ ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_galaxy_url( url ) return util.listify( repository_ids ) - def install_repositories_from_search_results( self, repositories, strings_displayed=[], strings_not_displayed=[], **kwd ): + def install_repositories_from_search_results( self, repositories, install_tool_dependencies=False, + strings_displayed=[], strings_not_displayed=[], **kwd ): ''' Normally, it would be possible to check the appropriate boxes in the search results, and click the install button. This works in a browser, but Twill manages to lose the 'toolshedgalaxyurl' cookie between one page and the next, so it's necessary to work @@ -640,15 +645,12 @@ form = tc.browser.get_form( 'select_tool_panel_section' ) checkbox = form.find_control( id="install_tool_dependencies" ) checkbox.disabled = False - if 'install_tool_dependencies' in kwd: - install_tool_dependencies = kwd[ 'install_tool_dependencies' ] - del kwd[ 'install_tool_dependencies' ] - else: - install_tool_dependencies = False if install_tool_dependencies: checkbox.selected = True + kwd[ 'install_tool_dependencies' ] = 'True' else: checkbox.selected = False + kwd[ 'install_tool_dependencies' ] = 'False' self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) repository_ids = self.initiate_installation_process() self.wait_for_repository_installation( repository_ids ) @@ -676,8 +678,10 @@ checkbox.disabled = False if install_tool_dependencies: checkbox.selected = True + kwd[ 'install_tool_dependencies' ] = 'True' else: checkbox.selected = False + kwd[ 'install_tool_dependencies' ] = 'False' if 'install_repository_dependencies' in self.last_page(): kwd[ 'install_repository_dependencies' ] = str( install_repository_dependencies ).lower() if 'shed_tool_conf' not in kwd: @@ -688,7 +692,7 @@ self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) else: - self.check_for_strings(strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] ) + self.check_for_strings( strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] ) args = dict( shed_tool_conf=self.shed_tool_conf ) self.submit_form( 1, 'select_shed_tool_panel_config_button', **args ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -60,15 +60,16 @@ commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' ) def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' - name = repository.name - owner = repository.user.username - changeset_revision = self.get_repository_tip( repository ) + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'Invalid tool shed %s defined for repository %s' % ( url, repository.name ) ] + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ] self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -77,16 +78,16 @@ strings_displayed=strings_displayed ) def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): '''Generate and upload a complex repository definition that specifies an invalid repository name.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' - owner = repository.user.username - changeset_revision = self.get_repository_tip( repository ) + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = 'Ignoring repository dependency definition for tool shed %s, name %s, owner %s' % ( url, name, owner ) - strings_displayed += ', changeset revision %s because the name is invalid.' % changeset_revision + strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -95,15 +96,16 @@ strings_displayed=[ strings_displayed ] ) def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): '''Generate and upload a complex repository definition that specifies an invalid owner.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = repository.name + name = tool_repository.name owner = 'invalid_owner!?' - changeset_revision = self.get_repository_tip( repository ) + changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'Invalid owner %s defined for repository %s. Repository dependencies will be ignored.' % ( owner, name ) ] + strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ] self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -112,16 +114,16 @@ strings_displayed=strings_displayed ) def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' - dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = repository.name - owner = repository.user.username + name = tool_repository.name + owner = tool_repository.user.username changeset_revision = '1234abcd' self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = 'Ignoring repository dependency definition for tool shed %s, name %s, owner %s' % ( url, name, owner ) - strings_displayed += ', changeset revision %s because the changeset revision is invalid.' % changeset_revision + strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision self.upload_file( repository, 'tool_dependencies.xml', valid_tools_only=False, @@ -129,13 +131,21 @@ commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.', strings_displayed=[ strings_displayed ] ) def test_0035_generate_complex_repository_dependency( self ): - '''Generate and upload a tool_dependencies.xml file that specifies a repository rather than a tool.''' + '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) - self.create_repository_complex_dependency( base_repository, - self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ), - depends_on=dict( package='bwa', version='0.5.9', repositories=[ tool_repository ] ) ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) + self.upload_file( base_repository, + 'tool_dependencies.xml', + valid_tools_only=True, + filepath=dependency_path, + commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) self.check_repository_dependency( base_repository, tool_repository ) self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) def test_0040_update_base_repository( self ): diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py @@ -0,0 +1,129 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'emboss_datatypes_0110' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss_0110' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +category_name = 'Test 0110 Invalid Repository Dependencies' +category_desc = 'Test 0110 Invalid Repository Dependencies' + +class TestBasicRepositoryDependencies( ShedTwillTestCase ): + '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( name=category_name, description=category_desc ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): + '''Create and populate the emboss_datatypes repository.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): + '''Verify that the emboss_datatypes repository contains datatype entries.''' + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): + '''Create and populate the emboss_5_0110 repository.''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + def test_0025_generate_repository_dependency_with_invalid_url( self ): + '''Generate a repository dependency for emboss 5 with an invalid URL.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = repository.name + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0030_generate_repository_dependency_with_invalid_name( self ): + '''Generate a repository dependency for emboss 5 with an invalid name.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = '!?invalid?!' + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0035_generate_repository_dependency_with_invalid_owner( self ): + '''Generate a repository dependency for emboss 5 with an invalid owner.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = '!?invalid?!' + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ): + '''Generate a repository dependency for emboss 5 with an invalid changeset revision.''' + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = repository.user.username + changeset_revision = '!?invalid?!' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -72,8 +72,8 @@ self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=strings_displayed ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' - strings_displayed=[ 'Never installed', 'can be automatically installed', 'Set the tool_dependency_dir' ] - strings_displayed.extend( [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] ) + strings_displayed=[ 'Never installed', 'dependencies can be automatically handled', 'Handle', 'tool dependencies' ] + strings_displayed.extend( [ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] ) self.install_repository( repository_name, common.test_user_1_name, category_name, diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -1,4 +1,4 @@ -from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os, logging +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util column_repository_name = 'column_maker_1087' @@ -12,8 +12,6 @@ category_name = 'Test 1087 Advanced Circular Dependencies' category_description = 'Test circular dependency features' -log = logging.getLogger( __name__ ) - class TestRepositoryDependencies( ShedTwillTestCase ): '''Test installing a repository, then updating it to include repository dependencies.''' def test_0000_create_or_login_admin_user( self ): @@ -91,7 +89,6 @@ convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) self.check_repository_dependency( column_repository, convert_repository ) - log.debug( [ repository.id for repository in test_db_util.get_all_installed_repositories() ] ) def test_0030_reinstall_column_repository( self ): '''Reinstall column_maker and verify that it now shows repository dependencies.''' installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -0,0 +1,228 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +bwa_base_repository_name = 'bwa_base_repository_0100' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" + +bwa_tool_repository_name = 'bwa_tool_repository_0100' +bwa_tool_repository_description = "BWA Tool" +bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." + +category_name = 'Test 0100 Complex Repository Dependencies' +category_description = 'Test 0100 Complex Repository Dependencies' +running_standalone = False + +class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ): + '''Test features related to installing repositories with complex repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_tool_repository( self ): + '''Create and populate bwa_tool_0100.''' + global running_standalone + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_tool_repository_name, + description=bwa_tool_repository_description, + long_description=bwa_tool_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'bwa/complex/tool_dependencies.xml', + strings_displayed=[], + commit_message='Uploaded tool_dependencies.xml.' ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) + def test_0010_create_bwa_base_repository( self ): + '''Create and populate bwa_base_0100.''' + global running_standalone + if running_standalone: + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_base_repository_name, + description=bwa_base_repository_description, + long_description=bwa_base_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'bwa/complex/bwa_base.tar', + strings_displayed=[], + commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' ) + def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): + '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ] + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid url.', + strings_displayed=strings_displayed ) + def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): + '''Generate and upload a complex repository definition that specifies an invalid repository name.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = 'invalid_repository!?' + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid repository name.', + strings_displayed=[ strings_displayed ] ) + def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): + '''Generate and upload a complex repository definition that specifies an invalid owner.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = tool_repository.name + owner = 'invalid_owner!?' + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ] + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid owner.', + strings_displayed=strings_displayed ) + def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): + '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = '1234abcd' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) + strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision + self.upload_file( repository, + 'tool_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.', + strings_displayed=[ strings_displayed ] ) + def test_0035_generate_valid_complex_repository_dependency( self ): + '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' + global running_standalone + if running_standalone: + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) + xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + url = self.url + name = tool_repository.name + owner = tool_repository.user.username + changeset_revision = self.get_repository_tip( tool_repository ) + self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) + self.upload_file( base_repository, + 'tool_dependencies.xml', + valid_tools_only=True, + filepath=dependency_path, + commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) + self.check_repository_dependency( base_repository, tool_repository ) + self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) + def test_0040_update_tool_repository( self ): + '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.''' + global running_standalone + if running_standalone: + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + previous_changeset = self.get_repository_tip( tool_repository ) + self.upload_file( tool_repository, + 'bwa/complex/readme/tool_dependencies.xml', + strings_displayed=[], + commit_message='Uploaded new tool_dependencies.xml.' ) + # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. + self.display_manage_repository_page( base_repository, + strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ], + strings_not_displayed=[ previous_changeset ] ) + def test_0045_install_base_repository( self ): + '''Verify installation of the repository with complex repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ] + self.install_repository( bwa_base_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=True, + preview_strings_displayed=preview_strings_displayed, + post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ], + includes_tools=True ) + def test_0050_verify_installed_repositories( self ): + '''Verify that the installed repositories are displayed properly.''' + base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + strings_displayed = [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision ] + strings_displayed.extend( [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ] ) + strings_displayed.append( self.url.replace( 'http://', '' ) ) + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] ) + checks = [ ( tool_repository, + [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'Missing tool dependencies' ] ), + ( base_repository, + [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision, tool_repository.name, + tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'Missing tool dependencies' ] ) ] + for repository, strings_displayed, strings_not_displayed in checks: + self.display_installed_repository_manage_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + def test_0055_verify_complex_tool_dependency( self ): + '''Verify that the generated env.sh contains the right data.''' + base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, + 'bwa', + '0.5.9', + base_repository.owner, + base_repository.name, + base_repository.installed_changeset_revision, + 'env.sh' ) + assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path + contents = file( env_sh_path, 'r' ).read() + if tool_repository.installed_changeset_revision not in contents or tool_repository.name not in contents: + raise AssertionError( 'The env.sh file was not correctly generated. Contents: %s' % contents ) + diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- /dev/null +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -0,0 +1,159 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'emboss_datatypes_0110' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss_0110' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +category_name = 'Test 0110 Invalid Repository Dependencies' +category_desc = 'Test 0110 Invalid Repository Dependencies' +running_standalone = False + +class TestBasicRepositoryDependencies( ShedTwillTestCase ): + '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( name=category_name, description=category_desc ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): + '''Create and populate the emboss_datatypes repository.''' + global running_standalone + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): + '''Verify that the emboss_datatypes repository contains datatype entries.''' + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): + '''Create and populate the emboss_5_0110 repository.''' + global running_standalone + if running_standalone: + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + def test_0025_generate_repository_dependency_with_invalid_url( self ): + '''Generate a repository dependency for emboss 5 with an invalid URL.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = 'http://http://this is not an url!' + name = repository.name + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', + strings_displayed=strings_displayed ) + def test_0030_generate_repository_dependency_with_invalid_name( self ): + '''Generate a repository dependency for emboss 5 with an invalid name.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = '!?invalid?!' + owner = repository.user.username + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid name.', + strings_displayed=strings_displayed ) + def test_0035_generate_repository_dependency_with_invalid_owner( self ): + '''Generate a repository dependency for emboss 5 with an invalid owner.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = '!?invalid?!' + changeset_revision = self.get_repository_tip( repository ) + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid owner.', + strings_displayed=strings_displayed ) + def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ): + '''Generate a repository dependency for emboss 5 with an invalid changeset revision.''' + global running_standalone + if running_standalone: + dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] ) + xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + url = self.url + name = repository.name + owner = repository.user.username + changeset_revision = '!?invalid?!' + self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ] + self.upload_file( emboss_repository, + 'repository_dependencies.xml', + valid_tools_only=False, + filepath=dependency_path, + commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid changeset revision.', + strings_displayed=strings_displayed ) + def test_0045_install_repository_with_invalid_repository_dependency( self ): + '''Install the repository and verify that galaxy detects invalid repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + preview_strings_displayed = [ repository.name, self.get_repository_tip( repository ), 'will be ignored' ] + self.install_repository( emboss_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + preview_strings_displayed=preview_strings_displayed, + post_submit_strings_displayed=[ repository.name, repository.name, 'new' ], + includes_tools=True ) + repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) + self.display_installed_repository_manage_page( repository, strings_not_displayed=[ 'Repository dependencies' ] ) diff -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 -r 596b4c29f84256767975caf9770d8c316d97386e test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -288,6 +288,7 @@ shed_tool_path = galaxy_shed_tool_path, template_path = "templates", tool_data_path = tool_data_path, + tool_dependency_dir = galaxy_tool_dependency_dir, tool_path = tool_path, tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file = galaxy_tool_sheds_conf_file, @@ -391,18 +392,18 @@ galaxyapp.shutdown() galaxyapp = None log.info( "Embedded galaxy application stopped" ) - if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: - try: - for dir in [ tool_shed_test_tmp_dir ]: - if os.path.exists( dir ): - log.info( "Cleaning up temporary files in %s" % dir ) - shutil.rmtree( dir ) - except: - pass - if success: - return 0 - else: - return 1 +# if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: +# try: +# for dir in [ tool_shed_test_tmp_dir ]: +# if os.path.exists( dir ): +# log.info( "Cleaning up temporary files in %s" % dir ) +# shutil.rmtree( dir ) +# except: +# pass +# if success: +# return 0 +# else: +# return 1 if __name__ == "__main__": sys.exit( main() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 04 Feb '13

04 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7627567df99c/ changeset: 7627567df99c user: jgoecks date: 2013-02-04 16:04:41 summary: Use from_work_dir for all Tophat2 output datasets rather than copying datasets in tool wrapper. affected #: 2 files diff -r cef2e9ff0960bab52fd481ec77585b6ecca8dfce -r 7627567df99c879146560ed523f903ed17d12fd6 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -260,11 +260,6 @@ if returncode != 0: raise Exception, stderr - # Copy output files from tmp directory to specified files. - shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), options.junctions_output_file ) - shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), options.accepted_hits_output_file ) - - # TODO: look for errors in program output. except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) diff -r cef2e9ff0960bab52fd481ec77585b6ecca8dfce -r 7627567df99c879146560ed523f903ed17d12fd6 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -356,7 +356,7 @@ </conditional></actions></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -375,7 +375,7 @@ </conditional></actions></data> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> https://bitbucket.org/galaxy/galaxy-central/commits/3de3a5a2d9b1/ changeset: 3de3a5a2d9b1 user: jgoecks date: 2013-02-04 16:06:13 summary: Use conditional so that from_work_dir is only active if file exists. This prevents spurious error messages when a tool fails. affected #: 1 file diff -r 7627567df99c879146560ed523f903ed17d12fd6 -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -34,11 +34,12 @@ if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - # -- Append commands to copy job outputs based on from_work_dir attribute. -- + # Append commands to copy job outputs based on from_work_dir attribute. if include_work_dir_outputs: work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) if work_dir_outputs: - commands += "; " + "; ".join( [ "cp %s %s" % ( source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) + commands += "; " + "; ".join( [ "if [ -f %s ] ; then cp %s %s ; fi" % + ( source_file, source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior 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: dan: Add sentry_dsn to Tool Shed config.py
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cef2e9ff0960/ changeset: cef2e9ff0960 user: dan date: 2013-02-04 12:48:48 summary: Add sentry_dsn to Tool Shed config.py affected #: 1 file diff -r 0ebd6f6f29553b4ac49f78d0106e412115948191 -r cef2e9ff0960bab52fd481ec77585b6ecca8dfce lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -92,6 +92,8 @@ self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] + # Error logging with sentry + self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root ) # Proxy features 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: dan: Backout 3189a1bf18af
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ebd6f6f2955/ changeset: 0ebd6f6f2955 user: dan date: 2013-02-04 12:43:35 summary: Backout 3189a1bf18af affected #: 15 files diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -59,7 +59,6 @@ <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/><datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/><datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> - <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/><datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"><converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/><converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -18,7 +18,6 @@ from galaxy.tools.genome_index import load_genome_index_tools from galaxy.sample_tracking import external_service_types from galaxy.openid.providers import OpenIDProviders -from galaxy.tools.data_manager.manager import DataManagers class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -94,8 +93,6 @@ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) # Search support for tools self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) - #datamanager - self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -75,10 +75,6 @@ except: self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) - self.enable_data_manager_user_view = string_as_bool( kwargs.get( "enable_data_manager_user_view", "False" ) ) - self.data_manager_config_file = resolve_path( kwargs.get(' data_manager_config_file', 'data_manager_conf.xml' ), self.root ) - self.data_manager_move_files = string_as_bool( kwargs.get( "data_manager_move_files", "False" ) ) - self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_dir', self.tool_data_path ) 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 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -44,7 +44,7 @@ log.debug( "%d workers ready", nworkers ) def run_next( self ): - """Run the next job, waiting until one is available if necessary""" + """Run the next job, waiting until one is available if neccesary""" while 1: job_wrapper = self.queue.get() if job_wrapper is self.STOP_SIGNAL: diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2996,20 +2996,6 @@ def set_item( self, visualization ): self.visualization = visualization -#Data Manager Classes -class DataManagerHistoryAssociation( object ): - def __init__( self, id=None, history=None, user=None ): - self.id = id - self.history = history - self.user = user - -class DataManagerJobAssociation( object ): - def __init__( self, id=None, job=None, data_manager_id=None ): - self.id = id - self.job = job - self.data_manager_id = data_manager_id -#end of Data Manager Classes - class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -930,23 +930,6 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) ) -#Data Manager tables -DataManagerHistoryAssociation.table = Table( "data_manager_history_association", metadata, - Column( "id", Integer, primary_key=True), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, index=True, default=now, onupdate=now ), - Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) - ) - -DataManagerJobAssociation.table = Table( "data_manager_job_association", metadata, - Column( "id", Integer, primary_key=True), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, index=True, default=now, onupdate=now ), - Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), - Column( "data_manager_id", TEXT, index=True ) - ) - # Tagging tables. Tag.table = Table( "tag", metadata, @@ -1916,17 +1899,6 @@ properties=dict( visualization=relation( Visualization ), user=relation( User ) ) ) -#Data Manager tables -assign_mapper( context, DataManagerHistoryAssociation, DataManagerHistoryAssociation.table, - properties=dict( history=relation( History ), - user=relation( User, backref='data_manager_histories' ) - ) - ) - -assign_mapper( context, DataManagerJobAssociation, DataManagerJobAssociation.table, - properties=dict( job=relation( Job, backref=backref('data_manager_association', uselist=False ), uselist=False ) ) - ) - # User tables. assign_mapper( context, UserPreference, UserPreference.table, diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -6,7 +6,7 @@ pkg_resources.require( "simplejson" ) pkg_resources.require( "Mako" ) -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re, pipes +import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re import simplejson import binascii from mako.template import Template @@ -25,7 +25,6 @@ from galaxy.util.expressions import ExpressionContext from galaxy.tools.test import ToolTestBuilder from galaxy.tools.actions import DefaultToolAction -from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager from galaxy.model import directory_hash_id from galaxy.model.orm import * @@ -80,7 +79,6 @@ # In-memory dictionary that defines the layout of the tool panel. self.tool_panel = odict() self.index = 0 - self.data_manager_tools = odict() # File that contains the XML section and tool tags from all tool panel config files integrated into a # single file that defines the tool panel layout. This file can be changed by the Galaxy administrator # (in a way similar to the single tool_conf.xml file in the past) to alter the layout of the tool panel. @@ -510,7 +508,7 @@ self.integrated_tool_panel[ key ] = integrated_section else: self.integrated_tool_panel.insert( index, key, integrated_section ) - def load_tool( self, config_file, guid=None, **kwds ): + def load_tool( self, config_file, guid=None ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element tree = util.parse_xml( config_file ) @@ -526,7 +524,7 @@ ToolClass = tool_types.get( root.get( 'tool_type' ) ) else: ToolClass = Tool - return ToolClass( config_file, root, self.app, guid=guid, **kwds ) + return ToolClass( config_file, root, self.app, guid=guid ) def reload_tool_by_id( self, tool_id ): """ Attempt to reload the tool identified by 'tool_id', if successful @@ -813,7 +811,6 @@ """ tool_type = 'default' - default_tool_action = DefaultToolAction def __init__( self, config_file, root, app, guid=None ): """Load a tool from the config named by `config_file`""" @@ -1054,7 +1051,7 @@ # Action action_elem = root.find( "action" ) if action_elem is None: - self.tool_action = self.default_tool_action() + self.tool_action = DefaultToolAction() else: module = action_elem.get( 'module' ) cls = action_elem.get( 'class' ) @@ -2573,24 +2570,18 @@ temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) try: a_files = os.listdir( temp_file_path ) - print 'a_files',a_files if len( a_files ) > 0: for f in a_files: - print 'f', f self.app.object_store.update_from_file(hda.dataset, extra_dir="dataset_%d_files" % hda.dataset.id, alt_name = f, file_name = os.path.join(temp_file_path, f), - create = True, - preserve_symlinks = True ) + create = True) # Clean up after being handled by object store. # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? - print 'before rmtree' shutil.rmtree(temp_file_path) - print 'after rm tree' - except Exception, e: - log.debug( "Error in collect_associated_files: %s" % ( e ) ) + except: continue def collect_child_datasets( self, output, job_working_directory ): """ @@ -2815,64 +2806,7 @@ return tool_dict - def get_default_history_by_trans( self, trans, create=False ): - return trans.get_history( create=create ) - - -class OutputParameterJSONTool( Tool ): - """ - Alternate implementation of Tool that provides parameters and other values - JSONified within the contents of an output dataset - """ - tool_type = 'output_parameter_json' - def _prepare_json_list( self, param_list ): - rval = [] - for value in param_list: - if isinstance( value, dict ): - rval.append( self._prepare_json_param_dict( value ) ) - elif isinstance( value, list ): - rval.append( self._prepare_json_list( value ) ) - else: - rval.append( str( value ) ) - return rval - def _prepare_json_param_dict( self, param_dict ): - rval = {} - for key, value in param_dict.iteritems(): - if isinstance( value, dict ): - rval[ key ] = self._prepare_json_param_dict( value ) - elif isinstance( value, list ): - rval[ key ] = self._prepare_json_list( value ) - else: - rval[ key ] = str( value ) - return rval - def exec_before_job( self, app, inp_data, out_data, param_dict=None ): - if param_dict is None: - param_dict = {} - json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? - json_params[ 'output_data' ] = [] - json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) - json_filename = None - for i, ( out_name, data ) in enumerate( out_data.iteritems() ): - #use wrapped dataset to access certain values - wrapped_data = param_dict.get( out_name ) - #allow multiple files to be created - file_name = str( wrapped_data ) - extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) - json_params[ 'output_data' ].append( data_dict ) - if json_filename is None: - json_filename = file_name - out = open( json_filename, 'w' ) - out.write( simplejson.dumps( json_params ) ) - out.close() - -class DataSourceTool( OutputParameterJSONTool ): +class DataSourceTool( Tool ): """ Alternate implementation of Tool for data_source tools -- those that allow the user to query and extract data from another web site. @@ -2882,10 +2816,29 @@ def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) def parse_inputs( self, root ): - super( DataSourceTool, self ).parse_inputs( root ) + Tool.parse_inputs( self, root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() - self.inputs_by_page[0][ 'GALAXY_URL' ] = self.inputs[ 'GALAXY_URL' ] + def _prepare_datasource_json_list( self, param_list ): + rval = [] + for value in param_list: + if isinstance( value, dict ): + rval.append( self._prepare_datasource_json_param_dict( value ) ) + elif isinstance( value, list ): + rval.append( self._prepare_datasource_json_list( value ) ) + else: + rval.append( str( value ) ) + return rval + def _prepare_datasource_json_param_dict( self, param_dict ): + rval = {} + for key, value in param_dict.iteritems(): + if isinstance( value, dict ): + rval[ key ] = self._prepare_datasource_json_param_dict( value ) + elif isinstance( value, list ): + rval[ key ] = self._prepare_datasource_json_list( value ) + else: + rval[ key ] = str( value ) + return rval def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} @@ -2895,7 +2848,7 @@ name = param_dict.get( 'name' ) json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -2986,186 +2939,9 @@ class GenomeIndexTool( Tool ): tool_type = 'index_genome' -class DataManagerTool( OutputParameterJSONTool ): - tool_type = 'manage_data' - default_tool_action = DataManagerToolAction - - def __init__( self, config_file, root, app, guid=None, data_manager_id=None, **kwds ): - self.data_manager_id = data_manager_id - super( DataManagerTool, self ).__init__( config_file, root, app, guid=guid, **kwds ) - if self.data_manager_id is None: - self.data_manager_id = self.id - - #def parse_inputs( self, root ): - # super( DataManagerTool, self ).parse_inputs( root ) - # ''' - # if '__GALAXY_MOVE_OUTPUT_FILES__' not in self.inputs: - # self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] = ToolParameter.build( self, ElementTree.XML( '<param name="__GALAXY_MOVE_OUTPUT_FILES__" label="Move created data to cache destination" type="boolean" truevalue="MOVE" falsevalue="DO_NOT_MOVE" checked="%s" />' % self.app.config.data_manager_move_files ) ) - # print 'self.inputs_by_page',self.inputs_by_page - # self.inputs_by_page[0][ '__GALAXY_MOVE_OUTPUT_FILES__' ] = self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] - # print 'self.inputs', self.inputs - # ''' - # #self.inputs[ '__DATA_MANAGER_ID__' ] = ToolParameter.build( self, ElementTree.XML( '<param name="__DATA_MANAGER_ID__" type="hidden" value="%s" />' % ( self.data_manager_id ) ) ) - # #self.inputs_by_page[0][ '__DATA_MANAGER_ID__' ] = self.inputs[ '__DATA_MANAGER_ID__' ] - - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): - #run original exec_after_process - super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) - #process results of tool - print 'exect after', self.id - print 'inp_data', inp_data - print 'out_data', out_data - print 'param_dict', param_dict - print 'job', job, job.state - if job and job.state == job.states.ERROR: - return - #print 'data_manager.output_ref',data_manager.output_ref - #data_manager = self.app.data_managers.get( self.id, None ) #fix me to not only use tool ID! - data_manager_id = job.data_manager_association.data_manager_id - data_manager = self.app.data_managers.get( data_manager_id, None ) - #TODO: need to be able to handle using a data manager tool for more than one manager - #manager id is currently same as tool id - assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id ) - data_manager_dicts = {} - data_manager_dict = {} - #TODO: fix this merging below - for output_name, output_dataset in out_data.iteritems(): - try: - output_dict = simplejson.loads( open( output_dataset.file_name ).read() ) - except Exception, e: - log.warning( 'Error reading DataManagerTool json for "%s": %s' % ( output_name, e ) ) - continue - data_manager_dicts[ output_name ] = output_dict - print 'data_manager_dicts', data_manager_dicts - for key, value in output_dict.iteritems(): - if key not in data_manager_dict: - data_manager_dict[ key ] = {} - print 'key', key - print ' data_manager_dict[ key ]', data_manager_dict[ key ] - print 'value', value - data_manager_dict[ key ].update( value ) - data_manager_dict.update( output_dict ) - - print 'data_manager_dicts',data_manager_dicts - print 'data_manager_dict', data_manager_dict - data_tables_dict = data_manager_dict.get( 'data_tables', {} ) - #for data_table_name, data_table_values in data_tables_dict.iteritems(): - for data_table_name, data_table_columns in data_manager.data_tables.iteritems(): - print 'data_table_name', data_table_name - data_table_values = data_tables_dict.pop( data_table_name, None ) #data_tables_dict.get( data_table_name, [] ) - if not data_table_values: - log.warning( 'No values for data table "%s" were returned by the data manager "%s".' % ( data_table_name, data_manager.id ) ) - continue #next data table - data_table = app.tool_data_tables.get( data_table_name, None ) - if data_table is None: - log.error( 'The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml' ) ) - continue #next table name - output_ref_values = {} - if data_table_name in data_manager.output_ref_by_data_table: - for data_table_column, output_ref in data_manager.output_ref_by_data_table[ data_table_name ].iteritems(): - output_ref_dataset = out_data.get( output_ref, None ) - assert output_ref_dataset is not None, "Referenced output was not found." - output_ref_values[ data_table_column ] = output_ref_dataset - print 'output_ref_values', output_ref_values - - final_data_table_values = [] - if not isinstance( data_table_values, list ): - data_table_values = [ data_table_values ] - columns = data_table.get_column_name_list() - - try: - data_table_fh = open( data_table.filename, 'r+b' ) - except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s' % ( data_table.filename, e ) ) - data_table_fh = open( data_table.filename, 'wb' ) - if os.stat( data_table.filename )[6] != 0: - # ensure last existing line ends with new line - data_table_fh.seek( -1, 2 ) #last char in file - last_char = data_table_fh.read() - if last_char not in [ '\n', '\r' ]: - data_table_fh.write( '\n' ) - for data_table_row in data_table_values: - data_table_value = dict( **data_table_row ) #keep original values here - for name, value in data_table_row.iteritems(): #FIXME: need to loop through here based upon order listed in data_manager config - if name in output_ref_values: - #TODO: Allow moving! - #if param_dict[ '__GALAXY_MOVE_OUTPUT_FILES__' ]: - # #FIXME: allow moving - # log.error( "\n\nShould be moving output files directory, but not implemented yet.\n" ) - # base_path = output_ref_values[ name ].extra_files_path - #else: - # base_path = output_ref_values[ name ].extra_files_path - moved = data_manager.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) - print 'moved', moved #should we always move? - data_table_value[ name ] = data_manager.process_value_translation( data_table_name, name, **data_table_value ) - final_data_table_values.append( data_table_value ) - fields = [] - for column_name in columns: - if column_name is None or column_name not in data_table_value: - fields.append( data_table.get_empty_field_by_name( column_name ) ) - else: - fields.append( data_table_value[ column_name ] ) - print 'fields', fields - #should we add a comment to file about automatically generated value here? - data_table_fh.write( "%s\n" % ( data_table.separator.join( self._replace_field_separators( fields, separator=data_table.separator ) ) ) ) #write out fields to disk - data_table.data.append( fields ) #add fields to loaded data table - print 'final_data_table_values', final_data_table_values - print 'data_table.data', data_table.data - data_table_fh.close() - for data_table_name, data_table_values in data_tables_dict.iteritems(): - #tool returned extra data table entries, but data table was not declared in data manager - #do not add these values, but do provide messages - log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, self.app.data_managers.filename ) ) - - def _replace_field_separators( self, fields, separator="\t", replace=None, comment_char=None ): - #make sure none of the fields contain separator - #make sure separator replace is different from comment_char, - #due to possible leading replace - if replace is None: - if separator == " ": - if comment_char == "\t": - replace = "_" - else: - replace = "\t" - else: - if comment_char == " ": - replace = "_" - else: - replace = " " - return map( lambda x: x.replace( separator, replace ), fields ) - - def get_default_history_by_trans( self, trans, create=False ): - def _create_data_manager_history( user ): - history = trans.app.model.History( name='Data Manager History (automatically created)', user=user ) - data_manager_association = trans.app.model.DataManagerHistoryAssociation( user=user, history=history ) - trans.sa_session.add_all( ( history, data_manager_association ) ) - trans.sa_session.flush() - return history - user = trans.user - assert user, 'You must be logged in to use this tool.' - history = user.data_manager_histories - if not history: - #create - if create: - history = _create_data_manager_history( user ) - else: - history = None - else: - for history in reversed( history ): - history = history.history - if not history.deleted: - break - if history.deleted: - if create: - history = _create_data_manager_history( user ) - else: - history = None - return history - - # Populate tool_type to ToolClass mappings tool_types = {} -for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]: +for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool ]: tool_types[ tool_class.tool_type ] = tool_class # ---- Utility classes to be factored out ----------------------------------- @@ -3207,12 +2983,6 @@ """ def __nonzero__( self ): return bool( self.value ) - def get_display_text( self, quote=True ): - print 'self.input',self.input - print 'self.input.tool.app', self.input.tool.app - print 'self.value', self.value - print 'self.input.value_to_display_text( self.value, self.input.tool.app )', self.input.value_to_display_text( self.value, self.input.tool.app ) - return pipes.quote( self.input.value_to_display_text( self.value, self.input.tool.app ) ) class RawObjectWrapper( ToolParameterValueWrapper ): """ diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -168,7 +168,7 @@ # Set history. if not history: - history = tool.get_default_history_by_trans( trans, create=True ) #trans..history + history = trans.history out_data = odict() # Collect any input datasets from the incoming parameters diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -28,11 +28,6 @@ return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) - def get( self, name, default=None ): - try: - return self[ name ] - except KeyError: - return default def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: @@ -130,8 +125,6 @@ def __init__( self, config_element, tool_data_path ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) - self.empty_field_value = config_element.get( 'empty_field_value', '' ) - self.empty_field_values = {} for file_elem in config_element.findall( 'file' ): # There should only be one file_elem. if 'path' in file_elem.attrib: @@ -141,8 +134,6 @@ self.tool_data_file = None self.tool_data_path = tool_data_path self.missing_index_file = None - def get_empty_field_by_name( self, name ): - return self.empty_field_values.get( name, self.empty_field_value ) class TabularToolDataTable( ToolDataTable ): """ @@ -185,7 +176,6 @@ if os.path.exists( filename ): found = True all_rows.extend( self.parse_file_fields( open( filename ) ) ) - self.filename = filename else: # Since the path attribute can include a hard-coded path to a specific directory # (e.g., <file path="tool-data/cg_crr_files.loc" />) which may not be the same value @@ -197,7 +187,6 @@ if os.path.exists( corrected_filename ): found = True all_rows.extend( self.parse_file_fields( open( corrected_filename ) ) ) - self.filename = corrected_filename if not found: self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) @@ -233,9 +222,6 @@ self.columns[name] = index if index > self.largest_index: self.largest_index = index - empty_field_value = column_elem.get( 'empty_field_value', None ) - if empty_field_value is not None: - self.empty_field_values[ name ] = empty_field_value assert 'value' in self.columns, "Required 'value' column missing from column def" if 'name' not in self.columns: self.columns['name'] = self.columns['value'] @@ -254,19 +240,7 @@ fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) - return rval - def get_column_name_list( self ): - rval = [] - for i in range( self.largest_index + 1 ): - found_column = False - for name, index in self.columns.iteritems(): - if index == i: - rval.append( name ) - found_column = True - break - if not found_column: - rval.append( None ) - return rval + return rval # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -880,9 +880,6 @@ >>> print p.filter_value( "hg17" ) hg17 """ - def __init__( self, *args, **kwds ): - super( GenomeBuildParameter, self ).__init__( *args, **kwds ) - self.static_options = [ ( value, key, False ) for key, value in util.dbnames ] def get_options( self, trans, other_values ): if not trans.history: yield 'unspecified', '?', False diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -567,22 +567,6 @@ return curdir return join( *rel_list ) -def relativize_symlinks( path, start=None, followlinks=False): - for root, dirs, files in os.walk( path, followlinks=followlinks ): - rel_start = None - for file_name in files: - symlink_file_name = os.path.join( root, file_name ) - if os.path.islink( symlink_file_name ): - symlink_target = os.readlink( symlink_file_name ) - if rel_start is None: - if start is None: - rel_start = root - else: - rel_start = start - rel_path = relpath( symlink_target, rel_start ) - os.remove( symlink_file_name ) - os.symlink( rel_path, symlink_file_name ) - def stringify_dictionary_keys( in_dict ): #returns a new dictionary #changes unicode keys into strings, only works on top level (does not recurse) diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -92,8 +92,6 @@ self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] - # Error logging with sentry - self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root ) # Proxy features diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -89,8 +89,7 @@ tool.input_translator.translate( params ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. - #history = trans.get_history( create=True ) - history = tool.get_default_history_by_trans( trans, create=True ) + history = trans.get_history( create=True ) template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -57,10 +57,8 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div><div class="toolTitle"><a href="${h.url_for( controller='library_admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> %if trans.app.config.enable_beta_job_managers: - <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage old local data</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage local data</a></div> %endif - ##how to name this? - <div class="toolTitle"><a href="${h.url_for( controller='data_manager' )}" target="galaxy_main">Manage local (cached) data (beta)</a></div></div></div><div class="toolSectionPad"></div> diff -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 -r 0ebd6f6f29553b4ac49f78d0106e412115948191 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -33,7 +33,7 @@ </param><param name="async_datasets" type="hidden" value="None"/><upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> - <param name="file_data" type="file" size="30" label="File" ajax-upload="False" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."><validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator></param><param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 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: dan: Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3189a1bf18af/ changeset: 3189a1bf18af user: dan date: 2013-02-04 12:33:19 summary: Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py affected #: 15 files diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -59,6 +59,7 @@ <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/><datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/><datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/><datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"><converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/><converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -18,6 +18,7 @@ from galaxy.tools.genome_index import load_genome_index_tools from galaxy.sample_tracking import external_service_types from galaxy.openid.providers import OpenIDProviders +from galaxy.tools.data_manager.manager import DataManagers class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -93,6 +94,8 @@ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) # Search support for tools self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + #datamanager + self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -75,6 +75,10 @@ except: self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) + self.enable_data_manager_user_view = string_as_bool( kwargs.get( "enable_data_manager_user_view", "False" ) ) + self.data_manager_config_file = resolve_path( kwargs.get(' data_manager_config_file', 'data_manager_conf.xml' ), self.root ) + self.data_manager_move_files = string_as_bool( kwargs.get( "data_manager_move_files", "False" ) ) + self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_dir', self.tool_data_path ) 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 d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -44,7 +44,7 @@ log.debug( "%d workers ready", nworkers ) def run_next( self ): - """Run the next job, waiting until one is available if neccesary""" + """Run the next job, waiting until one is available if necessary""" while 1: job_wrapper = self.queue.get() if job_wrapper is self.STOP_SIGNAL: diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2996,6 +2996,20 @@ def set_item( self, visualization ): self.visualization = visualization +#Data Manager Classes +class DataManagerHistoryAssociation( object ): + def __init__( self, id=None, history=None, user=None ): + self.id = id + self.history = history + self.user = user + +class DataManagerJobAssociation( object ): + def __init__( self, id=None, job=None, data_manager_id=None ): + self.id = id + self.job = job + self.data_manager_id = data_manager_id +#end of Data Manager Classes + class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -930,6 +930,23 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) ) +#Data Manager tables +DataManagerHistoryAssociation.table = Table( "data_manager_history_association", metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) + ) + +DataManagerJobAssociation.table = Table( "data_manager_job_association", metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "data_manager_id", TEXT, index=True ) + ) + # Tagging tables. Tag.table = Table( "tag", metadata, @@ -1899,6 +1916,17 @@ properties=dict( visualization=relation( Visualization ), user=relation( User ) ) ) +#Data Manager tables +assign_mapper( context, DataManagerHistoryAssociation, DataManagerHistoryAssociation.table, + properties=dict( history=relation( History ), + user=relation( User, backref='data_manager_histories' ) + ) + ) + +assign_mapper( context, DataManagerJobAssociation, DataManagerJobAssociation.table, + properties=dict( job=relation( Job, backref=backref('data_manager_association', uselist=False ), uselist=False ) ) + ) + # User tables. assign_mapper( context, UserPreference, UserPreference.table, diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -6,7 +6,7 @@ pkg_resources.require( "simplejson" ) pkg_resources.require( "Mako" ) -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re +import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re, pipes import simplejson import binascii from mako.template import Template @@ -25,6 +25,7 @@ from galaxy.util.expressions import ExpressionContext from galaxy.tools.test import ToolTestBuilder from galaxy.tools.actions import DefaultToolAction +from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager from galaxy.model import directory_hash_id from galaxy.model.orm import * @@ -79,6 +80,7 @@ # In-memory dictionary that defines the layout of the tool panel. self.tool_panel = odict() self.index = 0 + self.data_manager_tools = odict() # File that contains the XML section and tool tags from all tool panel config files integrated into a # single file that defines the tool panel layout. This file can be changed by the Galaxy administrator # (in a way similar to the single tool_conf.xml file in the past) to alter the layout of the tool panel. @@ -508,7 +510,7 @@ self.integrated_tool_panel[ key ] = integrated_section else: self.integrated_tool_panel.insert( index, key, integrated_section ) - def load_tool( self, config_file, guid=None ): + def load_tool( self, config_file, guid=None, **kwds ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element tree = util.parse_xml( config_file ) @@ -524,7 +526,7 @@ ToolClass = tool_types.get( root.get( 'tool_type' ) ) else: ToolClass = Tool - return ToolClass( config_file, root, self.app, guid=guid ) + return ToolClass( config_file, root, self.app, guid=guid, **kwds ) def reload_tool_by_id( self, tool_id ): """ Attempt to reload the tool identified by 'tool_id', if successful @@ -811,6 +813,7 @@ """ tool_type = 'default' + default_tool_action = DefaultToolAction def __init__( self, config_file, root, app, guid=None ): """Load a tool from the config named by `config_file`""" @@ -1051,7 +1054,7 @@ # Action action_elem = root.find( "action" ) if action_elem is None: - self.tool_action = DefaultToolAction() + self.tool_action = self.default_tool_action() else: module = action_elem.get( 'module' ) cls = action_elem.get( 'class' ) @@ -2570,18 +2573,24 @@ temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) try: a_files = os.listdir( temp_file_path ) + print 'a_files',a_files if len( a_files ) > 0: for f in a_files: + print 'f', f self.app.object_store.update_from_file(hda.dataset, extra_dir="dataset_%d_files" % hda.dataset.id, alt_name = f, file_name = os.path.join(temp_file_path, f), - create = True) + create = True, + preserve_symlinks = True ) # Clean up after being handled by object store. # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? + print 'before rmtree' shutil.rmtree(temp_file_path) - except: + print 'after rm tree' + except Exception, e: + log.debug( "Error in collect_associated_files: %s" % ( e ) ) continue def collect_child_datasets( self, output, job_working_directory ): """ @@ -2806,7 +2815,64 @@ return tool_dict -class DataSourceTool( Tool ): + def get_default_history_by_trans( self, trans, create=False ): + return trans.get_history( create=create ) + + +class OutputParameterJSONTool( Tool ): + """ + Alternate implementation of Tool that provides parameters and other values + JSONified within the contents of an output dataset + """ + tool_type = 'output_parameter_json' + def _prepare_json_list( self, param_list ): + rval = [] + for value in param_list: + if isinstance( value, dict ): + rval.append( self._prepare_json_param_dict( value ) ) + elif isinstance( value, list ): + rval.append( self._prepare_json_list( value ) ) + else: + rval.append( str( value ) ) + return rval + def _prepare_json_param_dict( self, param_dict ): + rval = {} + for key, value in param_dict.iteritems(): + if isinstance( value, dict ): + rval[ key ] = self._prepare_json_param_dict( value ) + elif isinstance( value, list ): + rval[ key ] = self._prepare_json_list( value ) + else: + rval[ key ] = str( value ) + return rval + def exec_before_job( self, app, inp_data, out_data, param_dict=None ): + if param_dict is None: + param_dict = {} + json_params = {} + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'output_data' ] = [] + json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) + json_filename = None + for i, ( out_name, data ) in enumerate( out_data.iteritems() ): + #use wrapped dataset to access certain values + wrapped_data = param_dict.get( out_name ) + #allow multiple files to be created + file_name = str( wrapped_data ) + extra_files_path = str( wrapped_data.files_path ) + data_dict = dict( out_data_name = out_name, + ext = data.ext, + dataset_id = data.dataset.id, + hda_id = data.id, + file_name = file_name, + extra_files_path = extra_files_path ) + json_params[ 'output_data' ].append( data_dict ) + if json_filename is None: + json_filename = file_name + out = open( json_filename, 'w' ) + out.write( simplejson.dumps( json_params ) ) + out.close() + +class DataSourceTool( OutputParameterJSONTool ): """ Alternate implementation of Tool for data_source tools -- those that allow the user to query and extract data from another web site. @@ -2816,29 +2882,10 @@ def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) def parse_inputs( self, root ): - Tool.parse_inputs( self, root ) + super( DataSourceTool, self ).parse_inputs( root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() - def _prepare_datasource_json_list( self, param_list ): - rval = [] - for value in param_list: - if isinstance( value, dict ): - rval.append( self._prepare_datasource_json_param_dict( value ) ) - elif isinstance( value, list ): - rval.append( self._prepare_datasource_json_list( value ) ) - else: - rval.append( str( value ) ) - return rval - def _prepare_datasource_json_param_dict( self, param_dict ): - rval = {} - for key, value in param_dict.iteritems(): - if isinstance( value, dict ): - rval[ key ] = self._prepare_datasource_json_param_dict( value ) - elif isinstance( value, list ): - rval[ key ] = self._prepare_datasource_json_list( value ) - else: - rval[ key ] = str( value ) - return rval + self.inputs_by_page[0][ 'GALAXY_URL' ] = self.inputs[ 'GALAXY_URL' ] def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} @@ -2848,7 +2895,7 @@ name = param_dict.get( 'name' ) json_params = {} - json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -2939,9 +2986,186 @@ class GenomeIndexTool( Tool ): tool_type = 'index_genome' +class DataManagerTool( OutputParameterJSONTool ): + tool_type = 'manage_data' + default_tool_action = DataManagerToolAction + + def __init__( self, config_file, root, app, guid=None, data_manager_id=None, **kwds ): + self.data_manager_id = data_manager_id + super( DataManagerTool, self ).__init__( config_file, root, app, guid=guid, **kwds ) + if self.data_manager_id is None: + self.data_manager_id = self.id + + #def parse_inputs( self, root ): + # super( DataManagerTool, self ).parse_inputs( root ) + # ''' + # if '__GALAXY_MOVE_OUTPUT_FILES__' not in self.inputs: + # self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] = ToolParameter.build( self, ElementTree.XML( '<param name="__GALAXY_MOVE_OUTPUT_FILES__" label="Move created data to cache destination" type="boolean" truevalue="MOVE" falsevalue="DO_NOT_MOVE" checked="%s" />' % self.app.config.data_manager_move_files ) ) + # print 'self.inputs_by_page',self.inputs_by_page + # self.inputs_by_page[0][ '__GALAXY_MOVE_OUTPUT_FILES__' ] = self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] + # print 'self.inputs', self.inputs + # ''' + # #self.inputs[ '__DATA_MANAGER_ID__' ] = ToolParameter.build( self, ElementTree.XML( '<param name="__DATA_MANAGER_ID__" type="hidden" value="%s" />' % ( self.data_manager_id ) ) ) + # #self.inputs_by_page[0][ '__DATA_MANAGER_ID__' ] = self.inputs[ '__DATA_MANAGER_ID__' ] + + def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): + #run original exec_after_process + super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) + #process results of tool + print 'exect after', self.id + print 'inp_data', inp_data + print 'out_data', out_data + print 'param_dict', param_dict + print 'job', job, job.state + if job and job.state == job.states.ERROR: + return + #print 'data_manager.output_ref',data_manager.output_ref + #data_manager = self.app.data_managers.get( self.id, None ) #fix me to not only use tool ID! + data_manager_id = job.data_manager_association.data_manager_id + data_manager = self.app.data_managers.get( data_manager_id, None ) + #TODO: need to be able to handle using a data manager tool for more than one manager + #manager id is currently same as tool id + assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id ) + data_manager_dicts = {} + data_manager_dict = {} + #TODO: fix this merging below + for output_name, output_dataset in out_data.iteritems(): + try: + output_dict = simplejson.loads( open( output_dataset.file_name ).read() ) + except Exception, e: + log.warning( 'Error reading DataManagerTool json for "%s": %s' % ( output_name, e ) ) + continue + data_manager_dicts[ output_name ] = output_dict + print 'data_manager_dicts', data_manager_dicts + for key, value in output_dict.iteritems(): + if key not in data_manager_dict: + data_manager_dict[ key ] = {} + print 'key', key + print ' data_manager_dict[ key ]', data_manager_dict[ key ] + print 'value', value + data_manager_dict[ key ].update( value ) + data_manager_dict.update( output_dict ) + + print 'data_manager_dicts',data_manager_dicts + print 'data_manager_dict', data_manager_dict + data_tables_dict = data_manager_dict.get( 'data_tables', {} ) + #for data_table_name, data_table_values in data_tables_dict.iteritems(): + for data_table_name, data_table_columns in data_manager.data_tables.iteritems(): + print 'data_table_name', data_table_name + data_table_values = data_tables_dict.pop( data_table_name, None ) #data_tables_dict.get( data_table_name, [] ) + if not data_table_values: + log.warning( 'No values for data table "%s" were returned by the data manager "%s".' % ( data_table_name, data_manager.id ) ) + continue #next data table + data_table = app.tool_data_tables.get( data_table_name, None ) + if data_table is None: + log.error( 'The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml' ) ) + continue #next table name + output_ref_values = {} + if data_table_name in data_manager.output_ref_by_data_table: + for data_table_column, output_ref in data_manager.output_ref_by_data_table[ data_table_name ].iteritems(): + output_ref_dataset = out_data.get( output_ref, None ) + assert output_ref_dataset is not None, "Referenced output was not found." + output_ref_values[ data_table_column ] = output_ref_dataset + print 'output_ref_values', output_ref_values + + final_data_table_values = [] + if not isinstance( data_table_values, list ): + data_table_values = [ data_table_values ] + columns = data_table.get_column_name_list() + + try: + data_table_fh = open( data_table.filename, 'r+b' ) + except IOError, e: + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s' % ( data_table.filename, e ) ) + data_table_fh = open( data_table.filename, 'wb' ) + if os.stat( data_table.filename )[6] != 0: + # ensure last existing line ends with new line + data_table_fh.seek( -1, 2 ) #last char in file + last_char = data_table_fh.read() + if last_char not in [ '\n', '\r' ]: + data_table_fh.write( '\n' ) + for data_table_row in data_table_values: + data_table_value = dict( **data_table_row ) #keep original values here + for name, value in data_table_row.iteritems(): #FIXME: need to loop through here based upon order listed in data_manager config + if name in output_ref_values: + #TODO: Allow moving! + #if param_dict[ '__GALAXY_MOVE_OUTPUT_FILES__' ]: + # #FIXME: allow moving + # log.error( "\n\nShould be moving output files directory, but not implemented yet.\n" ) + # base_path = output_ref_values[ name ].extra_files_path + #else: + # base_path = output_ref_values[ name ].extra_files_path + moved = data_manager.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) + print 'moved', moved #should we always move? + data_table_value[ name ] = data_manager.process_value_translation( data_table_name, name, **data_table_value ) + final_data_table_values.append( data_table_value ) + fields = [] + for column_name in columns: + if column_name is None or column_name not in data_table_value: + fields.append( data_table.get_empty_field_by_name( column_name ) ) + else: + fields.append( data_table_value[ column_name ] ) + print 'fields', fields + #should we add a comment to file about automatically generated value here? + data_table_fh.write( "%s\n" % ( data_table.separator.join( self._replace_field_separators( fields, separator=data_table.separator ) ) ) ) #write out fields to disk + data_table.data.append( fields ) #add fields to loaded data table + print 'final_data_table_values', final_data_table_values + print 'data_table.data', data_table.data + data_table_fh.close() + for data_table_name, data_table_values in data_tables_dict.iteritems(): + #tool returned extra data table entries, but data table was not declared in data manager + #do not add these values, but do provide messages + log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, self.app.data_managers.filename ) ) + + def _replace_field_separators( self, fields, separator="\t", replace=None, comment_char=None ): + #make sure none of the fields contain separator + #make sure separator replace is different from comment_char, + #due to possible leading replace + if replace is None: + if separator == " ": + if comment_char == "\t": + replace = "_" + else: + replace = "\t" + else: + if comment_char == " ": + replace = "_" + else: + replace = " " + return map( lambda x: x.replace( separator, replace ), fields ) + + def get_default_history_by_trans( self, trans, create=False ): + def _create_data_manager_history( user ): + history = trans.app.model.History( name='Data Manager History (automatically created)', user=user ) + data_manager_association = trans.app.model.DataManagerHistoryAssociation( user=user, history=history ) + trans.sa_session.add_all( ( history, data_manager_association ) ) + trans.sa_session.flush() + return history + user = trans.user + assert user, 'You must be logged in to use this tool.' + history = user.data_manager_histories + if not history: + #create + if create: + history = _create_data_manager_history( user ) + else: + history = None + else: + for history in reversed( history ): + history = history.history + if not history.deleted: + break + if history.deleted: + if create: + history = _create_data_manager_history( user ) + else: + history = None + return history + + # Populate tool_type to ToolClass mappings tool_types = {} -for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool ]: +for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]: tool_types[ tool_class.tool_type ] = tool_class # ---- Utility classes to be factored out ----------------------------------- @@ -2983,6 +3207,12 @@ """ def __nonzero__( self ): return bool( self.value ) + def get_display_text( self, quote=True ): + print 'self.input',self.input + print 'self.input.tool.app', self.input.tool.app + print 'self.value', self.value + print 'self.input.value_to_display_text( self.value, self.input.tool.app )', self.input.value_to_display_text( self.value, self.input.tool.app ) + return pipes.quote( self.input.value_to_display_text( self.value, self.input.tool.app ) ) class RawObjectWrapper( ToolParameterValueWrapper ): """ diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -168,7 +168,7 @@ # Set history. if not history: - history = trans.history + history = tool.get_default_history_by_trans( trans, create=True ) #trans..history out_data = odict() # Collect any input datasets from the incoming parameters diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -28,6 +28,11 @@ return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) + def get( self, name, default=None ): + try: + return self[ name ] + except KeyError: + return default def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: @@ -125,6 +130,8 @@ def __init__( self, config_element, tool_data_path ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) + self.empty_field_value = config_element.get( 'empty_field_value', '' ) + self.empty_field_values = {} for file_elem in config_element.findall( 'file' ): # There should only be one file_elem. if 'path' in file_elem.attrib: @@ -134,6 +141,8 @@ self.tool_data_file = None self.tool_data_path = tool_data_path self.missing_index_file = None + def get_empty_field_by_name( self, name ): + return self.empty_field_values.get( name, self.empty_field_value ) class TabularToolDataTable( ToolDataTable ): """ @@ -176,6 +185,7 @@ if os.path.exists( filename ): found = True all_rows.extend( self.parse_file_fields( open( filename ) ) ) + self.filename = filename else: # Since the path attribute can include a hard-coded path to a specific directory # (e.g., <file path="tool-data/cg_crr_files.loc" />) which may not be the same value @@ -187,6 +197,7 @@ if os.path.exists( corrected_filename ): found = True all_rows.extend( self.parse_file_fields( open( corrected_filename ) ) ) + self.filename = corrected_filename if not found: self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) @@ -222,6 +233,9 @@ self.columns[name] = index if index > self.largest_index: self.largest_index = index + empty_field_value = column_elem.get( 'empty_field_value', None ) + if empty_field_value is not None: + self.empty_field_values[ name ] = empty_field_value assert 'value' in self.columns, "Required 'value' column missing from column def" if 'name' not in self.columns: self.columns['name'] = self.columns['value'] @@ -240,7 +254,19 @@ fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) - return rval + return rval + def get_column_name_list( self ): + rval = [] + for i in range( self.largest_index + 1 ): + found_column = False + for name, index in self.columns.iteritems(): + if index == i: + rval.append( name ) + found_column = True + break + if not found_column: + rval.append( None ) + return rval # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -880,6 +880,9 @@ >>> print p.filter_value( "hg17" ) hg17 """ + def __init__( self, *args, **kwds ): + super( GenomeBuildParameter, self ).__init__( *args, **kwds ) + self.static_options = [ ( value, key, False ) for key, value in util.dbnames ] def get_options( self, trans, other_values ): if not trans.history: yield 'unspecified', '?', False diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -567,6 +567,22 @@ return curdir return join( *rel_list ) +def relativize_symlinks( path, start=None, followlinks=False): + for root, dirs, files in os.walk( path, followlinks=followlinks ): + rel_start = None + for file_name in files: + symlink_file_name = os.path.join( root, file_name ) + if os.path.islink( symlink_file_name ): + symlink_target = os.readlink( symlink_file_name ) + if rel_start is None: + if start is None: + rel_start = root + else: + rel_start = start + rel_path = relpath( symlink_target, rel_start ) + os.remove( symlink_file_name ) + os.symlink( rel_path, symlink_file_name ) + def stringify_dictionary_keys( in_dict ): #returns a new dictionary #changes unicode keys into strings, only works on top level (does not recurse) diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -92,6 +92,8 @@ self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] + # Error logging with sentry + self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root ) # Proxy features diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -89,7 +89,8 @@ tool.input_translator.translate( params ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. - history = trans.get_history( create=True ) + #history = trans.get_history( create=True ) + history = tool.get_default_history_by_trans( trans, create=True ) template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -57,8 +57,10 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div><div class="toolTitle"><a href="${h.url_for( controller='library_admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> %if trans.app.config.enable_beta_job_managers: - <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage local data</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage old local data</a></div> %endif + ##how to name this? + <div class="toolTitle"><a href="${h.url_for( controller='data_manager' )}" target="galaxy_main">Manage local (cached) data (beta)</a></div></div></div><div class="toolSectionPad"></div> diff -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 -r 3189a1bf18af72f750e476caa54d7e3ae2d3cc36 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -33,7 +33,7 @@ </param><param name="async_datasets" type="hidden" value="None"/><upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> - <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."> + <param name="file_data" type="file" size="30" label="File" ajax-upload="False" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."><validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator></param><param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 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.

1 0

commit/galaxy-central: james_taylor: error middleware: return writable from start_response correctly
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7f4d3a8d0b2/ changeset: d7f4d3a8d0b2 user: james_taylor date: 2013-02-04 06:09:23 summary: error middleware: return writable from start_response correctly affected #: 1 file diff -r 0c1b71a50ccb5b6f5aff233b40355d84141960c6 -r d7f4d3a8d0b273163ae3d04872e211b7dcfbeba9 lib/galaxy/web/framework/middleware/error.py --- a/lib/galaxy/web/framework/middleware/error.py +++ b/lib/galaxy/web/framework/middleware/error.py @@ -200,7 +200,9 @@ def __call__(self, *args): self.response_started = True - self.start_response(*args) + # Return whatever the wrapped start_response would have + # returned + return self.start_response(*args) class CatchingIter(object): 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.

1 0

commit/galaxy-central: james_taylor: genetrack: missed one reference to display application
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0c1b71a50ccb/ changeset: 0c1b71a50ccb user: james_taylor date: 2013-02-04 05:39:06 summary: genetrack: missed one reference to display application affected #: 1 file diff -r 898c9e140da953fe18ebfda5a96b9810d372706d -r 0c1b71a50ccb5b6f5aff233b40355d84141960c6 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -114,7 +114,6 @@ <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/> - <display file="genetrack.xml" inherit="True"/><display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/><display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/><display file="rviewer/bed.xml" inherit="True"/> 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.

1 0

commit/galaxy-central: james_taylor: remove comment from sentry middleware that is not a valid doctest
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/898c9e140da9/ changeset: 898c9e140da9 user: james_taylor date: 2013-02-04 05:27:04 summary: remove comment from sentry middleware that is not a valid doctest affected #: 1 file diff -r b59a3df615c3542cb05ad68dc851669928a586d8 -r 898c9e140da953fe18ebfda5a96b9810d372706d lib/galaxy/web/framework/middleware/sentry.py --- a/lib/galaxy/web/framework/middleware/sentry.py +++ b/lib/galaxy/web/framework/middleware/sentry.py @@ -16,9 +16,6 @@ """ A WSGI middleware which will attempt to capture any uncaught exceptions and send them to Sentry. - - >>> from raven.base import Client - >>> application = Sentry(application, Client()) """ def __init__(self, application, dsn): self.application = application 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.

1 0

commit/galaxy-central: james_taylor: Add some missing files
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b59a3df615c3/ changeset: b59a3df615c3 user: james_taylor date: 2013-02-04 05:22:16 summary: Add some missing files affected #: 2 files diff -r 17c40da527fe8fee481ead85bdf8069776fc8f44 -r b59a3df615c3542cb05ad68dc851669928a586d8 lib/galaxy/web/framework/middleware/request_id.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/request_id.py @@ -0,0 +1,12 @@ +import uuid + +class RequestIDMiddleware( object ): + """ + A WSGI middleware that creates a unique ID for the request and + puts it in the environment + """ + def __init__( self, app, global_conf=None ): + self.app = app + def __call__( self, environ, start_response ): + environ['request_id'] = uuid.uuid1().hex + return self.app( environ, start_response ) \ No newline at end of file diff -r 17c40da527fe8fee481ead85bdf8069776fc8f44 -r b59a3df615c3542cb05ad68dc851669928a586d8 static/scripts/packed/libs/jquery/select2.js --- /dev/null +++ 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?/,""))}this.container.css(s(E.containerCss));this.container.addClass(s(E.containerCssClass));this.opts.element.data("select2",this).hide().before(this.container);this.container.data("select2",this);this.dropdown=this.container.find(".select2-drop");this.dropdown.addClass(s(E.dropdownCssClass));this.dropdown.data("select2",this);this.results=D=this.container.find(F);this.search=C=this.container.find("input.select2-input");C.attr("tabIndex",this.opts.element.attr("tabIndex"));this.resultsPage=0;this.context=null;this.initContainer();this.initContainerWidth();u(this.results);this.dropdown.delegate(F,"mousemove-filtered",this.bind(this.highlightUnderEvent));g(80,this.results);this.dropdown.delegate(F,"scroll-debounced",this.bind(this.loadMoreIfNeeded));if(j.fn.mousewheel){D.mousewheel(function(K,L,I,H){var J=D.scrollTop(),G;if(H>0&&J-H<=0){D.scrollTop(0);d(K)}else{if(H<0&&D.get(0).scrollHeight-D.scrollTop()+H<=D.height()){D.scrollTop(D.get(0).scrollHeight-D.height());d(K)}}})}z(C);C.bind("keyup-change",this.bind(this.updateResults));C.bind("focus",function(){C.addClass("select2-focused");if(C.val()===" "){C.val("")}});C.bind("blur",function(){C.removeClass("select2-focused")});this.dropdown.delegate(F,"mouseup",this.bind(function(G){if(j(G.target).closest(".select2-result-selectable:not(.select2-disabled)").length>0){this.highlightUnderEvent(G);this.selectHighlighted(G)}else{this.focusSearch()}d(G)}));this.dropdown.bind("click mouseup mousedown",function(G){G.stopPropagation()});if(j.isFunction(this.opts.initSelection)){this.initSelection();this.monitorSource()}if(E.element.is(":disabled")||E.element.is("[readonly='readonly']")){this.disable()}},destroy:function(){var C=this.opts.element.data("select2");if(C!==l){C.container.remove();C.dropdown.remove();C.opts.element.removeData("select2").unbind(".select2").show()}},prepareOpts:function(G){var E,D,C,F;E=G.element;if(E.get(0).tagName.toLowerCase()==="select"){this.select=D=G.element}if(D){j.each(["id","multiple","ajax","query","createSearchChoice","initSelection","data","tags"],function(){if(this in G){throw new Error("Option '"+this+"' is not allowed for Select2 when attached to a <select> element.")}})}G=j.extend({},{populateResults:function(H,L,N){var M,K,P,J,I=this.opts.id,O=this;M=function(V,Q,U){var W,S,ab,Y,aa,R,Z,X,T;for(W=0,S=V.length;W<S;W=W+1){ab=V[W];Y=I(ab)!==l;aa=ab.children&&ab.children.length>0;R=j("<li></li>");R.addClass("select2-results-dept-"+U);R.addClass("select2-result");R.addClass(Y?"select2-result-selectable":"select2-result-unselectable");if(aa){R.addClass("select2-result-with-children")}R.addClass(O.opts.formatResultCssClass(ab));Z=j("<div></div>");Z.addClass("select2-result-label");T=G.formatResult(ab,Z,N);if(T!==l){Z.html(O.opts.escapeMarkup(T))}R.append(Z);if(aa){X=j("<ul></ul>");X.addClass("select2-result-sub");M(ab.children,X,U+1);R.append(X)}R.data("select2-data",ab);Q.append(R)}};M(L,H,0)}},j.fn.select2.defaults,G);if(typeof(G.id)!=="function"){C=G.id;G.id=function(H){return H[C]}}if(D){G.query=this.bind(function(K){var J={results:[],more:false},I=K.term,H,M,L;L=function(N,P){var 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G=this.container.offset(),O=this.container.outerHeight(),D=this.container.outerWidth(),F=this.dropdown.outerHeight(),K=j(window).scrollTop()+document.documentElement.clientHeight,C=G.top+O,N=G.left,L=C+F<=K,J=(G.top-F)>=this.body().scrollTop(),E=this.dropdown.hasClass("select2-drop-above"),H,M,I;if(this.body().css("position")!=="static"){H=this.body().offset();C-=H.top;N-=H.left}if(E){M=true;if(!J&&L){M=false}}else{M=false;if(!L&&J){M=true}}if(M){C=G.top-F;this.container.addClass("select2-drop-above");this.dropdown.addClass("select2-drop-above")}else{this.container.removeClass("select2-drop-above");this.dropdown.removeClass("select2-drop-above")}I=j.extend({top:C,left:N,width:D},s(this.opts.dropdownCss));this.dropdown.css(I)},shouldOpen:function(){var C;if(this.opened()){return false}C=j.Event("open");this.opts.element.trigger(C);return !C.isDefaultPrevented()},clearDropdownAlignmentPreference:function(){this.container.removeClass("select2-drop-above");this.dropdown.removeClass("select2-drop-above")},open:function(){if(!this.shouldOpen()){return false}window.setTimeout(this.bind(this.opening),1);return true},opening:function(){var F=this.containerId,D=this.containerSelector,C="scroll."+F,E="resize."+F;this.container.parents().each(function(){j(this).bind(C,function(){var G=j(D);if(G.length==0){j(this).unbind(C)}G.select2("close")})});j(window).bind(E,function(){var G=j(D);if(G.length==0){j(window).unbind(E)}G.select2("close")});this.clearDropdownAlignmentPreference();if(this.search.val()===" "){this.search.val("")}this.container.addClass("select2-dropdown-open").addClass("select2-container-active");this.updateResults(true);if(this.dropdown[0]!==this.body().children().last()[0]){this.dropdown.detach().appendTo(this.body())}this.dropdown.show();this.positionDropdown();this.dropdown.addClass("select2-drop-active");this.ensureHighlightVisible();this.focusSearch()},close:function(){if(!this.opened()){return}var C=this;this.container.parents().each(function(){j(this).unbind("scroll."+C.containerId)});j(window).unbind("resize."+this.containerId);this.clearDropdownAlignmentPreference();this.dropdown.hide();this.container.removeClass("select2-dropdown-open").removeClass("select2-container-active");this.results.empty();this.clearSearch();this.opts.element.trigger(j.Event("close"))},clearSearch:function(){},ensureHighlightVisible:function(){var F=this.results,E,C,J,I,G,H,D;C=this.highlight();if(C<0){return}if(C==0){F.scrollTop(0);return}E=F.find(".select2-result-selectable");J=j(E[C]);I=J.offset().top+J.outerHeight();if(C===E.length-1){D=F.find("li.select2-more-results");if(D.length>0){I=D.offset().top+D.outerHeight()}}G=F.offset().top+F.outerHeight();if(I>G){F.scrollTop(F.scrollTop()+(I-G))}H=J.offset().top-F.offset().top;if(H<0){F.scrollTop(F.scrollTop()+H)}},moveHighlight:function(F){var E=this.results.find(".select2-result-selectable"),D=this.highlight();while(D>-1&&D<E.length){D+=F;var C=j(E[D]);if(C.hasClass("select2-result-selectable")&&!C.hasClass("select2-disabled")){this.highlight(D);break}}},highlight:function(C){var D=this.results.find(".select2-result-selectable").not(".select2-disabled");if(arguments.length===0){return b(D.filter(".select2-highlighted")[0],D.get())}if(C>=D.length){C=D.length-1}if(C<0){C=0}D.removeClass("select2-highlighted");j(D[C]).addClass("select2-highlighted");this.ensureHighlightVisible()},countSelectableResults:function(){return this.results.find(".select2-result-selectable").not(".select2-disabled").length},highlightUnderEvent:function(D){var C=j(D.target).closest(".select2-result-selectable");if(C.length>0&&!C.is(".select2-highlighted")){var E=this.results.find(".select2-result-selectable");this.highlight(E.index(C))}else{if(C.length==0){this.results.find(".select2-highlighted").removeClass("select2-highlighted")}}},loadMoreIfNeeded:function(){var G=this.results,F=G.find("li.select2-more-results"),J,I=-1,H=this.resultsPage+1,C=this,E=this.search.val(),D=this.context;if(F.length===0){return}J=F.offset().top-G.offset().top-G.height();if(J<=0){F.addClass("select2-active");this.opts.query({term:E,page:H,context:D,matcher:this.opts.matcher,callback:this.bind(function(K){if(!C.opened()){return}C.opts.populateResults.call(this,G,K.results,{term:E,page:H,context:D});if(K.more===true){F.detach().appendTo(G).text(C.opts.formatLoadMore(H+1));window.setTimeout(function(){C.loadMoreIfNeeded()},10)}else{F.remove()}C.positionDropdown();C.resultsPage=H})})}},tokenize:function(){},updateResults:function(H){var K=this.search,F=this.results,C=this.opts,E,J=this,I;if(H!==true&&(this.showSearchInput===false||!this.opened())){return}K.addClass("select2-active");function G(){F.scrollTop(0);K.removeClass("select2-active");J.positionDropdown()}function D(L){F.html(J.opts.escapeMarkup(L));G()}if(C.maximumSelectionSize>=1){E=this.data();if(j.isArray(E)&&E.length>=C.maximumSelectionSize&&k(C.formatSelectionTooBig,"formatSelectionTooBig")){D("<li class='select2-selection-limit'>"+C.formatSelectionTooBig(C.maximumSelectionSize)+"</li>");return}}if(K.val().length<C.minimumInputLength&&k(C.formatInputTooShort,"formatInputTooShort")){D("<li class='select2-no-results'>"+C.formatInputTooShort(K.val(),C.minimumInputLength)+"</li>");return}else{D("<li class='select2-searching'>"+C.formatSearching()+"</li>")}I=this.tokenize();if(I!=l&&I!=null){K.val(I)}this.resultsPage=1;C.query({term:K.val(),page:this.resultsPage,context:null,matcher:C.matcher,callback:this.bind(function(M){var L;if(!this.opened()){return}this.context=(M.context===l)?null:M.context;if(this.opts.createSearchChoice&&K.val()!==""){L=this.opts.createSearchChoice.call(null,K.val(),M.results);if(L!==l&&L!==null&&J.id(L)!==l&&J.id(L)!==null){if(j(M.results).filter(function(){return q(J.id(this),J.id(L))}).length===0){M.results.unshift(L)}}}if(M.results.length===0&&k(C.formatNoMatches,"formatNoMatches")){D("<li class='select2-no-results'>"+C.formatNoMatches(K.val())+"</li>");return}F.empty();J.opts.populateResults.call(this,F,M.results,{term:K.val(),page:this.resultsPage,context:null});if(M.more===true&&k(C.formatLoadMore,"formatLoadMore")){F.append("<li class='select2-more-results'>"+J.opts.escapeMarkup(C.formatLoadMore(this.resultsPage))+"</li>");window.setTimeout(function(){J.loadMoreIfNeeded()},10)}this.postprocessResults(M,H);G()})})},cancel:function(){this.close()},blur:function(){this.close();this.container.removeClass("select2-container-active");this.dropdown.removeClass("select2-drop-active");if(this.search[0]===document.activeElement){this.search.blur()}this.clearSearch();this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")},focusSearch:function(){this.search.show();this.search.focus();window.setTimeout(this.bind(function(){this.search.show();this.search.focus();this.search.val(this.search.val())}),10)},selectHighlighted:function(){var C=this.highlight(),D=this.results.find(".select2-highlighted").not(".select2-disabled"),E=D.closest(".select2-result-selectable").data("select2-data");if(E){D.addClass("select2-disabled");this.highlight(C);this.onSelect(E)}},getPlaceholder:function(){return this.opts.element.attr("placeholder")||this.opts.element.attr("data-placeholder")||this.opts.element.data("placeholder")||this.opts.placeholder},initContainerWidth:function(){function D(){var H,F,I,G,E;if(this.opts.width==="off"){return null}else{if(this.opts.width==="element"){return this.opts.element.outerWidth()===0?"auto":this.opts.element.outerWidth()+"px"}else{if(this.opts.width==="copy"||this.opts.width==="resolve"){H=this.opts.element.attr("style");if(H!==l){F=H.split(";");for(G=0,E=F.length;G<E;G=G+1){I=F[G].replace(/\s/g,"").match(/width:(([-+]?([0-9]*\.)?[0-9]+)(px|em|ex|%|in|cm|mm|pt|pc))/);if(I!==null&&I.length>=1){return I[1]}}}if(this.opts.width==="resolve"){H=this.opts.element.css("width");if(H.indexOf("%")>0){return H}return(this.opts.element.outerWidth()===0?"auto":this.opts.element.outerWidth()+"px")}return null}else{if(j.isFunction(this.opts.width)){return this.opts.width()}else{return this.opts.width}}}}}var C=D.call(this);if(C!==null){this.container.attr("style","width: "+C)}}});v=w(e,{createContainer:function(){var C=j("<div></div>",{"class":"select2-container"}).html([" <a href='#' onclick='return false;' class='select2-choice'>"," <span></span><abbr class='select2-search-choice-close' style='display:none;'></abbr>"," <div><b></b></div>","</a>"," <div class='select2-drop select2-offscreen'>"," <div class='select2-search'>"," <input type='text' autocomplete='off' class='select2-input'/>"," </div>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return C},opening:function(){this.search.show();this.parent.opening.apply(this,arguments);this.dropdown.removeClass("select2-offscreen")},close:function(){if(!this.opened()){return}this.parent.close.apply(this,arguments);this.dropdown.removeAttr("style").addClass("select2-offscreen").insertAfter(this.selection).show()},focus:function(){this.close();this.selection.focus()},isFocused:function(){return this.selection[0]===document.activeElement},cancel:function(){this.parent.cancel.apply(this,arguments);this.selection.focus()},initContainer:function(){var E,D=this.container,F=this.dropdown,C=false;this.selection=E=D.find(".select2-choice");this.search.bind("keydown",this.bind(function(G){if(!this.enabled){return}if(G.which===c.PAGE_UP||G.which===c.PAGE_DOWN){d(G);return}if(this.opened()){switch(G.which){case c.UP:case c.DOWN:this.moveHighlight((G.which===c.UP)?-1:1);d(G);return;case c.TAB:case c.ENTER:this.selectHighlighted();d(G);return;case c.ESC:this.cancel(G);d(G);return}}else{if(G.which===c.TAB||c.isControl(G)||c.isFunctionKey(G)||G.which===c.ESC){return}if(this.opts.openOnEnter===false&&G.which===c.ENTER){return}this.open();if(G.which===c.ENTER){return}}}));this.search.bind("focus",this.bind(function(){this.selection.attr("tabIndex","-1")}));this.search.bind("blur",this.bind(function(){if(!this.opened()){this.container.removeClass("select2-container-active")}window.setTimeout(this.bind(function(){this.selection.attr("tabIndex",this.opts.element.attr("tabIndex"))}),10)}));E.bind("mousedown",this.bind(function(G){C=true;if(this.opened()){this.close();this.selection.focus()}else{if(this.enabled){this.open()}}C=false}));F.bind("mousedown",this.bind(function(){this.search.focus()}));E.bind("focus",this.bind(function(){this.container.addClass("select2-container-active");this.search.attr("tabIndex","-1")}));E.bind("blur",this.bind(function(){if(!this.opened()){this.container.removeClass("select2-container-active")}window.setTimeout(this.bind(function(){this.search.attr("tabIndex",this.opts.element.attr("tabIndex"))}),10)}));E.bind("keydown",this.bind(function(H){if(!this.enabled){return}if(H.which===c.PAGE_UP||H.which===c.PAGE_DOWN){d(H);return}if(H.which===c.TAB||c.isControl(H)||c.isFunctionKey(H)||H.which===c.ESC){return}if(this.opts.openOnEnter===false&&H.which===c.ENTER){return}if(H.which==c.DELETE){if(this.opts.allowClear){this.clear()}return}this.open();if(H.which===c.ENTER){d(H);return}if(H.which<48){d(H);return}var G=String.fromCharCode(H.which).toLowerCase();if(H.shiftKey){G=G.toUpperCase()}this.search.focus();this.search.val(G);d(H)}));E.delegate("abbr","mousedown",this.bind(function(G){if(!this.enabled){return}this.clear();d(G);this.close();this.triggerChange();this.selection.focus()}));this.setPlaceholder();this.search.bind("focus",this.bind(function(){this.container.addClass("select2-container-active")}))},clear:function(){this.opts.element.val("");this.selection.find("span").empty();this.selection.removeData("select2-data");this.setPlaceholder()},initSelection:function(){var D;if(this.opts.element.val()===""){this.close();this.setPlaceholder()}else{var C=this;this.opts.initSelection.call(null,this.opts.element,function(E){if(E!==l&&E!==null){C.updateSelection(E);C.close();C.setPlaceholder()}})}},prepareOpts:function(){var C=this.parent.prepareOpts.apply(this,arguments);if(C.element.get(0).tagName.toLowerCase()==="select"){C.initSelection=function(D,F){var E=D.find(":selected");if(j.isFunction(F)){F({id:E.attr("value"),text:E.text()})}}}return C},setPlaceholder:function(){var C=this.getPlaceholder();if(this.opts.element.val()===""&&C!==l){if(this.select&&this.select.find("option:first").text()!==""){return}this.selection.find("span").html(this.opts.escapeMarkup(C));this.selection.addClass("select2-default");this.selection.find("abbr").hide()}},postprocessResults:function(F,D){var E=0,C=this,G=true;this.results.find(".select2-result-selectable").each2(function(H,I){if(q(C.id(I.data("select2-data")),C.opts.element.val())){E=H;return false}});this.highlight(E);if(D===true){G=this.showSearchInput=h(F.results)>=this.opts.minimumResultsForSearch;this.dropdown.find(".select2-search")[G?"removeClass":"addClass"]("select2-search-hidden");j(this.dropdown,this.container)[G?"addClass":"removeClass"]("select2-with-searchbox")}},onSelect:function(D){var C=this.opts.element.val();this.opts.element.val(this.id(D));this.updateSelection(D);this.close();this.selection.focus();if(!q(C,this.id(D))){this.triggerChange()}},updateSelection:function(E){var C=this.selection.find("span"),D;this.selection.data("select2-data",E);C.empty();D=this.opts.formatSelection(E,C);if(D!==l){C.append(this.opts.escapeMarkup(D))}this.selection.removeClass("select2-default");if(this.opts.allowClear&&this.getPlaceholder()!==l){this.selection.find("abbr").show()}},val:function(){var E,D=null,C=this;if(arguments.length===0){return this.opts.element.val()}E=arguments[0];if(this.select){this.select.val(E).find(":selected").each2(function(F,G){D={id:G.attr("value"),text:G.text()};return false});this.updateSelection(D);this.setPlaceholder()}else{if(this.opts.initSelection===l){throw new Error("cannot call val() if initSelection() is not defined")}if(!E){this.clear();return}this.opts.element.val(E);this.opts.initSelection(this.opts.element,function(F){C.opts.element.val(!F?"":C.id(F));C.updateSelection(F);C.setPlaceholder()})}},clearSearch:function(){this.search.val("")},data:function(D){var C;if(arguments.length===0){C=this.selection.data("select2-data");if(C==l){C=null}return C}else{if(!D||D===""){this.clear()}else{this.opts.element.val(!D?"":this.id(D));this.updateSelection(D)}}}});B=w(e,{createContainer:function(){var C=j("<div></div>",{"class":"select2-container select2-container-multi"}).html([" <ul class='select2-choices'>"," <li class='select2-search-field'>"," <input type='text' autocomplete='off' class='select2-input'>"," </li>","</ul>","<div class='select2-drop select2-drop-multi' style='display:none;'>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return C},prepareOpts:function(){var C=this.parent.prepareOpts.apply(this,arguments);if(C.element.get(0).tagName.toLowerCase()==="select"){C.initSelection=function(D,F){var E=[];D.find(":selected").each2(function(G,H){E.push({id:H.attr("value"),text:H.text()})});if(j.isFunction(F)){F(E)}}}return C},initContainer:function(){var C=".select2-choices",D;this.searchContainer=this.container.find(".select2-search-field");this.selection=D=this.container.find(C);this.search.bind("keydown",this.bind(function(F){if(!this.enabled){return}if(F.which===c.BACKSPACE&&this.search.val()===""){this.close();var G,E=D.find(".select2-search-choice-focus");if(E.length>0){this.unselect(E.first());this.search.width(10);d(F);return}G=D.find(".select2-search-choice");if(G.length>0){G.last().addClass("select2-search-choice-focus")}}else{D.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")}if(this.opened()){switch(F.which){case c.UP:case c.DOWN:this.moveHighlight((F.which===c.UP)?-1:1);d(F);return;case c.ENTER:case c.TAB:this.selectHighlighted();d(F);return;case c.ESC:this.cancel(F);d(F);return}}if(F.which===c.TAB||c.isControl(F)||c.isFunctionKey(F)||F.which===c.BACKSPACE||F.which===c.ESC){return}if(this.opts.openOnEnter===false&&F.which===c.ENTER){return}this.open();if(F.which===c.PAGE_UP||F.which===c.PAGE_DOWN){d(F)}}));this.search.bind("keyup",this.bind(this.resizeSearch));this.search.bind("blur",this.bind(function(E){this.container.removeClass("select2-container-active");this.search.removeClass("select2-focused");this.clearSearch();E.stopImmediatePropagation()}));this.container.delegate(C,"mousedown",this.bind(function(E){if(!this.enabled){return}if(j(E.target).closest(".select2-search-choice").length>0){return}this.clearPlaceholder();this.open();this.focusSearch();E.preventDefault()}));this.container.delegate(C,"focus",this.bind(function(){if(!this.enabled){return}this.container.addClass("select2-container-active");this.dropdown.addClass("select2-drop-active");this.clearPlaceholder()}));this.clearSearch()},enable:function(){if(this.enabled){return}this.parent.enable.apply(this,arguments);this.search.removeAttr("disabled")},disable:function(){if(!this.enabled){return}this.parent.disable.apply(this,arguments);this.search.attr("disabled",true)},initSelection:function(){var D;if(this.opts.element.val()===""){this.updateSelection([]);this.close();this.clearSearch()}if(this.select||this.opts.element.val()!==""){var C=this;this.opts.initSelection.call(null,this.opts.element,function(E){if(E!==l&&E!==null){C.updateSelection(E);C.close();C.clearSearch()}})}},clearSearch:function(){var C=this.getPlaceholder();if(C!==l&&this.getVal().length===0&&this.search.hasClass("select2-focused")===false){this.search.val(C).addClass("select2-default");this.resizeSearch()}else{this.search.val(" ").width(10)}},clearPlaceholder:function(){if(this.search.hasClass("select2-default")){this.search.val("").removeClass("select2-default")}else{if(this.search.val()===" "){this.search.val("")}}},opening:function(){this.parent.opening.apply(this,arguments);this.clearPlaceholder();this.resizeSearch();this.focusSearch()},close:function(){if(!this.opened()){return}this.parent.close.apply(this,arguments)},focus:function(){this.close();this.search.focus()},isFocused:function(){return this.search.hasClass("select2-focused")},updateSelection:function(F){var E=[],D=[],C=this;j(F).each(function(){if(b(C.id(this),E)<0){E.push(C.id(this));D.push(this)}});F=D;this.selection.find(".select2-search-choice").remove();j(F).each(function(){C.addSelectedChoice(this)});C.postprocessResults()},tokenize:function(){var C=this.search.val();C=this.opts.tokenizer(C,this.data(),this.bind(this.onSelect),this.opts);if(C!=null&&C!=l){this.search.val(C);if(C.length>0){this.open()}}},onSelect:function(C){this.addSelectedChoice(C);if(this.select){this.postprocessResults()}if(this.opts.closeOnSelect){this.close();this.search.width(10)}else{if(this.countSelectableResults()>0){this.search.width(10);this.resizeSearch();this.positionDropdown()}else{this.close()}}this.triggerChange({added:C});this.focusSearch()},cancel:function(){this.close();this.focusSearch()},addSelectedChoice:function(E){var C=j("<li class='select2-search-choice'><div></div><a href='#' onclick='return false;' class='select2-search-choice-close' tabindex='-1'></a></li>"),G=this.id(E),F=this.getVal(),D;D=this.opts.formatSelection(E,C);C.find("div").replaceWith("<div>"+this.opts.escapeMarkup(D)+"</div>");C.find(".select2-search-choice-close").bind("mousedown",d).bind("click dblclick",this.bind(function(H){if(!this.enabled){return}j(H.target).closest(".select2-search-choice").fadeOut("fast",this.bind(function(){this.unselect(j(H.target));this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus");this.close();this.focusSearch()})).dequeue();d(H)})).bind("focus",this.bind(function(){if(!this.enabled){return}this.container.addClass("select2-container-active");this.dropdown.addClass("select2-drop-active")}));C.data("select2-data",E);C.insertBefore(this.searchContainer);F.push(G);this.setVal(F)},unselect:function(D){var F=this.getVal(),E,C;D=D.closest(".select2-search-choice");if(D.length===0){throw"Invalid argument: "+D+". Must be .select2-search-choice"}E=D.data("select2-data");C=b(this.id(E),F);if(C>=0){F.splice(C,1);this.setVal(F);if(this.select){this.postprocessResults()}}D.remove();this.triggerChange({removed:E})},postprocessResults:function(){var E=this.getVal(),F=this.results.find(".select2-result-selectable"),D=this.results.find(".select2-result-with-children"),C=this;F.each2(function(H,G){var I=C.id(G.data("select2-data"));if(b(I,E)>=0){G.addClass("select2-disabled").removeClass("select2-result-selectable")}else{G.removeClass("select2-disabled").addClass("select2-result-selectable")}});D.each2(function(G,H){if(H.find(".select2-result-selectable").length==0){H.addClass("select2-disabled")}else{H.removeClass("select2-disabled")}});F.each2(function(H,G){if(!G.hasClass("select2-disabled")&&G.hasClass("select2-result-selectable")){C.highlight(0);return false}})},resizeSearch:function(){var H,F,E,C,D,G=n(this.search);H=x(this.search)+10;F=this.search.offset().left;E=this.selection.width();C=this.selection.offset().left;D=E-(F-C)-G;if(D<H){D=E-G}if(D<40){D=E-G}this.search.width(D)},getVal:function(){var C;if(this.select){C=this.select.val();return C===null?[]:C}else{C=this.opts.element.val();return m(C,this.opts.separator)}},setVal:function(D){var C;if(this.select){this.select.val(D)}else{C=[];j(D).each(function(){if(b(this,C)<0){C.push(this)}});this.opts.element.val(C.length===0?"":C.join(this.opts.separator))}},val:function(){var E,D=[],C=this;if(arguments.length===0){return this.getVal()}E=arguments[0];if(!E){this.opts.element.val("");this.updateSelection([]);this.clearSearch();return}this.setVal(E);if(this.select){this.select.find(":selected").each(function(){D.push({id:j(this).attr("value"),text:j(this).text()})});this.updateSelection(D)}else{if(this.opts.initSelection===l){throw new Error("val() cannot be called if initSelection() is not defined")}this.opts.initSelection(this.opts.element,function(G){var F=j(G).map(C.id);C.setVal(F);C.updateSelection(G);C.clearSearch()})}this.clearSearch()},onSortStart:function(){if(this.select){throw new Error("Sorting of elements is not supported when attached to <select>. Attach to <input type='hidden'/> instead.")}this.search.width(0);this.searchContainer.hide()},onSortEnd:function(){var D=[],C=this;this.searchContainer.show();this.searchContainer.appendTo(this.searchContainer.parent());this.resizeSearch();this.selection.find(".select2-search-choice").each(function(){D.push(C.opts.id(j(this).data("select2-data")))});this.setVal(D);this.triggerChange()},data:function(D){var C=this,E;if(arguments.length===0){return this.selection.find(".select2-search-choice").map(function(){return j(this).data("select2-data")}).get()}else{if(!D){D=[]}E=j.map(D,function(F){return C.opts.id(F)});this.setVal(E);this.updateSelection(D);this.clearSearch()}}});j.fn.select2=function(){var F=Array.prototype.slice.call(arguments,0),G,E,H,D,C=["val","destroy","opened","open","close","focus","isFocused","container","onSortStart","onSortEnd","enable","disable","positionDropdown","data"];this.each(function(){if(F.length===0||typeof(F[0])==="object"){G=F.length===0?{}:j.extend({},F[0]);G.element=j(this);if(G.element.get(0).tagName.toLowerCase()==="select"){D=G.element.attr("multiple")}else{D=G.multiple||false;if("tags" in G){G.multiple=D=true}}E=D?new B():new v();E.init(G)}else{if(typeof(F[0])==="string"){if(b(F[0],C)<0){throw"Unknown method: "+F[0]}H=l;E=j(this).data("select2");if(E===l){return}if(F[0]==="container"){H=E.container}else{H=E[F[0]].apply(E,F.slice(1))}if(H!==l){return false}}else{throw"Invalid arguments to select2 plugin: "+F}}});return(H===l)?this:H};j.fn.select2.defaults={width:"copy",closeOnSelect:true,openOnEnter:true,containerCss:{},dropdownCss:{},containerCssClass:"",dropdownCssClass:"",formatResult:function(C,D,F){var E=[];i(C.text,F.term,E);return E.join("")},formatSelection:function(D,C){return D?D.text:l},formatResultCssClass:function(C){return l},formatNoMatches:function(){return"No matches found"},formatInputTooShort:function(C,D){return"Please enter "+(D-C.length)+" more characters"},formatSelectionTooBig:function(C){return"You can only select "+C+" item"+(C==1?"":"s")},formatLoadMore:function(C){return"Loading more results..."},formatSearching:function(){return"Searching..."},minimumResultsForSearch:0,minimumInputLength:0,maximumSelectionSize:0,id:function(C){return C.id},matcher:function(C,D){return D.toUpperCase().indexOf(C.toUpperCase())>=0},separator:",",tokenSeparators:[],tokenizer:y,escapeMarkup:function(C){if(C&&typeof(C)==="string"){return C.replace(/&/g,"&")}return C},blurOnChange:false};window.Select2={query:{ajax:p,local:r,tags:o},util:{debounce:f,markMatch:i},"class":{"abstract":e,single:v,multi:B}}}(jQuery)); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 04 Feb '13

04 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7e8d3695852/ changeset: b7e8d3695852 user: james_taylor date: 2013-02-04 05:12:58 summary: templates: Move external_services templates into templates/webapps/galaxy affected #: 6 files diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/generic_jquery_grid.mako --- a/templates/external_services/generic_jquery_grid.mako +++ /dev/null @@ -1,59 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="json_common.mako" import="display_item" /> - -<%def name="title()">${param_dict['service_instance'].name}: ${action.label}</%def> - -<%def name="display_json_grid_result( headers, rows )"> - %for row in rows: - %for name in headers: - <div class="form-row"> - <label>${name}</label> - ${display_item( row.get( name ) )} - <div style="clear: both"></div> - </div> - %endfor - %endfor -</%def> - -<% - #HACK!!!! need to use better method of displaying jqGrid here, needs to allow paging as optionally available. - if 'Rows' in result: #paged - records = result['Records'] - total = result['Total'] - rows = result['Rows'] - page = result['Page'] - else: - rows = result - records = None - total = None - page = None - headers = rows[0].keys() -%> - -<div class="toolForm"> - <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</div> - <div class="toolFormBody"> - %if records: - <div class="form-row"> - <label>Records</label> - ${records} - <div style="clear: both"></div> - </div> - %endif - %if total: - <div class="form-row"> - <label>Total</label> - ${total} - <div style="clear: both"></div> - </div> - %endif - %if page: - <div class="form-row"> - <label>Page</label> - ${page} - <div style="clear: both"></div> - </div> - %endif - ${display_json_grid_result( headers, rows )} - </div> -</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/generic_json.mako --- a/templates/external_services/generic_json.mako +++ /dev/null @@ -1,11 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="json_common.mako" import="display_item" /> - -<%def name="title()">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</%def> - -<div class="toolForm"> - <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</i></div> - <div class="toolFormBody"> - ${display_item( result )} - </div> -</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/json_common.mako --- a/templates/external_services/json_common.mako +++ /dev/null @@ -1,28 +0,0 @@ - -<%def name="display_dict( result_dict )"> - %for key, value in result_dict.items(): - <div class="form-row"> - <label>${key}</label> - ${display_item( value )} - <div style="clear: both"></div> - </div> - %endfor -</%def> - -<%def name="display_list( items )"> - <ul> - %for item in items: - <li>${display_item( item ) }</li> - %endfor - </ul> -</%def> - -<%def name="display_item( item )"> - %if isinstance( item, ( list, tuple ) ): - ${display_list( item )} - %elif isinstance( item, dict ): - ${display_dict( item )} - %else: - ${item} - %endif -</%def> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/generic_jquery_grid.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/generic_jquery_grid.mako @@ -0,0 +1,59 @@ +<%inherit file="/base.mako"/> +<%namespace file="json_common.mako" import="display_item" /> + +<%def name="title()">${param_dict['service_instance'].name}: ${action.label}</%def> + +<%def name="display_json_grid_result( headers, rows )"> + %for row in rows: + %for name in headers: + <div class="form-row"> + <label>${name}</label> + ${display_item( row.get( name ) )} + <div style="clear: both"></div> + </div> + %endfor + %endfor +</%def> + +<% + #HACK!!!! need to use better method of displaying jqGrid here, needs to allow paging as optionally available. + if 'Rows' in result: #paged + records = result['Records'] + total = result['Total'] + rows = result['Rows'] + page = result['Page'] + else: + rows = result + records = None + total = None + page = None + headers = rows[0].keys() +%> + +<div class="toolForm"> + <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</div> + <div class="toolFormBody"> + %if records: + <div class="form-row"> + <label>Records</label> + ${records} + <div style="clear: both"></div> + </div> + %endif + %if total: + <div class="form-row"> + <label>Total</label> + ${total} + <div style="clear: both"></div> + </div> + %endif + %if page: + <div class="form-row"> + <label>Page</label> + ${page} + <div style="clear: both"></div> + </div> + %endif + ${display_json_grid_result( headers, rows )} + </div> +</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/generic_json.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/generic_json.mako @@ -0,0 +1,11 @@ +<%inherit file="/base.mako"/> +<%namespace file="json_common.mako" import="display_item" /> + +<%def name="title()">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</%def> + +<div class="toolForm"> + <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</i></div> + <div class="toolFormBody"> + ${display_item( result )} + </div> +</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/json_common.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/json_common.mako @@ -0,0 +1,28 @@ + +<%def name="display_dict( result_dict )"> + %for key, value in result_dict.items(): + <div class="form-row"> + <label>${key}</label> + ${display_item( value )} + <div style="clear: both"></div> + </div> + %endfor +</%def> + +<%def name="display_list( items )"> + <ul> + %for item in items: + <li>${display_item( item ) }</li> + %endfor + </ul> +</%def> + +<%def name="display_item( item )"> + %if isinstance( item, ( list, tuple ) ): + ${display_list( item )} + %elif isinstance( item, dict ): + ${display_dict( item )} + %else: + ${item} + %endif +</%def> https://bitbucket.org/galaxy/galaxy-central/commits/17c40da527fe/ changeset: 17c40da527fe user: james_taylor date: 2013-02-04 05:21:17 summary: genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility affected #: 13 files diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,7 +26,6 @@ <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/><converter file="bed_to_fli_converter.xml" target_datatype="fli"/> - <display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> @@ -34,7 +33,6 @@ </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> - <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/></datatype><datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /><datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 display_applications/genetrack.xml --- a/display_applications/genetrack.xml +++ /dev/null @@ -1,18 +0,0 @@ -<display id="genetrack_interval" version="1.0.0" name="view in"> - <link id="genetrack" name="GeneTrack"> - <url target_frame="galaxy_main">http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}&h…</url> - <param type="data" name="bed_file" viewable="False" format="bed6,genetrack"/> - <param type="data" dataset="bed_file" name="genetrack_file" format="genetrack" viewable="False" /> - <param type="template" name="galaxy_url" strip="True" > - ${BASE_URL}/tool_runner?tool_id=predict2genetrack - </param> - <param type="template" name="hash_key" strip="True" > - #from galaxy.util.hash_util import hmac_new - ${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )} - </param> - <param type="template" name="encoded_filename" strip="True" > - #import binascii - ${binascii.hexlify( $genetrack_file.file_name )} - </param> - </link> -</display> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -143,7 +143,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") - self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/converters/bed_to_genetrack_converter.py --- a/lib/galaxy/datatypes/converters/bed_to_genetrack_converter.py +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env python - -#FIXME: THIS IS 1:1 COPY OF THE SAME FUNCTIONED TOOL - ALLOW REGULAR TOOLS TO MASCARADE AS CONVERTERS - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/converters/bed_to_genetrack_converter.xml --- a/lib/galaxy/datatypes/converters/bed_to_genetrack_converter.xml +++ /dev/null @@ -1,17 +0,0 @@ -<tool id="CONVERTER_bed_to_genetrack_0" name="Convert BED to GeneTrack Index" version="1.0.1"> - - - <command interpreter="python">bed_to_genetrack_converter.py -i $input1 -o $output1 -s 0 -v 0 -f BED -x</command> - <inputs> - <page> - <param format="bed6" name="input1" type="data" label="Choose BED file"/> - </page> - </inputs> - <outputs> - <data format="genetrack" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/tracks.py --- a/lib/galaxy/datatypes/tracks.py +++ b/lib/galaxy/datatypes/tracks.py @@ -10,27 +10,30 @@ log = logging.getLogger(__name__) +# GeneTrack is no longer supported but leaving the datatype since +# files of this type may still exist + class GeneTrack( binary.Binary ): file_ext = "genetrack" def __init__(self, **kwargs): super( GeneTrack, self ).__init__( **kwargs ) - self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) - def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): #Force target_frame to be 'galaxy_main' - return binary.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) - def genetrack_link( self, hda, type, app, base_url ): - ret_val = [] - if hda.dataset.has_data(): - # Get the disk file name and data id - file_name = hda.dataset.get_file_name() - data_id = quote_plus( str( hda.id ) ) - galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) - # Make it secure - hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) - encoded = quote_plus( binascii.hexlify( file_name ) ) - for name, url in util.get_genetrack_sites(): - if name.lower() in app.config.genetrack_display_sites: - # send both parameters filename and hashkey - link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) - ret_val.append( ( name, link ) ) - return ret_val + # self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) + # def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): #Force target_frame to be 'galaxy_main' + # return binary.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) + # def genetrack_link( self, hda, type, app, base_url ): + # ret_val = [] + # if hda.dataset.has_data(): + # # Get the disk file name and data id + # file_name = hda.dataset.get_file_name() + # data_id = quote_plus( str( hda.id ) ) + # galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) + # # Make it secure + # hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) + # encoded = quote_plus( binascii.hexlify( file_name ) ) + # for name, url in util.get_genetrack_sites(): + # if name.lower() in app.config.genetrack_display_sites: + # # send both parameters filename and hashkey + # link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) + # ret_val.append( ( name, link ) ) + # return ret_val diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -349,7 +349,7 @@ raise EggNotFetchable( missing ) class GalaxyConfig( object ): - always_conditional = ( 'GeneTrack', 'pysam', 'ctypes', 'python_daemon' ) + always_conditional = ( 'pysam', 'ctypes', 'python_daemon' ) def __init__( self, config_file ): if config_file is None: self.config = None @@ -387,7 +387,6 @@ "guppy": lambda: self.config.get( "app:main", "use_memdump" ), "python_openid": lambda: self.config.get( "app:main", "enable_openid" ), "python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ), - "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "ctypes": lambda: ( "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(",") ) and sys.version_info[:2] == ( 2, 4 ), "pysam": lambda: check_pysam() }.get( egg_name, lambda: True )() diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -432,11 +432,6 @@ if build in site['builds']: sites.append((site['name'],site['url'])) return sites -def get_genetrack_sites(): - sites = [] - for site in genetrack_sites: - sites.append( ( site['name'], site['url'] ) ) - return sites def read_dbnames(filename): """ Read build names from file """ @@ -773,7 +768,6 @@ ncbi_names = read_ncbi( os.path.join( galaxy_root_path, "tool-data", "shared", "ncbi", "builds.txt" ) ) ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) -genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False ) dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names) def galaxy_directory(): diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/base.html --- a/templates/genetrack/base.html +++ /dev/null @@ -1,29 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> -<title>${self.title()}</title> -<link rel="stylesheet" href="${h.url_for('/static/genetrack/genetrack.css')}" type="text/css" media="screen"> -<script type="text/javascript" src="${h.url_for('/static/genetrack/genetrack.js')}">var dummy1=0;</script> -</head> - -<%def name="title()"> - Title -</%def> - -<%def name="footer()"> - <div align="center" id="footer"> - <a href="/">Home</a>  |  <a href="${h.url_for(controller='genetrack',action='search',dataset_id=dataset_id)}">Search</a> - </div> - <div align="center" id="tag"> - Powered by <a href="http://genetrack.googlecode.com">GeneTrack</a> | - <a href="http://atlas.bx.psu.edu/">Penn State Genome Cartography (2008)</a> - </div> -</%def> - -<body> - ${self.body()} - ${self.footer()} -</body> - -</html> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/index.html --- a/templates/genetrack/index.html +++ /dev/null @@ -1,75 +0,0 @@ -## index.html -<%inherit file="base.html"/> -<%def name="title()"> - Index -</%def> - -<h1 align="center">${conf.TITLE}</h1> - -<form action="" method="get"> - -<table align="center" cellpadding="2" cellspacing="1" width="100%"> - - - % if form.errors(): - <tr class="error"><td align="center"> - % for ekey, evalue in form.errors().items(): - <b>ERROR:</b>    ${ekey}:    ${evalue}<br> - % endfor - </td></tr> - % endif - - <tr class="grey"> - <td colspan="4" align="center"> - <a href="javascript:toggle('options')">More</a><img src="/static/images/thumbtack_icon.png" align="absmiddle" border="0"> - - Chromosome: ${form.chrom.tag()}   - Feature: ${form.feature.tag()}   - Width: ${form.zoom.tag()}   - Plot: ${form.plot.tag()}   - <input type="submit" name="submit" value="Display!"> - <div id="options" style="display:none" class="selected"> - <table cellpadding="3"> - <tr> - <td> -  - Fit threshold: ${form.min_fit.tag()}    - Image width: ${form.img_size.tag()}    - </td> - </tr> - </table> - </div> - - </td> - </tr> - - <tr> - <td align="center"> - <input type="submit" name="move_left" value="<< Move Left"> -     - <input type="submit" name="zoom_out" value="Shrink -"> -     - <input type="submit" name="zoom_in" value="Magnify +"> -     - <input type="submit" name="move_right" value="Move Right >>"> - </td> - </tr> - - <tr> - <td align="center"> - <img src="${h.url_for('/static/genetrack/plots/' + param.fname)}" align="center" border="0"> - </td> - </tr> - - <tr> - <td align="center"> -  - </td> - </tr> - -</table> - -<input type="hidden" id="dataset_id" name="dataset_id" value="${dataset_id}" /> -</form> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/invalid.html --- a/templates/genetrack/invalid.html +++ /dev/null @@ -1,3 +0,0 @@ -## index.html -<%inherit file="base.html"/> -<h1>This dataset is not a valid GeneTrack dataset.</h1> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/search.html --- a/templates/genetrack/search.html +++ /dev/null @@ -1,55 +0,0 @@ -## search.html -<%! -from itertools import cycle -colors = cycle( [ 'even', 'odd' ] ) -%> - -<%inherit file="base.html"/> -<%def name="title()"> - Search -</%def> - -<h1 align="center">Search</h1> - -<div align="center"> - <form action="search" method="get"> - Search terms <input type="text" name="word" value="${param.word}"> - <input type="hidden" name="dataset_id" id="dataset_id" value="${dataset_id}" /> - <input type="submit" name="submit" value="Search!"> - </form> -</div> - -% if param.word: - - % if len(query)>0: - <h4 align="center">Showing the best ${len(query)} matches</h4> - - <table align="center" class="data_table" cellpadding="6" cellspacing="0"> - <tr align="center"> - <th width="25%">Name</td> - <th width="25%">Chromosome</td> - <th width="25%">Start:End</td> - <th width="25%">Type</td> - </tr> - % for color, row in zip(colors, query): - ${makerow(color, row)} - % endfor - </table> - - % else: - <h4 align="center">No results found</h4> - % endif - -%endif - -<br> -<%def name="makerow(color, row)"> - <tr class="${color}" align="center"> - <td><a href="${h.url_for(controller='genetrack', action='index', chrom=row.chrom, feature=row.start, dataset_id=dataset_id)}">${row.name}</a></td> - <td>${row.chrom}</td> - <td>${row.start}:${row.end}</td> - <td>${row.label.name}</td> - </tr> -</%def> - -</form> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 tool-data/shared/genetrack/genetrack_sites.txt --- a/tool-data/shared/genetrack/genetrack_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -# GeneTrack sites -# -# The key(s) should be added to universe_wsgi.ini as the value of -# genetrack_display_sites -# -# key site url -psu_galaxy http://genetrack.g2.bx.psu.edu/galaxy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: templates: Move tool_form templates into templates/webapps/galaxy
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35e476a0c0c4/ changeset: 35e476a0c0c4 user: james_taylor date: 2013-02-04 05:10:37 summary: templates: Move tool_form templates into templates/webapps/galaxy affected #: 4 files diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/tool_executed.mako --- a/templates/tool_executed.mako +++ /dev/null @@ -1,70 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - -<head> -<title>Galaxy</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<script type="text/javascript"> - var inside_galaxy_frameset = false; - - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}"; - inside_galaxy_frameset = true; - } - - %if trans.user: - if (inside_galaxy_frameset) - { - //parent.frames.galaxy_tools.update_recently_used(); - } - %endif - - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( -1 ); - } - - function main() { - // If called from outside the galaxy frameset, redirect there - %if tool.options.refresh: - if ( ! inside_galaxy_frameset ) { - setTimeout( "refresh()", 1000 ); - document.getElementById( "refresh_message" ).style.display = "block"; - } - %endif - } - - function refresh() { - top.location.href = '${h.url_for( "/" )}'; - } - -</script> - -</head> - -<body onLoad="main()"> - -<div class="donemessagelarge"> - -<p>The following job has been successfully added to the queue:</p> - -%for data in out_data.values(): - <div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div> -%endfor - -<p> -You can check the status of queued jobs and view the resulting -data by refreshing the <b>History</b> pane. When the job has been run -the status will change from 'running' to 'finished' if completed -successfully or 'error' if problems were encountered. -</p> - -%if tool.options.refresh: -<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${h.url_for( '/' )}">Galaxy</a></div> -%endif - -</div> - -</body> - -</html> diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/tool_form.mako --- a/templates/tool_form.mako +++ /dev/null @@ -1,357 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/base_panels.mako" import="overlay" /> - -<%def name="stylesheets()"> - ${h.css( "autocomplete_tagging", "base", "panel_layout", "library" )} - <style type="text/css"> - html, body { - background-color: #fff; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/jquery/select2", "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - $(window).bind("refresh_on_change", function() { - $(':file').each( function() { - var file = $(this); - var file_value = file.val(); - if (file_value) { - // disable file input, since we don't want to upload the file on refresh - var file_name = $(this).attr("name"); - file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); - // create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); - file.after(new_file_input); - } - }); - }); - - // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements - $( 'div.drilldown-container' ).each( function() { - $(this).find('span.form-toggle' ).each( function() { - var show_hide_click_elt = $(this); - var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); - $('#' + group_id + '-container').each( function() { - var show_hide_elt = $(this); - if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { - show_hide_elt.hide(); - } - show_hide_click_elt.click( function() { - if ( show_hide_click_elt.hasClass("toggle") ){ - show_hide_click_elt.addClass("toggle-expand"); - show_hide_click_elt.removeClass("toggle"); - show_hide_elt.slideUp( 'fast' ); - } - else { - show_hide_click_elt.addClass("toggle"); - show_hide_click_elt.removeClass("toggle-expand"); - show_hide_elt.slideDown( 'fast' ); - } - }); - }); - }); - }); - - function checkUncheckAll( name, check ) { - $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); - } - - // Inserts the Select All / Unselect All buttons for checkboxes - $("div.checkUncheckAllPlaceholder").each( function() { - var check_name = $(this).attr("checkbox_name"); - select_link = $("<a class='action-button'></a>").text("Select All").click(function() { - checkUncheckAll(check_name, true); - }); - unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { - checkUncheckAll(check_name, false); - }); - $(this).append(select_link).append(" ").append(unselect_link); - }); - - $(".add-librarydataset").live("click", function() { - var link = $(this); - $.ajax({ - url: "/visualization/list_libraries", - error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, - success: function(table_html) { - show_modal( - "Select Library Dataset", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Select": function() { - var names = []; - var ids = []; - counter = 1; - $('input[name=ldda_ids]:checked').each(function() { - var name = $.trim( $(this).siblings("label").text() ); - var id = $(this).val(); - names.push( counter + ". " + name ); - counter += 1; - ids.push(id); - }); - link.html( names.join("<br/>") ); - link.siblings("input[type=hidden]").val( ids.join("||") ); - hide_modal(); - } - } - ); - } - }); - }); - }); - - %if not add_frame.debug: - if( window.name != "galaxy_main" ) { - location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); - } - %endif - - </script> - -</%def> - -<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> - <% - from galaxy.util.expressions import ExpressionContext - other_values = ExpressionContext( tool_state, other_values ) - %> - %for input_index, input in enumerate( inputs.itervalues() ): - %if not input.visible: - <% pass %> - %elif input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.title_plural}</strong> - %if input.help: - <div class="toolParamHelp" style="clear: both;"> - ${input.help} - </div> - %endif - </div> - <% - repeat_state = tool_state[input.name] - num_repeats = len( repeat_state ) - %> - %for i in range( num_repeats ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - %if input.min < num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - %endif - </div> - %if rep_errors.has_key( '__index__' ): - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> - %endif - %endfor - %if input.max > num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - %endif - </div> - %elif input.type == "conditional": - <% - group_state = tool_state[input.name] - group_errors = errors.get( input.name, {} ) - current_case = group_state['__current_case__'] - group_prefix = prefix + input.name + "|" - %> - %if input.value_ref_in_group: - ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} - %endif - ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} - %elif input.type == "upload_dataset": - %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before - <% - if input.name in errors: - rep_errors = errors[input.name][0] - else: - rep_errors = dict() - %> - ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} - %else: - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> - <% - repeat_state = tool_state[input.name] - %> - %for i in range( len( repeat_state ) ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - </div> - %endfor - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - </div> - %endif - %else: - ${row_for_param( prefix, input, tool_state, errors, other_values )} - %endif - %endfor -</%def> - -<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> - <% - if parent_errors.has_key( param.name ): - cls = "form-row form-row-error" - else: - cls = "form-row" - - label = param.get_label() - - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change - - # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. - field_html = field.get_html( prefix ) - if type( field_html ) is not unicode: - field_html = unicode( field_html, 'utf-8', 'replace' ) - - if param.type == "hidden": - return field_html - %> - <div class="${cls}"> - %if label: - <label for="${param.name}">${label}:</label> - %endif - <div class="form-row-input">${field_html}</div> - %if parent_errors.has_key( param.name ): - <div class="form-row-error-message"> - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> - </div> - %endif - - %if param.help: - <div class="toolParamHelp" style="clear: both;"> - ${param.help} - </div> - %endif - - <div style="clear: both;"></div> - - </div> -</%def> - -<% overlay(visible=False) %> - -%if add_frame.from_noframe: - <div class="warningmessage"> - <strong>Welcome to Galaxy</strong> - <hr/> - It appears that you found this tool from a link outside of Galaxy. - If you're not familiar with Galaxy, please consider visiting the - <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. - To learn more about what Galaxy is and what it can do for you, please visit - the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. - </div> - <br/> -%endif - -<% - # Render an error message if a dynamically generated select list is missing a required - # index file or entry in the tool_data_table_conf.xml file. - message = "" - params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry - params_with_missing_index_file = tool.params_with_missing_index_file - if params_with_missing_data_table_entry: - param = params_with_missing_data_table_entry[0] - message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name - if tool.params_with_missing_index_file: - param = params_with_missing_index_file[0] - message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file - - # Handle calculating the redirect url for the special case where we have nginx proxy - # upload and need to do url_for on the redirect portion of the tool action. - try: - tool_url = h.url_for(tool.action) - except AttributeError: - assert len(tool.action) == 2 - tool_url = tool.action[0] + h.url_for(tool.action[1]) -%> - -<% - # Name of the tool in lower case - low_tool_name = tool.name.lower() -%> - -%if tool_id_version_message: - ${render_msg( tool_id_version_message, 'warning' )} -%endif - -<div class="toolForm" id="${tool.id}"> - <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) - %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version}) - %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} - %endif - %if trans.app.config.biostar: -  - <a href="${trans.app.config.biostar}/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> - <a href="${trans.app.config.biostar}/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> -  - %endif - </div> - <div class="toolFormBody"> - <input type="hidden" name="refresh" value="refresh"> - <input type="hidden" name="tool_id" value="${tool.id}"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - %if tool.display_by_page[tool_state.page]: - ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} - <div class="form-row form-actions"> - %if tool_state.page == tool.last_page: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> - %endif - </div> - %endif - </div> - </form> -</div> -%if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - %> - ${tool_help} - </div> - </div> -%endif diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/webapps/galaxy/tool_executed.mako --- /dev/null +++ b/templates/webapps/galaxy/tool_executed.mako @@ -0,0 +1,70 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<html> + +<head> +<title>Galaxy</title> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> +<script type="text/javascript"> + var inside_galaxy_frameset = false; + + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}"; + inside_galaxy_frameset = true; + } + + %if trans.user: + if (inside_galaxy_frameset) + { + //parent.frames.galaxy_tools.update_recently_used(); + } + %endif + + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( -1 ); + } + + function main() { + // If called from outside the galaxy frameset, redirect there + %if tool.options.refresh: + if ( ! inside_galaxy_frameset ) { + setTimeout( "refresh()", 1000 ); + document.getElementById( "refresh_message" ).style.display = "block"; + } + %endif + } + + function refresh() { + top.location.href = '${h.url_for( "/" )}'; + } + +</script> + +</head> + +<body onLoad="main()"> + +<div class="donemessagelarge"> + +<p>The following job has been successfully added to the queue:</p> + +%for data in out_data.values(): + <div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div> +%endfor + +<p> +You can check the status of queued jobs and view the resulting +data by refreshing the <b>History</b> pane. When the job has been run +the status will change from 'running' to 'finished' if completed +successfully or 'error' if problems were encountered. +</p> + +%if tool.options.refresh: +<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${h.url_for( '/' )}">Galaxy</a></div> +%endif + +</div> + +</body> + +</html> diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/webapps/galaxy/tool_form.mako --- /dev/null +++ b/templates/webapps/galaxy/tool_form.mako @@ -0,0 +1,357 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/base_panels.mako" import="overlay" /> + +<%def name="stylesheets()"> + ${h.css( "autocomplete_tagging", "base", "panel_layout", "library" )} + <style type="text/css"> + html, body { + background-color: #fff; + } + </style> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/jquery/select2", "libs/jquery/jstorage" )} + <script type="text/javascript"> + $(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $(document.createElement('input')); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); + file.after(new_file_input); + } + }); + }); + + // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements + $( 'div.drilldown-container' ).each( function() { + $(this).find('span.form-toggle' ).each( function() { + var show_hide_click_elt = $(this); + var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); + $('#' + group_id + '-container').each( function() { + var show_hide_elt = $(this); + if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { + show_hide_elt.hide(); + } + show_hide_click_elt.click( function() { + if ( show_hide_click_elt.hasClass("toggle") ){ + show_hide_click_elt.addClass("toggle-expand"); + show_hide_click_elt.removeClass("toggle"); + show_hide_elt.slideUp( 'fast' ); + } + else { + show_hide_click_elt.addClass("toggle"); + show_hide_click_elt.removeClass("toggle-expand"); + show_hide_elt.slideDown( 'fast' ); + } + }); + }); + }); + }); + + function checkUncheckAll( name, check ) { + $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); + } + + // Inserts the Select All / Unselect All buttons for checkboxes + $("div.checkUncheckAllPlaceholder").each( function() { + var check_name = $(this).attr("checkbox_name"); + select_link = $("<a class='action-button'></a>").text("Select All").click(function() { + checkUncheckAll(check_name, true); + }); + unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { + checkUncheckAll(check_name, false); + }); + $(this).append(select_link).append(" ").append(unselect_link); + }); + + $(".add-librarydataset").live("click", function() { + var link = $(this); + $.ajax({ + url: "/visualization/list_libraries", + error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, + success: function(table_html) { + show_modal( + "Select Library Dataset", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Select": function() { + var names = []; + var ids = []; + counter = 1; + $('input[name=ldda_ids]:checked').each(function() { + var name = $.trim( $(this).siblings("label").text() ); + var id = $(this).val(); + names.push( counter + ". " + name ); + counter += 1; + ids.push(id); + }); + link.html( names.join("<br/>") ); + link.siblings("input[type=hidden]").val( ids.join("||") ); + hide_modal(); + } + } + ); + } + }); + }); + }); + + %if not add_frame.debug: + if( window.name != "galaxy_main" ) { + location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); + } + %endif + + </script> + +</%def> + +<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( tool_state, other_values ) + %> + %for input_index, input in enumerate( inputs.itervalues() ): + %if not input.visible: + <% pass %> + %elif input.type == "repeat": + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.title_plural}</strong> + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif + </div> + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + %if input.min < num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif + </div> + %if rep_errors.has_key( '__index__' ): + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> + %endif + %endfor + %if input.max > num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif + </div> + %elif input.type == "conditional": + <% + group_state = tool_state[input.name] + group_errors = errors.get( input.name, {} ) + current_case = group_state['__current_case__'] + group_prefix = prefix + input.name + "|" + %> + %if input.value_ref_in_group: + ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %endif + ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} + %else: + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %endif + %else: + ${row_for_param( prefix, input, tool_state, errors, other_values )} + %endif + %endfor +</%def> + +<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> + <% + if parent_errors.has_key( param.name ): + cls = "form-row form-row-error" + else: + cls = "form-row" + + label = param.get_label() + + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if type( field_html ) is not unicode: + field_html = unicode( field_html, 'utf-8', 'replace' ) + + if param.type == "hidden": + return field_html + %> + <div class="${cls}"> + %if label: + <label for="${param.name}">${label}:</label> + %endif + <div class="form-row-input">${field_html}</div> + %if parent_errors.has_key( param.name ): + <div class="form-row-error-message"> + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + </div> + %endif + + %if param.help: + <div class="toolParamHelp" style="clear: both;"> + ${param.help} + </div> + %endif + + <div style="clear: both;"></div> + + </div> +</%def> + +<% overlay(visible=False) %> + +%if add_frame.from_noframe: + <div class="warningmessage"> + <strong>Welcome to Galaxy</strong> + <hr/> + It appears that you found this tool from a link outside of Galaxy. + If you're not familiar with Galaxy, please consider visiting the + <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. + To learn more about what Galaxy is and what it can do for you, please visit + the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. + </div> + <br/> +%endif + +<% + # Render an error message if a dynamically generated select list is missing a required + # index file or entry in the tool_data_table_conf.xml file. + message = "" + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file + + # Handle calculating the redirect url for the special case where we have nginx proxy + # upload and need to do url_for on the redirect portion of the tool action. + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) +%> + +<% + # Name of the tool in lower case + low_tool_name = tool.name.lower() +%> + +%if tool_id_version_message: + ${render_msg( tool_id_version_message, 'warning' )} +%endif + +<div class="toolForm" id="${tool.id}"> + <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> + %if tool.has_multiple_pages: + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) + %elif not tool_version_select_field: + <div class="toolFormTitle">${tool.name} (version ${tool.version}) + %else: + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} + %endif + %if trans.app.config.biostar: +  + <a href="${trans.app.config.biostar}/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="${trans.app.config.biostar}/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + %endif + </div> + <div class="toolFormBody"> + <input type="hidden" name="refresh" value="refresh"> + <input type="hidden" name="tool_id" value="${tool.id}"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + %if tool.display_by_page[tool_state.page]: + ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} + <div class="form-row form-actions"> + %if tool_state.page == tool.last_page: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> + %endif + </div> + %endif + </div> + </form> +</div> +%if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + %> + ${tool_help} + </div> + </div> +%endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c6e63dc04c9/ changeset: 4c6e63dc04c9 user: james_taylor date: 2013-02-04 05:07:11 summary: template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy affected #: 258 files diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ /dev/null @@ -1,291 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "autocomplete_tagging" )} - <style type="text/css"> - #new_history_p{ - line-height:2.5em; - margin:0em 0em .5em 0em; - } - #new_history_cbx{ - margin-right:.5em; - } - #new_history_input{ - display:none; - line-height:1em; - } - #ec_button_container{ - float:right; - } - #hidden_options{ - display:none; - } - div.toolForm{ - margin-top: 10px; - margin-bottom: 10px; - } - div.toolFormTitle{ - cursor:pointer; - } - .title_ul_text{ - text-decoration:underline; - } - .step-annotation { - margin-top: 0.25em; - font-weight: normal; - font-size: 97%; - } - .workflow-annotation { - margin-bottom: 1em; - } - #loading_indicator{ - position:fixed; - top:40px; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - var ACCOUNT_URL = "${h.url_for( controller='/cloudlaunch', action='get_account_info')}"; - var PKEY_DL_URL = "${h.url_for( controller='/cloudlaunch', action='get_pkey')}"; - var cloudlaunch_clusters = []; - - $(document).ready(function(){ - $('#id_existing_instance').change(function(){ - var ei_name = $(this).val(); - if (ei_name === "New Cluster"){ - //For new instances, need to see the cluster name field. - $('#id_cluster_name').val("New Cluster") - $('#cluster_name_wrapper').show('fast'); - }else{ - //Hide the Cluster Name field, but set the value - $('#id_cluster_name').val($(this).val()); - $('#cluster_name_wrapper').hide('fast'); - } - }); - //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("paste input propertychange", function(){ - secret_el = $("#id_secret"); - key_el = $("#id_key_id"); - if (secret_el.val().length === 40 && key_el.val().length === 20){ - //Submit these to get_account_info, unhide fields, and update as appropriate - $.ajax({type: "POST", - url: ACCOUNT_URL, - dataType: 'json', - data: {key_id: key_el.val(),secret:secret_el.val()}, - success: function(result){ - cloudlaunch_clusters = result.clusters; - var kplist = $("#id_keypair"); - var clusterlist = $("#id_existing_instance"); - kplist.find('option').remove(); - clusterlist.find('option').remove(); - //Update fields with appropriate elements - clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); - if (_.size(result.clusters) > 0){ - _.each(result.clusters, function(cluster, index){ - clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); - }); - $('#existing_instance_wrapper').show(); - } - if (!_.include(result.keypairs, '${default_keypair}')){ - kplist.append($('<option/>').val('${default_keypair}').text('Create New - ${default_keypair}')); - } - _.each(result.keypairs, function(keypair, index){ - kplist.append($('<option/>').val(keypair).text(keypair)); - }); - $('#hidden_options').show('fast'); - } - }); - } - }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show('fast'); - }).ajaxStop(function(){ - $(this).hide('fast'); - }); - $('form').ajaxForm({ - type: 'POST', - dataType: 'json', - beforeSubmit: function(data, form){ - if ($('#id_password').val() != $('#id_password_confirm').val()){ - //Passwords don't match. - form.prepend('<div class="errormessage">Passwords do not match</div>'); - return false; - }else{ - //Clear errors - $('.errormessage').remove() - //Hide the form, show pending box with spinner. - $('#launchFormContainer').hide('fast'); - $('#responsePanel').show('fast'); - } - //Dig up zone info for selected cluster, set hidden input. - //This is not necessary to present to the user though the interface may prove useful. - var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); - if( ei_val && (ei_val.value !== "New Cluster")){ - var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); - var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); - zdata.value = cluster.zone; - } - }, - success: function(data){ - //Success Message, link to key download if required, link to server itself. - $('#launchPending').hide('fast'); - //Set appropriate fields (dns, key, ami) and then display. - if(data.kp_material_tag){ - var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag) - .attr('target','_blank') - .text("Download your key now"); - $('#keypairInfo').append(kp_download_link); - $('#keypairInfo').show(); - } - $('.kp_name').text(data.kp_name); - $('#instance_id').text(data.instance_id); - $('#image_id').text(data.image_id); - $('#instance_link').html($('<a/>') - .attr('href', 'http://' + data.public_dns_name + '/cloud') - .attr('target','_blank') - .text(data.public_dns_name + '/cloud')); - $('#instance_dns').text(data.public_dns_name); - $('#launchSuccess').show('fast'); - }, - error: function(jqXHR, textStatus, errorThrown){ - $('#launchFormContainer').prepend('<div class="errormessage">' + errorThrown + " : " + jqXHR.responseText + '</div>'); - $('#responsePanel').hide('fast'); - $('#launchFormContainer').show('fast'); - } - }); - }); - </script> -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - <div id="loading_indicator"></div> - <h2>Launch a Galaxy Cloud Instance</h2> - <div id="launchFormContainer" class="toolForm"> - <form id="cloudlaunch_form" action="${h.url_for( controller='/cloudlaunch', action='launch_instance')}" method="post"> - - <p>To launch a Galaxy Cloud Cluster, enter your AWS Secret Key ID, and Secret Key. Galaxy will use - these to present appropriate options for launching your cluster. Note that using this form to - launch computational resources in the Amazon Cloud will result in costs to the account indicated - above. See <a href="http://aws.amazon.com/ec2/pricing/">Amazon's pricing</a> for more information. - options for launching your cluster.</p></p> - - <div class="form-row"> - <label for="id_key_id">Key ID</label> - <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/> - <div class="toolParamHelp"> - This is the text string that uniquely identifies your account, found in the - <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. - </div> - </div> - - <div class="form-row"> - <label for="id_secret">Secret Key</label> - <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/> - <div class="toolParamHelp"> - This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security -Credentials section of the AWS Console</a>. </div> - </div> - - <div id="hidden_options"> - <div id='existing_instance_wrapper' style="display:none;" class="form-row"> - <label for="id_existing_instance">Instances in your account</label> - <select name="existing_instance" id="id_existing_instance"> - </select> - <input id='id_zone' type='hidden' name='zone' value=''/> - </div> - <div id='cluster_name_wrapper' class="form-row"> - <label for="id_cluster_name">Cluster Name</label> - <input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/> - <div class="toolParamHelp"> - This is the name for your cluster. You'll use this when you want to restart. - </div> - </div> - - <div class="form-row"> - <label for="id_password">Cluster Password</label> - <input type="password" size="40" name="password" id="id_password"/><br/> - </div> - - <div class="form-row"> - <label for="id_password_confirm">Cluster Password - Confirmation</label> - <input type="password" size="40" name="password_confirm" id="id_password_confirm"/><br/> - </div> - - - <div class="form-row"> - <label for="id_keypair">Key Pair</label> - <select name="keypair" id="id_keypair"> - <option name="Create" value="cloudman_keypair">cloudman_keypair</option> - </select> - </div> - - %if share_string: - <input type='hidden' name='share_string' value='${share_string}'/> - %else: -  - <div class="form-row" style="display:none;"> - <label for="id_share_string">Instance Share String (optional)</label> - <input type="text" size="120" name="share_string" id="id_share_string"/><br/> - </div> - %endif - - <div class="form-row"> - <label for="id_instance_type">Instance Type</label> - <select name="instance_type" id="id_instance_type"> - <option value="m1.large">Large</option> - <option value="m1.xlarge">Extra Large</option> - <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> - </select> - </div> - <div class="form-row"> - <p>Requesting the instance may take a moment, please be patient. Do not refresh your browser or navigate away from the page</p> - <input type="submit" value="Submit" id="id_submit"/> - </div> - </div> - <div class="form-row"> - <div id="loading_indicator" style="position:relative;left:10px;right:0px"></div> - </div> - </form> - </div> - <div id="responsePanel" class="toolForm" style="display:none;"> - <div id="launchPending">Launch Pending, please be patient.</div> - <div id="launchSuccess" style="display:none;"> - <div id="keypairInfo" style="display:none;margin-bottom:20px;"> - <h3>Very Important Key Pair Information</h3> - <p>A new key pair named <strong><span class="kp_name">kp_name</span></strong> has been created in your AWS - account and will be used to access this instance via ssh. It is - <strong>very important</strong> that you save the following private key - as it is not saved on this Galaxy instance and will be permanently lost if not saved. Additionally, this link will - only allow a single download, after which the key is removed from the Galaxy server permanently.<br/> - </div> - <div> - <h3>Access Information</h3> - <ul> - <li>Your instance '<span id="instance_id">undefined</span>' has been successfully launched using the - '<span id="image_id">undefined</span>' AMI.</li> - <li>While it may take a few moments to boot, you will be able to access the cloud control - panel at <span id="instance_link">undefined.</span>.</li> - <li>SSH access is also available using your private key. From the terminal, you would execute something like:</br>    `ssh -i <span class="kp_name">undefined</span>.pem ubuntu@<span -id="instance_dns">undefined</span>`</li> - </ul> - </div> - </div> - </div> - </div> -</%def> - diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/run.mako --- a/templates/cloud/run.mako +++ /dev/null @@ -1,41 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - <h2>Launching a Galaxy Cloud Instance</h2> -%if error: - <p>${error}</p> -%elif instance: - %if kp_material: - <h3>Very Important Key Pair Information</h3> - <p>A new key pair named '${kp_name}' has been created in your AWS - account and will be used to access this instance via ssh. It is - <strong>very important</strong> that you save the following private key - as it is not saved on this Galaxy instance and will be permanently lost - once you leave this page. To do this, save the following key block as - a plain text file named '${kp_name}'.</p> - <pre>${kp_material}</pre> - %endif - <p>The instance '${instance.id} has been successfully launched using the - '${instance.image_id}' AMI.<br/> Access it at <a - href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p> - <p>SSH access is available using your private key '${kp_name}'.</p> -%else: - <p> Unknown failure, no instance. Please refer to your AWS console at <a - href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p> -%endif - </div> - </div> -</%def> - diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako +++ /dev/null @@ -1,141 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Copy History Items</%def> - -<%def name="javascripts()"> - - ${parent.javascripts()} - - <script type="text/javascript"> - $(function() { - $("#select-multiple").click(function() { - $("#single-dest-select").val(""); - $("#single-destination").hide(); - $("#multiple-destination").show(); - }); - }); - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - </script> - -</%def> - -%if error_msg: - <p> - <div class="errormessage">${error_msg}</div> - <div style="clear: both"></div> - </p> -%endif -%if done_msg: - <p> - <div class="donemessage">${done_msg}</div> - <div style="clear: both"></div> - </p> -%endif -<p> - <div class="infomessage">Copy any number of history items from one history to another.</div> - <div style="clear: both"></div> -</p> -<p> - <form method="post"> - <div class="toolForm" style="float: left; width: 45%; padding: 0px;"> - <div class="toolFormTitle">Source History:<br /> - <select id="source_history" name="source_history" refresh_on_change="true" style="font-weight: normal;"> - %for i, hist in enumerate(target_histories): - <% - selected = "" - current_history_text = "" - if hist == source_history: - selected = "selected='selected'" - if hist == current_history: - current_history_text = " (current history)" - - %> - <option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} - </option> - %endfor - </select> - </div> - <div class="toolFormBody"> - %if len(source_datasets) > 0: - %for data in source_datasets: - <% - checked = "" - encoded_id = trans.security.encode_id(data.id) - if data.id in source_dataset_ids: - checked = " checked='checked'" - %> - <div class="form-row"> - <input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> - </div> - %endfor - %else: - <div class="form-row">This history has no datasets.</div> - %endif - </div> - </div> - <div style="float: left; padding-left: 10px; font-size: 36px;">→</div> - <div class="toolForm" style="float: right; width: 45%; padding: 0px;"> - <div class="toolFormTitle">Destination History:</div> - <div class="toolFormBody"> - <div class="form-row" id="single-destination"> - <select id="single-dest-select" name="target_history_id"> - <option value=""></option> - %for i, hist in enumerate(target_histories): - <% - encoded_id = trans.security.encode_id(hist.id) - source_history_text = "" - selected = "" - if hist == source_history: - source_history_text = " (source history)" - if encoded_id == target_history_id: - selected = " selected='selected'" - %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> - %endfor - </select><br /><br /> - <a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> - </div> - <div id="multiple-destination" style="display: none;"> - %for i, hist in enumerate( target_histories ): - <% - cur_history_text = "" - encoded_id = trans.security.encode_id(hist.id) - if hist == source_history: - cur_history_text = " <strong>(source history)</strong>" - %> - <div class="form-row"> - <input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label> - </div> - %endfor - </div> - %if trans.get_user(): - <% - checked = "" - if "create_new_history" in target_history_ids: - checked = " checked='checked'" - %> - <hr /> - <div style="text-align: center; color: #888;">— OR —</div> - <div class="form-row"> - <label for="new_history_name" style="display: inline; font-weight:normal;">New history named:</label> - <input type="textbox" name="new_history_name" /> - </div> - %endif - </div> - </div> - <div style="clear: both"></div> - <div class="form-row" align="center"> - <input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/> - </div> - </form> - </div> -</p> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display.mako --- a/templates/dataset/display.mako +++ /dev/null @@ -1,111 +0,0 @@ -## Because HDAs do not have many of the properties that other sharable items have, we need to override most of the default code for display. -<%inherit file="/display_base.mako"/> -<%namespace file="/display_common.mako" import="*" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=True - self.message_box_visible=False - self.active_view="user" - self.overlay_visible=False -%> -</%def> - -<%def name="title()"> - Galaxy | ${get_class_display_name( item.__class__ )} | ${get_item_name( item ) | h} -</%def> - -<%def name="render_item_links( data )"> - ## Provide links to save data and import dataset. - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}" class="icon-button disk tooltip" title="Save dataset"></a> - <a - href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" - class="icon-button import tooltip" - title="Import dataset"></a> -</%def> - -<%def name="render_item( data, data_to_render )"> - %if truncated: - <div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below. | - <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> - </div> - %endif - ## TODO: why is the default font size so small? - <pre style="font-size: 135%">${ data_to_render | h }</pre> -</%def> - - -<%def name="center_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - ${get_class_display_name( item.__class__ )} - | ${get_item_name( item ) | h} - </div> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - <div class="page-body"> - <div style="float: right"> - ${self.render_item_links( item )} - </div> - <div> - ${self.render_item_header( item )} - </div> - - ${self.render_item( item, item_data )} - </div> - </div> - </div> -</%def> - -<%def name="right_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - About this ${get_class_display_name( item.__class__ )} - </div> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - <div style="padding: 10px;"> - <h4>Author</h4> - - <p>${item.history.user.username | h}</p> - - <div><img src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.email)}?d=iden…"></div> - - ## Page meta. - - ## No links for datasets right now. - - ## Tags. - <p> - <h4>Tags</h4> - <p> - ## Community tags. - <div> - Community: - ${render_community_tagging_element( tagged_item=item, tag_click_fn='community_tag_click', use_toggle_link=False )} - %if len ( item.tags ) == 0: - none - %endif - </div> - ## Individual tags. - <p> - <div> - Yours: - ${render_individual_tagging_element( user=trans.get_user(), tagged_item=item, elt_context='view.mako', use_toggle_link=False, tag_click_fn='community_tag_click' )} - </div> - </div> - </div> - </div> - -</%def> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display_application/display.mako --- a/templates/dataset/display_application/display.mako +++ /dev/null @@ -1,12 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Display Application: ${display_link.link.display_application.name} ${display_link.link.name}</%def> -%for message, status in msg: - ${render_msg( message, status )} -%endfor -%if refresh: -<%def name="metas()"><meta http-equiv="refresh" content="10" /></%def> -<p> -This page will <a href="${trans.request.url}">refresh</a> after 10 seconds. -</p> -%endif diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ /dev/null @@ -1,202 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/message.mako" name="message_ns" import="handle_refresh_frames" /> - -<%def name="title()">${_('Edit Dataset Attributes')}</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${message_ns.handle_refresh_frames()} - ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} -</%def> - -<%def name="datatype( dataset, datatypes )"> - <select name="datatype"> - %for ext in datatypes: - %if dataset.ext == ext: - <option value="${ext}" selected="yes">${_(ext)}</option> - %else: - <option value="${ext}">${_(ext)}</option> - %endif - %endfor - </select> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - - -<ul class="nav nav-tabs"> - <li class="active"><a href="#attributes" data-toggle="tab">Attributes</a></li> - <li><a href="#convert" data-toggle="tab">Convert Format</a></li> - <li><a href="#datatype" data-toggle="tab">Datatype</a></li> - <li><a href="#permissions" data-toggle="tab">Permissions</a></li> -</ul> - -<div class="tab-content"> - -<div class="tab-pane active toolForm" id="attributes"> - <div class="toolFormTitle">${_('Edit Attributes')}</div> - <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <label> - Name: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${data.get_display_name() | h}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label> - Info: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="info" cols="40" rows="2">${ util.unicodify( data.info ) | h}</textarea> - </div> - <div style="clear: both"></div> - </div> - %if trans.get_user() is not None: - <div class="form-row"> - <label> - Annotation / Notes: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="annotation" cols="40" rows="2">${data_annotation | h}</textarea> - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div> - </div> - %endif - %for name, spec in data.metadata.spec.items(): - %if spec.visible: - <div class="form-row"> - <label> - ${spec.desc}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${data.metadata.get_html_by_name( name, trans=trans )} - </div> - <div style="clear: both"></div> - </div> - %endif - %endfor - <div class="form-row"> - <input type="submit" name="save" value="${_('Save')}"/> - </div> - </form> - <form name="auto_detect" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="detect" value="${_('Auto-detect')}"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will inspect the dataset and attempt to correct the above column values if they are not accurate. - </div> - </div> - </form> - %if data.missing_meta(): - <div class="form-row"> - <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div> - </div> - %endif - </div> -</div> - -<div class="tab-pane toolForm" id="convert"> - <div class="toolFormTitle">${_('Convert to new format')}</div> - <div class="toolFormBody"> - <% converters = data.get_converter_types() %> - %if len( converters ) > 0: - <form name="convert_data" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <select name="target_type"> - %for key, value in converters.items(): - <option value="${key}">${value.name}</option> - %endfor - </select> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will create a new dataset with the contents of this dataset converted to a new format. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="convert_data" value="${_('Convert')}"/> - </div> - </form> - %else: - No conversions available - %endif - </div> -</div> - -<div class="tab-pane toolForm" id="datatype"> - <div class="toolFormTitle">${_('Change data type')}</div> - <div class="toolFormBody"> - %if data.datatype.allow_datatype_change: - <form name="change_datatype" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <label> - ${_('New Type')}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${datatype( data, datatypes )} - </div> - <div class="toolParamHelp" style="clear: both;"> - ${_('This will change the datatype of the existing dataset but <i>not</i> modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.')} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="change" value="${_('Save')}"/> - </div> - </form> - %else: - <div class="form-row"> - <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div> - </div> - %endif - </div> -</div> -<p /> - -<div class="tab-pane" id="permissions"> -%if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ): - <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='dataset', action='edit', dataset_id=dataset_id ), all_roles )} -%elif trans.user: - <div class="toolForm"> - <div class="toolFormTitle">View Permissions</div> - <div class="toolFormBody"> - <div class="form-row"> - %if data.dataset.actions: - <ul> - %for action, roles in trans.app.security_agent.get_permissions( data.dataset ).items(): - %if roles: - <li>${action.description}</li> - <ul> - %for role in roles: - <li>${role.name}</li> - %endfor - </ul> - %endif - %endfor - </ul> - %else: - <p>This dataset is accessible by everyone (it is public).</p> - %endif - </div> - </div> - </div> -%else: - Permissions not available (not logged in) -%endif -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/embed.mako --- a/templates/dataset/embed.mako +++ /dev/null @@ -1,19 +0,0 @@ -<%inherit file="/embed_base.mako"/> -<%! - from galaxy.web.framework.helpers import iff -%> - -<%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> - ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a> - <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> - -</%def> - -<%def name="render_summary_content( dataset, data )"> -## <ul> -## <li>Format : ${dataset.extension} -## <pre>${dataset.peek}</pre> -## </ul> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ /dev/null @@ -1,80 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - <head> - <title>Dataset generation errors</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link href="/static/style/base.css" rel="stylesheet" type="text/css" /> - <style> - pre - { - background: white; - color: black; - border: dotted black 1px; - overflow: auto; - padding: 10px; - } - </style> - </head> - - <body> - <h2>Dataset generation errors</h2> - <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> - <% job = hda.creating_job %> - %if job: - - %if job.traceback: - The Galaxy framework encountered the following error while attempting to run the tool: - <pre>${ util.unicodify( job.traceback ) | h}</pre> - %endif - %if job.stderr or job.info: - Tool execution generated the following error message: - %if job.stderr: - <pre>${ util.unicodify( job.stderr ) | h}</pre> - %elif job.info: - <pre>${ util.unicodify( job.info ) | h}</pre> - %endif - %else: - Tool execution did not generate any error messages. - %endif - %if job.stdout: - The tool produced the following additional output: - <pre>${ util.unicodify( job.stdout ) | h}</pre> - %endif - %else: - The tool did not create any additional job / error info. - %endif - <% - if trans.user: - user_email = trans.user.email - else: - user_email = '' - %> - <h2>Report this error to the Galaxy Team</h2> - <p> - The Galaxy team regularly reviews errors that occur in the application. - However, if you would like to provide additional information (such as - what you were trying to do when the error occurred) and a contact e-mail - address, we will be better able to investigate your problem and get back - to you. - </p> - <div class="toolForm"> - <div class="toolFormTitle">Error Report</div> - <div class="toolFormBody"> - <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > - <input type="hidden" name="id" value="${hda.id}" /> - <div class="form-row"> - <label>Your email</label> - <input type="text" name="email" size="40" value="${user_email}" /> - </div> - <div class="form-row"> - <label>Message</label> - <textarea name="message" rows="10" cols="40"></textarea> - </div> - <div class="form-row"> - <input type="submit" value="Report"/> - </div> - </form> - </div> - </div> - </body> -</html> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/grid.mako --- a/templates/dataset/grid.mako +++ /dev/null @@ -1,1 +0,0 @@ -<%inherit file="/grid_base.mako"/> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/item_content.mako --- a/templates/dataset/item_content.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="/dataset/display.mako" import="*" /> - -${render_item( item, item_data )} \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/large_file.mako --- a/templates/dataset/large_file.mako +++ /dev/null @@ -1,11 +0,0 @@ -<%inherit file="/base.mako"/> - -<div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below.<br /> - <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), filename='' )}">Show all</a> | - <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">Save</a> -</div> - -<pre> -${ unicode( truncated_data, 'utf-8' ) | h } -</pre> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/security_common.mako --- a/templates/dataset/security_common.mako +++ /dev/null @@ -1,130 +0,0 @@ -<%def name="render_select( current_actions, action_key, action, roles )"> - <% - import sets - in_roles = sets.Set() - for a in current_actions: - if a.action == action.action: - in_roles.add( a.role ) - out_roles = filter( lambda x: x not in in_roles, roles ) - %> - <p> - <b>${action.action}:</b> ${action.description} - %if action == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - <br/> - NOTE: Users must have every role associated with this dataset in order to access it - %endif - </p> - <div style="width: 100%; white-space: nowrap;"> - <div style="float: left; width: 50%;"> - Roles associated:<br /> - <select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> - %for role in in_roles: - <option value="${role.id}">${role.name}</option> - %endfor - </select><br /> - <div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> - </div> - <div style="width: 50%;"> - Roles not associated:<br /> - <select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> - %for role in out_roles: - <option value="${role.id}">${role.name}</option> - %endfor - </select><br /> - <input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> - </div> - </div> -</%def> - -## Any permission ( e.g., 'DATASET_ACCESS' ) included in the do_not_render param will not be rendered on the page. -<%def name="render_permission_form( obj, obj_name, form_url, roles, do_not_render=[], all_roles=[] )"> - <% - if isinstance( obj, trans.app.model.User ): - current_actions = obj.default_permissions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = 'user %s' % obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.History ): - current_actions = obj.default_permissions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = 'history %s' % obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.Dataset ): - current_actions = obj.actions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.LibraryDatasetDatasetAssociation ): - current_actions = obj.actions + obj.dataset.actions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() + trans.app.model.Library.permitted_actions.items() - obj_str = obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.Library ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library %s' % obj_name - obj_type = 'library' - elif isinstance( obj, trans.app.model.LibraryDataset ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library dataset %s' % obj_name - obj_type = 'library' - elif isinstance( obj, trans.app.model.LibraryFolder ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library folder %s' % obj_name - obj_type = 'library' - else: - current_actions = [] - permitted_actions = {}.items() - obj_str = 'unknown object %s' %obj_name - obj_type = '' - %> - <script type="text/javascript"> - $( document ).ready( function () { - $( '.role_add_button' ).click( function() { - var action = this.id.substring( 0, this.id.lastIndexOf( '_add_button' ) ) - var in_select = '#' + action + '_in_select'; - var out_select = '#' + action + '_out_select'; - return !$( out_select + ' option:selected' ).remove().appendTo( in_select ); - }); - $( '.role_remove_button' ).click( function() { - var action = this.id.substring( 0, this.id.lastIndexOf( '_remove_button' ) ) - var in_select = '#' + action + '_in_select'; - var out_select = '#' + action + '_out_select'; - return !$( in_select + ' option:selected' ).remove().appendTo( out_select ); - }); - $( 'form#edit_role_associations' ).submit( function() { - $( '.in_select option' ).each(function( i ) { - $( this ).attr( "selected", "selected" ); - }); - }); - }); - </script> - <div class="toolForm"> - <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div> - <div class="toolFormBody"> - <form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post"> - <div class="form-row"></div> - %for k, v in permitted_actions: - %if k not in do_not_render: - <div class="form-row"> - ## LIBRARY_ACCESS is a special case because we need to render all roles instead of - ## roles derived from the roles associated with LIBRARY_ACCESS. - <% render_all_roles = k == 'LIBRARY_ACCESS' %> - %if render_all_roles: - ${render_select( current_actions, k, v, all_roles )} - %else: - ${render_select( current_actions, k, v, roles )} - %endif - </div> - %endif - %endfor - <div class="form-row"> - <input type="submit" name="update_roles_button" value="Save"/> - </div> - </form> - </div> - </div> - <p/> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ /dev/null @@ -1,103 +0,0 @@ -<%inherit file="/base.mako"/> - - -<%def name="title()">Dataset Display</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var COLUMN_NUMBER = ${column_number}; - var COLUMN_TYPES = ${column_types}; - var COLUMN_NAMES = ${column_names}; - - var chunk = ${chunk}; - var current_chunk = 0; - - function renderCell(cell_contents, index, colspan){ - if (colspan !== undefined){ - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); - } - else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){ - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents);; - } - else{ - return $('<td>').text(cell_contents); - } - } - - function renderRow(line){ - /* Check length of cells to ensure this is a complete row. */ - var cells = line.split('\t'); - var row = $('<tr>'); - if (cells.length == COLUMN_NUMBER){ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - } - else if(cells.length > COLUMN_NUMBER){ - /* SAM file or like format with optional metadata included */ - $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1)); - } - else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){ - /* SAM file or like format with optional metadata missing */ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append($('<td>')); - } - else{ - /* Comment line, just return the one cell*/ - row.append(renderCell(line, 0, COLUMN_NUMBER)); - } - return row; - } - - function renderChunk(chunk){ - var table = $('#content_table'); - if (chunk.ck_data == ""){ - current_chunk = -1; - } - else if(chunk.ck_index === current_chunk + 1){ - if (current_chunk === 0 && COLUMN_NAMES){ - table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>'); - } - var lines = chunk.ck_data.split('\n'); - $.each(lines, function(index, line){ - table.append(renderRow(line)); - }); - current_chunk = chunk.ck_index; - } - } - - $(document).ready(function(){ - renderChunk(chunk); - $(window).scroll(function(){ - if ($(window).scrollTop() == $(document).height() - $(window).height()){ - if (current_chunk !== -1){ - $.getJSON(DATASET_URL, - {chunk: current_chunk}, - function(result){renderChunk(result)}); - } - } - }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show(); - }).ajaxStop(function(){ - $(this).hide(); - }); - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} -</%def> - -<div id="loading_indicator" ></div> -<table id="content_table" cellpadding="0"> -</table> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/copy.mako --- a/templates/history/copy.mako +++ /dev/null @@ -1,27 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">Copy History</%def> - -<div class="toolForm"> - <div class="toolFormTitle">Copy History</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='copy' )}" method="post" > - <div class="form-row"> - %if id_argument is not None: - <input type="hidden" name="id" value="${id_argument}"> - %endif - You can make a copy of the history that includes all datasets in the original history or just the active - (not deleted) datasets. - </div> - <div class="form-row"> - <input type="radio" name="copy_choice" value="activatable"> Copy all datasets, including deleted ones - </div> - <div class="form-row"> - <input type="radio" name="copy_choice" value="active"> Copy only active (not deleted) datasets - </div> - <div class="form-row"> - <input type="submit" name="copy_choice_button" value="Copy"> - </div> - </form> - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display.mako --- a/templates/history/display.mako +++ /dev/null @@ -1,84 +0,0 @@ -<%inherit file="/display_base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> - -## Set vars so that there's no need to change the code below. -<% - history = published_item - datasets = published_item_data -%> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history" )} - <style type="text/css"> - .historyItemBody { - display: none; - } - .column { - float: left; - padding: 10px; - margin: 20px; - background: #666; - border: 5px solid #ccc; - width: 300px; - } - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="render_item_links( history )"> - <a - href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" - class="icon-button import" - ## Needed to overwide initial width so that link is floated left appropriately. - style="width: 100%" - title="Import history">Import history</a> -</%def> - -<%def name="render_item( history, datasets )"> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - %else: - ## Render requested datasets, ordered from newest to oldest, including annotations. - <table class="annotated-item"> - <tr><th>Dataset</th><th class="annotation">Annotation</th></tr> - %for data in datasets: - <tr> - %if data.visible: - <td> - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - </td> - <td class="annotation"> - %if hasattr( data, "annotation") and data.annotation is not None: - ${data.annotation} - %endif - </td> - %endif - </tr> - %endfor - </table> - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("This history is empty.")} - </div> -</%def> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display_structured.mako --- a/templates/history/display_structured.mako +++ /dev/null @@ -1,132 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history" )} - <style type="text/css"> - body { - background: white; - padding: 5px; - } - - .clickable { - cursor: pointer; - } - - .workflow { - border: solid gray 1px; - margin: 5px 0; - border-left-width: 5px; - } - - .workflow > .header { - background: lightgray; - padding: 5px 10px; - - font-weight: bold; - } - - .workflow > .body { - border-top: solid gray 1px; - padding: 5px; - } - - div.toolForm { - margin: 5px 0; - border-left-width: 5px; - } - div.toolFormBody { - padding: 5px 5px; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - - $(".workflow, .tool").each( function() { - var body = $(this).children( ".body" ); - $(this).children( ".header" ).click( function() { - body.toggle(); - }).addClass( "clickable" ); - // body.hide(); - }); - - $(".historyItem").each( function() { - var id = this.id; - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - // Hiding stuff here - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - } else { - // Showing stuff here - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - } - return false; - }); - body.hide(); - }); - }); - </script> -</%def> - -<%def name="render_item( entity, children )"> -<% -entity_name = entity.__class__.__name__ -if entity_name == "HistoryDatasetAssociation": - render_item_hda( entity, children ) -elif entity_name == "Job": - render_item_job( entity, children ) -elif entity_name == "WorkflowInvocation": - render_item_wf( entity, children ) -%> -</%def> - -<%def name="render_item_hda( hda, children )"> - ${render_dataset( hda, hda.hid, display_structured=True )} -</%def> - -<%def name="render_item_job( job, children )"> - - <div class="tool toolForm"> - <% - tool = trans.app.toolbox.get_tool( job.tool_id ) - if tool: - tool_name = tool.name - else: - tool_name = "Unknown tool with id '%s'" % job.tool_id - %> - <div class="header toolFormTitle">Tool: ${tool_name}</div> - <div class="body toolFormBody"> - %for e, c in reversed( children ): - ${render_item( e, c )} - %endfor - </div> - </div> - -</%def> - -<%def name="render_item_wf( wf, children )"> - - <div class="workflow"> - <div class="header">Workflow: ${wf.workflow.name}</div> - <div class="body"> - %for e, c in reversed( children ): - ${render_item( e, c )} - %endfor - </div> - </div> - -</%def> - -%for entity, children in items: - ${render_item( entity, children )} -%endfor \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/embed.mako --- a/templates/history/embed.mako +++ /dev/null @@ -1,13 +0,0 @@ -<%inherit file="/embed_base.mako"/> -<%! - from galaxy.web.framework.helpers import iff -%> - -<%def name="render_summary_content( history, datasets )"> - -## <ul> -## <% num_datasets = len ( datasets ) %> -## <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )} -## <li>Operations: ... -## </ul> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/grid.mako --- a/templates/history/grid.mako +++ /dev/null @@ -1,25 +0,0 @@ -<%inherit file="../grid_base.mako"/> - -<%def name="grid_javascripts()"> - ${parent.grid_javascripts()} - <script type="text/javascript"> - %if refresh_frames: - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="grid_body( grid )"> - ${self.make_grid( grid )} - <br/> - <div class="toolParamHelp" style="clear: both;"> - Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted. - </div> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/item_content.mako --- a/templates/history/item_content.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="/history/display.mako" import="*" /> - -${render_item( item, item_data )} \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_as_xml.mako --- a/templates/history/list_as_xml.mako +++ /dev/null @@ -1,7 +0,0 @@ -<?xml version="1.0"?> -<history_ids> - %for i, history in enumerate( t.user.histories ): - <data id="${trans.security.encode_id( history.id )}" hid="${i+1}" num="${len(history.datasets)}" name="${history.name}" create="${history.create_time}" update="${history.update_time}" > - </data> - %endfor -</history_ids> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_published.mako --- a/templates/history/list_published.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - -<%def name="title()"> - Galaxy | Published Histories -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - <style> - .grid td { - min-width: 100px; - } - </style> -</%def> - -<%def name="center_panel()"> - - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - ${h.to_unicode( grid )} - </div> - </div> - - -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/options.mako --- a/templates/history/options.mako +++ /dev/null @@ -1,32 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">History options</%def> - -<h2>${_('History Options')}</h2> - -%if not user: -<div class="infomessage"> - <div>${_('You must be ')}<a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">${_('logged in')}</a>${_(' to store or switch histories.')}</div> -</div> -%endif - -<ul> - %if user: - <li><a href="${h.url_for( controller='history', action='list')}" target="galaxy_main">Previously</a> stored histories</li> - %if len( history.active_datasets ) > 0: - <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li> - <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from current history</li> - <li><a href="${h.url_for( controller='history', action='copy', id=trans.security.encode_id( history.id ) )}">Copy</a> current history</li> - %endif - <li><a href="${h.url_for( controller='history', action='share' )}" target="galaxy_main">Share</a> current history</div> - <li><a href="${h.url_for( controller='root', action='history_set_default_permissions' )}">Change default permissions</a> for current history</li> - %endif - %if len( history.activatable_datasets ) > 0: - <li><a href="${h.url_for( controller='root', action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in current history</li> - %endif - <li><a href="${h.url_for( controller='history', action='rename', id=trans.security.encode_id( history.id ) )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li> - <li><a href="${h.url_for( controller='history', action='delete_current' )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> - %if user and user.histories_shared_by_others: - <li><a href="${h.url_for( controller='history', action='list_shared')}" target="galaxy_main">Histories</a> shared with you by others</li> - %endif -</ul> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/permissions.mako --- a/templates/history/permissions.mako +++ /dev/null @@ -1,8 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default Permissions on New Datasets in This History</%def> -<%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - -%if trans.user: - <% history = trans.get_history() %> - ${render_permission_form( history, history.name, h.url_for(), trans.user.all_roles() )} -%endif diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/rename.mako --- a/templates/history/rename.mako +++ /dev/null @@ -1,38 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">${_('Rename History')}</%def> - -<div class="toolForm"> - <div class="toolFormTitle">${_('Rename')}</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='rename' )}" method="post" > - <div class="form-row"> - <table> - <thead> - <tr> - <th>${_('Current Name')}</th> - <th>${_('New Name')}</th> - </tr> - </thead> - <tbody> - %for history in histories: - <tr> - <td> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${history.get_display_name() | h} - </td> - <td> - <input type="text" name="name" value="${history.get_display_name() | h}" size="40"> - </td> - </tr> - %endfor - </tbody> - <tr> - <td colspan="2"> - <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> - </td> - </tr> - </table> - </div> - </form> - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/share.mako --- a/templates/history/share.mako +++ /dev/null @@ -1,192 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">Share histories</%def> - -<div class="toolForm"> - <div class="toolFormTitle">Share ${len( histories)} histories</div> - <div class="toolFormBody"> - %if not can_change and not cannot_change and not no_change_needed: - ## We are sharing histories that contain only public datasets - <form name='share' id='share' action="${h.url_for( action='share' )}" method="post" > - <div class="form-title-row"><b>Histories to be shared:</b></div> - <div class="form-row" style="padding-left: 2em;"> - <table width="100%"> - <thead> - <th>${_('History Name')}</th> - <th>${_('Number of Datasets')}</th> - </thead> - <tbody> - %for history in histories: - <tr> - <td> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${ util.unicodify( history.name )} - </td> - <td> - %if len( history.datasets ) < 1: - <div class="warningmark">${_('This history contains no data.')}</div> - %else: - ${len(history.datasets)} - %endif - </td> - </tr> - %endfor - </tbody> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> - <div class="toolParamHelp" style="clear: both;"> - Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users - </div> - </div> - %if send_to_err: - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage">${send_to_err}</div> - </div> - %endif - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="share_button" value="Submit"> - </div> - </form> - %else: - ## We are sharing restricted histories - %if no_change_needed or can_change: - <form name='share_restricted' id=share_restricted' action="${h.url_for( controller='history', action='share_restricted' )}" method="post"> - %if send_to_err: - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage">${send_to_err}</div> - </div> - %endif - ## Needed for rebuilding dicts - <input type="hidden" name="email" value="${email}" size="40"> - %for history in histories: - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - %endfor - %if no_change_needed: - ## no_change_needed looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="donemessage"> - The following datasets can be shared with ${email} with no changes - </div> - </div> - %for history, hdas in no_change_needed.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - %if can_change: - ## can_change looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="warningmessage"> - The following datasets can be shared with ${email} by updating their permissions - </div> - </div> - %for history, hdas in can_change.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - %if cannot_change: - ## cannot_change looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage"> - The following datasets cannot be shared with ${email} because you are not authorized to - change the permissions on them - </div> - </div> - %for history, hdas in cannot_change.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - <div class="toolFormTitle"></div> - <div class="form-row"> - <label>How would you like to proceed?</label> - </div> - %if can_change: - <div class="form-row"> - <input type="radio" name="action" value="public"> Make datasets public so anyone can access them - %if cannot_change: - (where possible) - %endif - </div> - <div class="form-row"> - %if no_change_needed: - <input type="radio" name="action" value="private"> Make datasets private to me and the user(s) with whom I am sharing - %else: - <input type="radio" name="action" value="private" checked> Make datasets private to me and the user(s) with whom I am sharing - %endif - %if cannot_change: - (where possible) - %endif - </div> - %endif - %if no_change_needed: - <div class="form-row"> - <input type="radio" name="action" value="share_anyway" checked> Share anyway - %if can_change: - (don't change any permissions) - %endif - </div> - %endif - <div class="form-row"> - <input type="submit" name="share_restricted_button" value="Go"><br/> - </div> - </form> - %endif - %endif - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/view.mako --- a/templates/history/view.mako +++ /dev/null @@ -1,140 +0,0 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - <style type="text/css"> - .historyItemContainer { - padding-right: 3px; - border-right-style: solid; - border-right-color: #66AA66; - } - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - </style> - - <style> - .historyItemBody { - display: none; - } - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-header" unselectable="on"> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged: - <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | - <a href="${get_history_link( history )}">${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> This diff is so big that we needed to truncate the remainder. 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: james_taylor: base_panels: no longer need to specify has_(left|right)_panel, determined depending on whether the blocks are set. Moved some CSS into base.css
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c714feaad115/ changeset: c714feaad115 user: james_taylor date: 2013-02-04 04:57:32 summary: base_panels: no longer need to specify has_(left|right)_panel, determined depending on whether the blocks are set. Moved some CSS into base.css affected #: 6 files diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -79,6 +79,7 @@ default_action=default_action, message=message, status=status ) + @web.expose def browse_libraries( self, trans, **kwd ): if 'operation' in kwd: diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -31,8 +31,19 @@ background-repeat: repeat-x; background-position: top; margin: 10px; + + // For panel layout pages + &.full-content { + overflow: hidden; + margin: 0; + padding: 0; + width: 100%; + height: 100%; + } + } + img { border: 0; } @@ -410,7 +421,7 @@ width:100%; min-width:900px; height:32px; - // background: @masthead_bg; + background: @masthead_bg; // color:#fff; border-bottom: solid @layout_masthead_border 1px; z-index: 15000; diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -892,7 +892,7 @@ .clear:after{clear:both;} .clear:before,.clear:after{display:table;content:"";line-height:0;} .clear:after{clear:both;} -body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} +body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;}body.full-content{overflow:hidden;margin:0;padding:0;width:100%;height:100%;} img{border:0;} a,a:link,a:visited,a:active{text-decoration:underline;color:#303030;} .nav-tabs a{text-decoration:none;} @@ -936,7 +936,7 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} .panel-done-message{background-image:url(ok_small.png);background-color:#ccffcc;} .panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} -#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} +#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2c3143;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} #masthead .nav>li>a{padding:8px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} #masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} #masthead .dropdown-toggle .caret{margin-top:7px;} diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -107,7 +107,6 @@ margin-left: -330px; } - .modal:after { content: ""; height: 0px; @@ -115,8 +114,7 @@ top: 50px; display: block; border: solid transparent 1px; -}; - +} .modal-body { height: auto; @@ -203,4 +201,4 @@ border-width: 0 @tooltipArrowWidth @tooltipArrowWidth; border-bottom-color: @tooltipArrowColor; } -} \ No newline at end of file +} diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -1,8 +1,8 @@ <!DOCTYPE HTML><% - self.has_left_panel=True - self.has_right_panel=True + self.has_left_panel = hasattr( self, 'left_panel' ) + self.has_right_panel = hasattr( self, 'right_panel' ) self.message_box_visible=False self.overlay_visible=False self.message_box_class="" @@ -17,15 +17,8 @@ ## Default stylesheets <%def name="stylesheets()"> - ${h.css('base','panel_layout','jquery.rating')} + ${h.css('base','jquery.rating')} <style type="text/css"> - body, html { - overflow: hidden; - margin: 0; - padding: 0; - width: 100%; - height: 100%; - } #center { %if not self.has_left_panel: left: 0 !important; @@ -270,7 +263,7 @@ ${self.javascripts()} </head> - <body scroll="no" class="${self.body_class}"> + <body scroll="no" class="full-content ${self.body_class}"> %if self.require_javascript: <noscript><div class="overlay overlay-background"> diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 templates/workflow/index.mako --- a/templates/workflow/index.mako +++ b/templates/workflow/index.mako @@ -2,10 +2,7 @@ <%def name="init()"><% - self.has_left_panel=False - self.has_right_panel=False self.active_view="workflow" - self.message_box_visible=False %></%def> 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: james_taylor: Customize errormiddleware with a better appearence for internal server errors, show sentry ID is enabled, modify sentry middleware to store id in environment and pass request_id with log messages
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2b192832826/ changeset: d2b192832826 user: james_taylor date: 2013-02-03 01:39:42 summary: Customize errormiddleware with a better appearence for internal server errors, show sentry ID is enabled, modify sentry middleware to store id in environment and pass request_id with log messages affected #: 3 files diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/web/framework/middleware/error.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/error.py @@ -0,0 +1,484 @@ +# Like many things, this started life as part of Paste + +# (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org) +# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php + +""" +Error handler middleware + +When an exception is thrown from the wrapper application, this logs +the exception and displays an error page. +""" +import sys +import traceback +import cgi +try: + from cStringIO import StringIO +except ImportError: + from StringIO import StringIO +from paste.exceptions import formatter, collector, reporter +from paste import wsgilib +from paste import request + +__all__ = ['ErrorMiddleware', 'handle_exception'] + +class _NoDefault(object): + def __repr__(self): + return '<NoDefault>' +NoDefault = _NoDefault() + +class ErrorMiddleware(object): + + """ + Error handling middleware + + Usage:: + + error_catching_wsgi_app = ErrorMiddleware(wsgi_app) + + Settings: + + ``debug``: + If true, then tracebacks will be shown in the browser. + + ``error_email``: + an email address (or list of addresses) to send exception + reports to + + ``error_log``: + a filename to append tracebacks to + + ``show_exceptions_in_wsgi_errors``: + If true, then errors will be printed to ``wsgi.errors`` + (frequently a server error log, or stderr). + + ``from_address``, ``smtp_server``, ``error_subject_prefix``, ``smtp_username``, ``smtp_password``, ``smtp_use_tls``: + variables to control the emailed exception reports + + ``error_message``: + When debug mode is off, the error message to show to users. + + ``xmlhttp_key``: + When this key (default ``_``) is in the request GET variables + (not POST!), expect that this is an XMLHttpRequest, and the + response should be more minimal; it should not be a complete + HTML page. + + Environment Configuration: + + ``paste.throw_errors``: + If this setting in the request environment is true, then this + middleware is disabled. This can be useful in a testing situation + where you don't want errors to be caught and transformed. + + ``paste.expected_exceptions``: + When this middleware encounters an exception listed in this + environment variable and when the ``start_response`` has not + yet occurred, the exception will be re-raised instead of being + caught. This should generally be set by middleware that may + (but probably shouldn't be) installed above this middleware, + and wants to get certain exceptions. Exceptions raised after + ``start_response`` have been called are always caught since + by definition they are no longer expected. + + """ + + def __init__(self, application, global_conf=None, + debug=NoDefault, + error_email=None, + error_log=None, + show_exceptions_in_wsgi_errors=NoDefault, + from_address=None, + smtp_server=None, + smtp_username=None, + smtp_password=None, + smtp_use_tls=False, + error_subject_prefix=None, + error_message=None, + xmlhttp_key=None): + from paste.util import converters + self.application = application + # @@: global_conf should be handled elsewhere in a separate + # function for the entry point + if global_conf is None: + global_conf = {} + if debug is NoDefault: + debug = converters.asbool(global_conf.get('debug')) + if show_exceptions_in_wsgi_errors is NoDefault: + show_exceptions_in_wsgi_errors = converters.asbool(global_conf.get('show_exceptions_in_wsgi_errors')) + self.debug_mode = converters.asbool(debug) + if error_email is None: + error_email = (global_conf.get('error_email') + or global_conf.get('admin_email') + or global_conf.get('webmaster_email') + or global_conf.get('sysadmin_email')) + self.error_email = converters.aslist(error_email) + self.error_log = error_log + self.show_exceptions_in_wsgi_errors = show_exceptions_in_wsgi_errors + if from_address is None: + from_address = global_conf.get('error_from_address', 'errors@localhost') + self.from_address = from_address + if smtp_server is None: + smtp_server = global_conf.get('smtp_server', 'localhost') + self.smtp_server = smtp_server + self.smtp_username = smtp_username or global_conf.get('smtp_username') + self.smtp_password = smtp_password or global_conf.get('smtp_password') + self.smtp_use_tls = smtp_use_tls or converters.asbool(global_conf.get('smtp_use_tls')) + self.error_subject_prefix = error_subject_prefix or '' + if error_message is None: + error_message = global_conf.get('error_message') + self.error_message = error_message + if xmlhttp_key is None: + xmlhttp_key = global_conf.get('xmlhttp_key', '_') + self.xmlhttp_key = xmlhttp_key + + def __call__(self, environ, start_response): + """ + The WSGI application interface. + """ + # We want to be careful about not sending headers twice, + # and the content type that the app has committed to (if there + # is an exception in the iterator body of the response) + if environ.get('paste.throw_errors'): + return self.application(environ, start_response) + environ['paste.throw_errors'] = True + + try: + __traceback_supplement__ = Supplement, self, environ + sr_checker = ResponseStartChecker(start_response) + app_iter = self.application(environ, sr_checker) + return self.make_catching_iter(app_iter, environ, sr_checker) + except: + exc_info = sys.exc_info() + try: + for expect in environ.get('paste.expected_exceptions', []): + if isinstance(exc_info[1], expect): + raise + start_response('500 Internal Server Error', + [('content-type', 'text/html')], + exc_info) + # @@: it would be nice to deal with bad content types here + response = self.exception_handler(exc_info, environ) + return [response] + finally: + # clean up locals... + exc_info = None + + def make_catching_iter(self, app_iter, environ, sr_checker): + if isinstance(app_iter, (list, tuple)): + # These don't raise + return app_iter + return CatchingIter(app_iter, environ, sr_checker, self) + + def exception_handler(self, exc_info, environ): + simple_html_error = False + if self.xmlhttp_key: + get_vars = wsgilib.parse_querystring(environ) + if dict(get_vars).get(self.xmlhttp_key): + simple_html_error = True + return handle_exception( + exc_info, environ['wsgi.errors'], + html=True, + debug_mode=self.debug_mode, + error_email=self.error_email, + error_log=self.error_log, + show_exceptions_in_wsgi_errors=self.show_exceptions_in_wsgi_errors, + error_email_from=self.from_address, + smtp_server=self.smtp_server, + smtp_username=self.smtp_username, + smtp_password=self.smtp_password, + smtp_use_tls=self.smtp_use_tls, + error_subject_prefix=self.error_subject_prefix, + error_message=self.error_message, + simple_html_error=simple_html_error, + environ=environ) + +class ResponseStartChecker(object): + def __init__(self, start_response): + self.start_response = start_response + self.response_started = False + + def __call__(self, *args): + self.response_started = True + self.start_response(*args) + +class CatchingIter(object): + + """ + A wrapper around the application iterator that will catch + exceptions raised by the a generator, or by the close method, and + display or report as necessary. + """ + + def __init__(self, app_iter, environ, start_checker, error_middleware): + self.app_iterable = app_iter + self.app_iterator = iter(app_iter) + self.environ = environ + self.start_checker = start_checker + self.error_middleware = error_middleware + self.closed = False + + def __iter__(self): + return self + + def next(self): + __traceback_supplement__ = ( + Supplement, self.error_middleware, self.environ) + if self.closed: + raise StopIteration + try: + return self.app_iterator.next() + except StopIteration: + self.closed = True + close_response = self._close() + if close_response is not None: + return close_response + else: + raise StopIteration + except: + self.closed = True + close_response = self._close() + exc_info = sys.exc_info() + response = self.error_middleware.exception_handler( + exc_info, self.environ) + if close_response is not None: + response += ( + '<hr noshade>Error in .close():<br>%s' + % close_response) + + if not self.start_checker.response_started: + self.start_checker('500 Internal Server Error', + [('content-type', 'text/html')], + exc_info) + + return response + + def close(self): + # This should at least print something to stderr if the + # close method fails at this point + if not self.closed: + self._close() + + def _close(self): + """Close and return any error message""" + if not hasattr(self.app_iterable, 'close'): + return None + try: + self.app_iterable.close() + return None + except: + close_response = self.error_middleware.exception_handler( + sys.exc_info(), self.environ) + return close_response + + +class Supplement(object): + + """ + This is a supplement used to display standard WSGI information in + the traceback. + """ + + def __init__(self, middleware, environ): + self.middleware = middleware + self.environ = environ + self.source_url = request.construct_url(environ) + + def extraData(self): + data = {} + cgi_vars = data[('extra', 'CGI Variables')] = {} + wsgi_vars = data[('extra', 'WSGI Variables')] = {} + hide_vars = ['paste.config', 'wsgi.errors', 'wsgi.input', + 'wsgi.multithread', 'wsgi.multiprocess', + 'wsgi.run_once', 'wsgi.version', + 'wsgi.url_scheme'] + for name, value in self.environ.items(): + if name.upper() == name: + if value: + cgi_vars[name] = value + elif name not in hide_vars: + wsgi_vars[name] = value + if self.environ['wsgi.version'] != (1, 0): + wsgi_vars['wsgi.version'] = self.environ['wsgi.version'] + proc_desc = tuple([int(bool(self.environ[key])) + for key in ('wsgi.multiprocess', + 'wsgi.multithread', + 'wsgi.run_once')]) + wsgi_vars['wsgi process'] = self.process_combos[proc_desc] + wsgi_vars['application'] = self.middleware.application + if 'paste.config' in self.environ: + data[('extra', 'Configuration')] = dict(self.environ['paste.config']) + return data + + process_combos = { + # multiprocess, multithread, run_once + (0, 0, 0): 'Non-concurrent server', + (0, 1, 0): 'Multithreaded', + (1, 0, 0): 'Multiprocess', + (1, 1, 0): 'Multi process AND threads (?)', + (0, 0, 1): 'Non-concurrent CGI', + (0, 1, 1): 'Multithread CGI (?)', + (1, 0, 1): 'CGI', + (1, 1, 1): 'Multi thread/process CGI (?)', + } + +def handle_exception(exc_info, error_stream, html=True, + debug_mode=False, + error_email=None, + error_log=None, + show_exceptions_in_wsgi_errors=False, + error_email_from='errors@localhost', + smtp_server='localhost', + smtp_username=None, + smtp_password=None, + smtp_use_tls=False, + error_subject_prefix='', + error_message=None, + simple_html_error=False, + environ=None + ): + """ + For exception handling outside of a web context + + Use like:: + + import sys + from paste.exceptions.errormiddleware import handle_exception + try: + do stuff + except: + handle_exception( + sys.exc_info(), sys.stderr, html=False, ...other config...) + + If you want to report, but not fully catch the exception, call + ``raise`` after ``handle_exception``, which (when given no argument) + will reraise the exception. + """ + reported = False + exc_data = collector.collect_exception(*exc_info) + extra_data = '' + if error_email: + rep = reporter.EmailReporter( + to_addresses=error_email, + from_address=error_email_from, + smtp_server=smtp_server, + smtp_username=smtp_username, + smtp_password=smtp_password, + smtp_use_tls=smtp_use_tls, + subject_prefix=error_subject_prefix) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + if error_log: + rep = reporter.LogReporter( + filename=error_log) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + if show_exceptions_in_wsgi_errors: + rep = reporter.FileReporter( + file=error_stream) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + else: + error_stream.write('Error - %s: %s\n' % ( + exc_data.exception_type, exc_data.exception_value)) + if html: + if debug_mode and simple_html_error: + return_error = formatter.format_html( + exc_data, include_hidden_frames=False, + include_reusable=False, show_extra_data=False) + reported = True + elif debug_mode and not simple_html_error: + error_html = formatter.format_html( + exc_data, + include_hidden_frames=True, + include_reusable=False) + head_html = formatter.error_css + formatter.hide_display_js + return_error = error_template( + head_html, error_html, extra_data) + extra_data = '' + reported = True + else: + msg = error_message or ''' + An error occurred. + ''' + extra = "<p><b>The error has been logged to our team.</b>" + if 'sentry_event_id' in environ: + extra += " If you want to contact us about this error, please reference the following<br><br>" + extra += "<b><large>GURU MEDITATION: #" + environ['sentry_event_id'] + "</large></b>" + extra += "</p>" + return_error = error_template('', msg, extra) + else: + return_error = None + if not reported and error_stream: + err_report = formatter.format_text(exc_data, show_hidden_frames=True) + err_report += '\n' + '-'*60 + '\n' + error_stream.write(err_report) + if extra_data: + error_stream.write(extra_data) + return return_error + +def send_report(rep, exc_data, html=True): + try: + rep.report(exc_data) + except: + output = StringIO() + traceback.print_exc(file=output) + if html: + return """ + <p>Additionally an error occurred while sending the %s report: + + <pre>%s</pre> + </p>""" % ( + cgi.escape(str(rep)), output.getvalue()) + else: + return ( + "Additionally an error occurred while sending the " + "%s report:\n%s" % (str(rep), output.getvalue())) + else: + return '' + +def error_template(head_html, exception, extra): + return ''' + <!DOCTYPE HTML> + <html> + <head> + <style type="text/css"> + body { color: #303030; background: #dfe5f9; font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif; font-size:12px; line-height:16px; } + .content { max-width: 720px; margin: auto; margin-top: 50px; } + </style> + <title>Internal Server Error</title> + %s + </head> + <body> + <div class="content"> + <h1>Internal Server Error</h1> + + <h2>Galaxy was unable to sucessfully complete your request</h2> + + <p>%s</p> + + This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. + + %s + </div> + </body> + </html>''' % (head_html, exception, extra) + +def make_error_middleware(app, global_conf, **kw): + return ErrorMiddleware(app, global_conf=global_conf, **kw) + +doc_lines = ErrorMiddleware.__doc__.splitlines(True) +for i in range(len(doc_lines)): + if doc_lines[i].strip().startswith('Settings'): + make_error_middleware.__doc__ = ''.join(doc_lines[i:]) + break +del i, doc_lines \ No newline at end of file diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/web/framework/middleware/sentry.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/sentry.py @@ -0,0 +1,70 @@ +""" +raven.middleware +~~~~~~~~~~~~~~~~~~~~~~~~ + +:copyright: (c) 2010-2012 by the Sentry Team, see AUTHORS for more details. +:license: BSD, see LICENSE for more details. +""" + +import galaxy.eggs; galaxy.eggs.require( "raven" ) + +from raven import Client +from raven.utils.wsgi import get_current_url, get_headers, \ + get_environ + +class Sentry(object): + """ + A WSGI middleware which will attempt to capture any + uncaught exceptions and send them to Sentry. + + >>> from raven.base import Client + >>> application = Sentry(application, Client()) + """ + def __init__(self, application, dsn): + self.application = application + self.client = Client( dsn ) + + def __call__(self, environ, start_response): + try: + iterable = self.application(environ, start_response) + except Exception: + self.handle_exception(environ) + raise + + try: + for event in iterable: + yield event + except Exception: + self.handle_exception(environ) + raise + finally: + # wsgi spec requires iterable to call close if it exists + # see http://blog.dscpl.com.au/2012/10/obligations-for-calling-close-on.html + if iterable and hasattr(iterable, 'close') and callable(iterable.close): + try: + iterable.close() + except Exception: + self.handle_exception(environ) + + def handle_exception(self, environ): + event_id = self.client.captureException( + data={ + 'sentry.interfaces.Http': { + 'method': environ.get('REQUEST_METHOD'), + 'url': get_current_url(environ, strip_querystring=True), + 'query_string': environ.get('QUERY_STRING'), + # TODO + # 'data': environ.get('wsgi.input'), + 'headers': dict(get_headers(environ)), + 'env': dict(get_environ(environ)), + } + }, + # Galaxy: add request id from environment if available + extra={ + 'request_id': environ.get( 'request_id', 'Unknown' ) + } + ) + # Galaxy: store event_id in environment so we can show it to the user + environ['sentry_event_id'] = event_id[0] + + return event_id \ No newline at end of file diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -242,12 +242,10 @@ log.debug( "Enabling 'recursive' middleware" ) # If sentry logging is enabled, log here before propogating up to # the error middleware - sentry_url = conf.get( 'sentry_url', None ) - if sentry_url: - pkg_resources.require( "raven") - from raven import Client - from raven.middleware import Sentry - app = Sentry( app, Client( sentry_url ) ) + sentry_dsn = conf.get( 'sentry_dsn', None ) + if sentry_dsn: + from galaxy.web.framework.middleware.sentry import Sentry + app = Sentry( app, sentry_dsn ) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance @@ -275,11 +273,11 @@ # Not in interactive debug mode, just use the regular error middleware if sys.version_info[:2] >= ( 2, 6 ): warnings.filterwarnings( 'ignore', '.*', DeprecationWarning, '.*serial_number_generator', 11, True ) - from paste.exceptions import errormiddleware + import galaxy.web.framework.middleware.error warnings.filters.pop() else: - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) + import galaxy.web.framework.middleware.error + app = galaxy.web.framework.middleware.error.ErrorMiddleware( app, conf ) log.debug( "Enabling 'error' middleware" ) # Transaction logging (apache access.log style) if asbool( conf.get( 'use_translogger', True ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: Fix leftover debug code
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc99a36f9d21/ changeset: fc99a36f9d21 user: james_taylor date: 2013-02-03 00:29:05 summary: Fix leftover debug code affected #: 2 files diff -r 708d0ccee63fc75eb88e5dc3a9e0d6d3e5ff72e7 -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -54,7 +54,7 @@ ${h.js( "mvc/ui" )} - + <script type="text/javascript"> // console protection window.console = window.console || { diff -r 708d0ccee63fc75eb88e5dc3a9e0d6d3e5ff72e7 -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -74,7 +74,7 @@ }); */ - $( '.tooltip' ).tooltip().foasdasdasdoo(); + $( '.tooltip' ).tooltip(); // TODO: is this necessary? $( "a[minsizehint]" ).click( function() { 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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