diff --git a/job_conf.xml.sample_advanced b/job_conf.xml.sample_advanced index 2637c7ce319..8c9741241bb 100644 --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -6,7 +6,19 @@ --> - + + + ok + 0 + ok + 0 + + + + /sge/lib/libdrmaa.so + @@ -14,6 +26,7 @@ + + + + + diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index eb81d47df39..6b5c30df296 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -86,6 +86,7 @@ class JobConfiguration( object ): self.app = app self.runner_plugins = [] self.handlers = {} + self.handler_runner_plugins = {} self.default_handler_id = None self.destinations = {} self.destination_tags = {} @@ -138,6 +139,10 @@ class JobConfiguration( object ): else: log.debug("Read definition for handler '%s'" % id) self.handlers[id] = (id,) + for plugin in handler.findall('plugin'): + if id not in self.handler_runner_plugins: + self.handler_runner_plugins[id] = [] + self.handler_runner_plugins[id].append( plugin.get('id') ) if handler.get('tags', None) is not None: for tag in [ x.strip() for x in handler.get('tags').split(',') ]: if tag in self.handlers: @@ -420,13 +425,19 @@ class JobConfiguration( object ): """ return self.destinations.get(id_or_tag, None) - def get_job_runner_plugins(self): + def get_job_runner_plugins(self, handler_id): """Load all configured job runner plugins :returns: list of job runner plugins """ rval = {} - for runner in self.runner_plugins: + if handler_id in self.handler_runner_plugins: + plugins_to_load = [ rp for rp in self.runner_plugins if rp['id'] in self.handler_runner_plugins[handler_id] ] + log.info( "Handler '%s' will load specified runner plugins: %s", handler_id, ', '.join( [ rp['id'] for rp in plugins_to_load ] ) ) + else: + plugins_to_load = self.runner_plugins + log.info( "Handler '%s' will load all configured runner plugins", handler_id ) + for runner in plugins_to_load: class_names = [] module = None id = runner['id'] @@ -477,7 +488,7 @@ class JobConfiguration( object ): try: rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) except TypeError: - log.warning( "Job runner '%s:%s' has not been converted to a new-style runner" % ( module_name, class_name ) ) + log.exception( "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load" % ( module_name, class_name ) ) rval[id] = runner_class( self.app ) log.debug( "Loaded job runner '%s:%s' as '%s'" % ( module_name, class_name, id ) ) return rval diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py index ae6f2ac3d38..5a262ec4633 100644 --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -565,7 +565,7 @@ class JobHandlerStopQueue( object ): class DefaultJobDispatcher( object ): def __init__( self, app ): self.app = app - self.job_runners = self.app.job_config.get_job_runner_plugins() + self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) # Once plugins are loaded, all job destinations that were created from # URLs can have their URL params converted to the destination's param # dict by the plugin. diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index 2b412a6db31..334b20c4850 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -22,13 +22,39 @@ log = logging.getLogger( __name__ ) STOP_SIGNAL = object() + +class RunnerParams( object ): + + def __init__( self, specs = None, params = None ): + self.specs = specs or dict() + self.params = params or dict() + for name, value in self.params.items(): + assert name in self.specs, 'Invalid job runner parameter for this plugin: %s' % name + if 'map' in self.specs[ name ]: + try: + self.params[ name ] = self.specs[ name ][ 'map' ]( value ) + except Exception, e: + raise Exception( 'Job runner parameter "%s" value "%s" could not be converted to the correct type: %s' % ( name, value, e ) ) + if 'valid' in self.specs[ name ]: + assert self.specs[ name ][ 'valid' ]( value ), 'Job runner parameter %s failed validation' % name + + def __getattr__( self, name ): + return self.params.get( name, self.specs[ name ][ 'default' ] ) + + class BaseJobRunner( object ): - def __init__( self, app, nworkers ): + def __init__( self, app, nworkers, **kwargs ): """Start the job runner """ self.app = app self.sa_session = app.model.context self.nworkers = nworkers + runner_param_specs = dict( recheck_missing_job_retries = dict( map = int, valid = lambda x: x >= 0, default = 0 ) ) + if 'runner_param_specs' in kwargs: + runner_param_specs.update( kwargs.pop( 'runner_param_specs' ) ) + if kwargs: + log.debug( 'Loading %s with params: %s', self.runner_name, kwargs ) + self.runner_params = RunnerParams( specs = runner_param_specs, params = kwargs ) def _init_worker_threads(self): """Start ``nworkers`` worker threads. @@ -115,7 +141,7 @@ class BaseJobRunner( object ): job_wrapper.cleanup() return False elif job_state != model.Job.states.QUEUED: - log.info( "(%d) Job is in state %s, skipping execution" % ( job_id, job_state ) ) + log.info( "(%s) Job is in state %s, skipping execution" % ( job_id, job_state ) ) # cleanup may not be safe in all states return False @@ -226,6 +252,10 @@ class BaseJobRunner( object ): options.update(**kwds) return job_script(**options) + def _complete_terminal_job( self, ajs, **kwargs ): + if ajs.job_wrapper.get_state() != model.Job.states.DELETED: + self.work_queue.put( ( self.finish_job, ajs ) ) + class AsynchronousJobState( object ): """ @@ -287,8 +317,8 @@ class AsynchronousJobRunner( BaseJobRunner ): to the correct methods (queue, finish, cleanup) at appropriate times.. """ - def __init__( self, app, nworkers ): - super( AsynchronousJobRunner, self ).__init__( app, nworkers ) + def __init__( self, app, nworkers, **kwargs ): + super( AsynchronousJobRunner, self ).__init__( app, nworkers, **kwargs ) # 'watched' and 'queue' are both used to keep track of jobs to watch. # 'queue' is used to add new watched jobs, and can be called from # any thread (usually by the 'queue_job' method). 'watched' must only diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 5e111ca4710..dfda8b23f25 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -16,27 +16,12 @@ from galaxy.jobs import JobDestination from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner eggs.require( "drmaa" ) -# We foolishly named this file the same as the name exported by the drmaa -# library... 'import drmaa' imports itself. -drmaa = __import__( "drmaa" ) log = logging.getLogger( __name__ ) __all__ = [ 'DRMAAJobRunner' ] -drmaa_state = { - drmaa.JobState.UNDETERMINED: 'process status cannot be determined', - drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active', - drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold', - drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold', - drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', - drmaa.JobState.RUNNING: 'job is running', - drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended', - drmaa.JobState.USER_SUSPENDED: 'job is user suspended', - drmaa.JobState.DONE: 'job finished normally', - drmaa.JobState.FAILED: 'job finished, but failed', -} - +drmaa = None DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification', 'jobName', 'email', 'project' ] @@ -48,8 +33,50 @@ class DRMAAJobRunner( AsynchronousJobRunner ): """ runner_name = "DRMAARunner" - def __init__( self, app, nworkers ): + def __init__( self, app, nworkers, **kwargs ): """Start the job runner""" + + global drmaa + + runner_param_specs = dict( + drmaa_library_path = dict( map = str, default = os.environ.get( 'DRMAA_LIBRARY_PATH', None ) ), + invalidjobexception_state = dict( map = str, valid = lambda x: x in ( model.Job.states.OK, model.Job.states.ERROR ), default = model.Job.states.OK ), + invalidjobexception_retries = dict( map = int, valid = lambda x: int >= 0, default = 0 ), + internalexception_state = dict( map = str, valid = lambda x: x in ( model.Job.states.OK, model.Job.states.ERROR ), default = model.Job.states.OK ), + internalexception_retries = dict( map = int, valid = lambda x: int >= 0, default = 0 ) ) + + if 'runner_param_specs' not in kwargs: + kwargs[ 'runner_param_specs' ] = dict() + kwargs[ 'runner_param_specs' ].update( runner_param_specs ) + + super( DRMAAJobRunner, self ).__init__( app, nworkers, **kwargs ) + + # This allows multiple drmaa runners (although only one per handler) in the same job config file + if 'drmaa_library_path' in kwargs: + log.info( 'Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: %s', self.runner_params.drmaa_library_path ) + os.environ['DRMAA_LIBRARY_PATH'] = self.runner_params.drmaa_library_path + + # We foolishly named this file the same as the name exported by the drmaa + # library... 'import drmaa' imports itself. + drmaa = __import__( "drmaa" ) + + # Subclasses may need access to state constants + self.drmaa_job_states = drmaa.JobState + + # Descriptive state strings pulled from the drmaa lib itself + self.drmaa_job_state_strings = { + drmaa.JobState.UNDETERMINED: 'process status cannot be determined', + drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active', + drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold', + drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold', + drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', + drmaa.JobState.RUNNING: 'job is running', + drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended', + drmaa.JobState.USER_SUSPENDED: 'job is user suspended', + drmaa.JobState.DONE: 'job finished normally', + drmaa.JobState.FAILED: 'job finished, but failed', + } + self.ds = drmaa.Session() self.ds.initialize() @@ -58,7 +85,6 @@ class DRMAAJobRunner( AsynchronousJobRunner ): self.external_killJob_script = app.config.drmaa_external_killjob_script self.userid = None - super( DRMAAJobRunner, self ).__init__( app, nworkers ) self._init_monitor_thread() self._init_worker_threads() @@ -137,8 +163,10 @@ class DRMAAJobRunner( AsynchronousJobRunner ): job_wrapper.cleanup() return - log.debug( "(%s) submitting file %s" % ( galaxy_id_tag, ajs.job_file ) ) - log.debug( "(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) + log.debug( "(%s) submitting file %s", galaxy_id_tag, ajs.job_file ) + log.debug( "(%s) command is: %s", galaxy_id_tag, command_line ) + if native_spec: + log.debug( "(%s) native specification is: %s", galaxy_id_tag, native_spec ) # runJob will raise if there's a submit problem if self.external_runJob_script is None: @@ -175,6 +203,20 @@ class DRMAAJobRunner( AsynchronousJobRunner ): # Add to our 'queue' of jobs to monitor self.monitor_queue.put( ajs ) + def _complete_terminal_job( self, ajs, drmaa_state, **kwargs ): + """ + Handle a job upon its termination in the DRM. This method is meant to + be overridden by subclasses to improve post-mortem and reporting of + failures. + """ + if drmaa_state == drmaa.JobState.FAILED: + if ajs.job_wrapper.get_state() != model.Job.states.DELETED: + ajs.stop_job = False + ajs.fail_message = "The cluster DRM system terminated this job" + self.work_queue.put( ( self.fail_job, ajs ) ) + elif drmaa_state == drmaa.JobState.DONE: + super( DRMAAJobRunner, self )._complete_terminal_job( ajs ) + def check_watched_items( self ): """ Called by the monitor thread to look at each watched job and deal @@ -188,16 +230,27 @@ class DRMAAJobRunner( AsynchronousJobRunner ): try: assert external_job_id not in ( None, 'None' ), '(%s/%s) Invalid job id' % ( galaxy_id_tag, external_job_id ) state = self.ds.jobStatus( external_job_id ) - # InternalException was reported to be necessary on some DRMs, but - # this could cause failures to be detected as completion! Please - # report if you experience problems with this. - except ( drmaa.InvalidJobException, drmaa.InternalException ), e: - # we should only get here if an orphaned job was put into the queue at app startup - log.info( "(%s/%s) job left DRM queue with following message: %s" % ( galaxy_id_tag, external_job_id, e ) ) - self.work_queue.put( ( self.finish_job, ajs ) ) + except ( drmaa.InternalException, drmaa.InvalidJobException ), e: + ecn = e.__class__.__name__ + retry_param = ecn.lower() + '_retries' + state_param = ecn.lower() + '_state' + retries = getattr( ajs, retry_param, 0 ) + if self.runner_params[ retry_param ] > 0: + if retries < self.runner_params[ retry_param ]: + # will retry check on next iteration + setattr( ajs, retry_param, retries + 1 ) + continue + if self.runner_params[ state_param ] == model.Job.states.OK: + log.info( "(%s/%s) job left DRM queue with following message: %s", galaxy_id_tag, external_job_id, e ) + self.work_queue.put( ( self.finish_job, ajs ) ) + elif self.runner_params[ state_param ] == model.Job.states.ERROR: + log.info( "(%s/%s) job check resulted in %s after %s tries: %s", galaxy_id_tag, external_job_id, ecn, retries, e ) + self.work_queue.put( ( self.fail_job, ajs ) ) + else: + raise Exception( "%s is set to an invalid value (%s), this should not be possible. See galaxy.jobs.drmaa.__init__()", state_param, self.runner_params[ state_param ] ) continue except drmaa.DrmCommunicationException, e: - log.warning( "(%s/%s) unable to communicate with DRM: %s" % ( galaxy_id_tag, external_job_id, e )) + log.warning( "(%s/%s) unable to communicate with DRM: %s", galaxy_id_tag, external_job_id, e ) new_watched.append( ajs ) continue except Exception, e: @@ -208,19 +261,12 @@ class DRMAAJobRunner( AsynchronousJobRunner ): self.work_queue.put( ( self.fail_job, ajs ) ) continue if state != old_state: - log.debug( "(%s/%s) state change: %s" % ( galaxy_id_tag, external_job_id, drmaa_state[state] ) ) + log.debug( "(%s/%s) state change: %s" % ( galaxy_id_tag, external_job_id, self.drmaa_job_state_strings[state] ) ) if state == drmaa.JobState.RUNNING and not ajs.running: ajs.running = True ajs.job_wrapper.change_state( model.Job.states.RUNNING ) - if state == drmaa.JobState.FAILED: - if ajs.job_wrapper.get_state() != model.Job.states.DELETED: - ajs.stop_job = False - ajs.fail_message = "The cluster DRM system terminated this job" - self.work_queue.put( ( self.fail_job, ajs ) ) - continue - if state == drmaa.JobState.DONE: - if ajs.job_wrapper.get_state() != model.Job.states.DELETED: - self.work_queue.put( ( self.finish_job, ajs ) ) + if state in ( drmaa.JobState.FAILED, drmaa.JobState.DONE ): + self._complete_terminal_job( ajs, drmaa_state = state ) continue ajs.old_state = state new_watched.append( ajs ) diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py new file mode 100644 index 00000000000..51b7df56c79 --- /dev/null +++ b/lib/galaxy/jobs/runners/slurm.py @@ -0,0 +1,57 @@ +""" +SLURM job control via the DRMAA API. +""" + +import time +import logging +import subprocess + +from galaxy import model +from galaxy.jobs.runners.drmaa import DRMAAJobRunner + +log = logging.getLogger( __name__ ) + +__all__ = [ 'SlurmJobRunner' ] + + +class SlurmJobRunner( DRMAAJobRunner ): + runner_name = "SlurmRunner" + + def _complete_terminal_job( self, ajs, drmaa_state, **kwargs ): + def __get_jobinfo(): + scontrol_out = subprocess.check_output( ( 'scontrol', '-o', 'show', 'job', ajs.job_id ) ) + return dict( [ out_param.split( '=', 1 ) for out_param in scontrol_out.split() ] ) + if drmaa_state == self.drmaa_job_states.FAILED: + try: + job_info = __get_jobinfo() + sleep = 1 + while job_info['JobState'] == 'COMPLETING': + log.debug( '(%s/%s) Waiting %s seconds for failed job to exit COMPLETING state for post-mortem', ajs.job_wrapper.get_id_tag(), ajs.job_id, sleep ) + time.sleep( sleep ) + sleep *= 2 + if sleep > 64: + ajs.fail_message = "This job failed and the system timed out while trying to determine the cause of the failure." + break + job_info = __get_jobinfo() + if job_info['JobState'] == 'TIMEOUT': + ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time." + elif job_info['JobState'] == 'NODE_FAIL': + log.warning( '(%s/%s) Job failed due to node failure, attempting resubmission', ajs.job_wrapper.get_id_tag(), ajs.job_id ) + ajs.job_wrapper.change_state( model.Job.states.QUEUED, info = 'Job was resubmitted due to node failure' ) + try: + self.queue_job( ajs.job_wrapper ) + return + except: + ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed." + elif job_info['JobState'] == 'CANCELLED': + ajs.fail_message = "This job failed because it was cancelled by an administrator." + else: + ajs.fail_message = "This job failed for reasons that could not be determined." + ajs.fail_message += '\nPlease click the bug icon to report this problem if you need help.' + ajs.stop_job = False + self.work_queue.put( ( self.fail_job, ajs ) ) + except Exception, e: + log.exception( '(%s/%s) Unable to inspect failed slurm job using scontrol, job will be unconditionally failed: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, e ) + super( SlurmJobRunner, self )._complete_terminal_job( ajs, drmaa_state = drmaa_state ) + elif drmaa_state == self.drmaa_job_states.DONE: + super( SlurmJobRunner, self )._complete_terminal_job( ajs, drmaa_state = drmaa_state ) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 7075562f274..7c4dc29e196 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -18,6 +18,7 @@ import json import socket import time from string import Template +from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -42,6 +43,11 @@ datatypes_registry = galaxy.datatypes.registry.Registry() # Default Value Required for unit tests datatypes_registry.load_datatypes() +# When constructing filters with in for a fixed set of ids, maximum +# number of items to place in the IN statement. Different databases +# are going to have different limits so it is likely best to not let +# this be unlimited - filter in Python if over this limit. +MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -892,6 +898,33 @@ class History( object, Dictifiable, UsesAnnotations ): rval = galaxy.datatypes.data.nice_size( rval ) return rval + def contents_iter( self, **kwds ): + """ + Fetch filtered list of contents of history. + """ + python_filter = None + db_session = object_session( self ) + assert db_session != None + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + query = query.order_by( HistoryDatasetAssociation.table.c.hid.asc() ) + deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) + if deleted is not None: + query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) + visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) + if visible is not None: + query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) + if 'ids' in kwds: + ids = kwds['ids'] + max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) + if len(ids) < max_in_filter_length: + query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) + else: + python_filter = lambda hda: hda.id in ids + if python_filter: + return ifilter(python_filter, query) + else: + return query + def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index 25a65e45c39..e77f05d9841 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,47 +51,28 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - # if ids, return _FULL_ data (as show) for each id passed + contents_kwds = {} if ids: - ids = ids.split( ',' ) - for index, hda in enumerate( history.datasets ): - encoded_hda_id = trans.security.encode_id( hda.id ) - if encoded_hda_id in ids: - #TODO: share code with show - rval.append( self._detailed_hda_dict( trans, hda ) ) - - # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) + contents_kwds[ 'ids' ] = ids + # If explicit ids given, always used detailed result. + details = 'all' else: + contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) + contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) - # if specified return those datasets that match the setting - # backwards compat - return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) - return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) - - for hda in history.datasets: - # if either return_ setting has been requested (!= None), skip hdas that don't match the request - if return_deleted is not None: - if( ( return_deleted and not hda.deleted ) - or ( not return_deleted and hda.deleted ) ): - continue - if return_visible is not None: - if( ( return_visible and not hda.visible ) - or ( not return_visible and hda.visible ) ): - continue - - encoded_hda_id = trans.security.encode_id( hda.id ) - if( ( encoded_hda_id in details ) - or ( details == 'all' ) ): - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) - + for hda in history.contents_iter( **contents_kwds ): + encoded_hda_id = trans.security.encode_id( hda.id ) + detailed = details == 'all' or ( encoded_hda_id in details ) + if detailed: + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 7d30c4cbbfb..795183b562e 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -19,11 +19,6 @@ import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) -def default_tool_shed_repository_value_mapper( trans, tool_shed_repository ): - value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ), - 'error_message' : tool_shed_repository.error_message or '' } - return value_mapper - def get_message_for_no_shed_tool_config(): # This Galaxy instance is not configured with a shed-related tool panel configuration file. message = 'The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a ' @@ -48,8 +43,8 @@ class ToolShedRepositoriesController( BaseAPIController ): :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/f2db41e1fa331b3e/exported_workflows - # Since exported workflows are dictionaries with very few attributes that differentiate them from each other, we'll build the - # list based on the following dictionary of those few attributes. + # Since exported workflows are dictionaries with very few attributes that differentiate them from each + # other, we'll build the list based on the following dictionary of those few attributes. exported_workflows = [] repository = suc.get_tool_shed_repository_by_id( trans, id ) metadata = repository.metadata @@ -58,17 +53,23 @@ class ToolShedRepositoriesController( BaseAPIController ): else: exported_workflow_tups = [] for index, exported_workflow_tup in enumerate( exported_workflow_tups ): - # The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of relative_path is the location - # on disk (relative to the root of the installed repository) where the exported_workflow_dict file (.ga file) is located. + # The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of + # relative_path is the location on disk (relative to the root of the installed repository) where the + # exported_workflow_dict file (.ga file) is located. exported_workflow_dict = exported_workflow_tup[ 1 ] annotation = exported_workflow_dict.get( 'annotation', '' ) format_version = exported_workflow_dict.get( 'format-version', '' ) workflow_name = exported_workflow_dict.get( 'name', '' ) - # Since we don't have an in-memory object with an id, we'll identify the exported workflow via it's location (i.e., index) in the list. + # Since we don't have an in-memory object with an id, we'll identify the exported workflow via it's + # location (i.e., index) in the list. display_dict = dict( index=index, annotation=annotation, format_version=format_version, workflow_name=workflow_name ) exported_workflows.append( display_dict ) return exported_workflows + def __get_value_mapper( self, trans ): + value_mapper = { 'id' : trans.security.encode_id } + return value_mapper + @web.expose_api def import_workflow( self, trans, payload, **kwd ): """ @@ -96,13 +97,11 @@ class ToolShedRepositoriesController( BaseAPIController ): # Since we don't have an in-memory object with an id, we'll identify the exported workflow via it's location (i.e., index) in the list. exported_workflow = exported_workflows[ int( index ) ] workflow_name = exported_workflow[ 'workflow_name' ] - workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) + workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name ) if status == 'error': - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - else: - return workflow.to_dict( view='element' ) + log.debug( error_message ) + return {} + return workflow.to_dict( view='element' ) @web.expose_api def import_workflows( self, trans, **kwd ): @@ -125,11 +124,9 @@ class ToolShedRepositoriesController( BaseAPIController ): imported_workflow_dicts = [] for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict[ 'workflow_name' ] - workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) + workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name ) if status == 'error': - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + log.debug( error_message ) else: imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) return imported_workflow_dicts @@ -142,22 +139,15 @@ class ToolShedRepositoriesController( BaseAPIController ): """ # Example URL: http://localhost:8763/api/tool_shed_repositories tool_shed_repository_dicts = [] - try: - query = trans.install_model.context.query( trans.app.install_model.ToolShedRepository ) \ - .order_by( trans.app.install_model.ToolShedRepository.table.c.name ) \ - .all() - for tool_shed_repository in query: - tool_shed_repository_dict = tool_shed_repository.to_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) - tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', - action='show', - id=trans.security.encode_id( tool_shed_repository.id ) ) - tool_shed_repository_dicts.append( tool_shed_repository_dict ) - return tool_shed_repository_dicts - except Exception, e: - message = "Error in the tool_shed_repositories API in index: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + for tool_shed_repository in trans.install_model.context.query( trans.app.install_model.ToolShedRepository ) \ + .order_by( trans.app.install_model.ToolShedRepository.table.c.name ): + tool_shed_repository_dict = \ + tool_shed_repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', + action='show', + id=trans.security.encode_id( tool_shed_repository.id ) ) + tool_shed_repository_dicts.append( tool_shed_repository_dict ) + return tool_shed_repository_dicts @web.expose_api def install_repository_revision( self, trans, payload, **kwd ): @@ -208,8 +198,7 @@ class ToolShedRepositoriesController( BaseAPIController ): # Make sure this Galaxy instance is configured with a shed-related tool panel configuration file. if not suc.have_shed_tool_conf_for_install( trans ): message = get_message_for_no_shed_tool_config() - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( message ) return dict( status='error', error=message ) # Make sure the current user's API key proves he is an admin user in this Galaxy instance. if not trans.user_is_admin(): @@ -225,18 +214,20 @@ class ToolShedRepositoriesController( BaseAPIController ): except Exception, e: message = "Error attempting to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s: %s" % \ ( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) ) - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( message ) return dict( status='error', error=message ) if raw_text: + # If successful, the response from get_repository_revision_install_info will be 3 + # dictionaries, a dictionary defining the Repository, a dictionary defining the + # Repository revision (RepositoryMetadata), and a dictionary including the additional + # information required to install the repository. items = json.from_json_string( raw_text ) repository_revision_dict = items[ 1 ] repo_info_dict = items[ 2 ] else: message = "Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s: %s" % \ ( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) ) - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( message ) return dict( status='error', error=message ) repo_info_dicts = [ repo_info_dict ] # Make sure the tool shed returned everything we need for installing the repository. @@ -345,7 +336,7 @@ class ToolShedRepositoriesController( BaseAPIController ): tool_path, install_tool_dependencies, reinstalling=False ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) @@ -394,8 +385,7 @@ class ToolShedRepositoriesController( BaseAPIController ): if not suc.have_shed_tool_conf_for_install( trans ): # This Galaxy instance is not configured with a shed-related tool panel configuration file. message = get_message_for_no_shed_tool_config() - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( message ) return dict( status='error', error=message ) if not trans.user_is_admin(): raise HTTPForbidden( detail='You are not authorized to install a tool shed repository into this Galaxy instance.' ) @@ -410,8 +400,7 @@ class ToolShedRepositoriesController( BaseAPIController ): len( changeset_revisions ) != num_specified_repositories: message = 'Error in tool_shed_repositories API in install_repository_revisions: the received parameters must be ordered ' message += 'lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.' - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( message ) return dict( status='error', error=message ) # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain information # about each of the repositories being installed. @@ -482,7 +471,7 @@ class ToolShedRepositoriesController( BaseAPIController ): repair_dict = repository_util.repair_tool_shed_repository( trans, repository, encoding_util.tool_shed_encode( repo_info_dict ) ) - repository_dict = repository.to_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) ) + repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( repository.id ) ) @@ -502,39 +491,39 @@ class ToolShedRepositoriesController( BaseAPIController ): :param key: the API key of the Galaxy admin user. """ - try: - start_time = strftime( "%Y-%m-%d %H:%M:%S" ) - results = dict( start_time=start_time, - successful_count=0, - unsuccessful_count=0, - repository_status=[] ) - # Make sure the current user's API key proves he is an admin user in this Galaxy instance. - if not trans.user_is_admin(): - raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' ) - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=False ) - # Now reset metadata on all remaining repositories. - for repository in query: - repository_id = trans.security.encode_id( repository.id ) - try: - invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_installed_repository( trans, repository_id ) - if invalid_file_tups: - message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) - results[ 'unsuccessful_count' ] += 1 - else: - message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.owner ) ) - results[ 'successful_count' ] += 1 - except Exception, e: - message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.owner ), str( e ) ) + start_time = strftime( "%Y-%m-%d %H:%M:%S" ) + results = dict( start_time=start_time, + successful_count=0, + unsuccessful_count=0, + repository_status=[] ) + # Make sure the current user's API key proves he is an admin user in this Galaxy instance. + if not trans.user_is_admin(): + raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' ) + query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=False ) + # Now reset metadata on all remaining repositories. + for repository in query: + repository_id = trans.security.encode_id( repository.id ) + try: + invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_installed_repository( trans, repository_id ) + if invalid_file_tups: + message = tool_util.generate_message_for_invalid_tools( trans, + invalid_file_tups, + repository, + None, + as_html=False ) results[ 'unsuccessful_count' ] += 1 - results[ 'repository_status' ].append( message ) - stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) - results[ 'stop_time' ] = stop_time - return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) - except Exception, e: - message = "Error in the Galaxy tool_shed_repositories API in reset_metadata_on_installed_repositories: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + else: + message = "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) + results[ 'successful_count' ] += 1 + except Exception, e: + message = "Error resetting metadata on repository %s owned by %s: %s" % \ + ( str( repository.name ), str( repository.owner ), str( e ) ) + results[ 'unsuccessful_count' ] += 1 + results[ 'repository_status' ].append( message ) + stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) + results[ 'stop_time' ] = stop_time + return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) @web.expose_api def show( self, trans, id, **kwd ): @@ -545,15 +534,12 @@ class ToolShedRepositoriesController( BaseAPIController ): :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e - try: - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) - tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', - action='show', - id=trans.security.encode_id( tool_shed_repository.id ) ) - return tool_shed_repository_dict - except Exception, e: - message = "Error in tool_shed_repositories API in index: " + str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id ) + if tool_shed_repository is None: + log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) + return {} + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', + action='show', + id=trans.security.encode_id( tool_shed_repository.id ) ) + return tool_shed_repository_dict diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 726d744687f..61dffc14979 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -36,22 +36,27 @@ class RepositoriesController( BaseAPIController ): :param name: the name of the Repository :param owner: the owner of the Repository - Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the - list is ordered oldest to newest. + Returns the ordered list of changeset revision hash strings that are associated with installable revisions. + As in the changelog, the list is ordered oldest to newest. """ # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test - try: + if name and owner: # Get the repository information. repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if repository is None: + error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: " + error_message += "cannot locate repository %s owned by %s." % ( str( name ), str( owner ) ) + log.debug( error_message ) + return [] repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) return ordered_installable_revisions - except Exception, e: - message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + else: + error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: " + error_message += "invalid name %s or owner %s received." % ( str( name ), str( owner ) ) + log.debug( error_message ) + return [] @web.expose_api_anonymous def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ): @@ -106,49 +111,65 @@ class RepositoriesController( BaseAPIController ): ] } """ - repository_value_mapper = { 'id' : trans.security.encode_id, - 'user_id' : trans.security.encode_id } - # Example URL: http://localhost:9009/api/repositories/get_repository_revision_install_info?name=add_column&owner=test&changeset_revision=3a08cc21466f - try: + # Example URL: + # http:///api/repositories/get_repository_revision_install_info?name=&owner=&changeset_revision= + if name and owner and changeset_revision: # Get the repository information. repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if repository is None: + log.debug( 'Cannot locate repository %s owned by %s' % ( str( name ), str( owner ) ) ) + return {}, {}, {} encoded_repository_id = trans.security.encode_id( repository.id ) - repository_dict = repository.to_dict( view='element', value_mapper=repository_value_mapper ) + repository_dict = repository.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) repository_dict[ 'url' ] = web.url_for( controller='repositories', action='show', id=encoded_repository_id ) # Get the repository_metadata information. - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_repository_id, + changeset_revision ) if not repository_metadata: - # The changeset_revision column in the repository_metadata table has been updated with a new value value, so find the - # changeset_revision to which we need to update. + # The changeset_revision column in the repository_metadata table has been updated with a new + # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, new_changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_repository_id, + new_changeset_revision ) changeset_revision = new_changeset_revision if repository_metadata: encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id ) repository_metadata_dict = repository_metadata.to_dict( view='collection', - value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) + value_mapper=self.__get_value_mapper( trans ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=encoded_repository_metadata_id ) # Get the repo_info_dict for installing the repository. - repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ - has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + repo_info_dict, \ + includes_tools, \ + includes_tool_dependencies, \ + includes_tools_for_display_in_tool_panel, \ + has_repository_dependencies, \ + has_repository_dependencies_only_if_compiling_contained_td = \ repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision ) return repository_dict, repository_metadata_dict, repo_info_dict else: - message = "Unable to locate repository_metadata record for repository id %d and changeset_revision %s" % ( repository.id, changeset_revision ) - log.error( message, exc_info=True ) - trans.response.status = 500 + log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \ + ( str( repository.id ), str( changeset_revision ) ) ) return repository_dict, {}, {} - except Exception, e: - message = "Error in the Tool Shed repositories API in get_repository_revision_install_info: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + else: + debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: " + debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % \ + ( str( name ), str( owner ), str( changeset_revision ) ) + log.debug( debug_msg ) + return {}, {}, {} + + def __get_value_mapper( self, trans ): + value_mapper = { 'id' : trans.security.encode_id, + 'repository_id' : trans.security.encode_id } + return value_mapper @web.expose_api def import_capsule( self, trans, payload, **kwd ): @@ -177,29 +198,27 @@ class RepositoriesController( BaseAPIController ): uploaded_file=None, capsule_file_name=None ) if os.path.getsize( os.path.abspath( capsule_file_name ) ) == 0: - message = 'Your capsule file is empty.' - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + log.debug( 'Your capsule file %s is empty.' % str( capsule_file_name ) ) + return {} try: # Open for reading with transparent compression. tar_archive = tarfile.open( capsule_file_path, 'r:*' ) except tarfile.ReadError, e: - message = 'Error opening file %s: %s' % ( str( capsule_file_name ), str( e ) ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) ) + return {} capsule_dict[ 'tar_archive' ] = tar_archive capsule_dict[ 'capsule_file_name' ] = capsule_file_name capsule_dict = import_util.extract_capsule_files( trans, **capsule_dict ) capsule_dict = import_util.validate_capsule( trans, **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': - message = 'The capsule contents are invalid and cannpt be imported:
%s' % str( capsule_dict.get( 'error_message', '' ) ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + log.debug( 'The capsule contents are invalid and cannpt be imported:
%s' % \ + str( capsule_dict.get( 'error_message', '' ) ) ) + return {} encoded_file_path = capsule_dict.get( 'encoded_file_path', None ) + if encoded_file_path is None: + log.debug( 'The capsule_dict %s is missing the required encoded_file_path entry.' % str( capsule_dict ) ) + return {} file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) export_info_dict = import_util.get_export_info_dict( export_info_file_path ) @@ -216,12 +235,14 @@ class RepositoriesController( BaseAPIController ): # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = repository_maintenance_util.create_repository_and_import_archive( trans, - repository_status_info_dict, - import_results_tups ) + import_results_tups = \ + repository_maintenance_util.create_repository_and_import_archive( trans, + repository_status_info_dict, + import_results_tups ) import_util.check_status_and_reset_downloadable( trans, import_results_tups ) suc.remove_dir( file_path ) - # NOTE: the order of installation is defined in import_results_tups, but order will be lost when transferred to return_dict. + # NOTE: the order of installation is defined in import_results_tups, but order will be lost + # when transferred to return_dict. return_dict = {} for import_results_tup in import_results_tups: ok, name_owner, message = import_results_tup @@ -237,28 +258,19 @@ class RepositoriesController( BaseAPIController ): GET /api/repositories Displays a collection (list) of repositories. """ - value_mapper = { 'id' : trans.security.encode_id, - 'user_id' : trans.security.encode_id } # Example URL: http://localhost:9009/api/repositories repository_dicts = [] - deleted = util.string_as_bool( deleted ) - try: - query = trans.sa_session.query( trans.app.model.Repository ) \ - .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ - .order_by( trans.app.model.Repository.table.c.name ) \ - .all() - for repository in query: - repository_dict = repository.to_dict( view='collection', value_mapper=value_mapper ) - repository_dict[ 'url' ] = web.url_for( controller='repositories', - action='show', - id=trans.security.encode_id( repository.id ) ) - repository_dicts.append( repository_dict ) - return repository_dicts - except Exception, e: - message = "Error in the Tool Shed repositories API in index: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + deleted = util.asbool( deleted ) + for repository in trans.sa_session.query( trans.app.model.Repository ) \ + .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ + .order_by( trans.app.model.Repository.table.c.name ): + repository_dict = repository.to_dict( view='collection', + value_mapper=self.__get_value_mapper( trans ) ) + repository_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository.id ) ) + repository_dicts.append( repository_dict ) + return repository_dicts @web.expose_api def repository_ids_for_setting_metadata( self, trans, my_writable=False, **kwd ): @@ -273,28 +285,22 @@ class RepositoriesController( BaseAPIController ): in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. """ - try: - if trans.user_is_admin(): - my_writable = util.asbool( my_writable ) - else: - my_writable = True - handled_repository_ids = [] - repository_ids = [] - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) - # Make sure repositories of type tool_dependency_definition are first in the list. - for repository in query: - if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - repository_ids.append( trans.security.encode_id( repository.id ) ) - # Now add all remaining repositories to the list. - for repository in query: - if repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - repository_ids.append( trans.security.encode_id( repository.id ) ) - return repository_ids - except Exception, e: - message = "Error in the Tool Shed repositories API in repository_ids_for_setting_metadata: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + if trans.user_is_admin(): + my_writable = util.asbool( my_writable ) + else: + my_writable = True + handled_repository_ids = [] + repository_ids = [] + query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + # Make sure repositories of type tool_dependency_definition are first in the list. + for repository in query: + if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: + repository_ids.append( trans.security.encode_id( repository.id ) ) + # Now add all remaining repositories to the list. + for repository in query: + if repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: + repository_ids.append( trans.security.encode_id( repository.id ) ) + return repository_ids @web.expose_api def reset_metadata_on_repositories( self, trans, payload, **kwd ): @@ -318,6 +324,7 @@ class RepositoriesController( BaseAPIController ): :param skip_file (optional): A local file name that contains the encoded repository ids associated with repositories to skip. This param can be used as an alternative to the above encoded_ids_to_skip. """ + def handle_repository( trans, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) @@ -335,53 +342,48 @@ class RepositoriesController( BaseAPIController ): status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - try: - start_time = strftime( "%Y-%m-%d %H:%M:%S" ) - results = dict( start_time=start_time, - repository_status=[], - successful_count=0, - unsuccessful_count=0 ) - handled_repository_ids = [] - encoded_ids_to_skip = payload.get( 'encoded_ids_to_skip', [] ) - skip_file = payload.get( 'skip_file', None ) - if skip_file and os.path.exists( skip_file ) and not encoded_ids_to_skip: - # Load the list of encoded_ids_to_skip from the skip_file. - # Contents of file must be 1 encoded repository id per line. - lines = open( skip_file, 'rb' ).readlines() - for line in lines: - if line.startswith( '#' ): - # Skip comments. - continue - encoded_ids_to_skip.append( line.rstrip( '\n' ) ) - if trans.user_is_admin(): - my_writable = util.asbool( payload.get( 'my_writable', False ) ) - else: - my_writable = True - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) - # First reset metadata on all repositories of type repository_dependency_definition. - for repository in query: - encoded_id = trans.security.encode_id( repository.id ) - if encoded_id in encoded_ids_to_skip: - log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ - ( str( repository.id ), str( encoded_ids_to_skip ) ) ) - elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) - # Now reset metadata on all remaining repositories. - for repository in query: - encoded_id = trans.security.encode_id( repository.id ) - if encoded_id in encoded_ids_to_skip: - log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ - ( str( repository.id ), str( encoded_ids_to_skip ) ) ) - elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) - stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) - results[ 'stop_time' ] = stop_time - return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) - except Exception, e: - message = "Error in the Tool Shed repositories API in reset_metadata_on_repositories: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + + start_time = strftime( "%Y-%m-%d %H:%M:%S" ) + results = dict( start_time=start_time, + repository_status=[], + successful_count=0, + unsuccessful_count=0 ) + handled_repository_ids = [] + encoded_ids_to_skip = payload.get( 'encoded_ids_to_skip', [] ) + skip_file = payload.get( 'skip_file', None ) + if skip_file and os.path.exists( skip_file ) and not encoded_ids_to_skip: + # Load the list of encoded_ids_to_skip from the skip_file. + # Contents of file must be 1 encoded repository id per line. + lines = open( skip_file, 'rb' ).readlines() + for line in lines: + if line.startswith( '#' ): + # Skip comments. + continue + encoded_ids_to_skip.append( line.rstrip( '\n' ) ) + if trans.user_is_admin(): + my_writable = util.asbool( payload.get( 'my_writable', False ) ) + else: + my_writable = True + query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + # First reset metadata on all repositories of type repository_dependency_definition. + for repository in query: + encoded_id = trans.security.encode_id( repository.id ) + if encoded_id in encoded_ids_to_skip: + log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ + ( str( repository.id ), str( encoded_ids_to_skip ) ) ) + elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: + results = handle_repository( trans, repository, results ) + # Now reset metadata on all remaining repositories. + for repository in query: + encoded_id = trans.security.encode_id( repository.id ) + if encoded_id in encoded_ids_to_skip: + log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ + ( str( repository.id ), str( encoded_ids_to_skip ) ) ) + elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: + results = handle_repository( trans, repository, results ) + stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) + results[ 'stop_time' ] = stop_time + return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) @web.expose_api def reset_metadata_on_repository( self, trans, payload, **kwd ): @@ -395,6 +397,7 @@ class RepositoriesController( BaseAPIController ): The following parameters must be included in the payload. :param repository_id: the encoded id of the repository on which metadata is to be reset. """ + def handle_repository( trans, start_time, repository ): results = dict( start_time=start_time, repository_status=[] ) @@ -410,21 +413,16 @@ class RepositoriesController( BaseAPIController ): status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - try: - repository_id = payload.get( 'repository_id', None ) - if repository_id is not None: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - start_time = strftime( "%Y-%m-%d %H:%M:%S" ) - log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) ) - results = handle_repository( trans, start_time, repository ) - stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) - results[ 'stop_time' ] = stop_time - return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) - except Exception, e: - message = "Error in the Tool Shed repositories API in reset_metadata_on_repositories: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + + repository_id = payload.get( 'repository_id', None ) + if repository_id is not None: + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + start_time = strftime( "%Y-%m-%d %H:%M:%S" ) + log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) ) + results = handle_repository( trans, start_time, repository ) + stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) + results[ 'stop_time' ] = stop_time + return json.to_json_string( results, sort_keys=True, indent=4 * ' ' ) @web.expose_api_anonymous def show( self, trans, id, **kwd ): @@ -434,27 +432,14 @@ class RepositoriesController( BaseAPIController ): :param id: the encoded id of the Repository object """ - value_mapper = { 'id' : trans.security.encode_id, - 'user_id' : trans.security.encode_id } # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 - try: - repository = suc.get_repository_in_tool_shed( trans, id ) - repository_dict = repository.to_dict( view='element', value_mapper=value_mapper ) - repository_dict[ 'url' ] = web.url_for( controller='repositories', - action='show', - id=trans.security.encode_id( repository.id ) ) - return repository_dict - except Exception, e: - message = "Error in the Tool Shed repositories API in show: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - - def __get_value_mapper( self, trans, repository_metadata ): - value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } - if repository_metadata.time_last_tested is not None: - # For some reason the Dictifiable.to_dict() method in ~/galaxy/model/item_attrs.py requires - # a function rather than a mapped value, so just pass the time_ago function here. - value_mapper[ 'time_last_tested' ] = time_ago - return value_mapper + repository = suc.get_repository_in_tool_shed( trans, id ) + if repository is None: + log.debug( "Unable to locate repository record for id %s." % ( str( id ) ) ) + return {} + repository_dict = repository.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + repository_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository.id ) ) + return repository_dict diff --git a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py index a93b51178cb..19c26cf1824 100644 --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -1,6 +1,5 @@ import datetime import logging -from galaxy.web.framework.helpers import time_ago from tool_shed.util import metadata_util from galaxy import web from galaxy import util @@ -48,61 +47,29 @@ class RepositoryRevisionsController( BaseAPIController ): if not changeset_revision: raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." ) export_repository_dependencies = payload.get( 'export_repository_dependencies', False ) - try: - # We'll currently support only gzip-compressed tar archives. - file_type = 'gz' - export_repository_dependencies = util.string_as_bool( export_repository_dependencies ) - # Get the repository information. - repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - repository_id = trans.security.encode_id( repository.id ) - response = export_util.export_repository( trans, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=True ) - return response - except Exception, e: - message = "Error in the Tool Shed repository_revisions API in export: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + # We'll currently support only gzip-compressed tar archives. + file_type = 'gz' + export_repository_dependencies = util.asbool( export_repository_dependencies ) + # Get the repository information. + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if repository is None: + error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) ) + log.debug( error_message ) + return None, error_message + repository_id = trans.security.encode_id( repository.id ) + return export_util.export_repository( trans, + tool_shed_url, + repository_id, + str( repository.name ), + changeset_revision, + file_type, + export_repository_dependencies, + api=True ) - @web.expose_api_anonymous - def repository_dependencies( self, trans, id, **kwd ): - """ - GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies - Displays information about a repository_metadata record in the Tool Shed. - - :param id: the encoded id of the `RepositoryMetadata` object - """ - # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620 + def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, - 'user_id' : trans.security.encode_id } - repository_dependencies_dicts = [] - try: - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) - metadata = repository_metadata.metadata - if metadata and 'repository_dependencies' in metadata: - rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] - repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) - # We have to add the changeset_revision of of the repository dependency. - repository_dependency_dict[ 'changeset_revision' ] = changeset_revision - repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', - action='show', - id=trans.security.encode_id( repository_dependency.id ) ) - repository_dependencies_dicts.append( repository_dependency_dict ) - return repository_dependencies_dicts - except Exception, e: - message = "Error in the Tool Shed repository_revisions API in repository_dependencies: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + 'repository_id' : trans.security.encode_id } + return value_mapper @web.expose_api_anonymous def index( self, trans, **kwd ): @@ -117,59 +84,94 @@ class RepositoryRevisionsController( BaseAPIController ): # Filter by downloadable if received. downloadable = kwd.get( 'downloadable', None ) if downloadable is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.downloadable == util.string_as_bool( downloadable ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.downloadable == util.asbool( downloadable ) ) # Filter by malicious if received. malicious = kwd.get( 'malicious', None ) if malicious is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.malicious == util.string_as_bool( malicious ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.malicious == util.asbool( malicious ) ) # Filter by tools_functionally_correct if received. tools_functionally_correct = kwd.get( 'tools_functionally_correct', None ) if tools_functionally_correct is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.tools_functionally_correct == util.string_as_bool( tools_functionally_correct ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.tools_functionally_correct == util.asbool( tools_functionally_correct ) ) # Filter by missing_test_components if received. missing_test_components = kwd.get( 'missing_test_components', None ) if missing_test_components is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.missing_test_components == util.string_as_bool( missing_test_components ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.missing_test_components == util.asbool( missing_test_components ) ) # Filter by do_not_test if received. do_not_test = kwd.get( 'do_not_test', None ) if do_not_test is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.do_not_test == util.string_as_bool( do_not_test ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.do_not_test == util.asbool( do_not_test ) ) # Filter by includes_tools if received. includes_tools = kwd.get( 'includes_tools', None ) if includes_tools is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.includes_tools == util.string_as_bool( includes_tools ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.includes_tools == util.asbool( includes_tools ) ) # Filter by test_install_error if received. test_install_error = kwd.get( 'test_install_error', None ) if test_install_error is not None: - clause_list.append( trans.model.RepositoryMetadata.table.c.test_install_error == util.string_as_bool( test_install_error ) ) + clause_list.append( trans.model.RepositoryMetadata.table.c.test_install_error == util.asbool( test_install_error ) ) # Filter by skip_tool_test if received. skip_tool_test = kwd.get( 'skip_tool_test', None ) if skip_tool_test is not None: - skip_tool_test = util.string_as_bool( skip_tool_test ) + skip_tool_test = util.asbool( skip_tool_test ) skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] ) if skip_tool_test: clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) else: clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) ) - # Generate and execute the query. - try: - query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ - .filter( and_( *clause_list ) ) \ - .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id.desc() ) \ - .all() - for repository_metadata in query: - repository_metadata_dict = repository_metadata.to_dict( view='collection', - value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) - repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', - action='show', - id=trans.security.encode_id( repository_metadata.id ) ) - repository_metadata_dicts.append( repository_metadata_dict ) - return repository_metadata_dicts - except Exception, e: - message = "Error in the Tool Shed repository_revisions API in index: " + str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + for repository_metadata in trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ + .filter( and_( *clause_list ) ) \ + .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id.desc() ): + repository_metadata_dict = repository_metadata.to_dict( view='collection', + value_mapper=self.__get_value_mapper( trans ) ) + repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', + action='show', + id=trans.security.encode_id( repository_metadata.id ) ) + repository_metadata_dicts.append( repository_metadata_dict ) + return repository_metadata_dicts + + @web.expose_api_anonymous + def repository_dependencies( self, trans, id, **kwd ): + """ + GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies + Displays information about a repository_metadata record in the Tool Shed. + + :param id: the encoded id of the `RepositoryMetadata` object + """ + # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620 + repository_dependencies_dicts = [] + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + if repository_metadata is None: + log.debug( 'Invalid repository_metadata id received: %s' % str( id ) ) + return repository_dependencies_dicts + metadata = repository_metadata.metadata + if metadata is None: + log.debug( 'The repository_metadata record with id %s has no metadata.' % str ( id ) ) + return repository_dependencies_dicts + if 'repository_dependencies' in metadata: + rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] + repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if repository_dependency is None: + log.dbug( 'Cannot locate repository dependency %s owned by %s.' % ( name, owner ) ) + continue + repository_dependency_id = trans.security.encode_id( repository_dependency.id ) + repository_dependency_repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, repository_dependency_id, changeset_revision ) + if repository_dependency_repository_metadata is None: + log.debug( 'Cannot locate repository_metadata with id %s for repository dependency %s owned by %s.' % \ + ( str( repository_dependency_id ), str( name ), str( owner ) ) ) + continue + repository_dependency_repository_metadata_id = trans.security.encode_id( repository_dependency_repository_metadata.id ) + repository_dependency_dict = repository_dependency.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + # We have to add the changeset_revision of of the repository dependency. + repository_dependency_dict[ 'changeset_revision' ] = changeset_revision + repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=repository_dependency_repository_metadata_id ) + repository_dependencies_dicts.append( repository_dependency_dict ) + return repository_dependencies_dicts @web.expose_api_anonymous def show( self, trans, id, **kwd ): @@ -180,19 +182,16 @@ class RepositoryRevisionsController( BaseAPIController ): :param id: the encoded id of the `RepositoryMetadata` object """ # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620 - try: - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) - repository_metadata_dict = repository_metadata.to_dict( view='element', - value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) - repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', - action='show', - id=trans.security.encode_id( repository_metadata.id ) ) - return repository_metadata_dict - except Exception, e: - message = "Error in the Tool Shed repository_revisions API in show: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + if repository_metadata is None: + log.debug( 'Cannot locate repository_metadata with id %s' % str( id ) ) + return {} + repository_metadata_dict = repository_metadata.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', + action='show', + id=trans.security.encode_id( repository_metadata.id ) ) + return repository_metadata_dict @web.expose_api def update( self, trans, payload, **kwd ): @@ -201,41 +200,32 @@ class RepositoryRevisionsController( BaseAPIController ): Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload. """ repository_metadata_id = kwd.get( 'id', None ) - try: - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) - flush_needed = False - for key, new_value in payload.items(): - if key == 'time_last_tested': - repository_metadata.time_last_tested = datetime.datetime.utcnow() - flush_needed = True - elif hasattr( repository_metadata, key ): - # log information when setting attributes associated with the Tool Shed's install and test framework. - if key in [ 'do_not_test', 'includes_tools', 'missing_test_components', 'test_install_error', - 'tools_functionally_correct' ]: - log.debug( 'Setting repository_metadata table column %s to value %s for changeset_revision %s via the Tool Shed API.' % \ - ( str( key ), str( new_value ), str( repository_metadata.changeset_revision ) ) ) - setattr( repository_metadata, key, new_value ) - flush_needed = True - if flush_needed: - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - except Exception, e: - message = "Error in the Tool Shed repository_revisions API in update: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message + if repository_metadata_id is None: + raise HTTPBadRequest( detail="Missing required parameter 'id'." ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) + if repository_metadata is None: + log.debug( 'Cannot locate repository_metadata with id %s' % str( repository_metadata_id ) ) + return {} + flush_needed = False + for key, new_value in payload.items(): + if key == 'time_last_tested': + repository_metadata.time_last_tested = datetime.datetime.utcnow() + flush_needed = True + elif hasattr( repository_metadata, key ): + # log information when setting attributes associated with the Tool Shed's install and test framework. + if key in [ 'do_not_test', 'includes_tools', 'missing_test_components', 'test_install_error', + 'tools_functionally_correct' ]: + log.debug( 'Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.' % \ + ( str( key ), str( new_value ), str( repository_metadata.changeset_revision ) ) ) + setattr( repository_metadata, key, new_value ) + flush_needed = True + if flush_needed: + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + trans.sa_session.refresh( repository_metadata ) repository_metadata_dict = repository_metadata.to_dict( view='element', - value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) + value_mapper=self.__get_value_mapper( trans ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) return repository_metadata_dict - - def __get_value_mapper( self, trans, repository_metadata ): - value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } - if repository_metadata.time_last_tested is not None: - # For some reason the Dictifiable.to_dict() method in ~/galaxy/model/item_attrs.py requires - # a function rather than a mapped value, so just pass the time_ago function here. - value_mapper[ 'time_last_tested' ] = time_ago - return value_mapper diff --git a/lib/galaxy/webapps/tool_shed/controllers/hg.py b/lib/galaxy/webapps/tool_shed/controllers/hg.py index 4e1e5ffc8f6..c6fd4f8b71a 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -2,6 +2,7 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController from tool_shed.util.shed_util_common import get_repository_by_name_and_owner +from tool_shed.util.shed_util_common import update_repository from tool_shed.util.metadata_util import set_repository_metadata from galaxy import eggs @@ -9,6 +10,8 @@ eggs.require('mercurial') import mercurial.__version__ from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication +from mercurial import hg +from mercurial import ui log = logging.getLogger(__name__) @@ -36,6 +39,11 @@ class HgController( BaseUIController ): repository = get_repository_by_name_and_owner( trans.app, name, owner ) if repository: if hg_version >= '2.2.3': + # Update the repository on disk to the tip revision, because the web upload form uses the on-disk working + # directory. If the repository is not updated on disk, pushing from the command line and then uploading + # via the web interface will result in a new head being created. + repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) + update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. error_message, status = set_repository_metadata( trans, repository ) if status == 'ok' and error_message: diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py index d01d2d2e100..2872d0591a1 100644 --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -567,14 +567,17 @@ class InstallManager( object ): def order_repositories_for_installation( self, tool_shed_repositories, repository_dependencies_dict ): """ - Some repositories may have repository dependencies that are required to be installed before the dependent repository. This method will - inspect the list of repositories about to be installed and make sure to order them appropriately. For each repository about to be installed, - if required repositories are not contained in the list of repositories about to be installed, then they are not considered. Repository - dependency definitions that contain circular dependencies should not result in an infinite loop, but obviously prior installation will not be - handled for one or more of the repositories that require prior installation. This process is similar to the process used when installing tool - shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not handle - managing tool panel sections and other components since repository dependency definitions contained in tool shed repositories with migrated - tools must never define a relationship to a repository dependency that contains a tool. + Some repositories may have repository dependencies that are required to be installed before the dependent + repository. This method will inspect the list of repositories about to be installed and make sure to order + them appropriately. For each repository about to be installed, if required repositories are not contained + in the list of repositories about to be installed, then they are not considered. Repository dependency + definitions that contain circular dependencies should not result in an infinite loop, but obviously prior + installation will not be handled for one or more of the repositories that require prior installation. This + process is similar to the process used when installing tool shed repositories (i.e., the + order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not + handle managing tool panel sections and other components since repository dependency definitions contained + in tool shed repositories with migrated tools must never define a relationship to a repository dependency + that contains a tool. """ ordered_tool_shed_repositories = [] ordered_tsr_ids = [] diff --git a/lib/tool_shed/scripts/api/common.py b/lib/tool_shed/scripts/api/common.py index 9ed77d7c5aa..460f2711078 100644 --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -8,28 +8,18 @@ new_path = [ os.path.join( os.path.dirname( __file__ ), '..', '..', '..', '..', new_path.extend( sys.path[ 1: ] ) sys.path = new_path +import tool_shed.util.shed_util_common as suc + from galaxy import eggs import pkg_resources -pkg_resources.require( "pycrypto" ) -from Crypto.Cipher import Blowfish -from Crypto.Util.randpool import RandomPool -from Crypto.Util import number - -def encode_id( config_id_secret, obj_id ): - # Utility method to encode ID's - id_cipher = Blowfish.new( config_id_secret ) - # Convert to string - s = str( obj_id ) - # Pad to a multiple of 8 with leading "!" - s = ( "!" * ( 8 - len(s) % 8 ) ) + s - # Encrypt - return id_cipher.encrypt( s ).encode( 'hex' ) - def delete( api_key, url, data, return_formatted=True ): - # Sends an API DELETE request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy. + """ + Sends an API DELETE request and acts as a generic formatter for the JSON response. The + 'data' will become the JSON payload read by the Tool Shed. + """ try: - url = make_url( api_key, url ) + url = make_url( url, api_key=api_key, args=None ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data )) req.get_method = lambda: 'DELETE' r = json.loads( urllib2.urlopen( req ).read() ) @@ -47,12 +37,13 @@ def delete( api_key, url, data, return_formatted=True ): print r def display( url, api_key=None, return_formatted=True ): - # Sends an API GET request and acts as a generic formatter for the JSON response. + """Sends an API GET request and acts as a generic formatter for the JSON response.""" try: r = get( url, api_key=api_key ) except urllib2.HTTPError, e: print e - print e.read( 1024 ) # Only return the first 1K of errors. + # Only return the first 1K of errors. + print e.read( 1024 ) sys.exit( 1 ) if type( r ) == unicode: print 'error: %s' % r @@ -84,16 +75,94 @@ def display( url, api_key=None, return_formatted=True ): print 'response is unknown type: %s' % type( r ) def get( url, api_key=None ): - # Do the actual GET. - url = make_url( url, api_key=api_key ) + """Do the GET.""" + url = make_url( url, api_key=api_key, args=None ) try: return json.loads( urllib2.urlopen( url ).read() ) except ValueError, e: print "URL did not return JSON data" - sys.exit(1) + sys.exit( 1 ) + +def get_api_url( base, parts=[], params=None ): + """Compose and return a URL for the Tool Shed API.""" + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = suc.url_join( base, *parts ) + if params is not None: + try: + query_string = urllib.urlencode( params ) + except Exception, e: + # The value of params must be a string. + query_string = params + url += '?%s' % query_string + return url + +def get_latest_downloadable_changeset_revision_via_api( url, name, owner ): + """ + Return the latest downloadable changeset revision for the repository defined by the received + name and owner. + """ + error_message = '' + parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + params = dict( name=name, owner=owner ) + api_url = get_api_url( base=url, parts=parts, params=params ) + changeset_revisions, error_message = json_from_url( api_url ) + if changeset_revisions is None or error_message: + return None, error_message + if len( changeset_revisions ) >= 1: + return changeset_revisions[ -1 ], error_message + return suc.INITIAL_CHANGELOG_HASH, error_message + +def get_repository_dict( url, repository_dict ): + """ + Send a request to the Tool Shed to get additional information about the repository defined + by the received repository_dict. Add the information to the repository_dict and return it. + """ + error_message = '' + if not isinstance( repository_dict, dict ): + error_message = 'Invalid repository_dict received: %s' % str( repository_dict ) + return None, error_message + repository_id = repository_dict.get( 'repository_id', None ) + if repository_id is None: + error_message = 'Invalid repository_dict does not contain a repository_id entry: %s' % str( repository_dict ) + return None, error_message + parts = [ 'api', 'repositories', repository_id ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict, error_message = json_from_url( api_url ) + if extended_dict is None or error_message: + return None, error_message + name = extended_dict.get( 'name', None ) + owner = extended_dict.get( 'owner', None ) + if name is not None and owner is not None: + name = str( name ) + owner = str( owner ) + latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision_via_api( url, name, owner ) + if latest_changeset_revision is None or error_message: + return None, error_message + extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) + return extended_dict, error_message + else: + error_message = 'Invalid extended_dict does not contain name or woner entries: %s' % str( extended_dict ) + return None, error_message + +def json_from_url( url ): + """Send a request to the Tool Shed via the Tool Shed API and handle the response.""" + error_message = '' + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + try: + parsed_json = simplejson.loads( url_contents ) + except Exception, e: + error_message = str( url_contents ) + print 'Error parsing JSON data in json_from_url(): ', str( e ) + return None, error_message + return parsed_json, error_message def make_url( url, api_key=None, args=None ): - # Adds the API Key to the URL if it's not already there. + """Adds the API Key to the URL if it's not already there.""" if args is None: args = [] argsep = '&' @@ -105,20 +174,23 @@ def make_url( url, api_key=None, args=None ): return url + argsep + '&'.join( [ '='.join( t ) for t in args ] ) def post( url, data, api_key=None ): - # Do the actual POST. - url = make_url( url, api_key=api_key ) + """Do the POST.""" + url = make_url( url, api_key=api_key, args=None ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) ) return json.loads( urllib2.urlopen( req ).read() ) def put( url, data, api_key=None ): - # Do the actual PUT. - url = make_url( url, api_key=api_key ) + """Do the PUT.""" + url = make_url( url, api_key=api_key, args=None ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data )) req.get_method = lambda: 'PUT' return json.loads( urllib2.urlopen( req ).read() ) def submit( url, data, api_key=None, return_formatted=True ): - # Sends an API POST request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy. + """ + Sends an API POST request and acts as a generic formatter for the JSON response. The + 'data' will become the JSON payload read by the Tool Shed. + """ try: r = post( url, data, api_key=api_key ) except urllib2.HTTPError, e: @@ -133,7 +205,8 @@ def submit( url, data, api_key=None, return_formatted=True ): print 'Response' print '--------' if type( r ) == list: - # Currently the only implemented responses are lists of dicts, because submission creates some number of collection elements. + # Currently the only implemented responses are lists of dicts, because submission creates + # some number of collection elements. for i in r: if type( i ) == dict: if 'url' in i: @@ -150,9 +223,12 @@ def submit( url, data, api_key=None, return_formatted=True ): print r def update( api_key, url, data, return_formatted=True ): - # Sends an API PUT request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy. + """ + Sends an API PUT request and acts as a generic formatter for the JSON response. The + 'data' will become the JSON payload read by the Tool Shed. + """ try: - r = put( api_key, url, data ) + r = put( url, data, api_key=api_key ) except urllib2.HTTPError, e: if return_formatted: print e diff --git a/lib/tool_shed/scripts/api/get_filtered_repository_revisions.py b/lib/tool_shed/scripts/api/get_filtered_repository_revisions.py index 447b8ca62e7..3a4cdff9165 100644 --- a/lib/tool_shed/scripts/api/get_filtered_repository_revisions.py +++ b/lib/tool_shed/scripts/api/get_filtered_repository_revisions.py @@ -26,69 +26,19 @@ import sys import urllib sys.path.insert( 0, os.path.dirname( __file__ ) ) + from common import get +from common import get_api_url +from common import get_repository_dict +from common import json_from_url + +from galaxy.util import asbool from galaxy.util.json import from_json_string import tool_shed.util.shed_util_common as suc -def get_api_url( base, parts=[], params=None ): - if 'api' in parts and parts.index( 'api' ) != 0: - parts.pop( parts.index( 'api' ) ) - parts.insert( 0, 'api' ) - elif 'api' not in parts: - parts.insert( 0, 'api' ) - url = suc.url_join( base, *parts ) - if params: - url += '?%s' % params - return url - -def get_latest_downloadable_changeset_revision( url, name, owner ): - error_message = '' - parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = urllib.urlencode( dict( name=name, owner=owner ) ) - api_url = get_api_url( base=url, parts=parts, params=params ) - changeset_revisions, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - if changeset_revisions: - return changeset_revisions[ -1 ], error_message - else: - return suc.INITIAL_CHANGELOG_HASH, error_message - -def get_repository_dict( url, repository_dict ): - error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) - extended_dict, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - name = str( extended_dict[ 'name' ] ) - owner = str( extended_dict[ 'owner' ] ) - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) - if error_message: - print error_message - extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) - return extended_dict, error_message - -def json_from_url( url ): - error_message = '' - url_handle = urllib.urlopen( url ) - url_contents = url_handle.read() - try: - parsed_json = from_json_string( url_contents ) - except Exception, e: - error_message = str( url_contents ) - return None, error_message - return parsed_json, error_message - -def string_as_bool( string ): - if str( string ).lower() in [ 'true' ]: - return True - else: - return False - def main( options ): base_tool_shed_url = options.tool_shed_url.rstrip( '/' ) - latest_revision_only = string_as_bool( options.latest_revision_only ) + latest_revision_only = asbool( options.latest_revision_only ) do_not_test = str( options.do_not_test ) downloadable = str( options.downloadable ) includes_tools = str( options.includes_tools ) @@ -108,30 +58,31 @@ def main( options ): tools_functionally_correct=tools_functionally_correct ) ) api_url = get_api_url( base=base_tool_shed_url, parts=parts, params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) - if error_message: + if baseline_repository_dicts is None or error_message: print error_message - repository_dicts = [] - for baseline_repository_dict in baseline_repository_dicts: - # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the - # module that will generate the install methods. - repository_dict, error_message = get_repository_dict( base_tool_shed_url, baseline_repository_dict ) - if error_message: - print 'Error getting additional details from the API: ', error_message - repository_dicts.append( baseline_repository_dict ) - else: - # Don't test empty repositories. - changeset_revision = baseline_repository_dict[ 'changeset_revision' ] - if changeset_revision != suc.INITIAL_CHANGELOG_HASH: - # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and - # append it to the list of repository_dicts to install and test. - if latest_revision_only: - latest_revision = repository_dict[ 'latest_revision' ] - if changeset_revision == latest_revision: + else: + repository_dicts = [] + for baseline_repository_dict in baseline_repository_dicts: + # We need to get additional details from the tool shed API to pass on to the + # module that will generate the install methods. + repository_dict, error_message = get_repository_dict( base_tool_shed_url, baseline_repository_dict ) + if error_message: + print 'Error getting additional details from the API: ', error_message + repository_dicts.append( baseline_repository_dict ) + else: + # Don't test empty repositories. + changeset_revision = baseline_repository_dict.get( 'changeset_revision', suc.INITIAL_CHANGELOG_HASH ) + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and + # append it to the list of repository_dicts to install and test. + if latest_revision_only: + latest_revision = repository_dict.get( 'latest_revision', suc.INITIAL_CHANGELOG_HASH ) + if changeset_revision == latest_revision: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + else: repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - else: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - print '\n\n', repository_dicts - print '\nThe url:\n\n', api_url, '\n\nreturned ', len( repository_dicts ), ' repository dictionaries...' + print '\n\n', repository_dicts + print '\nThe url:\n\n', api_url, '\n\nreturned ', len( repository_dicts ), ' repository dictionaries...' if __name__ == '__main__': parser = argparse.ArgumentParser( description='Get a filtered list of repository dictionaries.' ) diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py index acaa8bf7c36..1b319576d5f 100644 --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -313,6 +313,9 @@ def handle_repository_dependency_elem( trans, elem, unpopulate=False ): if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH: elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision revised = True + else: + error_message = 'Invalid latest installable changeset_revision %s ' % str( lastest_installable_changeset_revision ) + error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) else: error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) return revised, elem, error_message diff --git a/lib/tool_shed/util/container_util.py b/lib/tool_shed/util/container_util.py index 0dd81ff2f7b..7b7668bd2e0 100644 --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -744,7 +744,8 @@ def build_repository_containers_for_galaxy( trans, repository, datatypes, invali lock.release() return containers_dict -def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None ): +def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, + exclude=None ): """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed.""" if exclude is None: exclude = [] @@ -806,11 +807,12 @@ def build_repository_containers_for_tool_shed( trans, repository, changeset_revi containers_dict[ 'readme_files' ] = readme_files_root_folder if 'repository_dependencies' not in exclude: # Repository dependencies container. - folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( trans=trans, - folder_id=folder_id, - repository_dependencies=repository_dependencies, - label='Repository dependencies', - installed=False ) + folder_id, repository_dependencies_root_folder = \ + build_repository_dependencies_folder( trans=trans, + folder_id=folder_id, + repository_dependencies=repository_dependencies, + label='Repository dependencies', + installed=False ) if repository_dependencies_root_folder: containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Tool dependencies container. @@ -868,11 +870,13 @@ def build_repository_containers_for_tool_shed( trans, repository, changeset_revi if metadata: if 'data_manager' not in exclude and 'data_manager' in metadata: data_managers = metadata['data_manager'].get( 'data_managers', None ) - folder_id, data_managers_root_folder = build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) + folder_id, data_managers_root_folder = \ + build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) containers_dict[ 'valid_data_managers' ] = data_managers_root_folder error_messages = metadata['data_manager'].get( 'error_messages', None ) data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) - folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) + folder_id, data_managers_root_folder = \ + build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder except Exception, e: log.exception( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) @@ -890,15 +894,22 @@ def build_repository_dependencies_folder( trans, folder_id, repository_dependenc folder_id += 1 # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] - repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) + repository_dependencies_folder = Folder( id=folder_id, + key=repository_dependencies_folder_key, + label=label, + parent=repository_dependencies_root_folder ) del repository_dependencies[ 'root_key' ] - # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. - # We want the description value associated with the repository_dependencies_folder. + # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more + # repository_dependency keys. We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) del repository_dependencies[ 'description' ] repository_dependencies_folder, folder_id, repository_dependency_id = \ - populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ) + populate_repository_dependencies_container( trans, + repository_dependencies_folder, + repository_dependencies, + folder_id, + repository_dependency_id ) repository_dependencies_folder = prune_repository_dependencies( repository_dependencies_folder ) else: repository_dependencies_root_folder = None @@ -985,11 +996,13 @@ def build_tools_folder( trans, folder_id, tool_dicts, repository, changeset_revi tools_root_folder = None return folder_id, tools_root_folder -def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False ): +def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, + new_install=False, reinstalling=False ): """Return a folder hierarchy containing tool dependencies.""" - # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, they are considered missing. The tool - # dependency status will be displayed only if a record exists for the tool dependency in the Galaxy database, but the tool dependency is not installed. - # The value for new_install will be True only if the associated repository in being installed for the first time. This value is used in setting the + # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, + # they are considered missing. The tool dependency status will be displayed only if a record exists for the tool + # dependency in the Galaxy database, but the tool dependency is not installed. The value for new_install will be + # True only if the associated repository in being installed for the first time. This value is used in setting the # container description. if tool_dependencies: tool_dependency_id = 0 @@ -1138,7 +1151,10 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l else: containing_folder = tool_test_results_root_folder folder_id += 1 - test_environment_folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + test_environment_folder = Folder( id=folder_id, + key='test_environment', + label='Automated test environment', + parent=containing_folder ) containing_folder.folders.append( test_environment_folder ) try: architecture = test_environment_dict.get( 'architecture', '' ) @@ -1184,7 +1200,10 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if len( passed_tests_dicts ) > 0: folder_id += 1 - passed_tests_folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) + passed_tests_folder = Folder( id=folder_id, + key='passed_tests', + label='Tests that passed successfully', + parent=containing_folder ) containing_folder.folders.append( passed_tests_folder ) passed_test_id = 0 for passed_tests_dict in passed_tests_dicts: @@ -1395,7 +1414,8 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l rd_tool_shed = str( repository_dependency_successful_installation_dict.get( 'tool_shed', '' ) ) rd_name = str( repository_dependency_successful_installation_dict.get( 'name', '' ) ) rd_owner = str( repository_dependency_successful_installation_dict.get( 'owner', '' ) ) - rd_changeset_revision = str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) + rd_changeset_revision = \ + str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) except Exception, e: rd_tool_shed = 'unknown' rd_name = 'unknown' @@ -1495,7 +1515,8 @@ def can_display_tool_test_results( tool_test_results_dicts, exclude=None ): # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other # entry that may be added in the future. - display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', 'not_tested', 'passed_tests', 'skipped_tests' ] + display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', + 'not_tested', 'passed_tests', 'skipped_tests' ] for k, v in tool_test_results_dict.items(): if k in display_entries: # We've discovered an entry that can be displayed, so see if it has a value since displaying @@ -1506,8 +1527,9 @@ def can_display_tool_test_results( tool_test_results_dicts, exclude=None ): def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): """ - Change any empty folders contained within the repository dependencies container into a repository dependency since it has no repository dependencies - of it's own. This method is not used (and may not be needed), but here it is just in case. + Change any empty folders contained within the repository dependencies container into a repository dependency + since it has no repository dependencies of it's own. This method is not used (and may not be needed), but here + it is just in case. """ if not folder.folders and not folder.repository_dependencies: repository_dependency_id += 1 @@ -1519,10 +1541,14 @@ def cast_empty_repository_dependency_folders( folder, repository_dependency_id ) return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) return folder, repository_dependency_id -def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td, key ): +def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td, key ): """Return a repository dependency label based on the repository dependency key.""" - if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ): + if key_is_current_repositorys_key( repository_name, + repository_owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, key ): label = 'Repository dependencies' else: if galaxy.util.asbool( prior_installation_required ): @@ -1533,8 +1559,8 @@ def generate_repository_dependencies_folder_label_from_key( repository_name, rep ( repository_name, changeset_revision, repository_owner, prior_installation_required_str ) return label -def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td ): +def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td ): """Assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported.""" return '%s%s%s%s%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ), STRSEP, @@ -1551,13 +1577,6 @@ def generate_repository_dependencies_key_for_repository( toolshed_base_url, repo def generate_tool_dependencies_key( name, version, type ): return '%s%s%s%s%s' % ( str( name ), STRSEP, str( version ), STRSEP, str( type ) ) -def get_folder( folder, key ): - if folder.key == key: - return folder - for sub_folder in folder.folders: - return get_folder( sub_folder, key ) - return None - def get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ): """Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page.""" # Default prior_installation_required and only_if_compiling_contained_td to False. @@ -1610,7 +1629,15 @@ def get_components_from_key( key ): # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions. return toolshed_base_url, repository_name, repository_owner, changeset_revision -def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): +def get_folder( folder, key ): + if folder.key == key: + return folder + for sub_folder in folder.folders: + return get_folder( sub_folder, key ) + return None + +def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, + repository_dependency_id, folder_keys ): repository_components_tuple = get_components_from_key( rd_key ) components_list = suc.extract_components_from_tuple( repository_components_tuple ) toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ] @@ -1713,11 +1740,21 @@ def key_is_current_repositorys_key( repository_name, repository_owner, changeset return True return False -def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ): - folder_keys = repository_dependencies.keys() +def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, + repository_dependency_id ): + folder_keys = [] + for key in repository_dependencies.keys(): + if key not in folder_keys: + folder_keys.append( key ) for key, value in repository_dependencies.items(): repository_dependencies_folder, folder_id, repository_dependency_id = \ - handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, key, value, folder_id, repository_dependency_id, folder_keys ) + handle_repository_dependencies_container_entry( trans, + repository_dependencies_folder, + key, + value, + folder_id, + repository_dependency_id, + folder_keys ) return repository_dependencies_folder, folder_id, repository_dependency_id def print_folders( pad, folder ): @@ -1731,19 +1768,22 @@ def print_folders( pad, folder ): for sub_folder in folder.folders: print_folders( pad+5, sub_folder ) +def prune_folder( folder, repository_dependency ): + listified_repository_dependency = repository_dependency.listify + if is_subfolder_of( folder, listified_repository_dependency ): + folder.repository_dependencies.remove( repository_dependency ) + def prune_repository_dependencies( folder ): """ - Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be json-serialize-able), the - order in which the dictionary is processed to create the container sometimes results in repository dependency entries in a folder that also - includes the repository dependency as a sub-folder (if the repository dependency has it's own repository dependency). This method will remove - all repository dependencies from folder that are also sub-folders of folder. + Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be + json-serialize-able), the order in which the dictionary is processed to create the container sometimes results in + repository dependency entries in a folder that also includes the repository dependency as a sub-folder (if the + repository dependency has it's own repository dependency). This method will remove all repository dependencies from + folder that are also sub-folders of folder. """ repository_dependencies = [ rd for rd in folder.repository_dependencies ] for repository_dependency in repository_dependencies: - listified_repository_dependency = repository_dependency.listify - if is_subfolder_of( folder, listified_repository_dependency ): - repository_dependencies.remove( repository_dependency ) - folder.repository_dependencies = repository_dependencies + prune_folder( folder, repository_dependency ) for sub_folder in folder.folders: return prune_repository_dependencies( sub_folder ) return folder diff --git a/lib/tool_shed/util/export_util.py b/lib/tool_shed/util/export_util.py index 4572519fab8..cd997931401 100644 --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -55,7 +55,8 @@ def clean_tool_shed_url( base_url ): base = base.rstrip( '/' ) return base -def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, export_repository_dependencies, api=False ): +def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, + export_repository_dependencies, api=False ): repository = suc.get_repository_in_tool_shed( trans, repository_id ) repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, str( repository.name ), @@ -67,7 +68,8 @@ def export_repository( trans, tool_shed_url, repository_id, repository_name, cha if export_repository_dependencies: repo_info_dicts = get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ) repository_ids = get_repository_ids( trans, repo_info_dicts ) - ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = order_components_for_import( trans, repository_ids, repo_info_dicts ) + ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ + order_components_for_import( trans, repository_id, repository_ids, repo_info_dicts ) else: ordered_repository_ids = [] ordered_repositories = [] @@ -193,8 +195,8 @@ def generate_export_elem( tool_shed_url, repository, changeset_revision, export_ def get_components_from_repo_info_dict( trans, repo_info_dict ): """ - Return the repository and the associated latest installable changeset_revision (including updates) for the repository defined by the received - repo_info_dict. + Return the repository and the associated latest installable changeset_revision (including updates) for the + repository defined by the received repo_info_dict. """ for repository_name, repo_info_tup in repo_info_dict.items(): # There should only be one entry in the received repo_info_dict. @@ -208,8 +210,9 @@ def get_components_from_repo_info_dict( trans, repo_info_dict ): def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids, repo_info_dicts ): """ - The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each location in the list. This method will return the element - from repo_info_dicts associated with the received encoded_repository_id by determining it's location in the received encoded_repository_ids list. + The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each + location in the list. This method will return the element from repo_info_dicts associated with the received + encoded_repository_id by determining it's location in the received encoded_repository_ids list. """ for index, repository_id in enumerate( encoded_repository_ids ): if repository_id == encoded_repository_id: @@ -218,6 +221,10 @@ def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids return None def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ): + """ + Return a list of dictionaries defining repositories that are required by the repository associated with the + received repository_id. + """ repository = suc.get_repository_in_tool_shed( trans, repository_id ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. @@ -246,8 +253,9 @@ def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision def get_repository_attributes_and_sub_elements( repository, archive_name ): """ - Get the information about a repository to create and populate an XML tag set. The generated attributes will be contained within the - tag, while the sub_elements will be tag sets contained within the tag set. + Get the information about a repository to create and populate an XML tag set. The generated attributes will + be contained within the tag, while the sub_elements will be tag sets contained within the + tag set. """ attributes = odict() sub_elements = odict() @@ -268,6 +276,7 @@ def get_repository_attributes_and_sub_elements( repository, archive_name ): return attributes, sub_elements def get_repository_ids( trans, repo_info_dicts ): + """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" repository_ids = [] for repo_info_dict in repo_info_dicts: for repository_name, repo_info_tup in repo_info_dict.items(): @@ -277,23 +286,36 @@ def get_repository_ids( trans, repo_info_dicts ): repository_ids.append( trans.security.encode_id( repository.id ) ) return repository_ids -def order_components_for_import( trans, repository_ids, repo_info_dicts ): +def order_components_for_import( trans, primary_repository_id, repository_ids, repo_info_dicts ): """ - Some repositories may have repository dependencies that must be imported and have metadata set on them before the dependent repository is imported. This method - will inspect the list of repositories about to be exported and make sure to order them appropriately for proper import. For each repository about to be exported, - if required repositories are not contained in the list of repositories about to be exported, then they are not considered. Repository dependency definitions that - contain circular dependencies should not result in an infinite loop, but obviously ordering the list will not be handled for one or more of the repositories that - require prior import. + Some repositories may have repository dependencies that must be imported and have metadata set on + them before the dependent repository is imported. This method will inspect the list of repositories + about to be exported and make sure to order them appropriately for proper import. For each repository + about to be exported, if required repositories are not contained in the list of repositories about to + be exported, then they are not considered. Repository dependency definitions that contain circular + dependencies should not result in an infinite loop, but obviously ordering the list will not be handled + for one or more of the repositories that require prior import. """ + # The received primary_repository_id is the id of the repository being exported, with the received list + # of repository_ids being only the ids of all of its repository dependencies. The primary repository will + # always be last in the returned lists. ordered_repository_ids = [] ordered_repositories = [] ordered_changeset_revisions = [] - # Create a dictionary whose keys are the received repository_ids and whose values are a list of repository_ids, each of which is contained in the received list of - # repository_ids and whose associated repository must be imported prior to the repository associated with the repository_id key. + # Create a dictionary whose keys are the received repository_ids and whose values are a list of + # repository_ids, each of which is contained in the received list of repository_ids and whose associated + # repository must be imported prior to the repository associated with the repository_id key. prior_import_required_dict = suc.get_prior_import_or_install_required_dict( trans, repository_ids, repo_info_dicts ) processed_repository_ids = [] + # Process the list of repository dependencies defined for the repository associated with the received + # primary_repository_id. while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, processed_repository_ids ) + if repository_id == primary_repository_id: + # Append the primary_repository_id without processing it since it must be returned last in the order. + # It will be processed below after all dependencies are processed. + processed_repository_ids.append( primary_repository_id ) + continue processed_repository_ids.append( repository_id ) if repository_id not in ordered_repository_ids: prior_import_required_ids = prior_import_required_dict[ repository_id ] @@ -312,4 +334,11 @@ def order_components_for_import( trans, repository_ids, repo_info_dicts ): ordered_repository_ids.append( repository_id ) ordered_repositories.append( repository ) ordered_changeset_revisions.append( changeset_revision ) + # Process the repository associated with the received primary_repository_id last. + repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = get_components_from_repo_info_dict( trans, repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions diff --git a/lib/tool_shed/util/repository_maintenance_util.py b/lib/tool_shed/util/repository_maintenance_util.py index 7e52ab9749f..96c51fc9d58 100644 --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -154,6 +154,9 @@ def create_repository_and_import_archive( trans, repository_archive_dict, import # Populate the new repository with the contents of exported repository archive. results_dict = import_util.import_repository_archive( trans, repository, repository_archive_dict ) ok = results_dict.get( 'ok', False ) + error_message = results_dict.get( 'error_message', '' ) + if error_message: + results_message += error_message import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) else: # The repository either already exists in this Tool Shed or the current user is not authorized to create it. diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index f7b030fc093..bf83152e1cc 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -745,10 +745,11 @@ def get_next_downloadable_changeset_revision( repository, repo, after_changeset_ def get_next_prior_import_or_install_required_dict_entry( prior_required_dict, processed_tsr_ids ): """ - This method is used in the Tool Shed when exporting a repository and it's dependencies, and in Galaxy when a repository and it's dependencies - are being installed. The order in which the prior_required_dict is processed is critical in order to ensure that the ultimate repository import - or installation order is correctly defined. This method determines the next key / value pair from the received prior_required_dict that should - be processed. + This method is used in the Tool Shed when exporting a repository and it's dependencies, and in Galaxy + when a repository and it's dependencies are being installed. The order in which the prior_required_dict + is processed is critical in order to ensure that the ultimate repository import or installation order is + correctly defined. This method determines the next key / value pair from the received prior_required_dict + that should be processed. """ # Return the first key / value pair that is not yet processed and whose value is an empty list. for key, value in prior_required_dict.items(): @@ -756,7 +757,8 @@ def get_next_prior_import_or_install_required_dict_entry( prior_required_dict, p continue if not value: return key - # Return the first key / value pair that is not yet processed and whose ids in value are all included in processed_tsr_ids. + # Return the first key / value pair that is not yet processed and whose ids in value are all included + # in processed_tsr_ids. for key, value in prior_required_dict.items(): if key in processed_tsr_ids: continue @@ -767,7 +769,8 @@ def get_next_prior_import_or_install_required_dict_entry( prior_required_dict, p break if all_contained: return key - # Return the first key / value pair that is not yet processed. Hopefully this is all that is necessary at this point. + # Return the first key / value pair that is not yet processed. Hopefully this is all that is necessary + # at this point. for key, value in prior_required_dict.items(): if key in processed_tsr_ids: continue @@ -862,9 +865,10 @@ def get_prior_import_or_install_required_dict( trans, tsr_ids, repo_info_dicts ) def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=True ): """ - Return a query containing repositories for resetting metadata. This method is called from both the Tool Shed and Galaxy. The - my_writable parameter is ignored unless called from the Tool Shed, and the order parameter is used for displaying the list of - repositories ordered alphabetically for display on a page. When called from wither the Tool Shed or Galaxy API, order is False. + Return a query containing repositories for resetting metadata. This method is called from both the + Tool Shed and Galaxy. The my_writable parameter is ignored unless called from the Tool Shed, and the + order parameter is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from either the Tool Shed or Galaxy API, order is False. """ if trans.webapp.name == 'tool_shed': # When called from the Tool Shed API, the metadata is reset on all repositories of type tool_dependency_definition in addition @@ -873,7 +877,8 @@ def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, or username = trans.user.username clause_list = [] for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): # Always reset metadata on all repositories of type tool_dependency_definition. if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION: clause_list.append( trans.model.Repository.table.c.id == repository.id ) @@ -900,12 +905,14 @@ def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, or else: if order: return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ) \ .order_by( trans.model.Repository.table.c.name, trans.model.Repository.table.c.user_id ) else: return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ) else: # We're in Galaxy. if order: diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py index fb4a2a106be..03bc5a07eb2 100755 --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -105,7 +105,7 @@ class Cleanup(object): url = make_url(self.config.database_connection) log.info('Connecting to database with URL: %s' % url) - args = url.translate_connect_args() + args = url.translate_connect_args( username='user' ) args.update(url.query) assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.' diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py index 9cb9f281bec..995783004ef 100644 --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -313,6 +313,7 @@ def main(): file_path = os.path.join( galaxy_db_path, 'files' ) new_file_path = tempfile.mkdtemp( prefix='new_files_path_', dir=tempdir ) job_working_directory = tempfile.mkdtemp( prefix='job_working_directory_', dir=tempdir ) + install_database_connection = os.environ.get( 'GALAXY_TEST_INSTALL_DBURI', None ) if 'GALAXY_TEST_DBURI' in os.environ: database_connection = os.environ['GALAXY_TEST_DBURI'] else: @@ -372,6 +373,8 @@ def main(): user_library_import_dir=user_library_import_dir, master_api_key=master_api_key, ) + if install_database_connection is not None: + kwargs[ 'install_database_connection' ] = install_database_connection if psu_production: kwargs[ 'global_conf' ] = None if not database_connection.startswith( 'sqlite://' ): diff --git a/static/scripts/galaxy.library.js b/static/scripts/galaxy.library.js index d133fb8cef3..1ff2f6e6063 100644 --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -90,7 +90,7 @@ define([ // === VIEWS ==== // MMMMMMMMMMMMMM -// galaxy folder +//main view for folder browsing var FolderContentView = Backbone.View.extend({ // main element definition el : '#center', @@ -116,7 +116,7 @@ var FolderContentView = Backbone.View.extend({ // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM - // set up + // main template for folder browsing templateFolder : function (){ var tmpl_array = []; @@ -162,7 +162,7 @@ var FolderContentView = Backbone.View.extend({ tmpl_array.push(' name'); tmpl_array.push(' data type'); tmpl_array.push(' size'); - tmpl_array.push(' date'); + tmpl_array.push(' date (UTC)'); tmpl_array.push(' '); tmpl_array.push(' '); tmpl_array.push(' '); @@ -184,7 +184,7 @@ var FolderContentView = Backbone.View.extend({ tmpl_array.push(' (empty folder)'); tmpl_array.push(' <% } %>'); tmpl_array.push(' '); - tmpl_array.push(' folder'); // data type + tmpl_array.push(' folder'); tmpl_array.push(' <%= _.escape(content_item.get("item_count")) %> item(s)'); // size tmpl_array.push(' <% } else { %>'); tmpl_array.push(' '); @@ -228,7 +228,7 @@ var FolderContentView = Backbone.View.extend({ tmpl_array.push(' <%= _.escape(size) %>'); tmpl_array.push(' '); tmpl_array.push(' '); - tmpl_array.push(' Date uploaded'); + tmpl_array.push(' Date uploaded (UTC)'); tmpl_array.push(' <%= _.escape(item.get("date_uploaded")) %>'); tmpl_array.push(' '); tmpl_array.push(' '); @@ -240,7 +240,7 @@ var FolderContentView = Backbone.View.extend({ tmpl_array.push(' <%= _.escape(item.get("metadata_data_lines")) %>'); tmpl_array.push(' '); tmpl_array.push(' Comment Lines'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); tmpl_array.push(' <%= _.escape(item.get("metadata_comment_lines")) %>'); tmpl_array.push(' <% } else { %>'); tmpl_array.push(' unknown'); @@ -296,19 +296,34 @@ var FolderContentView = Backbone.View.extend({ return tmpl_array.join(''); }, - // convert size to nice string - size_to_string : function (size) - { - // 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"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('
'); + tmpl_array.push('Importing selected datasets to history <%= _.escape(history_name) %>'); + tmpl_array.push('
'); + tmpl_array.push('
'); + tmpl_array.push('
'); + tmpl_array.push(' 0% Complete'); + tmpl_array.push('
'); + tmpl_array.push('
'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + templateNewFolderInModal: function(){ + tmpl_array = []; + + tmpl_array.push('
'); + tmpl_array.push('
'); + tmpl_array.push(''); + tmpl_array.push(''); + tmpl_array.push('
'); + tmpl_array.push('
'); + + return tmpl_array.join(''); + }, // MMMMMMMMMMMMMMM // === EVENTS ==== @@ -325,6 +340,10 @@ var FolderContentView = Backbone.View.extend({ 'click .btn_open_folder' : 'navigateToFolder' }, +// MMMMMMMMMMMMMMMMMM +// === FUNCTIONS ==== +// MMMMMMMMMMMMMMMMMM + //render the folder view render: function (options) { //hack to show scrollbars @@ -360,10 +379,27 @@ var FolderContentView = Backbone.View.extend({ // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); that.$el.html(template); - } + }, + error: function(){ + mod_toastr.error('An error occured :('); + } }) }, + // convert size to nice string + size_to_string : function (size) + { + // 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"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + // handles the click on 'open' and 'upper' folder icons navigateToFolder : function(event){ var folder_id = $(event.target).attr('data-id'); @@ -398,9 +434,18 @@ var FolderContentView = Backbone.View.extend({ // TODO can render here already //fetch user histories for import purposes histories.fetch({ - success: function (histories){self.renderModalAfterFetch(item, histories)} + success: function (histories){ + self.renderModalAfterFetch(item, histories) + }, + error: function(){ + mod_toastr.error('An error occured during fetching histories:('); + self.renderModalAfterFetch(item) + } }); - } + }, + error: function(){ + mod_toastr.error('An error occured during loading dataset details :('); + } }); }, @@ -422,16 +467,17 @@ var FolderContentView = Backbone.View.extend({ }); $(".peek").html(item.get("peek")); - var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - - // preset last selected history if we know it - if (self.lastSelectedHistory.length > 0) { - $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); - } + // show the import-into-history footer only if the request for histories succeeded + if (typeof history.models !== undefined){ + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + } this.modal.bindEvents(); - // show the prepared modal this.modal.show(); }, @@ -555,7 +601,6 @@ var FolderContentView = Backbone.View.extend({ $('#toolbtn_bulk_import').hide(); $('#toolbtn_dl').hide(); } - }, // show bulk import modal @@ -577,8 +622,10 @@ var FolderContentView = Backbone.View.extend({ } }); self.modal.bindEvents(); - // show the prepared modal self.modal.show(); + }, + error: function(){ + mod_toastr.error('An error occured :('); } }); }, @@ -616,7 +663,7 @@ var FolderContentView = Backbone.View.extend({ datasets_to_import.push(historyItem); }; - // call the recursive function to call ajax one after each other + // call the recursive function to call ajax one after each other (request FIFO queue) this.chainCall(datasets_to_import); }, @@ -646,22 +693,7 @@ var FolderContentView = Backbone.View.extend({ $('.completion_span').text(txt_representation); }, - // progress bar - templateProgressBar : function (){ - var tmpl_array = []; - tmpl_array.push('
'); - tmpl_array.push('Importing selected datasets to history <%= _.escape(history_name) %>'); - tmpl_array.push('
'); - tmpl_array.push('
'); - tmpl_array.push('
'); - tmpl_array.push(' 0% Complete'); - tmpl_array.push('
'); - tmpl_array.push('
'); - tmpl_array.push(''); - - return tmpl_array.join(''); - }, // download selected datasets download : function(folder_id, format){ @@ -706,14 +738,13 @@ var FolderContentView = Backbone.View.extend({ this.modal = new mod_modal.GalaxyModal({ destructible : true, title : 'Create New Folder', - body : this.template_new_folder(), + body : this.templateNewFolderInModal(), buttons : { 'Create' : function() {self.create_new_folder_event()}, 'Close' : function() {self.modal.hideOrDestroy(); self.modal = null;} } }); this.modal.bindEvents(); - // show prepared modal this.modal.show(); }, @@ -726,7 +757,7 @@ var FolderContentView = Backbone.View.extend({ url_items = Backbone.history.fragment.split('/'); current_folder_id = url_items[url_items.length-1]; folder.url = folder.urlRoot + '/' + current_folder_id ; - + var self = this; folder.save(folderDetails, { success: function (folder) { @@ -755,20 +786,6 @@ var FolderContentView = Backbone.View.extend({ // validate new library info validate_new_folder: function(folderDetails){ return folderDetails.name !== ''; - }, - - // template for new library modal - template_new_folder: function(){ - tmpl_array = []; - - tmpl_array.push('
'); - tmpl_array.push('
'); - tmpl_array.push(''); - tmpl_array.push(''); - tmpl_array.push('
'); - tmpl_array.push('
'); - - return tmpl_array.join(''); } }); @@ -785,11 +802,13 @@ var GalaxyLibraryview = Backbone.View.extend({ initialize : function(){ }, - // template - template_library_list : function (){ +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + templateLibraryList: function(){ tmpl_array = []; tmpl_array.push('
'); - tmpl_array.push(''); tmpl_array.push('

New Data Libraries. This is work in progress. Report problems & ideas to Marten.

'); tmpl_array.push('New Library'); @@ -814,14 +833,27 @@ var GalaxyLibraryview = Backbone.View.extend({ tmpl_array.push(' <% }); %>'); tmpl_array.push(' '); tmpl_array.push(''); - tmpl_array.push('
'); + + return tmpl_array.join(''); + }, + + templateNewLibraryInModal: function(){ + tmpl_array = []; + + tmpl_array.push('
'); + tmpl_array.push('
'); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push('
'); + tmpl_array.push('
'); + return tmpl_array.join(''); }, - // render render: function () { - //hack to show scrollbars due to #center element inheritance + // modification of upper DOM element to show scrollbars due to the #center element inheritance $("#center").css('overflow','auto'); var that = this; @@ -829,7 +861,7 @@ var GalaxyLibraryview = Backbone.View.extend({ libraries.fetch({ success: function (libraries) { - var template = _.template(that.template_library_list(), { libraries : libraries.models }); + var template = _.template(that.templateLibraryList(), { libraries : libraries.models }); that.$el.html(template); }, error: function(model, response){ @@ -863,14 +895,13 @@ var GalaxyLibraryview = Backbone.View.extend({ this.modal = new mod_modal.GalaxyModal({ destructible : true, title : 'Create New Library', - body : this.template_new_library(), + body : this.templateNewLibraryInModal(), buttons : { 'Create' : function() {self.create_new_library_event()}, 'Close' : function() {self.modal.hideOrDestroy();} } }); this.modal.bindEvents(); - // show prepared modal this.modal.show(); }, @@ -916,21 +947,6 @@ var GalaxyLibraryview = Backbone.View.extend({ // validate new library info validate_new_library: function(libraryDetails){ return libraryDetails.name !== ''; - }, - - // template for new library modal - template_new_library: function(){ - tmpl_array = []; - - tmpl_array.push('
'); - tmpl_array.push('
'); - tmpl_array.push(''); - tmpl_array.push(''); - tmpl_array.push(''); - tmpl_array.push('
'); - tmpl_array.push('
'); - - return tmpl_array.join(''); } }); @@ -938,6 +954,7 @@ var GalaxyLibraryview = Backbone.View.extend({ var GalaxyLibrary = Backbone.View.extend({ folderContentView : null, galaxyLibraryview : null, + initialize : function(){ folderContentView = new FolderContentView(); diff --git a/static/scripts/galaxy.modal.js b/static/scripts/galaxy.modal.js index f35a0a859d2..2d3c84a8ff4 100644 --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -19,7 +19,9 @@ var GalaxyModal = Backbone.View.extend( // options options : { - destructible: false // by default the modal cannot be removed by theself.destroy() method + // by default the modal cannot be removed by the self.destroy() method + // but only hidden through self.hide() + destructible: false }, // initialize @@ -99,9 +101,9 @@ var GalaxyModal = Backbone.View.extend( hide: function(){ // fade out this.$el.fadeOut('fast'); - // set flag this.visible = false; + // unbind events this.unbindEvents(); }, @@ -109,8 +111,8 @@ var GalaxyModal = Backbone.View.extend( destroy: function(){ // set flag this.visible = false; + // unbind events this.unbindEvents(); - // remove this.$el.remove(); }, diff --git a/static/scripts/mvc/dataset/hda-base.js b/static/scripts/mvc/dataset/hda-base.js index 11e749cc89a..10434c96dec 100644 --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -215,7 +215,8 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( // return either: a single download icon-button (if there are no meta files) if( _.isEmpty( meta_files ) ){ return $([ - '', + '', '', '' ].join( '' ) ); @@ -239,7 +240,8 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( '', '
', - '', + '', '', // join these w/o whitespace or there'll be a gap when rendered '', @@ -257,6 +259,7 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( // gen. safe to show in all cases return faIconButton({ title : _l( 'View details' ), + classes : 'dataset-params-btn', href : this.urls.show_params, target : this.linkTarget, faIcon : 'fa-info-circle' diff --git a/static/scripts/mvc/dataset/hda-edit.js b/static/scripts/mvc/dataset/hda-edit.js index d464ba49cad..1e1353405a1 100644 --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -72,7 +72,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( var purged = this.model.get( 'purged' ), deleted = this.model.get( 'deleted' ), editBtnData = { - title : _l( 'Edit Attributes' ), + title : _l( 'Edit attributes' ), href : this.urls.edit, target : this.linkTarget, classes : 'dataset-edit' @@ -138,6 +138,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( return faIconButton({ title : _l( 'View or report this error' ), href : this.urls.report_error, + classes : 'dataset-report-error-btn', target : this.linkTarget, faIcon : 'fa-bug' }); @@ -150,6 +151,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( return faIconButton({ title : _l( 'Run this job again' ), href : this.urls.rerun, + classes : 'dataset-rerun-btn', target : this.linkTarget, faIcon : 'fa-refresh' }); @@ -189,6 +191,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( var $icon = faIconButton({ title : _l( 'Visualize' ), + classes : 'dataset-visualize-btn', faIcon : 'fa-bar-chart-o' }); @@ -242,6 +245,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( } var $icon = faIconButton({ title : _l( 'Visualize' ), + classes : 'dataset-visualize-btn', faIcon : 'fa-bar-chart-o' }); $icon.addClass( 'visualize-icon' ); // needed? @@ -364,8 +368,10 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( // make the dbkey a link to editing if( this.model.get( 'metadata_dbkey' ) === '?' && !this.model.isDeletedOrPurged() ){ - $body.find( '.dataset-dbkey .value' ).replaceWith( - $( '?' ).attr( 'href', this.urls.edit ) ); + var editableDbkey = $( '?' ) + .attr( 'href', this.urls.edit ) + .attr( 'target', this.linkTarget ); + $body.find( '.dataset-dbkey .value' ).replaceWith( editableDbkey ); } }, diff --git a/static/scripts/packed/galaxy.library.js b/static/scripts/packed/galaxy.library.js index 83f857ee9b8..20a6df10c17 100644 --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1 +1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
');r.push('

New Data Libraries. This is work in progress. Report problems & ideas to Marten.

');r.push('
');r.push(' ');r.push(' ');r.push(' ");r.push("
");r.push('
');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
");r.push('');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
viewnamedata typesizedate
<%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
");r.push("
");return r.join("")},templateDatasetModal:function(){var r=[];r.push('
');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" <% } %>");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push("
">Name<%= _.escape(item.get("name")) %>
Data type<%= _.escape(item.get("data_type")) %>
Genome build<%= _.escape(item.get("genome_build")) %>
Size<%= _.escape(size) %>
Date uploaded<%= _.escape(item.get("date_uploaded")) %>
Uploaded by<%= _.escape(item.get("uploaded_by")) %>
Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
Number of Columns<%= _.escape(item.get("metadata_columns")) %>
Column Types<%= _.escape(item.get("metadata_column_types")) %>
Miscellaneous information<%= _.escape(item.get("misc_blurb")) %>
");r.push(' 
');r.push("
");r.push("
");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var r=[];r.push('
');r.push("Importing selected datasets to history <%= _.escape(history_name) %>");r.push("
");r.push('
');r.push('
');r.push(' 0% Complete');r.push("
");r.push("
");r.push("");return r.join("")},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+=''});$('
'+r+"
").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.template_new_folder(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""},template_new_folder:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("
");tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
");tmpl_array.push("
");return tmpl_array.join("")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("");tmpl_array.push('

New Data Libraries. This is work in progress. Report problems & ideas to Marten.

');tmpl_array.push('New Library');tmpl_array.push('');tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" <% }); %>");tmpl_array.push(" ");tmpl_array.push("
namedescriptionsynopsismodel type
<%- library.get("name") %><%= _.escape(library.get("description")) %><%= _.escape(library.get("synopsis")) %><%= _.escape(library.get("model_class")) %>
");tmpl_array.push("
");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.template_library_list(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("
");tmpl_array.push('');tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
");tmpl_array.push("
");return tmpl_array.join("")}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
');r.push('

New Data Libraries. This is work in progress. Report problems & ideas to Marten.

');r.push('
');r.push(' ');r.push(' ');r.push(' ");r.push("
");r.push('
');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
");r.push('');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
viewnamedata typesizedate (UTC)
<%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
");r.push("
");return r.join("")},templateDatasetModal:function(){var r=[];r.push('
');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" <% } %>");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push("
">Name<%= _.escape(item.get("name")) %>
Data type<%= _.escape(item.get("data_type")) %>
Genome build<%= _.escape(item.get("genome_build")) %>
Size<%= _.escape(size) %>
Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
Uploaded by<%= _.escape(item.get("uploaded_by")) %>
Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
Number of Columns<%= _.escape(item.get("metadata_columns")) %>
Column Types<%= _.escape(item.get("metadata_column_types")) %>
Miscellaneous information<%= _.escape(item.get("misc_blurb")) %>
");r.push(' 
');r.push("
");r.push("
");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateProgressBar:function(){var r=[];r.push('
');r.push("Importing selected datasets to history <%= _.escape(history_name) %>");r.push("
");r.push('
');r.push('
');r.push(' 0% Complete');r.push("
");r.push("
");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("
");tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
");tmpl_array.push("
");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+=''});$('
'+r+"
").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("");tmpl_array.push('

New Data Libraries. This is work in progress. Report problems & ideas to Marten.

');tmpl_array.push('New Library');tmpl_array.push('');tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" <% }); %>");tmpl_array.push(" ");tmpl_array.push("
namedescriptionsynopsismodel type
<%- library.get("name") %><%= _.escape(library.get("description")) %><%= _.escape(library.get("synopsis")) %><%= _.escape(library.get("model_class")) %>
");tmpl_array.push("
");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('
');tmpl_array.push("
");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push("
");tmpl_array.push("
");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-base.js b/static/scripts/packed/mvc/dataset/hda-base.js index 56a462c3af2..ae9e4189a56 100644 --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
",'
','','','','',"","
"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
Error: unknown dataset state "'+this.model.get("state")+'".
'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
"+_l("This is a new dataset and not all of its data are available yet")+"
")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
"+_l("You do not have permission to view this dataset")+"
")},_render_body_discarded:function(){return this._render_stateBodyHelper("
"+_l("The job creating this dataset was cancelled before completion")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
"+_l("This job is waiting to run")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
"+_l("This dataset is currently uploading")+"
")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
"+_l("Metadata is being auto-detected")+"
")},_render_body_running:function(){return this._render_stateBodyHelper("
"+_l("This job is currently running")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['',_l("An error occurred with this dataset"),":",'
',$.trim(this.model.get("misc_info")),"
"].join("");if(!this.model.get("purged")){c="
"+this.model.get("misc_blurb")+"
"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("
"+_l("No data")+": "+this.model.get("misc_blurb")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
",'
','','','','',"","
"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
Error: unknown dataset state "'+this.model.get("state")+'".
'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
"+_l("This is a new dataset and not all of its data are available yet")+"
")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
"+_l("You do not have permission to view this dataset")+"
")},_render_body_discarded:function(){return this._render_stateBodyHelper("
"+_l("The job creating this dataset was cancelled before completion")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
"+_l("This job is waiting to run")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
"+_l("This dataset is currently uploading")+"
")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
"+_l("Metadata is being auto-detected")+"
")},_render_body_running:function(){return this._render_stateBodyHelper("
"+_l("This job is currently running")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['',_l("An error occurred with this dataset"),":",'
',$.trim(this.model.get("misc_info")),"
"].join("");if(!this.model.get("purged")){c="
"+this.model.get("misc_blurb")+"
"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("
"+_l("No data")+": "+this.model.get("misc_blurb")+"
",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-edit.js b/static/scripts/packed/mvc/dataset/hda-edit.js index 2b0e61c4f78..e63ece180a3 100644 --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click here to undelete it or here to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click here to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click here to undelete it or here to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click here to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(h){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var g=$('?').attr("href",this.urls.edit).attr("target",this.linkTarget);h.find(".dataset-dbkey .value").replaceWith(g)}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako index 74e7a2c1db4..970b78d8a01 100644 --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -1,9 +1,7 @@ <%inherit file="/webapps/galaxy/base_panels.mako"/> <%namespace file="/root/tool_menu.mako" import="*" /> -<%namespace file="/history/history_panel.mako" import="history_panel_javascripts" /> <%namespace file="/history/history_panel.mako" import="current_history_panel" /> -<%namespace file="/history/history_panel.mako" import="history_panel" /> <%def name="stylesheets()"> ${parent.stylesheets()} diff --git a/test-data/8.tabular b/test-data/8.tabular deleted file mode 100644 index 6e39b95e24a..00000000000 --- a/test-data/8.tabular +++ /dev/null @@ -1,29 +0,0 @@ -AF099740 ENST00000296869 -AF377960 ENST00000160373 -AK131266 ENST00000350908 -BC005078 ENST00000319432 -BC007833 ENST00000349792 -NM_000054 ENST00000337474 -NM_000127 ENST00000333324 -NM_000425 ENST00000361699 -NM_000492 ENST00000003084 -NM_000588 ENST00000296870 -NM_001167 ENST00000245836 -NM_001666 ENST00000350060 -NM_001927 ENST00000273074 -NM_002651 ENST00000271657 -NM_002796 ENST00000290541 -NM_003269 ENST00000230083 -NM_003391 ENST00000265441 -NM_003687 ENST00000253754 -NM_004199 ENST00000166534 -NM_005997 ENST00000295315 -NM_006773 ENST00000263239 -NM_007214 ENST00000027474 -NM_014908 ENST00000308871 -NM_015354 ENST00000259310 -NM_020145 ENST00000291931 -NM_024536 ENST00000243776 -NM_145315 ENST00000258002 -NM_152827 ENST00000230085 -NM_174933 ENST00000308941 diff --git a/test-data/aggregate_binned_scores_in_intervals.bed b/test-data/aggregate_binned_scores_in_intervals.bed deleted file mode 100644 index 4cf6bbb19b2..00000000000 --- a/test-data/aggregate_binned_scores_in_intervals.bed +++ /dev/null @@ -1 +0,0 @@ -chr7 60000002 60000010 diff --git a/test-data/library/3.bed b/test-data/library/3.bed deleted file mode 100644 index 124167d1871..00000000000 --- a/test-data/library/3.bed +++ /dev/null @@ -1,25 +0,0 @@ -chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, -chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, -chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, -chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, -chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, -chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, -chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, -chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, -chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, -chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, -chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, -chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, -chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, -chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, -chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, -chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, -chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, -chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, -chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, -chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, -chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, -chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, -chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, -chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, -chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, diff --git a/test-data/library/4.bed b/test-data/library/4.bed deleted file mode 100644 index 6f32a4fb5a3..00000000000 --- a/test-data/library/4.bed +++ /dev/null @@ -1 +0,0 @@ -chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff --git a/test-data/library/5.bed b/test-data/library/5.bed deleted file mode 100644 index 646dca7a428..00000000000 --- a/test-data/library/5.bed +++ /dev/null @@ -1,134 +0,0 @@ -chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + -chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + -chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + -chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + -chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + -chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + -chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + -chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + -chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + -chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + -chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + -chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + -chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 + -chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 + -chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 + -chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 + -chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 + -chr7 115739975 115740164 CCDS5765.1_cds_1_0_chr7_115739976_f 0 + -chr7 115759067 115759097 CCDS5767.1_cds_0_0_chr7_115759068_f 0 + -chr7 115760529 115760694 CCDS5767.1_cds_1_0_chr7_115760530_f 0 + -chr7 115792950 115793292 CCDS5767.1_cds_2_0_chr7_115792951_f 0 + -chr7 116096616 116096655 CCDS5768.1_cds_0_0_chr7_116096617_f 0 + -chr7 116122131 116122195 CCDS5768.1_cds_1_0_chr7_116122132_f 0 + -chr7 116126998 116127050 CCDS5768.1_cds_2_0_chr7_116126999_f 0 + -chr7 116132776 116132840 CCDS5768.1_cds_3_0_chr7_116132777_f 0 + -chr7 116138181 116138388 CCDS5768.1_cds_4_0_chr7_116138182_f 0 + -chr7 116140267 116140347 CCDS5768.1_cds_5_0_chr7_116140268_f 0 + -chr7 116144237 116144316 CCDS5768.1_cds_6_0_chr7_116144238_f 0 + -chr7 116146073 116146145 CCDS5768.1_cds_7_0_chr7_116146074_f 0 + -chr7 116150064 116150127 CCDS5768.1_cds_8_0_chr7_116150065_f 0 + -chr7 116151731 116151872 CCDS5768.1_cds_9_0_chr7_116151732_f 0 + -chr7 116187545 116187696 CCDS5770.1_cds_0_0_chr7_116187546_f 0 + -chr7 116333766 116333849 CCDS5770.1_cds_1_0_chr7_116333767_f 0 + -chr7 116353565 116353725 CCDS5770.1_cds_2_0_chr7_116353566_f 0 + -chr7 116363797 116363852 CCDS5770.1_cds_3_0_chr7_116363798_f 0 + -chr7 116364495 116364611 CCDS5770.1_cds_4_0_chr7_116364496_f 0 + -chr7 116365889 116365965 CCDS5770.1_cds_5_0_chr7_116365890_f 0 + -chr7 116368128 116368197 CCDS5770.1_cds_6_0_chr7_116368129_f 0 + -chr7 116370085 116370240 CCDS5770.1_cds_7_0_chr7_116370086_f 0 + -chr7 116372439 116372537 CCDS5770.1_cds_8_0_chr7_116372440_f 0 + -chr7 116404866 116404981 CCDS5770.1_cds_9_0_chr7_116404867_f 0 + -chr7 116423325 116423398 CCDS5770.1_cds_10_0_chr7_116423326_f 0 + -chr7 116424838 116424941 CCDS5770.1_cds_11_0_chr7_116424839_f 0 + -chr7 116443791 116443942 CCDS5770.1_cds_12_0_chr7_116443792_f 0 + -chr7 116453088 116453181 CCDS5770.1_cds_13_0_chr7_116453089_f 0 + -chr7 116455927 116456067 CCDS5770.1_cds_14_0_chr7_116455928_f 0 + -chr7 116456865 116456985 CCDS5770.1_cds_15_0_chr7_116456866_f 0 + -chr7 116187545 116187696 CCDS5769.1_cds_0_0_chr7_116187546_f 0 + -chr7 116333766 116333849 CCDS5769.1_cds_1_0_chr7_116333767_f 0 + -chr7 116353565 116353725 CCDS5769.1_cds_2_0_chr7_116353566_f 0 + -chr7 116363797 116363852 CCDS5769.1_cds_3_0_chr7_116363798_f 0 + -chr7 116364495 116364611 CCDS5769.1_cds_4_0_chr7_116364496_f 0 + -chr7 116365889 116365965 CCDS5769.1_cds_5_0_chr7_116365890_f 0 + -chr7 116370085 116370240 CCDS5769.1_cds_6_0_chr7_116370086_f 0 + -chr7 116372439 116372537 CCDS5769.1_cds_7_0_chr7_116372440_f 0 + -chr7 116404866 116404981 CCDS5769.1_cds_8_0_chr7_116404867_f 0 + -chr7 116423325 116423398 CCDS5769.1_cds_9_0_chr7_116423326_f 0 + -chr7 116424838 116424941 CCDS5769.1_cds_10_0_chr7_116424839_f 0 + -chr7 116443791 116443942 CCDS5769.1_cds_11_0_chr7_116443792_f 0 + -chr7 116453088 116453181 CCDS5769.1_cds_12_0_chr7_116453089_f 0 + -chr7 116455927 116456067 CCDS5769.1_cds_13_0_chr7_116455928_f 0 + -chr7 116463766 116463862 CCDS5769.1_cds_14_0_chr7_116463767_f 0 + -chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - -chr7 116531616 116531881 CCDS5771.1_cds_1_0_chr7_116531617_r 0 - -chr7 116549075 116549353 CCDS5771.1_cds_2_0_chr7_116549076_r 0 - -chr7 116554571 116554798 CCDS5771.1_cds_3_0_chr7_116554572_r 0 - -chr7 116556911 116556994 CCDS5771.1_cds_4_0_chr7_116556912_r 0 - -chr7 116597600 116597753 CCDS5772.1_cds_0_0_chr7_116597601_r 0 - -chr7 116601356 116601470 CCDS5772.1_cds_1_0_chr7_116601357_r 0 - -chr7 116602616 116602722 CCDS5772.1_cds_2_0_chr7_116602617_r 0 - -chr7 116613942 116614052 CCDS5772.1_cds_3_0_chr7_116613943_r 0 - -chr7 116615015 116615072 CCDS5772.1_cds_4_0_chr7_116615016_r 0 - -chr7 116616073 116616149 CCDS5772.1_cds_5_0_chr7_116616074_r 0 - -chr7 116616990 116617115 CCDS5772.1_cds_6_0_chr7_116616991_r 0 - -chr7 116618730 116618865 CCDS5772.1_cds_7_0_chr7_116618731_r 0 - -chr7 116619702 116619814 CCDS5772.1_cds_8_0_chr7_116619703_r 0 - -chr7 116654167 116654279 CCDS5772.1_cds_9_0_chr7_116654168_r 0 - -chr7 116656241 116656364 CCDS5772.1_cds_10_0_chr7_116656242_r 0 - -chr7 116660840 116660940 CCDS5772.1_cds_11_0_chr7_116660841_r 0 - -chr7 116661360 116661465 CCDS5772.1_cds_12_0_chr7_116661361_r 0 - -chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + -chr7 116738257 116738368 CCDS5773.1_cds_1_0_chr7_116738258_f 0 + -chr7 116743038 116743147 CCDS5773.1_cds_2_0_chr7_116743039_f 0 + -chr7 116764903 116765119 CCDS5773.1_cds_3_0_chr7_116764904_f 0 + -chr7 116768280 116768370 CCDS5773.1_cds_4_0_chr7_116768281_f 0 + -chr7 116769252 116769416 CCDS5773.1_cds_5_0_chr7_116769253_f 0 + -chr7 116770552 116770678 CCDS5773.1_cds_6_0_chr7_116770553_f 0 + -chr7 116774104 116774351 CCDS5773.1_cds_7_0_chr7_116774105_f 0 + -chr7 116776020 116776113 CCDS5773.1_cds_8_0_chr7_116776021_f 0 + -chr7 116782645 116782828 CCDS5773.1_cds_9_0_chr7_116782646_f 0 + -chr7 116793468 116793660 CCDS5773.1_cds_10_0_chr7_116793469_f 0 + -chr7 116821743 116821838 CCDS5773.1_cds_11_0_chr7_116821744_f 0 + -chr7 116824357 116824444 CCDS5773.1_cds_12_0_chr7_116824358_f 0 + -chr7 116825938 116826662 CCDS5773.1_cds_13_0_chr7_116825939_f 0 + -chr7 116828934 116829063 CCDS5773.1_cds_14_0_chr7_116828935_f 0 + -chr7 116836830 116836868 CCDS5773.1_cds_15_0_chr7_116836831_f 0 + -chr7 116837536 116837787 CCDS5773.1_cds_16_0_chr7_116837537_f 0 + -chr7 116840678 116840758 CCDS5773.1_cds_17_0_chr7_116840679_f 0 + -chr7 116844523 116844674 CCDS5773.1_cds_18_0_chr7_116844524_f 0 + -chr7 116845585 116845813 CCDS5773.1_cds_19_0_chr7_116845586_f 0 + -chr7 116848617 116848718 CCDS5773.1_cds_20_0_chr7_116848618_f 0 + -chr7 116861526 116861775 CCDS5773.1_cds_21_0_chr7_116861527_f 0 + -chr7 116876442 116876598 CCDS5773.1_cds_22_0_chr7_116876443_f 0 + -chr7 116886846 116886936 CCDS5773.1_cds_23_0_chr7_116886847_f 0 + -chr7 116898692 116898865 CCDS5773.1_cds_24_0_chr7_116898693_f 0 + -chr7 116899463 116899569 CCDS5773.1_cds_25_0_chr7_116899464_f 0 + -chr7 116900912 116901113 CCDS5773.1_cds_26_0_chr7_116900913_f 0 + -chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - -chr7 116952022 116952124 CCDS5774.1_cds_1_0_chr7_116952023_r 0 - -chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 - -chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 - -chr7 116958551 116958737 CCDS5774.1_cds_4_0_chr7_116958552_r 0 - -chr7 116959056 116959262 CCDS5774.1_cds_5_0_chr7_116959057_r 0 - -chr7 116962093 116962272 CCDS5774.1_cds_6_0_chr7_116962094_r 0 - -chr7 116968917 116969105 CCDS5774.1_cds_7_0_chr7_116968918_r 0 - -chr7 116969273 116969426 CCDS5774.1_cds_8_0_chr7_116969274_r 0 - -chr7 116979835 116979935 CCDS5774.1_cds_9_0_chr7_116979836_r 0 - -chr7 116980017 116980104 CCDS5774.1_cds_10_0_chr7_116980018_r 0 - -chr7 116990559 116990639 CCDS5774.1_cds_11_0_chr7_116990560_r 0 - -chr7 116991879 116991975 CCDS5774.1_cds_12_0_chr7_116991880_r 0 - -chr7 116994439 116994715 CCDS5774.1_cds_13_0_chr7_116994440_r 0 - -chr7 117001063 117001181 CCDS5774.1_cds_14_0_chr7_117001064_r 0 - -chr7 117011515 117011770 CCDS5774.1_cds_15_0_chr7_117011516_r 0 - -chr7 117014445 117014596 CCDS5774.1_cds_16_0_chr7_117014446_r 0 - -chr7 117016866 117016966 CCDS5774.1_cds_17_0_chr7_117016867_r 0 - -chr7 117018255 117018459 CCDS5774.1_cds_18_0_chr7_117018256_r 0 - -chr7 117025132 117026786 CCDS5774.1_cds_19_0_chr7_117025133_r 0 - -chr7 117044769 117044994 CCDS5774.1_cds_20_0_chr7_117044770_r 0 - -chr7 117095213 117095321 CCDS5774.1_cds_21_0_chr7_117095214_r 0 - -chr7 117107339 117107420 CCDS5774.1_cds_22_0_chr7_117107340_r 0 - -chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + -chr5 131424558 131424600 CCDS4149.1_cds_1_0_chr5_131424559_f 0 + -chr5 131425903 131425993 CCDS4149.1_cds_2_0_chr5_131425904_f 0 + -chr5 131426117 131426159 CCDS4149.1_cds_3_0_chr5_131426118_f 0 + diff --git a/test-data/taxonomyGI.tabular b/test-data/taxonomyGI.tabular deleted file mode 100644 index 4c4af7c9e08..00000000000 --- a/test-data/taxonomyGI.tabular +++ /dev/null @@ -1,5 +0,0 @@ -33001686 9443 -23236241 9604 -12583 9606 -410771 40674 -2286205 63221 diff --git a/test-data/users/test1@bx.psu.edu/1.fasta b/test-data/users/test1@bx.psu.edu/1.fasta deleted file mode 100644 index c9ecbb612dd..00000000000 --- a/test-data/users/test1@bx.psu.edu/1.fasta +++ /dev/null @@ -1,2 +0,0 @@ ->hg17 -gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAGGACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAcccccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC----------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTACCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCCGAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAGCAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGCCGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGGCATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTCCTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCAGGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATTGGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGACATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCCTGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAGTAGAGGTGGGGGGAAACAAGTGTCAGGAAGA--------------------------------------------CTCAAA---------ATCTTC--------------------------------------------------------------CAGAGAAATTGT-----GCAGGGTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATGAGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAACTTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTATAGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACACTCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACAGTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAGG----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAGAGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GTGCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGGTGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGATTGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAATGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGGCAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCCCAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCCTCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAATATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGACAGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGTCTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAGGAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGCACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCATCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCCTTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGCTTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTGACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTGTTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATTTCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGGG-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---GGGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCCAGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGATGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCACATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCATTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCAAAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTTACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagatatttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttctgagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaattgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaaggcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaaccccatctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagctacttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgagccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacacacacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-tatctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCTGTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTGGTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTGTGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTGAATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGAAAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCCTGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCTCACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTCTGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAATGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCCACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAGGAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGTAGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgtgtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCCTACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTCTACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttggcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagttcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTTTGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGTTGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAACTTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGAGTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCAAATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT-------CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTGGG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAAGAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCATCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTTGTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAGGGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAACTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGCAGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTATATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatcttttttggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtgatcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcccaagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggctcaagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacacccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTTCTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GCCAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AGGGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCTCCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC--------TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAATGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACAGCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACAGCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGACTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGGACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAGTTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TGCTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGATTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCCACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctctcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatctcctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gcattggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcagccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaaaactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATAGCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACCCAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaatgcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacaaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaaggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcctatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccagctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgagccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaagaaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggaggatgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaacactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaataaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGCACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAATCAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATCCCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTGGCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATTATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtggtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGAATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTTCTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTAATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtttggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtctctcacacacacccagcacaagtccaag-------------------------accagcatggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagttgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccatatctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacgacaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttagtcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatggccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaagatattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgtgtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GATTCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATAGGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAGCTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTGGTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATTTGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGGGGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTGGAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCACTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTAACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGGAAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAAATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGGA---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc--------------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctgagccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAACATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCCTACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAATATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATTGGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtctttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccatatttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgccttccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcccattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgttgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcagtaagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAGTGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATGGGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACACCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagatagatatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatgcagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AGCATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAGCTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCTAAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGATGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTGGTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCTGTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCACTGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctgaatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTCTGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG--------------------------------------------------------TTCTAATTCTAAACCACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggctgggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcattcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaataataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggctgagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgccaccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaataaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttaggaggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggcaagacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGATTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCGATTAGCTGAGC----------CACATGCAGGCACAG------------------------CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCCTCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCTTG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------CTCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tgtagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccctttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtcttttctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaattaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaagttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA diff --git a/test-data/users/test3@bx.psu.edu/run1/2.fasta b/test-data/users/test3@bx.psu.edu/run1/2.fasta deleted file mode 100644 index c2a830c75ed..00000000000 --- a/test-data/users/test3@bx.psu.edu/run1/2.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt -tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac -cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg -aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg -gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt -tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac -ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt -ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt -tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa -aacaattcta atggtcaaaa a diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index f486b4c198e..fa5be27b591 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -335,6 +335,7 @@ class TwillTestCase( unittest.TestCase ): self.visit_page( "history?show_deleted=False" ) else: self.visit_page( "history" ) + json_data = {} try: tc.find( pattern, flags=( 'm' if multiline else '' ) ) # twill stores the regex match in a special stack variable @@ -541,7 +542,6 @@ class TwillTestCase( unittest.TestCase ): self.home() self.visit_page( "history/list" ) self.check_page_for_string( 'Saved Histories' ) - self.check_page_for_string( ' same history -spaceghost.user.loginOrRegisterUser( email, password ); -spaceghost.thenOpen( spaceghost.baseUrl, function(){ +spaceghost.user.loginOrRegisterUser( email, password ).openHomePage( function(){ this.test.comment( 'anon-user should login and be associated with previous history' ); var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); this.historypanel.waitForHdas( function(){ - var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.hdaElement.text ); + var hdaInfo = this.historypanel.hdaElementInfoByTitle( filenameToUpload ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, @@ -146,8 +130,7 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ }); // ------------------------------------------------------------------- logs out -> new history -spaceghost.user.logout(); -spaceghost.thenOpen( spaceghost.baseUrl, function(){ +spaceghost.user.logout().openHomePage( function(){ this.test.comment( 'logging out should create a new, anonymous history' ); this.historypanel.waitForHdas( function(){ diff --git a/test/casperjs/api-history-tests.js b/test/casperjs/api-history-tests.js index 9b31ad6f14e..76ec3071416 100644 --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -304,13 +304,15 @@ spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ //this.debug( 'returned:\n' + this.jsonStr( returned ) ); historyShow = this.api.histories.show( newFirstHistory.id ); this.test.assert( historyShow.genome_build === unicodeBuild, - "Update accepted unicode genome_build: " + historyShow.name ); + "Update accepted unicode genome_build: " + historyShow.genome_build ); } catch( err ){ //this.debug( this.jsonStr( err ) ); if( ( err instanceof this.api.APIError ) && ( err.status === 500 ) && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } else { + throw err; } } diff --git a/test/casperjs/hda-state-tests.js b/test/casperjs/hda-state-tests.js index 73b00a42ce1..b6dee0e2802 100644 --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -56,23 +56,20 @@ var utils = require( 'utils' ), filepathToUpload = '../../test-data/1.txt', testUploadInfo = {}, //TODO: get from the api module - that doesn't exist yet - summaryShouldBeArray = [ '10 lines', 'format: txt' ], + summaryShouldBeArray = [ '10 lines', 'format', 'txt' ], infoShouldBe = 'uploaded txt file', metadataFiles = null, peekShouldBeArray = []; // ------------------------------------------------------------------- set up -// start a new user +// start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); - -// upload a file spaceghost.then( function upload(){ spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ testUploadInfo = _uploadInfo; }); }); - // =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) @@ -104,13 +101,14 @@ function testIconButton( hdaDbId, containerSelector, buttonName, expectedButtonD if( expectedButtonData.hrefTpl ){ var href = buttonElement.attributes.href, - hrefShouldBe = utils.format( expectedButtonData.hrefTpl, hdaDbId ); + hrefShouldBe = ( expectedButtonData.hrefTpl.indexOf( '%s' ) !== -1 )? + ( utils.format( expectedButtonData.hrefTpl, hdaDbId ) ):( expectedButtonData.hrefTpl ); this.assertTextContains( href, hrefShouldBe, buttonName + ' has proper href (' + hrefShouldBe + '): ' + href ); } if( expectedButtonData.tooltip ){ - this.historypanel.hoverOver( btnSelector ); + this.hoverOver( btnSelector ); var tooltipText = expectedButtonData.tooltip; this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); this.test.assertSelectorHasText( tooltipSelector, tooltipText, @@ -159,7 +157,7 @@ function testDbkey( hdaSelector, dbkeySetTo ){ this.test.assertSelectorHasText( dbkeySelector, dbkeySetTo, 'dbkey is specified: ' + dbkey.text ); this.test.assert( dbkey.nodeName === specifiedDbkeyNodeName, - 'dbkey has proper nodeName (' + specifiedDbkeyNodeName + '):' + dbkey.nodeName ); + 'dbkey has proper nodeName (' + specifiedDbkeyNodeName + '): ' + dbkey.nodeName ); // dbkey expected to be not set } else { @@ -305,7 +303,7 @@ function testExpandedBody( hdaSelector, expectedSummaryTextArray, expectedInfoTe // =================================================================== TESTS // ------------------------------------------------------------------- ok state -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; @@ -329,13 +327,10 @@ spaceghost.withHistoryPanel( function(){ this.test.comment( 'clicking the hda title should expand its body' ); this.historypanel.thenExpandHda( uploadSelector, function(){ - // ugh. - this.jumpToHistory( function(){ - testExpandedBody.call( spaceghost, uploadSelector, - summaryShouldBeArray, infoShouldBe, false, metadataFiles ); - //testExpandedBody.call( spaceghost, uploadSelector, - // summaryShouldBeArray, infoShouldBe, false ); - }); + testExpandedBody.call( spaceghost, uploadSelector, + summaryShouldBeArray, infoShouldBe, false, metadataFiles ); + //testExpandedBody.call( spaceghost, uploadSelector, + // summaryShouldBeArray, infoShouldBe, false ); }); }); // restore to collapsed @@ -350,7 +345,7 @@ spaceghost.then( function(){ }); // ------------------------------------------------------------------- new state -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ // set state directly through model, wait for re-render //TODO: not ideal to test this this.evaluate( function(){ @@ -385,7 +380,7 @@ spaceghost.withHistoryPanel( function(){ 'HDA body has text: ' + expectedBodyText ); }); - this.historypanel.then( function(){ + this.then( function(){ this.test.comment( 'a simulated error on a new dataset should appear in a message box' ); // datasets that error on fetching their data appear as 'new', so do this here // more of a unit test, but ok @@ -410,7 +405,7 @@ spaceghost.withHistoryPanel( function(){ }); }); // restore state, collapse -spaceghost.withHistoryPanel( function revertStateAndCollapse(){ +spaceghost.then( function revertStateAndCollapse(){ var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.historypanel.thenCollapseHda( uploadSelector, function(){ diff --git a/test/casperjs/history-options-tests.js b/test/casperjs/history-options-tests.js index 6f5d83582bd..699e8840b49 100644 --- a/test/casperjs/history-options-tests.js +++ b/test/casperjs/history-options-tests.js @@ -47,9 +47,8 @@ var filepathToUpload = '../../test-data/1.txt', // =================================================================== TESTS // ------------------------------------------------------------------- set up -// start a new user +// start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ testUploadInfo = _uploadInfo; }); @@ -114,8 +113,15 @@ spaceghost.then( function(){ this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); }); +}); + +spaceghost.then( function(){ // undelete the uploaded file - this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); + this.historyoptions.includeDeleted( function(){ + this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); + spaceghost.debug( 'undeleted' ); + }); + }); // ------------------------------------------------------------------- hidden hdas aren't shown @@ -132,10 +138,8 @@ spaceghost.then( function(){ this.historyoptions.collapseExpanded( function(){ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withHistoryPanel( function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); diff --git a/test/casperjs/history-panel-tests.js b/test/casperjs/history-panel-tests.js index 08d9c10a149..b9b22668315 100644 --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -40,7 +40,7 @@ if( spaceghost.fixtureData.testUser ){ // selectors and labels var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, editableTextClass = spaceghost.data.selectors.editableText, - editableTextInput = spaceghost.data.selectors.editableTextInput, + editableTextInput = spaceghost.historypanel.data.selectors.history.nameEditableTextInput, nameSelector = spaceghost.historypanel.data.selectors.history.name, subtitleSelector = spaceghost.historypanel.data.selectors.history.subtitle, @@ -56,8 +56,7 @@ var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, nameTooltip = spaceghost.historypanel.data.text.history.tooltips.name, refreshButtonSelector = 'a#history-refresh-button', - refreshButtonIconSelector = 'span.fa-icon-refresh', - refreshButtonHref = '/history', + refreshButtonIconSelector = 'span.fa-refresh', includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; @@ -74,11 +73,8 @@ var newHistoryName = "Test History", spaceghost.user.loginOrRegisterUser( email, password ); // ------------------------------------------------------------------- check structure of empty history -spaceghost.thenOpen( spaceghost.baseUrl ).historypanel.waitForHdas( function(){ +spaceghost.openHomePage().historypanel.waitForHdas( function(){ this.test.comment( 'history panel with a new, empty history should be well formed' ); - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); this.test.assertExists( nameSelector, nameSelector + ' exists' ); @@ -103,11 +99,11 @@ spaceghost.thenOpen( spaceghost.baseUrl ).historypanel.waitForHdas( function(){ }); // ------------------------------------------------------------------- name editing -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'history panel, editing the history name' ); this.test.comment( 'name should have a tooltip with proper info on name editing' ); - this.historypanel.hoverOver( nameSelector ); + this.hoverOver( nameSelector ); this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); // clear the tooltip @@ -116,6 +112,7 @@ spaceghost.withHistoryPanel( function(){ this.test.comment( 'name should be create an input when clicked' ); this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); this.click( nameSelector ); + spaceghost.debug( editableTextInput ); this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); this.test.comment( 'name should be editable by entering keys and pressing enter' ); @@ -129,7 +126,7 @@ spaceghost.withHistoryPanel( function(){ }); }); -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'name should revert if user clicks away while editing' ); this.click( nameSelector ); @@ -142,7 +139,7 @@ spaceghost.withHistoryPanel( function(){ }); }); -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'name should revert if user hits ESC while editing' ); this.click( nameSelector ); @@ -168,7 +165,7 @@ spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadI testUploadInfo = _uploadInfo; }); -spaceghost.withHistoryPanel( function checkPanelStructure(){ +spaceghost.then( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); @@ -176,9 +173,9 @@ spaceghost.withHistoryPanel( function checkPanelStructure(){ this.test.assertVisible( nameSelector, 'History name is visible' ); this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), expectedSubtitle = onetxtFilesize + ' bytes'; + this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, @@ -196,7 +193,7 @@ spaceghost.withHistoryPanel( function checkPanelStructure(){ // ------------------------------------------------------------------- tags // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.withHistoryPanel( function openTags(){ +spaceghost.then( function openTags(){ this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); this.click( tagIconSelector ); @@ -204,7 +201,7 @@ spaceghost.withHistoryPanel( function openTags(){ this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); }); }); -spaceghost.withHistoryPanel( function closeAnnotation(){ +spaceghost.then( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); this.click( tagIconSelector ); @@ -216,7 +213,7 @@ spaceghost.withHistoryPanel( function closeAnnotation(){ // ------------------------------------------------------------------- annotation // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.withHistoryPanel( function openAnnotation(){ +spaceghost.then( function openAnnotation(){ this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); this.click( annoIconSelector ); @@ -224,7 +221,7 @@ spaceghost.withHistoryPanel( function openAnnotation(){ this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); }); }); -spaceghost.withHistoryPanel( function closeAnnotation(){ +spaceghost.then( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); this.click( annoIconSelector ); @@ -240,12 +237,10 @@ spaceghost.then( function refreshButton(){ this.test.assertExists( refreshButtonSelector, "Found refresh button" ); this.test.assertVisible( refreshButtonSelector, "Refresh button is visible" ); this.test.assertVisible( refreshButtonSelector + ' ' + refreshButtonIconSelector, "Refresh icon is visible" ); - this.test.assert( this.getElementAttribute( refreshButtonSelector, 'href' ) === refreshButtonHref, - "Refresh button has href: " + refreshButtonHref ); - this.assertNavigationRequested( refreshButtonHref, "History refreshed when clicking refresh icon", function(){ - this.click( refreshButtonSelector ); - }); + //this.assertNavigationRequested( refreshButtonHref, "History refreshed when clicking refresh icon", function(){ + // this.click( refreshButtonSelector ); + //}); }); // ------------------------------------------------------------------- hdas can be expanded by clicking on the hda name @@ -275,7 +270,7 @@ spaceghost.then( function(){ }); // ------------------------------------------------------------------- expanded hdas collapse by clicking name again -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; diff --git a/test/casperjs/login-tests.js b/test/casperjs/login-tests.js index efb8d583218..7ac4f993535 100644 --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -1,5 +1,3 @@ -// have to handle errors here - or phantom/casper won't bail but _HANG_ -//TODO: global error handler? try { var utils = require( 'utils' ), xpath = require( 'casper' ).selectXPath, @@ -25,12 +23,6 @@ try { phantom.exit( 1 ); } -// =================================================================== -/* TODO: - move selectors and assertText strings into global object for easier editing - - -*/ // =================================================================== globals and helpers var email = spaceghost.user.getRandomEmail(), password = '123456'; @@ -39,22 +31,17 @@ if( spaceghost.fixtureData.testUser ){ password = spaceghost.fixtureData.testUser.password; } -var userEmailSelector = '//a[contains(text(),"Logged in as")]/span["id=#user-email"]'; +var userEmailSelector = '//a[contains(text(),"Logged in as")]'; // =================================================================== TESTS // register a user (again...) -spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.test.comment( 'registering: ' + email ); - spaceghost.user.registerUser( email, password ); -}); +spaceghost.openHomePage() + .user.registerUser( email, password ) + .user.logout(); -// log them out - check for empty logged in text -spaceghost.then( function(){ - this.test.comment( 'logging out: ' + email ); - spaceghost.user.logout(); -}); -spaceghost.then( function(){ - this.test.assertSelectorDoesntHaveText( xpath( userEmailSelector ), /\w/ ); +spaceghost.openHomePage( function(){ + this.test.comment( 'log out should be reflected in user menu' ); + this.test.assertDoesntExist( xpath( userEmailSelector ) ); this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); }); @@ -63,16 +50,13 @@ spaceghost.then( function(){ this.test.comment( 'logging back in: ' + email ); spaceghost.user._submitLogin( email, password ); //No such user }); -spaceghost.thenOpen( spaceghost.baseUrl, function(){ +spaceghost.openHomePage( function(){ this.test.assertSelectorHasText( xpath( userEmailSelector ), email ); this.test.assert( spaceghost.user.loggedInAs() === email, 'loggedInAs() matches email' ); }); // finally log back out for next tests -spaceghost.then( function(){ - this.test.comment( 'logging out: ' + email ); - spaceghost.user.logout(); -}); +spaceghost.user.logout(); // ------------------------------------------------------------------- shouldn't work // can't log in: users that don't exist, bad emails, sql injection (hurhur) @@ -118,10 +102,6 @@ spaceghost.then( function(){ }); }); }); - -spaceghost.then( function(){ - this.user.logout(); -}); /* */ // =================================================================== diff --git a/test/casperjs/modules/api.js b/test/casperjs/modules/api.js index 7741ea359ef..b30aeb29940 100644 --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -1,12 +1,4 @@ // =================================================================== module object, exports -/** Creates a new api module object. - * @param {SpaceGhost} spaceghost a spaceghost instance - * @exported - */ -exports.create = function createAPI( spaceghost, apikey ){ - return new API( spaceghost ); -}; - /** User object constructor. * @param {SpaceGhost} spaceghost a spaceghost instance * @param {String} apikey apikey for use when not using session authentication @@ -28,14 +20,21 @@ var API = function API( spaceghost, apikey ){ }; exports.API = API; +/** Creates a new api module object. + * @param {SpaceGhost} spaceghost a spaceghost instance + * @exported + */ +exports.create = function createAPI( spaceghost, apikey ){ + return new API( spaceghost ); +}; + + API.prototype.toString = function toString(){ return ( this.spaceghost + '.API:' + (( this.apikey )?( this.apikey ):( '(session)' )) ); }; // ------------------------------------------------------------------- APIError -APIError.prototype = new Error(); -APIError.prototype.constructor = Error; /** @class Thrown when Galaxy the API returns an error from a request */ function APIError( msg, status ){ Error.apply( this, arguments ); @@ -43,6 +42,8 @@ function APIError( msg, status ){ this.message = msg; this.status = status; } +APIError.prototype = new Error(); +APIError.prototype.constructor = Error; API.prototype.APIError = APIError; exports.APIError = APIError; diff --git a/test/casperjs/modules/historyoptions.js b/test/casperjs/modules/historyoptions.js index ac29f7a6557..9474b2c0747 100644 --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -34,8 +34,11 @@ var xpath = require( 'casper' ).selectXPath; * @returns {Any} the return value of fn */ HistoryOptions.prototype.openMenu = function openMenu( fn ){ + return this.spaceghost.jumpToTop( function(){ - this.click( this.historyoptions.data.selectors.button ); + if( !spaceghost.visible( this.historyoptions.data.selectors.menu ) ){ + this.click( this.historyoptions.data.selectors.button ); + } return fn.call( this ); }); }; @@ -170,41 +173,32 @@ HistoryOptions.prototype.collapseExpanded = function collapseExpanded( then ){ * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.includeDeleted = function includeDeleted( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, true ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeDeleted, true ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Deleted Datasets' to off * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.excludeDeleted = function excludeDeleted( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, false ); - //TODO:?? this puts in the history frame. Is that what we want? - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeDeleted, false ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Hidden Datasets' to on * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.includeHidden = function includeHidden( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, true ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeHidden, true ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Hidden Datasets' to off * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.excludeHidden = function excludeHidden( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, false ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeHidden, false ); + this.spaceghost.historypanel.waitForHdas( then ); }; @@ -213,14 +207,14 @@ HistoryOptions.prototype.excludeHidden = function excludeHidden( then ){ HistoryOptions.prototype.data = { selectors : { button : '#history-options-button', - buttonIcon : '#history-options-button span.fa-icon-cog', + buttonIcon : '#history-options-button span.fa-cog', menu : '#history-options-button-menu', optionXpathByLabelFn : function optionXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); }, optionIsOnXpathByLabelFn : function optionIsOnXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' - + '/span[@class="fa-icon-ok"]' ); + + '/span[@class="fa fa-check"]' ); } }, labels : { diff --git a/test/casperjs/modules/historypanel.js b/test/casperjs/modules/historypanel.js index 455d7afa0a0..bfa8c7ca737 100644 --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -33,64 +33,38 @@ var xpath = require( 'casper' ).selectXPath; // =================================================================== API (external) // ------------------------------------------------------------------- frame control -/** Is casper currently 'in' the history frame? - * @returns {Boolean} - */ -HistoryPanel.prototype.inFrame = function inFrame(){ - return ( ( this.spaceghost.page.frameName === this.spaceghost.data.selectors.frames.history ) - && ( this.spaceghost.page.frameTitle === this.data.text.frameTitle ) ); -}; - -/** Hover over an element in the history panel. - * @param {String} selector a css or xpath selector for an historyItemWrapper - */ -HistoryPanel.prototype.hoverOver = function hoverOver( selector ){ - var spaceghost = this.spaceghost, - historyFrameInfo = spaceghost.jumpToTop( function(){ - return spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); - }); - //spaceghost.debug( 'historyFrameInfo:\n' + spaceghost.jsonStr( historyFrameInfo ) ); - - spaceghost.jumpToHistory( function(){ - var elementInfo = spaceghost.getElementInfo( selector ), - newCoords = { x: ( historyFrameInfo.x + elementInfo.x ), - y: ( historyFrameInfo.y + elementInfo.y ) }; - spaceghost.page.sendEvent( 'mousemove', newCoords.x + 1, newCoords.y + 1 ); - }); - return spaceghost; -}; +///** Hover over an element in the history panel. +// * @param {String} selector a css or xpath selector for an historyItemWrapper +// */ +//HistoryPanel.prototype.hoverOver = function hoverOver( selector ){ +// var spaceghost = this.spaceghost, +// elementInfo = spaceghost.getElementInfo( selector ); +// spaceghost.page.sendEvent( 'mousemove', elementInfo.x + 1, elementInfo.y + 1 ); +// return spaceghost; +//}; // ------------------------------------------------------------------- hdas -/** Parse the hid and name from an HDA title. - * NOTE: if more than one is found, will return the first found. - * @param {String} title the title of the hda - * @returns {Object} of the form { hid: , name: } - */ -HistoryPanel.prototype.hdaHidAndNameFromTitle = function hdaHidAndNameFromTitle( title ){ - var sep = ': ', split = title.split( sep, 1 ); - return { - name : (( split.length >= 2 )?( split[1] ):( split[0] )), - hid : (( split.length >= 2 )?( parseInt( split[0], 10 ) ):( undefined )) - }; -}; +///** Parse the hid and name from an HDA title. +// * NOTE: if more than one is found, will return the first found. +// * @param {String} title the title of the hda +// * @returns {Object} of the form { hid: , name: } +// */ +//HistoryPanel.prototype.hdaHidAndNameFromTitle = function hdaHidAndNameFromTitle( title ){ +// var sep = ': ', split = title.split( sep, 1 ); +// return { +// name : (( split.length >= 2 )?( split[1] ):( split[0] )), +// hid : (( split.length >= 2 )?( parseInt( split[0], 10 ) ):( undefined )) +// }; +//}; -/** Find the casper element info of the hda wrapper given the hda title and hid. +/** Find the casper element info of the hda wrapper given the hda title. * NOTE: if more than one is found, will return the first found. * @param {String} title the title of the hda - * @param {Int} hid (optional) the hid of the hda to look for * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found */ -HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ - var spaceghost = this.spaceghost, - titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ); - //TODO: this would fail if we named/uploaded a file that has quotations - - // we can use underscore.un/escape to solve that - - return spaceghost.jumpToHistory( function getWrapperInfo(){ - var wrapperXpath = xpath( '//span[@class="historyItemTitle" ' + - 'and contains(text(),"' + titleContains + '")]/../..' ); - return spaceghost.elementInfoOrNull( wrapperXpath ); - }); +HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title ){ + var wrapperXpath = xpath( '//span[@class="dataset-name" and contains(text(),"' + title + '")]/../../..' ); + return this.spaceghost.elementInfoOrNull( wrapperXpath ); }; /** Get the state string of the given hda. @@ -99,12 +73,10 @@ HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( t * @returns {String|undefined} class string of the historyItemWrapper found, undefined if not found or set */ HistoryPanel.prototype.getHdaState = function getHdaState( hdaSelector ){ - return this.spaceghost.jumpToHistory( function(){ - var found = null, - hdaInfo = this.elementInfoOrNull( hdaSelector ); - if( !hdaInfo ){ return undefined; } - return (( found = hdaInfo.attributes[ 'class' ].match( /historyItem\-(\w+)/ ) )?( found[1] ):( undefined )); - }); + var found = null, + hdaInfo = this.spaceghost.elementInfoOrNull( hdaSelector ); + if( !hdaInfo ){ return undefined; } + return (( found = hdaInfo.attributes[ 'class' ].match( /state\-(\w+)/ ) )?( found[1] ):( undefined )); }; /** Get the encoded database/API id of the given hda. @@ -119,20 +91,20 @@ HistoryPanel.prototype.getHdaEncodedId = function getHdaEncodedId( hdaSelector ) }; // ------------------------------------------------------------------- step functions -/** Version of Casper#withFrame for the history iframe. - * Hopefully will allow easier test transition if/when frames are removed - * (i.e. -> just call the function). - * NOTE: is more than one Casper step. - * @param {Function} then function called when in the history frame - */ -HistoryPanel.prototype.then = function then( thenFn ){ - if( this.inFrame() ){ - thenFn.call( this.spaceghost ); - } else { - this.spaceghost.withHistoryPanel( thenFn ); - } -}; - +///** Version of Casper#withFrame for the history iframe. +// * Hopefully will allow easier test transition if/when frames are removed +// * (i.e. -> just call the function). +// * NOTE: is more than one Casper step. +// * @param {Function} then function called when in the history frame +// */ +//HistoryPanel.prototype.then = function then( thenFn ){ +// if( this.inFrame() ){ +// thenFn.call( this.spaceghost ); +// } else { +// this.spaceghost.withHistoryPanel( thenFn ); +// } +//}; +// /** Moves into history iframe and waits until hdas are visible or empty message is. * NOTE: is more than one Casper step. * @see Casper@waitFor @@ -140,13 +112,13 @@ HistoryPanel.prototype.then = function then( thenFn ){ HistoryPanel.prototype.waitForHdas = function waitForHdas( then, timeout, maxWait ){ //TODO:?? should this wait until the seletors are in AND they are opaque? var spaceghost = this.spaceghost; - this.then( function waitingForHdas(){ + spaceghost.then( function waitingForHdas(){ this.waitFor( function checkHpanel(){ - // trying a subtitle opacity test for page.isloaded var subtitleOpacity = this.evaluate( function( selector ){ return $( selector ).css( 'opacity' ); }, this.historypanel.data.selectors.history.subtitle ); + // wait until the subtitle is faded in and either the hdas or the empty history msg is displayed return ( subtitleOpacity !== 1 && ( ( this.visible( this.historypanel.data.selectors.hda.wrapper.itemClass ) ) ||( this.visible( this.historypanel.data.selectors.history.emptyMsg ) ) ) ); @@ -164,7 +136,7 @@ HistoryPanel.prototype.waitForHdas = function waitForHdas( then, timeout, maxWai */ HistoryPanel.prototype._thenExpandOrCollapseHda = function _thenExpandOrCollapseHda( hdaSelector, then, desiredClosed ){ // using a step here (instead of a jump) bc we need the wait for function - this.then( function checkingHda(){ + this.spaceghost.then( function checkingHda(){ this.info( (( desiredClosed )?( 'collapsing' ):( 'expanding' )) + ' hda: ' + hdaSelector ); // click to open if the body isn't visible and call wait to account for opening animation @@ -218,7 +190,7 @@ HistoryPanel.prototype.waitForHdaState = function waitForHdaState( hdaSelector, var hpanel = this, spaceghost = this.spaceghost; - this.then( function(){ + this.spaceghost.then( function(){ // get initial state, cache old timeout, set new timeout var prevState = hpanel.getHdaState( hdaSelector ), oldWaitTimeout = spaceghost.options.waitTimeout; @@ -269,7 +241,7 @@ HistoryPanel.prototype.waitForHdaState = function waitForHdaState( hdaSelector, * @param {Function} timeoutFn function to be called if/when the deleted attempted times out (optional) */ HistoryPanel.prototype.deleteHda = function deleteHda( hdaSelector, whenDeletedFn, timeoutFn ){ - this.then( function deletingHda(){ + this.spaceghost.then( function deletingHda(){ var hdaId = this.getElementInfo( hdaSelector ).attributes.id, deleteIconSelector = '#' + hdaId + ' ' + this.historypanel.data.hdaTitleButtons['delete'].selector; this.click( deleteIconSelector ); @@ -299,7 +271,7 @@ HistoryPanel.prototype.deleteHda = function deleteHda( hdaSelector, whenDeletedF */ HistoryPanel.prototype.undeleteHda = function undeleteHda( hdaSelector, whenUndeletedFn ){ this.spaceghost.historyoptions.includeDeleted( function(){ - this.click( hdaSelector + ' ' + this.historypanel.data.selectors.history.undeleteLink ); + this.click( hdaSelector + ' ' + this.historypanel.data.selectors.hda.undeleteLink ); this.historyoptions.excludeDeleted( function(){ this.info( 'hda undeleted: ' + hdaSelector ); if( utils.isFunction( whenUndeletedFn ) ){ whenUndeletedFn.call( this ); } @@ -314,39 +286,39 @@ HistoryPanel.prototype.data = { hdaTitleButtons : { // mixing text and selectors here display : { - selector : '.icon-button.display', + selector : '.icon-btn.dataset-display', tooltip : 'View data', hrefTpl : '/datasets/%s/display', nodeName : 'a' }, edit : { - selector : '.icon-button.edit', - tooltip : 'Edit Attributes', + selector : '.icon-btn.dataset-edit', + tooltip : 'Edit attributes', hrefTpl : '/datasets/%s/edit', nodeName : 'a' }, 'delete' : { - selector : '.icon-button.delete', + selector : '.icon-btn.dataset-delete', tooltip : 'Delete', - hrefTpl : '/datasets/%s/delete_async', + hrefTpl : 'javascript:void(0);', nodeName : 'a' } }, hdaPrimaryActionButtons : { download : { - selector : '.icon-button.disk', + selector : '.icon-btn.dataset-download-btn', tooltip : 'Download', hrefTpl : '/datasets/%s/display?to_ext=', nodeName : 'a' }, info : { - selector : '.icon-button.information', + selector : '.icon-btn.dataset-params-btn', tooltip : 'View details', hrefTpl : '/datasets/%s/show_params', nodeName : 'a' }, rerun : { - selector : '.icon-button.arrow-circle', + selector : '.icon-btn.dataset-rerun-btn', tooltip : 'Run this job again', hrefTpl : '/tool_runner/rerun?id=%s', nodeName : 'a' @@ -356,39 +328,42 @@ HistoryPanel.prototype.data = { }, selectors : { history : { - name : 'div#history-name', - subtitle : 'div#history-subtitle-area', - tagIcon : '#history-tag.icon-button', - tagArea : '#history-tag-area', - annoIcon : '#history-annotate.icon-button', - annoArea : '#history-annotation-area', - // weak - emptyMsg : '.infomessagesmall', - undeleteLink : '.historyItemUndelete', - hdaContainer : '.history-datasets-list' + title : '.history-title', + name : '.history-title .history-name', + nameEditableTextInput : '.history-name input', + subtitle : '.history-subtitle', + tagIcon : '.history-secondary-actions .history-tag-btn', + tagArea : '.history-controls .tags-display', + annoIcon : '.history-secondary-actions .history-annotate-btn', + annoArea : '.history-controls .annotation-display', + emptyMsg : '.empty-history-message', + hdaContainer: '.datasets-list' }, hda : { wrapper : { - itemClass : '.historyItem', + itemClass : '.hda', stateClasses : { - prefix : 'historyItem-', - ok : 'historyItem-ok', - 'new' : 'historyItem-new' + prefix : 'state-', + ok : 'state-ok', + 'new' : 'state-new' } }, errorMessage : '.errormessagesmall', - title : '.historyItemTitle', - titleButtonArea : '.historyItemButtons', - body : '.historyItemBody', - summary : '.hda-summary', - dbkey : '.metadata-dbkey', - info : '.hda-info', + title : '.dataset-title', + titleButtonArea : '.dataset-primary-actions', + summary : '.dataset-summary', + dbkey : '.dataset-dbkey .value', + info : '.dataset-info', + body : '.dataset-body', - primaryActionButtons : 'div[id^="primary-actions"]', - secondaryActionButtons : 'div[id^="secondary-actions"]', + primaryActionButtons : '.dataset-actions .left', + secondaryActionButtons : '.dataset-actions .right', - peek : 'pre.peek' + undeleteLink : '.dataset-undelete', + purgeLink : '.dataset-purge', + + peek : '.dataset-peek' } }, labels : { @@ -399,7 +374,7 @@ HistoryPanel.prototype.data = { }, text : { windowTitle : 'History', - frameTitle : 'Galaxy History', + //frameTitle : 'Galaxy History', anonymous : { tooltips : { name : 'You must be logged in to edit your history name' diff --git a/test/casperjs/modules/tools.js b/test/casperjs/modules/tools.js index d2c56ed9703..85d2f84e848 100644 --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -86,10 +86,10 @@ Tools.prototype._uploadFile = function _uploadFile( filepath ){ uploadInfo = {}; uploadInfo[ spaceghost.data.selectors.tools.upload.fileInput ] = filepath; - // click the upload tool - spaceghost.thenOpen( spaceghost.baseUrl, function(){ - // we can apprently click a tool label without expanding the tool container for it - this.clickLabel( spaceghost.data.labels.tools.upload.panelLabel ); + spaceghost.openHomePage( function(){ + // load the upload tool form + // (we can apprently click a tool label without expanding the tool container for it) + this.click( xpath( '//a[contains(text(),"Upload File")]' ) ); this.jumpToMain( function(){ this.waitForSelector( 'body' ); }); @@ -108,7 +108,7 @@ Tools.prototype._uploadFile = function _uploadFile( filepath ){ // wait for main panel, history reload ////NOTE!: assumes tool execution reloads the history panel - this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message', 'history' ], + this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message' ], function thenAfterUploadRefreshes(){ // debugging this.jumpToMain( function(){ diff --git a/test/casperjs/modules/user.js b/test/casperjs/modules/user.js index 2d7e0a434e1..dff2915e8f1 100644 --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -43,11 +43,11 @@ User.prototype._submitRegistration = function _submitRegistration( email, passwo confirm : ( confirm !== undefined )?( confirm ):( password ) }; - spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.waitForMasthead( function() { - this.clickLabel( spaceghost.data.labels.masthead.menus.user ); - this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); + spaceghost.openHomePage( function(){ + this.clickLabel( spaceghost.data.labels.masthead.menus.user ); + this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); + this.waitForNavigation( 'user/create', function beforeRegister(){ this.withMainPanel( function mainBeforeRegister(){ spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') registering user:\n' + spaceghost.jsonStr( userInfo ) ); @@ -56,11 +56,13 @@ User.prototype._submitRegistration = function _submitRegistration( email, passwo this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); }); }); - //// debugging - //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterRegister(){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); - //}); + + this.waitForNavigation( 'user/create', function afterRegister(){ + // this.withMainPanel( function mainAfterRegister(){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); + // }); + }); }); }; @@ -79,25 +81,23 @@ User.prototype._submitLogin = function _submitLogin( email, password ){ password: password }; - spaceghost.thenOpen( spaceghost.baseUrl, function(){ - spaceghost.waitForMasthead( function() { - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); + spaceghost.openHomePage( function(){ + this.clickLabel( spaceghost.data.labels.masthead.menus.user ); + this.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); - spaceghost.withMainPanel( function mainBeforeLogin(){ + this.waitForNavigation( 'user/login', function beforeLogin(){ + this.withMainPanel( function mainBeforeLogin(){ spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' + spaceghost.jsonStr( loginInfo ) ); spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); }); + }); - //// debugging - //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ - // //TODO: prob. could use a more generalized form of this for url breakdown/checking - // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); - // } + this.waitForNavigation( 'user/login', function afterLogin(){ + //this.withMainPanel( function mainAfterLogin(){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); //}); }); }); @@ -123,6 +123,9 @@ User.prototype.registerUser = function registerUser( email, password, username ) this.warning( 'Registration failed: ' + messageInfo.text ); throw new spaceghost.GalaxyError( 'RegistrationError: ' + messageInfo.text ); } + + this.clickLabel( 'Return to the home page.' ); + this.waitForNavigation( '' ); }); return spaceghost; }; @@ -136,19 +139,21 @@ User.prototype.login = function login( email, password ){ var spaceghost = this.spaceghost; this._submitLogin( email, password ); - spaceghost.waitForMasthead( function() { - spaceghost.withMainPanel( function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ - var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ - this.warning( 'Login failed: ' + messageInfo.text ); - throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); - } - } - if( spaceghost.user.loggedInAs() === email ){ - spaceghost.info( 'logged in as ' + email ); - } - }); + //spaceghost.withMainPanel( function mainAfterLogin(){ + // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ + // this.warning( 'Login failed: ' + messageInfo.text ); + // throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); + // } + // } + //}); + this.spaceghost.then( function checkLogin(){ + if( spaceghost.user.loggedInAs() !== email ){ + throw new spaceghost.GalaxyError( 'LoginError' ); + } else { + spaceghost.info( 'logged in as ' + email ); + } }); return spaceghost; }; @@ -157,17 +162,19 @@ User.prototype.login = function login( email, password ){ * @returns {String} email of currently logged in user or '' if no one logged in */ User.prototype.loggedInAs = function loggedInAs(){ - var spaceghost = this.spaceghost, - userEmail = ''; - try { - var loggedInInfo = spaceghost.getElementInfo( - xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ) ); - userEmail = loggedInInfo.text; - } catch( err ){ - spaceghost.error( err ); - } - //console.debug( 'loggedInInfo:', spaceghost.jsonStr( loggedInInfo ) ); - return userEmail; + return this.spaceghost.jumpToTop( function(){ + var userEmail = ''; + try { + var emailSelector = xpath( this.data.selectors.masthead.userMenu.userEmail_xpath ), + loggedInInfo = this.elementInfoOrNull( emailSelector ); + if( loggedInInfo !== null ){ + userEmail = loggedInInfo.text.replace( 'Logged in as ', '' ); + } + } catch( err ){ + this.warn( err ); + } + return userEmail; + }); }; /** Log out the current user @@ -175,13 +182,15 @@ User.prototype.loggedInAs = function loggedInAs(){ */ User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; - spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.info( 'user logging out' ); - //TODO: handle already logged out - spaceghost.waitForMasthead( function _logout() { + this.spaceghost.openHomePage( function(){ + if( spaceghost.user.loggedInAs() ){ spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); - }); + spaceghost.waitForNavigation( 'user/logout', function _toLogoutPage() { + spaceghost.clickLabel( 'go to the home page' ); + spaceghost.waitForNavigation( '' ); + }); + } }); return spaceghost; }; @@ -196,10 +205,10 @@ User.prototype.loginOrRegisterUser = function loginOrRegisterUser( email, passwo var spaceghost = this.spaceghost; // attempt a login, if that fails - register spaceghost.tryStepsCatch( function tryToLogin(){ - spaceghost.open( spaceghost.baseUrl ).user.login( email, password ); + spaceghost.openHomePage().user.login( email, password ); }, function failedLoginRegister(){ - spaceghost.open( spaceghost.baseUrl ).user.registerUser( email, password, username ); + spaceghost.openHomePage().user.registerUser( email, password, username ); }); return spaceghost; }; @@ -214,7 +223,8 @@ User.prototype.getAdminData = function getAdminData(){ // check for the setting in sg and the universe_wsgi.ini file var adminData = this.spaceghost.options.adminUser, iniAdminEmails = this.spaceghost.getUniverseSetting( 'admin_users' ); - iniAdminEmails = ( iniAdminEmails )?( iniAdminEmails.split( ',' ).map( function( email ) { return email.trim(); } ) ):( null ); + iniAdminEmails = ( iniAdminEmails )? + ( iniAdminEmails.split( ',' ).map( function( email ) { return email.trim(); } ) ):( null ); //TODO: seems like we only need the wsgi setting - that's the only thing we can't change if( adminData ){ diff --git a/test/casperjs/registration-tests.js b/test/casperjs/registration-tests.js index b5b35dd12bb..457f9f5f423 100644 --- a/test/casperjs/registration-tests.js +++ b/test/casperjs/registration-tests.js @@ -1,4 +1,3 @@ -// have to handle errors here - or phantom/casper won't bail but _HANG_ try { var utils = require( 'utils' ), xpath = require( 'casper' ).selectXPath, @@ -24,13 +23,6 @@ try { phantom.exit( 1 ); } -// =================================================================== -/* TODO: - move selectors and assertText strings into global object for easier editing - pass email, etc. for first (successful) registration (for use with other tests) - - -*/ // =================================================================== globals and helpers var email = spaceghost.user.getRandomEmail(), password = '123456', @@ -38,48 +30,27 @@ var email = spaceghost.user.getRandomEmail(), username = 'test' + Date.now(); // =================================================================== TESTS -spaceghost.thenOpen( spaceghost.baseUrl, function(){ +spaceghost.openHomePage( function(){ this.test.comment( 'loading galaxy homepage' ); - // can we load galaxy? this.test.assertTitle( 'Galaxy' ); - // xpath selector use: this.test.assertExists( xpath( "//div[@id='masthead']" ), 'found masthead' ); }); -// failing tests for...testing...the tests -//spaceghost.thenOpen( spaceghost.baseUrl, function(){ -// this.test.comment( 'loading galaxy homepage' ); -// // can we load galaxy? -// this.test.assertTitle( 'Blorgo' ); -// // xpath selector use: -// this.test.assertExists( xpath( "//div[@id='facebook']" ), 'found facebook' ); -//}); - - // ------------------------------------------------------------------- register a new user spaceghost.then( function(){ this.test.comment( 'registering user: ' + email ); this.user._submitRegistration( email, password, username, confirm ); }); -spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.waitForMasthead( function() { - this.clickLabel( 'User' ); - this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); - }); +spaceghost.openHomePage( function(){ + this.clickLabel( 'User' ); + var loggedInAs = this.fetchText( xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ) ); + this.test.assert( loggedInAs.indexOf( email ) !== -1, 'found proper email in user menu: ' + loggedInAs ); }); // ------------------------------------------------------------------- log out that user -spaceghost.then( function(){ - this.waitForMasthead( function() { - this.test.comment( 'logging out user: ' + email ); - this.user.logout(); - }); -}); -spaceghost.then( function(){ - this.waitForMasthead( function() { - this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); - this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); - }); +spaceghost.user.logout().openHomePage( function(){ + var emailSelector = xpath( this.data.selectors.masthead.userMenu.userEmail_xpath ); + this.test.assert( !this.elementInfoOrNull( emailSelector ), 'user email not found' ); }); // ------------------------------------------------------------------- bad user registrations @@ -99,7 +70,7 @@ spaceghost.each( badEmails, function( self, badEmail ){ this.user._submitRegistration( badEmail, password, username, confirm ); }); self.then(function(){ - this.assertErrorMessage( 'Enter a real email address' ); + this.assertErrorMessage( 'Please enter your valid email address' ); }); }); @@ -108,10 +79,10 @@ var badPasswords = [ '1234' ]; spaceghost.each( badPasswords, function( self, badPassword ){ self.then( function(){ this.test.comment( 'attempting bad password: ' + badPassword ); - this.user._submitRegistration( spaceghost.user.getRandomEmail(), badPassword, username, confirm ); + this.user._submitRegistration( spaceghost.user.getRandomEmail(), badPassword, username, badPassword ); }); self.then(function(){ - this.assertErrorMessage( 'Use a password of at least 6 characters' ); + this.assertErrorMessage( 'Please use a password of at least 6 characters' ); }); }); @@ -123,7 +94,7 @@ spaceghost.each( badConfirms, function( self, badConfirm ){ this.user._submitRegistration( spaceghost.user.getRandomEmail(), password, username, badConfirm ); }); self.then(function(){ - this.assertErrorMessage( 'Passwords do not match' ); + this.assertErrorMessage( 'Passwords don\'t match' ); }); }); @@ -149,7 +120,7 @@ spaceghost.each( badUsernames, function( self, badUsername ){ this.user._submitRegistration( newEmail, password, badUsername, confirm ); }); self.then(function(){ - this.assertErrorMessage( "Public name must contain only lower-case letters, numbers and '-'" ); + this.assertErrorMessage( 'Public name must contain only lowercase letters, numbers and "-"' ); }); }); @@ -163,7 +134,6 @@ spaceghost.then(function(){ this.assertErrorMessage( 'Public name is taken; please choose another' ); }); - // ------------------------------------------------------------------- test the convenience fns // these versions are for conv. use in other tests, they should throw errors if used improperly spaceghost.then( function(){ @@ -175,11 +145,6 @@ spaceghost.then( function(){ }); }); -spaceghost.then( function(){ - //??: necessary? - this.user.logout(); -}); - // =================================================================== spaceghost.run( function(){ this.test.done(); diff --git a/test/casperjs/spaceghost.js b/test/casperjs/spaceghost.js index a478723f41f..03730ba212b 100644 --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -507,6 +507,38 @@ SpaceGhost.prototype.run = function run( onComplete, time ){ Casper.prototype.run.call( this, new_onComplete, time ); }; +// ------------------------------------------------------------------- home page +/** Wait for the homepage/index/Analyze Data to load fully. + */ +SpaceGhost.prototype.openHomePage = function openHomePage( then, delay ){ +//TODO: delay doesn't seem to work + this.thenOpen( this.baseUrl, function _openHomePage(){ + this.waitFor( + function waitForCheck(){ + return this.homePageIsLoaded(); + }, + then, + function openHomePageTimeout(){ + throw new GalaxyError( 'Homepage timed out' ); + }, + delay + ); + }); + return this; +}; + +/** Check for visibility of main home page elements: masthead, tool menu, history panel. + */ +SpaceGhost.prototype.homePageIsLoaded = function homePageIsLoaded(){ + //this.debug( 'homePageIsLoaded: ' + [ + // this.visible( '#masthead' ), + // this.visible( this.data.selectors.toolMenu.container ), + // this.visible( '#current-history-panel' )].join( ', ' ) ); + return ( this.visible( '#masthead' ) + && this.visible( this.data.selectors.toolMenu.container ) + && this.visible( '#current-history-panel' ) ); +}; + // ------------------------------------------------------------------- try step /** Install a function as an error handler temporarily, run a function with steps, then remove the handler. * A rough stand-in for try catch with steps. @@ -549,6 +581,7 @@ SpaceGhost.prototype.tryStepsCatch = function tryStepsCatch( stepsFn, catchFn ){ }); }; + // ------------------------------------------------------------------- misc /** Hover over an element. * NOTE: not for use with iframes (main, tool, history) - they need to re-calc @@ -559,7 +592,7 @@ SpaceGhost.prototype.tryStepsCatch = function tryStepsCatch( stepsFn, catchFn ){ SpaceGhost.prototype.hoverOver = function hoverOver( selector, whenHovering ){ var elementInfo = this.getElementInfo( selector ); this.page.sendEvent( 'mousemove', elementInfo.x + 1, elementInfo.y + 1 ); - whenHovering.call( this ); + if( whenHovering ){ whenHovering.call( this ); } return this; }; @@ -626,15 +659,6 @@ SpaceGhost.prototype.waitForMultipleNavigation = function waitForMultipleNavigat // ------------------------------------------------------------------- iframes, damnable iframes -/** Version of Casper#withFrame for the history iframe. - * Hopefully will allow easier test transition if/when frames are removed - * (i.e. -> just call the function). - * @param {Function} then function called when in the history frame - */ -SpaceGhost.prototype.withHistoryPanel = function withHistoryPanel( then ){ - return this.withFrame( this.data.selectors.frames.history, then ); -}; - /** Version of Casper#withFrame for the main iframe. * @param {Function} then function called when in the frame */ @@ -671,15 +695,6 @@ SpaceGhost.prototype.jumpToFrame = function jumpToFrame( frame, fn ){ return returned; }; -/** Jumps into history frame, exectutes fn, and jumps back to original frame. - * @param {Selector} frame the selector for the frame to jump to - * @param {Function} fn function called when in the frame - * @returns {Any} the return value of fn - */ -SpaceGhost.prototype.jumpToHistory = function jumpToHistory( fn ){ - return this.jumpToFrame( this.data.selectors.frames.history, fn ); -}; - /** Jumps into main frame, exectutes fn, and jumps back to original frame. * @param {Selector} frame the selector for the frame to jump to * @param {Function} fn function called when in the frame @@ -793,7 +808,7 @@ SpaceGhost.prototype.assertVisibleWithText = function assertVisibleWithText( sel * @param {CasperJS selector} messageSelector what element in which to search for the text * (defaults to '.errormessage') */ -SpaceGhost.prototype.assertErrorMessage = function assertSelectorAndTextInFrame( message, frame, messageSelector ){ +SpaceGhost.prototype.assertErrorMessage = function assertErrorMessage( message, frame, messageSelector ){ messageSelector = messageSelector || this.data.selectors.messages.error; frame = frame || this.data.selectors.frames.main; this.assertSelectorAndTextInFrame( messageSelector, message, frame ); @@ -871,6 +886,7 @@ SpaceGhost.prototype.assertDoesntHaveClass = function assertDoesntHaveClass( sel this.test.assert( classes.indexOf( className ) === -1, msg ); }; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. * @param {String} selector css or xpath selector for the element to find @@ -1105,7 +1121,7 @@ SpaceGhost.prototype.getUniverseSetting = function getUniverseSetting( iniKey ){ SpaceGhost.prototype.waitForMasthead = function wait( then ) { return this.waitForText( this.data.labels.masthead.menus.user, then ); -} +}; // =================================================================== TEST DATA @@ -1116,7 +1132,6 @@ SpaceGhost.prototype.data = { tooltipBalloon : '.tooltip', editableText : '.editable-text', - editableTextInput : 'input#renaming-active', messages : { all : '[class*="message"]', @@ -1128,17 +1143,23 @@ SpaceGhost.prototype.data = { }, frames : { - main : 'galaxy_main', - history : 'galaxy_history' + main : 'galaxy_main' }, masthead : { - adminLink : '#masthead a[href="/admin/index"]', - userMenu : { - userEmail : 'a #user-email', - userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' + id : '#masthead', + adminLink : '#masthead a[href="/admin/index"]', + userMenu : { + userEmail_xpath : '//a[contains(text(),"Logged in as")]' } }, + toolMenu : { + container : '.toolMenuContainer' + }, + historyPanel : { + current : '#current-history-panel' + }, + loginPage : { form : 'form#login', submit_xpath : "//input[@value='Login']", @@ -1146,7 +1167,8 @@ SpaceGhost.prototype.data = { }, registrationPage : { form : 'form#registration', - submit_xpath : "//input[@value='Submit']" + submit_xpath : "//input[@value='Submit']", + returnLink : '//a[contains(text(),"Return to the home page")]' }, tools : { general : { diff --git a/test/casperjs/upload-tests.js b/test/casperjs/upload-tests.js index bd638eb2a92..12b2ace50a4 100644 --- a/test/casperjs/upload-tests.js +++ b/test/casperjs/upload-tests.js @@ -43,23 +43,18 @@ var testUploadInfo = {}; // =================================================================== TESTS // ------------------------------------------------------------------- start a new user -spaceghost.user.loginOrRegisterUser( email, password ); -//??: why is a reload needed here? If we don't, loggedInAs === '' ... -spaceghost.thenOpen( spaceghost.baseUrl, function(){ +spaceghost.user.loginOrRegisterUser( email, password ).openHomePage( function(){ var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); - // ------------------------------------------------------------------- long form - // upload a file... spaceghost.then( function(){ this.test.comment( 'Test uploading a file' ); var filename = '1.txt', filepath = this.options.scriptDir + '/../../test-data/' + filename; - this.tools._uploadFile( filepath ); // when an upload begins successfully main should reload with a infomessagelarge @@ -83,6 +78,7 @@ spaceghost.historypanel.waitForHdas( function(){ this.test.fail( 'Could not locate new hda: ' + testUploadInfo.name ); } else { + spaceghost.debugElement( spaceghost.jsonStr( hdaInfo ) ); this.historypanel.waitForHdaState( '#' + hdaInfo.attributes.id, 'ok', function whenInStateFn( newHdaInfo ){ //this.debug( 'newHdaInfo:\n' + this.jsonStr( newHdaInfo ) ); diff --git a/test/functional/test_history_functions.py b/test/functional/test_history_functions.py index b48495152f0..cf38b5fa5a4 100644 --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -82,6 +82,7 @@ class TestHistory( TwillTestCase ): .first() assert historyB is not None, "Problem retrieving historyB from database" assert historyA.id == historyB.id, "After the same user logged out and back in, their last used history was not associated with their new session" + def test_005_deleting_histories( self ): """Testing deleting histories""" # Logged in as admin_user @@ -144,6 +145,7 @@ class TestHistory( TwillTestCase ): raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history2.id # Current history is empty self.history_options( user=True ) + def test_010_history_rename( self ): """Testing renaming a history""" # Logged in as admin_user @@ -157,10 +159,12 @@ class TestHistory( TwillTestCase ): raise AssertionError, "History id %d deleted when it should not be" % latest_history.id self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) ) sa_session.refresh( history3 ) + def test_015_history_list( self ): """Testing viewing previously stored active histories""" # Logged in as admin_user self.view_stored_active_histories() + def test_020_share_current_history( self ): """Testing sharing the current history which contains only public datasets""" # Logged in as admin_user @@ -210,10 +214,13 @@ class TestHistory( TwillTestCase ): # Test sharing history3 with an invalid user self.share_current_history( 'jack@jill.com', strings_displayed_after_submit=[ 'jack@jill.com is not a valid Galaxy user.' ] ) + def test_025_delete_shared_current_history( self ): """Testing deleting the current history after it was shared""" # Logged in as admin_user - self.delete_current_history( strings_displayed=[ "History (%s) has been shared with others, unshare it before deleting it." % history3.name ] ) + self.delete_current_history( + strings_displayed=[ "History (%s) has been shared with others, unshare it before deleting it." % history3.name ] ) + def test_030_clone_shared_history( self ): """Testing copying a shared history""" # logged in as admin user @@ -656,7 +663,7 @@ class TestHistory( TwillTestCase ): if hda[ 'id' ] == self.security.encode_id( hda_2_bed.id ): return ( not hda[ 'accessible' ] ) return False - self.check_history_json( r'\bhdaJson\s*=\s*(.*);', hda_2_bed_is_inaccessible ) + self.check_history_json( r'\bhdaJSON\s*=\s*(.*);', hda_2_bed_is_inaccessible ) # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin self.logout() @@ -734,7 +741,7 @@ class TestHistory( TwillTestCase ): log.info( 'deleting last hda' ) self.delete_history_item( str( latest_hda.id ) ) # check the historyPanel settings.show_deleted for a null json value (no show_deleted in query string) - self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == None ) + self.check_history_json( r'\bshow_deleted\s*:\s*(.*),', lambda x: x == None ) # reload this history with the show_deleted flag set in the query string # the deleted dataset should be there with the proper 'deleted' text @@ -742,7 +749,7 @@ class TestHistory( TwillTestCase ): log.info( 'turning show_deleted on' ) #self.visit_url( "%s/history/?show_deleted=True" % self.url ) # check the historyPanel settings.show_deleted for a true json value - self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == True, show_deleted=True ) + self.check_history_json( r'\bshow_deleted\s*:\s*(.*),', lambda x: x == True, show_deleted=True ) # reload this history again with the show_deleted flag set TO FALSE in the query string # make sure the 'history empty' message shows @@ -750,7 +757,7 @@ class TestHistory( TwillTestCase ): log.info( 'turning show_deleted off' ) #self.visit_url( "%s/history/?show_deleted=False" % self.url ) # check the historyPanel settings.show_deleted for a false json value - self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == False, show_deleted=False ) + self.check_history_json( r'\bshow_deleted\s*:\s*(.*),', lambda x: x == False, show_deleted=False ) # delete this history self.delete_history( self.security.encode_id( latest_history.id ) ) diff --git a/test/install_and_test_tool_shed_repositories/base/util.py b/test/install_and_test_tool_shed_repositories/base/util.py index cb023004f24..3f2128a62e0 100644 --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -3,10 +3,9 @@ import sys cwd = os.getcwd() sys.path.append( cwd ) -new_path = [ os.path.join( cwd, "scripts" ), - os.path.join( cwd, "lib" ), +new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ), - os.path.join( cwd, 'scripts', 'api' ) ] + os.path.join( cwd, 'lib', 'tool_shed', 'scripts', 'api' ) ] new_path.extend( sys.path ) sys.path = new_path @@ -27,6 +26,10 @@ import urllib from datetime import datetime from datetime import timedelta +from common import get_api_url +from common import get_latest_downloadable_changeset_revision_via_api +from common import get_repository_dict +from common import json_from_url from common import update from galaxy.util import asbool @@ -267,18 +270,6 @@ def display_tool_dependencies_by_name( tool_dependency_dicts ): version = str( tool_dependency_dict[ 'version' ] ) print "# %s %s version %s" % ( type, name, version ) -def get_api_url( base, parts=[], params=None ): - if 'api' in parts and parts.index( 'api' ) != 0: - parts.pop( parts.index( 'api' ) ) - parts.insert( 0, 'api' ) - elif 'api' not in parts: - parts.insert( 0, 'api' ) - url = suc.url_join( base, *parts ) - if params is not None: - query_string = urllib.urlencode( params ) - url += '?%s' % query_string - return url - def get_database_version( app ): ''' This method returns the value of the version column from the migrate_version table, using the provided app's SQLAlchemy session to determine @@ -296,19 +287,6 @@ def get_database_version( app ): break return version -def get_latest_downloadable_changeset_revision( url, name, owner ): - error_message = '' - parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = dict( name=name, owner=owner ) - api_url = get_api_url( base=url, parts=parts, params=params ) - changeset_revisions, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - if changeset_revisions: - return changeset_revisions[ -1 ], error_message - else: - return suc.INITIAL_CHANGELOG_HASH, error_message - def get_missing_repository_dependencies( repository ): """ Return the entire list of missing repository dependencies for the received repository. The entire @@ -467,21 +445,6 @@ def get_repository_dependencies_for_changeset_revision( tool_shed_url, encoded_r return None, error_message return repository_dependency_dicts, error_message -def get_repository_dict( url, repository_dict ): - error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) - extended_dict, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - name = str( extended_dict[ 'name' ] ) - owner = str( extended_dict[ 'owner' ] ) - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) - if error_message: - return None, error_message - extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) - return extended_dict, error_message - def get_repository_dependencies_dicts( url, encoded_repository_metadata_id ): """ Return a list if dictionaries that define the repository dependencies of the repository defined by the @@ -702,23 +665,23 @@ def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_re return False, None def is_latest_downloadable_revision( url, repository_dict ): - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - latest_revision = get_latest_downloadable_changeset_revision( url, name=name, owner=owner ) - return changeset_revision == str( latest_revision ) - -def json_from_url( url ): + """ + Return True if the changeset_revision defined in the received repository_dict is the latest + installable revision for the repository. + """ error_message = '' - url_handle = urllib.urlopen( url ) - url_contents = url_handle.read() - try: - parsed_json = from_json_string( url_contents ) - except Exception, e: - error_message = str( url_contents ) - log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) - return None, error_message - return parsed_json, error_message + name = repository_dict.get( 'name', None ) + owner = repository_dict.get( 'owner', None ) + changeset_revision = repository_dict.get( 'changeset_revision', None ) + if name is not None and owner is not None and changeset_revision is not None: + name = str( name ) + owner = str( owner ) + changeset_revision = str( changeset_revision ) + latest_revision, error_message = get_latest_downloadable_changeset_revision_via_api( url, name=name, owner=owner ) + if latest_revision is None or error_message: + return None, error_message + is_latest_downloadable = changeset_revision == str( latest_revision ) + return is_latest_downloadable, error_message def parse_exclude_list( xml_filename ): """Return a list of repositories to exclude from testing.""" @@ -882,9 +845,19 @@ def populate_install_containers_for_repository_dependencies( app, repository, re log.debug( 'due to the following error getting repository_dependencies_dicts:\n%s' % str( error_message ) ) else: for repository_dependencies_dict in repository_dependencies_dicts: - name = str( repository_dependencies_dict[ 'name' ] ) - owner = str( repository_dependencies_dict[ 'owner' ] ) - changeset_revision = str( repository_dependencies_dict[ 'changeset_revision' ] ) + if not isinstance( repository_dependencies_dict, dict ): + log.debug( 'Skipping invalid repository_dependencies_dict: %s' % str( repository_dependencies_dict ) ) + continue + name = repository_dependencies_dict.get( 'name', None ) + owner = repository_dependencies_dict.get( 'owner', None ) + changeset_revision = repository_dependencies_dict.get( 'changeset_revision', None ) + if name is None or owner is None or changeset_revision is None: + log.debug( 'Skipping invalid repository_dependencies_dict due to missing name,owner or changeset_revision: %s' % \ + str( repository_dependencies_dict ) ) + continue + name = str( name ) + owner = str( owner ) + changeset_revision = str( changeset_revision ) log.debug( 'Checking installation containers for revision %s of repository dependency %s owned by %s' % \ ( changeset_revision, name, owner ) ) required_repository_metadata_id = repository_dependencies_dict[ 'id' ] @@ -898,22 +871,23 @@ def populate_install_containers_for_repository_dependencies( app, repository, re log.debug( 'due to the following error getting tool_test_results:\n%s' % str( error_message ) ) else: # Check the required repository's time_last_tested value to see if its tool_test_results column - # has been updated within the past 12 hours. - twelve_hours_ago = datetime.utcnow() - timedelta( hours=12 ) + # has been updated within the past 12 hours. The RepositoryMetadata class's to_dict() method + # returns the value of time_last_tested in datetime.isoformat(). + twenty_hours_ago = ( datetime.utcnow() - timedelta( hours=20 ) ).isoformat() time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, repository_metadata_id ) - if time_last_tested is not None and time_last_tested < twelve_hours_ago: + if time_last_tested is not None and time_last_tested < twenty_hours_ago: log.debug( 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ ( changeset_revision, name, owner ) ) - log.debug( 'populated within the past 12 hours (likely in this test run), so skipping this check.' ) + log.debug( 'populated within the past 20 hours (likely in this test run), so skipping this check.' ) continue - if time_last_tested is None: + elif time_last_tested is None: log.debug( 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ ( changeset_revision, name, owner ) ) - elif time_last_tested < twelve_hours_ago: - log.debug( 'Version %s of repository dependency %s owned by %s was last tested less than 12 hours ago.' % \ + elif time_last_tested < twenty_hours_ago: + log.debug( 'Version %s of repository dependency %s owned by %s was last tested less than 20 hours ago.' % \ ( changeset_revision, name, owner ) ) else: - log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 12 hours ago.' % \ + log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 20 hours ago.' % \ ( changeset_revision, name, owner ) ) # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: @@ -975,8 +949,8 @@ def populate_install_containers_for_repository_dependencies( app, repository, re else: log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) ) - log.debug( 'so tool_test_results cannot be saved.' ) - log.debug( 'The attributes used to retrieve the record are:\n' ) + log.debug( 'so tool_test_results cannot be saved at this time.' ) + log.debug( 'The attributes used to retrieve the record are:' ) log.debug( 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \ ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) @@ -1006,9 +980,15 @@ def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool if can_update_tool_shed: metadata_revision_id = repository_dict.get( 'id', None ) if metadata_revision_id is not None: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + name = repository_dict.get( 'name', None ) + owner = repository_dict.get( 'owner', None ) + changeset_revision = repository_dict.get( 'changeset_revision', None ) + if name is None or owner is None or changeset_revision is None: + log.debug( 'Entries for name, owner or changeset_revision missing from repository_dict %s' % str( repository_dict ) ) + return {} + name = str( name ) + owner = str( owner ) + changeset_revision = str( changeset_revision ) log.debug('\n=============================================================\n' ) log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) diff --git a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py index f864cb4f94d..b3bcef719c5 100644 --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -685,9 +685,16 @@ def test_repository_tools( app, repository, repository_dict, tool_test_results_d tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - set_do_not_test = \ - not install_and_test_base_util.is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, - repository_dict ) + is_latest_downloadable_revision, error_message = \ + install_and_test_base_util.is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, + repository_dict ) + if is_latest_downloadable_revision is None or error_message: + log.debug( 'Error attempting to determine if revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'is the latest downloadable revision: %s' % str( error_message ) ) + set_do_not_test = False + else: + set_do_not_test = not is_latest_downloadable_revision params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) diff --git a/test/tool_shed/base/twilltestcase.py b/test/tool_shed/base/twilltestcase.py index 4e282e6b215..748852e47a4 100644 --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -382,7 +382,17 @@ class ShedTwillTestCase( TwillTestCase ): except: pass return previously_created, username_taken, invalid_username - + + def deactivate_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): + url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( installed_repository.id ) + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + form = tc.browser.get_form( 'deactivate_or_uninstall_repository' ) + kwd = self.set_form_value( form, {}, 'remove_from_disk', False ) + tc.submit( 'deactivate_or_uninstall_repository_button' ) + strings_displayed = [ 'The repository named', 'has been deactivated' ] + self.check_for_strings( strings_displayed, strings_not_displayed=[] ) + def delete_files_from_repository( self, repository, filenames=[], strings_displayed=[ 'were deleted from the repository' ], strings_not_displayed=[] ): files_to_delete = [] basepath = self.get_repo_path( repository ) @@ -1203,18 +1213,14 @@ class ShedTwillTestCase( TwillTestCase ): self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def uninstall_repository( self, installed_repository, remove_from_disk=True, is_required=False, strings_displayed=[], strings_not_displayed=[] ): + def uninstall_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) form = tc.browser.get_form( 'deactivate_or_uninstall_repository' ) - kwd = self.set_form_value( form, {}, 'remove_from_disk', remove_from_disk ) + kwd = self.set_form_value( form, {}, 'remove_from_disk', True ) tc.submit( 'deactivate_or_uninstall_repository_button' ) - strings_displayed = [ 'The repository named' ] - if remove_from_disk and not is_required: - strings_displayed.append( 'has been uninstalled' ) - else: - strings_displayed.append( 'has been deactivated' ) + strings_displayed = [ 'The repository named', 'has been uninstalled' ] self.check_for_strings( strings_displayed, strings_not_displayed=[] ) def update_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): diff --git a/test/tool_shed/functional/test_0490_export_import_repositories.py b/test/tool_shed/functional/test_0490_export_import_repositories.py index f8aa2073605..2d57ce0bda4 100644 --- a/test/tool_shed/functional/test_0490_export_import_repositories.py +++ b/test/tool_shed/functional/test_0490_export_import_repositories.py @@ -65,7 +65,7 @@ class TestExportImportRepository( ShedTwillTestCase ): global capsule_filepath repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) capsule_filepath = self.export_capsule( repository ) - log.debug( os.path.exists( capsule_filepath ) ) + assert os.path.exists( capsule_filepath ), 'Exported repository capsule file path %s not found.' % capsule_filepath def test_0015_verify_exported_capsule( self ): '''Verify the exported capsule contents.''' diff --git a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py index 026b394cd1d..1929a242435 100644 --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -121,7 +121,7 @@ class ToolWithRepositoryDependencies( ShedTwillTestCase ): global base_datatypes_count installed_repository = self.test_db_util.get_installed_repository_by_name_owner( datatypes_repository_name, common.test_user_1_name ) old_datatypes_count = int( self.get_datatypes_count() ) - self.uninstall_repository( installed_repository, remove_from_disk=False ) + self.deactivate_repository( installed_repository ) current_datatypes = int( self.get_datatypes_count() ) assert current_datatypes < old_datatypes_count, 'Uninstalling emboss did not remove datatypes.' diff --git a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py index 0fea5aa30ad..6525fa2ee57 100644 --- a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -109,7 +109,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ): installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( installed_freebayes_repository ) self.display_installed_repository_manage_page( installed_filtering_repository ) - self.uninstall_repository( installed_filtering_repository, remove_from_disk=False ) + self.deactivate_repository( installed_filtering_repository ) self.test_db_util.ga_refresh( installed_filtering_repository ) self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' ) strings_displayed = [ 'Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040" ] @@ -134,7 +134,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ): installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( installed_freebayes_repository ) self.display_installed_repository_manage_page( installed_filtering_repository ) - self.uninstall_repository( installed_freebayes_repository, remove_from_disk=False ) + self.deactivate_repository( installed_freebayes_repository ) self.test_db_util.ga_refresh( installed_freebayes_repository ) self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, '' ) strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ] @@ -149,7 +149,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ): installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( installed_freebayes_repository ) self.display_installed_repository_manage_page( installed_filtering_repository ) - self.uninstall_repository( installed_filtering_repository, remove_from_disk=False ) + self.deactivate_repository( installed_filtering_repository ) self.test_db_util.ga_refresh( installed_filtering_repository ) self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' ) strings_displayed = [ 'Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040" ] diff --git a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py index 27ce05f1f56..293b023c53f 100644 --- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -315,7 +315,7 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ): '''Deactivate emboss_datatypes and verify that the datatypes count is reduced.''' original_datatypes = self.get_datatypes_count() repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) - self.uninstall_repository( repository, remove_from_disk=False ) + self.deactivate_repository( repository ) assert original_datatypes > self.get_datatypes_count(), 'Deactivating emboss_datatypes did not remove datatypes.' # Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), @@ -330,7 +330,7 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ): def test_0070_uninstall_emboss_repository( self ): '''Uninstall the emboss_5 repository.''' repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.uninstall_repository( repository, remove_from_disk=True ) + self.uninstall_repository( repository ) strings_not_displayed = [ repository.name, repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) self.test_db_util.ga_refresh( repository ) diff --git a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py index 2548aec64ab..d91e0f0e5ed 100644 --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -162,7 +162,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) + self.deactivate_repository( installed_convert_repository ) strings_displayed = [ 'column_maker_0080', 'Add column', self.url.replace( 'http://', '' ), @@ -199,7 +199,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=False ) + self.deactivate_repository( installed_column_repository ) strings_displayed = [ 'convert_chars_0080', 'Convert delimiters', self.url.replace( 'http://', '' ), @@ -217,7 +217,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) + self.deactivate_repository( installed_convert_repository ) strings_not_displayed = [ 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'convert_chars_0080', @@ -274,7 +274,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + self.uninstall_repository( installed_column_repository ) strings_displayed = [ 'convert_chars_0080', 'Convert delimiters', self.url.replace( 'http://', '' ), @@ -320,7 +320,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) + self.deactivate_repository( installed_convert_repository ) strings_displayed = [ 'column_maker_0080', 'Add column', self.url.replace( 'http://', '' ), @@ -340,7 +340,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=False ) + self.deactivate_repository( installed_column_repository ) strings_displayed = [ 'convert_chars_0080', 'Convert delimiters', self.url.replace( 'http://', '' ), @@ -387,8 +387,8 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=False ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) + self.deactivate_repository( installed_column_repository ) + self.deactivate_repository( installed_convert_repository ) self.test_db_util.install_session.refresh( installed_column_repository ) self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, '' ) diff --git a/test/tool_shed/functional/test_1085_repository_dependency_handling.py b/test/tool_shed/functional/test_1085_repository_dependency_handling.py index 42b1d4d9c9f..ae73e8b51ee 100644 --- a/test/tool_shed/functional/test_1085_repository_dependency_handling.py +++ b/test/tool_shed/functional/test_1085_repository_dependency_handling.py @@ -124,14 +124,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ): '''uninstall column_maker, verify same section''' installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + self.uninstall_repository( installed_column_repository ) self.test_db_util.ga_refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' ) def test_0030_uninstall_convert_repository( self ): installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=True ) + self.uninstall_repository( installed_convert_repository ) self.test_db_util.ga_refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'column_maker' ) @@ -173,8 +173,8 @@ class TestRepositoryDependencies( ShedTwillTestCase ): common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_convert_repository, remove_from_disk=True ) - self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + self.uninstall_repository( installed_convert_repository ) + self.uninstall_repository( installed_column_repository ) self.test_db_util.ga_refresh( installed_convert_repository ) self.test_db_util.ga_refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' ) diff --git a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py index 9ae6f02b640..c9a10d0fffa 100644 --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -89,7 +89,7 @@ class TestRepositoryDependencies( ShedTwillTestCase ): new_tool_panel_section_label='column_maker', strings_not_displayed=[ 'install_repository_dependencies' ] ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + self.uninstall_repository( installed_column_repository ) def test_0020_upload_dependency_xml( self ): '''Upload a repository_dependencies.xml file to column_maker that specifies convert_chars.''' diff --git a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py index e8770860f5b..4dd6f7cf94d 100644 --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -251,7 +251,7 @@ class TestToolSearchAndInstall( ShedTwillTestCase ): self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories ) filtering_repository = self.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) - self.uninstall_repository( filtering_repository, remove_from_disk=False ) + self.deactivate_repository( filtering_repository ) strings_displayed = [ 'freebayes_0090' ] strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) @@ -278,7 +278,7 @@ class TestToolSearchAndInstall( ShedTwillTestCase ): self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) self.verify_installed_repositories( installed_repositories ) datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) - self.uninstall_repository( datatypes_repository, remove_from_disk=True ) + self.uninstall_repository( datatypes_repository ) strings_displayed = [ 'freebayes_0090' ] strings_not_displayed = [ 'emboss_datatypes_0090', 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090' ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) diff --git 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 index 76036b116f6..b61ec2ad4b2 100644 --- 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 @@ -278,7 +278,7 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ): ''' base_repository = self.test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = self.test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) - self.uninstall_repository( tool_repository, remove_from_disk=False ) + self.deactivate_repository( tool_repository ) env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 'bwa', '0.5.9', diff --git a/test/tool_shed/functional/test_1130_datatype_converters.py b/test/tool_shed/functional/test_1130_datatype_converters.py index 71095f36deb..ec987e6661d 100644 --- a/test/tool_shed/functional/test_1130_datatype_converters.py +++ b/test/tool_shed/functional/test_1130_datatype_converters.py @@ -87,5 +87,5 @@ class TestDatatypeConverters( ShedTwillTestCase ): so we have to uninstall it first, then verify that it was not assigned a tool panel section. ''' repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - self.uninstall_repository( repository, remove_from_disk=True ) + self.uninstall_repository( repository ) self.verify_installed_repository_no_tool_panel_section( repository ) diff --git a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py index 298ba42d93e..197ed013f7c 100644 --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -217,19 +217,19 @@ class TestSimplePriorInstallation( ShedTwillTestCase ): assert filter_repository.update_time > convert_repository.update_time, 'Error: convert_chars_0160 shows a later update time than filtering_0160' assert filter_repository.update_time > column_repository.update_time, 'Error: column_maker_0160 shows a later update time than filtering_0160' - def test_0040_uninstall_all_repositories( self ): + def test_0040_deactivate_all_repositories( self ): '''Uninstall convert_chars_0160, column_maker_0160, and filtering_0160.''' filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) - self.uninstall_repository( filter_repository, remove_from_disk=False ) - self.uninstall_repository( column_repository, remove_from_disk=False ) - self.uninstall_repository( convert_repository, remove_from_disk=False ) + self.deactivate_repository( filter_repository ) + self.deactivate_repository( column_repository ) + self.deactivate_repository( convert_repository ) - def test_0045_reinstall_filter_repository( self ): + def test_0045_reactivate_filter_repository( self ): '''Reinstall the filtering_0160 repository.''' filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) - self.reinstall_repository( filter_repository ) + self.reactivate_repository( filter_repository ) strings_displayed = [ 'filtering_0160', "Galaxy's filtering tool for test 0160", 'user1', @@ -242,6 +242,7 @@ class TestSimplePriorInstallation( ShedTwillTestCase ): def test_0050_verify_reinstallation_order( self ): '''Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160.''' + # Fixme: this test is not covering any important behavior since repositories were only deactivated and not uninstalled. filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) diff --git a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py index d7799123055..81b22ef8d98 100644 --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -1,7 +1,9 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os + class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): '''Test uninstalling and reinstalling a basic repository.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -19,6 +21,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): galaxy_admin_user = self.test_db_util.get_galaxy_user( common.admin_email ) assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email galaxy_admin_user_private_role = self.test_db_util.get_galaxy_private_role( galaxy_admin_user ) + def test_0005_ensure_repositories_and_categories_exist( self ): '''Create the 0000 category and upload the filtering repository to the tool shed, if necessary.''' category = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) @@ -67,6 +70,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): commit_message='Uploaded readme for 2.2.0', strings_displayed=[], strings_not_displayed=[] ) + def test_0010_install_filtering_repository( self ): '''Install the filtering repository into the Galaxy instance.''' self.galaxy_logout() @@ -82,14 +86,16 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + def test_0015_uninstall_filtering_repository( self ): '''Uninstall the filtering repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=True ) + self.uninstall_repository( installed_repository ) strings_not_displayed = [ 'filtering_0000', "Galaxy's filtering tool for test 0000", installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0020_reinstall_filtering_repository( self ): '''Reinstall the filtering repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) @@ -103,14 +109,16 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0025_deactivate_filtering_repository( self ): '''Deactivate the filtering repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=False ) + self.deactivate_repository( installed_repository ) strings_not_displayed = [ 'filtering_0000', "Galaxy's filtering tool for test 0000", installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0030_reactivate_filtering_repository( self ): '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) diff --git a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py index eac2833c149..ad52353f381 100644 --- a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -1,7 +1,9 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os + class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): '''Test uninstalling and reinstalling a repository with tool dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.galaxy_logout() @@ -19,6 +21,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): admin_user = self.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 = self.test_db_util.get_private_role( admin_user ) + def test_0005_ensure_repositories_and_categories_exist( self ): '''Create the 0010 category and upload the freebayes repository to the tool shed, if necessary.''' category = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' ) @@ -84,6 +87,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): commit_message='Uploaded valid tool dependency XML.', strings_displayed=[], strings_not_displayed=[] ) + def test_0010_install_freebayes_repository( self ): '''Install the freebayes repository into the Galaxy instance.''' self.galaxy_logout() @@ -101,12 +105,14 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + def test_0015_uninstall_freebayes_repository( self ): '''Uninstall the freebayes repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=True ) + self.uninstall_repository( installed_repository ) strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0020_reinstall_freebayes_repository( self ): '''Reinstall the freebayes repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) @@ -120,12 +126,14 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0025_deactivate_freebayes_repository( self ): '''Deactivate the freebayes repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=False ) + self.deactivate_repository( installed_repository ) strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0030_reactivate_freebayes_repository( self ): '''Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) diff --git a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py index 5cb03e1284c..c36e543f892 100644 --- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py @@ -108,7 +108,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): def test_0015_uninstall_emboss_repository( self ): '''Uninstall the emboss repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=True ) + self.uninstall_repository( installed_repository ) strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) @@ -129,7 +129,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): def test_0025_deactivate_emboss_repository( self ): '''Deactivate the emboss repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=False ) + self.deactivate_repository( installed_repository ) strings_not_displayed = [ 'emboss_0020', installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) diff --git a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py index 4f5cdd18fab..0c60ae17355 100644 --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -144,7 +144,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): def test_0015_uninstall_emboss_repository( self ): '''Uninstall the emboss repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=True ) + self.uninstall_repository( installed_repository ) strings_not_displayed = [ installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) @@ -165,7 +165,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ): def test_0025_deactivate_emboss_repository( self ): '''Deactivate the emboss repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.uninstall_repository( installed_repository, remove_from_disk=False ) + self.deactivate_repository( installed_repository ) strings_not_displayed = [ installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) diff --git a/test/tool_shed/functional/test_1430_repair_installed_repository.py b/test/tool_shed/functional/test_1430_repair_installed_repository.py index 8fa7aaf8321..2465e4c9b93 100644 --- a/test/tool_shed/functional/test_1430_repair_installed_repository.py +++ b/test/tool_shed/functional/test_1430_repair_installed_repository.py @@ -146,10 +146,9 @@ class TestRepairRepository( ShedTwillTestCase ): installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) strings_displayed = [ 'This repository cannot be uninstalled' ] strings_not_displayed = [ 'Check to uninstall' ] - self.uninstall_repository( installed_repository, - remove_from_disk=False, - strings_displayed=strings_displayed, - strings_not_displayed=strings_not_displayed ) + self.deactivate_repository( installed_repository, + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) strings_not_displayed = [ 'filter_1430', "Galaxy's filter tool for test 1430", installed_repository.installed_changeset_revision ] diff --git a/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py b/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py index 1defaa5c6a0..42df6fe445c 100644 --- a/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py +++ b/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py @@ -119,7 +119,7 @@ class TestInstallDatatypesSniffers( ShedTwillTestCase ): global repository_datatypes_count global base_datatypes_count global base_sniffers_count - self.uninstall_repository( repository, remove_from_disk=False ) + self.deactivate_repository( repository ) new_datatypes_count = self.get_datatypes_count() assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % ( base_datatypes_count, new_datatypes_count ) current_sniffers = self.get_sniffers_count() @@ -157,7 +157,7 @@ class TestInstallDatatypesSniffers( ShedTwillTestCase ): repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) global repository_datatypes_count global base_datatypes_count - self.uninstall_repository( repository, remove_from_disk=True ) + self.uninstall_repository( repository ) new_datatypes_count = self.get_datatypes_count() assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % ( base_datatypes_count, new_datatypes_count ) current_sniffers = self.get_sniffers_count() diff --git a/test/unit/test_galaxy_mapping.py b/test/unit/test_galaxy_mapping.py index acc6c14f5d0..f218451e5f5 100644 --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -180,6 +180,41 @@ class MappingTests( unittest.TestCase ): assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. + def test_history_contents( self ): + model = self.model + u = model.User( email="contents@foo.bar.baz", password="password" ) + # gs = model.GalaxySession() + h1 = model.History( name="HistoryContentsHistory1", user=u) + + self.persist( u, h1, expunge=False ) + + d1 = self.new_hda( h1, name="1" ) + d2 = self.new_hda( h1, name="2", visible=False ) + d3 = self.new_hda( h1, name="3", deleted=True ) + d4 = self.new_hda( h1, name="4", visible=False, deleted=True ) + + self.session().flush() + + def contents_iter_names(**kwds): + history = model.context.query( model.History ).filter( + model.History.name == "HistoryContentsHistory1" + ).first() + return list( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) ) + + self.assertEquals(contents_iter_names(), [ "1", "2", "3", "4" ]) + assert contents_iter_names( deleted=False ) == [ "1", "2" ] + assert contents_iter_names( visible=True ) == [ "1", "3" ] + assert contents_iter_names( visible=False ) == [ "2", "4" ] + assert contents_iter_names( deleted=True, visible=False ) == [ "4" ] + + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == [ "1", "2", "3", "4" ] + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == [ "1", "2", "3", "4" ] + + assert contents_iter_names( ids=[ d1.id, d3.id ] ) == [ "1", "3" ] + + def new_hda( self, history, **kwds ): + return history.add_dataset( self.model.HistoryDatasetAssociation( create_dataset=True, sa_session=self.model.session, **kwds ) ) + @classmethod def setUpClass(cls): # Start the database and connect the mapping @@ -191,10 +226,20 @@ class MappingTests( unittest.TestCase ): return cls.model.session.query( type ) @classmethod - def persist(cls, *args): + def persist(cls, *args, **kwargs): + session = cls.session() + flush = kwargs.get('flush', True) for arg in args: - cls.model.session.add( arg ) - cls.expunge() + session.add( arg ) + if flush: + session.flush() + if kwargs.get('expunge', not flush): + cls.expunge() + return arg # Return last or only arg. + + @classmethod + def session(cls): + return cls.model.session @classmethod def expunge(cls): diff --git a/tools/genomespace/genomespace_file_browser.py b/tools/genomespace/genomespace_file_browser.py index 7b1ce406ef0..fe0e88f3a81 100644 --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -9,11 +9,16 @@ import urllib2 import urlparse +import galaxy.model # need to import model before sniff to resolve a circular import dependency +from galaxy.datatypes import sniff +from galaxy.datatypes.registry import Registry + GENOMESPACE_API_VERSION_STRING = "v1.0" GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb +AUTO_GALAXY_EXT = "auto" DEFAULT_GALAXY_EXT = "data" #genomespace format identifier is the URL @@ -40,6 +45,9 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles', 'gmt': 'gmt', 'gct': 'gct'} +GENOMESPACE_UNKNOWN_FORMAT_KEY = 'unknown' +GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = None + VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ ' def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ): @@ -68,7 +76,7 @@ def get_galaxy_ext_from_genomespace_format_url( url_opener, file_format_url ): ext = GENOMESPACE_EXT_TO_GALAXY_EXT.get( ext, None ) if ext is None: #could check content type, etc here - ext = DEFAULT_GALAXY_EXT + ext = AUTO_GALAXY_EXT return ext def get_genomespace_site_urls(): @@ -91,6 +99,8 @@ def set_genomespace_format_identifiers( url_opener, dm_site ): genomespace_formats = json.loads( opened_gs_request.read() ) for format in genomespace_formats: GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name'] + global GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN + GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = dict( map( lambda x: ( x[1], x[0] ) , GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.iteritems() ) ).get( GENOMESPACE_UNKNOWN_FORMAT_KEY, GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN ) def download_from_genomespace_file_browser( json_parameter_file, genomespace_site ): json_params = json.loads( open( json_parameter_file, 'r' ).read() ) @@ -109,6 +119,11 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit file_url_prefix = "fileUrl" file_type_prefix = "fileFormat" metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' ) + + #setup datatypes registry for sniffing + datatypes_registry = Registry() + datatypes_registry.load_datatypes( root_dir = json_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = json_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] ) + file_numbers = [] for name in datasource_params.keys(): if name.startswith( file_url_prefix ): @@ -144,28 +159,47 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit filename = urllib.unquote_plus( parsed_url[2].split( '/' )[-1] ) if not filename: filename = download_url + metadata_dict = None + original_filename = filename if output_filename is None: - original_filename = filename filename = ''.join( c in VALID_CHARS and c or '-' for c in filename ) while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) - metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset', - base_dataset_id = dataset_id, - ext = galaxy_ext, - filename = output_filename, - name = "GenomeSpace import on %s" % ( original_filename ) ) ) ) + + metadata_dict = dict( type = 'new_primary_dataset', + base_dataset_id = dataset_id, + ext = galaxy_ext, + filename = output_filename, + name = "GenomeSpace import on %s" % ( original_filename ) ) else: if dataset_id is not None: - metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'dataset', - dataset_id = dataset_id, - ext = galaxy_ext, - name = "GenomeSpace import on %s" % ( filename ) ) ) ) + metadata_dict = dict( type = 'dataset', + dataset_id = dataset_id, + ext = galaxy_ext, + name = "GenomeSpace import on %s" % ( filename ) ) output_file = open( output_filename, 'wb' ) chunk_write( target_download_url, output_file ) output_file.close() + + if ( galaxy_ext == AUTO_GALAXY_EXT or filetype_url == GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN ) and metadata_dict: + #try to sniff datatype + try: + galaxy_ext = sniff.handle_uploaded_dataset_file( output_filename, datatypes_registry ) + except: + #sniff failed + galaxy_ext = original_filename.rsplit( '.', 1 )[-1] + if galaxy_ext not in datatypes_registry.datatypes_by_extension: + galaxy_ext = DEFAULT_GALAXY_EXT + metadata_dict[ 'ext' ] = galaxy_ext + output_filename = None #only have one filename available + + #write out metadata info + if metadata_dict: + metadata_parameter_file.write( "%s\n" % json.dumps( metadata_dict ) ) + metadata_parameter_file.close() return True