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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6fdf96b4aef0/ Changeset: 6fdf96b4aef0 User: jmchilton Date: 2013-10-11 17:40:43 Summary: Refactor building command lines out of job runner base into its own module. Add unit tests. Test skipping metadata, using metadata, return code patch, dependency shell commands. Affected #: 3 files diff -r 829c047e05776fb2a6568f0d1076856fe6255fab -r 6fdf96b4aef00174938470f945d6931746e319f2 lib/galaxy/jobs/command_factory.py --- /dev/null +++ b/lib/galaxy/jobs/command_factory.py @@ -0,0 +1,70 @@ +from os import getcwd +from os.path import abspath + + +def build_command( job, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): + """ + Compose the sequence of commands necessary to execute a job. This will + currently include: + + - environment settings corresponding to any requirement tags + - preparing input files + - command line taken from job wrapper + - commands to set metadata (if include_metadata is True) + """ + + commands = job_wrapper.get_command_line() + + # All job runners currently handle this case which should never occur + if not commands: + return None + + # Prepend version string + if job_wrapper.version_string_cmd: + commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands + + # prepend getting input files (if defined) + if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: + commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) + + # Prepend dependency injection + if job_wrapper.dependency_shell_commands: + commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) + + # Coping work dir outputs or setting metadata will mask return code of + # tool command. If these are used capture the return code and ensure + # the last thing that happens is an exit with return code. + capture_return_code_command = "; return_code=$?" + captured_return_code = False + + # Append commands to copy job outputs based on from_work_dir attribute. + if include_work_dir_outputs: + work_dir_outputs = job.get_work_dir_outputs( job_wrapper ) + if work_dir_outputs: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True + + 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 + if include_metadata and job_wrapper.requires_setting_metadata: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True + commands += "; cd %s; " % abspath( getcwd() ) + commands += job_wrapper.setup_external_metadata( + exec_dir=abspath( getcwd() ), + tmp_dir=job_wrapper.working_directory, + dataset_files_path=job.app.model.Dataset.file_path, + output_fnames=job_wrapper.get_output_fnames(), + set_extension=False, + kwds={ 'overwrite' : False } + ) + + if captured_return_code: + commands += '; sh -c "exit $return_code"' + + return commands diff -r 829c047e05776fb2a6568f0d1076856fe6255fab -r 6fdf96b4aef00174938470f945d6931746e319f2 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -12,6 +12,7 @@ from Queue import Queue, Empty import galaxy.jobs +from galaxy.jobs.command_factory import build_command from galaxy import model from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size @@ -142,67 +143,7 @@ raise NotImplementedError() def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): - """ - Compose the sequence of commands necessary to execute a job. This will - currently include: - - - environment settings corresponding to any requirement tags - - preparing input files - - command line taken from job wrapper - - commands to set metadata (if include_metadata is True) - """ - - commands = job_wrapper.get_command_line() - # All job runners currently handle this case which should never - # occur - if not commands: - return None - # Prepend version string - if job_wrapper.version_string_cmd: - commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands - # prepend getting input files (if defined) - if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) - # Prepend dependency injection - if job_wrapper.dependency_shell_commands: - commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - - # Coping work dir outputs or setting metadata will mask return code of - # tool command. If these are used capture the return code and ensure - # the last thing that happens is an exit with return code. - capture_return_code_command = "; return_code=$?" - captured_return_code = False - - # 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: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True - 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 - if include_metadata and job_wrapper.requires_setting_metadata: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True - commands += "; cd %s; " % os.path.abspath( os.getcwd() ) - commands += job_wrapper.setup_external_metadata( - exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = job_wrapper.working_directory, - dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = job_wrapper.get_output_fnames(), - set_extension = False, - kwds = { 'overwrite' : False } ) - - - if captured_return_code: - commands += '; sh -c "exit $return_code"' - - return commands + return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) def get_work_dir_outputs( self, job_wrapper ): """ diff -r 829c047e05776fb2a6568f0d1076856fe6255fab -r 6fdf96b4aef00174938470f945d6931746e319f2 test/unit/test_command_factory.py --- /dev/null +++ b/test/unit/test_command_factory.py @@ -0,0 +1,79 @@ +from os import getcwd +from unittest import TestCase + +from galaxy.jobs.command_factory import build_command +from galaxy.util.bunch import Bunch + +MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat" + + +class TestCommandFactory(TestCase): + + def setUp(self): + self.job_wrapper = MockJobWrapper() + self.job = Bunch(app=Bunch(model=Bunch(Dataset=Bunch(file_path="file_path")))) + self.include_metadata = False + self.include_work_dir_outputs = True + + def test_simplest_command(self): + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_shell_commands(self): + self.include_work_dir_outputs = False + dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] + self.job_wrapper.dependency_shell_commands = dep_commands + self.__assert_command_is( "%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE) ) + + def test_set_metadata_skipped_if_unneeded(self): + self.include_metadata = True + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_set_metadata(self): + self.include_metadata = True + self.include_work_dir_outputs = False + metadata_line = "set_metadata_and_stuff.sh" + self.job_wrapper.metadata_line = metadata_line + expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), metadata_line) + self.__assert_command_is( expected_command ) + + def __assert_command_is(self, expected_command): + command = self.__command() + self.assertEqual(command, expected_command) + + def __command(self): + kwds = dict( + job=self.job, + job_wrapper=self.job_wrapper, + include_metadata=self.include_metadata, + include_work_dir_outputs=self.include_work_dir_outputs, + ) + return build_command(**kwds) + + +class MockJobWrapper(object): + + def __init__(self): + self.version_string_cmd = None + self.command_line = MOCK_COMMAND_LINE + self.dependency_shell_commands = [] + self.metadata_line = None + self.working_directory = "job1" + + def get_command_line(self): + return self.command_line + + @property + def requires_setting_metadata(self): + return self.metadata_line is not None + + def setup_external_metadata(self, *args, **kwds): + return self.metadata_line + + def get_output_fnames(self): + return [] + + +class MockJob(object): + app = Bunch() https://bitbucket.org/galaxy/galaxy-central/commits/e0016057e164/ Changeset: e0016057e164 User: jmchilton Date: 2013-10-11 17:40:43 Summary: Fix bug related to trailing semi-colon in tools. Thanks to Bjoern, Nicola, Nate for helping track this down. Affected #: 2 files diff -r 6fdf96b4aef00174938470f945d6931746e319f2 -r e0016057e1648d7f4d29fbaf14252cbefff6d0bd lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -19,6 +19,10 @@ if not commands: return None + # Remove trailing semi-colon so we can start hacking up this command. + # TODO: Refactor to compose a list and join with ';', would be more clean. + commands = commands.rstrip(";") + # Prepend version string if job_wrapper.version_string_cmd: commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands diff -r 6fdf96b4aef00174938470f945d6931746e319f2 -r e0016057e1648d7f4d29fbaf14252cbefff6d0bd test/unit/test_command_factory.py --- a/test/unit/test_command_factory.py +++ b/test/unit/test_command_factory.py @@ -31,6 +31,13 @@ self.__assert_command_is( MOCK_COMMAND_LINE ) def test_set_metadata(self): + self._test_set_metadata() + + def test_strips_trailing_semicolons(self): + self.job_wrapper.command_line = "%s;" % MOCK_COMMAND_LINE + self._test_set_metadata() + + def _test_set_metadata(self): self.include_metadata = True self.include_work_dir_outputs = False metadata_line = "set_metadata_and_stuff.sh" https://bitbucket.org/galaxy/galaxy-central/commits/e8fbf32ba1cc/ Changeset: e8fbf32ba1cc User: jmchilton Date: 2013-10-16 19:48:50 Summary: Merge pull request #235. Fix for tools with trailing semi-colons. Affected #: 3 files diff -r e4d476ccf7832df0b1f65048d3784b010f84e59a -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be lib/galaxy/jobs/command_factory.py --- /dev/null +++ b/lib/galaxy/jobs/command_factory.py @@ -0,0 +1,74 @@ +from os import getcwd +from os.path import abspath + + +def build_command( job, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): + """ + Compose the sequence of commands necessary to execute a job. This will + currently include: + + - environment settings corresponding to any requirement tags + - preparing input files + - command line taken from job wrapper + - commands to set metadata (if include_metadata is True) + """ + + commands = job_wrapper.get_command_line() + + # All job runners currently handle this case which should never occur + if not commands: + return None + + # Remove trailing semi-colon so we can start hacking up this command. + # TODO: Refactor to compose a list and join with ';', would be more clean. + commands = commands.rstrip(";") + + # Prepend version string + if job_wrapper.version_string_cmd: + commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands + + # prepend getting input files (if defined) + if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: + commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) + + # Prepend dependency injection + if job_wrapper.dependency_shell_commands: + commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) + + # Coping work dir outputs or setting metadata will mask return code of + # tool command. If these are used capture the return code and ensure + # the last thing that happens is an exit with return code. + capture_return_code_command = "; return_code=$?" + captured_return_code = False + + # Append commands to copy job outputs based on from_work_dir attribute. + if include_work_dir_outputs: + work_dir_outputs = job.get_work_dir_outputs( job_wrapper ) + if work_dir_outputs: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True + + 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 + if include_metadata and job_wrapper.requires_setting_metadata: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True + commands += "; cd %s; " % abspath( getcwd() ) + commands += job_wrapper.setup_external_metadata( + exec_dir=abspath( getcwd() ), + tmp_dir=job_wrapper.working_directory, + dataset_files_path=job.app.model.Dataset.file_path, + output_fnames=job_wrapper.get_output_fnames(), + set_extension=False, + kwds={ 'overwrite' : False } + ) + + if captured_return_code: + commands += '; sh -c "exit $return_code"' + + return commands diff -r e4d476ccf7832df0b1f65048d3784b010f84e59a -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -12,6 +12,7 @@ from Queue import Queue, Empty import galaxy.jobs +from galaxy.jobs.command_factory import build_command from galaxy import model from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size @@ -142,67 +143,7 @@ raise NotImplementedError() def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): - """ - Compose the sequence of commands necessary to execute a job. This will - currently include: - - - environment settings corresponding to any requirement tags - - preparing input files - - command line taken from job wrapper - - commands to set metadata (if include_metadata is True) - """ - - commands = job_wrapper.get_command_line() - # All job runners currently handle this case which should never - # occur - if not commands: - return None - # Prepend version string - if job_wrapper.version_string_cmd: - commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands - # prepend getting input files (if defined) - if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) - # Prepend dependency injection - if job_wrapper.dependency_shell_commands: - commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - - # Coping work dir outputs or setting metadata will mask return code of - # tool command. If these are used capture the return code and ensure - # the last thing that happens is an exit with return code. - capture_return_code_command = "; return_code=$?" - captured_return_code = False - - # 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: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True - 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 - if include_metadata and job_wrapper.requires_setting_metadata: - if not captured_return_code: - commands += capture_return_code_command - captured_return_code = True - commands += "; cd %s; " % os.path.abspath( os.getcwd() ) - commands += job_wrapper.setup_external_metadata( - exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = job_wrapper.working_directory, - dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = job_wrapper.get_output_fnames(), - set_extension = False, - kwds = { 'overwrite' : False } ) - - - if captured_return_code: - commands += '; sh -c "exit $return_code"' - - return commands + return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) def get_work_dir_outputs( self, job_wrapper ): """ diff -r e4d476ccf7832df0b1f65048d3784b010f84e59a -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be test/unit/test_command_factory.py --- /dev/null +++ b/test/unit/test_command_factory.py @@ -0,0 +1,86 @@ +from os import getcwd +from unittest import TestCase + +from galaxy.jobs.command_factory import build_command +from galaxy.util.bunch import Bunch + +MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat" + + +class TestCommandFactory(TestCase): + + def setUp(self): + self.job_wrapper = MockJobWrapper() + self.job = Bunch(app=Bunch(model=Bunch(Dataset=Bunch(file_path="file_path")))) + self.include_metadata = False + self.include_work_dir_outputs = True + + def test_simplest_command(self): + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_shell_commands(self): + self.include_work_dir_outputs = False + dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] + self.job_wrapper.dependency_shell_commands = dep_commands + self.__assert_command_is( "%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE) ) + + def test_set_metadata_skipped_if_unneeded(self): + self.include_metadata = True + self.include_work_dir_outputs = False + self.__assert_command_is( MOCK_COMMAND_LINE ) + + def test_set_metadata(self): + self._test_set_metadata() + + def test_strips_trailing_semicolons(self): + self.job_wrapper.command_line = "%s;" % MOCK_COMMAND_LINE + self._test_set_metadata() + + def _test_set_metadata(self): + self.include_metadata = True + self.include_work_dir_outputs = False + metadata_line = "set_metadata_and_stuff.sh" + self.job_wrapper.metadata_line = metadata_line + expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), metadata_line) + self.__assert_command_is( expected_command ) + + def __assert_command_is(self, expected_command): + command = self.__command() + self.assertEqual(command, expected_command) + + def __command(self): + kwds = dict( + job=self.job, + job_wrapper=self.job_wrapper, + include_metadata=self.include_metadata, + include_work_dir_outputs=self.include_work_dir_outputs, + ) + return build_command(**kwds) + + +class MockJobWrapper(object): + + def __init__(self): + self.version_string_cmd = None + self.command_line = MOCK_COMMAND_LINE + self.dependency_shell_commands = [] + self.metadata_line = None + self.working_directory = "job1" + + def get_command_line(self): + return self.command_line + + @property + def requires_setting_metadata(self): + return self.metadata_line is not None + + def setup_external_metadata(self, *args, **kwds): + return self.metadata_line + + def get_output_fnames(self): + return [] + + +class MockJob(object): + app = Bunch() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Restore improvements to job output checking code.
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4d476ccf783/ Changeset: e4d476ccf783 User: jmchilton Date: 2013-10-16 19:46:59 Summary: Restore improvements to job output checking code. Affected #: 5 files diff -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e -r e4d476ccf7832df0b1f65048d3784b010f84e59a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -25,6 +25,7 @@ from galaxy.util.bunch import Bunch from galaxy.util.expressions import ExpressionContext from galaxy.util.json import from_json_string +from .output_checker import check_output log = logging.getLogger( __name__ ) @@ -1079,158 +1080,7 @@ self.cleanup() def check_tool_output( self, stdout, stderr, tool_exit_code, job ): - """ - Check the output of a tool - given the stdout, stderr, and the tool's - exit code, return True if the tool exited succesfully and False - otherwise. No exceptions should be thrown. If this code encounters - an exception, it returns True so that the workflow can continue; - otherwise, a bug in this code could halt workflow progress. - Note that, if the tool did not define any exit code handling or - any stdio/stderr handling, then it reverts back to previous behavior: - if stderr contains anything, then False is returned. - Note that the job id is just for messages. - """ - # By default, the tool succeeded. This covers the case where the code - # has a bug but the tool was ok, and it lets a workflow continue. - success = True - - try: - # Check exit codes and match regular expressions against stdout and - # stderr if this tool was configured to do so. - # If there is a regular expression for scanning stdout/stderr, - # then we assume that the tool writer overwrote the default - # behavior of just setting an error if there is *anything* on - # stderr. - if ( len( self.tool.stdio_regexes ) > 0 or - len( self.tool.stdio_exit_codes ) > 0 ): - # Check the exit code ranges in the order in which - # they were specified. Each exit_code is a StdioExitCode - # that includes an applicable range. If the exit code was in - # that range, then apply the error level and add a message. - # If we've reached a fatal error rule, then stop. - max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR - if tool_exit_code != None: - for stdio_exit_code in self.tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - # Tack on a generic description of the code - # plus a specific code description. For example, - # this might prepend "Job 42: Warning (Out of Memory)\n". - code_desc = stdio_exit_code.desc - if ( None == code_desc ): - code_desc = "" - tool_msg = ( "%s: Exit code %d (%s)" % ( - galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ), - tool_exit_code, - code_desc ) ) - log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) - stderr = tool_msg + "\n" + stderr - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if ( max_error_level >= - galaxy.tools.StdioErrorLevel.FATAL ): - break - - if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: - # We'll examine every regex. Each regex specifies whether - # it is to be run on stdout, stderr, or both. (It is - # possible for neither stdout nor stderr to be scanned, - # but those regexes won't be used.) We record the highest - # error level, which are currently "warning" and "fatal". - # If fatal, then we set the job's state to ERROR. - # If warning, then we still set the job's state to OK - # but include a message. We'll do this if we haven't seen - # a fatal error yet - for regex in self.tool.stdio_regexes: - # If ( this regex should be matched against stdout ) - # - Run the regex's match pattern against stdout - # - If it matched, then determine the error level. - # o If it was fatal, then we're done - break. - # Repeat the stdout stuff for stderr. - # TODO: Collapse this into a single function. - if ( regex.stdout_match ): - regex_match = re.search( regex.match, stdout, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = self.regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stdout = rexmsg + "\n" + stdout - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - galaxy.tools.StdioErrorLevel.FATAL ): - break - - if ( regex.stderr_match ): - regex_match = re.search( regex.match, stderr, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = self.regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stderr = rexmsg + "\n" + stderr - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - galaxy.tools.StdioErrorLevel.FATAL ): - break - - # If we encountered a fatal error, then we'll need to set the - # job state accordingly. Otherwise the job is ok: - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - success = False - else: - success = True - - # When there are no regular expressions and no exit codes to check, - # default to the previous behavior: when there's anything on stderr - # the job has an error, and the job is ok otherwise. - else: - # TODO: Add in the tool and job id: - # log.debug( "Tool did not define exit code or stdio handling; " - # + "checking stderr for success" ) - if stderr: - success = False - else: - success = True - - # On any exception, return True. - except: - tb = traceback.format_exc() - log.warning( "Tool check encountered unexpected exception; " - + "assuming tool was successful: " + tb ) - success = True - - # Store the modified stdout and stderr in the job: - if None != job: - job.stdout = stdout - job.stderr = stderr - - return success - - def regex_err_msg( self, match, regex ): - """ - Return a message about the match on tool output using the given - ToolStdioRegex regex object. The regex_match is a MatchObject - that will contain the string matched on. - """ - # Get the description for the error level: - err_msg = galaxy.tools.StdioErrorLevel.desc( regex.error_level ) + ": " - # If there's a description for the regular expression, then use it. - # Otherwise, we'll take the first 256 characters of the match. - if None != regex.desc: - err_msg += regex.desc - else: - mstart = match.start() - mend = match.end() - err_msg += "Matched on " - # TODO: Move the constant 256 somewhere else besides here. - if mend - mstart > 256: - err_msg += match.string[ mstart : mstart+256 ] + "..." - else: - err_msg += match.string[ mstart: mend ] - return err_msg + return check_output( self.tool, stdout, stderr, tool_exit_code, job ) def cleanup( self ): # remove temporary files diff -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e -r e4d476ccf7832df0b1f65048d3784b010f84e59a lib/galaxy/jobs/error_level.py --- /dev/null +++ b/lib/galaxy/jobs/error_level.py @@ -0,0 +1,25 @@ + + +# These determine stdio-based error levels from matching on regular expressions +# and exit codes. They are meant to be used comparatively, such as showing +# that warning < fatal. This is really meant to just be an enum. +class StdioErrorLevel( object ): + NO_ERROR = 0 + 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" + if ( error_level > 0 and + error_level <= StdioErrorLevel.MAX ): + err_msg = StdioErrorLevel.descs[ error_level ] + return err_msg diff -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e -r e4d476ccf7832df0b1f65048d3784b010f84e59a lib/galaxy/jobs/output_checker.py --- /dev/null +++ b/lib/galaxy/jobs/output_checker.py @@ -0,0 +1,164 @@ +import re +from .error_level import StdioErrorLevel +import traceback + +from logging import getLogger +log = getLogger( __name__ ) + + +def check_output( tool, stdout, stderr, tool_exit_code, job ): + """ + Check the output of a tool - given the stdout, stderr, and the tool's + exit code, return True if the tool exited succesfully and False + otherwise. No exceptions should be thrown. If this code encounters + an exception, it returns True so that the workflow can continue; + otherwise, a bug in this code could halt workflow progress. + + Note that, if the tool did not define any exit code handling or + any stdio/stderr handling, then it reverts back to previous behavior: + if stderr contains anything, then False is returned. + + Note that the job id is just for messages. + """ + # By default, the tool succeeded. This covers the case where the code + # has a bug but the tool was ok, and it lets a workflow continue. + success = True + + try: + # Check exit codes and match regular expressions against stdout and + # stderr if this tool was configured to do so. + # If there is a regular expression for scanning stdout/stderr, + # then we assume that the tool writer overwrote the default + # behavior of just setting an error if there is *anything* on + # stderr. + if ( len( tool.stdio_regexes ) > 0 or + len( tool.stdio_exit_codes ) > 0 ): + # Check the exit code ranges in the order in which + # they were specified. Each exit_code is a StdioExitCode + # that includes an applicable range. If the exit code was in + # that range, then apply the error level and add a message. + # If we've reached a fatal error rule, then stop. + max_error_level = StdioErrorLevel.NO_ERROR + if tool_exit_code != None: + for stdio_exit_code in tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + # Tack on a generic description of the code + # plus a specific code description. For example, + # this might prepend "Job 42: Warning (Out of Memory)\n". + code_desc = stdio_exit_code.desc + if ( None == code_desc ): + code_desc = "" + tool_msg = ( "%s: Exit code %d (%s)" % ( + StdioErrorLevel.desc( stdio_exit_code.error_level ), + tool_exit_code, + code_desc ) ) + log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) + stderr = tool_msg + "\n" + stderr + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if ( max_error_level >= + StdioErrorLevel.FATAL ): + break + + if max_error_level < StdioErrorLevel.FATAL: + # We'll examine every regex. Each regex specifies whether + # it is to be run on stdout, stderr, or both. (It is + # possible for neither stdout nor stderr to be scanned, + # but those regexes won't be used.) We record the highest + # error level, which are currently "warning" and "fatal". + # If fatal, then we set the job's state to ERROR. + # If warning, then we still set the job's state to OK + # but include a message. We'll do this if we haven't seen + # a fatal error yet + for regex in tool.stdio_regexes: + # If ( this regex should be matched against stdout ) + # - Run the regex's match pattern against stdout + # - If it matched, then determine the error level. + # o If it was fatal, then we're done - break. + # Repeat the stdout stuff for stderr. + # TODO: Collapse this into a single function. + if ( regex.stdout_match ): + regex_match = re.search( regex.match, stdout, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = __regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stdout = rexmsg + "\n" + stdout + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + StdioErrorLevel.FATAL ): + break + + if ( regex.stderr_match ): + regex_match = re.search( regex.match, stderr, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = __regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stderr = rexmsg + "\n" + stderr + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + StdioErrorLevel.FATAL ): + break + + # If we encountered a fatal error, then we'll need to set the + # job state accordingly. Otherwise the job is ok: + if max_error_level >= StdioErrorLevel.FATAL: + success = False + else: + success = True + + # When there are no regular expressions and no exit codes to check, + # default to the previous behavior: when there's anything on stderr + # the job has an error, and the job is ok otherwise. + else: + # TODO: Add in the tool and job id: + # log.debug( "Tool did not define exit code or stdio handling; " + # + "checking stderr for success" ) + if stderr: + success = False + else: + success = True + + # On any exception, return True. + except: + tb = traceback.format_exc() + log.warning( "Tool check encountered unexpected exception; " + + "assuming tool was successful: " + tb ) + success = True + + # Store the modified stdout and stderr in the job: + if None != job: + job.stdout = stdout + job.stderr = stderr + + return success + + +def __regex_err_msg( match, regex ): + """ + Return a message about the match on tool output using the given + ToolStdioRegex regex object. The regex_match is a MatchObject + that will contain the string matched on. + """ + # Get the description for the error level: + err_msg = StdioErrorLevel.desc( regex.error_level ) + ": " + # If there's a description for the regular expression, then use it. + # Otherwise, we'll take the first 256 characters of the match. + if None != regex.desc: + err_msg += regex.desc + else: + mstart = match.start() + mend = match.end() + err_msg += "Matched on " + # TODO: Move the constant 256 somewhere else besides here. + if mend - mstart > 256: + err_msg += match.string[ mstart : mstart + 256 ] + "..." + else: + err_msg += match.string[ mstart: mend ] + return err_msg diff -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e -r e4d476ccf7832df0b1f65048d3784b010f84e59a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -34,6 +34,7 @@ from sqlalchemy import and_ from galaxy import jobs, model +from galaxy.jobs.error_level import StdioErrorLevel from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo from galaxy.tools.actions import DefaultToolAction @@ -64,33 +65,11 @@ from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params + log = logging.getLogger( __name__ ) WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) -# These determine stdio-based error levels from matching on regular expressions -# and exit codes. They are meant to be used comparatively, such as showing -# that warning < fatal. This is really meant to just be an enum. -class StdioErrorLevel( object ): - NO_ERROR = 0 - 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" - if ( error_level > 0 and - error_level <= StdioErrorLevel.MAX ): - err_msg = StdioErrorLevel.descs[ error_level ] - return err_msg - class ToolNotFoundException( Exception ): pass diff -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e -r e4d476ccf7832df0b1f65048d3784b010f84e59a test/unit/test_job_output_checker.py --- /dev/null +++ b/test/unit/test_job_output_checker.py @@ -0,0 +1,62 @@ +from unittest import TestCase +from galaxy.util.bunch import Bunch +from galaxy.jobs.output_checker import check_output +from galaxy.jobs.error_level import StdioErrorLevel + + +class OutputCheckerTestCase( TestCase ): + + def setUp( self ): + self.tool = Bunch( + stdio_regexes=[], + stdio_exit_codes=[], + ) + self.job = Bunch( + stdout=None, + stderr=None, + get_id_tag=lambda: "test_id", + ) + self.stdout = '' + self.stderr = '' + self.tool_exit_code = None + + def test_default_no_stderr_success( self ): + self.__assertSuccessful() + + def test_default_stderr_failure( self ): + self.stderr = 'foo' + self.__assertNotSuccessful() + + def test_exit_code_error( self ): + mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_exit_codes.append( mock_exit_code ) + self.tool_exit_code = 1 + self.__assertNotSuccessful() + + def test_exit_code_success( self ): + mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_exit_codes.append( mock_exit_code ) + self.tool_exit_code = 0 + self.__assertSuccessful() + + def test_problematic_strings( self ): + problematic_str = '\x80abc' + regex_rule = Bunch( match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_regexes = [ regex_rule ] + self.stderr = problematic_str + self.__assertNotSuccessful() + + problematic_str = '\x80abc' + regex_rule = Bunch( match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) + self.tool.stdio_regexes = [ regex_rule ] + self.stderr = problematic_str + self.__assertSuccessful() + + def __assertSuccessful( self ): + self.assertTrue( self.__check_output() ) + + def __assertNotSuccessful( self ): + self.assertFalse( self.__check_output() ) + + def __check_output( self ): + return check_output( self.tool, self.stdout, self.stderr, self.tool_exit_code, self.job ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove tipsy because it has been replaced by bootstrap tooltips.
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d966d09f77d9/ Changeset: d966d09f77d9 User: jgoecks Date: 2013-10-16 19:03:47 Summary: Remove tipsy because it has been replaced by bootstrap tooltips. Affected #: 4 files diff -r 2d78abc47928918a14f56711657696724cd9af72 -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -666,11 +666,6 @@ }); // Tooltips - // if ( $.fn.tipsy ) { - // // FIXME: tipsy gravity cannot be updated, so need classes that specify N/S gravity and - // // initialize each separately. - // $(".tooltip").tipsy( { gravity: 's' } ); - // } if ( $.fn.tooltip ) { // Put tooltips below items in panel header so that they do not overlap masthead. $(".unified-panel-header [title]").tooltip( { placement: 'bottom' } ); diff -r 2d78abc47928918a14f56711657696724cd9af72 -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e static/scripts/libs/jquery/jquery.tipsy.js --- a/static/scripts/libs/jquery/jquery.tipsy.js +++ /dev/null @@ -1,172 +0,0 @@ -/* NOTE: MODIFIED FROM ORIGINAL! */ - -(function($) { - function fixTitle($ele) { - if ($ele.attr('title') || typeof($ele.attr('original-title')) != 'string') { - $ele.attr('original-title', $ele.attr('title') || '').removeAttr('title'); - } - } - - $.fn.tipsy = function(options) { - - options = $.extend({}, $.fn.tipsy.defaults, options); - - return this.each(function() { - - fixTitle($(this)); - var opts = $.fn.tipsy.elementOptions(this, options); - var timeout = null; - - $(this).hover(function() { - var self = this; - timeout = setTimeout(function() { - $.data(self, 'cancel.tipsy', true); - - var tip = $.data(self, 'active.tipsy'); - if (!tip) { - tip = $('<div class="tipsy"><div class="tipsy-inner"/></div>'); - tip.css({position: 'absolute', zIndex: 100000}); - $.data(self, 'active.tipsy', tip); - } - - fixTitle($(self)); - - var title; - if (typeof opts.title == 'string') { - title = $(self).attr(opts.title == 'title' ? 'original-title' : opts.title); - } else if (typeof opts.title == 'function') { - title = opts.title.call(self); - } - - tip.find('.tipsy-inner')[opts.html ? 'html' : 'text'](title || opts.fallback); - - - var pos = $.extend({}, $(self).offset(), {width: self.offsetWidth, height: self.offsetHeight}); - tip.get(0).className = 'tipsy'; // reset classname in case of dynamic gravity - tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).appendTo(document.body); - - tip.css( { width: tip.width() + 1, height: tip.height() } ); - - var actualWidth = tip[0].offsetWidth, actualHeight = tip[0].offsetHeight; - var gravity = (typeof opts.gravity == 'function') ? opts.gravity.call(self) : opts.gravity; - - var top, left; - switch (gravity.charAt(0)) { - case 'n': - top = pos.top + pos.height; - left = pos.left + pos.width / 2 - actualWidth / 2; - tip.addClass('tipsy-north'); - break; - case 's': - top = pos.top - actualHeight; - left = pos.left + pos.width / 2 - actualWidth / 2; - tip.addClass('tipsy-south'); - break; - case 'e': - top = pos.top + pos.height / 2 - actualHeight / 2; - left = pos.left - actualWidth; - tip.addClass('tipsy-east'); - break; - case 'w': - top = pos.top + pos.height / 2 - actualHeight / 2; - left = pos.left + pos.width; - tip.addClass('tipsy-west'); - break; - } - // Shift if off screen - var w = $(window); - - // If off the top of the screen, flip - if ( top < w.scrollTop() && gravity.charAt( 0 ) == 's' ) { - top = pos.top + pos.height; - gravity = 'north'; - tip.removeClass('tipsy-south').addClass('tipsy-north'); - } - - // If off bottom, just shift for now - top = Math.min( top, w.scrollTop() + w.height() - tip.outerHeight() ); - - - // Shift left or right - var left_shift = 0; - if ( left < w.scrollLeft() ) { - left_shift = left - w.scrollLeft(); - } - var t = w.scrollLeft() + w.width() - tip.outerWidth(); - if ( left > t ) { - left_shift = left - t; - } - - left -= left_shift; - - tip.css( { left: left, top: top } ); - - // Shift background to center over element (not implemented for east/west) - switch (gravity.charAt(0)) { - case 'n': - tip.css( 'background-position', - ( 250 - tip.outerWidth() / 2 ) + left_shift + "px top" ); - break; - case 's': - tip.css( 'background-position', - ( 250 - tip.outerWidth() / 2 ) + left_shift + "px bottom" ); - break; - case 'e': - break; - case 'w': - break; - } - - if (opts.fade) { - tip.stop().css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: opts.opacity}); - } else { - tip.css({visibility: 'visible', opacity: opts.opacity}); - } - }, opts.delayIn); - - }, function() { - $.data(this, 'cancel.tipsy', false); - var self = this; - clearTimeout(timeout); - setTimeout(function() { - if ($.data(this, 'cancel.tipsy')) { return; } - var tip = $.data(self, 'active.tipsy'); - if (opts.fade) { - tip.stop().fadeOut(function() { $(this).remove(); }); - } else if (tip) { - tip.remove(); - } - }, opts.delayOut); - - }); - - }); - - }; - - // Overwrite this method to provide options on a per-element basis. - // For example, you could store the gravity in a 'tipsy-gravity' attribute: - // return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' }); - // (remember - do not modify 'options' in place!) - $.fn.tipsy.elementOptions = function(ele, options) { - return $.metadata ? $.extend({}, options, $(ele).metadata()) : options; - }; - - $.fn.tipsy.defaults = { - delayIn: 0, - delayOut: 100, - fade: false, - fallback: '', - gravity: 'n', - html: false, - opacity: 0.8, - title: 'title' - }; - - $.fn.tipsy.autoNS = function() { - return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n'; - }; - - $.fn.tipsy.autoWE = function() { - return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w'; - }; - -})(jQuery); diff -r 2d78abc47928918a14f56711657696724cd9af72 -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e static/scripts/packed/libs/jquery/jquery.tipsy.js --- a/static/scripts/packed/libs/jquery/jquery.tipsy.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(b){function a(c){if(c.attr("title")||typeof(c.attr("original-title"))!="string"){c.attr("original-title",c.attr("title")||"").removeAttr("title")}}b.fn.tipsy=function(c){c=b.extend({},b.fn.tipsy.defaults,c);return this.each(function(){a(b(this));var d=b.fn.tipsy.elementOptions(this,c);var e=null;b(this).hover(function(){var f=this;e=setTimeout(function(){b.data(f,"cancel.tipsy",true);var o=b.data(f,"active.tipsy");if(!o){o=b('<div class="tipsy"><div class="tipsy-inner"/></div>');o.css({position:"absolute",zIndex:100000});b.data(f,"active.tipsy",o)}a(b(f));var m;if(typeof d.title=="string"){m=b(f).attr(d.title=="title"?"original-title":d.title)}else{if(typeof d.title=="function"){m=d.title.call(f)}}o.find(".tipsy-inner")[d.html?"html":"text"](m||d.fallback);var k=b.extend({},b(f).offset(),{width:f.offsetWidth,height:f.offsetHeight});o.get(0).className="tipsy";o.remove().css({top:0,left:0,visibility:"hidden",display:"block"}).appendTo(document.body);o.css({width:o.width()+1,height:o.height()});var h=o[0].offsetWidth,j=o[0].offsetHeight;var q=(typeof d.gravity=="function")?d.gravity.call(f):d.gravity;var l,i;switch(q.charAt(0)){case"n":l=k.top+k.height;i=k.left+k.width/2-h/2;o.addClass("tipsy-north");break;case"s":l=k.top-j;i=k.left+k.width/2-h/2;o.addClass("tipsy-south");break;case"e":l=k.top+k.height/2-j/2;i=k.left-h;o.addClass("tipsy-east");break;case"w":l=k.top+k.height/2-j/2;i=k.left+k.width;o.addClass("tipsy-west");break}var n=b(window);if(l<n.scrollTop()&&q.charAt(0)=="s"){l=k.top+k.height;q="north";o.removeClass("tipsy-south").addClass("tipsy-north")}l=Math.min(l,n.scrollTop()+n.height()-o.outerHeight());var g=0;if(i<n.scrollLeft()){g=i-n.scrollLeft()}var p=n.scrollLeft()+n.width()-o.outerWidth();if(i>p){g=i-p}i-=g;o.css({left:i,top:l});switch(q.charAt(0)){case"n":o.css("background-position",-(250-o.outerWidth()/2)+g+"px top");break;case"s":o.css("background-position",-(250-o.outerWidth()/2)+g+"px bottom");break;case"e":break;case"w":break}if(d.fade){o.stop().css({opacity:0,display:"block",visibility:"visible"}).animate({opacity:d.opacity})}else{o.css({visibility:"visible",opacity:d.opacity})}},d.delayIn)},function(){b.data(this,"cancel.tipsy",false);var f=this;clearTimeout(e);setTimeout(function(){if(b.data(this,"cancel.tipsy")){return}var g=b.data(f,"active.tipsy");if(d.fade){g.stop().fadeOut(function(){b(this).remove()})}else{if(g){g.remove()}}},d.delayOut)})})};b.fn.tipsy.elementOptions=function(d,c){return b.metadata?b.extend({},c,b(d).metadata()):c};b.fn.tipsy.defaults={delayIn:0,delayOut:100,fade:false,fallback:"",gravity:"n",html:false,opacity:0.8,title:"title"};b.fn.tipsy.autoNS=function(){return b(this).offset().top>(b(document).scrollTop()+b(window).height()/2)?"s":"n"};b.fn.tipsy.autoWE=function(){return b(this).offset().left>(b(document).scrollLeft()+b(window).width()/2)?"e":"w"}})(jQuery); \ No newline at end of file diff -r 2d78abc47928918a14f56711657696724cd9af72 -r d966d09f77d9a3fed4401eb1e5e64d17a57d684e static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -292,7 +292,7 @@ title: "Remove", css_class: "remove-icon", on_click_fn: function(drawable) { - // Tipsy for remove icon must be deleted when drawable is deleted. + // Tooltip for remove icon must be deleted when drawable is deleted. $(".tooltip").remove(); drawable.remove(); } @@ -642,7 +642,7 @@ title: "Filters", css_class: "filters-icon", on_click_fn: function(group) { - // TODO: update tipsy text. + // TODO: update Tooltip text. if (group.filters_manager.visible()) { // Hiding filters. group.filters_manager.clear_filters(); @@ -2409,7 +2409,7 @@ title: "Filters", css_class: "filters-icon", on_click_fn: function(drawable) { - // TODO: update tipsy text. + // TODO: update Tooltip text. if (drawable.filters_manager.visible()) { drawable.filters_manager.clear_filters(); } @@ -2425,7 +2425,7 @@ title: "Tool", css_class: "hammer", on_click_fn: function(track) { - // TODO: update tipsy text. + // TODO: update Tooltip text. track.tool.toggle(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: honeypot trap for bot registering accounts
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d78abc47928/ Changeset: 2d78abc47928 User: martenson Date: 2013-10-16 17:40:02 Summary: honeypot trap for bot registering accounts Affected #: 2 files diff -r d3d4210d0abee42c4c7cb8d66b8a325f340899c1 -r 2d78abc47928918a14f56711657696724cd9af72 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -594,6 +594,12 @@ @web.expose def create( self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd ): params = util.Params( kwd ) + + # If the honeypot field is not empty we are dealing with a bot. + honeypot_field = params.get( 'bear_field', '' ) + if honeypot_field != '': + return trans.show_error_message( "You are considered a bot. If you are not one please try registering again and follow the form's legend. <a target=\"_top\" href=\"%s\">Go to the home page</a>." ) % url_for( '/' ) + message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) ) diff -r d3d4210d0abee42c4c7cb8d66b8a325f340899c1 -r 2d78abc47928918a14f56711657696724cd9af72 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -162,7 +162,7 @@ %endif <div id="for_bears"> If you see this, please leave following field blank. - <input type="text" name="please leave this field blank" size="1" value=""/> + <input type="text" name="bear_field" size="1" value=""/></div><div class="form-row"><input type="submit" id="send" name="create_user_button" value="Submit"/> 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: guerler: Modify bowtie error handler
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d3d4210d0abe/ Changeset: d3d4210d0abe User: guerler Date: 2013-10-16 17:03:51 Summary: Modify bowtie error handler Affected #: 3 files diff -r 940a310179c4ad9cfe7dabae2ac71402608a636a -r d3d4210d0abee42c4c7cb8d66b8a325f340899c1 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1129,7 +1129,7 @@ .upload-box .table th{text-align:center;white-space:nowrap} .upload-box .table td{margin:0px;paddign:0px} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px} -.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit} +.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000} .upload-box .text .text-info{font-size:11px;color:#999} .upload-box .extension{width:100px;font-size:11px} .upload-box .genome{width:150px;font-size:11px} diff -r 940a310179c4ad9cfe7dabae2ac71402608a636a -r d3d4210d0abee42c4c7cb8d66b8a325f340899c1 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -45,10 +45,11 @@ .text-content { font-size : @font-size-small; - width : 100%; - height : 50px; - resize : none; - background : inherit; + width: 100%; + height: 50px; + resize: none; + background: inherit; + color: @black; } .text-info { diff -r 940a310179c4ad9cfe7dabae2ac71402608a636a -r d3d4210d0abee42c4c7cb8d66b8a325f340899c1 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -109,7 +109,7 @@ <stdio> - <regex match="Exception" source="stderr" level="fatal" description="Tool exception"/> + <exit_code range="1:" level="fatal" description="Tool exception" /></stdio><inputs> 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: guerler: Fix textarea background color in new upload front end
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/940a310179c4/ Changeset: 940a310179c4 User: guerler Date: 2013-10-16 11:16:55 Summary: Fix textarea background color in new upload front end Affected #: 2 files diff -r f7760ffba1883eb14617890066778f38021f2d50 -r 940a310179c4ad9cfe7dabae2ac71402608a636a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1129,7 +1129,7 @@ .upload-box .table th{text-align:center;white-space:nowrap} .upload-box .table td{margin:0px;paddign:0px} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px} -.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none} +.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit} .upload-box .text .text-info{font-size:11px;color:#999} .upload-box .extension{width:100px;font-size:11px} .upload-box .genome{width:150px;font-size:11px} diff -r f7760ffba1883eb14617890066778f38021f2d50 -r 940a310179c4ad9cfe7dabae2ac71402608a636a static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -48,6 +48,7 @@ width : 100%; height : 50px; resize : none; + background : inherit; } .text-info { 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: guerler: Fix for Firefox
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7760ffba188/ Changeset: f7760ffba188 User: guerler Date: 2013-10-16 10:53:59 Summary: Fix for Firefox Affected #: 1 file diff -r 41d3434f8506bb13380bd072e64194519e32a36e -r f7760ffba1883eb14617890066778f38021f2d50 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -164,15 +164,17 @@ // get text component var text = it.find('#text'); + // get padding + var padding = 8; + // get dimensions - var padding = parseInt($(text.parent()).css('padding')); var width = it.width() - 2 * padding; - var height = it.height(); - + var height = it.height() - padding; + // set dimensions - text.width(width); + text.css('width', width + 'px'); text.css('top', height + 'px'); - it.height(height + text.height() + padding); + it.height(height + text.height() + 2 * padding); // show text field text.show(); @@ -471,7 +473,7 @@ 'Close' : function() {self.modal.hide()}, }, height : '400', - width : '850' + width : '900' }); // set element @@ -611,11 +613,13 @@ { // construct template var tmpl = '<tr id="' + id.substr(1) + '" class="upload-item">' + - '<td style="position: relative;">' + - '<div id="title" class="title"></div>' + - '<div id="text" class="text">' + - '<div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div>' + - '<textarea id="text-content" class="text-content form-control"></textarea>' + + '<td>' + + '<div style="position: relative;">' + + '<div id="title" class="title"></div>' + + '<div id="text" class="text">' + + '<div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div>' + + '<textarea id="text-content" class="text-content form-control"></textarea>' + + '</div>' + '</div>' + '</td>' + '<td><div id="size" class="size"></div></td>'; 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: guerler: Show file size for manually created files
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41d3434f8506/ Changeset: 41d3434f8506 User: guerler Date: 2013-10-16 10:05:53 Summary: Show file size for manually created files Affected #: 1 file diff -r f170cf78702b3913a5e09ada1c75db2800ebc982 -r 41d3434f8506bb13380bd072e64194519e32a36e static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -144,6 +144,10 @@ // add functionality to remove button var self = this; it.find('#symbol').on('click', function() { self.event_remove (index) }); + it.find('#text-content').on('keyup', function() { + var count = it.find('#text-content').val().length; + it.find('#size').html(self.size_to_string (count)); + }); // initialize progress this.event_progress(index, file, 0); @@ -437,8 +441,8 @@ } }, - // add (pseudo) file - event_add : function () + // create (pseudo) file + event_create : function () { this.uploadbox.add([{ name : 'New File', size : -1 }]); }, @@ -460,7 +464,7 @@ body : this.template('upload-box', 'upload-info'), buttons : { 'Select' : function() {self.uploadbox.select()}, - 'Create' : function() {self.event_add()}, + 'Create' : function() {self.event_create()}, 'Upload' : function() {self.event_start()}, 'Pause' : function() {self.event_stop()}, 'Reset' : function() {self.event_reset()}, @@ -511,7 +515,8 @@ if (size >= 100000000) { size = size / 100000000; unit = 'GB'; } else if (size >= 100000) { size = size / 100000; unit = 'MB'; } else if (size >= 100) { size = size / 100; unit = 'KB'; } else - if (size > 0) { size = size * 10; unit = 'b'; } else return '?'; + if (size > 0) { size = size * 10; unit = 'b'; } else + return '<strong>-</strong>'; // return formatted string return '<strong>' + (Math.round(size) / 10) + '</strong> ' + unit; 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: guerler: Add url, text input field to upload form
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f170cf78702b/ Changeset: f170cf78702b User: guerler Date: 2013-10-16 09:36:17 Summary: Add url, text input field to upload form Affected #: 4 files diff -r ecd1fe4c471d2cf9ede923c43f27d4e380f961d1 -r f170cf78702b3913a5e09ada1c75db2800ebc982 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -71,7 +71,7 @@ on_click : function(e) { self.event_show(e) }, on_unload : function() { if (self.counter.running > 0) - return "Currently uploads are running."; + return "Several uploads are still processing."; }, with_number : true }); @@ -129,9 +129,6 @@ // add upload item $(this.el).find('tbody:last').append(this.template_row(id)); - // scroll to bottom - //$(this.el).scrollTop($(this.el).prop('scrollHeight')); - // access upload item var it = this.get_upload_item(index); @@ -156,6 +153,26 @@ // update screen this.update_screen(); + + // activate text field if file content is zero + if (file.size == -1) + { + // get text component + var text = it.find('#text'); + + // get dimensions + var padding = parseInt($(text.parent()).css('padding')); + var width = it.width() - 2 * padding; + var height = it.height(); + + // set dimensions + text.width(width); + text.css('top', height + 'px'); + it.height(height + text.height() + padding); + + // show text field + text.show(); + } }, // start @@ -175,8 +192,13 @@ var current_history = Galaxy.currHistoryPanel.model.get('id'); var file_type = it.find('#extension').val(); var genome = it.find('#genome').val(); + var url_paste = it.find('#text-content').val(); var space_to_tabs = it.find('#space_to_tabs').is(':checked'); + // validate + if (!url_paste && !(file.size > 0)) + return null; + // configure uploadbox this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"}); @@ -186,6 +208,7 @@ tool_input['file_type'] = file_type; tool_input['files_0|NAME'] = file.name; tool_input['files_0|type'] = 'upload_dataset'; + tool_input['files_0|url_paste'] = url_paste; tool_input['space_to_tabs'] = space_to_tabs; // setup data @@ -193,7 +216,7 @@ data['history_id'] = current_history; data['tool_id'] = 'upload1'; data['inputs'] = JSON.stringify(tool_input); - + // return additional data to be send with file return data; }, @@ -288,7 +311,7 @@ }, // start upload process - event_upload : function() + event_start : function() { // check if (this.counter.announce == 0 || this.counter.running > 0) @@ -307,6 +330,7 @@ symbol.addClass(self.state.queued); // disable options + $(this).find('#text-content').attr('disabled', true); $(this).find('#genome').attr('disabled', true); $(this).find('#extension').attr('disabled', true); $(this).find('#space_to_tabs').attr('disabled', true); @@ -318,21 +342,21 @@ this.update_screen(); // initiate upload procedure in plugin - this.uploadbox.upload(); + this.uploadbox.start(); }, // pause upload process - event_pause : function() + event_stop : function() { // check if (this.counter.running == 0) return; // request pause - this.uploadbox.pause(); + this.uploadbox.stop(); // set html content - $('#upload-info').html('Queueing will pause after completing the current file...'); + $('#upload-info').html('Queue will pause after completing the current file...'); }, // queue is done @@ -355,6 +379,7 @@ symbol.addClass(self.state.init); // disable options + $(this).find('#text-content').attr('disabled', false); $(this).find('#genome').attr('disabled', false); $(this).find('#extension').attr('disabled', false); $(this).find('#space_to_tabs').attr('disabled', false); @@ -412,6 +437,12 @@ } }, + // add (pseudo) file + event_add : function () + { + this.uploadbox.add([{ name : 'New File', size : -1 }]); + }, + // show/hide upload frame event_show : function (e) { @@ -428,13 +459,14 @@ title : 'Upload files from your local drive', body : this.template('upload-box', 'upload-info'), buttons : { - 'Select' : function() {self.uploadbox.select()}, - 'Upload' : function() {self.event_upload()}, - 'Pause' : function() {self.event_pause()}, - 'Reset' : function() {self.event_reset()}, - 'Close' : function() {self.modal.hide()} + 'Select' : function() {self.uploadbox.select()}, + 'Create' : function() {self.event_add()}, + 'Upload' : function() {self.event_start()}, + 'Pause' : function() {self.event_stop()}, + 'Reset' : function() {self.event_reset()}, + 'Close' : function() {self.modal.hide()}, }, - height : '350', + height : '400', width : '850' }); @@ -475,13 +507,14 @@ { // identify unit var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } + if (size >= 100000000000) { size = size / 100000000000; unit = 'TB'; } else + if (size >= 100000000) { size = size / 100000000; unit = 'GB'; } else + if (size >= 100000) { size = size / 100000; unit = 'MB'; } else + if (size >= 100) { size = size / 100; unit = 'KB'; } else + if (size > 0) { size = size * 10; unit = 'b'; } else return '?'; + // return formatted string - return "<strong>" + (Math.round(size) / 10) + "</strong> " + unit; + return '<strong>' + (Math.round(size) / 10) + '</strong> ' + unit; }, // set screen @@ -494,7 +527,7 @@ // check default message if(this.counter.announce == 0) { - if (this.uploadbox.compatible) + if (this.uploadbox.compatible()) message = 'Drag&drop files into this box or click \'Select\' to select files!'; else message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.' @@ -532,10 +565,14 @@ // select upload button if (this.counter.running == 0) + { this.modal.enableButton('Select'); - else + this.modal.enableButton('Create'); + } else { this.modal.disableButton('Select'); - + this.modal.disableButton('Create'); + } + // table visibility if (this.counter.announce + this.counter.success + this.counter.error > 0) $(this.el).find('table').show(); @@ -569,7 +606,13 @@ { // construct template var tmpl = '<tr id="' + id.substr(1) + '" class="upload-item">' + - '<td><div id="title" class="title"></div></td>' + + '<td style="position: relative;">' + + '<div id="title" class="title"></div>' + + '<div id="text" class="text">' + + '<div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div>' + + '<textarea id="text-content" class="text-content form-control"></textarea>' + + '</div>' + + '</td>' + '<td><div id="size" class="size"></div></td>'; // add file type selectore diff -r ecd1fe4c471d2cf9ede923c43f27d4e380f961d1 -r f170cf78702b3913a5e09ada1c75db2800ebc982 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -25,7 +25,8 @@ error_default : "Please make sure the file is available.", error_server : "Upload request failed.", error_toomany : "You can only queue <20 files per upload session.", - error_login : "Uploads require you to log in." + error_login : "Uploads require you to log in.", + error_missing : "No upload content available." } // options @@ -42,7 +43,7 @@ // indicates if queue is currently running var queue_running = false; - var queue_pause = false; + var queue_stop = false; // element var el = null; @@ -159,21 +160,15 @@ // process an upload, recursive function process() { - // log - //console.log("Processing queue..." + queue_length + " (" + queue_running + " / " + queue_pause + ")"); - // validate - if (queue_length == 0 || queue_pause) + if (queue_length == 0 || queue_stop) { - queue_pause = false; + queue_stop = false; queue_running = false; opts.complete(); return; } else queue_running = true; - - // log - //console.log("Looking for file..."); // get an identifier from the queue var index = -1; @@ -188,9 +183,6 @@ // remove from queue remove(index) - - // log - //console.log("Initializing ('" + file.name + "')."); // identify maximum file size var filesize = file.size; @@ -199,8 +191,14 @@ // check file size if (filesize < maxfilesize) { - // send data - send(index, file, opts.initialize(index, file)) + // get parameters + var data = opts.initialize(index, file); + + // validate + if (data) + send(index, file, data); + else + error(index, file, opts.error_missing); } else { // skip file error(index, file, opts.error_filesize); @@ -214,7 +212,10 @@ var formData = new FormData(); for (var key in data) formData.append(key, data[key]); - formData.append(opts.paramname, file, file.name); + + // check file size + if (file.size > 0) + formData.append(opts.paramname, file, file.name); // prepare request xhr = new XMLHttpRequest(); @@ -226,9 +227,6 @@ // captures state changes xhr.onreadystatechange = function() { - // status change - //console.log("Status changed: " + xhr.readyState + "."); - // check for request completed, server connection closed if (xhr.readyState != xhr.DONE) return; @@ -271,9 +269,6 @@ // send request xhr.send(formData); - - // sending file - //console.log("Sending file ('" + file.name + "')."); } // success @@ -314,7 +309,7 @@ } // initiate upload process - function upload() + function start() { if (!queue_running) { @@ -323,11 +318,11 @@ } } - // pause upload process - function pause() + // stop upload process + function stop() { - // request pause - queue_pause = true; + // request stop + queue_stop = true; } // set options @@ -349,9 +344,10 @@ // export functions return { 'select' : select, + 'add' : add, 'remove' : remove, - 'upload' : upload, - 'pause' : pause, + 'start' : start, + 'stop' : stop, 'reset' : reset, 'configure' : configure, 'compatible' : compatible diff -r ecd1fe4c471d2cf9ede923c43f27d4e380f961d1 -r f170cf78702b3913a5e09ada1c75db2800ebc982 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1129,6 +1129,8 @@ .upload-box .table th{text-align:center;white-space:nowrap} .upload-box .table td{margin:0px;paddign:0px} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px} +.upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none} +.upload-box .text .text-info{font-size:11px;color:#999} .upload-box .extension{width:100px;font-size:11px} .upload-box .genome{width:150px;font-size:11px} .upload-box .size{width:60px;white-space:nowrap} diff -r ecd1fe4c471d2cf9ede923c43f27d4e380f961d1 -r f170cf78702b3913a5e09ada1c75db2800ebc982 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -39,6 +39,23 @@ font-size : @font-size-small; } + .text { + position: absolute; + display: none; + + .text-content { + font-size : @font-size-small; + width : 100%; + height : 50px; + resize : none; + } + + .text-info { + font-size : @font-size-small; + color : @gray-light; + } + } + .extension { width: 100px; font-size : @font-size-small; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Sort genomes in genome selector
by commits-noreply＠bitbucket.org 16 Oct '13

16 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ecd1fe4c471d/ Changeset: ecd1fe4c471d User: guerler Date: 2013-10-16 05:40:46 Summary: Sort genomes in genome selector Affected #: 1 file diff -r 443c97b1017eae9374ab91c0d87a19252db8a0e0 -r ecd1fe4c471d2cf9ede923c43f27d4e380f961d1 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.modal", "galaxy.master", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_master, mod_util) { +define(["galaxy.modal", "galaxy.master", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_master, mod_utils) { // galaxy upload var GalaxyUpload = Backbone.View.extend( @@ -18,14 +18,10 @@ uploadbox: null, // extension types - select_extension : { - 'auto' : 'Auto-detect' - }, + select_extension :[['Auto-detect', 'auto']], // genomes - select_genome : { - '?' : 'Unspecified' - }, + select_genome : [['Unspecified (?)', '?']], // states state : { @@ -85,17 +81,32 @@ // load extension var self = this; - mod_util.jsonFromUrl(galaxy_config.root + "api/datatypes", + mod_utils.jsonFromUrl(galaxy_config.root + "api/datatypes", function(datatypes) { for (key in datatypes) - self.select_extension[datatypes[key]] = datatypes[key]; + self.select_extension.push([datatypes[key], datatypes[key]]); }); // load genomes - mod_util.jsonFromUrl(galaxy_config.root + "api/genomes", + mod_utils.jsonFromUrl(galaxy_config.root + "api/genomes", function(genomes) { + // backup default + var def = self.select_genome[0]; + + // fill array + self.select_genome = []; for (key in genomes) - self.select_genome[genomes[key][1]] = genomes[key][0]; + if (genomes[key].length > 1) + if (genomes[key][1] !== def[1]) + self.select_genome.push(genomes[key]); + + // sort + self.select_genome.sort(function(a, b) { + return a[0] > b[0] ? 1 : a[0] < b[0] ? -1 : 0; + }); + + // insert default back to array + self.select_genome.unshift(def); }); }, @@ -565,7 +576,7 @@ tmpl += '<td>' + '<select id="extension" class="extension">'; for (key in this.select_extension) - tmpl += '<option value="' + key + '">' + this.select_extension[key] + '</option>'; + tmpl += '<option value="' + this.select_extension[key][1] + '">' + this.select_extension[key][0] + '</option>'; tmpl += '</select>' + '</td>'; @@ -573,7 +584,7 @@ tmpl += '<td>' + '<select id="genome" class="genome">'; for (key in this.select_genome) - tmpl += '<option value="' + key + '">' + this.select_genome[key] + '</option>'; + tmpl += '<option value="' + this.select_genome[key][1] + '">' + this.select_genome[key][0] + '</option>'; tmpl += '</select>' + '</td>'; 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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