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commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 18 Aug '14

18 Aug '14

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40d8d9e3ebd5/ Changeset: 40d8d9e3ebd5 User: jmchilton Date: 2014-08-18 00:43:54 Summary: Dynamic destinations - extend RuleHelper for reasoning about groups of destinations... If multiple destinations map to the same underlying resource (a very typical case), this could allow rule developer to reason about cluster as a whole - though perhaps clunkily - by supplying all destination ids mapping to that cluster. Affected #: 2 files diff -r 572a8d5ee218aeb37f77660948cb75a439936868 -r 40d8d9e3ebd57820aac97115950818d97019ba17 lib/galaxy/jobs/rule_helper.py --- a/lib/galaxy/jobs/rule_helper.py +++ b/lib/galaxy/jobs/rule_helper.py @@ -58,16 +58,23 @@ query, for_user_email=None, for_destination=None, + for_destinations=None, for_job_states=None, created_in_last=None, updated_in_last=None, ): + if for_destination is not None: + for_destinations = [ for_destination ] + query = query.join( model.User ) if for_user_email is not None: query = query.filter( model.User.table.c.email == for_user_email ) - if for_destination is not None: - query = query.filter( model.Job.table.c.destination_id == for_destination ) + if for_destinations is not None: + if len( for_destinations ) == 1: + query = query.filter( model.Job.table.c.destination_id == for_destinations[ 0 ] ) + else: + query = query.filter( model.Job.table.c.destination_id.in_( for_destinations ) ) if created_in_last is not None: end_date = datetime.now() diff -r 572a8d5ee218aeb37f77660948cb75a439936868 -r 40d8d9e3ebd57820aac97115950818d97019ba17 test/unit/jobs/test_rule_helper.py --- a/test/unit/jobs/test_rule_helper.py +++ b/test/unit/jobs/test_rule_helper.py @@ -24,9 +24,12 @@ __assert_job_count_is( 2, rule_helper, for_destination="local" ) __assert_job_count_is( 7, rule_helper, for_destination="cluster1" ) + __assert_job_count_is( 9, rule_helper, for_destinations=["cluster1", "local"] ) + # Test per user destination counts __assert_job_count_is( 5, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1 ) __assert_job_count_is( 2, rule_helper, for_destination="local", for_user_email=USER_EMAIL_1 ) + __assert_job_count_is( 7, rule_helper, for_destinations=["cluster1", "local"], for_user_email=USER_EMAIL_1 ) __assert_job_count_is( 2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_2 ) __assert_job_count_is( 0, rule_helper, for_destination="local", for_user_email=USER_EMAIL_2 ) https://bitbucket.org/galaxy/galaxy-central/commits/ae77e648918a/ Changeset: ae77e648918a User: jmchilton Date: 2014-08-18 00:43:54 Summary: Dynamic destinations - pass job_conf.xml params to rule functions. In other words, send extra job destination parameters to dynamic rule functions as arguments (in addition to those dynamically populated by Galaxy itself). This enables greater parameterization of rule functions and should lead to cleaner separation of logic and data (i.e. sites can program rules that restrict access to users, but which users can be populated at a higher level in `job_conf.xml`). For example the following dynamic job rule: def cluster1(app, memory="4096", cores="1", hours="48"): native_spec = "--time=%s:00:00 --nodes=1 --ntasks=%s --mem=%s" % ( hours, cores, memory ) return JobDestination( "cluster1", params=dict( native_specification=native_spec ) ) Could then be called with various parameters in job_conf.xml as follows: <destination id="short_job" type="dyanmic"><param id="function">cluster1</param><param id="hours">1</param></destination><destination id="big_job" type="dynamic"><param id="function">cluster1</param><param id="cores">8</param><param id="memory">32768</param></destination> Affected #: 3 files diff -r 40d8d9e3ebd57820aac97115950818d97019ba17 -r ae77e648918aa881618e196bd6b036ae4095b6db lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -69,7 +69,7 @@ names.append( rule_module_name ) return names - def __invoke_expand_function( self, expand_function ): + def __invoke_expand_function( self, expand_function, destination_params ): function_arg_names = inspect.getargspec( expand_function ).args app = self.job_wrapper.app possible_args = { @@ -83,6 +83,11 @@ actual_args = {} + # Send through any job_conf.xml defined args to function + for destination_param in destination_params.keys(): + if destination_param in function_arg_names: + actual_args[ destination_param ] = destination_params[ destination_param ] + # Populate needed args for possible_arg_name in possible_args: if possible_arg_name in function_arg_names: @@ -179,12 +184,12 @@ raise Exception( message ) expand_function = self.__get_expand_function( expand_function_name ) - return self.__handle_rule( expand_function ) + return self.__handle_rule( expand_function, destination ) else: raise Exception( "Unhandled dynamic job runner type specified - %s" % expand_type ) - def __handle_rule( self, rule_function ): - job_destination = self.__invoke_expand_function( rule_function ) + def __handle_rule( self, rule_function, destination ): + job_destination = self.__invoke_expand_function( rule_function, destination.params ) if not isinstance(job_destination, galaxy.jobs.JobDestination): job_destination_rep = str(job_destination) # Should be either id or url if '://' in job_destination_rep: diff -r 40d8d9e3ebd57820aac97115950818d97019ba17 -r ae77e648918aa881618e196bd6b036ae4095b6db test/unit/jobs/test_mapper.py --- a/test/unit/jobs/test_mapper.py +++ b/test/unit/jobs/test_mapper.py @@ -46,6 +46,12 @@ assert mapper.job_config.rule_response == "tool1_dest_id" +def test_dynamic_mapping_job_conf_params(): + mapper = __mapper( __dynamic_destination( dict( function="check_job_conf_params", param1="7" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "sent_7_dest_id" + + def test_dynamic_mapping_function_parameters(): mapper = __mapper( __dynamic_destination( dict( function="check_rule_params" ) ) ) assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION diff -r 40d8d9e3ebd57820aac97115950818d97019ba17 -r ae77e648918aa881618e196bd6b036ae4095b6db test/unit/jobs/test_rules/10_site.py --- a/test/unit/jobs/test_rules/10_site.py +++ b/test/unit/jobs/test_rules/10_site.py @@ -40,6 +40,11 @@ return "all_passed" +def check_job_conf_params( param1 ): + assert param1 == "7" + return "sent_7_dest_id" + + def check_resource_params( resource_params ): assert resource_params["memory"] == "8gb" return "have_resource_params" https://bitbucket.org/galaxy/galaxy-central/commits/ec6a5e37d428/ Changeset: ec6a5e37d428 User: jmchilton Date: 2014-08-18 00:43:54 Summary: Dynamic destinations - allow dispatching on workflow invocation. Generate a workflow invocation UUID that is stored with each job in the workflow and allow dynamic job destinations to consume these. Should allow for grouping jobs from the same workflow together during resource allocation (a sort of first attempt at dealing with data locality in workflows). Affected #: 6 files diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -95,7 +95,7 @@ # Don't hit the DB to load the job object if not needed require_db = False - for param in ["job", "user", "user_email", "resource_params"]: + for param in ["job", "user", "user_email", "resource_params", "workflow_invocation_uuid"]: if param in function_arg_names: require_db = True break @@ -127,6 +127,11 @@ pass actual_args[ "resource_params" ] = resource_params + if "workflow_invocation_uuid" in function_arg_names: + param_values = job.raw_param_dict( ) + workflow_invocation_uuid = param_values.get( "__workflow_invocation_uuid__", None ) + actual_args[ "workflow_invocation_uuid" ] = workflow_invocation_uuid + return expand_function( **actual_args ) def __job_params( self, job ): diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -482,10 +482,13 @@ Read encoded parameter values from the database and turn back into a dict of tool parameter values. """ - param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + param_dict = self.raw_param_dict() tool = app.toolbox.get_tool( self.tool_id ) param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) return param_dict + def raw_param_dict( self ): + param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + return param_dict def check_if_output_datasets_deleted( self ): """ Return true if all of the output datasets associated with this job are diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd lib/galaxy/tools/execute.py --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -10,13 +10,19 @@ log = logging.getLogger( __name__ ) -def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None ): +def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None ): """ Execute a tool and return object containing summary (output data, number of failures, etc...). """ execution_tracker = ToolExecutionTracker( tool, param_combinations, collection_info ) for params in execution_tracker.param_combinations: + if workflow_invocation_uuid: + params[ '__workflow_invocation_uuid__' ] = workflow_invocation_uuid + elif '__workflow_invocation_uuid__' in params: + # Only workflow invocation code gets to set this, ignore user supplied + # values or rerun parameters. + del params[ '__workflow_invocation_uuid__' ] job, result = tool.handle_single_execution( trans, rerun_remap_job_id, params, history ) if job: execution_tracker.record_success( job, result ) diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -1,3 +1,5 @@ +import uuid + from galaxy import model from galaxy import exceptions from galaxy import util @@ -41,6 +43,8 @@ self.param_map = workflow_run_config.param_map self.outputs = odict() + # TODO: Attach to actual model object and persist someday... + self.invocation_uuid = uuid.uuid1().hex def invoke( self ): workflow_invocation = model.WorkflowInvocation() @@ -132,6 +136,7 @@ param_combinations=param_combinations, history=self.target_history, collection_info=collection_info, + workflow_invocation_uuid=self.invocation_uuid ) if collection_info: outputs[ step.id ] = dict( execution_tracker.created_collections ) diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd test/unit/jobs/test_mapper.py --- a/test/unit/jobs/test_mapper.py +++ b/test/unit/jobs/test_mapper.py @@ -1,3 +1,5 @@ +import uuid + import jobs.test_rules from galaxy.jobs.mapper import ( @@ -9,7 +11,7 @@ from galaxy.util import bunch - +WORKFLOW_UUID = uuid.uuid1().hex TOOL_JOB_DESTINATION = JobDestination() DYNAMICALLY_GENERATED_DESTINATION = JobDestination() @@ -64,6 +66,12 @@ assert mapper.job_config.rule_response == "have_resource_params" +def test_dynamic_mapping_workflow_invocation_parameter(): + mapper = __mapper( __dynamic_destination( dict( function="check_workflow_invocation_uuid" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == WORKFLOW_UUID + + def test_dynamic_mapping_no_function(): dest = __dynamic_destination( dict( ) ) mapper = __mapper( dest ) @@ -130,21 +138,26 @@ return True def get_job(self): + raw_params = { + "threshold": 8, + "__workflow_invocation_uuid__": WORKFLOW_UUID, + } + def get_param_values( app, ignore_errors ): assert app == self.app - return { - "threshold": 8, - "__job_resource": { - "__job_resource__select": "True", - "memory": "8gb" - } + params = raw_params.copy() + params[ "__job_resource" ] = { + "__job_resource__select": "True", + "memory": "8gb" } + return params return bunch.Bunch( user=bunch.Bunch( id=6789, email="test(a)example.com" ), + raw_param_dict=lambda: raw_params, get_param_values=get_param_values ) diff -r ae77e648918aa881618e196bd6b036ae4095b6db -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd test/unit/jobs/test_rules/10_site.py --- a/test/unit/jobs/test_rules/10_site.py +++ b/test/unit/jobs/test_rules/10_site.py @@ -48,3 +48,7 @@ def check_resource_params( resource_params ): assert resource_params["memory"] == "8gb" return "have_resource_params" + + +def check_workflow_invocation_uuid( workflow_invocation_uuid ): + return workflow_invocation_uuid https://bitbucket.org/galaxy/galaxy-central/commits/05b550588d9d/ Changeset: 05b550588d9d User: jmchilton Date: 2014-08-18 00:43:54 Summary: Dynamic destinations - easier, high-level reasoning about data locality. ... if only in a limitted sort of way. Provide ability to hash jobs by history, workflow, user, etc... and choose among various destinations semi-randomly based on that to distribute work across destinations based on these factors. Add a stock rule as in the form of a new dynamic destination type ("choose_one") that demonstrate using this to quickly proxy to some fixed static destinations. Add examples to job_conf.xml.sample_advanced. Affected #: 5 files diff -r ec6a5e37d428cc5d97b4d8f65487a7505a0ea5fd -r 05b550588d9dcf1502f141e7f1c5c896930e64bc job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -235,6 +235,21 @@ <param id="function">foo</param></destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination><destination id="secure_pulsar_rest_dest" runner="pulsar_rest"><param id="url">https://examle.com:8913/</param> + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination><destination id="secure_pulsar_rest_dest" runner="pulsar_rest"><param id="url">https://examle.com:8913/</param></destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination><destination id="secure_pulsar_rest_dest" runner="pulsar_rest"><param id="url">https://examle.com:8913/</param><param id="function">foo</param></destination> + <destination id="load_balance" runner="dynamic"> + <param id="type">choose_one</param> +  + <param id="destination_ids">cluster1,cluster2,cluster3</param> + </destination> + <destination id="load_balance_with_data_locality" runner="dynamic"> +  + <param id="type">choose_one</param> + <param id="destination_ids">cluster1,cluster2,cluster3</param> + <param id="hash_by">workflow_invocation,history</param> + </destination> + <destination id="burst_out" runner="dynamic"> +  + <param id="type">burst</param> + <param id="from_destination_ids">local_cluster_8_core,local_cluster_1_core,local_cluster_16_core</param> + <param id="to_destination_id">shared_cluster_8_core</param> + <param id="num_jobs">50</param> +  + </destination> + <destination id="docker_dispatch" runner="dynamic"> +  + <param id="type">docker_dispatch</param> + <param id="docker_destination_id">docker_cluster</param> + <param id="default_destination_id">normal_cluster</param> + </destination><destination id="secure_pulsar_rest_dest" runner="pulsar_rest"><param id="url">https://examle.com:8913/</param><!-- If set, private_token must match token in remote Pulsar's diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -5,6 +5,8 @@ log = logging.getLogger( __name__ ) import galaxy.jobs.rules +from galaxy.jobs import stock_rules + from .rule_helper import RuleHelper DYNAMIC_RUNNER_NAME = "dynamic" @@ -27,6 +29,13 @@ self.message = message +STOCK_RULES = dict( + choose_one=stock_rules.choose_one, + burst=stock_rules.burst, + docker_dispatch=stock_rules.docker_dispatch, +) + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs @@ -69,7 +78,7 @@ names.append( rule_module_name ) return names - def __invoke_expand_function( self, expand_function ): + def __invoke_expand_function( self, expand_function, destination_params ): function_arg_names = inspect.getargspec( expand_function ).args app = self.job_wrapper.app possible_args = { @@ -83,6 +92,11 @@ actual_args = {} + # Send through any job_conf.xml defined args to function + for destination_param in destination_params.keys(): + if destination_param in function_arg_names: + actual_args[ destination_param ] = destination_params[ destination_param ] + # Populate needed args for possible_arg_name in possible_args: if possible_arg_name in function_arg_names: @@ -90,7 +104,7 @@ # Don't hit the DB to load the job object if not needed require_db = False - for param in ["job", "user", "user_email", "resource_params"]: + for param in ["job", "user", "user_email", "resource_params", "workflow_invocation_uuid"]: if param in function_arg_names: require_db = True break @@ -122,6 +136,11 @@ pass actual_args[ "resource_params" ] = resource_params + if "workflow_invocation_uuid" in function_arg_names: + param_values = job.raw_param_dict( ) + workflow_invocation_uuid = param_values.get( "__workflow_invocation_uuid__", None ) + actual_args[ "workflow_invocation_uuid" ] = workflow_invocation_uuid + return expand_function( **actual_args ) def __job_params( self, job ): @@ -172,6 +191,7 @@ def __handle_dynamic_job_destination( self, destination ): expand_type = destination.params.get('type', "python") + expand_function = None if expand_type == "python": expand_function_name = self.__determine_expand_function_name( destination ) if not expand_function_name: @@ -179,12 +199,15 @@ raise Exception( message ) expand_function = self.__get_expand_function( expand_function_name ) - return self.__handle_rule( expand_function ) + elif expand_type in STOCK_RULES: + expand_function = STOCK_RULES[ expand_type ] else: raise Exception( "Unhandled dynamic job runner type specified - %s" % expand_type ) - def __handle_rule( self, rule_function ): - job_destination = self.__invoke_expand_function( rule_function ) + return self.__handle_rule( expand_function, destination ) + + def __handle_rule( self, rule_function, destination ): + job_destination = self.__invoke_expand_function( rule_function, destination.params ) if not isinstance(job_destination, galaxy.jobs.JobDestination): job_destination_rep = str(job_destination) # Should be either id or url if '://' in job_destination_rep: diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/jobs/rule_helper.py --- a/lib/galaxy/jobs/rule_helper.py +++ b/lib/galaxy/jobs/rule_helper.py @@ -1,4 +1,6 @@ from datetime import datetime +import hashlib +import random from sqlalchemy import ( and_, @@ -6,10 +8,13 @@ ) from galaxy import model +from galaxy import util import logging log = logging.getLogger( __name__ ) +VALID_JOB_HASH_STRATEGIES = ["job", "user", "history", "workflow_invocation"] + class RuleHelper( object ): """ Utillity to allow job rules to interface cleanly with the rest of @@ -22,6 +27,24 @@ def __init__( self, app ): self.app = app + def supports_docker( self, job_or_tool ): + """ Job rules can pass this function a job, job_wrapper, or tool and + determine if the underlying tool believes it can be containered. + """ + # Not a ton of logic in this method - but the idea is to shield rule + # developers from the details and they shouldn't have to know how to + # interrogate tool or job to figure out if it can be run in a + # container. + if hasattr( job_or_tool, 'containers' ): + tool = job_or_tool + elif hasattr( job_or_tool, 'tool' ): + # Have a JobWrapper-like + tool = job_or_tool.tool + else: + # Have a Job object. + tool = self.app.toolbox.get_tool( job_or_tool.tool_id ) + return any( [ c.type == "docker" for c in tool.containers ] ) + def job_count( self, **kwds @@ -58,16 +81,23 @@ query, for_user_email=None, for_destination=None, + for_destinations=None, for_job_states=None, created_in_last=None, updated_in_last=None, ): + if for_destination is not None: + for_destinations = [ for_destination ] + query = query.join( model.User ) if for_user_email is not None: query = query.filter( model.User.table.c.email == for_user_email ) - if for_destination is not None: - query = query.filter( model.Job.table.c.destination_id == for_destination ) + if for_destinations is not None: + if len( for_destinations ) == 1: + query = query.filter( model.Job.table.c.destination_id == for_destinations[ 0 ] ) + else: + query = query.filter( model.Job.table.c.destination_id.in_( for_destinations ) ) if created_in_last is not None: end_date = datetime.now() @@ -89,3 +119,81 @@ query = query.filter( model.Job.table.c.state.in_( for_job_states ) ) return query + + def should_burst( self, destination_ids, num_jobs, job_states=None ): + """ Check if the specified destinations ``destination_ids`` have at + least ``num_jobs`` assigned to it - send in ``job_state`` as ``queued`` + to limit this check to number of jobs queued. + + See stock_rules for an simple example of using this function - but to + get the most out of it - it should probably be used with custom job + rules that can respond to the bursting by allocatin resources, + launching cloud nodes, etc.... + """ + if job_states is None: + job_states = "queued,running" + from_destination_job_count = self.job_count( + for_destinations=destination_ids, + for_job_states=util.listify( job_states ) + ) + # Would this job push us over maximum job count before requiring + # bursting (roughly... very roughly given many handler threads may be + # scheduling jobs). + return ( from_destination_job_count + 1 ) > int( num_jobs ) + + def choose_one( self, lst, hash_value=None ): + """ Choose a random value from supplied list. If hash_value is passed + in then every request with that same hash_value would produce the same + choice from the supplied list. + """ + if hash_value is None: + return random.choice( lst ) + + if not isinstance( hash_value, int ): + # Convert hash_value string into index + as_hex = hashlib.md5( hash_value ).hexdigest() + hash_value = int(as_hex, 16) + # else assumed to be 'random' int from 0-~Inf + random_index = hash_value % len( lst ) + return lst[ random_index ] + + def job_hash( self, job, hash_by=None ): + """ Produce a reproducible hash for the given job on various + criteria - for instance if hash_by is "workflow_invocation,history" - + all jobs within the same workflow invocation will recieve the same + hash - for jobs outside of workflows all jobs within the same history + will recieve the same hash, other jobs will be hashed on job's id + randomly. + + Primarily intended for use with ``choose_one`` above - to consistent + route or schedule related jobs. + """ + if hash_by is None: + hash_by = [ "job" ] + hash_bys = util.listify( hash_by ) + for hash_by in hash_bys: + job_hash = self._try_hash_for_job( job, hash_by ) + if job_hash: + return job_hash + + # Fallback to just hashing by job id, should always return a value. + return self._try_hash_for_job( job, "job" ) + + def _try_hash_for_job( self, job, hash_by ): + """ May return False or None if hash type is invalid for that job - + e.g. attempting to hash by user for anonymous job or by workflow + invocation for jobs outside of workflows. + """ + if hash_by not in VALID_JOB_HASH_STRATEGIES: + message = "Do not know how to hash jobs by %s, must be one of %s" % ( hash_by, VALID_JOB_HASH_STRATEGIES ) + raise Exception( message ) + + if hash_by == "workflow_invocation": + return job.raw_param_dict().get( "__workflow_invocation_uuid__", None ) + elif hash_by == "history": + return job.history_id + elif hash_by == "user": + user = job.user + return user and user.id + elif hash_by == "job": + return job.id diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/jobs/stock_rules.py --- /dev/null +++ b/lib/galaxy/jobs/stock_rules.py @@ -0,0 +1,25 @@ +""" Stock job 'dynamic' rules for use in job_conf.xml - these may cover some +simple use cases but will just proxy into functions in rule_helper so similar +functionality - but more tailored and composable can be utilized in custom +rules. +""" + +from galaxy import util + + +def choose_one( rule_helper, job, destination_ids, hash_by="job" ): + destination_id_list = util.listify( destination_ids ) + job_hash = rule_helper.job_hash( job, hash_by ) + return rule_helper.choose_one( destination_id_list, hash_value=job_hash ) + + +def burst( rule_helper, job, from_destination_ids, to_destination_id, num_jobs, job_states=None): + from_destination_ids = util.listify( from_destination_ids ) + if rule_helper.should_burst( from_destination_ids, num_jobs=num_jobs, job_states=job_states ): + return to_destination_id + else: + return from_destination_ids[ 0 ] + + +def docker_dispatch( rule_helper, tool, docker_destination_id, default_destination_id ): + return docker_destination_id if rule_helper.supports_docker( tool ) else default_destination_id diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -482,10 +482,13 @@ Read encoded parameter values from the database and turn back into a dict of tool parameter values. """ - param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + param_dict = self.raw_param_dict() tool = app.toolbox.get_tool( self.tool_id ) param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) return param_dict + def raw_param_dict( self ): + param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) + return param_dict def check_if_output_datasets_deleted( self ): """ Return true if all of the output datasets associated with this job are diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/tools/execute.py --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -10,13 +10,19 @@ log = logging.getLogger( __name__ ) -def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None ): +def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None ): """ Execute a tool and return object containing summary (output data, number of failures, etc...). """ execution_tracker = ToolExecutionTracker( tool, param_combinations, collection_info ) for params in execution_tracker.param_combinations: + if workflow_invocation_uuid: + params[ '__workflow_invocation_uuid__' ] = workflow_invocation_uuid + elif '__workflow_invocation_uuid__' in params: + # Only workflow invocation code gets to set this, ignore user supplied + # values or rerun parameters. + del params[ '__workflow_invocation_uuid__' ] job, result = tool.handle_single_execution( trans, rerun_remap_job_id, params, history ) if job: execution_tracker.record_success( job, result ) diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -1,3 +1,5 @@ +import uuid + from galaxy import model from galaxy import exceptions from galaxy import util @@ -41,6 +43,8 @@ self.param_map = workflow_run_config.param_map self.outputs = odict() + # TODO: Attach to actual model object and persist someday... + self.invocation_uuid = uuid.uuid1().hex def invoke( self ): workflow_invocation = model.WorkflowInvocation() @@ -132,6 +136,7 @@ param_combinations=param_combinations, history=self.target_history, collection_info=collection_info, + workflow_invocation_uuid=self.invocation_uuid ) if collection_info: outputs[ step.id ] = dict( execution_tracker.created_collections ) diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd test/unit/jobs/test_mapper.py --- a/test/unit/jobs/test_mapper.py +++ b/test/unit/jobs/test_mapper.py @@ -1,3 +1,5 @@ +import uuid + import jobs.test_rules from galaxy.jobs.mapper import ( @@ -9,7 +11,7 @@ from galaxy.util import bunch - +WORKFLOW_UUID = uuid.uuid1().hex TOOL_JOB_DESTINATION = JobDestination() DYNAMICALLY_GENERATED_DESTINATION = JobDestination() @@ -46,6 +48,12 @@ assert mapper.job_config.rule_response == "tool1_dest_id" +def test_dynamic_mapping_job_conf_params(): + mapper = __mapper( __dynamic_destination( dict( function="check_job_conf_params", param1="7" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "sent_7_dest_id" + + def test_dynamic_mapping_function_parameters(): mapper = __mapper( __dynamic_destination( dict( function="check_rule_params" ) ) ) assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION @@ -58,6 +66,12 @@ assert mapper.job_config.rule_response == "have_resource_params" +def test_dynamic_mapping_workflow_invocation_parameter(): + mapper = __mapper( __dynamic_destination( dict( function="check_workflow_invocation_uuid" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == WORKFLOW_UUID + + def test_dynamic_mapping_no_function(): dest = __dynamic_destination( dict( ) ) mapper = __mapper( dest ) @@ -124,21 +138,26 @@ return True def get_job(self): + raw_params = { + "threshold": 8, + "__workflow_invocation_uuid__": WORKFLOW_UUID, + } + def get_param_values( app, ignore_errors ): assert app == self.app - return { - "threshold": 8, - "__job_resource": { - "__job_resource__select": "True", - "memory": "8gb" - } + params = raw_params.copy() + params[ "__job_resource" ] = { + "__job_resource__select": "True", + "memory": "8gb" } + return params return bunch.Bunch( user=bunch.Bunch( id=6789, email="test(a)example.com" ), + raw_param_dict=lambda: raw_params, get_param_values=get_param_values ) diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd test/unit/jobs/test_rule_helper.py --- a/test/unit/jobs/test_rule_helper.py +++ b/test/unit/jobs/test_rule_helper.py @@ -1,3 +1,5 @@ +import uuid + from galaxy.util import bunch from galaxy import model from galaxy.model import mapping @@ -24,9 +26,12 @@ __assert_job_count_is( 2, rule_helper, for_destination="local" ) __assert_job_count_is( 7, rule_helper, for_destination="cluster1" ) + __assert_job_count_is( 9, rule_helper, for_destinations=["cluster1", "local"] ) + # Test per user destination counts __assert_job_count_is( 5, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1 ) __assert_job_count_is( 2, rule_helper, for_destination="local", for_user_email=USER_EMAIL_1 ) + __assert_job_count_is( 7, rule_helper, for_destinations=["cluster1", "local"], for_user_email=USER_EMAIL_1 ) __assert_job_count_is( 2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_2 ) __assert_job_count_is( 0, rule_helper, for_destination="local", for_user_email=USER_EMAIL_2 ) @@ -69,10 +74,98 @@ app.add( __new_job( user=user2, destination_id="cluster1", state="running" ) ) -def __rule_helper(): - app = MockApp() - rule_helper = RuleHelper( app ) - return rule_helper +def test_choose_one_unhashed(): + rule_helper = __rule_helper() + + # Random choices if hash not set. + chosen_ones = set([]) + __do_a_bunch( lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'])) ) + + assert chosen_ones == set(['a', 'b']) + + +def test_choose_one_hashed(): + rule_helper = __rule_helper() + + # Hashed, so all choosen ones should be the same... + chosen_ones = set([]) + __do_a_bunch( lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value=1234)) ) + assert len( chosen_ones ) == 1 + + # ... also can verify hashing on strings + chosen_ones = set([]) + __do_a_bunch( lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value="i am a string")) ) + + assert len( chosen_ones ) == 1 + + +def test_job_hash_unique_by_default( ): + rule_helper = __rule_helper() + job1, job2 = __two_jobs_in_a_history() + + rule_helper.job_hash( job1 ) != rule_helper.job_hash( job2 ) + + +def test_job_hash_history( ): + rule_helper = __rule_helper() + job1, job2 = __two_jobs_in_a_history() + + __assert_same_hash( rule_helper, job1, job2, hash_by="history" ) + + +def test_job_hash_workflow_invocation(): + rule_helper = __rule_helper() + job1, job2 = __two_jobs() + wi_uuid = uuid.uuid1().hex + + job1.add_parameter( "__workflow_invocation_uuid__", wi_uuid ) + job2.add_parameter( "__workflow_invocation_uuid__", wi_uuid ) + + __assert_same_hash( rule_helper, job1, job2, hash_by="workflow_invocation" ) + + +def test_job_hash_fallback(): + rule_helper = __rule_helper() + job1, job2 = __two_jobs_in_a_history() + + __assert_same_hash( rule_helper, job1, job2, hash_by="workflow_invocation,history" ) + + +def test_should_burst( ): + rule_helper = __rule_helper() + __setup_fixtures( rule_helper.app ) + # cluster1 fixture has 4 queued jobs, 3 running + assert rule_helper.should_burst( [ "cluster1" ], "7" ) + assert not rule_helper.should_burst( [ "cluster1" ], "10" ) + + assert rule_helper.should_burst( [ "cluster1" ], "2", job_states="queued" ) + assert not rule_helper.should_burst( [ "cluster1" ], "6", job_states="queued" ) + + +def __assert_same_hash( rule_helper, job1, job2, hash_by ): + job1_hash = rule_helper.job_hash( job1, hash_by=hash_by ) + job2_hash = rule_helper.job_hash( job2, hash_by=hash_by ) + assert job1_hash == job2_hash + + +def __two_jobs_in_a_history(): + job1, job2 = __two_jobs() + job1.history_id = 4 + job2.history_id = 4 + return job1, job2 + + +def __two_jobs( ): + job1 = model.Job() + job1.id = 1 + job2 = model.Job() + job2.id = 2 + return job1, job2 + + +def __do_a_bunch( work ): + for i in range( 20 ): + work() def __new_job( **kwds ): @@ -82,6 +175,12 @@ return job +def __rule_helper(): + app = MockApp() + rule_helper = RuleHelper( app ) + return rule_helper + + class MockApp( object ): def __init__( self ): diff -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 -r 3c9a169936720219b60be32dd790fa2f14a139cd test/unit/jobs/test_rules/10_site.py --- a/test/unit/jobs/test_rules/10_site.py +++ b/test/unit/jobs/test_rules/10_site.py @@ -40,6 +40,15 @@ return "all_passed" +def check_job_conf_params( param1 ): + assert param1 == "7" + return "sent_7_dest_id" + + def check_resource_params( resource_params ): assert resource_params["memory"] == "8gb" return "have_resource_params" + + +def check_workflow_invocation_uuid( workflow_invocation_uuid ): + return workflow_invocation_uuid Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merged in kellrott/galaxy-farm/federation_ids (pull request #462)
by commits-noreply＠bitbucket.org 18 Aug '14

18 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d06d852093f/ Changeset: 0d06d852093f User: dannon Date: 2014-08-18 19:38:24 Summary: Merged in kellrott/galaxy-farm/federation_ids (pull request #462) UUIDs as valid inputs for workflows Affected #: 2 files diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -188,6 +188,15 @@ content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'uuid': + dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first() + if dataset is None: + #this will need to be changed later. If federation code is avalible, then a missing UUID + #could be found amoung fereration partners + message = "Input cannot find UUID: %s." % input_id + raise exceptions.RequestParameterInvalidException( message ) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) + content = history.add_dataset(dataset) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -23,7 +23,7 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% + <% try: current_case = param_values[input.name]['__current_case__'] is_valid = True @@ -53,7 +53,7 @@ <td></td></tr> %elif input.visible: - <% + <% if hasattr( input, "label" ) and input.label: label = input.label else: @@ -70,7 +70,7 @@ ## Parameter does not have a stored value. <tr><% - # Get parameter label. + # Get parameter label. if input.type == "conditional": label = input.test_param.label elif input.type == "repeat": @@ -83,7 +83,7 @@ <td></td></tr> %endif - + %endfor </%def> @@ -91,7 +91,7 @@ <%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> ${text | h} - </td> + </td></%def><table class="tabletip"> @@ -120,6 +120,9 @@ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> + %if hda.dataset.uuid: + <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr> + %endif %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif @@ -168,4 +171,3 @@ '${dep[0].name | h}' in ${dep[1]}<br/></div> % endfor - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Aug '14

18 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce24adaae994/ Changeset: ce24adaae994 Branch: federation_ids User: kellrott Date: 2014-08-14 22:19:43 Summary: Adding method for workflows to use input with 'src' set as 'uuid', it will then scan datasets for a matching uuid. Affected #: 2 files diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r ce24adaae9941568a414f80b5f16da37e55fa192 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -188,6 +188,15 @@ content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'uuid': + dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first() + if dataset is None: + #this will need to be changed later. If federation code is avalible, then a missing UUID + #could be found amoung fereration partners + message = "Input cannot find UUID: %s." % input_id + raise exceptions.RequestParameterInvalidException( message ) + content = history.add_dataset(dataset) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r ce24adaae9941568a414f80b5f16da37e55fa192 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -23,7 +23,7 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% + <% try: current_case = param_values[input.name]['__current_case__'] is_valid = True @@ -53,7 +53,7 @@ <td></td></tr> %elif input.visible: - <% + <% if hasattr( input, "label" ) and input.label: label = input.label else: @@ -70,7 +70,7 @@ ## Parameter does not have a stored value. <tr><% - # Get parameter label. + # Get parameter label. if input.type == "conditional": label = input.test_param.label elif input.type == "repeat": @@ -83,7 +83,7 @@ <td></td></tr> %endif - + %endfor </%def> @@ -91,7 +91,7 @@ <%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> ${text | h} - </td> + </td></%def><table class="tabletip"> @@ -120,6 +120,9 @@ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> + %if hda.dataset.uuid: + <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr> + %endif %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif @@ -168,4 +171,3 @@ '${dep[0].name | h}' in ${dep[1]}<br/></div> % endfor - https://bitbucket.org/galaxy/galaxy-central/commits/9440196009e1/ Changeset: 9440196009e1 Branch: federation_ids User: kellrott Date: 2014-08-14 22:38:55 Summary: Checking security before creating the HDA Affected #: 1 file diff -r ce24adaae9941568a414f80b5f16da37e55fa192 -r 9440196009e1efdd69df90a406e49a4fc6d7655b lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -195,8 +195,8 @@ #could be found amoung fereration partners message = "Input cannot find UUID: %s." % input_id raise exceptions.RequestParameterInvalidException( message ) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) content = history.add_dataset(dataset) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, https://bitbucket.org/galaxy/galaxy-central/commits/0d06d852093f/ Changeset: 0d06d852093f User: dannon Date: 2014-08-18 19:38:24 Summary: Merged in kellrott/galaxy-farm/federation_ids (pull request #462) UUIDs as valid inputs for workflows Affected #: 2 files diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -188,6 +188,15 @@ content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'uuid': + dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first() + if dataset is None: + #this will need to be changed later. If federation code is avalible, then a missing UUID + #could be found amoung fereration partners + message = "Input cannot find UUID: %s." % input_id + raise exceptions.RequestParameterInvalidException( message ) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) + content = history.add_dataset(dataset) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -23,7 +23,7 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% + <% try: current_case = param_values[input.name]['__current_case__'] is_valid = True @@ -53,7 +53,7 @@ <td></td></tr> %elif input.visible: - <% + <% if hasattr( input, "label" ) and input.label: label = input.label else: @@ -70,7 +70,7 @@ ## Parameter does not have a stored value. <tr><% - # Get parameter label. + # Get parameter label. if input.type == "conditional": label = input.test_param.label elif input.type == "repeat": @@ -83,7 +83,7 @@ <td></td></tr> %endif - + %endfor </%def> @@ -91,7 +91,7 @@ <%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> ${text | h} - </td> + </td></%def><table class="tabletip"> @@ -120,6 +120,9 @@ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> + %if hda.dataset.uuid: + <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr> + %endif %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif @@ -168,4 +171,3 @@ '${dep[0].name | h}' in ${dep[1]}<br/></div> % endfor - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Aug '14

18 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/162b355ae974/ Changeset: 162b355ae974 User: jmchilton Date: 2014-08-18 16:28:40 Summary: Minor trans-related changes for jobs. Remove a couple unused references on the job execution path through the code and require 'less' from the object to run jobs (i.e. try to use only trans.user and not trans.get_user() and make access to the underlying session optional in galaxy.tools.actions). Affected #: 3 files diff -r e66936a92febf952017586742db36ed44be4d08b -r 162b355ae974e9082ae013640632d534579add6c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1610,7 +1610,7 @@ except KeyError: depends_list = [] # See if converted dataset already exists, either in metadata in conversions. - converted_dataset = self.get_metadata_dataset( trans, target_ext ) + converted_dataset = self.get_metadata_dataset( target_ext ) if converted_dataset: return converted_dataset converted_dataset = self.get_converted_files_by_type( target_ext ) @@ -1641,7 +1641,7 @@ session.add( assoc ) session.flush() return None - def get_metadata_dataset( self, trans, dataset_ext ): + def get_metadata_dataset( self, dataset_ext ): """ Returns an HDA that points to a metadata file which contains a converted data with the requested extension. diff -r e66936a92febf952017586742db36ed44be4d08b -r 162b355ae974e9082ae013640632d534579add6c lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -133,7 +133,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets - def collect_input_dataset_collections( self, tool, param_values, trans ): + def collect_input_dataset_collections( self, tool, param_values ): input_dataset_collections = dict() def visitor( prefix, input, value, parent=None ): @@ -167,7 +167,7 @@ out_data = odict() # Track input dataset collections - but replace with simply lists so collect # input datasets can process these normally. - inp_dataset_collections = self.collect_input_dataset_collections( tool, incoming, trans ) + inp_dataset_collections = self.collect_input_dataset_collections( tool, incoming ) # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans ) @@ -331,10 +331,12 @@ trans.sa_session.flush() # Create the job object job = trans.app.model.Job() - galaxy_session = trans.get_galaxy_session() - # If we're submitting from the API, there won't be a session. - if type( galaxy_session ) == trans.model.GalaxySession: - job.session_id = galaxy_session.id + + if hasattr( trans, "get_galaxy_session" ): + galaxy_session = trans.get_galaxy_session() + # If we're submitting from the API, there won't be a session. + if type( galaxy_session ) == trans.model.GalaxySession: + job.session_id = galaxy_session.id if trans.user is not None: job.user_id = trans.user.id job.history_id = history.id diff -r e66936a92febf952017586742db36ed44be4d08b -r 162b355ae974e9082ae013640632d534579add6c lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -36,7 +36,7 @@ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) - user = trans.get_user() + user = trans.user if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): https://bitbucket.org/galaxy/galaxy-central/commits/eaf8920f999b/ Changeset: eaf8920f999b User: jmchilton Date: 2014-08-18 16:28:40 Summary: Extract some mixin's out of trans allowing trans-like functionilty outside web threads... In particular break out mixins defining context-based utilities for interacting with app, an user, and a history. In downstream work on workflow scheduling this proves nessecary and sufficient to create an context for 'execute'-ing tools (create jobs) outside of web threads in response to workflow requests. Unit tests for some of this. Affected #: 2 files diff -r 162b355ae974e9082ae013640632d534579add6c -r eaf8920f999bab18a44c938565b643e0612f6e15 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -491,7 +491,178 @@ return T( app ) -class GalaxyWebTransaction( base.DefaultWebTransaction ): +class ProvidesAppContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + database and event handling. + + Mixed in class must provide `app` property. + """ + + def log_action( self, user=None, action=None, context=None, params=None): + """ + Application-level logging of user actions. + """ + if self.app.config.log_actions: + action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) + try: + if user: + action.user = user + else: + action.user = self.user + except: + action.user = None + try: + action.session_id = self.galaxy_session.id + except: + action.session_id = None + self.sa_session.add( action ) + self.sa_session.flush() + + def log_event( self, message, tool_id=None, **kwargs ): + """ + Application level logging. Still needs fleshing out (log levels and such) + Logging events is a config setting - if False, do not log. + """ + if self.app.config.log_events: + event = self.app.model.Event() + event.tool_id = tool_id + try: + event.message = message % kwargs + except: + event.message = message + try: + event.history = self.get_history() + except: + event.history = None + try: + event.history_id = self.history.id + except: + event.history_id = None + try: + event.user = self.user + except: + event.user = None + try: + event.session_id = self.galaxy_session.id + except: + event.session_id = None + self.sa_session.add( event ) + self.sa_session.flush() + + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.app.model.context.current + + def expunge_all( self ): + app = self.app + context = app.model.context + context.expunge_all() + # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all() + if hasattr(app, 'install_model'): + install_model = app.install_model + if install_model != app.model: + install_model.context.expunge_all() + + def get_toolbox(self): + """Returns the application toolbox""" + return self.app.toolbox + + @property + def model( self ): + return self.app.model + + @property + def install_model( self ): + return self.app.install_model + + def request_types(self): + if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: + return True + return False + + +class ProvidesUserContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + reasoning about users. + + Mixed in class must provide `user`, `api_inherit_admin`, and `app` + properties. + """ + + @property + def anonymous( self ): + return self.user is None and not self.api_inherit_admin + + def get_current_user_roles( self ): + user = self.user + if user: + roles = user.all_roles() + else: + roles = [] + return roles + + def user_is_admin( self ): + if self.api_inherit_admin: + return True + return self.user and self.user.email in self.app.config.admin_users_list + + def user_can_do_run_as( self ): + run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ] + if not run_as_users: + return False + user_in_run_as_users = self.user and self.user.email in run_as_users + # Can do if explicitly in list or master_api_key supplied. + can_do_run_as = user_in_run_as_users or self.api_inherit_admin + return can_do_run_as + + @property + def user_ftp_dir( self ): + identifier = self.app.config.ftp_upload_dir_identifier + return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) + + +class ProvidesHistoryContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + reasoning about histories. + + Mixed in class must provide `user`, `history`, and `app` + properties. + """ + + def db_dataset_for( self, dbkey ): + """ + Returns the db_file dataset associated/needed by `dataset`, or `None`. + """ + # If no history, return None. + if self.history is None: + return None + if isinstance(self.history, Bunch): + # The API presents a Bunch for a history. Until the API is + # more fully featured for handling this, also return None. + return None + datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ + .filter_by( deleted=False, history_id=self.history.id, extension="len" ) + for ds in datasets: + if dbkey == ds.dbkey: + return ds + return None + + @property + def db_builds( self ): + """ + Returns the builds defined by galaxy and the builds defined by + the user (chromInfo in history). + """ + # FIXME: This method should be removed + return self.app.genome_builds.get_genome_build_names( trans=self ) + + +class GalaxyWebTransaction( base.DefaultWebTransaction, ProvidesAppContext, ProvidesUserContext, ProvidesHistoryContext ): """ Encapsulates web transaction specific state for the Galaxy application (specifically the user's "cookie" session and history) @@ -552,29 +723,6 @@ t = Translations.load( dirname='locale', locales=locales, domain='ginga' ) self.template_context.update( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) ) - @property - def anonymous( self ): - return self.user is None and not self.api_inherit_admin - - @property - def sa_session( self ): - """ - Returns a SQLAlchemy session -- currently just gets the current - session from the threadlocal session context, but this is provided - to allow migration toward a more SQLAlchemy 0.4 style of use. - """ - return self.app.model.context.current - - def expunge_all( self ): - app = self.app - context = app.model.context - context.expunge_all() - # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all() - if hasattr(app, 'install_model'): - install_model = app.install_model - if install_model != app.model: - install_model.context.expunge_all() - def get_user( self ): """Return the current user if logged in or None.""" if self.galaxy_session: @@ -592,57 +740,6 @@ user = property( get_user, set_user ) - def log_action( self, user=None, action=None, context=None, params=None): - """ - Application-level logging of user actions. - """ - if self.app.config.log_actions: - action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) - try: - if user: - action.user = user - else: - action.user = self.user - except: - action.user = None - try: - action.session_id = self.galaxy_session.id - except: - action.session_id = None - self.sa_session.add( action ) - self.sa_session.flush() - - def log_event( self, message, tool_id=None, **kwargs ): - """ - Application level logging. Still needs fleshing out (log levels and such) - Logging events is a config setting - if False, do not log. - """ - if self.app.config.log_events: - event = self.app.model.Event() - event.tool_id = tool_id - try: - event.message = message % kwargs - except: - event.message = message - try: - event.history = self.get_history() - except: - event.history = None - try: - event.history_id = self.history.id - except: - event.history_id = None - try: - event.user = self.user - except: - event.user = None - try: - event.session_id = self.galaxy_session.id - except: - event.session_id = None - self.sa_session.add( event ) - self.sa_session.flush() - def get_cookie( self, name='galaxysession' ): """Convenience method for getting a session cookie""" try: @@ -1100,44 +1197,10 @@ self.sa_session.flush() return history - def get_current_user_roles( self ): - user = self.get_user() - if user: - roles = user.all_roles() - else: - roles = [] - return roles - - def user_is_admin( self ): - if self.api_inherit_admin: - return True - return self.user and self.user.email in self.app.config.admin_users_list - - def user_can_do_run_as( self ): - run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ] - if not run_as_users: - return False - user_in_run_as_users = self.user and self.user.email in run_as_users - # Can do if explicitly in list or master_api_key supplied. - can_do_run_as = user_in_run_as_users or self.api_inherit_admin - return can_do_run_as - - def get_toolbox(self): - """Returns the application toolbox""" - return self.app.toolbox - @base.lazy_property def template_context( self ): return dict() - @property - def model( self ): - return self.app.model - - @property - def install_model( self ): - return self.app.install_model - def make_form_data( self, name, **kwargs ): rval = self.template_context[name] = FormData() rval.values.update( kwargs ) @@ -1250,43 +1313,6 @@ searchList=[context or kwargs, dict(caller=self)] ) return str(template) - @property - def db_builds( self ): - """ - Returns the builds defined by galaxy and the builds defined by - the user (chromInfo in history). - """ - # FIXME: This method should be removed - return self.app.genome_builds.get_genome_build_names( trans=self ) - - @property - def user_ftp_dir( self ): - identifier = self.app.config.ftp_upload_dir_identifier - return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) - - def db_dataset_for( self, dbkey ): - """ - Returns the db_file dataset associated/needed by `dataset`, or `None`. - """ - # If no history, return None. - if self.history is None: - return None - if isinstance(self.history, Bunch): - # The API presents a Bunch for a history. Until the API is - # more fully featured for handling this, also return None. - return None - datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ - .filter_by( deleted=False, history_id=self.history.id, extension="len" ) - for ds in datasets: - if dbkey == ds.dbkey: - return ds - return None - - def request_types(self): - if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: - return True - return False - class FormBuilder( object ): """ diff -r 162b355ae974e9082ae013640632d534579add6c -r eaf8920f999bab18a44c938565b643e0612f6e15 test/unit/test_galaxy_transactions.py --- /dev/null +++ b/test/unit/test_galaxy_transactions.py @@ -0,0 +1,74 @@ +from galaxy import model +from galaxy.model import mapping +from galaxy.util import bunch +from galaxy.web import framework + + +class TestTransaction( framework.ProvidesAppContext ): + + def __init__( self ): + self.app = TestApp() + + +def test_logging_events_off(): + trans = TestTransaction() + trans.log_event( "test event 123" ) + assert len( trans.sa_session.query( model.Event ).all() ) == 0 + + +def test_logging_events_on(): + trans = TestTransaction() + trans.app.config.log_events = True + trans.log_event( "test event 123" ) + events = trans.sa_session.query( model.Event ).all() + assert len( events ) == 1 + assert events[ 0 ].message == "test event 123" + + +def test_logging_actions_off(): + trans = TestTransaction() + trans.log_action( "test action 123" ) + assert len( trans.sa_session.query( model.Event ).all() ) == 0 + + +def test_logging_actions_on(): + trans = TestTransaction() + trans.app.config.log_actions = True + trans.log_action( None, "test action 123", context="the context", params=dict(foo="bar") ) + actions = trans.sa_session.query( model.UserAction ).all() + assert len( actions ) == 1 + assert actions[ 0 ].action == "test action 123" + + +def test_expunge_all(): + trans = TestTransaction() + + user = model.User( "foo", "bar1" ) + trans.sa_session.add( user ) + + user.password = "bar2" + trans.sa_session.flush() + + assert trans.sa_session.query( model.User ).first().password == "bar2" + + trans.sa_session.expunge_all() + + user.password = "bar3" + trans.sa_session.flush() + + # Password unchange because not attached to session/context. + assert trans.sa_session.query( model.User ).first().password == "bar2" + + +class TestApp( object ): + + def __init__( self ): + self.config = bunch.Bunch( + log_events=False, + log_actions=False, + ) + self.model = mapping.init( + "/tmp", + "sqlite:///:memory:", + create_tables=True + ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix for running LSF DRMAA jobs as 'real' user.
by commits-noreply＠bitbucket.org 18 Aug '14

18 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e66936a92feb/ Changeset: e66936a92feb User: jmchilton Date: 2014-08-18 14:43:37 Summary: Fix for running LSF DRMAA jobs as 'real' user. Fix thanks to Chong Chen at IBM - "When invoking the LSF drmma api to submit a job, the API will print the message like 'Job <78> is submitted to default queue <normal>'. So if the Galaxy want to use this API, need modify the drmaa_external_runner.py script to handle this message. LSF already support a env variable to disable this message print out, "BSUB_QUIET", set this into env can disable this message output." A second issue was related to subsequent querying of the job state as a user other than the submitter - according to Chong Chen this has been fixed in latest LSF DRMAA changes on github (https://github.com/PlatformLSF/lsf-drmaa/commit/43e62546172b90d9f95e90273d7…) Affected #: 1 file diff -r 572a8d5ee218aeb37f77660948cb75a439936868 -r e66936a92febf952017586742db36ed44be4d08b scripts/drmaa_external_runner.py --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -124,6 +124,9 @@ userid, json_filename, assign_all_groups = validate_paramters() set_user(userid, assign_all_groups) json_file_exists(json_filename) + # Added to disable LSF generated messages that would interfer with this + # script. Fix thank to Chong Chen at IBM. + os.environ['BSUB_QUIET'] = 'Y' s = drmaa.Session() s.initialize() jt = s.createJobTemplate() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 17 Aug '14

17 Aug '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae0dd02c419c/ Changeset: ae0dd02c419c User: jmchilton Date: 2014-08-17 22:38:34 Summary: PEP-8 fixes for galaxy.jobs.mapper. Affected #: 1 file diff -r 109f40daa21ad0348662805f93f1cf1c9fbd6003 -r ae0dd02c419c0cc781c8601ffc5fd9bf4f8af2ca lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -10,6 +10,7 @@ DYNAMIC_RUNNER_NAME = "dynamic" DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url" + class JobMappingException( Exception ): def __init__( self, failure_message ): @@ -65,12 +66,14 @@ def __invoke_expand_function( self, expand_function ): function_arg_names = inspect.getargspec( expand_function ).args app = self.job_wrapper.app - possible_args = { "job_id" : self.job_wrapper.job_id, - "tool" : self.job_wrapper.tool, - "tool_id" : self.job_wrapper.tool.id, - "job_wrapper" : self.job_wrapper, - "rule_helper": RuleHelper( app ), - "app" : app } + possible_args = { + "job_id": self.job_wrapper.job_id, + "tool": self.job_wrapper.tool, + "tool_id": self.job_wrapper.tool.id, + "job_wrapper": self.job_wrapper, + "rule_helper": RuleHelper( app ), + "app": app + } actual_args = {} @@ -82,7 +85,6 @@ # Don't hit the DB to load the job object if not needed if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names: job = self.job_wrapper.get_job() - history = job.history user = job.user user_email = user and str(user.email) https://bitbucket.org/galaxy/galaxy-central/commits/cfb0c443884f/ Changeset: cfb0c443884f User: jmchilton Date: 2014-08-17 22:38:34 Summary: Small refactor of galaxy.jobs.mapper to make it more testable. Affected #: 1 file diff -r ae0dd02c419c0cc781c8601ffc5fd9bf4f8af2ca -r cfb0c443884f65a6297699b35b323962e2b74539 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -35,6 +35,8 @@ self.url_to_destination = url_to_destination self.job_config = job_config + self.rules_module = galaxy.jobs.rules + def __get_rule_modules( self ): unsorted_module_names = self.__get_rule_module_names( ) ## Load modules in reverse order to allow hierarchical overrides @@ -55,11 +57,12 @@ return modules def __get_rule_module_names( self ): - rules_dir = galaxy.jobs.rules.__path__[0] + rules_dir = self.rules_module.__path__[0] names = [] for fname in os.listdir( rules_dir ): if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): - rule_module_name = "galaxy.jobs.rules.%s" % fname[:-len(".py")] + base_name = self.rules_module.__name__ + rule_module_name = "%s.%s" % (base_name, fname[:-len(".py")]) names.append( rule_module_name ) return names https://bitbucket.org/galaxy/galaxy-central/commits/949be0b9ef72/ Changeset: 949be0b9ef72 User: jmchilton Date: 2014-08-17 22:38:34 Summary: Job mapping unit tests. A bunch of unit tests for galaxy.jobs.mapper and galaxy.jobs.rule_helper testing various aspects of static and dynamic job mapping and the utility class (RuleHelper) that can be supplied to dynamic job rules. Affected #: 5 files diff -r cfb0c443884f65a6297699b35b323962e2b74539 -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa test/unit/jobs/test_mapper.py --- /dev/null +++ b/test/unit/jobs/test_mapper.py @@ -0,0 +1,129 @@ +import jobs.test_rules + +from galaxy.jobs.mapper import JobRunnerMapper +from galaxy.jobs import JobDestination + +from galaxy.util import bunch + + +TOOL_JOB_DESTINATION = JobDestination() +DYNAMICALLY_GENERATED_DESTINATION = JobDestination() + + +def test_static_mapping(): + mapper = __mapper() + assert mapper.get_job_destination( {} ) is TOOL_JOB_DESTINATION + + +def test_caching(): + mapper = __mapper() + mapper.get_job_destination( {} ) + mapper.get_job_destination( {} ) + assert mapper.job_wrapper.tool.call_count == 1 + + +def test_dynamic_mapping(): + mapper = __mapper( __dynamic_destination( dict( function="upload" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "local_runner" + + +def test_dynamic_mapping_priorities(): + mapper = __mapper( __dynamic_destination( dict( function="tophat" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + # Next line verifies we using definition in 20_instance.py instead of + # 10_site.py. + assert mapper.job_config.rule_response == "instance_dest_id" + + +def test_dynamic_mapping_defaults_to_tool_id_as_rule(): + mapper = __mapper( __dynamic_destination( ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "tool1_dest_id" + + +def test_dynamic_mapping_function_parameters(): + mapper = __mapper( __dynamic_destination( dict( function="check_rule_params" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "all_passed" + + +def test_dynamic_mapping_resource_parameters(): + mapper = __mapper( __dynamic_destination( dict( function="check_resource_params" ) ) ) + assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION + assert mapper.job_config.rule_response == "have_resource_params" + + +def __mapper( tool_job_destination=TOOL_JOB_DESTINATION ): + job_wrapper = MockJobWrapper( tool_job_destination ) + job_config = MockJobConfig() + + mapper = JobRunnerMapper( + job_wrapper, + {}, + job_config + ) + mapper.rules_module = jobs.test_rules + return mapper + + +def __dynamic_destination( params={} ): + return JobDestination( runner="dynamic", params=params ) + + +class MockJobConfig( object ): + + def __init__( self ): + self.rule_response = None + + def get_destination( self, rep ): + # Called to transform dynamic job destination rule response + # from destination id/runner url into a dynamic job destination. + self.rule_response = rep + return DYNAMICALLY_GENERATED_DESTINATION + + +class MockJobWrapper( object ): + + def __init__( self, tool_job_destination ): + self.tool = MockTool( tool_job_destination ) + self.job_id = 12345 + self.app = object() + + def is_mock_job_wrapper( self ): + return True + + def get_job(self): + def get_param_values( app, ignore_errors ): + assert app == self.app + return { + "threshold": 8, + "__job_resource": { + "__job_resource__select": "True", + "memory": "8gb" + } + } + + return bunch.Bunch( + user=bunch.Bunch( + id=6789, + email="test(a)example.com" + ), + get_param_values=get_param_values + ) + + +class MockTool( object ): + + def __init__( self, tool_job_destination ): + self.id = "testtoolshed/devteam/tool1/23abcd13123" + self.call_count = 0 + self.tool_job_destination = tool_job_destination + self.all_ids = [ "testtoolshed/devteam/tool1/23abcd13123", "tool1" ] + + def get_job_destination( self, params ): + self.call_count += 1 + return self.tool_job_destination + + def is_mock_tool( self ): + return True diff -r cfb0c443884f65a6297699b35b323962e2b74539 -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa test/unit/jobs/test_rule_helper.py --- /dev/null +++ b/test/unit/jobs/test_rule_helper.py @@ -0,0 +1,98 @@ +from galaxy.util import bunch +from galaxy import model +from galaxy.model import mapping + +from galaxy.jobs.rule_helper import RuleHelper + +USER_EMAIL_1 = "u1(a)example.com" +USER_EMAIL_2 = "u2(a)example.com" +USER_EMAIL_3 = "u3(a)example.com" + + +def test_job_count(): + rule_helper = __rule_helper() + __assert_job_count_is( 0, rule_helper ) + + __setup_fixtures( rule_helper.app ) + + # Test raw counts for users... + __assert_job_count_is( 7, rule_helper, for_user_email=USER_EMAIL_1 ) + __assert_job_count_is( 2, rule_helper, for_user_email=USER_EMAIL_2 ) + __assert_job_count_is( 0, rule_helper, for_user_email=USER_EMAIL_3 ) + + # Test desitnation counts + __assert_job_count_is( 2, rule_helper, for_destination="local" ) + __assert_job_count_is( 7, rule_helper, for_destination="cluster1" ) + + # Test per user destination counts + __assert_job_count_is( 5, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1 ) + __assert_job_count_is( 2, rule_helper, for_destination="local", for_user_email=USER_EMAIL_1 ) + + __assert_job_count_is( 2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_2 ) + __assert_job_count_is( 0, rule_helper, for_destination="local", for_user_email=USER_EMAIL_2 ) + + # Test per user, per state destination counts + __assert_job_count_is( 3, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=[ "queued" ] ) + __assert_job_count_is( 2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=[ "running" ] ) + __assert_job_count_is( 0, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=[ "error" ] ) + __assert_job_count_is( 5, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=[ "queued", "running", "error" ] ) + + +def __assert_job_count_is( expected_count, rule_helper, **kwds ): + acutal_count = rule_helper.job_count( **kwds ) + + if expected_count != acutal_count: + template = "Expected job count %d, actual job count %s for params %s" + raise AssertionError( template % ( expected_count, acutal_count, kwds ) ) + + +def __setup_fixtures( app ): + # user1 has 3 jobs queued and 2 jobs running on cluster1 and one queued and + # on running job on local. user2 has a queued and running job on the cluster. + # user3 has no jobs. + user1 = model.User( email=USER_EMAIL_1, password="pass1" ) + user2 = model.User( email=USER_EMAIL_2, password="pass2" ) + user3 = model.User( email=USER_EMAIL_2, password="pass2" ) + + app.add( user1, user2, user3 ) + + app.add( __new_job( user=user1, destination_id="cluster1", state="queued" ) ) + app.add( __new_job( user=user1, destination_id="cluster1", state="queued" ) ) + app.add( __new_job( user=user1, destination_id="cluster1", state="queued" ) ) + app.add( __new_job( user=user1, destination_id="cluster1", state="running" ) ) + app.add( __new_job( user=user1, destination_id="cluster1", state="running" ) ) + + app.add( __new_job( user=user1, destination_id="local", state="queued" ) ) + app.add( __new_job( user=user1, destination_id="local", state="running" ) ) + + app.add( __new_job( user=user2, destination_id="cluster1", state="queued" ) ) + app.add( __new_job( user=user2, destination_id="cluster1", state="running" ) ) + + +def __rule_helper(): + app = MockApp() + rule_helper = RuleHelper( app ) + return rule_helper + + +def __new_job( **kwds ): + job = model.Job() + for key, value in kwds.items(): + setattr( job, key, value ) + return job + + +class MockApp( object ): + + def __init__( self ): + self.config = bunch.Bunch( ) + self.model = mapping.init( + "/tmp", + "sqlite:///:memory:", + create_tables=True + ) + + def add( self, *args ): + for arg in args: + self.model.context.add( arg ) + self.model.context.flush() diff -r cfb0c443884f65a6297699b35b323962e2b74539 -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa test/unit/jobs/test_rules/10_site.py --- /dev/null +++ b/test/unit/jobs/test_rules/10_site.py @@ -0,0 +1,45 @@ + + +def upload(): + return 'local_runner' + + +def tophat(): + return 'site_dest_id' + + +def tool1(): + # tool1 is id to test tool mocked out in test_mapper.py, without specify + # function name in dynamic destination - this function should be used by + # default. + return 'tool1_dest_id' + + +def check_rule_params( + job_id, + tool, + tool_id, + job_wrapper, + rule_helper, + app, + job, + user, + user_email, +): + assert job_id == 12345 + assert tool.is_mock_tool() + assert tool_id == "testtoolshed/devteam/tool1/23abcd13123" + assert job_wrapper.is_mock_job_wrapper() + assert app == job_wrapper.app + assert rule_helper is not None + + assert job.user == user + assert user.id == 6789 + assert user_email == "test(a)example.com" + + return "all_passed" + + +def check_resource_params( resource_params ): + assert resource_params["memory"] == "8gb" + return "have_resource_params" diff -r cfb0c443884f65a6297699b35b323962e2b74539 -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa test/unit/jobs/test_rules/20_instance.py --- /dev/null +++ b/test/unit/jobs/test_rules/20_instance.py @@ -0,0 +1,6 @@ + + +def tophat(): + # This should override definition in 10_site.py + return 'instance_dest_id' + https://bitbucket.org/galaxy/galaxy-central/commits/47efdb818f41/ Changeset: 47efdb818f41 User: jmchilton Date: 2014-08-17 22:38:34 Summary: Improved error handling for dynamic job destinations. More and more verbose error messages with updated terminology and error conditions unit tested. Affected #: 2 files diff -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa -r 47efdb818f41227c4c4ff179a0c9a28e9e154acd lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -10,6 +10,9 @@ DYNAMIC_RUNNER_NAME = "dynamic" DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url" +ERROR_MESSAGE_NO_RULE_FUNCTION = "Galaxy misconfigured - cannot find dynamic rule function name for destination %s." +ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = "Galaxy misconfigured - no rule function named %s found in dynamic rule modules." + class JobMappingException( Exception ): @@ -150,7 +153,8 @@ expand_function = getattr( matching_rule_module, expand_function_name ) return expand_function else: - raise Exception( "Dynamic job runner cannot find function to expand job runner type - %s" % expand_function_name ) + message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % ( expand_function_name ) + raise Exception( message ) def __last_rule_module_with_function( self, function_name ): # self.rule_modules is sorted in reverse order, so find first @@ -164,6 +168,10 @@ expand_type = destination.params.get('type', "python") if expand_type == "python": expand_function_name = self.__determine_expand_function_name( destination ) + if not expand_function_name: + message = ERROR_MESSAGE_NO_RULE_FUNCTION % destination + raise Exception( message ) + expand_function = self.__get_expand_function( expand_function_name ) job_destination = self.__invoke_expand_function( expand_function ) if not isinstance(job_destination, galaxy.jobs.JobDestination): diff -r 949be0b9ef72b54ea7d1584055f563e2209aeeaa -r 47efdb818f41227c4c4ff179a0c9a28e9e154acd test/unit/jobs/test_mapper.py --- a/test/unit/jobs/test_mapper.py +++ b/test/unit/jobs/test_mapper.py @@ -1,6 +1,10 @@ import jobs.test_rules -from galaxy.jobs.mapper import JobRunnerMapper +from galaxy.jobs.mapper import ( + JobRunnerMapper, + ERROR_MESSAGE_NO_RULE_FUNCTION, + ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND, +) from galaxy.jobs import JobDestination from galaxy.util import bunch @@ -54,6 +58,32 @@ assert mapper.job_config.rule_response == "have_resource_params" +def test_dynamic_mapping_no_function(): + dest = __dynamic_destination( dict( ) ) + mapper = __mapper( dest ) + mapper.job_wrapper.tool.all_ids = [ "no_such_function" ] + error_message = ERROR_MESSAGE_NO_RULE_FUNCTION % dest + __assert_mapper_errors_with_message( mapper, error_message ) + + +def test_dynamic_mapping_missing_function(): + dest = __dynamic_destination( dict( function="missing_func" ) ) + mapper = __mapper( dest ) + mapper.job_wrapper.tool.all_ids = [ "no_such_function" ] + error_message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % ( "missing_func" ) + __assert_mapper_errors_with_message( mapper, error_message ) + + +def __assert_mapper_errors_with_message( mapper, message ): + exception = None + try: + mapper.get_job_destination( {} ) + except Exception as e: + exception = e + assert exception + assert str( exception ) == message, "%s != %s" % ( str( exception ), message ) + + def __mapper( tool_job_destination=TOOL_JOB_DESTINATION ): job_wrapper = MockJobWrapper( tool_job_destination ) job_config = MockJobConfig() https://bitbucket.org/galaxy/galaxy-central/commits/ef7107f56ffb/ Changeset: ef7107f56ffb User: jmchilton Date: 2014-08-17 22:38:34 Summary: galaxy.job.mapper refactoring and cleanup. Affected #: 1 file diff -r 47efdb818f41227c4c4ff179a0c9a28e9e154acd -r ef7107f56ffb6377d0cb0bd04a5cfae9e6b22a2f lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -89,7 +89,12 @@ actual_args[ possible_arg_name ] = possible_args[ possible_arg_name ] # Don't hit the DB to load the job object if not needed - if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names: + require_db = False + for param in ["job", "user", "user_email", "resource_params"]: + if param in function_arg_names: + require_db = True + break + if require_db: job = self.job_wrapper.get_job() user = job.user user_email = user and str(user.email) @@ -106,16 +111,12 @@ if "resource_params" in function_arg_names: # Find the dymically inserted resource parameters and give them # to rule. - app = self.job_wrapper.app - param_values = job.get_param_values( app, ignore_errors=True ) + param_values = self.__job_params( job ) resource_params = {} try: resource_params_raw = param_values[ "__job_resource" ] if resource_params_raw[ "__job_resource__select" ].lower() in [ "1", "yes", "true" ]: for key, value in resource_params_raw.iteritems(): - #if key.startswith( "__job_resource_param__" ): - # resource_key = key[ len( "__job_resource_param__" ): ] - # resource_params[ resource_key ] = value resource_params[ key ] = value except KeyError: pass @@ -123,6 +124,11 @@ return expand_function( **actual_args ) + def __job_params( self, job ): + app = self.job_wrapper.app + param_values = job.get_param_values( app, ignore_errors=True ) + return param_values + def __convert_url_to_destination( self, url ): """ Job runner URLs are deprecated, but dynamic mapper functions may still @@ -173,28 +179,28 @@ raise Exception( message ) expand_function = self.__get_expand_function( expand_function_name ) - job_destination = self.__invoke_expand_function( expand_function ) - if not isinstance(job_destination, galaxy.jobs.JobDestination): - job_destination_rep = str(job_destination) # Should be either id or url - if '://' in job_destination_rep: - job_destination = self.__convert_url_to_destination(job_destination_rep) - else: - job_destination = self.job_config.get_destination(job_destination_rep) - return job_destination + return self.__handle_rule( expand_function ) else: raise Exception( "Unhandled dynamic job runner type specified - %s" % expand_type ) + def __handle_rule( self, rule_function ): + job_destination = self.__invoke_expand_function( rule_function ) + if not isinstance(job_destination, galaxy.jobs.JobDestination): + job_destination_rep = str(job_destination) # Should be either id or url + if '://' in job_destination_rep: + job_destination = self.__convert_url_to_destination(job_destination_rep) + else: + job_destination = self.job_config.get_destination(job_destination_rep) + return job_destination + def __cache_job_destination( self, params, raw_job_destination=None ): if raw_job_destination is None: raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) - #raw_job_destination_id_or_tag = self.job_wrapper.tool.get_job_destination_id_or_tag( params ) if raw_job_destination.runner == DYNAMIC_RUNNER_NAME: job_destination = self.__handle_dynamic_job_destination( raw_job_destination ) else: job_destination = raw_job_destination - #job_destination_id_or_tag = raw_job_destination_id_or_tag self.cached_job_destination = job_destination - #self.cached_job_destination_id_or_tag = job_destination_id_or_tag def get_job_destination( self, params ): """ https://bitbucket.org/galaxy/galaxy-central/commits/572a8d5ee218/ Changeset: 572a8d5ee218 User: jmchilton Date: 2014-08-17 22:38:34 Summary: Small optimization in galaxy.jobs.rule_helper. Affected #: 1 file diff -r ef7107f56ffb6377d0cb0bd04a5cfae9e6b22a2f -r 572a8d5ee218aeb37f77660948cb75a439936868 lib/galaxy/jobs/rule_helper.py --- a/lib/galaxy/jobs/rule_helper.py +++ b/lib/galaxy/jobs/rule_helper.py @@ -82,6 +82,10 @@ query = query.filter( model.Job.table.c.update_time >= start_date ) if for_job_states is not None: - query = query.filter( model.Job.table.c.state.in_( for_job_states ) ) + # Optimize the singleton case - can be much more performant in my experience. + if len( for_job_states ) == 1: + query = query.filter( model.Job.table.c.state == for_job_states[ 0 ] ) + else: + query = query.filter( model.Job.table.c.state.in_( for_job_states ) ) return query Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add c3.2xlarge instances to the cloudlaunch list. This list is being moved to bioblend.cloudman and will be updated there in the future, but this is a stopgap measure enabling use of this particularly useful instance type.
by commits-noreply＠bitbucket.org 15 Aug '14

15 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/109f40daa21a/ Changeset: 109f40daa21a User: dannon Date: 2014-08-15 22:35:02 Summary: Add c3.2xlarge instances to the cloudlaunch list. This list is being moved to bioblend.cloudman and will be updated there in the future, but this is a stopgap measure enabling use of this particularly useful instance type. Affected #: 1 file diff -r 2d509288d484025de4f882b28b2c22069f12422e -r 109f40daa21ad0348662805f93f1cf1c9fbd6003 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -240,6 +240,7 @@ <select name="instance_type" id="id_instance_type"><option value="m1.large">Large</option><option value="m1.xlarge">Extra Large</option> + <option value="c3.2xlarge">Compute Optimized Double Extra Large</option><option value="m2.4xlarge">High-Memory Quadruple Extra Large</option></select></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Core, controllers: Remove test method from root controller
by commits-noreply＠bitbucket.org 15 Aug '14

15 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d509288d484/ Changeset: 2d509288d484 User: carlfeberhard Date: 2014-08-15 16:46:54 Summary: Core, controllers: Remove test method from root controller Affected #: 1 file diff -r 5f7aab7158fd26bfb07835fef66b051d480f40cc -r 2d509288d484025de4f882b28b2c22069f12422e lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -514,8 +514,3 @@ raise HTTPBadGateway() trans.response.status = code return { 'error': 'Fake error!' } - - @web.expose - def test( self, trans, **kwargs ): - #trans.response.headers[ 'Content-Type' ] = 'text/plain' - return trans.fill_template( 'test/test.mako', **kwargs ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, History: add copy method to model; fill out history collection; pack scripts
by commits-noreply＠bitbucket.org 15 Aug '14

15 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f7aab7158fd/ Changeset: 5f7aab7158fd User: carlfeberhard Date: 2014-08-15 15:58:15 Summary: UI, History: add copy method to model; fill out history collection; pack scripts Affected #: 5 files diff -r 4a55f350a68d65d7e076505af575ca112894f677 -r 5f7aab7158fd26bfb07835fef66b051d480f40cc static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -187,6 +187,36 @@ return xhr; }, + /** Make a copy of this history on the server + * @param {Boolean} current if true, set the copy as the new current history (default: true) + * @param {String} name name of new history (default: none - server sets to: Copy of <current name>) + * @fires copied passed this history and the response JSON from the copy + * @returns {xhr} + */ + copy : function( current, name ){ + current = ( current !== undefined )?( current ):( true ); + if( !this.id ){ + throw new Error( 'You must set the history ID before copying it.' ); + } + + var postData = { history_id : this.id }; + if( current ){ + postData.current = true; + } + if( name ){ + postData.name = name; + } + + //TODO:?? all datasets? + + var history = this, + xhr = jQuery.post( this.urlRoot, postData ); + xhr.done( function( newData ){ + history.trigger( 'copied', history, newData ); + }); + return xhr; + }, + // ........................................................................ misc toString : function(){ return 'History(' + this.get( 'id' ) + ',' + this.get( 'name' ) + ')'; @@ -280,10 +310,55 @@ var HistoryCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - urlRoot : galaxy_config.root + 'api/histories' /** logger used to record this.log messages, commonly set to console */ //logger : console, + + urlRoot : ( window.galaxy_config? galaxy_config.root : '/' ) + 'api/histories', + //url : function(){ return this.urlRoot; }, + + initialize : function( models, options ){ + options = options || {}; + this.log( 'HistoryCollection.initialize', arguments ); + this.includeDeleted = options.includeDeleted || false; + + //this.on( 'all', function(){ + // console.info( 'event:', arguments ); + //}); + + this.setUpListeners(); + }, + + setUpListeners : function setUpListeners(){ + var collection = this; + + // when a history is deleted, remove it from the collection (if optionally set to do so) + this.on( 'change:deleted', function( history ){ + this.debug( 'change:deleted', collection.includeDeleted, history.get( 'deleted' ) ); + if( !collection.includeDeleted && history.get( 'deleted' ) ){ + collection.remove( history ); + } + }); + + // listen for a history copy, adding it to the beginning of the collection + this.on( 'copied', function( original, newData ){ + this.unshift( new History( newData, [] ) ); + }); + }, + + create : function create( data, hdas, historyOptions, xhrOptions ){ + var collection = this, + history = new History( data || {}, hdas || [], historyOptions || {} ); + return history.save( xhrOptions ).done( function( newData ){ + // new histories go in the front +//TODO: (implicit ordering by update time...) + collection.unshift( history ); + }); + }, + + toString: function toString(){ + return 'HistoryCollection(' + this.length + ')'; + } }); //============================================================================== diff -r 4a55f350a68d65d7e076505af575ca112894f677 -r 5f7aab7158fd26bfb07835fef66b051d480f40cc static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length==0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()==0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length===0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()===0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file diff -r 4a55f350a68d65d7e076505af575ca112894f677 -r 5f7aab7158fd26bfb07835fef66b051d480f40cc static/scripts/packed/mvc/dataset/dataset-li.js --- a/static/scripts/packed/mvc/dataset/dataset-li.js +++ b/static/scripts/packed/mvc/dataset/dataset-li.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDetailMessages:function(){var f=this,h=$('<div class="detail-messages"></div>'),g=f.model.toJSON();_.each(f.templates.detailMessages,function(i){h.append($(i(g,f)))});return h},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var h=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var i=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var g=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var j={};j[a.OK]=j[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");j[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");j[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");j[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");j[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");j[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");j[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");j[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");j[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");j[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");j[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");j.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var k={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:h,details:i,noAccess:g,summaries:j,detailMessages:k,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){require(["mvc/data"],function(k){var l=new k.TabularDataset({id:f.model.get("id")});$.when(l.fetch()).then(function(){k.createTabularDatasetChunkedView({model:l,parent_elt:j,embedded:true,height:"100%"})})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDetailMessages:function(){var f=this,h=$('<div class="detail-messages"></div>'),g=f.model.toJSON();_.each(f.templates.detailMessages,function(i){h.append($(i(g,f)))});return h},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var h=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var i=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var g=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var j={};j[a.OK]=j[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");j[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");j[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");j[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");j[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");j[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");j[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");j[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");j[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");j[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");j[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");j.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var k={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:h,details:i,noAccess:g,summaries:j,detailMessages:k,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file diff -r 4a55f350a68d65d7e076505af575ca112894f677 -r 5f7aab7158fd26bfb07835fef66b051d480f40cc static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(e,a,b){var d=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.log("creating history contents:",i);this.contents=new e.HistoryContents(i||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.contents){this.contents.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||d.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.contents.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});d.UPDATE_DELAY=4000;d.getHistoryData=function f(g,s){s=s||{};var m=s.hdaDetailIds||[];var i=s.hdcaDetailIds||[];var o=jQuery.Deferred(),n=null;function h(t){return jQuery.ajax(galaxy_config.root+"api/histories/"+g)}function l(t){return t&&t.empty}function r(u){if(l(u)){return[]}if(_.isFunction(m)){m=m(u)}if(_.isFunction(i)){i=i(u)}var t={};if(m.length){t.dataset_details=m.join(",")}if(i.length){t.dataset_collection_details=i.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+u.id+"/contents",{data:t})}var q=s.historyFn||h,p=s.hdaFn||r;var k=q(g);k.done(function(t){n=t;o.notify({status:"history data retrieved",historyJSON:n})});k.fail(function(v,t,u){o.reject(v,"loading the history")});var j=k.then(p);j.then(function(t){o.notify({status:"dataset data retrieved",historyJSON:n,hdaJSON:t});o.resolve(n,t)});j.fail(function(v,t,u){o.reject(v,"loading the datasets",{history:n})});return o};var c=Backbone.Collection.extend(a.LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories"});return{History:d,HistoryCollection:c}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);n.done(function(o){l.trigger("copied",l,o)});return n},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var p=v.hdaDetailIds||[];var l=v.hdcaDetailIds||[];var r=jQuery.Deferred(),q=null;function k(w){return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function u(x){if(o(x)){return[]}if(_.isFunction(p)){p=p(x)}if(_.isFunction(l)){l=l(x)}var w={};if(p.length){w.dataset_details=p.join(",")}if(l.length){w.dataset_collection_details=l.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,s=v.hdaFn||u;var n=t(j);n.done(function(w){q=w;r.notify({status:"history data retrieved",historyJSON:q})});n.fail(function(y,w,x){r.reject(y,"loading the history")});var m=n.then(s);m.then(function(w){r.notify({status:"dataset data retrieved",historyJSON:q,hdaJSON:w});r.resolve(q,w)});m.fail(function(y,w,x){r.reject(y,"loading the datasets",{history:q})});return r};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=new e(m||{},k||[],j||{});return n.save(l).done(function(p){o.unshift(n)})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file diff -r 4a55f350a68d65d7e076505af575ca112894f677 -r 5f7aab7158fd26bfb07835fef66b051d480f40cc static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set_data(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(z,A){var B=A.get("start")-x.region.get("start");return x.data.slice(B,B+A.length())}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));var x=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",p.ConfigSettingCollection.from_models_and_saved_values(x,v.prefs));var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));var w=[];this.set("config",p.ConfigSettingCollection.from_models_and_saved_values(w,v.prefs));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,j,l,o){var e={toJSON:function(){var u=this,v={};s.each(u.constructor.to_json_keys,function(w){var x=u.get(w);if(w in u.constructor.to_json_mappers){x=u.constructor.to_json_mappers[w](x,u)}v[w]=x});return v}};var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){Galaxy.modal.show({title:"Select datasets for new tracks",body:y,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});Galaxy.modal.hide()}}})}})};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var c=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(l.is_deferred(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(l.is_deferred(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!l.is_deferred(C)){var F=this.subset_entry(C,B);this.set_data(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){B=B.copy();var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(y,z){var A=z.get("start")-w.region.get("start");return w.data.slice(A,A+z.length())}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=c.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?c.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var d=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(u){this.set("region",new g(u.region))}});var r=Backbone.Collection.extend({model:d});var t=Backbone.Model.extend(e).extend({defaults:{mode:"Auto"},initialize:function(u){this.set("dataset",new j.Dataset(u.dataset));var w=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",o.ConfigSettingCollection.from_models_and_saved_values(w,u.prefs));var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new c({dataset:this.get("dataset"),init_data:v}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(v,u){if(s.size(v)===0){v={name:u.get("config").get("name").get("value"),color:u.get("config").get("color").get("value")}}return v},dataset:function(u){return{id:u.id,hda_ldda:u.get("hda_ldda")}}}});var i=Backbone.Collection.extend({model:t});var n=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend(e).extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(u){this.set("drawables",new i(u.tracks));var v=[];this.set("config",o.ConfigSettingCollection.from_models_and_saved_values(v,u.prefs));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(u){this.get("drawables").add(u)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(v,u){return{obj_type:"View",prefs:{name:u.get("title"),content_visible:true},drawables:u.get("drawables")}}}});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:d,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:b,GenomeDataManager:c,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,Visualization:n,select_datasets:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Build: add grunt-contrib-clean to styles builder, remove tmp-site-config.less on build
by commits-noreply＠bitbucket.org 15 Aug '14

15 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a55f350a68d/ Changeset: 4a55f350a68d User: carlfeberhard Date: 2014-08-15 15:28:27 Summary: Build: add grunt-contrib-clean to styles builder, remove tmp-site-config.less on build Affected #: 2 files diff -r e4ce04f7e7447d9f4d6a736d8f64ad2575a88813 -r 4a55f350a68d65d7e076505af575ca112894f677 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,16 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue'; - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster', 'circster' ]; + var lessFiles = [ + 'base', + 'autocomplete_tagging', + 'embed_item', + 'iphone', + 'masthead', + 'library', + 'trackster', + 'circster' + ]; var _ = grunt.util._; var fmt = _.sprintf; @@ -46,23 +55,29 @@ paths: [ out ] }, dist: { - files: _.reduce( lessFiles, function( d, s ) { - d[ fmt( '%s/%s.css', out, s ) ] = [ fmt( 'src/less/%s.less', s ) ]; return d + files: _.reduce( lessFiles, function( d, s ) { + d[ fmt( '%s/%s.css', out, s ) ] = [ fmt( 'src/less/%s.less', s ) ]; return d; }, {} ) } }, + + // remove tmp files + clean: { + clean : [ fmt('%s/tmp-site-config.less', out) ] + } }); // Write theme variable for less grunt.registerTask('less-site-config', 'Write site configuration for less', function() { - grunt.file.write( fmt('%s/tmp-site-config.less', out), fmt( "@theme-name: %s;", theme ) ) + grunt.file.write( fmt('%s/tmp-site-config.less', out), fmt( "@theme-name: %s;", theme ) ); }); // These plugins provide necessary tasks. grunt.loadNpmTasks('grunt-contrib-less'); grunt.loadNpmTasks('grunt-spritesmith'); + grunt.loadNpmTasks('grunt-contrib-clean'); // Default task. - grunt.registerTask('default', ['sprite', 'less-site-config', 'less']); + grunt.registerTask('default', ['sprite', 'less-site-config', 'less', 'clean']); }; diff -r e4ce04f7e7447d9f4d6a736d8f64ad2575a88813 -r 4a55f350a68d65d7e076505af575ca112894f677 static/style/package.json --- a/static/style/package.json +++ b/static/style/package.json @@ -4,6 +4,7 @@ "grunt": "~0.4.1", "grunt-recess": "~0.3.5", "grunt-spritesmith": "~1.7.0", - "grunt-contrib-less": "~0.7.0" + "grunt-contrib-less": "~0.7.0", + "grunt-contrib-clean": "0.6.0" } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: fix display of overlapping reads by correctly resolving read length regardless of data loading/tile drawing order. Unfortunately, the easiest way to accomplish this required refactoring, hence the large commit. Pack scripts.
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7f754e611031/ Changeset: 7f754e611031 Branch: stable User: jgoecks Date: 2014-08-13 23:25:35 Summary: Trackster: fix display of overlapping reads by correctly resolving read length regardless of data loading/tile drawing order. Unfortunately, the easiest way to accomplish this required refactoring, hence the large commit. Pack scripts. Affected #: 4 files diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 7f754e6110313cb35cfe96c6653509a5b39214f5 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,rect_y+(draw_height-1)/2,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,draw_height=(mode==="Pack"?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;var line_height=y_start+1+(draw_height-1)/2;dashedLine(ctx,b1_end,line_height,b2_start,line_height)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid].slot:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,rect_y+(draw_height-1)/2,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,draw_height=(mode==="Pack"?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;var line_height=y_start+1+(draw_height-1)/2;dashedLine(ctx,b1_end,line_height,b2_start,line_height)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 7f754e6110313cb35cfe96c6653509a5b39214f5 static/scripts/packed/viz/trackster/slotting.js --- a/static/scripts/packed/viz/trackster/slotting.js +++ b/static/scripts/packed/viz/trackster/slotting.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(b){var e=b.extend;var c=2,a=5;var d=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(d.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(c+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}});return{FeatureSlotter:d}}); \ No newline at end of file +define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){console.log(x[3],g.slot,this._find_slot(this._get_draw_coords(x)));var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}}); \ No newline at end of file diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 7f754e6110313cb35cfe96c6653509a5b39214f5 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -396,7 +396,7 @@ feature_end = feature[2], // Slot valid only if features are slotted and this feature is slotted; // feature may not be due to lack of space. - slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null); + slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid].slot : null); // Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and // (b) there's overlap between the feature and drawing region. diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 7f754e6110313cb35cfe96c6653509a5b39214f5 static/scripts/viz/trackster/slotting.js --- a/static/scripts/viz/trackster/slotting.js +++ b/static/scripts/viz/trackster/slotting.js @@ -7,6 +7,14 @@ PACK_SPACING = 5; /** + * Hold slotting information for a feature. + */ +var SlottedInfo = function(slot, feature) { + this.slot = slot; + this.feature = feature; +}; + +/** * FeatureSlotter determines slots in which to draw features for vertical * packing. * @@ -28,118 +36,148 @@ * the largest slot required for the passed set of features is returned */ extend( FeatureSlotter.prototype, { + /** + * Get drawing coordinate for a feature. + */ + _get_draw_coords: function(feature) { + // Get initial draw coordinates using w_scale. + var draw_start = Math.floor(feature[1] * this.w_scale), + draw_end = Math.ceil(feature[2] * this.w_scale), + f_name = feature[3], + text_align; + + // Update start, end drawing locations to include feature name. + // Try to put the name on the left, if not, put on right. + if (f_name !== undefined && this.include_label ) { + // Add gap for label spacing and extra pack space padding + // TODO: Fix constants + var text_len = this.measureText(f_name).width + (LABEL_SPACING + PACK_SPACING); + if (draw_start - text_len >= 0) { + draw_start -= text_len; + text_align = "left"; + } else { + draw_end += text_len; + text_align = "right"; + } + } + + /* + if (slot_num < 0) { + + TODO: this is not yet working -- + console.log(feature_uid, "looking for slot with text on the right"); + // Slot not found. If text was on left, try on right and see + // if slot can be found. + // TODO: are there any checks we need to do to ensure that text + // will fit on tile? + if (text_align === "left") { + draw_start -= text_len; + draw_end -= text_len; + text_align = "right"; + slot_num = find_slot(draw_start, draw_end); + } + if (slot_num >= 0) { + console.log(feature_uid, "found slot with text on the right"); + } + + } + */ + + return [draw_start, draw_end]; + }, + + /** + * Find the first slot such that current feature doesn't overlap any other features in that slot. + * Returns -1 if no slot was found. + */ + _find_slot: function(draw_coords) { + // TODO: Use a data structure for faster searching of available slots. + var draw_start = draw_coords[0], + draw_end = draw_coords[1]; + for (var slot_num = 0; slot_num <= this.max_rows; slot_num++) { + var has_overlap = false, + slot = this.start_end_dct[slot_num]; + if (slot !== undefined) { + // Iterate through features already in slot to see if current feature will fit. + for (var k = 0, k_len = slot.length; k < k_len; k++) { + var s_e = slot[k]; + if (draw_end > s_e[0] && draw_start < s_e[1]) { + // There is overlap + has_overlap = true; + break; + } + } + } + if (!has_overlap) { + return slot_num; + } + } + return -1; + }, + + /** + * Slot features. + */ slot_features: function( features ) { - var w_scale = this.w_scale, - start_end_dct = this.start_end_dct, + var start_end_dct = this.start_end_dct, undone = [], - slotted = [], - highest_slot = 0, - max_rows = this.max_rows; - - // If feature already exists in slots (from previously seen tiles), use the same slot, - // otherwise if not seen, add to "undone" list for slot calculation. - - // TODO: Should calculate zoom tile index, which will improve performance - // by only having to look at a smaller subset - // if (this.start_end_dct[0] === undefined) { this.start_end_dct[0] = []; } + highest_slot = 0, + feature, + feature_uid; + + // Loop through features to (a) find those that are not yet slotted and (b) update + // those that are slotted if new information is availabe. For (a), features already + // slotted (based on slotting from other tiles) will retain their current slot. for (var i = 0, len = features.length; i < len; i++) { - var feature = features[i], - feature_uid = feature[0]; - if (this.slots[feature_uid] !== undefined) { - highest_slot = Math.max(highest_slot, this.slots[feature_uid]); - slotted.push(this.slots[feature_uid]); - } else { + feature = features[i]; + feature_uid = feature[0]; + var slotted_info = this.slots[feature_uid]; + + // Separate and handle slotted vs. unslotted features. + if (slotted_info) { + // Feature is slotted; if feature now has larger start/end coordinates, + // update drawing coordinates. + if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) { + console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature))); + // Feature has changed (e.g. a single read now has its pair), so recalculate its + // drawing coordinates. + var old_draw_coords = this._get_draw_coords(slotted_info.feature), + new_draw_coords = this._get_draw_coords(feature), + slotted_coords = this.start_end_dct[slotted_info.slot]; + for (var k = 0; k < slotted_coords.length; k++) { + var dc = slotted_coords[k]; + if (dc[0] === old_draw_coords[0] && dc[1] === old_draw_coords[1]) { + // Replace old drawing coordinates with new ones. + slotted_coords[k] = new_draw_coords; + } + } + } + highest_slot = Math.max(highest_slot, this.slots[feature_uid].slot); + } + else { undone.push(i); } } - + // Slot unslotted features. - // Find the first slot such that current feature doesn't overlap any other features in that slot. - // Returns -1 if no slot was found. - var find_slot = function(f_start, f_end) { - // TODO: Fix constants - for (var slot_num = 0; slot_num <= max_rows; slot_num++) { - var has_overlap = false, - slot = start_end_dct[slot_num]; - if (slot !== undefined) { - // Iterate through features already in slot to see if current feature will fit. - for (var k = 0, k_len = slot.length; k < k_len; k++) { - var s_e = slot[k]; - if (f_end > s_e[0] && f_start < s_e[1]) { - // There is overlap - has_overlap = true; - break; - } - } - } - if (!has_overlap) { - return slot_num; - } - } - return -1; - }; - // Do slotting. for (var i = 0, len = undone.length; i < len; i++) { - var feature = features[undone[i]], - feature_uid = feature[0], - feature_start = feature[1], - feature_end = feature[2], - feature_name = feature[3], - // Where to start, end drawing on screen. - f_start = Math.floor( feature_start * w_scale ), - f_end = Math.ceil( feature_end * w_scale ), - text_len = this.measureText(feature_name).width, - text_align; - - // Update start, end drawing locations to include feature name. - // Try to put the name on the left, if not, put on right. - if (feature_name !== undefined && this.include_label ) { - // Add gap for label spacing and extra pack space padding - // TODO: Fix constants - text_len += (LABEL_SPACING + PACK_SPACING); - if (f_start - text_len >= 0) { - f_start -= text_len; - text_align = "left"; - } else { - f_end += text_len; - text_align = "right"; - } - } + feature = features[undone[i]]; + feature_uid = feature[0]; + var draw_coords = this._get_draw_coords(feature); // Find slot. - var slot_num = find_slot(f_start, f_end); + var slot_num = this._find_slot(draw_coords); - /* - if (slot_num < 0) { - - TODO: this is not yet working -- - console.log(feature_uid, "looking for slot with text on the right"); - // Slot not found. If text was on left, try on right and see - // if slot can be found. - // TODO: are there any checks we need to do to ensure that text - // will fit on tile? - if (text_align === "left") { - f_start -= text_len; - f_end -= text_len; - text_align = "right"; - slot_num = find_slot(f_start, f_end); - } - if (slot_num >= 0) { - console.log(feature_uid, "found slot with text on the right"); - } - - } - */ // Do slotting. if (slot_num >= 0) { // Add current feature to slot. if (start_end_dct[slot_num] === undefined) { start_end_dct[slot_num] = []; } - start_end_dct[slot_num].push([f_start, f_end]); - this.slots[feature_uid] = slot_num; + start_end_dct[slot_num].push(draw_coords); + this.slots[feature_uid] = new SlottedInfo(slot_num, feature); highest_slot = Math.max(highest_slot, slot_num); } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Code cleanup: semicolons and identity rather than equality.
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4ce04f7e744/ Changeset: e4ce04f7e744 User: jgoecks Date: 2014-08-14 23:14:46 Summary: Code cleanup: semicolons and identity rather than equality. Affected #: 1 file diff -r 86c487b0c65f0d4ba4ce0c33432f3727c619921c -r e4ce04f7e7447d9f4d6a736d8f64ad2575a88813 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -32,7 +32,7 @@ { icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', - onclick : function() { self._activate() }, + onclick : function() { self._activate(); }, onunload : function() { if (self.frames.length() > 0) { return "You opened " + self.frames.length() + " frame(s) which will be lost."; @@ -50,9 +50,9 @@ tooltip : 'Show/Hide Scratchbook', onclick : function(e) { if (self.frames.visible) { - self.frames.hide() + self.frames.hide(); } else { - self.frames.show() + self.frames.show(); } }, with_number : true @@ -70,7 +70,7 @@ // refresh menu this.frames.setOnChange(function() { self._refresh(); - }) + }); this._refresh(); }, @@ -98,7 +98,7 @@ var $galaxy_main = $(window.parent.document).find('#galaxy_main'); if (options.target == 'galaxy_main' || options.target == 'center') { - if ($galaxy_main.length == 0) + if ($galaxy_main.length === 0) { var href = options.content; if (href.indexOf('?') == -1) @@ -151,7 +151,7 @@ this.button_load.number(this.frames.length()); // check - if(this.frames.length() == 0) + if(this.frames.length() === 0) this.button_load.hide(); else this.button_load.show(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Readd data module that is needed to display dataset contents in Scratchbook.
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86c487b0c65f/ Changeset: 86c487b0c65f User: jgoecks Date: 2014-08-14 23:04:06 Summary: Readd data module that is needed to display dataset contents in Scratchbook. Affected #: 1 file diff -r de58677d81111fc0e84580607f1919f02c21f221 -r 86c487b0c65f0d4ba4ce0c33432f3727c619921c static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -177,13 +177,15 @@ title : "Data Viewer: " + self.model.get( 'name' ), type : "other", content : function( parent_elt ){ - var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); - $.when( new_dataset.fetch() ).then( function(){ - DATA.createTabularDatasetChunkedView({ - model: new_dataset, - parent_elt: parent_elt, - embedded: true, - height: '100%' + require(['mvc/data'], function(DATA) { + var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); + $.when( new_dataset.fetch() ).then( function(){ + DATA.createTabularDatasetChunkedView({ + model: new_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); }); }); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Remove unused code from client-side visualization library.
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de58677d8111/ Changeset: de58677d8111 User: jgoecks Date: 2014-08-14 22:41:37 Summary: Remove unused code from client-side visualization library. Affected #: 1 file diff -r 882673a409055ade1614d28b15d677f5ce257a36 -r de58677d81111fc0e84580607f1919f02c21f221 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1034,13 +1034,6 @@ ); /** - * Configuration data for a Trackster track. - */ -var TrackConfig = Backbone.Model.extend({ - -}); - -/** * -- Routers -- */ @@ -1081,7 +1074,6 @@ GenomeVisualization: GenomeVisualization, GenomeReferenceDataManager: GenomeReferenceDataManager, TrackBrowserRouter: TrackBrowserRouter, - TrackConfig: TrackConfig, Visualization: Visualization, select_datasets: select_datasets }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to 3179b324e9d5: remove debugging statements
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/882673a40905/ Changeset: 882673a40905 User: carlfeberhard Date: 2014-08-14 20:19:33 Summary: Fix to 3179b324e9d5: remove debugging statements Affected #: 2 files diff -r 3179b324e9d5886962fe2acda12c1b481bbd1e6a -r 882673a409055ade1614d28b15d677f5ce257a36 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1207,10 +1207,8 @@ toggleExtensions : function( force ){ var creator = this; creator.removeExtensions = ( force !== undefined )?( force ):( !creator.removeExtensions ); - console.debug( 'toggleExtensions:', creator.removeExtensions ); _.each( creator.paired, function( pair ){ - console.debug( pair ); // don't overwrite custom names if( pair.customizedName ){ return; } pair.name = creator._guessNameForPair( pair.forward, pair.reverse ); diff -r 3179b324e9d5886962fe2acda12c1b481bbd1e6a -r 882673a409055ade1614d28b15d677f5ce257a36 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.removeExtensions=true;this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(h){var g=new RegExp(this.filters[0]);return g.test(h.name)},_filterRevFn:function(h){var g=new RegExp(this.filters[1]);return g.test(h.name)},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g,j){j=(j!==undefined)?(j):(this.removeExtensions);var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));if(j){var k=h.lastIndexOf(".");if(k>0){h=h.slice(0,k)}}return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(g)}).fail(function(l,j,k){i._ajaxErrHandler(l,j,k)}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},_ajaxErrHandler:function(j,g,i){console.error(j,g,i);var h=d("An error occurred while creating this collection");if(j){if(j.readyState===0&&j.status===0){h+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(j.responseJSON){h+="<br /><pre>"+JSON.stringify(j.responseJSON)+"</pre>"}else{h+=": "+i}}}creator._showAlert(h,"alert-danger")},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(g);return g},_renderUnpairedNotShown:function(){var g=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}else{this.$(".remove-extensions-link").show()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",d("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',d("Forward"),": ",k,", ",d("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var g,h=null;if(this.paired.length){h="alert-success";g=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){g+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .paired-column .dataset-name":"_clickPairName","mouseover .dataset.paired":"_hoverPaired","mouseout .dataset.paired":"_hoverOutPaired","click .unpair-btn":"_clickUnpair","change .remove-extensions":function(g){this.toggleExtensions()},"change .collection-name":"_changeName","click .cancel-create":function(g){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(g).show().find(".alert-message").html(h)},_hideAlert:function(g){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(g){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(g){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(g,h){g=g||0;this.$(".unpaired-columns").hide(g,h);this.$(".paired-columns").show(g).css("flex","1 0 auto");this.unpairedPanelHidden=true},hidePaired:function(g,h){g=g||0;this.$(".unpaired-columns").show(g).css("flex","1 0 auto");this.$(".paired-columns").hide(g,h);this.pairedPanelHidden=true},splitView:function(g,h){g=g||0;this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(g);return this},_clickUnpairAll:function(g){this.unpairAll()},_clickAutopair:function(h){var g=this.autoPair();this.trigger("autopair",g)},_clickFilterChoice:function(h){var g=$(h.currentTarget);this.$(".forward-unpaired-filter input").val(g.data("forward"));this.$(".reverse-unpaired-filter input").val(g.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(g){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(g){g.stopPropagation();return this.toggleSelectUnpaired($(g.currentTarget))},toggleSelectUnpaired:function(i,h){h=h||{};var j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var i=this,j=[],g=[],k=[];i.$(".unpaired-columns .forward-column .dataset.selected").each(function(){j.push($(this).data("dataset"))});i.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){g.push($(this).data("dataset"))});j.length=g.length=Math.min(j.length,g.length);j.forEach(function(m,l){try{k.push(i._pair(m,g[l],{silent:true}))}catch(n){console.error(n)}});if(k.length&&!h.silent){this.trigger("pair:new",k)}return k},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_clickPairRow:function(i){var j=$(i.currentTarget).index(),h=$(".unpaired-columns .forward-column .dataset").eq(j).data("dataset"),g=$(".unpaired-columns .reverse-column .dataset").eq(j).data("dataset");this._pair(h,g)},_startPartitionDrag:function(h){var g=this,k=h.pageY;$("body").css("cursor","ns-resize");g.$(".flexible-partition-drag").css("color","black");function j(l){g.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",i)}function i(l){var m=l.pageY-k;if(!g.adjPartition(m)){$("body").trigger("mouseup")}k+=m}$("body").mousemove(i);$("body").one("mouseup",j)},adjPartition:function(h){var g=this.$(".unpaired-columns"),i=this.$(".paired-columns"),j=parseInt(g.css("height"),10),k=parseInt(i.css("height"),10);j=Math.max(10,j+h);k=k-h;if(j<=10){this.hideUnpaired();return false}else{if(!g.is("visible")){g.show()}}if(k<=15){this.hidePaired();if(k<10){return false}}else{if(!i.is("visible")){i.show()}}g.css({height:j+"px",flex:"0 0 auto"});return true},_clickPairName:function(i){var h=$(i.currentTarget),j=this.paired[h.parent().index()],g=prompt("Enter a new name for the 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.dataset.paired").eq(g)).removeClass("emphasized")},toggleExtensions:function(h){var g=this;g.removeExtensions=(h!==undefined)?(h):(!g.removeExtensions);console.debug("toggleExtensions:",g.removeExtensions);_.each(g.paired,function(i){console.debug(i);if(i.customizedName){return}i.name=g._guessNameForPair(i.forward,i.reverse)});g._renderPaired();g._renderFooter()},_changeName:function(g){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(h){var g=this._getName();if(!g){this._validationWarning("name")}else{this.createList()}},_printList:function(h){var g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row 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btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.removeExtensions=true;this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return 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k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g,j){j=(j!==undefined)?(j):(this.removeExtensions);var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));if(j){var k=h.lastIndexOf(".");if(k>0){h=h.slice(0,k)}}return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(g)}).fail(function(l,j,k){i._ajaxErrHandler(l,j,k)}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},_ajaxErrHandler:function(j,g,i){console.error(j,g,i);var h=d("An error occurred while creating this collection");if(j){if(j.readyState===0&&j.status===0){h+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(j.responseJSON){h+="<br /><pre>"+JSON.stringify(j.responseJSON)+"</pre>"}else{h+=": "+i}}}creator._showAlert(h,"alert-danger")},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column 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.create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(g).show().find(".alert-message").html(h)},_hideAlert:function(g){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(g){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(g){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(g,h){g=g||0;this.$(".unpaired-columns").hide(g,h);this.$(".paired-columns").show(g).css("flex","1 0 auto");this.unpairedPanelHidden=true},hidePaired:function(g,h){g=g||0;this.$(".unpaired-columns").show(g).css("flex","1 0 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j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var i=this,j=[],g=[],k=[];i.$(".unpaired-columns .forward-column .dataset.selected").each(function(){j.push($(this).data("dataset"))});i.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){g.push($(this).data("dataset"))});j.length=g.length=Math.min(j.length,g.length);j.forEach(function(m,l){try{k.push(i._pair(m,g[l],{silent:true}))}catch(n){console.error(n)}});if(k.length&&!h.silent){this.trigger("pair:new",k)}return k},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_clickPairRow:function(i){var j=$(i.currentTarget).index(),h=$(".unpaired-columns .forward-column .dataset").eq(j).data("dataset"),g=$(".unpaired-columns .reverse-column .dataset").eq(j).data("dataset");this._pair(h,g)},_startPartitionDrag:function(h){var g=this,k=h.pageY;$("body").css("cursor","ns-resize");g.$(".flexible-partition-drag").css("color","black");function j(l){g.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",i)}function i(l){var m=l.pageY-k;if(!g.adjPartition(m)){$("body").trigger("mouseup")}k+=m}$("body").mousemove(i);$("body").one("mouseup",j)},adjPartition:function(h){var g=this.$(".unpaired-columns"),i=this.$(".paired-columns"),j=parseInt(g.css("height"),10),k=parseInt(i.css("height"),10);j=Math.max(10,j+h);k=k-h;if(j<=10){this.hideUnpaired();return false}else{if(!g.is("visible")){g.show()}}if(k<=15){this.hidePaired();if(k<10){return false}}else{if(!i.is("visible")){i.show()}}g.css({height:j+"px",flex:"0 0 auto"});return true},_clickPairName:function(i){var h=$(i.currentTarget),j=this.paired[h.parent().index()],g=prompt("Enter a new name for the pair:",j.name);if(g){j.name=g;j.customizedName=true;h.text(j.name)}},_clickUnpair:function(h){var g=Math.floor($(h.currentTarget).index()/2);this._unpair(this.paired[g])},_hoverPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.emphasizePair(h)},_hoverOutPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.deemphasizePair(h)},emphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).addClass("emphasized")},deemphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).removeClass("emphasized")},toggleExtensions:function(h){var g=this;g.removeExtensions=(h!==undefined)?(h):(!g.removeExtensions);_.each(g.paired,function(i){if(i.customizedName){return}i.name=g._guessNameForPair(i.forward,i.reverse)});g._renderPaired();g._renderFooter()},_changeName:function(g){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(h){var g=this._getName();if(!g){this._validationWarning("name")}else{this.createList()}},_printList:function(h){var g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',d("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>"].join("")),footer:_.template(['<div class="attributes clear">','<div class="clear">','<label class="remove-extensions-prompt pull-right">',d("Remove file extensions from pair names"),"?",'<input class="remove-extensions pull-right" type="checkbox" />',"</label>","</div>",'<div class="clear">','<input class="collection-name form-control pull-right" ','placeholder="',d("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',d("Name"),":</div>","</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',d("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',d("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',d("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',d("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new e(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});window.PCC=h;return h};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9c62f54cf16/ Changeset: c9c62f54cf16 User: carlfeberhard Date: 2014-08-14 20:16:07 Summary: Paired collection creator: add option to remove file extensions from pair names (note: will not change any manually changed names) Affected #: 3 files diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -50,6 +50,10 @@ this.strategy = attributes.strategy; } + /** remove file extensions (\.*) from created pair names? */ + this.removeExtensions = true; + //this.removeExtensions = false; + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ this.oncancel = attributes.oncancel; /** fn to call when the collection is created (scoped to this) */ @@ -423,11 +427,19 @@ }, /** try to find a good pair name for the given fwd and rev datasets */ - _guessNameForPair : function( fwd, rev ){ + _guessNameForPair : function( fwd, rev, removeExtensions ){ + removeExtensions = ( removeExtensions !== undefined )?( removeExtensions ):( this.removeExtensions ); var lcs = this._naiveStartingAndEndingLCS( +//TODO: won't work with regex fwd.name.replace( this.filters[0], '' ), rev.name.replace( this.filters[1], '' ) ); + if( removeExtensions ){ + var lastDotIndex = lcs.lastIndexOf( '.' ); + if( lastDotIndex > 0 ){ + lcs = lcs.slice( 0, lastDotIndex ); + } + } //TODO: optionally remove extension return lcs || ( fwd.name + ' & ' + rev.name ); }, @@ -579,12 +591,15 @@ /** render the middle including unpaired and paired sections (which may be hidden) */ _renderMiddle : function( speed, callback ){ var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() ); + + // (re-) hide the un/paired panels based on instance vars //TODO: use replaceWith if( this.unpairedPanelHidden ){ this.$( '.unpaired-columns' ).hide(); } else if( this.pairedPanelHidden ){ this.$( '.paired-columns' ).hide(); } + this._renderUnpaired(); this._renderPaired(); return $middle; @@ -666,7 +681,7 @@ //console.debug( '-- renderUnpairedEmpty' ); var $msg = $( '<div class="empty-message"></div>' ) .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' ); - this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg ); + this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg ); return $msg; }, /** a message to display when no unpaired can be shown with the current filters */ @@ -674,7 +689,7 @@ //console.debug( '-- renderUnpairedEmpty' ); var $msg = $( '<div class="empty-message"></div>' ) .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' ); - this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg ); + this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg ); return $msg; }, @@ -691,6 +706,9 @@ if( this.paired.length === 0 ){ this._renderPairedEmpty(); //TODO: would be best to return here (the $columns) + } else { + // show/hide 'remove extensions link' when any paired and they seem to have extensions + this.$( '.remove-extensions-link' ).show(); } this.paired.forEach( function( pair, i ){ @@ -721,6 +739,7 @@ /** render the footer, completion controls, and cancel controls */ _renderFooter : function( speed, callback ){ var $footer = this.$( '.footer' ).empty().html( PairedCollectionCreator.templates.footer() ); + this.$( '.remove-extensions' ).prop( 'checked', this.removeExtensions ); if( typeof this.oncancel === 'function' ){ this.$( '.cancel-create.btn' ).show(); } @@ -861,12 +880,12 @@ 'mousedown .flexible-partition-drag' : '_startPartitionDrag', // paired 'click .paired-columns .paired-column .dataset-name' : '_clickPairName', + 'mouseover .dataset.paired' : '_hoverPaired', + 'mouseout .dataset.paired' : '_hoverOutPaired', 'click .unpair-btn' : '_clickUnpair', - 'mouseover .dataset.paired' : '_hoverPaired', - 'mouseout .dataset.paired' : '_hoverOutPaired', - // footer + 'change .remove-extensions' : function( ev ){ this.toggleExtensions(); }, 'change .collection-name' : '_changeName', 'click .cancel-create' : function( ev ){ if( typeof this.oncancel === 'function' ){ @@ -1130,6 +1149,10 @@ response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; + // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these + // when adding/removing extensions + //TODO: kinda hacky + pair.customizedName = true; $control.text( pair.name ); } }, @@ -1181,6 +1204,22 @@ }, // ........................................................................ footer + toggleExtensions : function( force ){ + var creator = this; + creator.removeExtensions = ( force !== undefined )?( force ):( !creator.removeExtensions ); + console.debug( 'toggleExtensions:', creator.removeExtensions ); + + _.each( creator.paired, function( pair ){ + console.debug( pair ); + // don't overwrite custom names + if( pair.customizedName ){ return; } + pair.name = creator._guessNameForPair( pair.forward, pair.reverse ); + }); + + creator._renderPaired(); + creator._renderFooter(); + }, + /** handle a collection name change */ _changeName : function( ev ){ this._validationWarning( 'name', !!this._getName() ); @@ -1330,9 +1369,17 @@ /** creation and cancel controls */ footer : _.template([ '<div class="attributes clear">', - '<input class="collection-name form-control pull-right" ', - 'placeholder="', _l( 'Enter a name for your new list' ), '" />', - '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>', + '<div class="clear">', + '<label class="remove-extensions-prompt pull-right">', + _l( 'Remove file extensions from pair names' ), '?', + '<input class="remove-extensions pull-right" type="checkbox" />', + '</label>', + '</div>', + '<div class="clear">', + '<input class="collection-name form-control pull-right" ', + 'placeholder="', _l( 'Enter a name for your new list' ), '" />', + '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>', + '</div>', '</div>', '<div class="actions clear vertically-spaced">', @@ -1411,6 +1458,10 @@ 'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.' ].join( '' )), '</p>', '<p>', _l([ + 'You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ', + '<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.' + ].join( '' )), '</p>', + '<p>', _l([ 'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ', 'click <i data-target=".create-collection">"Create list"</i>. ', '(Note: you do not have to pair all unpaired datasets to finish.)' diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1840,16 +1840,19 @@ .collection-creator .unpaired-columns .paired-column .dataset.unpaired{border-color:lightgrey;color:lightgrey}.collection-creator .unpaired-columns .paired-column .dataset.unpaired:hover{border-color:black;color:black} .collection-creator .unpaired-columns .reverse-column .dataset.unpaired{text-align:right;margin-left:32px} .collection-creator .flexible-partition .flexible-partition-drag{width:100%;height:8px;cursor:ns-resize}.collection-creator .flexible-partition .flexible-partition-drag:hover{background:lightgrey} -.collection-creator .flexible-partition .column-header{width:100%;text-align:center}.collection-creator .flexible-partition .column-header .column-title{display:inline;margin-right:8px} +.collection-creator .flexible-partition .column-header{width:100%;text-align:center}.collection-creator .flexible-partition .column-header .column-title{display:inline} +.collection-creator .flexible-partition .column-header>*:not(:last-child){margin-right:8px} +.collection-creator .flexible-partition .column-header .remove-extensions-link{display:none} .collection-creator .paired-columns .dataset.paired{background:#AFF1AF;border-color:grey;border-width:2px}.collection-creator .paired-columns .dataset.paired:hover,.collection-creator .paired-columns .dataset.paired.emphasized{border-color:black} .collection-creator .paired-columns .forward-column .dataset.paired{margin-left:32px;border-radius:3px 0 0 3px;border-right-color:grey;border-right-width:1px;text-align:right}.collection-creator .paired-columns .forward-column .dataset.paired:after{margin-left:8px;font-family:FontAwesome;content:'\f061'} .collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline} .collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'} .collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE} -.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} -.collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red} -.collection-creator .footer .other-options>*{display:none;margin-left:4px} -.collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0} +.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .attributes .remove-extensions-prompt{line-height:32px}.collection-creator .footer .attributes .remove-extensions-prompt .remove-extensions{display:inline-block;width:24px;height:24px} +.collection-creator .footer .attributes .collection-name-prompt{margin:5px 4px 0 0} +.collection-creator .footer .attributes .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} +.collection-creator .footer .attributes .collection-name{width:50%}.collection-creator .footer .attributes .collection-name.validation-warning{border-color:red} +.collection-creator .footer .actions .other-options>*{display:none;margin-left:4px} .toolMenuContainer{color:#000;background:#dfe5f9;min-height:100%;padding:5px 10px} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px} div.toolSectionWrapper{margin-bottom:5px} diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -301,8 +301,13 @@ text-align: center; .column-title { display: inline; + } + & > *:not(:last-child) { margin-right: 8px; } + .remove-extensions-link { + display: none; + } } } @@ -372,26 +377,39 @@ // ------------------------------------------------------------------------ footer .footer { - .collection-name-prompt.validation-warning:before { - //TODO: localize (somehow) - content: '(required)'; - margin-right: 4px; - color: red; - } - .collection-name { - width: 50%; - &.validation-warning { - border-color: red; + .attributes { + .remove-extensions-prompt { + //margin-right: 32px; + line-height: 32px; + .remove-extensions { + display: inline-block; + width: 24px; + height: 24px; + } + } + // actually appears/floats to the left of the input + .collection-name-prompt { + margin: 5px 4px 0 0; + } + .collection-name-prompt.validation-warning:before { + //TODO: localize (somehow) + content: '(required)'; + margin-right: 4px; + color: red; + } + .collection-name { + width: 50%; + &.validation-warning { + border-color: red; + } } } - .other-options > * { - // do not display the links to create other collections yet - display: none; - margin-left: 4px; - } - // actually appears/floats to the left of the input - .collection-name-prompt { - margin: 5px 4px 0 0; + .actions { + .other-options > * { + // do not display the links to create other collections yet + display: none; + margin-left: 4px; + } } padding-bottom: 8px; } https://bitbucket.org/galaxy/galaxy-central/commits/3179b324e9d5/ Changeset: 3179b324e9d5 User: carlfeberhard Date: 2014-08-14 20:16:34 Summary: (pack scripts) Affected #: 1 file diff -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac -r 3179b324e9d5886962fe2acda12c1b481bbd1e6a static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(h){var g=new RegExp(this.filters[0]);return g.test(h.name)},_filterRevFn:function(h){var g=new RegExp(this.filters[1]);return g.test(h.name)},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(g)}).fail(function(l,j,k){i._ajaxErrHandler(l,j,k)}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},_ajaxErrHandler:function(j,g,i){console.error(j,g,i);var h=d("An error occurred while creating this collection");if(j){if(j.readyState===0&&j.status===0){h+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(j.responseJSON){h+="<br /><pre>"+JSON.stringify(j.responseJSON)+"</pre>"}else{h+=": "+i}}}creator._showAlert(h,"alert-danger")},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderUnpairedNotShown:function(){var g=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",d("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(e.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',d("Forward"),": ",k,", ",d("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var g,h=null;if(this.paired.length){h="alert-success";g=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){g+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .paired-column .dataset-name":"_clickPairName","click .unpair-btn":"_clickUnpair","mouseover .dataset.paired":"_hoverPaired","mouseout .dataset.paired":"_hoverOutPaired","change .collection-name":"_changeName","click .cancel-create":function(g){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(g).show().find(".alert-message").html(h)},_hideAlert:function(g){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(g){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(g){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(g,h){g=g||0;this.$(".unpaired-columns").hide(g,h);this.$(".paired-columns").show(g).css("flex","1 0 auto");this.unpairedPanelHidden=true},hidePaired:function(g,h){g=g||0;this.$(".unpaired-columns").show(g).css("flex","1 0 auto");this.$(".paired-columns").hide(g,h);this.pairedPanelHidden=true},splitView:function(g,h){g=g||0;this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(g);return this},_clickUnpairAll:function(g){this.unpairAll()},_clickAutopair:function(h){var g=this.autoPair();this.trigger("autopair",g)},_clickFilterChoice:function(h){var g=$(h.currentTarget);this.$(".forward-unpaired-filter input").val(g.data("forward"));this.$(".reverse-unpaired-filter input").val(g.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(g){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(g){g.stopPropagation();return this.toggleSelectUnpaired($(g.currentTarget))},toggleSelectUnpaired:function(i,h){h=h||{};var j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var i=this,j=[],g=[],k=[];i.$(".unpaired-columns .forward-column .dataset.selected").each(function(){j.push($(this).data("dataset"))});i.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){g.push($(this).data("dataset"))});j.length=g.length=Math.min(j.length,g.length);j.forEach(function(m,l){try{k.push(i._pair(m,g[l],{silent:true}))}catch(n){console.error(n)}});if(k.length&&!h.silent){this.trigger("pair:new",k)}return k},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_clickPairRow:function(i){var j=$(i.currentTarget).index(),h=$(".unpaired-columns .forward-column .dataset").eq(j).data("dataset"),g=$(".unpaired-columns .reverse-column .dataset").eq(j).data("dataset");this._pair(h,g)},_startPartitionDrag:function(h){var g=this,k=h.pageY;$("body").css("cursor","ns-resize");g.$(".flexible-partition-drag").css("color","black");function j(l){g.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",i)}function i(l){var m=l.pageY-k;if(!g.adjPartition(m)){$("body").trigger("mouseup")}k+=m}$("body").mousemove(i);$("body").one("mouseup",j)},adjPartition:function(h){var g=this.$(".unpaired-columns"),i=this.$(".paired-columns"),j=parseInt(g.css("height"),10),k=parseInt(i.css("height"),10);j=Math.max(10,j+h);k=k-h;if(j<=10){this.hideUnpaired();return false}else{if(!g.is("visible")){g.show()}}if(k<=15){this.hidePaired();if(k<10){return false}}else{if(!i.is("visible")){i.show()}}g.css({height:j+"px",flex:"0 0 auto"});return true},_clickPairName:function(i){var h=$(i.currentTarget),j=this.paired[h.parent().index()],g=prompt("Enter a new name for the pair:",j.name);if(g){j.name=g;h.text(j.name)}},_clickUnpair:function(h){var g=Math.floor($(h.currentTarget).index()/2);this._unpair(this.paired[g])},_hoverPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.emphasizePair(h)},_hoverOutPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.deemphasizePair(h)},emphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).addClass("emphasized")},deemphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).removeClass("emphasized")},_changeName:function(g){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(h){var g=this._getName();if(!g){this._validationWarning("name")}else{this.createList()}},_printList:function(h){var g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new e(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});window.PCC=h;return h};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 83c74e7d67f5: open regex tutorial in new tab
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3be5658bc5da/ Changeset: 3be5658bc5da User: carlfeberhard Date: 2014-08-14 18:21:11 Summary: Fix to 83c74e7d67f5: open regex tutorial in new tab Affected #: 2 files diff -r 83c74e7d67f5d8f5c3853f9b3dd1ca07ad88eafb -r 3be5658bc5da1831860b367ad57deec0140cc10e static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1396,9 +1396,8 @@ '<i data-target=".choose-filters-link">"Choose filters" link</i>.', '</li>', '<li>Entering regular expressions to match dataset names. See: ', - '<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…">', - 'MDN\'s JavaScript Regular Expression Tutorial', - '</a>. ', + '<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"', + ' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ', 'Note: forward slashes (\\) are not needed.', '</li>', '<li>Clearing the filters by clicking the ', diff -r 83c74e7d67f5d8f5c3853f9b3dd1ca07ad88eafb -r 3be5658bc5da1831860b367ad57deec0140cc10e static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(h){var g=new RegExp(this.filters[0]);return g.test(h.name)},_filterRevFn:function(h){var g=new RegExp(this.filters[1]);return g.test(h.name)},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var 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"+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(g)}).fail(function(l,j,k){i._ajaxErrHandler(l,j,k)}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},_ajaxErrHandler:function(j,g,i){console.error(j,g,i);var h=d("An error occurred while creating this collection");if(j){if(j.readyState===0&&j.status===0){h+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(j.responseJSON){h+="<br /><pre>"+JSON.stringify(j.responseJSON)+"</pre>"}else{h+=": "+i}}}creator._showAlert(h,"alert-danger")},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" 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g,h=null;if(this.paired.length){h="alert-success";g=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){g+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new e(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});window.PCC=h;return h};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Paired collection creator: use regex string matching for dataset filtering (by default - we'll see if that's the right choice), extract ajax error handler
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83c74e7d67f5/ Changeset: 83c74e7d67f5 User: carlfeberhard Date: 2014-08-14 18:17:28 Summary: Paired collection creator: use regex string matching for dataset filtering (by default - we'll see if that's the right choice), extract ajax error handler Affected #: 2 files diff -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 -r 83c74e7d67f5d8f5c3853f9b3dd1ca07ad88eafb static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -146,13 +146,16 @@ /** filter fn to apply to forward datasets */ _filterFwdFn : function( dataset ){ - // simple contains for now - add more when new feat. are added (regex, etc.) - return dataset.name.indexOf( this.filters[0] ) >= 0; +//TODO: this treats *all* strings as regex which may confuse people + var regexp = new RegExp( this.filters[0] ); + return regexp.test( dataset.name ); + //return dataset.name.indexOf( this.filters[0] ) >= 0; }, /** filter fn to apply to reverse datasets */ _filterRevFn : function( dataset ){ - return dataset.name.indexOf( this.filters[1] ) >= 0; + var regexp = new RegExp( this.filters[1] ); + return regexp.test( dataset.name ); }, /** add a dataset to the unpaired list in it's proper order */ @@ -500,7 +503,7 @@ // } - //var xhr = jQuery.ajax({ +//TODO:?? Can't we use ListPairedCollection.create() var ajaxData = { type : 'dataset_collection', collection_type : 'list:paired', @@ -513,23 +516,11 @@ return jQuery.ajax( url, { type : 'POST', contentType : 'application/json', + dataType : 'json', data : JSON.stringify( ajaxData ) }) .fail( function( xhr, status, message ){ - //TODO: extract method - console.error( xhr, status, message ); - var content = _l( 'An error occurred while creating this collection' ); - if( xhr ){ - if( xhr.readyState === 0 && xhr.status === 0 ){ - content += ': ' + _l( 'Galaxy could not be reached and may be updating.' ) - + _l( ' Try again in a few minutes.' ); - } else if( xhr.responseJSON ){ - content += '<br /><pre>' + JSON.stringify( xhr.responseJSON ) + '</pre>'; - } else { - content += ': ' + message; - } - } - creator._showAlert( content, 'alert-danger' ); + creator._ajaxErrHandler( xhr, status, message ); }) .done( function( response, message, xhr ){ //console.info( 'ok', response, message, xhr ); @@ -540,6 +531,23 @@ }); }, + /** handle ajax errors with feedback and details to the user (if available) */ + _ajaxErrHandler : function( xhr, status, message ){ + console.error( xhr, status, message ); + var content = _l( 'An error occurred while creating this collection' ); + if( xhr ){ + if( xhr.readyState === 0 && xhr.status === 0 ){ + content += ': ' + _l( 'Galaxy could not be reached and may be updating.' ) + + _l( ' Try again in a few minutes.' ); + } else if( xhr.responseJSON ){ + content += '<br /><pre>' + JSON.stringify( xhr.responseJSON ) + '</pre>'; + } else { + content += ': ' + message; + } + } + creator._showAlert( content, 'alert-danger' ); + }, + // ------------------------------------------------------------------------ rendering /** render the entire interface */ render : function( speed, callback ){ @@ -1387,6 +1395,12 @@ '<li>Choosing from a list of preset filters by clicking the ', '<i data-target=".choose-filters-link">"Choose filters" link</i>.', '</li>', + '<li>Entering regular expressions to match dataset names. See: ', + '<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…">', + 'MDN\'s JavaScript Regular Expression Tutorial', + '</a>. ', + 'Note: forward slashes (\\) are not needed.', + '</li>', '<li>Clearing the filters by clicking the ', '<i data-target=".clear-filters-link">"Clear filters" link</i>.', '</li>', diff -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 -r 83c74e7d67f5d8f5c3853f9b3dd1ca07ad88eafb static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=d("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderUnpairedNotShown:function(){var g=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",d("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(e.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',d("Forward"),": ",k,", ",d("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var g,h=null;if(this.paired.length){h="alert-success";g=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){g+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .paired-column .dataset-name":"_clickPairName","click .unpair-btn":"_clickUnpair","mouseover .dataset.paired":"_hoverPaired","mouseout .dataset.paired":"_hoverOutPaired","change .collection-name":"_changeName","click .cancel-create":function(g){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header 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g=this.autoPair();this.trigger("autopair",g)},_clickFilterChoice:function(h){var g=$(h.currentTarget);this.$(".forward-unpaired-filter input").val(g.data("forward"));this.$(".reverse-unpaired-filter input").val(g.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(g){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(g){g.stopPropagation();return this.toggleSelectUnpaired($(g.currentTarget))},toggleSelectUnpaired:function(i,h){h=h||{};var j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Use floating instead of float as member id, pack code
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fbcb1e26af34/ Changeset: fbcb1e26af34 User: guerler Date: 2014-08-14 17:21:37 Summary: Use floating instead of float as member id, pack code Affected #: 9 files diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" 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t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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$.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url 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Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})}); \ No newline at end of file diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -10,7 +10,7 @@ // create form view var View = Backbone.View.extend({ // base element - body: 'body', + main_el: 'body', // initialize initialize: function(options) { @@ -31,13 +31,13 @@ title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'), buttons: { execute: new Ui.ButtonIcon({ - icon : 'fa-check', - tooltip : 'Execute the tool', - title : 'Execute', - float :'clear', - onclick : function() { + icon : 'fa-check', + tooltip : 'Execute the tool', + title : 'Execute', + floating : 'clear', + onclick : function() { } - }), + }) } }); @@ -49,7 +49,7 @@ self.portlet.append(self.message.$el); // append portlet - $(self.body).append(self.portlet.$el); + $(self.main_el).append(self.portlet.$el); self.setElement(self.portlet.content()); self.portlet.append(self.table.$el); self.render(); diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/mvc/ui/ui-button-menu.js --- a/static/scripts/mvc/ui/ui-button-menu.js +++ b/static/scripts/mvc/ui/ui-button-menu.js @@ -10,7 +10,7 @@ // same as Ui.ButtonIcon id : '', title : '', - float : 'right', + floating : 'right', icon : null, onclick : null, cls : 'icon-btn', @@ -150,7 +150,7 @@ } // string - var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">'; + var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">'; // title if (options.title) { diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -66,7 +66,7 @@ var Icon = Backbone.View.extend({ // options optionsDefault: { - float : 'right', + floating : 'right', icon : '', tooltip : '', placement : 'bottom', @@ -99,11 +99,11 @@ var Button = Backbone.View.extend({ // options optionsDefault: { - id : null, - title : '', - float : 'right', - cls : 'btn btn-default', - icon : '' + id : null, + title : '', + floating : 'right', + cls : 'btn btn-default', + icon : '' }, // initialize @@ -123,7 +123,7 @@ // element _template: function(options) { - var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.float + ';" type="button" class="ui-button ' + options.cls + '">'; + var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.floating + ';" type="button" class="ui-button ' + options.cls + '">'; if (options.icon) { str += '<i class="icon fa ' + options.icon + '"></i> ' ; } @@ -137,13 +137,13 @@ var ButtonIcon = Backbone.View.extend({ // options optionsDefault: { - id : null, - title : '', - float : 'right', - cls : 'icon-btn', - icon : '', - tooltip : '', - onclick : null + id : null, + title : '', + floating : 'right', + cls : 'icon-btn', + icon : '', + tooltip : '', + onclick : null }, // initialize @@ -170,7 +170,7 @@ } // string - var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon ' + options.cls + '">'; + var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="ui-button-icon ' + options.cls + '">'; // title if (options.title) { diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/packed/mvc/tools/tools-form.js --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -0,0 +1,1 @@ +define(["mvc/tools","mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc"],function(b,c,a,f){var e=Backbone.Model.extend({initialize:function(g){this.url=galaxy_config.root+"api/tools/"+g.id+"?io_details=true"}});var d=Backbone.View.extend({main_el:"body",initialize:function(h){var g=this;this.model=new e({id:h.id});this.model.fetch({success:function(){g.portlet=new c.View({icon:"fa-wrench",title:"<b>"+g.model.get("name")+"</b> "+g.model.get("description"),buttons:{execute:new f.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});g.table=new a.View();g.message=new f.Message();g.portlet.append(g.message.$el);$(g.main_el).append(g.portlet.$el);g.setElement(g.portlet.content());g.portlet.append(g.table.$el);g.render()}})},render:function(){var g=this.model.get("inputs");this.table.delAll();this.list=[];var h=new Backbone.Model();for(var i in g){this._add(g[i],h)}for(var i in this.list){this.list[i].trigger("change")}},_add:function(g,j){var h=this;var m=g.name;console.debug(g);var k=null;var i=g.type;switch(i){case"text":k=this.field_text(g,j);break;case"select":k=this.field_select(g,j);break;case"radiobutton":k=this.field_radio(g,j);break;case"data":k=this.field_select(g,j);break;case"textarea":k=this.field_textarea(g,j);break;default:k=new f.Input({id:"field-"+m,placeholder:g.placeholder,type:g.type,onchange:function(){j.set(m,k.value())}})}if(!j.get(m)){j.set(m,g.value)}k.value(j.get(m));this.list[m]=k;var l=$("<div/>");l.append(k.$el);if(g.info){l.append('<div class="ui-table-form-info">'+g.info+"</div>")}if(this.options.style=="bold"){this.table.add(new f.Label({title:g.title,cls:"form-label"}).$el);this.table.add(l)}else{this.table.add('<span class="ui-table-form-title">'+g.label+"</span>","25%");this.table.add(l)}this.table.append(m);if(g.hide){this.table.get(m).hide()}},field_text:function(g,h){var i=g.name;return new f.Input({id:"field-"+i,value:h.get(i),onchange:function(j){h.set(i,j)}})},field_textarea:function(g,h){var i=g.name;return new f.Textarea({id:"field-"+i,onchange:function(){h.set(i,field.value())}})},field_select:function(g,l){var h=[];for(var j in g.options){var k=g.options[j];h.push({label:k[0],value:k[1]})}var m=g.name;return new f.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(p){l.set(m,p);var r=_.findWhere(h,{value:p});if(r&&r.operations){var n=r.operations;for(var o in n.show){var q=n.show[o];self.table.get(q).show()}for(var o in n.hide){var q=n.hide[o];self.table.get(q).hide()}}}})},field_radio:function(g,h){var i=g.name;return new f.RadioButton({id:"field-"+i,data:g.data,value:h.get(i),onchange:function(l){h.set(i,l);var n=_.findWhere(g.data,{value:l});if(n&&n.operations){var j=n.operations;for(var k in j.show){var m=j.show[k];self.table.get(m).show()}for(var k in j.hide){var m=j.hide[k];self.table.get(m).hide()}}}})}});return{View:d}}); \ No newline at end of file diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/packed/mvc/ui/ui-button-menu.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-button-menu.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:true,tag:""},$menu:null,initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($(this._template(this.options)));var d=$(this.el).find(".root");var b=this;d.on("click",function(f){$(".tooltip").hide();f.preventDefault();if(b.options.onclick){b.options.onclick()}});if(!this.options.visible){this.hide()}d.tooltip({title:c.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(c){var d={title:"",target:"",href:"",onclick:null,divider:false,icon:null,cls:"button-menu btn-group"};d=a.merge(c,d);if(!this.$menu){$(this.el).append(this._templateMenu());this.$menu=$(this.el).find(".menu")}var b=$(this._templateMenuItem(d));b.on("click",function(f){f.preventDefault();if(d.onclick){d.onclick()}});this.$menu.append(b);if(d.divider){this.$menu.append($(this._templateDivider()))}},_templateMenuItem:function(c){var b='<li><a href="'+c.href+'" target="'+c.target+'">';if(c.icon){b+='<i class="fa '+c.icon+'"></i>'}b+=" "+c.title+"</a></li>";return b},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(b){var c="";if(b.title){c="width: auto;"}var d='<div id="'+b.id+'" style="float: '+b.floating+"; "+c+'" class="ui-button-icon dropdown '+b.cls+'">';if(b.title){d+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+b.icon+'"/> <span class="title">'+b.title+"</span></div>"}else{d+='<i class="icon fa '+b.icon+'"/>'}d+="</div>";return d}})}); \ No newline at end of file diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/packed/mvc/ui/ui-misc.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -0,0 +1,1 @@ +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,o,m){var c=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(p){return'<img class="ui-image '+p.cls+'" src="'+p.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},title:function(p){this.$el.html(p)},_template:function(p){return'<label class="ui-label '+p.cls+'">'+p.title+"</label>"},value:function(){return options.title}});var d=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){return'<div><span class="fa '+p.icon+'" class="ui-icon"/> '+p.title+"</div>"}});var f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q='<button id="'+p.id+'" type="submit" style="float: '+p.floating+';" type="button" class="ui-button '+p.cls+'">';if(p.icon){q+='<i class="icon fa '+p.icon+'"></i> '}q+=p.title+"</button>";return q}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q="";if(p.title){q="width: auto;"}var r='<div id="'+p.id+'" style="float: '+p.floating+"; "+q+'" class="ui-button-icon '+p.cls+'">';if(p.title){r+='<div class="button"><i class="icon fa '+p.icon+'"/> <span class="title">'+p.title+"</span></div>"}else{r+='<i class="icon fa '+p.icon+'"/>'}r+="</div>";return r}});var e=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick)},_template:function(p){return'<div><a href="javascript:void(0)" class="ui-anchor '+p.cls+'">'+p.title+"</a></div>"}});var n=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement("<div></div>")},update:function(q){this.options=k.merge(q,this.optionsDefault);if(q.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(q.message);this.$el.fadeIn();if(!q.persistent){var p=this;window.setTimeout(function(){if(p.$el.is(":visible")){p.$el.fadeOut()}else{p.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(p){return'<div class="ui-message alert alert-'+p.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));var p=this;if(this.options.onclick){this.$el.on("submit",function(s){var r=p.$el.find("#search");p.options.onclick(r.val())})}},_template:function(p){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+p.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return'<input id="'+p.id+'" type="'+p.type+'" value="'+p.value+'" placeholder="'+p.placeholder+'" class="ui-input '+p.cls+'">'}});var h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return'<textarea id="'+p.id+'" class="ui-textarea '+p.cls+'" rows="5"></textarea>'}});var l=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:k.uuid()},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var p=this;this.$el.find("input").on("change",function(){p.value(p._getValue())})},value:function(p){var q=this.current;if(p!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+p+'"]').closest("label").addClass("active");this.current=p}var r=this.current;if(r!=q&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var p=this.$el.find(":checked");var q=null;if(p.length>0){q=p.val()}return q},_template:function(q){var p='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in q.data){var r=q.data[key];p+='<label class="btn btn-default"><input type="radio" name="'+q.id+'" value="'+r.value+'" selected>'+r.label+"</label>"}p+="</div>";return p}});return{Anchor:e,Button:f,ButtonIcon:g,ButtonMenu:o,Icon:d,Image:c,Input:i,Label:j,Message:n,Modal:m,RadioButton:l,Searchbox:a,Select:b,Textarea:h}}); \ No newline at end of file diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/packed/mvc/ui/ui-select-default.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false},selected:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.selected=this.options.value;this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");var c=this;this.$select.on("change",function(){c.value(c.$select.val())});this.on("change",function(){if(c.options.onchange){c.options.onchange(c.value())}});this._refresh();if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}},value:function(c){var d=this.selected;if(c!==undefined){this.selected=c;this.$select.val(c)}var e=this.selected;if(e){if(e!=d&&this.options.onchange){this.options.onchange(e)}}return e},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh()},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}if(this.selected){this.$select.val(this.selected)}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(e){var d='<div id="'+e.id+'" class="ui-select"><div class="button"><i id="icon"/></div><select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var f=e.data[key];var c="";if(f.value==e.value||f.value==""){c="selected"}d+='<option value="'+f.value+'" '+c+">"+f.label+"</option>"}d+="</select></div>";return d}});return{View:b}}); \ No newline at end of file diff -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 -r fbcb1e26af34d388a5583628b0812aa2d2cb3179 static/scripts/packed/mvc/ui/ui-table.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-table.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);var d=$(this._template(this.options));this.$thead=d.find("thead");this.$tbody=d.find("tbody");this.$tmessage=d.find("tmessage");this.setElement(d);this.row=$("<tr></tr>")},addHeader:function(c){var d=$("<th></th>");d.append(c);this.row.append(d)},appendHeader:function(){this.$thead.append(this.row);this.row=$("<tr></tr>")},add:function(c,d,f){var e=$("<td></td>");if(d){e.css("width",d)}if(f){e.css("text-align",f)}e.append(c);this.row.append(e)},append:function(c){this._commit(c)},prepend:function(c){this._commit(c,true)},get:function(c){return this.$el.find("#"+c)},del:function(d){var c=this.$tbody.find("#"+d);if(c.length>0){c.remove();this.row_count--;this._refresh()}},delAll:function(){this.$tbody.empty();this.row_count=0;this._refresh()},value:function(c){this.before=this.$tbody.find(".current").attr("id");if(c!==undefined){this.$tbody.find("tr").removeClass("current");if(c){this.$tbody.find("#"+c).addClass("current")}}var d=this.$tbody.find(".current").attr("id");if(d===undefined){return null}else{if(d!=this.before&&this.options.onchange){this.options.onchange(c)}return d}},size:function(){return this.$tbody.find("tr").length},_commit:function(d,c){this.del(d);this.row.attr("id",d);if(c){this.$tbody.prepend(this.row)}else{this.$tbody.append(this.row)}this.row=$("<tr></tr>");this.row_count++;this._refresh()},_onclick:function(f){var c=this.value();var d=$(f.target).closest("tr").attr("id");if(d!=""){if(d&&c!=d){if(this.options.onconfirm){this.options.onconfirm(d)}else{this.value(d)}}}},_ondblclick:function(d){var c=this.value();if(c&&this.options.ondblclick){this.options.ondblclick(c)}},_refresh:function(){if(this.row_count==0){this.$tmessage.show()}else{this.$tmessage.hide()}},_template:function(c){return'<div><table class="ui-table '+c.cls+'"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+c.content+"</tmessage><div>"}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA, history panel: better error details: full url, ajax data, Raven/Sentry id if available; galaxy-app-base: add global listeners
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32f451ba2202/ Changeset: 32f451ba2202 User: carlfeberhard Date: 2014-08-14 16:57:41 Summary: QA, history panel: better error details: full url, ajax data, Raven/Sentry id if available; galaxy-app-base: add global listeners Affected #: 4 files diff -r f58d8cf6018a536470275b400c711ff74f9b4dc3 -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 static/scripts/galaxy-app-base.js --- a/static/scripts/galaxy-app-base.js +++ b/static/scripts/galaxy-app-base.js @@ -59,6 +59,8 @@ // options.onload(); //} + self._setUpListeners(); + return self; }; @@ -122,6 +124,28 @@ return self; }; +/** Set up DOM/jQuery/Backbone event listeners enabled for all pages */ +GalaxyApp.prototype._setUpListeners = function _setUpListeners(){ + var self = this; + + // hook to jq beforeSend to record the most recent ajax call and cache some data about it + /** cached info about the last ajax call made through jQuery */ + self.lastAjax = {}; + $( document ).bind( 'ajaxSend', function( ev, xhr, options ){ + var data = options.data; + try { + data = JSON.parse( data ); + } catch( err ){} + + self.lastAjax = { + url : location.href.slice( 0, -1 ) + options.url, + data : data + }; + //TODO:?? we might somehow manage to *retry* ajax using either this hook or Backbone.sync + }); + +}; + /** string rep */ GalaxyApp.prototype.toString = function toString(){ var userEmail = this.user.get( 'email' ) || '(anonymous)'; diff -r f58d8cf6018a536470275b400c711ff74f9b4dc3 -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -190,6 +190,7 @@ // this.hdaViews = null; //}, +//TODO: break this out // ........................................................................ error handling /** Event handler for errors (from the panel, the history, or the history's HDAs) * @param {Model or View} model the (Backbone) source of the error @@ -202,6 +203,8 @@ this.error( model, xhr, options, msg, details ); //TODO: getting JSON parse errors from jq migrate + window.xhr = xhr; + // interrupted ajax if( xhr && xhr.status === 0 && xhr.readyState === 0 ){ @@ -211,6 +214,7 @@ // otherwise, show an error message inside the panel } else { + // if sentry is available, attempt to get the event id var parsed = this._parseErrorMessage( model, xhr, options, msg, details ); // it's possible to have a triggered error before the message container is rendered - wait for it to show if( !this.$messages().is( ':visible' ) ){ @@ -226,18 +230,25 @@ /** Parse an error event into an Object usable by displayMessage based on the parameters * note: see errorHandler for more info on params */ - _parseErrorMessage : function( model, xhr, options, msg, details ){ + _parseErrorMessage : function( model, xhr, options, msg, details, sentryId ){ var user = Galaxy.currUser, // add the args (w/ some extra info) into an obj parsed = { message : this._bePolite( msg ), details : { - user : ( user instanceof USER.User )?( user.toJSON() ):( user + '' ), - source : ( model instanceof Backbone.Model )?( model.toJSON() ):( model + '' ), + message : msg, + raven : ( window.Raven )?( Raven.lastEventId() ):( undefined ), + agent : navigator.userAgent, + // add ajax data from Galaxy object cache + url : ( window.Galaxy )?( Galaxy.lastAjax.url ):( undefined ), + data : ( window.Galaxy )?( Galaxy.lastAjax.data ):( undefined ), + options : ( xhr )?( _.omit( options, 'xhr' ) ):( options ), xhr : xhr, - options : ( xhr )?( _.omit( options, 'xhr' ) ):( options ) + source : ( _.isFunction( model.toJSON ) )?( model.toJSON() ):( model + '' ), + user : ( user instanceof USER.User )?( user.toJSON() ):( user + '' ) } }; + // add any extra details passed in _.extend( parsed.details, details || {} ); // fancy xhr.header parsing (--> obj) diff -r f58d8cf6018a536470275b400c711ff74f9b4dc3 -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 static/scripts/packed/galaxy-app-base.js --- a/static/scripts/packed/galaxy-app-base.js +++ b/static/scripts/packed/galaxy-app-base.js @@ -1,1 +1,1 @@ -define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","bootstrapped-data"],function(b,d,g,e,a){function h(n){var m=this;return m._init(n||{})}g(h,"GalaxyApp");h.prototype.defaultOptions={patchExisting:true,root:"/"};h.prototype._init=function k(n){var m=this;_.extend(m,Backbone.Events);m._processOptions(n);m.debug("GalaxyApp.options: ",m.options);m._patchGalaxy(window.Galaxy);m._initLogger(n.loggerOptions||{});m.debug("GalaxyApp.logger: ",m.logger);m._initLocale();m.debug("GalaxyApp.localize: ",m.localize);m.config=n.config||a.config||{};m.debug("GalaxyApp.config: ",m.config);m._initUser(n.user||a.user||{});m.debug("GalaxyApp.user: ",m.user);m.trigger("ready",m);return m};h.prototype._processOptions=function f(o){var n=this,p=n.defaultOptions;n.debug("_processOptions: ",o);n.options={};for(var m in p){if(p.hasOwnProperty(m)){n.options[m]=(o.hasOwnProperty(m))?(o[m]):(p[m])}}return n};h.prototype._patchGalaxy=function f(m){var o=this;if(o.options.patchExisting&&m){o.debug("found existing Galaxy object:",m);for(var n in m){if(m.hasOwnProperty(n)){o.debug("\t patching in "+n+" to Galaxy");o[n]=m[n]}}}};h.prototype._initLogger=function l(n){var m=this;m.debug("_initLogger:",n);m.logger=new d.MetricsLogger(n);return m};h.prototype._initLocale=function j(n){var m=this;m.debug("_initLocale:",n);m.localize=e;window._l=m.localize;return m};h.prototype._initUser=function i(n){var m=this;m.debug("_initUser:",n);m.user=new b.User(n);m.currUser=m.user;return m};h.prototype.toString=function c(){var m=this.user.get("email")||"(anonymous)";return"GalaxyApp("+m+")"};return{GalaxyApp:h}}); \ No newline at end of file +define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","bootstrapped-data"],function(b,d,h,e,a){function i(o){var n=this;return n._init(o||{})}h(i,"GalaxyApp");i.prototype.defaultOptions={patchExisting:true,root:"/"};i.prototype._init=function l(o){var n=this;_.extend(n,Backbone.Events);n._processOptions(o);n.debug("GalaxyApp.options: ",n.options);n._patchGalaxy(window.Galaxy);n._initLogger(o.loggerOptions||{});n.debug("GalaxyApp.logger: ",n.logger);n._initLocale();n.debug("GalaxyApp.localize: ",n.localize);n.config=o.config||a.config||{};n.debug("GalaxyApp.config: ",n.config);n._initUser(o.user||a.user||{});n.debug("GalaxyApp.user: ",n.user);n.trigger("ready",n);n._setUpListeners();return n};i.prototype._processOptions=function g(p){var o=this,q=o.defaultOptions;o.debug("_processOptions: ",p);o.options={};for(var n in q){if(q.hasOwnProperty(n)){o.options[n]=(p.hasOwnProperty(n))?(p[n]):(q[n])}}return o};i.prototype._patchGalaxy=function g(n){var p=this;if(p.options.patchExisting&&n){p.debug("found existing Galaxy object:",n);for(var o in n){if(n.hasOwnProperty(o)){p.debug("\t patching in "+o+" to Galaxy");p[o]=n[o]}}}};i.prototype._initLogger=function m(o){var n=this;n.debug("_initLogger:",o);n.logger=new d.MetricsLogger(o);return n};i.prototype._initLocale=function k(o){var n=this;n.debug("_initLocale:",o);n.localize=e;window._l=n.localize;return n};i.prototype._initUser=function j(o){var n=this;n.debug("_initUser:",o);n.user=new b.User(o);n.currUser=n.user;return n};i.prototype._setUpListeners=function f(){var n=this;n.lastAjax={};$(document).bind("ajaxSend",function(q,s,o){var r=o.data;try{r=JSON.parse(r)}catch(p){}n.lastAjax={url:location.href.slice(0,-1)+o.url,data:r}})};i.prototype.toString=function c(){var n=this.user.get("email")||"(anonymous)";return"GalaxyApp("+n+")"};return{GalaxyApp:i}}); \ No newline at end of file diff -r f58d8cf6018a536470275b400c711ff74f9b4dc3 -r 32f451ba2202e11d7aee80667d6882c56ae2e3f5 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(e,b,a,f,k,d){var i=k.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(m){var n="expandedHdas";this.save(n,_.extend(this.get(n),_.object([m.id],[m.get("id")])))},removeExpandedHda:function(m){var n="expandedHdas";this.save(n,_.omit(this.get(n),m.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function g(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(k.LoggableMixin).extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){this.error(o,r,n,q,p);if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(p,t,o,s,r){var n=Galaxy.currUser,m={message:this._bePolite(s),details:{user:(n instanceof f.User)?(n.toJSON()):(n+""),source:(p instanceof Backbone.Model)?(p.toJSON()):(p+""),xhr:t,options:(t)?(_.omit(o,"xhr")):(o)}};_.extend(m.details,r||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var q=t.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(u){return u.split(": ")});m.details.xhr.responseHeaders=_.object(q)}return m},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.values(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=e.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new e.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.contents)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.contents.on("add",this.addContentView,this);this.model.on("error error:contents",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.id,s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(p){var n=this._getContentClass(p),m=_.extend(this._getContentOptions(p),{model:p}),o=new n(m);this._setUpHdaListeners(o);return o},_getContentClass:function(m){var n=m.get("history_content_type");switch(n){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+n)},_getContentOptions:function(m){return{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedHdas")[m.id],hasUser:this.model.ownedByCurrUser(),logger:this.logger}},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("expanded",function(o){m.storage.addExpandedHda(o.model)});n.on("collapsed",function(o){m.storage.removeExpandedHda(o.model)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},views:function(m){var n=this,o=this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);if(m!==undefined){return n.hdaViews[o.at(m).id]}return o.map(function(p){return n.hdaViews[p.id]})},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},hdaViewRange:function(p,o){if(p===o){return[p]}var m=this,n=false,q=[];this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters).each(function(r){if(n){q.push(m.hdaViews[r.id]);if(r===p.model||r===o.model){n=false}}else{if(r===p.model||r===o.model){n=true;q.push(m.hdaViews[r.id])}}});return q},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.collapse()});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.contents.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.contents.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.contents.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},print:function(){var m=this;m.debug(this);_.each(this.hdaViews,function(n,o){m.debug("\t "+o,n)})},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(e,b,a,f,k,d){var i=k.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(m){var n="expandedHdas";this.save(n,_.extend(this.get(n),_.object([m.id],[m.get("id")])))},removeExpandedHda:function(m){var n="expandedHdas";this.save(n,_.omit(this.get(n),m.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});i.storageKeyPrefix="history:";i.historyStorageKey=function g(m){if(!m){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+m)}return(i.storageKeyPrefix+m)};i.get=function c(m){return new i({id:i.historyStorageKey(m)})};i.clearAll=function h(n){for(var m in sessionStorage){if(m.indexOf(i.storageKeyPrefix)===0){sessionStorage.removeItem(m)}}};var j=Backbone.View.extend(k.LoggableMixin).extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:d("This history is empty"),noneFoundMsg:d("No matching datasets found"),initialize:function(m){m=m||{};if(m.logger){this.logger=m.logger}this.log(this+".initialize:",m);this.linkTarget=m.linkTarget||"_blank";this.fxSpeed=_.has(m,"fxSpeed")?(m.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=m.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var n=_.pick(m,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,n,false);if(m.onready){m.onready.call(this)}},_setUpListeners:function(){this.on("error",function(n,q,m,p,o){this.errorHandler(n,q,m,p,o)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(m){this.log(this+"",arguments)},this)}return this},errorHandler:function(o,r,n,q,p){this.error(o,r,n,q,p);window.xhr=r;if(r&&r.status===0&&r.readyState===0){}else{if(r&&r.status===502){}else{var m=this._parseErrorMessage(o,r,n,q,p);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",m.message,m.details)})}else{this.displayMessage("error",m.message,m.details)}}}},_parseErrorMessage:function(q,t,u,o,m,r){var p=Galaxy.currUser,s={message:this._bePolite(o),details:{message:o,raven:(window.Raven)?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(t)?(_.omit(u,"xhr")):(u),xhr:t,source:(_.isFunction(q.toJSON))?(q.toJSON()):(q+""),user:(p instanceof f.User)?(p.toJSON()):(p+"")}};_.extend(s.details,m||{});if(t&&_.isFunction(t.getAllResponseHeaders)){var n=t.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(v){return v.split(": ")});s.details.xhr.responseHeaders=_.object(n)}return s},_bePolite:function(m){m=m||d("An error occurred while getting updates from the server");return m+". "+d("Please contact a Galaxy administrator if the problem persists")+"."},loadHistoryWithHDADetails:function(o,n,m,q){var p=function(r){return _.values(i.get(r.id).get("expandedHdas"))};return this.loadHistory(o,n,m,q,p)},loadHistory:function(p,o,n,s,q){var m=this;o=o||{};m.trigger("loading-history",m);var r=e.History.getHistoryData(p,{historyFn:n,hdaFn:s,hdaDetailIds:o.initiallyExpanded||q});return m._loadHistoryFromXHR(r,o).fail(function(v,t,u){m.trigger("error",m,v,o,d("An error was encountered while "+t),{historyId:p,history:u||{}})}).always(function(){m.trigger("loading-done",m)})},_loadHistoryFromXHR:function(o,n){var m=this;o.then(function(p,q){m.JSONToModel(p,q,n)});o.fail(function(q,p){m.render()});return o},JSONToModel:function(p,m,n){this.log("JSONToModel:",p,m,n);n=n||{};var o=new e.History(p,m,n);this.setModel(o);return this},setModel:function(n,m,o){m=m||{};o=(o!==undefined)?(o):(true);this.log("setModel:",n,m,o);this.freeModel();this.selectedHdaIds=[];if(n){this.model=n;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(m.initiallyExpanded,m.show_deleted,m.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(o){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.contents)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(n,m,o){this.storage=new i({id:i.historyStorageKey(this.model.get("id"))});if(_.isObject(n)){this.storage.set("exandedHdas",n)}if(_.isBoolean(m)){this.storage.set("show_deleted",m)}if(_.isBoolean(o)){this.storage.set("show_hidden",o)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.contents.on("add",this.addContentView,this);this.model.on("error error:contents",function(n,p,m,o){this.errorHandler(n,p,m,o)},this);return this},render:function(o,p){this.log("render:",o,p);o=(o===undefined)?(this.fxSpeed):(o);var m=this,n;if(this.model){n=this.renderModel()}else{n=this.renderWithoutModel()}$(m).queue("fx",[function(q){if(o&&m.$el.is(":visible")){m.$el.fadeOut(o,q)}else{q()}},function(q){m.$el.empty();if(n){m.$el.append(n.children())}q()},function(q){if(o&&!m.$el.is(":visible")){m.$el.fadeIn(o,q)}else{q()}},function(q){if(p){p.call(this)}m.trigger("rendered",this);q()}]);return this},renderWithoutModel:function(){var m=$("<div/>"),n=$("<div/>").addClass("message-container").css({margin:"4px"});return m.append(n)},renderModel:function(){var m=$("<div/>");m.append(j.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(m).text(this.emptyMsg);m.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(m);this.renderHdas(m);return m},_renderEmptyMsg:function(o){var n=this,m=n.$emptyMessage(o);if(!_.isEmpty(n.hdaViews)){m.hide()}else{if(n.searchFor){m.text(n.noneFoundMsg).show()}else{m.text(n.emptyMsg).show()}}return this},_renderSearchButton:function(m){return faIconButton({title:d("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(m){m=m||this.$el;m.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(m.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(m){return(m||this.$el).find(".datasets-list")},$messages:function(m){return(m||this.$el).find(".message-container")},$emptyMessage:function(m){return(m||this.$el).find(".empty-history-message")},renderHdas:function(n){n=n||this.$el;var m=this,p={},o=this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(n).empty();if(o.length){o.each(function(r){var q=r.id,s=m._createContentView(r);p[q]=s;if(_.contains(m.selectedHdaIds,q)){s.selected=true}m.attachContentView(s.render(),n)})}this.hdaViews=p;this._renderEmptyMsg(n);return this.hdaViews},_createContentView:function(p){var n=this._getContentClass(p),m=_.extend(this._getContentOptions(p),{model:p}),o=new n(m);this._setUpHdaListeners(o);return o},_getContentClass:function(m){var n=m.get("history_content_type");switch(n){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+n)},_getContentOptions:function(m){return{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedHdas")[m.id],hasUser:this.model.ownedByCurrUser(),logger:this.logger}},_setUpHdaListeners:function(n){var m=this;n.on("error",function(p,r,o,q){m.errorHandler(p,r,o,q)});n.on("expanded",function(o){m.storage.addExpandedHda(o.model)});n.on("collapsed",function(o){m.storage.removeExpandedHda(o.model)});return this},attachContentView:function(o,n){n=n||this.$el;var m=this.$datasetsList(n);m.prepend(o.$el);return this},addContentView:function(p){this.log("add."+this,p);var n=this;if(!p.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return n}$({}).queue([function o(r){var q=n.$emptyMessage();if(q.is(":visible")){q.fadeOut(n.fxSpeed,r)}else{r()}},function m(q){var r=n._createContentView(p);n.hdaViews[p.id]=r;r.render().$el.hide();n.scrollToTop();n.attachContentView(r);r.$el.slideDown(n.fxSpeed)}]);return n},views:function(m){var n=this,o=this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);if(m!==undefined){return n.hdaViews[o.at(m).id]}return o.map(function(p){return n.hdaViews[p.id]})},refreshContents:function(n,m){if(this.model){return this.model.refresh(n,m)}return $.when()},hdaViewRange:function(p,o){if(p===o){return[p]}var m=this,n=false,q=[];this.model.contents.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters).each(function(r){if(n){q.push(m.hdaViews[r.id]);if(r===p.model||r===o.model){n=false}}else{if(r===p.model||r===o.model){n=true;q.push(m.hdaViews[r.id])}}});return q},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(m){m.collapse()});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",m);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(m){m=(m!==undefined)?(m):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",m);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(n){var o=this,p=".history-search-input";function m(q){if(o.model.contents.haveDetails()){o.searchHdas(q);return}o.$el.find(p).searchInput("toggle-loading");o.model.contents.fetchAllDetails({silent:true}).always(function(){o.$el.find(p).searchInput("toggle-loading")}).done(function(){o.searchHdas(q)})}n.searchInput({initialVal:o.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:m,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return n},toggleSearchControls:function(o,m){var n=this.$el.find(".history-search-controls"),p=(jQuery.type(o)==="number")?(o):(this.fxSpeed);m=(m!==undefined)?(m):(!n.is(":visible"));if(m){n.slideDown(p,function(){$(this).find("input").focus()})}else{n.slideUp(p)}return m},searchHdas:function(m){var n=this;this.searchFor=m;this.filters=[function(o){return o.matchesAll(n.searchFor)}];this.trigger("search:searching",m,this);this.renderHdas();return this},clearHdaSearch:function(m){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(n,m,o){m=(m!==undefined)?(m):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,o)}else{this.$el.fadeOut(m);this.indicator.show(n,m,o)}},_hideLoadingIndicator:function(m,n){m=(m!==undefined)?(m):(this.fxSpeed);if(this.indicator){this.indicator.hide(m,n)}},displayMessage:function(r,s,q){var o=this;this.scrollToTop();var p=this.$messages(),m=$("<div/>").addClass(r+"message").html(s);if(!_.isEmpty(q)){var n=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(o._messageToModalOptions(r,s,q));return false});m.append(" ",n)}return p.html(m)},_messageToModalOptions:function(q,s,p){var m=this,r=$("<div/>"),o={title:"Details"};function n(t){t=_.omit(t,_.functions(t));return["<table>",_.map(t,function(v,u){v=(_.isObject(v))?(n(v)):(v);return'<tr><td style="vertical-align: top; color: grey">'+u+'</td><td style="padding-left: 8px">'+v+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(p)){o.body=r.append(n(p))}else{o.body=r.html(p)}o.buttons={Ok:function(){Galaxy.modal.hide();m.clearMessages()}};return o},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(m){this.$container().scrollTop(m);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(n){if((!n)||(!this.hdaViews[n])){return this}var m=this.hdaViews[n];this.scrollTo(m.el.offsetTop);return this},scrollToHid:function(m){var n=this.model.contents.getByHid(m);if(!n){return this}return this.scrollToId(n.id)},print:function(){var m=this;m.debug(this);_.each(this.hdaViews,function(n,o){m.debug("\t "+o,n)})},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var l=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',d("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',d("You are over your disk quota"),". ",d("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',d("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',d("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',d("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',d("This history is empty"),"</div>"].join("");j.templates={historyPanel:function(m){return _.template(l,m,{variable:"history"})}};return{ReadOnlyHistoryPanel:j}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc0769d68f40/ Changeset: fc0769d68f40 User: jmchilton Date: 2014-08-14 04:52:59 Summary: PEP-8 fixes and comments for workflow_util.py. Affected #: 1 file diff -r 08e25f0ffc06543bd76efbe7bca8a329bb1858cb -r fc0769d68f4071701bca612823587b1ccea1cbef lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -1,3 +1,6 @@ +""" Tool shed helper methods for dealing with workflows - only two methods are +utilized outside of this modules - generate_workflow_image and import_workflow. +""" import logging import os @@ -6,7 +9,7 @@ import galaxy.webapps.galaxy.controllers.workflow from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html -from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING +from galaxy.workflow.render import WorkflowCanvas from galaxy.workflow.modules import InputDataModule from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory @@ -106,6 +109,7 @@ def get_data_inputs( self ): data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, galaxy.tools.parameters.DataToolParameter ): data_inputs.append( dict( name=prefixed_name, @@ -125,16 +129,16 @@ if self.tool: data_inputs = None for name, tool_output in self.tool.outputs.iteritems(): - if tool_output.format_source != None: + if tool_output.format_source is not None: # Default to special name "input" which remove restrictions on connections formats = [ 'input' ] - if data_inputs == None: + if data_inputs is None: data_inputs = self.get_data_inputs() # Find the input parameter referenced by format_source for di in data_inputs: # Input names come prefixed with conditional and repeat names separated by '|', # so remove prefixes when comparing with format_source. - if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + if di[ 'name' ] is not None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: formats = di[ 'extensions' ] else: formats = [ tool_output.format ] @@ -170,6 +174,7 @@ module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ): """ Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called @@ -225,6 +230,7 @@ trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() + def get_workflow_data_inputs( step, module ): if module.type == 'tool': if module.tool: @@ -240,6 +246,7 @@ return data_inputs return module.get_data_inputs() + def get_workflow_data_outputs( step, module, steps ): if module.type == 'tool': if module.tool: @@ -264,6 +271,7 @@ return data_outputs return module.get_data_outputs() + def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): """ Return an in-memory Workflow object from the dictionary object created when it was exported. This method is called from @@ -334,6 +342,7 @@ # Return the in-memory Workflow object for display or later persistence to the Galaxy database. return workflow, missing_tool_tups + def get_workflow_module_name( module, missing_tool_tups ): module_name = module.get_name() if module.type == 'tool' and module_name == 'unavailable': @@ -344,6 +353,7 @@ break return module_name + def import_workflow( trans, repository, workflow_name ): """Import a workflow contained in an installed tool shed repository into Galaxy (this method is called only from Galaxy).""" status = 'done' @@ -402,14 +412,15 @@ status = 'error' return workflow, status, message -def save_workflow( trans, workflow, workflow_dict = None): + +def save_workflow( trans, workflow, workflow_dict=None): """Use the received in-memory Workflow object for saving to the Galaxy database.""" stored = trans.model.StoredWorkflow() stored.name = workflow.name workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user - if workflow_dict and workflow_dict.get('annotation',''): + if workflow_dict and workflow_dict.get('annotation', ''): annotation = sanitize_html( workflow_dict['annotation'], 'utf-8', 'text/html' ) new_annotation = trans.model.StoredWorkflowAnnotationAssociation() new_annotation.annotation = annotation https://bitbucket.org/galaxy/galaxy-central/commits/c627f39b9b99/ Changeset: c627f39b9b99 User: jmchilton Date: 2014-08-14 04:52:59 Summary: Remove unused method. Affected #: 1 file diff -r fc0769d68f4071701bca612823587b1ccea1cbef -r c627f39b9b997b526a1e4adfca4ec6c10587c8e4 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -156,11 +156,6 @@ def __init__( self, module_types ): self.module_types = module_types - def new( self, trans, type, tools_metadata=None, tool_id=None ): - """Return module for type and (optional) tool_id initialized with new / default state.""" - assert type in self.module_types - return self.module_types[ type ].new( trans, tool_id ) - def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): """Return module initialized from the data in dictionary `step_dict`.""" type = step_dict[ 'type' ] https://bitbucket.org/galaxy/galaxy-central/commits/3874a0ab5e3d/ Changeset: 3874a0ab5e3d User: jmchilton Date: 2014-08-14 04:52:59 Summary: Rearrange module arguments to bring ts workflow modules more inline with Galaxy. Will enable remove tool shed specific input module in a subsequent changeset. Affected #: 1 file diff -r c627f39b9b997b526a1e4adfca4ec6c10587c8e4 -r 3874a0ab5e3d71f34f29cc9bd2883c3b9165dec5 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -35,14 +35,14 @@ return module @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): + def from_dict( Class, trans, step_dict, repository_id, changeset_revision, tools_metadata=None, secure=True ): module = Class( trans ) state = json.from_json_string( step_dict[ "tool_state" ] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) return module @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + def from_workflow_step( Class, trans, step, repository_id, changeset_revision, tools_metadata ): module = Class( trans ) module.state = dict( name="Input Dataset" ) if step.tool_inputs and "name" in step.tool_inputs: @@ -87,7 +87,7 @@ return module @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): + def from_dict( Class, trans, step_dict, repository_id, changeset_revision, tools_metadata, secure=True ): tool_id = step_dict[ 'tool_id' ] module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) module.state = galaxy.tools.DefaultToolState() @@ -97,7 +97,7 @@ return module @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + def from_workflow_step( Class, trans, step, repository_id, changeset_revision, tools_metadata ): module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) module.state = galaxy.tools.DefaultToolState() if module.tool: @@ -160,12 +160,12 @@ """Return module initialized from the data in dictionary `step_dict`.""" type = step_dict[ 'type' ] assert type in self.module_types - return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + return self.module_types[ type ].from_dict( trans, step_dict, repository_id=repository_id, changeset_revision=changeset_revision, **kwd ) def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): """Return module initialized from the WorkflowStep object `step`.""" type = step.type - return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + return self.module_types[ type ].from_workflow_step( trans, step, repository_id=repository_id, changeset_revision=changeset_revision, tools_metadata=tools_metadata ) module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) https://bitbucket.org/galaxy/galaxy-central/commits/f8b0a85a04c0/ Changeset: f8b0a85a04c0 User: jmchilton Date: 2014-08-14 04:52:59 Summary: Remove unused methods. Affected #: 1 file diff -r 3874a0ab5e3d71f34f29cc9bd2883c3b9165dec5 -r f8b0a85a04c0e4d8d84aebf2cd52adbef5fa6e29 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -29,12 +29,6 @@ name = "Input dataset" @classmethod - def new( Class, trans, tools_metadata=None, tool_id=None ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - return module - - @classmethod def from_dict( Class, trans, step_dict, repository_id, changeset_revision, tools_metadata=None, secure=True ): module = Class( trans ) state = json.from_json_string( step_dict[ "tool_state" ] ) @@ -81,12 +75,6 @@ self.state = None @classmethod - def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): - module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) - module.state = module.tool.new_state( trans, all_pages=True ) - return module - - @classmethod def from_dict( Class, trans, step_dict, repository_id, changeset_revision, tools_metadata, secure=True ): tool_id = step_dict[ 'tool_id' ] module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) https://bitbucket.org/galaxy/galaxy-central/commits/a03e7b90d953/ Changeset: a03e7b90d953 User: jmchilton Date: 2014-08-14 04:52:59 Summary: Rework tool shed's workflow module factory so only tool module needs to be different. Fixes dataset collection inputs in the tool shed. Furthermore, this will allow all all future non-tool modules to be the same between Galaxy and the Tool Shed as well. May seem hacky - but it is removing duplication and it makes some intuitive sense that only the tool module would need to function differently between Galaxy and the tool shed anyway - input parameters, if statements, stop and review steps, etc... will all likely not depend on tool shed artifacts. Affected #: 2 files diff -r f8b0a85a04c0e4d8d84aebf2cd52adbef5fa6e29 -r a03e7b90d9534ae7a495f76bc320fb81d764d2bb lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -536,4 +536,5 @@ type = step.type return self.module_types[type].from_workflow_step( trans, step ) -module_factory = WorkflowModuleFactory( dict( data_input=InputDataModule, data_collection_input=InputDataCollectionModule, tool=ToolModule ) ) +module_types = dict( data_input=InputDataModule, data_collection_input=InputDataCollectionModule, tool=ToolModule ) +module_factory = WorkflowModuleFactory( module_types ) diff -r f8b0a85a04c0e4d8d84aebf2cd52adbef5fa6e29 -r a03e7b90d9534ae7a495f76bc320fb81d764d2bb lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -10,7 +10,7 @@ from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html from galaxy.workflow.render import WorkflowCanvas -from galaxy.workflow.modules import InputDataModule +from galaxy.workflow.modules import module_types from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory @@ -23,27 +23,6 @@ log = logging.getLogger( __name__ ) -class RepoInputDataModule( InputDataModule ): - - type = "data_input" - name = "Input dataset" - - @classmethod - def from_dict( Class, trans, step_dict, repository_id, changeset_revision, tools_metadata=None, secure=True ): - module = Class( trans ) - state = json.from_json_string( step_dict[ "tool_state" ] ) - module.state = dict( name=state.get( "name", "Input Dataset" ) ) - return module - - @classmethod - def from_workflow_step( Class, trans, step, repository_id, changeset_revision, tools_metadata ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - if step.tool_inputs and "name" in step.tool_inputs: - module.state[ 'name' ] = step.tool_inputs[ 'name' ] - return module - - class RepoToolModule( ToolModule ): type = "tool" @@ -144,18 +123,30 @@ def __init__( self, module_types ): self.module_types = module_types - def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): + def from_dict( self, trans, repository_id, changeset_revision, step_dict, tools_metadata, **kwd ): """Return module initialized from the data in dictionary `step_dict`.""" type = step_dict[ 'type' ] assert type in self.module_types - return self.module_types[ type ].from_dict( trans, step_dict, repository_id=repository_id, changeset_revision=changeset_revision, **kwd ) + module_method_kwds = dict( **kwd ) + if type == "tool": + module_method_kwds[ 'repository_id' ] = repository_id + module_method_kwds[ 'changeset_revision' ] = changeset_revision + module_method_kwds[ 'tools_metadata' ] = tools_metadata + return self.module_types[ type ].from_dict( trans, step_dict, **module_method_kwds ) def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): """Return module initialized from the WorkflowStep object `step`.""" type = step.type - return self.module_types[ type ].from_workflow_step( trans, step, repository_id=repository_id, changeset_revision=changeset_revision, tools_metadata=tools_metadata ) + module_method_kwds = dict( ) + if type == "tool": + module_method_kwds[ 'repository_id' ] = repository_id + module_method_kwds[ 'changeset_revision' ] = changeset_revision + module_method_kwds[ 'tools_metadata' ] = tools_metadata + return self.module_types[ type ].from_workflow_step( trans, step, **module_method_kwds ) -module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) +tool_shed_module_types = module_types.copy() +tool_shed_module_types[ 'tool' ] = RepoToolModule +module_factory = RepoWorkflowModuleFactory( tool_shed_module_types ) def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ): https://bitbucket.org/galaxy/galaxy-central/commits/f58d8cf6018a/ Changeset: f58d8cf6018a User: jmchilton Date: 2014-08-14 04:52:59 Summary: Make run_tool_shed.sh executable. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #457)
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08e25f0ffc06/ Changeset: 08e25f0ffc06 User: jmchilton Date: 2014-08-14 03:53:30 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #457) Allow cheetah tool templates to reason polymorphically about datatypes. Affected #: 1 file diff -r be407987417297cb1543864e8448d49bb93851ab -r 08e25f0ffc06543bd76efbe7bca8a329bb1858cb lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -194,6 +194,7 @@ else: self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) + self.datatypes_registry = datatypes_registry self.false_path = getattr( dataset_path, "false_path", None ) self.false_extra_files_path = getattr( dataset_path, "false_extra_files_path", None ) @@ -201,6 +202,10 @@ def is_collection( self ): return False + def is_of_type( self, *exts ): + datatypes = [ self.datatypes_registry.get_datatype_by_extension( e ) for e in exts ] + return self.dataset.datatype.matches_any( datatypes ) + def __str__( self ): if self.false_path is not None: return self.false_path Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/94105d1ea20c/ Changeset: 94105d1ea20c User: jmchilton Date: 2014-08-12 18:26:20 Summary: Allow cheetah tool templates to reason polymorphically about datatypes. Adds a $input.is_of_type( 'ext' ) method to dataset wrappers. Peter brought this issue up on galaxy-dev here http://dev.list.galaxyproject.org/Determining-datatype-inheritance-in-tool-…. There are some hacks if you are willing to import the datatype or use $__app__ but both of these are exposing details and frankly internals of Galaxy that we should not want to expose to tools or tool authors. Bad ways and new good way: #import galaxy.datatypes.sequence ; echo "${isinstance($input1.datatype, galaxy.datatypes.sequence.Fastq )}" ; echo "$input1.datatype.matches_any([galaxy.datatypes.sequence.Fastq])" ; echo "$input1.datatype.matches_any([ $__app__.datatypes_registry.get_datatype_by_extension( 'fastq' )])" ; echo "$input1.is_of_type( 'fastq' )" Affected #: 1 file diff -r f926988f8e0a480c09d3462002f482b5ac806682 -r 94105d1ea20c2cc9a5e5643db191178260a770cb lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -194,6 +194,7 @@ else: self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) + self.datatypes_registry = datatypes_registry self.false_path = getattr( dataset_path, "false_path", None ) self.false_extra_files_path = getattr( dataset_path, "false_extra_files_path", None ) @@ -201,6 +202,10 @@ def is_collection( self ): return False + def is_of_type( self, ext ): + datatype = self.datatypes_registry.get_datatype_by_extension( ext ) + return self.dataset.datatype.matches_any( [ datatype ] ) + def __str__( self ): if self.false_path is not None: return self.false_path https://bitbucket.org/galaxy/galaxy-central/commits/1b28e2bd5bad/ Changeset: 1b28e2bd5bad User: jmchilton Date: 2014-08-12 19:08:11 Summary: Extend dataset_wrapper.is_of_type to allow multiple arguments. Affected #: 1 file diff -r 94105d1ea20c2cc9a5e5643db191178260a770cb -r 1b28e2bd5badd94c9e94053d1a80f98b4eb6a4e6 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -202,9 +202,9 @@ def is_collection( self ): return False - def is_of_type( self, ext ): - datatype = self.datatypes_registry.get_datatype_by_extension( ext ) - return self.dataset.datatype.matches_any( [ datatype ] ) + def is_of_type( self, *exts ): + datatypes = [ self.datatypes_registry.get_datatype_by_extension( e ) for e in exts ] + return self.dataset.datatype.matches_any( datatypes ) def __str__( self ): if self.false_path is not None: https://bitbucket.org/galaxy/galaxy-central/commits/08e25f0ffc06/ Changeset: 08e25f0ffc06 User: jmchilton Date: 2014-08-14 03:53:30 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #457) Allow cheetah tool templates to reason polymorphically about datatypes. Affected #: 1 file diff -r be407987417297cb1543864e8448d49bb93851ab -r 08e25f0ffc06543bd76efbe7bca8a329bb1858cb lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -194,6 +194,7 @@ else: self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) + self.datatypes_registry = datatypes_registry self.false_path = getattr( dataset_path, "false_path", None ) self.false_extra_files_path = getattr( dataset_path, "false_extra_files_path", None ) @@ -201,6 +202,10 @@ def is_collection( self ): return False + def is_of_type( self, *exts ): + datatypes = [ self.datatypes_registry.get_datatype_by_extension( e ) for e in exts ] + return self.dataset.datatype.matches_any( datatypes ) + def __str__( self ): if self.false_path is not None: return self.false_path Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 10 new changesets
by commits-noreply＠bitbucket.org 14 Aug '14

14 Aug '14

10 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/91110971f1b3/ Changeset: 91110971f1b3 User: jmchilton Date: 2014-08-14 03:36:10 Summary: Add galaxy.workflow.render module - try to decrease dup between ts and gx. Affected #: 3 files diff -r fb6a06ce35f08f516b8a5d80d2105225c243201b -r 91110971f1b37f121e177cc983d26f777805c1c4 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -39,6 +39,7 @@ edgelist_for_workflow_steps, order_workflow_steps_with_levels, ) +from galaxy.worklfow.render import WorkflowCanvas class StoredWorkflowListGrid( grids.Grid ): @@ -1554,11 +1555,11 @@ def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow data = [] - canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left") - text = svgfig.SVG("g") - connectors = svgfig.SVG("g") - boxes = svgfig.SVG("g") - svgfig.Text.defaults["font-size"] = "10px" + workflow_canvas = WorkflowCanvas() + canvas = workflow_canvas.canvas + text = workflow_canvas.text + connectors = workflow_canvas.connectors + boxes = workflow_canvas.boxes in_pos = {} out_pos = {} margin = 5 @@ -1641,14 +1642,7 @@ text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) - canvas.append(connectors) - canvas.append(boxes) - canvas.append(text) - width, height = (max_x + max_width + 50), max_y + 300 - canvas['width'] = "%spx" % width - canvas['height'] = "%spx" % height - canvas['viewBox'] = "0 0 %s %s" % (width, height) - + workflow_canvas.finish( max_x, max_width, max_y ) return canvas diff -r fb6a06ce35f08f516b8a5d80d2105225c243201b -r 91110971f1b37f121e177cc983d26f777805c1c4 lib/galaxy/workflow/render.py --- /dev/null +++ b/lib/galaxy/workflow/render.py @@ -0,0 +1,25 @@ +from galaxy import eggs + +eggs.require( "SVGFig" ) +import svgfig + + +class WorkflowCanvas( object ): + + def __init__( self ): + self.canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) + self.text = svgfig.SVG( "g" ) + self.connectors = svgfig.SVG( "g" ) + self.boxes = svgfig.SVG( "g" ) + + svgfig.Text.defaults[ "font-size" ] = "10px" + + def finish( self, max_x, max_width, max_y ): + canvas = self.canvas + canvas.append( self.connectors ) + canvas.append( self.boxes ) + canvas.append( self.text ) + width, height = ( max_x + max_width + 50 ), max_y + 300 + canvas[ 'width' ] = "%s px" % width + canvas[ 'height' ] = "%s px" % height + canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) diff -r fb6a06ce35f08f516b8a5d80d2105225c243201b -r 91110971f1b37f121e177cc983d26f777805c1c4 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -7,6 +7,7 @@ from galaxy import eggs from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html +from galaxy.worklfow.render import WorkflowCanvas from galaxy.workflow.modules import InputDataModule from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory @@ -207,11 +208,12 @@ repository_id=repository_id, changeset_revision=changeset_revision ) data = [] - canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) - text = svgfig.SVG( "g" ) - connectors = svgfig.SVG( "g" ) - boxes = svgfig.SVG( "g" ) - svgfig.Text.defaults[ "font-size" ] = "10px" + workflow_canvas = WorkflowCanvas() + canvas = workflow_canvas.canvas + text = workflow_canvas.text + connectors = workflow_canvas.connectors + boxes = workflow_canvas.boxes + in_pos = {} out_pos = {} margin = 5 @@ -311,13 +313,7 @@ in_coords[ 0 ] - 10, in_coords[ 1 ], arrow_end = "true" ).SVG() ) - canvas.append( connectors ) - canvas.append( boxes ) - canvas.append( text ) - width, height = ( max_x + max_width + 50 ), max_y + 300 - canvas[ 'width' ] = "%s px" % width - canvas[ 'height' ] = "%s px" % height - canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + workflow_canvas.finish( max_x, max_width, max_y ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/e88f0fe18454/ Changeset: e88f0fe18454 User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Affected #: 3 files diff -r 91110971f1b37f121e177cc983d26f777805c1c4 -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -39,7 +39,7 @@ edgelist_for_workflow_steps, order_workflow_steps_with_levels, ) -from galaxy.worklfow.render import WorkflowCanvas +from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING class StoredWorkflowListGrid( grids.Grid ): @@ -1559,14 +1559,7 @@ canvas = workflow_canvas.canvas text = workflow_canvas.text connectors = workflow_canvas.connectors - boxes = workflow_canvas.boxes - in_pos = {} - out_pos = {} - margin = 5 - line_px = 16 # how much spacing between input/outputs - widths = {} # store px width for boxes of each step - max_width, max_x, max_y = 0, 0, 0 - + margin = MARGIN for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) @@ -1588,61 +1581,27 @@ data.append(step_dict) x, y = step.position['left'], step.position['top'] - count = 0 max_len = len(module.get_name()) * 1.5 text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() ) - y += 45 - for di in module.get_data_inputs(): - cur_y = y + count * line_px - if step.order_index not in in_pos: - in_pos[step.order_index] = {} - in_pos[step.order_index][di['name']] = (x, cur_y) - text.append( svgfig.Text(x, cur_y, di['label']).SVG() ) - count += 1 - max_len = max(max_len, len(di['label'])) - - if len(module.get_data_inputs()) > 0: - y += 15 - - for do in module.get_data_outputs(): - cur_y = y + count * line_px - if step.order_index not in out_pos: - out_pos[step.order_index] = {} - out_pos[step.order_index][do['name']] = (x, cur_y) - text.append( svgfig.Text(x, cur_y, do['name']).SVG() ) - count += 1 - max_len = max(max_len, len(do['name'])) - - widths[step.order_index] = max_len * 5.5 - max_x = max(max_x, step.position['left']) - max_y = max(max_y, step.position['top']) - max_width = max(max_width, widths[step.order_index]) + module_data_inputs = module.get_data_inputs() + module_data_outputs = module.get_data_outputs() + order_index = step.order_index + workflow_canvas.add_text( module_data_inputs, module_data_outputs, order_index, x, y, max_len ) for step_dict in data: - width = widths[step_dict['id']] - x, y = step_dict['position']['left'], step_dict['position']['top'] - boxes.append( svgfig.Rect(x - margin, y, x + width - margin, y + 30, fill="#EBD9B2").SVG() ) - box_height = (len(step_dict['data_inputs']) + len(step_dict['data_outputs'])) * line_px + margin - - # Draw separator line - if len(step_dict['data_inputs']) > 0: - box_height += 15 - sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG() ) - - # input/output box - boxes.append( svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG() ) - + fill = "#EBD9B2" + width = workflow_canvas.widths[step_dict['id']] + workflow_canvas.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict['input_connections'].iteritems(): - in_coords = in_pos[step_dict['id']][conn] - out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] - adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) - text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) + in_coords = workflow_canvas.in_pos[step_dict['id']][conn] + out_conn_pos = workflow_canvas.out_pos[output_dict['id']][output_dict['output_name']] + adjusted = (out_conn_pos[0] + workflow_canvas.widths[output_dict['id']], out_conn_pos[1]) + text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + workflow_canvas.widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) - workflow_canvas.finish( max_x, max_width, max_y ) + workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) return canvas diff -r 91110971f1b37f121e177cc983d26f777805c1c4 -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -3,6 +3,9 @@ eggs.require( "SVGFig" ) import svgfig +MARGIN = 5 +LINE_SPACING = 15 + class WorkflowCanvas( object ): @@ -14,6 +17,13 @@ svgfig.Text.defaults[ "font-size" ] = "10px" + self.in_pos = {} + self.out_pos = {} + self.widths = {} + self.max_x = 0 + self.max_y = 0 + self.max_width = 0 + def finish( self, max_x, max_width, max_y ): canvas = self.canvas canvas.append( self.connectors ) @@ -23,3 +33,50 @@ canvas[ 'width' ] = "%s px" % width canvas[ 'height' ] = "%s px" % height canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + + def add_boxes( self, step_dict, width, name_fill ): + margin = MARGIN + line_px = LINE_SPACING + + x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] + self.boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=name_fill ).SVG() ) + box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin + # Draw separator line. + if len( step_dict[ 'data_inputs' ] ) > 0: + box_height += 15 + sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 + self.text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) + # Define an input/output box. + self.boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + + def add_text( self, module_data_inputs, module_data_outputs, order_index, left, top, max_len ): + x, y = left, top + y += 45 + + count = 0 + line_px = LINE_SPACING + in_pos = self.in_pos + out_pos = self.out_pos + + for di in module_data_inputs: + cur_y = y + count * line_px + if order_index not in in_pos: + in_pos[ order_index ] = {} + in_pos[ order_index ][ di[ 'name' ] ] = ( x, cur_y ) + self.text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( di[ 'label' ] ) ) + if len( module_data_inputs ) > 0: + y += 15 + for do in module_data_outputs: + cur_y = y + count * line_px + if order_index not in out_pos: + out_pos[ order_index ] = {} + out_pos[ order_index ][ do[ 'name' ] ] = ( x, cur_y ) + self.text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( do['name' ] ) ) + self.widths[ order_index ] = max_len * 5.5 + self.max_x = max( self.max_x, left ) + self.max_y = max( self.max_y, top ) + self.max_width = max( self.max_width, self.widths[ order_index ] ) diff -r 91110971f1b37f121e177cc983d26f777805c1c4 -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -7,7 +7,7 @@ from galaxy import eggs from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html -from galaxy.worklfow.render import WorkflowCanvas +from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING from galaxy.workflow.modules import InputDataModule from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory @@ -212,16 +212,9 @@ canvas = workflow_canvas.canvas text = workflow_canvas.text connectors = workflow_canvas.connectors - boxes = workflow_canvas.boxes - in_pos = {} - out_pos = {} - margin = 5 - # Spacing between input/outputs. - line_px = 16 + margin = MARGIN # Store px width for boxes of each step. - widths = {} - max_width, max_x, max_y = 0, 0, 0 for step in workflow.steps: step.upgrade_messages = {} module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) @@ -239,72 +232,42 @@ step_dict[ 'input_connections' ] = input_conn_dict data.append( step_dict ) x, y = step.position[ 'left' ], step.position[ 'top' ] - count = 0 module_name = get_workflow_module_name( module, missing_tool_tups ) max_len = len( module_name ) * 1.5 text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) - y += 45 - for di in module_data_inputs: - cur_y = y + count * line_px - if step.order_index not in in_pos: - in_pos[ step.order_index ] = {} - in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) - text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) - count += 1 - max_len = max( max_len, len( di[ 'label' ] ) ) - if len( module.get_data_inputs() ) > 0: - y += 15 - for do in module_data_outputs: - cur_y = y + count * line_px - if step.order_index not in out_pos: - out_pos[ step.order_index ] = {} - out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) - text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) - count += 1 - max_len = max( max_len, len( do['name' ] ) ) - widths[ step.order_index ] = max_len * 5.5 - max_x = max( max_x, step.position[ 'left' ] ) - max_y = max( max_y, step.position[ 'top' ] ) - max_width = max( max_width, widths[ step.order_index ] ) + order_index = step.order_index + workflow_canvas.add_text( module_data_inputs, module_data_outputs, order_index, x, y, max_len ) for step_dict in data: + # Only highlight missing tools if displaying in the tool shed. tool_unavailable = step_dict[ 'tool_errors' ] - width = widths[ step_dict[ 'id' ] ] - x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] - # Only highlight missing tools if displaying in the tool shed. if trans.webapp.name == 'tool_shed' and tool_unavailable: fill = "#EBBCB2" else: fill = "#EBD9B2" - boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) - box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin - # Draw separator line. - if len( step_dict[ 'data_inputs' ] ) > 0: - box_height += 15 - sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 - text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) - # Define an input/output box. - boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + + width = workflow_canvas.widths[ step_dict[ 'id' ] ] + workflow_canvas.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): - in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] + in_coords = workflow_canvas.in_pos[ step_dict[ 'id' ] ][ conn ] # out_pos_index will be a step number like 1, 2, 3... out_pos_index = output_dict[ 'id' ] # out_pos_name will be a string like 'o', 'o2', etc. out_pos_name = output_dict[ 'output_name' ] - if out_pos_index in out_pos: + if out_pos_index in workflow_canvas.out_pos: # out_conn_index_dict will be something like: # 7: {'o': (824.5, 618)} - out_conn_index_dict = out_pos[ out_pos_index ] + out_conn_index_dict = workflow_canvas.out_pos[ out_pos_index ] if out_pos_name in out_conn_index_dict: - out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ] + out_conn_pos = workflow_canvas.out_pos[ out_pos_index ][ out_pos_name ] else: # Take any key / value pair available in out_conn_index_dict. # A problem will result if the dictionary is empty. if out_conn_index_dict.keys(): key = out_conn_index_dict.keys()[0] - out_conn_pos = out_pos[ out_pos_index ][ key ] - adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + out_conn_pos = workflow_canvas.out_pos[ out_pos_index ][ key ] + adjusted = ( out_conn_pos[ 0 ] + workflow_canvas.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) text.append( svgfig.SVG( "circle", - cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, + cx=out_conn_pos[ 0 ] + workflow_canvas.widths[ output_dict[ 'id' ] ] - margin, cy=out_conn_pos[ 1 ] - margin, r = 5, fill="#ffffff" ) ) @@ -313,7 +276,7 @@ in_coords[ 0 ] - 10, in_coords[ 1 ], arrow_end = "true" ).SVG() ) - workflow_canvas.finish( max_x, max_width, max_y ) + workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/b9858d6d9a22/ Changeset: b9858d6d9a22 User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Affected #: 3 files diff -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 -r b9858d6d9a22f8d8c177ed39e51c35e2b6e9325c lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1580,15 +1580,10 @@ data.append(step_dict) - x, y = step.position['left'], step.position['top'] - - max_len = len(module.get_name()) * 1.5 - text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() ) - + module_name = module.get_name() module_data_inputs = module.get_data_inputs() module_data_outputs = module.get_data_outputs() - order_index = step.order_index - workflow_canvas.add_text( module_data_inputs, module_data_outputs, order_index, x, y, max_len ) + workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) for step_dict in data: fill = "#EBD9B2" diff -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 -r b9858d6d9a22f8d8c177ed39e51c35e2b6e9325c lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -49,8 +49,13 @@ # Define an input/output box. self.boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) - def add_text( self, module_data_inputs, module_data_outputs, order_index, left, top, max_len ): + def add_text( self, module_data_inputs, module_data_outputs, step, module_name ): + left, top = step.position[ 'left' ], step.position[ 'top' ] x, y = left, top + order_index = step.order_index + max_len = len( module_name ) * 1.5 + self.text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) + y += 45 count = 0 diff -r e88f0fe184543ce8c64d11e6af445ba4f7ea2a82 -r b9858d6d9a22f8d8c177ed39e51c35e2b6e9325c lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -231,12 +231,8 @@ input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) step_dict[ 'input_connections' ] = input_conn_dict data.append( step_dict ) - x, y = step.position[ 'left' ], step.position[ 'top' ] module_name = get_workflow_module_name( module, missing_tool_tups ) - max_len = len( module_name ) * 1.5 - text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) - order_index = step.order_index - workflow_canvas.add_text( module_data_inputs, module_data_outputs, order_index, x, y, max_len ) + workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) for step_dict in data: # Only highlight missing tools if displaying in the tool shed. tool_unavailable = step_dict[ 'tool_errors' ] https://bitbucket.org/galaxy/galaxy-central/commits/c12e8b96a97c/ Changeset: c12e8b96a97c User: jmchilton Date: 2014-08-14 03:36:10 Summary: Refactor ts/gx workflow svg rendering slightly so they look more similar. Affected #: 2 files diff -r b9858d6d9a22f8d8c177ed39e51c35e2b6e9325c -r c12e8b96a97c802d33c3d276232350e59cafb506 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1591,7 +1591,14 @@ workflow_canvas.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = workflow_canvas.in_pos[step_dict['id']][conn] - out_conn_pos = workflow_canvas.out_pos[output_dict['id']][output_dict['output_name']] + # out_pos_index will be a step number like 1, 2, 3... + out_pos_index = output_dict[ 'id' ] + # out_pos_name will be a string like 'o', 'o2', etc. + out_pos_name = output_dict[ 'output_name' ] + # out_conn_index_dict will be something like: + # 7: {'o': (824.5, 618)} + out_conn_index_dict = workflow_canvas.out_pos[ out_pos_index ] + out_conn_pos = out_conn_index_dict[out_pos_name] adjusted = (out_conn_pos[0] + workflow_canvas.widths[output_dict['id']], out_conn_pos[1]) text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + workflow_canvas.widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) diff -r b9858d6d9a22f8d8c177ed39e51c35e2b6e9325c -r c12e8b96a97c802d33c3d276232350e59cafb506 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -254,7 +254,7 @@ # 7: {'o': (824.5, 618)} out_conn_index_dict = workflow_canvas.out_pos[ out_pos_index ] if out_pos_name in out_conn_index_dict: - out_conn_pos = workflow_canvas.out_pos[ out_pos_index ][ out_pos_name ] + out_conn_pos = out_conn_index_dict[ out_pos_name ] else: # Take any key / value pair available in out_conn_index_dict. # A problem will result if the dictionary is empty. https://bitbucket.org/galaxy/galaxy-central/commits/287b8c5c6f8e/ Changeset: 287b8c5c6f8e User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Using more conservative logic from the tool shed - not sure picking random connections the way it is doing however is appropriate. Affected #: 3 files diff -r c12e8b96a97c802d33c3d276232350e59cafb506 -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1590,18 +1590,7 @@ width = workflow_canvas.widths[step_dict['id']] workflow_canvas.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict['input_connections'].iteritems(): - in_coords = workflow_canvas.in_pos[step_dict['id']][conn] - # out_pos_index will be a step number like 1, 2, 3... - out_pos_index = output_dict[ 'id' ] - # out_pos_name will be a string like 'o', 'o2', etc. - out_pos_name = output_dict[ 'output_name' ] - # out_conn_index_dict will be something like: - # 7: {'o': (824.5, 618)} - out_conn_index_dict = workflow_canvas.out_pos[ out_pos_index ] - out_conn_pos = out_conn_index_dict[out_pos_name] - adjusted = (out_conn_pos[0] + workflow_canvas.widths[output_dict['id']], out_conn_pos[1]) - text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + workflow_canvas.widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) - connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) + workflow_canvas.add_connection( step_dict, conn, output_dict ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) return canvas diff -r c12e8b96a97c802d33c3d276232350e59cafb506 -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -85,3 +85,35 @@ self.max_x = max( self.max_x, left ) self.max_y = max( self.max_y, top ) self.max_width = max( self.max_width, self.widths[ order_index ] ) + + def add_connection( self, step_dict, conn, output_dict): + margin = MARGIN + + in_coords = self.in_pos[ step_dict[ 'id' ] ][ conn ] + # out_pos_index will be a step number like 1, 2, 3... + out_pos_index = output_dict[ 'id' ] + # out_pos_name will be a string like 'o', 'o2', etc. + out_pos_name = output_dict[ 'output_name' ] + if out_pos_index in self.out_pos: + # out_conn_index_dict will be something like: + # 7: {'o': (824.5, 618)} + out_conn_index_dict = self.out_pos[ out_pos_index ] + if out_pos_name in out_conn_index_dict: + out_conn_pos = out_conn_index_dict[ out_pos_name ] + else: + # Take any key / value pair available in out_conn_index_dict. + # A problem will result if the dictionary is empty. + if out_conn_index_dict.keys(): + key = out_conn_index_dict.keys()[0] + out_conn_pos = self.out_pos[ out_pos_index ][ key ] + adjusted = ( out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + self.text.append( svgfig.SVG( "circle", + cx=out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ] - margin, + cy=out_conn_pos[ 1 ] - margin, + r=5, + fill="#ffffff" ) ) + self.connectors.append( svgfig.Line( adjusted[ 0 ], + adjusted[ 1 ] - margin, + in_coords[ 0 ] - 10, + in_coords[ 1 ], + arrow_end="true" ).SVG() ) diff -r c12e8b96a97c802d33c3d276232350e59cafb506 -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -244,34 +244,7 @@ width = workflow_canvas.widths[ step_dict[ 'id' ] ] workflow_canvas.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): - in_coords = workflow_canvas.in_pos[ step_dict[ 'id' ] ][ conn ] - # out_pos_index will be a step number like 1, 2, 3... - out_pos_index = output_dict[ 'id' ] - # out_pos_name will be a string like 'o', 'o2', etc. - out_pos_name = output_dict[ 'output_name' ] - if out_pos_index in workflow_canvas.out_pos: - # out_conn_index_dict will be something like: - # 7: {'o': (824.5, 618)} - out_conn_index_dict = workflow_canvas.out_pos[ out_pos_index ] - if out_pos_name in out_conn_index_dict: - out_conn_pos = out_conn_index_dict[ out_pos_name ] - else: - # Take any key / value pair available in out_conn_index_dict. - # A problem will result if the dictionary is empty. - if out_conn_index_dict.keys(): - key = out_conn_index_dict.keys()[0] - out_conn_pos = workflow_canvas.out_pos[ out_pos_index ][ key ] - adjusted = ( out_conn_pos[ 0 ] + workflow_canvas.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) - text.append( svgfig.SVG( "circle", - cx=out_conn_pos[ 0 ] + workflow_canvas.widths[ output_dict[ 'id' ] ] - margin, - cy=out_conn_pos[ 1 ] - margin, - r = 5, - fill="#ffffff" ) ) - connectors.append( svgfig.Line( adjusted[ 0 ], - adjusted[ 1 ] - margin, - in_coords[ 0 ] - 10, - in_coords[ 1 ], - arrow_end = "true" ).SVG() ) + workflow_canvas.add_connection( step_dict, conn, output_dict ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/c9b972306e77/ Changeset: c9b972306e77 User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Affected #: 3 files diff -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b -r c9b972306e7730c9bede45ef60abb4073ad0cf31 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1585,13 +1585,7 @@ module_data_outputs = module.get_data_outputs() workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) - for step_dict in data: - fill = "#EBD9B2" - width = workflow_canvas.widths[step_dict['id']] - workflow_canvas.add_boxes( step_dict, width, fill ) - for conn, output_dict in step_dict['input_connections'].iteritems(): - workflow_canvas.add_connection( step_dict, conn, output_dict ) - + workflow_canvas.add_steps( data ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) return canvas diff -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b -r c9b972306e7730c9bede45ef60abb4073ad0cf31 lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -117,3 +117,17 @@ in_coords[ 0 ] - 10, in_coords[ 1 ], arrow_end="true" ).SVG() ) + + def add_steps( self, data, highlight_errors=False ): + # Only highlight missing tools if displaying in the tool shed. + for step_dict in data: + tool_unavailable = step_dict[ 'tool_errors' ] + if highlight_errors and tool_unavailable: + fill = "#EBBCB2" + else: + fill = "#EBD9B2" + + width = self.widths[ step_dict[ 'id' ] ] + self.add_boxes( step_dict, width, fill ) + for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): + self.add_connection( step_dict, conn, output_dict ) diff -r 287b8c5c6f8e05c29dc5c8c262e28aaa621cd77b -r c9b972306e7730c9bede45ef60abb4073ad0cf31 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -233,18 +233,7 @@ data.append( step_dict ) module_name = get_workflow_module_name( module, missing_tool_tups ) workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) - for step_dict in data: - # Only highlight missing tools if displaying in the tool shed. - tool_unavailable = step_dict[ 'tool_errors' ] - if trans.webapp.name == 'tool_shed' and tool_unavailable: - fill = "#EBBCB2" - else: - fill = "#EBD9B2" - - width = workflow_canvas.widths[ step_dict[ 'id' ] ] - workflow_canvas.add_boxes( step_dict, width, fill ) - for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): - workflow_canvas.add_connection( step_dict, conn, output_dict ) + workflow_canvas.add_steps( data, highlight_errors=True ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/6482359d4a7c/ Changeset: 6482359d4a7c User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Affected #: 3 files diff -r c9b972306e7730c9bede45ef60abb4073ad0cf31 -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1554,7 +1554,6 @@ def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow - data = [] workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas text = workflow_canvas.text @@ -1563,29 +1562,17 @@ for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) - - # Pack attributes into plain dictionary - step_dict = { - 'id': step.order_index, - 'data_inputs': module.get_data_inputs(), - 'data_outputs': module.get_data_outputs(), - 'position': step.position - } - - input_conn_dict = {} - for conn in step.input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) - step_dict['input_connections'] = input_conn_dict - - data.append(step_dict) - module_name = module.get_name() module_data_inputs = module.get_data_inputs() module_data_outputs = module.get_data_outputs() - workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) + workflow_canvas.populate_data_for_step( + step, + module_name, + module_data_inputs, + module_data_outputs, + ) - workflow_canvas.add_steps( data ) + workflow_canvas.add_steps( ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) return canvas diff -r c9b972306e7730c9bede45ef60abb4073ad0cf31 -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -24,6 +24,8 @@ self.max_y = 0 self.max_width = 0 + self.data = [] + def finish( self, max_x, max_width, max_y ): canvas = self.canvas canvas.append( self.connectors ) @@ -118,9 +120,9 @@ in_coords[ 1 ], arrow_end="true" ).SVG() ) - def add_steps( self, data, highlight_errors=False ): + def add_steps( self, highlight_errors=False ): # Only highlight missing tools if displaying in the tool shed. - for step_dict in data: + for step_dict in self.data: tool_unavailable = step_dict[ 'tool_errors' ] if highlight_errors and tool_unavailable: fill = "#EBBCB2" @@ -131,3 +133,22 @@ self.add_boxes( step_dict, width, fill ) for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): self.add_connection( step_dict, conn, output_dict ) + + def populate_data_for_step( self, step, module_name, module_data_inputs, module_data_outputs, tool_errors=None ): + step_dict = { + 'id': step.order_index, + 'data_inputs': module_data_inputs, + 'data_outputs': module_data_outputs, + 'position': step.position + } + if tool_errors: + step_dict[ 'tool_errors' ] = tool_errors + + input_conn_dict = {} + for conn in step.input_connections: + input_conn_dict[ conn.input_name ] = \ + dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict['input_connections'] = input_conn_dict + + self.data.append(step_dict) + self.add_text( module_data_inputs, module_data_outputs, step, module_name ) diff -r c9b972306e7730c9bede45ef60abb4073ad0cf31 -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -207,7 +207,6 @@ tools_metadata=tools_metadata, repository_id=repository_id, changeset_revision=changeset_revision ) - data = [] workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas text = workflow_canvas.text @@ -221,19 +220,15 @@ tool_errors = module.type == 'tool' and not module.tool module_data_inputs = get_workflow_data_inputs( step, module ) module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps ) - step_dict = { 'id' : step.order_index, - 'data_inputs' : module_data_inputs, - 'data_outputs' : module_data_outputs, - 'position' : step.position, - 'tool_errors' : tool_errors } - input_conn_dict = {} - for conn in step.input_connections: - input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) - step_dict[ 'input_connections' ] = input_conn_dict - data.append( step_dict ) module_name = get_workflow_module_name( module, missing_tool_tups ) - workflow_canvas.add_text( module_data_inputs, module_data_outputs, step, module_name ) - workflow_canvas.add_steps( data, highlight_errors=True ) + workflow_canvas.populate_data_for_step( + step, + module_name, + module_data_inputs, + module_data_outputs, + tool_errors=tool_errors + ) + workflow_canvas.add_steps( highlight_errors=True ) workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/a464ba73488c/ Changeset: a464ba73488c User: jmchilton Date: 2014-08-14 03:36:10 Summary: More SVG rendering de-dup. Affected #: 3 files diff -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 -r a464ba73488cb4fc82e398d1c84bd019bf128524 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1,12 +1,8 @@ -import pkg_resources -pkg_resources.require( "SVGFig" ) - import base64 import httplib import json import os import sgmllib -import svgfig import urllib2 from sqlalchemy import and_ @@ -1556,9 +1552,6 @@ workflow = stored.latest_workflow workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas - text = workflow_canvas.text - connectors = workflow_canvas.connectors - margin = MARGIN for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) @@ -1573,7 +1566,7 @@ ) workflow_canvas.add_steps( ) - workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) + workflow_canvas.finish( ) return canvas diff -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 -r a464ba73488cb4fc82e398d1c84bd019bf128524 lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -26,7 +26,9 @@ self.data = [] - def finish( self, max_x, max_width, max_y ): + def finish( self ): + max_x, max_y, max_width = self.max_x, self.max_y, self.max_width + canvas = self.canvas canvas.append( self.connectors ) canvas.append( self.boxes ) diff -r 6482359d4a7c429574ae4c4631eebf3f7bcf3350 -r a464ba73488cb4fc82e398d1c84bd019bf128524 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -4,7 +4,6 @@ import galaxy.tools import galaxy.tools.parameters import galaxy.webapps.galaxy.controllers.workflow -from galaxy import eggs from galaxy.util import json from galaxy.util.sanitize_html import sanitize_html from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING @@ -18,9 +17,6 @@ from tool_shed.util import metadata_util from tool_shed.util import shed_util_common as suc -eggs.require( "SVGFig" ) -import svgfig - log = logging.getLogger( __name__ ) @@ -209,10 +205,6 @@ changeset_revision=changeset_revision ) workflow_canvas = WorkflowCanvas() canvas = workflow_canvas.canvas - text = workflow_canvas.text - connectors = workflow_canvas.connectors - - margin = MARGIN # Store px width for boxes of each step. for step in workflow.steps: step.upgrade_messages = {} @@ -229,7 +221,7 @@ tool_errors=tool_errors ) workflow_canvas.add_steps( highlight_errors=True ) - workflow_canvas.finish( workflow_canvas.max_x, workflow_canvas.max_width, workflow_canvas.max_y ) + workflow_canvas.finish( ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/57980600c4e3/ Changeset: 57980600c4e3 User: jmchilton Date: 2014-08-14 03:36:10 Summary: Add unit test to merely walk through new workflow render module... ...small fix found by test. Affected #: 2 files diff -r a464ba73488cb4fc82e398d1c84bd019bf128524 -r 57980600c4e34d5a5097ebc2aac72d3ff709031b lib/galaxy/workflow/render.py --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -125,7 +125,7 @@ def add_steps( self, highlight_errors=False ): # Only highlight missing tools if displaying in the tool shed. for step_dict in self.data: - tool_unavailable = step_dict[ 'tool_errors' ] + tool_unavailable = step_dict.get( 'tool_errors', False ) if highlight_errors and tool_unavailable: fill = "#EBBCB2" else: diff -r a464ba73488cb4fc82e398d1c84bd019bf128524 -r 57980600c4e34d5a5097ebc2aac72d3ff709031b test/unit/workflows/test_render.py --- /dev/null +++ b/test/unit/workflows/test_render.py @@ -0,0 +1,80 @@ +from galaxy import model +from galaxy.util import bunch +from galaxy.workflow import render + + +def test_render(): + # Doesn't check anything about the render code - just exercises to + # ensure that obvious errors aren't thrown. + workflow_canvas = render.WorkflowCanvas() + + workflow = model.Workflow() + workflow.steps = [] + + def add_step( **kwds ): + workflow_step = model.WorkflowStep() + for key, value in kwds.iteritems(): + setattr(workflow_step, key, value) + workflow.steps.append( workflow_step ) + return workflow_step + + step_0 = add_step( + type="data_input", + order_index=0, + tool_inputs={"name": "input1"}, + input_connections=[], + position={"top": 3, "left": 3} + ) + step_1 = add_step( + type="data_input", + order_index=1, + tool_inputs={"name": "input2"}, + input_connections=[], + position={"top": 6, "left": 4} + ) + step_2 = add_step( + type="tool", + tool_id="cat1", + order_index=2, + input_connections=[ + bunch.Bunch(input_name="input1", output_step=step_0, output_name="di1") + ], + position={"top": 13, "left": 10} + ) + step_3 = add_step( + type="tool", + tool_id="cat1", + order_index=3, + input_connections=[ + bunch.Bunch(input_name="input1", output_step=step_0, output_name="di1") + ], + position={"top": 33, "left": 103} + ) + + workflow_canvas.populate_data_for_step( + step_0, + "input1", + [], + [{"name": "di1"}], + ) + workflow_canvas.populate_data_for_step( + step_1, + "input2", + [], + [{"name": "di1"}], + ) + workflow_canvas.populate_data_for_step( + step_2, + "cat wrapper", + [{"name": "input1", "label": "i1"}], + [{"name": "out1"}] + ) + workflow_canvas.populate_data_for_step( + step_3, + "cat wrapper", + [{"name": "input1", "label": "i1"}], + [{"name": "out1"}] + ) + workflow_canvas.add_steps() + workflow_canvas.finish() + assert workflow_canvas.canvas.standalone_xml() https://bitbucket.org/galaxy/galaxy-central/commits/be4079874172/ Changeset: be4079874172 User: jmchilton Date: 2014-08-14 03:36:10 Summary: Ensure elementtree is available (required) in workflow modules. Affected #: 1 file diff -r 57980600c4e34d5a5097ebc2aac72d3ff709031b -r be407987417297cb1543864e8448d49bb93851ab lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -5,6 +5,9 @@ import logging import re +from galaxy import eggs +eggs.require( "elementtree" ) + from elementtree.ElementTree import Element import galaxy.tools Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Core, histories: when deleting/purging the current history, set the most recent history as the new current. If the user is anonymous or there are no non-deleted histories remaining: create a new, blank history
by commits-noreply＠bitbucket.org 13 Aug '14

13 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb6a06ce35f0/ Changeset: fb6a06ce35f0 User: carlfeberhard Date: 2014-08-13 21:24:21 Summary: Core, histories: when deleting/purging the current history, set the most recent history as the new current. If the user is anonymous or there are no non-deleted histories remaining: create a new, blank history Affected #: 2 files diff -r 898a172941b10e435a6616c8cc04ccec6c7984d3 -r fb6a06ce35f08f516b8a5d80d2105225c243201b lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -221,6 +221,19 @@ return history_dict + def most_recent( self, trans, user=None, deleted=False ): + user = user or trans.user + if not user: + return None if trans.history.deleted else trans.history + + #TODO: dup with by_user - should return query from there and call first and not all + history_model = trans.model.History + query = ( trans.sa_session.query( history_model ) + .filter( history_model.user == user ) + .order_by( orm.desc( history_model.table.c.update_time ) ) ) + if not deleted: + query = query.filter( history_model.deleted == False ) + return query.first() # ============================================================================= class HistorySerializer( manager_base.ModelSerializer ): diff -r 898a172941b10e435a6616c8cc04ccec6c7984d3 -r fb6a06ce35f08f516b8a5d80d2105225c243201b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -1034,7 +1034,14 @@ # No need to check other outputs since the job's parent history is this history job.mark_deleted( trans.app.config.track_jobs_in_database ) trans.app.job_manager.job_stop_queue.put( job.id ) - # Regardless of whether it was previously deleted, get or create default history. + + # Regardless of whether it was previously deleted, get the most recent history or create a new one. + most_recent_history = self.mgrs.histories.most_recent( trans, user=trans.user, deleted=False ) + if most_recent_history: + trans.set_history( most_recent_history ) + return trans.show_ok_message( "History deleted, your most recent history is now active", + refresh_frames=['history'] ) + trans.get_or_create_default_history() return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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