diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js index 7a143f9555b..9a6cd1ab24e 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js @@ -200,6 +200,7 @@ var View = Backbone.View.extend({ this._renderMessage(); this._renderParameters(); this._renderHistory(); + this._renderUseCachedJob(); _.each(this.steps, step => { self._renderStep(step); }); @@ -311,6 +312,36 @@ var View = Backbone.View.extend({ this._append(this.$steps, this.history_form.$el); }, + /** Render job caching option */ + _renderUseCachedJob: function() { + var extra_user_preferences = {}; + if (Galaxy.user.attributes.preferences && 'extra_user_preferences' in Galaxy.user.attributes.preferences){ + extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences); + } + var display_use_cached_job_checkbox = 'use_cached_job|use_cached_job_checkbox' in extra_user_preferences ? extra_user_preferences['use_cached_job|use_cached_job_checkbox'] : false ; + this.display_use_cached_job_checkbox = display_use_cached_job_checkbox === 'true'; + if (this.display_use_cached_job_checkbox){ + this.job_options_form = new Form({ + cls: "ui-portlet-narrow", + title: "Job re-use Options", + inputs: [ + { + type: "conditional", + name: "use_cached_job", + test_param: { + name: "check", + label: "BETA: Attempt to reuse jobs with identical parameters?", + type: "boolean", + value: "false", + help: "This may skip executing jobs that you have already run." + }, + } + ] + }); + this._append(this.$steps, this.job_options_form.$el); + } + }, + /** Render step */ _renderStep: function(step) { var self = this; @@ -510,6 +541,9 @@ var View = Backbone.View.extend({ // so that inputs can be batched. batch: true }; + if (this.display_use_cached_job_checkbox) { + job_def['use_cached_job'] = this.job_options_form.data.create()["use_cached_job|check"] === 'true'; + } var validated = true; for (var i in this.forms) { var form = this.forms[i]; diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js index 6e0d5132d3d..e0038c3c97c 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form.js +++ b/client/galaxy/scripts/mvc/tool/tool-form.js @@ -148,6 +148,25 @@ var View = Backbone.View.extend({ "The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run." }); } + + // Job Re-use Options + var extra_user_preferences = {}; + if (Galaxy.user.attributes.preferences && 'extra_user_preferences' in Galaxy.user.attributes.preferences) { + extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences); + } + var use_cached_job = 'use_cached_job|use_cached_job_checkbox' in extra_user_preferences ? extra_user_preferences['use_cached_job|use_cached_job_checkbox'] : false ; + if (use_cached_job === 'true'){ + options.inputs.push({ + label: "BETA: Attempt to re-use jobs with identical parameters ?", + help: "This may skip executing jobs that you have already run", + name: "use_cached_job", + type: "select", + display: "radio", + ignore: "__ignore__", + value: "__ignore__", + options: [["No", false], ["Yes", true]], + }); + } }, /** Submit a regular job. diff --git a/config/user_preferences_extra_conf.yml.sample b/config/user_preferences_extra_conf.yml.sample index 8f8ef07670a..0718773e478 100644 --- a/config/user_preferences_extra_conf.yml.sample +++ b/config/user_preferences_extra_conf.yml.sample @@ -39,3 +39,13 @@ preferences: label: Maximum number of search results type: text required: False + + use_cached_job: + description: Do you want to be able to re-use previously run jobs ? + inputs: + - name: use_cached_job_checkbox + label: Do you want to be able to re-use equivalent jobs ? + type: boolean + checked: false + value: false + help: If you select yes, you will be able to select for each tool and workflow run if you would like to use this feature. diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py index 80585c103d6..d03b930d6ba 100644 --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -305,6 +305,21 @@ class JobHandlerQueue(Monitors, object): try: # Check the job's dependencies, requeue if they're not done. # Some of these states will only happen when using the in-memory job queue + if job.copied_from_job_id: + copied_from_job = self.sa_session.query(model.Job).get(job.copied_from_job_id) + job.numeric_metrics = copied_from_job.numeric_metrics + job.text_metrics = copied_from_job.text_metrics + job.dependencies = copied_from_job.dependencies + job.state = copied_from_job.state + job.stderr = copied_from_job.stderr + job.stdout = copied_from_job.stdout + job.command_line = copied_from_job.command_line + job.traceback = copied_from_job.traceback + job.tool_version = copied_from_job.tool_version + job.exit_code = copied_from_job.exit_code + job.job_runner_name = copied_from_job.job_runner_name + job.job_runner_external_id = copied_from_job.job_runner_external_id + continue job_state = self.__check_job_state(job) if job_state == JOB_WAIT: new_waiting_jobs.append(job.id) diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py index b17fa922f1b..d845ae1296e 100644 --- a/lib/galaxy/managers/jobs.py +++ b/lib/galaxy/managers/jobs.py @@ -49,11 +49,10 @@ class JobSearch(object): self.ldda_manager = LDDAManager(app) self.decode_id = self.app.security.decode_id - def by_tool_input(self, trans, tool_id, param_dump=None, job_state='ok', is_workflow_step=False): + def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state='ok'): """Search for jobs producing same results using the 'inputs' part of a tool POST.""" user = trans.user input_data = defaultdict(list) - input_ids = defaultdict(dict) def populate_input_data_input_id(path, key, value): """Traverses expanded incoming using remap and collects input_ids and input_data.""" @@ -63,187 +62,205 @@ class JobSearch(object): for p in path: current_case = current_case[p] src = current_case['src'] - input_data[path_key].append({'src': src, 'id': value}) - input_ids[src][value] = True - return key, value + current_case = param + for i, p in enumerate(path): + if p == 'values' and i == len(path) - 2: + continue + if isinstance(current_case, (list, dict)): + current_case = current_case[p] + identifier = getattr(current_case, "element_identifier", None) + input_data[path_key].append({'src': src, + 'id': value, + 'identifier': identifier, + }) + return key, "__id_wildcard__" return key, value - remap(param_dump, visit=populate_input_data_input_id) + wildcard_param_dump = remap(param_dump, visit=populate_input_data_input_id) return self.__search(tool_id=tool_id, + tool_version=tool_version, user=user, input_data=input_data, job_state=job_state, param_dump=param_dump, - input_ids=input_ids, - is_workflow_step=is_workflow_step) + wildcard_param_dump=wildcard_param_dump) - def __search(self, tool_id, user, input_data, input_ids=None, job_state=None, param_dump=None, is_workflow_step=False): + def __search(self, tool_id, tool_version, user, input_data, job_state=None, param_dump=None, wildcard_param_dump=None): search_timer = ExecutionTimer() - query = self.sa_session.query(model.Job).filter( - model.Job.tool_id == tool_id, - model.Job.user == user - ) + + def replace_dataset_ids(path, key, value): + """Exchanges dataset_ids (HDA, LDA, HDCA, not Dataset) in param_dump with dataset ids used in job.""" + if key == 'id': + current_case = param_dump + for p in path: + current_case = current_case[p] + src = current_case['src'] + value = job_input_ids[src][value] + return key, value + return key, value + + conditions = [and_(model.Job.tool_id == tool_id, + model.Job.user == user)] + + if tool_version: + conditions.append(model.Job.tool_version == str(tool_version)) if job_state is None: - query = query.filter( - or_( - model.Job.state == 'running', - model.Job.state == 'queued', - model.Job.state == 'waiting', - model.Job.state == 'running', - model.Job.state == 'ok', - ) + conditions.append( + model.Job.state.in_([model.Job.states.NEW, + model.Job.states.QUEUED, + model.Job.states.WAITING, + model.Job.states.RUNNING, + model.Job.states.OK]) ) else: if isinstance(job_state, string_types): - query = query.filter(model.Job.state == job_state) + conditions.append(model.Job.state == job_state) elif isinstance(job_state, list): o = [] for s in job_state: o.append(model.Job.state == s) - query = query.filter( + conditions.append( or_(*o) ) + # We now build the query filters that relate to the input datasets + # that this job uses. We keep track of the requested dataset id in `requested_ids`, + # the type (hda, hdca or lda) in `data_types` + # and the ids that have been used in the job that has already been run in `used_ids`. + requested_ids = [] + data_types = [] + used_ids = [] for k, input_list in input_data.items(): for type_values in input_list: t = type_values['src'] v = type_values['id'] + requested_ids.append(v) + data_types.append(t) + identifier = type_values['identifier'] if t == 'hda': a = aliased(model.JobToInputDatasetAssociation) b = aliased(model.HistoryDatasetAssociation) c = aliased(model.HistoryDatasetAssociation) - query = query.filter(and_( + d = aliased(model.JobParameter) + e = aliased(model.HistoryDatasetAssociationHistory) + conditions.append(and_( model.Job.id == a.job_id, a.name == k, a.dataset_id == b.id, c.dataset_id == b.dataset_id, - c.id == v, + c.id == v, # c is the requested job input HDA + # We can compare input dataset names and metadata for a job + # if we know that the input dataset hasn't changed since the job was run, + # or if the job recorded a dataset_version and name and metadata of the current + # job request matches those that were recorded for the job in question (introduced in release 18.01) + or_(and_( + b.update_time < model.Job.create_time, + b.name == c.name, + b.extension == c.extension, + b.metadata == c.metadata, + ), and_( + b.id == e.history_dataset_association_id, + a.dataset_version == e.version, + e.name == c.name, + e.extension == c.extension, + e._metadata == c._metadata, + )), or_(b.deleted == false(), c.deleted == false()) )) + if identifier: + conditions.append(and_(model.Job.id == d.job_id, + d.name == "%s|__identifier__" % k, + d.value == json.dumps(identifier))) + used_ids.append(a.dataset_id) elif t == 'ldda': a = aliased(model.JobToInputLibraryDatasetAssociation) - query = query.filter(and_( + conditions.append(and_( model.Job.id == a.job_id, a.name == k, a.ldda_id == v )) + used_ids.append(a.ldda_id) elif t == 'hdca': a = aliased(model.JobToInputDatasetCollectionAssociation) b = aliased(model.HistoryDatasetCollectionAssociation) c = aliased(model.HistoryDatasetCollectionAssociation) - query = query.filter(and_( + conditions.append(and_( model.Job.id == a.job_id, a.name == k, b.id == a.dataset_collection_id, c.id == v, + b.name == c.name, or_(and_(b.deleted == false(), b.id == v), and_(or_(c.copied_from_history_dataset_collection_association_id == b.id, b.copied_from_history_dataset_collection_association_id == c.id), - c.deleted == false() + c.deleted == false(), ) ) )) + used_ids.append(a.dataset_collection_id) else: return [] + for k, v in wildcard_param_dump.items(): + wildcard_value = json.dumps(v).replace('"id": "__id_wildcard__"', '"id": %') + a = aliased(model.JobParameter) + conditions.append(and_( + model.Job.id == a.job_id, + a.name == k, + a.value.like(wildcard_value) + )) + + conditions.append(and_( + model.Job.any_output_dataset_collection_instances_deleted == false(), + model.Job.any_output_dataset_deleted == false() + )) + + query = self.sa_session.query(model.Job.id, *used_ids).filter(and_(*conditions)) for job in query.all(): # We found a job that is equal in terms of tool_id, user, state and input datasets, # but to be able to verify that the parameters match we need to modify all instances of # dataset_ids (HDA, LDDA, HDCA) in the incoming param_dump to point to those used by the # possibly equivalent job, which may have been run on copies of the original input data. - replacement_timer = ExecutionTimer() job_input_ids = {} - for src, items in input_ids.items(): - for dataset_id in items: - if src in job_input_ids and dataset_id in job_input_ids[src]: - continue - if src == 'hda': - a = aliased(model.JobToInputDatasetAssociation) - b = aliased(model.HistoryDatasetAssociation) - c = aliased(model.HistoryDatasetAssociation) - - (job_dataset_id,) = self.sa_session.query(b.id).filter( - and_( - a.job_id == job.id, - b.id == a.dataset_id, - c.dataset_id == b.dataset_id, - c.id == dataset_id - ) - ).first() - elif src == 'hdca': - a = aliased(model.JobToInputDatasetCollectionAssociation) - b = aliased(model.HistoryDatasetCollectionAssociation) - c = aliased(model.HistoryDatasetCollectionAssociation) - - (job_dataset_id,) = self.sa_session.query(b.id).filter( - and_( - a.job_id == job.id, - b.id == a.dataset_collection_id, - c.id == dataset_id, - or_(b.id == c.id, or_(c.copied_from_history_dataset_collection_association_id == b.id, - b.copied_from_history_dataset_collection_association_id == c.id) - ) - ) - ).first() - elif src == 'ldda': - job_dataset_id = dataset_id - else: - return [] + if len(job) > 1: + # We do have datasets to check + job_id, current_jobs_data_ids = job[0], job[1:] + job_parameter_conditions = [model.Job.id == job_id] + for src, requested_id, used_id in zip(data_types, requested_ids, current_jobs_data_ids): if src not in job_input_ids: - job_input_ids[src] = {dataset_id: job_dataset_id} + job_input_ids[src] = {requested_id: used_id} else: - job_input_ids[src][dataset_id] = job_dataset_id - - def replace_dataset_ids(path, key, value): - """Exchanges dataset_ids (HDA, LDA, HDCA, not Dataset) in param_dump with dataset ids used in job.""" - if key == 'id': - current_case = param_dump - for p in path: - current_case = current_case[p] - src = current_case['src'] - value = job_input_ids[src][value] - return key, value - return key, value - - new_param_dump = remap(param_dump, visit=replace_dataset_ids) - log.info("Parameter replacement finished %s", replacement_timer) - # new_param_dump has its dataset ids remapped to those used by the job. - # We now ask if the remapped job parameters match the current job. - query = self.sa_session.query(model.Job).filter(model.Job.id == job.id) - for k, v in new_param_dump.items(): - a = aliased(model.JobParameter) - query = query.filter(and_( - a.job_id == job.id, - a.name == k, - a.value == json.dumps(v) - )) - if query.first() is None: - continue - if is_workflow_step: - add_n_parameters = 3 + job_input_ids[src][requested_id] = used_id + new_param_dump = remap(param_dump, visit=replace_dataset_ids) + # new_param_dump has its dataset ids remapped to those used by the job. + # We now ask if the remapped job parameters match the current job. + for k, v in new_param_dump.items(): + a = aliased(model.JobParameter) + job_parameter_conditions.append(and_( + a.name == k, + a.value == json.dumps(v) + )) else: - add_n_parameters = 2 - if not len(job.parameters) == (len(new_param_dump) + add_n_parameters): - # Verify that equivalent jobs had the same number of job parameters - # We add 2 or 3 to new_param_dump because chrominfo and dbkey (and __workflow_invocation_uuid__) are not passed - # as input parameters + job_parameter_conditions = [model.Job.id == job] + query = self.sa_session.query(model.Job).filter(*job_parameter_conditions) + job = query.first() + if job is None: continue - # check to make sure none of the output datasets or collections have been deleted - # TODO: refactors this into the initial job query - outputs_deleted = False - for hda in job.output_datasets: - if hda.dataset.deleted: - outputs_deleted = True - break - if not outputs_deleted: - for collection_instance in job.output_dataset_collection_instances: - if collection_instance.dataset_collection_instance.deleted: - outputs_deleted = True - break - if not outputs_deleted: - log.info("Searching jobs finished %s", search_timer) - return job + n_parameters = 0 + # Verify that equivalent jobs had the same number of job parameters + # We skip chrominfo, dbkey, __workflow_invocation_uuid__ and identifer + # parameter as these are not passed along when expanding tool parameters + # and they can differ without affecting the resulting dataset. + for parameter in job.parameters: + if parameter.name in {'__workflow_invocation_uuid__', 'chromInfo', 'dbkey'} or parameter.name.endswith('|__identifier__'): + continue + n_parameters += 1 + if not n_parameters == len(param_dump): + continue + log.info("Found equivalent job %s", search_timer) + return job + log.info("No equivalent jobs found %s", search_timer) return None diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 68610b8eabd..984dfb883b1 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -5,6 +5,7 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ import errno +import json import logging import numbers import operator @@ -16,11 +17,21 @@ from string import Template from uuid import UUID, uuid4 from six import string_types -from sqlalchemy import (and_, func, join, not_, or_, select, true, type_coerce, - types) +from sqlalchemy import ( + and_, + func, + inspect, + join, + not_, + or_, + select, + true, + type_coerce, + types) from sqlalchemy.ext import hybrid from sqlalchemy.orm import aliased, joinedload, object_session + import galaxy.model.metadata import galaxy.model.orm.now import galaxy.security.passwords @@ -201,6 +212,17 @@ class User(object, Dictifiable): self.credentials = [] # ? self.roles = [] + @property + def extra_preferences(self): + data = {} + extra_user_preferences = self.preferences.get('extra_user_preferences') + if extra_user_preferences: + try: + data = json.loads(extra_user_preferences) + except Exception: + pass + return data + def set_password_cleartext(self, cleartext): """ Set user password to the digest of `cleartext`. @@ -474,6 +496,7 @@ class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable): self.user_id = None self.tool_id = None self.tool_version = None + self.copied_from_job_id = None self.command_line = None self.dependencies = [] self.param_filename = None @@ -542,6 +565,9 @@ class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable): def get_parameters(self): return self.parameters + def get_copied_from_job_id(self): + return self.copied_from_job_id + def get_input_datasets(self): return self.input_datasets @@ -625,6 +651,9 @@ class Job(object, JobLike, UsesCreateAndUpdateTime, Dictifiable): def set_parameters(self, parameters): self.parameters = parameters + def set_copied_from_job_id(self, job_id): + self.copied_from_job_id = job_id + def set_input_datasets(self, input_datasets): self.input_datasets = input_datasets @@ -993,6 +1022,7 @@ class JobToInputDatasetAssociation(object): def __init__(self, name, dataset): self.name = name self.dataset = dataset + self.dataset_version = dataset.version if dataset else None class JobToOutputDatasetAssociation(object): @@ -1957,7 +1987,7 @@ class DatasetInstance(object): self.metadata = metadata or dict() self.extended_metadata = extended_metadata if dbkey: # dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' - self.dbkey = dbkey + self._metadata['dbkey'] = dbkey self.deleted = deleted self.visible = visible # Relationships @@ -2043,8 +2073,6 @@ class DatasetInstance(object): if "dbkey" in self.datatype.metadata_spec: if not isinstance(value, list): self.metadata.dbkey = [value] - else: - self.metadata.dbkey = value dbkey = property(get_dbkey, set_dbkey) def change_datatype(self, new_ext): @@ -2394,6 +2422,36 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot self.copied_from_history_dataset_association = copied_from_history_dataset_association self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + def __create_version__(self, session): + state = inspect(self) + changes = {} + + for attr in state.attrs: + hist = state.get_history(attr.key, True) + + if not hist.has_changes(): + continue + + # hist.deleted holds old value(s) + changes[attr.key] = hist.deleted + if self.update_time and self.state == self.states.OK: + # We only record changes to HDAs that exist in the database and have a update_time + new_values = {} + new_values['name'] = changes.get('name', self.name) + new_values['dbkey'] = changes.get('dbkey', self.dbkey) + new_values['extension'] = changes.get('extension', self.extension) + new_values['extended_metadata_id'] = changes.get('extended_metadata_id', self.extended_metadata_id) + for k, v in new_values.items(): + if isinstance(v, list): + new_values[k] = v[0] + new_values['update_time'] = self.update_time + new_values['version'] = self.version or 1 + new_values['metadata'] = self._metadata + past_hda = HistoryDatasetAssociationHistory(history_dataset_association_id=self.id, + **new_values) + self.version = self.version + 1 if self.version else 1 + session.add(past_hda) + def copy(self, parent_id=None): """ Create a copy of this HDA. @@ -2609,6 +2667,27 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot self.tags.append(new_tag_assoc) +class HistoryDatasetAssociationHistory(object): + def __init__(self, + history_dataset_association_id, + name, + dbkey, + update_time, + version, + extension, + extended_metadata_id, + metadata, + ): + self.history_dataset_association_id = history_dataset_association_id + self.name = name + self.dbkey = dbkey + self.update_time = update_time + self.version = version + self.extension = extension + self.extended_metadata_id = extended_metadata_id + self._metadata = metadata + + class HistoryDatasetAssociationDisplayAtAuthorization(object): def __init__(self, hda=None, user=None, site=None): self.history_dataset_association = hda diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py index 01e834619da..016fdc80291 100644 --- a/lib/galaxy/model/base.py +++ b/lib/galaxy/model/base.py @@ -7,6 +7,7 @@ from inspect import ( isclass ) +from sqlalchemy import event from sqlalchemy.orm import ( scoped_session, sessionmaker @@ -20,7 +21,9 @@ class ModelMapping(Bunch): def __init__(self, model_modules, engine): self.engine = engine - context = scoped_session(sessionmaker(autoflush=False, autocommit=True)) + Session = sessionmaker(autoflush=False, autocommit=True) + versioned_session(Session) + context = scoped_session(Session) # For backward compatibility with "context.current" # deprecated? context.current = context @@ -44,3 +47,18 @@ class ModelMapping(Bunch): For backward compat., deprecated. """ return self.context + + +def versioned_objects(iter): + for obj in iter: + if hasattr(obj, '__create_version__'): + yield obj + + +def versioned_session(session): + @event.listens_for(session, 'before_flush') + def before_flush(session, flush_context, instances): + for obj in versioned_objects(session.dirty): + obj.__create_version__(session) + for obj in versioned_objects(session.deleted): + obj.__create_version__(session, deleted=True) diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index 22c96af3964..8ab7ca9c82f 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -29,8 +29,9 @@ from sqlalchemy import ( ) from sqlalchemy.ext.associationproxy import association_proxy from sqlalchemy.ext.orderinglist import ordering_list -from sqlalchemy.orm import backref, class_mapper, deferred, mapper, object_session, relation +from sqlalchemy.orm import backref, class_mapper, column_property, deferred, mapper, object_session, relation from sqlalchemy.orm.collections import attribute_mapped_collection +from sqlalchemy.sql import exists from sqlalchemy.types import BigInteger from galaxy import model @@ -142,11 +143,26 @@ model.HistoryDatasetAssociation.table = Table( Column("deleted", Boolean, index=True, default=False), Column("visible", Boolean), Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True), + Column("version", Integer, default=1, nullable=True, index=True), Column("hid", Integer), Column("purged", Boolean, index=True, default=False), Column("hidden_beneath_collection_instance_id", ForeignKey("history_dataset_collection_association.id"), nullable=True)) + +model.HistoryDatasetAssociationHistory.table = Table( + "history_dataset_association_history", metadata, + Column("id", Integer, primary_key=True), + Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True), + Column("update_time", DateTime, default=now), + Column("version", Integer), + Column("name", TrimmedString(255)), + Column("extension", TrimmedString(64)), + Column("metadata", MetadataType(), key="_metadata"), + Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True), +) + + model.Dataset.table = Table( "dataset", metadata, Column("id", Integer, primary_key=True), @@ -464,6 +480,7 @@ model.Job.table = Table( Column("tool_version", TEXT, default="1.0.0"), Column("state", String(64), index=True), Column("info", TrimmedString(255)), + Column("copied_from_job_id", Integer, nullable=True), Column("command_line", TEXT), Column("dependencies", JSONType, nullable=True), Column("param_filename", String(1024)), @@ -504,6 +521,7 @@ model.JobToInputDatasetAssociation.table = Table( Column("id", Integer, primary_key=True), Column("job_id", Integer, ForeignKey("job.id"), index=True), Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True), + Column("dataset_version", Integer), Column("name", String(255))) model.JobToOutputDatasetAssociation.table = Table( @@ -1474,6 +1492,8 @@ simple_mapping(model.Dataset, backref='datasets') ) +mapper(model.HistoryDatasetAssociationHistory, model.HistoryDatasetAssociationHistory.table) + mapper(model.HistoryDatasetAssociationDisplayAtAuthorization, model.HistoryDatasetAssociationDisplayAtAuthorization.table, properties=dict( history_dataset_association=relation(model.HistoryDatasetAssociation), user=relation(model.User) @@ -1965,6 +1985,20 @@ mapper(model.Job, model.Job.table, properties=dict( input_datasets=relation(model.JobToInputDatasetAssociation), input_dataset_collections=relation(model.JobToInputDatasetCollectionAssociation, lazy=True), output_datasets=relation(model.JobToOutputDatasetAssociation, lazy=True), + any_output_dataset_deleted=column_property( + exists([model.HistoryDatasetAssociation], + and_(model.Job.table.c.id == model.JobToOutputDatasetAssociation.table.c.job_id, + model.HistoryDatasetAssociation.table.c.id == model.JobToOutputDatasetAssociation.table.c.dataset_id, + model.HistoryDatasetAssociation.table.c.deleted == true()) + ) + ), + any_output_dataset_collection_instances_deleted=column_property( + exists([model.HistoryDatasetCollectionAssociation.table.c.id], + and_(model.Job.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.job_id, + model.HistoryDatasetCollectionAssociation.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.dataset_collection_id, + model.HistoryDatasetCollectionAssociation.table.c.deleted == true()) + ) + ), output_dataset_collection_instances=relation(model.JobToOutputDatasetCollectionAssociation, lazy=True), output_dataset_collections=relation(model.JobToImplicitOutputDatasetCollectionAssociation, lazy=True), post_job_actions=relation(model.PostJobActionAssociation, lazy=False), diff --git a/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py b/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py new file mode 100644 index 00000000000..bb2c2030dd7 --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py @@ -0,0 +1,40 @@ +""" +Add copied_from_job_id column to jobs table +""" +from __future__ import print_function + +import logging + +from sqlalchemy import Column, Integer, MetaData, Table + +log = logging.getLogger(__name__) +copied_from_job_id_column = Column("copied_from_job_id", Integer, nullable=True) + + +def upgrade(migrate_engine): + print(__doc__) + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Add the copied_from_job_id column to the job table + try: + jobs_table = Table("job", metadata, autoload=True) + copied_from_job_id_column.create(jobs_table) + assert copied_from_job_id_column is jobs_table.c.copied_from_job_id + except Exception: + log.exception("Adding column 'copied_from_job_id_column' to job table failed.") + + +def downgrade(migrate_engine): + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Drop the job table's copied_from_job_id column. + try: + jobs_table = Table("job", metadata, autoload=True) + copied_from_job_id = jobs_table.c.copied_from_job_id_column + copied_from_job_id.drop() + except Exception: + log.exception("Dropping 'copied_from_job_id_column' column from job table failed.") diff --git a/lib/galaxy/model/migrate/versions/0138_add_hda_version.py b/lib/galaxy/model/migrate/versions/0138_add_hda_version.py new file mode 100644 index 00000000000..55db96d4fc3 --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0138_add_hda_version.py @@ -0,0 +1,40 @@ +""" +Add version column to history_dataset_association table +""" +from __future__ import print_function + +import logging + +from sqlalchemy import Column, Integer, MetaData, Table + +log = logging.getLogger(__name__) +version_column = Column("version", Integer, default=1) + + +def upgrade(migrate_engine): + print(__doc__) + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Add the version column to the history_dataset_association table + try: + hda_table = Table("history_dataset_association", metadata, autoload=True) + version_column.create(hda_table) + assert version_column is hda_table.c.version + except Exception: + log.exception("Adding column 'copied_from_job_id_column' to job table failed.") + + +def downgrade(migrate_engine): + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Drop the history_dataset_association table's version column. + try: + hda_table = Table("history_dataset_association", metadata, autoload=True) + version_column = hda_table.c.version + version_column.drop() + except Exception: + log.exception("Dropping 'copied_from_job_id_column' column from job table failed.") diff --git a/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py b/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py new file mode 100644 index 00000000000..8c8175a8c73 --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py @@ -0,0 +1,49 @@ +""" +Migration script to add the history_dataset_association_history table. +""" +from __future__ import print_function + +import datetime +import logging + +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table + +from galaxy.model.custom_types import MetadataType, TrimmedString + +now = datetime.datetime.utcnow +log = logging.getLogger(__name__) +log.setLevel(logging.DEBUG) +metadata = MetaData() + +HistoryDatasetAssociationHistory_table = Table( + "history_dataset_association_history", metadata, + Column("id", Integer, primary_key=True), + Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True), + Column("update_time", DateTime, default=now), + Column("version", Integer, index=True), + Column("name", TrimmedString(255)), + Column("extension", TrimmedString(64)), + Column("metadata", MetadataType(), key='_metadata'), + Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True), +) + + +def upgrade(migrate_engine): + print(__doc__) + metadata.bind = migrate_engine + metadata.reflect() + try: + HistoryDatasetAssociationHistory_table.create() + log.debug("Created history_dataset_association_history table") + except Exception: + log.exception("Creating history_dataset_association_history table failed.") + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + HistoryDatasetAssociationHistory_table.drop() + log.debug("Dropped history_dataset_association_history table") + except Exception: + log.exception("Dropping history_dataset_association_history table failed.") diff --git a/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py b/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py new file mode 100644 index 00000000000..e4b8276ffa1 --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py @@ -0,0 +1,40 @@ +""" +Add dataset_version column to job_to_input_dataset table +""" +from __future__ import print_function + +import logging + +from sqlalchemy import Column, Integer, MetaData, Table + +log = logging.getLogger(__name__) +dataset_version_column = Column("dataset_version", Integer) + + +def upgrade(migrate_engine): + print(__doc__) + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Add the version column to the job_to_input_dataset table + try: + job_to_input_dataset_table = Table("job_to_input_dataset", metadata, autoload=True) + dataset_version_column.create(job_to_input_dataset_table) + assert dataset_version_column is job_to_input_dataset_table.c.dataset_version + except Exception: + log.exception("Adding column 'dataset_history_id' to job_to_input_dataset table failed.") + + +def downgrade(migrate_engine): + metadata = MetaData() + metadata.bind = migrate_engine + metadata.reflect() + + # Drop the job_to_input_dataset table's version column. + try: + job_to_input_dataset_table = Table("job_to_input_dataset", metadata, autoload=True) + dataset_version_column = job_to_input_dataset_table.c.dataset_version + dataset_version_column.drop() + except Exception: + log.exception("Dropping 'dataset_version' column from job_to_input_dataset table failed.") diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 52b42f94fdf..d0d1fcc1d81 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -26,6 +26,7 @@ from galaxy import ( ) from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.managers import histories +from galaxy.managers.jobs import JobSearch from galaxy.queue_worker import send_control_task from galaxy.tools.actions import DefaultToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction @@ -438,6 +439,7 @@ class Tool(object, Dictifiable): raise e self.history_manager = histories.HistoryManager(app) self._view = views.DependencyResolversView(app) + self.job_search = JobSearch(app=self.app) @property def version_object(self): @@ -1279,7 +1281,7 @@ class Tool(object, Dictifiable): log.debug('Validated and populated state for tool request %s' % validation_timer) return all_params, all_errors, rerun_remap_job_id, collection_info - def handle_input(self, trans, incoming, history=None): + def handle_input(self, trans, incoming, history=None, use_cached_job=False): """ Process incoming parameters for this tool from the dict `incoming`, update the tool state (or create if none existed), and either return @@ -1294,7 +1296,20 @@ class Tool(object, Dictifiable): raise exceptions.MessageException(', '.join(msg for msg in err_data.values()), err_data=err_data) else: mapping_params = MappingParameters(incoming, all_params) - execution_tracker = execute_job(trans, self, mapping_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info) + completed_jobs = {} + for i, param in enumerate(all_params): + if use_cached_job: + completed_jobs[i] = self.job_search.by_tool_input( + trans=trans, + tool_id=self.id, + tool_version=self.version, + param=param, + param_dump=self.params_to_strings(param, self.app, nested=True), + job_state=None, + ) + else: + completed_jobs[i] = None + execution_tracker = execute_job(trans, self, mapping_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info, completed_jobs=completed_jobs) # Raise an exception if there were jobs to execute and none of them were submitted, # if at least one is submitted or there are no jobs to execute - return aggregate # information including per-job errors. Arguably we should just always return the @@ -1311,7 +1326,7 @@ class Tool(object, Dictifiable): output_collections=execution_tracker.output_collections, implicit_collections=execution_tracker.implicit_collections) - def handle_single_execution(self, trans, rerun_remap_job_id, execution_slice, history, execution_cache=None): + def handle_single_execution(self, trans, rerun_remap_job_id, execution_slice, history, execution_cache=None, completed_job=None): """ Return a pair with whether execution is successful as well as either resulting output data or an error message indicating the problem. @@ -1324,6 +1339,7 @@ class Tool(object, Dictifiable): rerun_remap_job_id=rerun_remap_job_id, execution_cache=execution_cache, dataset_collection_elements=execution_slice.dataset_collection_elements, + completed_job=completed_job, ) except httpexceptions.HTTPFound as e: # if it's a paste redirect exception, pass it up the stack diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index a0088e8344e..5ff1a25b0e6 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -195,7 +195,7 @@ class DefaultToolAction(object): return history, inp_data, inp_dataset_collections - def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, execution_cache=None, dataset_collection_elements=None): + def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, execution_cache=None, dataset_collection_elements=None, completed_job=None): """ Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use @@ -223,7 +223,7 @@ class DefaultToolAction(object): continue # Convert LDDA to an HDA. - if isinstance(data, LibraryDatasetDatasetAssociation): + if isinstance(data, LibraryDatasetDatasetAssociation) and not completed_job: data = data.to_history_dataset_association(None) inp_data[name] = data @@ -246,13 +246,14 @@ class DefaultToolAction(object): inp_data.update({"chromInfo": db_dataset}) incoming["chromInfo"] = chrom_info - # Determine output dataset permission/roles list - existing_datasets = [inp for inp in inp_data.values() if inp] - if existing_datasets: - output_permissions = app.security_agent.guess_derived_permissions_for_datasets(existing_datasets) - else: - # No valid inputs, we will use history defaults - output_permissions = app.security_agent.history_get_default_permissions(history) + if not completed_job: + # Determine output dataset permission/roles list + existing_datasets = [inp for inp in inp_data.values() if inp] + if existing_datasets: + output_permissions = app.security_agent.guess_derived_permissions_for_datasets(existing_datasets) + else: + # No valid inputs, we will use history defaults + output_permissions = app.security_agent.history_get_default_permissions(history) # Add the dbkey to the incoming parameters incoming["dbkey"] = input_dbkey @@ -301,7 +302,18 @@ class DefaultToolAction(object): inp_dataset_collections, input_ext ) - data = app.model.HistoryDatasetAssociation(extension=ext, create_dataset=True, flush=False) + create_datasets = True + dataset = None + + if completed_job: + for output_dataset in completed_job.output_datasets: + if output_dataset.name == name: + create_datasets = False + completed_data = output_dataset.dataset + dataset = output_dataset.dataset.dataset + break + + data = app.model.HistoryDatasetAssociation(extension=ext, dataset=dataset, create_dataset=create_datasets, flush=False) if hidden is None: hidden = output.hidden if not hidden and dataset_collection_elements is not None: # Mapping over a collection - hide datasets @@ -311,14 +323,17 @@ class DefaultToolAction(object): if dataset_collection_elements is not None and name in dataset_collection_elements: dataset_collection_elements[name].hda = data trans.sa_session.add(data) - trans.app.security_agent.set_all_dataset_permissions(data.dataset, output_permissions, new=True) + if not completed_job: + trans.app.security_agent.set_all_dataset_permissions(data.dataset, output_permissions, new=True) for _, tag in preserved_tags.items(): data.tags.append(tag.copy()) # Must flush before setting object store id currently. # TODO: optimize this. + trans.sa_session.flush() - object_store_populator.set_object_store_id(data) + if not completed_job: + object_store_populator.set_object_store_id(data) # This may not be neccesary with the new parent/child associations data.designation = name @@ -338,7 +353,12 @@ class DefaultToolAction(object): # Take dbkey from LAST input data.dbkey = str(input_dbkey) # Set state - data.blurb = "queued" + if completed_job: + data.blurb = completed_data.blurb + data.peek = completed_data.peek + data._metadata = completed_data._metadata + else: + data.blurb = "queued" # Set output label data.name = self.get_output_name(output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params) # Store output @@ -447,6 +467,8 @@ class DefaultToolAction(object): if job_params: job.params = dumps(job_params) job.set_handler(tool.get_job_handler(job_params)) + if completed_job: + job.set_copied_from_job_id(completed_job.id) trans.sa_session.add(job) # Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs # This functionality requires tracking jobs in the database. diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index 1a83a0d245f..880bc4a38c3 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -31,7 +31,7 @@ class PartialJobExecution(Exception): MappingParameters = collections.namedtuple("MappingParameters", ["param_template", "param_combinations"]) -def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None, job_callback=None): +def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None, job_callback=None, completed_jobs=None): """ Execute a tool and return object containing summary (output data, number of failures, etc...). @@ -49,7 +49,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle app = trans.app execution_cache = ToolExecutionCache(trans) - def execute_single_job(execution_slice): + def execute_single_job(execution_slice, completed_job): job_timer = ExecutionTimer() params = execution_slice.param_combination if workflow_invocation_uuid: @@ -59,7 +59,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle # values or rerun parameters. del params['__workflow_invocation_uuid__'] - job, result = tool.handle_single_execution(trans, rerun_remap_job_id, execution_slice, history, execution_cache) + job, result = tool.handle_single_execution(trans, rerun_remap_job_id, execution_slice, history, execution_cache, completed_job) if job: message = EXECUTION_SUCCESS_MESSAGE % (tool.id, job.id, job_timer) log.debug(message) @@ -89,13 +89,12 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle has_remaining_jobs = False if (job_count < burst_at or burst_threads < 2): - for execution_slice in execution_tracker.new_execution_slices(): + for i, execution_slice in enumerate(execution_tracker.new_execution_slices()): if max_num_jobs and jobs_executed >= max_num_jobs: has_remaining_jobs = True break else: - execute_single_job(execution_slice) - jobs_executed += 1 + execute_single_job(execution_slice, completed_jobs[i]) else: # TODO: re-record success... q = Queue() @@ -111,12 +110,12 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle t.daemon = True t.start() - for execution_slice in execution_tracker.new_execution_slices(): + for i, execution_slice in enumerate(execution_tracker.new_execution_slices()): if max_num_jobs and jobs_executed >= max_num_jobs: has_remaining_jobs = True break else: - q.put(execution_slice) + q.put(execution_slice, completed_jobs[i]) jobs_executed += 1 q.join() diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 5ae79a7e303..e57989ae3c7 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -3,6 +3,7 @@ Basic tool parameters. """ from __future__ import print_function +import cgi import logging import os import os.path @@ -543,6 +544,8 @@ class FileToolParameter(ToolParameter): return value['local_filename'] except KeyError: return None + elif isinstance(value, cgi.FieldStorage): + return value.filename raise Exception("FileToolParameter cannot be persisted") def to_python(self, value, app): diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index e92dd35c402..9330359ef55 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -302,9 +302,11 @@ class JobController(BaseAPIController, UsesLibraryMixinItems): return [] params_dump = [tool.params_to_strings(param, self.app, nested=True) for param in all_params] jobs = [] - for param_dump in params_dump: + for param_dump, param in zip(params_dump, all_params): job = self.job_search.by_tool_input(trans=trans, tool_id=tool_id, + tool_version=tool.version, + param=param, param_dump=param_dump, job_state=payload.get('state')) if job: diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index 41578548888..412cc4082d8 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -346,7 +346,12 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin): # TODO: handle dbkeys params = util.Params(inputs, sanitize=False) incoming = params.__dict__ - vars = tool.handle_input(trans, incoming, history=target_history) + + # use_cached_job can be passed in via the top-level payload or among the tool inputs. + # I think it should be a top-level parameter, but because the selector is implemented + # as a regular tool parameter we accept both. + use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false')) + vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job) # TODO: check for errors and ensure that output dataset(s) are available. output_datasets = vars.get('out_data', []) diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py index faced8ccf5b..c3adcc95b26 100644 --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -296,21 +296,21 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cre """ if not preferences: return [] - data = [] - # Get data if present - data_key = "extra_user_preferences" - if data_key in user.preferences: - data = json.loads(user.preferences[data_key]) extra_pref_inputs = list() # Build sections for different categories of inputs for item, value in preferences.items(): if value is not None: for input in value["inputs"]: - input['help'] = 'Required' if input['required'] else '' + help = input.get('help', '') + required = 'Required' if util.string_as_bool(input.get('required')) else '' + if help: + input['help'] = "%s %s" % (help, required) + else: + input['help'] = required field = item + '|' + input['name'] - for data_item in data: + for data_item in user.extra_preferences: if field in data_item: - input['value'] = data[data_item] + input['value'] = user.extra_preferences[data_item] extra_pref_inputs.append({'type': 'section', 'title': value['description'], 'name': item, 'expanded': True, 'inputs': value['inputs']}) return extra_pref_inputs @@ -455,9 +455,9 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cre # Update values for extra user preference items extra_user_pref_data = dict() - get_extra_pref_keys = self._get_extra_user_preferences(trans) - if get_extra_pref_keys is not None: - for key in get_extra_pref_keys: + extra_pref_keys = self._get_extra_user_preferences(trans) + if extra_pref_keys is not None: + for key in extra_pref_keys: key_prefix = key + '|' for item in payload: if item.startswith(key_prefix): @@ -465,7 +465,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cre if payload[item] == "": # Raise an exception when a required field is empty while saving the form keys = item.split("|") - section = get_extra_pref_keys[keys[0]] + section = extra_pref_keys[keys[0]] for input in section['inputs']: if input['name'] == keys[1] and input['required']: raise MessageException("Please fill the required field") diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 1db5d3df3b4..6e6233173ce 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -255,6 +255,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn :param allow_tool_state_corrections: If set to True, any Tool parameter changes will not prevent running workflow, defaults to False :type allow_tool_state_corrections: bool + + :param use_cached_job: If set to True galaxy will attempt to find previously executed steps for all workflow steps with the exact same parameter combinations + and will copy the outputs of the previously executed step. """ ways_to_create = set([ 'workflow_id', @@ -336,10 +339,12 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn rval = {} rval['history'] = trans.security.encode_id(history.id) rval['outputs'] = [] - for step in workflow.steps: - if step.type == 'tool' or step.type is None: - for v in outputs[step.id].values(): - rval['outputs'].append(trans.security.encode_id(v.id)) + if outputs: + # Newer outputs don't necessarily fill outputs (?) + for step in workflow.steps: + if step.type == 'tool' or step.type is None: + for v in outputs[step.id].values(): + rval['outputs'].append(trans.security.encode_id(v.id)) # Newer version of this API just returns the invocation as a dict, to # facilitate migration - produce the newer style response and blend in diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index 6f4d92c5c17..28fdba1c6b8 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -214,7 +214,7 @@ class WorkflowModule(object): state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs()), self.trans.app) return state - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): """ Execute the given workflow invocation step. Use the supplied workflow progress object to track outputs, find @@ -333,13 +333,13 @@ class SubWorkflowModule(WorkflowModule): def get_content_id(self): return self.trans.security.encode_id(self.subworkflow.id) - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): """ Execute the given workflow step in the given workflow invocation. Use the supplied workflow progress object to track outputs, find inputs, etc... """ step = invocation_step.workflow_step - subworkflow_invoker = progress.subworkflow_invoker(trans, step) + subworkflow_invoker = progress.subworkflow_invoker(trans, step, use_cached_job=use_cached_job) subworkflow_invoker.invoke() subworkflow = subworkflow_invoker.workflow subworkflow_progress = subworkflow_invoker.progress @@ -367,7 +367,7 @@ class InputModule(WorkflowModule): def get_data_inputs(self): return [] - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): invocation = invocation_step.workflow_invocation step = invocation_step.workflow_step step_outputs = dict(output=step.state.inputs['input']) @@ -504,7 +504,7 @@ class InputParameterModule(WorkflowModule): def get_data_inputs(self): return [] - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): step = invocation_step.workflow_step step_outputs = dict(output=step.state.inputs['input']) progress.set_outputs_for_input(invocation_step, step_outputs) @@ -535,7 +535,7 @@ class PauseModule(WorkflowModule): state.inputs = dict() return state - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): step = invocation_step.workflow_step progress.mark_step_outputs_delayed(step, why="executing pause step") @@ -805,7 +805,7 @@ class ToolModule(WorkflowModule): else: raise ToolMissingException("Tool %s missing. Cannot recover runtime state." % self.tool_id) - def execute(self, trans, progress, invocation_step): + def execute(self, trans, progress, invocation_step, use_cached_job=False): invocation = invocation_step.workflow_invocation step = invocation_step.workflow_step tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version) @@ -873,6 +873,19 @@ class ToolModule(WorkflowModule): param_combinations.append(execution_state.inputs) complete = False + completed_jobs = {} + for i, param in enumerate(param_combinations): + if use_cached_job: + completed_jobs[i] = tool.job_search.by_tool_input( + trans=trans, + tool_id=tool.id, + tool_version=tool.version, + param=param, + param_dump=tool.params_to_strings(param, trans.app, nested=True), + job_state=None, + ) + else: + completed_jobs[i] = None try: mapping_params = MappingParameters(tool_state.inputs, param_combinations) max_num_jobs = progress.maximum_jobs_to_schedule_or_none @@ -886,6 +899,7 @@ class ToolModule(WorkflowModule): invocation_step=invocation_step, max_num_jobs=max_num_jobs, job_callback=lambda job: self._handle_post_job_actions(step, job, invocation.replacement_dict), + completed_jobs=completed_jobs ) complete = True except PartialJobExecution as pje: diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index a97bf4bf067..8271a4c4458 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -136,6 +136,7 @@ class WorkflowInvoker(object): self.workflow_invocation = workflow_invocation self.workflow_invocation.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history + self.workflow_invocation.use_cached_job = workflow_run_config.use_cached_job self.workflow_invocation.replacement_dict = workflow_run_config.replacement_dict module_injector = modules.WorkflowModuleInjector(trans) @@ -255,7 +256,10 @@ class WorkflowInvoker(object): pass def _invoke_step(self, invocation_step): - incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans, self.progress, invocation_step) + incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans, + self.progress, + invocation_step, + use_cached_job=self.workflow_invocation.use_cached_job) return incomplete_or_none @@ -437,7 +441,7 @@ class WorkflowProgress(object): raise Exception("Failed to find persisted workflow invocation for step [%s]" % step.id) return subworkflow_invocation - def subworkflow_invoker(self, trans, step): + def subworkflow_invoker(self, trans, step, use_cached_job=False): subworkflow_progress = self.subworkflow_progress(step) subworkflow_invocation = subworkflow_progress.workflow_invocation workflow_run_config = WorkflowRunConfig( @@ -446,6 +450,7 @@ class WorkflowProgress(object): inputs={}, param_map={}, copy_inputs_to_history=False, + use_cached_job=use_cached_job ) return WorkflowInvoker( trans, diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py index 6cee1620673..fca6a3e199a 100644 --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -41,13 +41,20 @@ class WorkflowRunConfig(object): :type param_map: dict """ - def __init__(self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={}, allow_tool_state_corrections=False): + def __init__(self, target_history, + replacement_dict, + copy_inputs_to_history=False, + inputs={}, + param_map={}, + allow_tool_state_corrections=False, + use_cached_job=False): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history self.inputs = inputs self.param_map = param_map self.allow_tool_state_corrections = allow_tool_state_corrections + self.use_cached_job = use_cached_job def _normalize_inputs(steps, inputs, inputs_by): @@ -197,6 +204,7 @@ def _get_target_history(trans, workflow, payload, param_keys=[], index=0): def build_workflow_run_configs(trans, workflow, payload): app = trans.app allow_tool_state_corrections = payload.get('allow_tool_state_corrections', False) + use_cached_job = payload.get('use_cached_job', False) # Sanity checks. if len(workflow.steps) == 0: @@ -301,7 +309,8 @@ def build_workflow_run_configs(trans, workflow, payload): replacement_dict=payload.get('replacement_params', {}), inputs=normalized_inputs, param_map=param_map, - allow_tool_state_corrections=allow_tool_state_corrections + allow_tool_state_corrections=allow_tool_state_corrections, + use_cached_job=use_cached_job, )) return run_configs @@ -338,6 +347,7 @@ def workflow_run_config_to_request(trans, run_config, workflow): target_history=run_config.target_history, replacement_dict=run_config.replacement_dict, copy_inputs_to_history=False, + use_cached_job=run_config.use_cached_job, inputs={}, param_map={}, allow_tool_state_corrections=run_config.allow_tool_state_corrections @@ -363,6 +373,7 @@ def workflow_run_config_to_request(trans, run_config, workflow): workflow_invocation.add_input(content, step_id) add_parameter("copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS) + add_parameter("use_cached_job", "true" if run_config.use_cached_job else "false", param_types.META_PARAMETERS) return workflow_invocation @@ -373,6 +384,7 @@ def workflow_request_to_run_config(work_request_context, workflow_invocation): inputs = {} param_map = {} copy_inputs_to_history = None + use_cached_job = False for parameter in workflow_invocation.input_parameters: parameter_type = parameter.type @@ -381,6 +393,8 @@ def workflow_request_to_run_config(work_request_context, workflow_invocation): elif parameter_type == param_types.META_PARAMETERS: if parameter.name == "copy_inputs_to_history": copy_inputs_to_history = (parameter.value == "true") + if parameter.name == 'use_cached_job': + use_cached_job = (parameter.value == 'true') for input_association in workflow_invocation.input_datasets: inputs[input_association.workflow_step_id] = input_association.dataset for input_association in workflow_invocation.input_dataset_collections: @@ -395,6 +409,7 @@ def workflow_request_to_run_config(work_request_context, workflow_invocation): inputs=inputs, param_map=param_map, copy_inputs_to_history=copy_inputs_to_history, + use_cached_job=use_cached_job, ) return workflow_run_config diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js index e8977269dd4..310f3be5be7 100644 --- a/static/scripts/bundled/analysis.bundled.js +++ b/static/scripts/bundled/analysis.bundled.js @@ -1,3 +1,3 @@ webpackJsonp([1],[,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var 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e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){s.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return _.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,g.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,g.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,g.default)("This dataset is not yet 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',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'
',(0,g.default)("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
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','
',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
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"],"dataset"),n=p.default.wrapTemplate(['
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"],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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"],"dataset"),s[c.default.DISCARDED]=p.default.wrapTemplate(["
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"],"dataset"),s[c.default.UPLOAD]=p.default.wrapTemplate(["
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"],"dataset"),s[c.default.SETTING_METADATA]=p.default.wrapTemplate(["
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<%- dataset.misc_blurb %>
","<% } %>",'',(0,g.default)("An error occurred with this dataset"),":",'
<%- dataset.misc_info %>
'],"dataset"),s[c.default.EMPTY]=p.default.wrapTemplate(["
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"],"dataset"),s.unknown=p.default.wrapTemplate(['
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'],"dataset");var a={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'
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'),i=e.model.toJSON();return s.each(e.templates.warnings,function(s){t.append(n(s(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:r.default.wrapTemplate(['
','
','
','',"
",'
','
','
',"
"]),warnings:{},titleBar:r.default.wrapTemplate(['
','','
','<%- element.name %>',"
",'
',"
"],"element"),subtitle:r.default.wrapTemplate(['
']),details:r.default.wrapTemplate(['
'])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(s.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=r.default.wrapTemplate(['
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this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,s){var a;try{a=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var s={history_id:this.id};e&&(s.current=!0),t&&(s.name=t),i||(s.all_datasets=!1),s.view="dev-detailed";var a=this,o=n.post(this.urlRoot,s);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){a.trigger("copied",a,e)})}):o.done(function(e){a.trigger("copied",a,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,y=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return s.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),s.defaults(t,i)},fetchFirst:function(e){var t=this,i=a.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:s.extend(s.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,s.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,s){var a=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){a.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:y}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(4),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return a.storageKeyPrefix+e},get:function(e){return new a({id:a.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(a.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:a}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function i(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function n(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof 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Please try again in a few minutes.")+" "+h,(0,u.default)("Cannot connect to Galaxy"))}function r(e,t,i,n,s){return n=n||f,n+=" "+h,s=s||(0,u.default)("An error occurred"),a(n,s,d(e,t,i))}function d(e,t,i){return{raven:n.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:n.result(Galaxy.config,"version_major"),xhr:n.omit(t,n.functions(t)),options:n.omit(i,"xhr"),url:n.result(Galaxy.lastAjax,"url"),data:n.result(Galaxy.lastAjax,"data"),model:n.result(e,"toJSON",""+e),user:n.omit(n.result(Galaxy.user,"toJSON"),"email")}}Object.defineProperty(t,"__esModule",{value:!0});var c=i(3),u=function(e){return e&&e.__esModule?e:{default:e}}(c),h=(0,u.default)("Please contact a Galaxy administrator if the problem persists."),f=(0,u.default)("An error occurred while updating information with the server."),p=(0,u.default)("The following information can assist the developers in finding the source of the error:");t.default={errorModal:a,offlineErrorModal:o,badGatewayErrorModal:l,ajaxErrorModal:r}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(50),a=n(s),o=i(51),l=n(o),r=i(4),d=n(r),c=i(3),u=(n(c),a.default.DatasetAssociation),h=l.default.HistoryContentMixin,f=u.extend(d.default.mixin(h,{defaults:e.extend({},u.prototype.defaults,h.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));t.default={HistoryDatasetAssociation:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(21),l=a(o),r=i(95),d=a(r),c=i(4),u=a(c),h=i(3),f=a(h);i(39);var p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:l.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 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e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),s(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['
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n.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=n.extend(this._getItemViewOptions(e),{model:e}),s=new t(i);return this._setUpItemViewListeners(s),s},_destroyItemView:function(e){this.stopListening(e),this.views=n.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:n.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){n.each(this.views,function(e){e.expand()})},collapseAll:function(){n.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,a=n._filterCollection().indexOf(e);if(-1!==a){var o=n._createItemView(e);return s(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,a),e()}]),o}},_attachView:function(e,t,i){i=!!n.isUndefined(i)||i,t=t||0;var s=this;return s.views.splice(t,0,e),s._insertIntoListAt(t,s._renderItemView$el(e).hide()),s.trigger("view:attached",e),i?e.$el.slideDown(s.fxSpeed,function(){s.trigger("view:attached:rendered")}):(e.$el.show(),s.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var a=this,o=n.find(a.views,function(t){return t.model===e});if(o)return a.views=n.without(a.views,o),a.trigger("view:removed",o),s({}).queue("fx",[function(e){o.$el.fadeOut(a.fxSpeed,e)},function(e){o.remove(),a.trigger("view:removed:rendered"),a.views.length?e():a._renderEmptyMessage().fadeIn(a.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),controls:u.default.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=s(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function s(){return['"].join("")}var r=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===a.default.type(t)&&(t=a.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(s()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===r&&t.escWillClear)i.call(this,e);else{var s=o(this).val();(e.which===d||t.minSearchLen&&s.length>=t.minSearchLen)&&n.call(this,e,s)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default,l=window._l||function(e){return e};a.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=n(s),o=i(4),l=n(o),r=i(58),d=n(r),c=i(3),u=n(c),h=a.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+"\n            
    \n            
    \n            "+d.default.nametagTemplate(t)+"\n        
    \n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',(0,u.default)("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=n(s),o=i(33),l=n(o),r=i(59),d=n(r),c=i(4),u=(n(c),i(58)),h=n(u),f=i(3),p=n(f),m=l.default.DCListItemView,g=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?a.default.OK:a.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),s=e.jobStatesSummary;if(t&&"Job"!=t){if(s&&s.hasDetails()){var a=s.new(),o=a?null:s.jobCount();if(a)return'\n                        
    \n                            Creating jobs...\n                            
    \n                        
    ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n                        
    \n                            '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n                            
    \n                            
    \n                            
    \n                        
    '}return'\n                    
    \n                        Loading job data for '+i+'...\n                        
    \n                    
    '}return n},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+'\n            
    \n            
    \n            
    \n            '+h.default.nametagTemplate(t)+"\n        
    \n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),l=a(o),r=i(42),d=a(r),c=i(9),u=a(c),h=i(5),f=a(h),p=e.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(t){var i=this;this.config=n.defaults(t.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new l.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),s=t[n];if(s){var a=new s(i,t);i[a.toString()]=a,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:a})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return s(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=s("").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['
    ','
    ','
    ','
    ','
    ','
    ','
    ','",'
    '].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=s("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?s.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(2),i(1),i(0))},,,,,,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(8),l=a(o),r=i(4),d=a(r),c=i(3),u=a(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:l.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
 //!! this state is not in trans.app.model.Dataset.states - set it here -
-this.get("accessible")||this.set("state",l.default.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/edit?dataset_id="+e,download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return n.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return n.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=n.contains(l.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var i=this;return e.Model.prototype.fetch.call(this,t).always(function(){i._generateUrls()})},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},save:function(t,i){return i=i||{},i.wait=!!n.isUndefined(i.wait)||i.wait,e.Model.prototype.save.call(this,t,i)},delete:function(e){return this.get("deleted")?s.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?s.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return s.when();e=e||{},e.url=this.urls.purge;var t=this,i=s.ajax(e);return i.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),i.fail(function(i,n,s){var a=(0,u.default)("Unable to purge dataset");i.responseJSON&&i.responseJSON.error?a=i.responseJSON.error:-1!==i.responseText.indexOf("Removal of datasets by users is not allowed in this Galaxy instance")&&(a="Removal of datasets by users is not allowed in this Galaxy instance"),i.responseText=a,t.trigger("error",t,i,e,(0,u.default)(a),{error:a})}),i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=s.Deferred(),n=this.length,a=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(s,l){return function(){var r=e.call(s,t);r.done(function(e){i.notify({curr:l,total:n,response:e,model:s})}),r.always(function(e){a.push(e),o.length?o.shift()():i.resolve(a)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=(n(s),i(4)),o=(n(a),i(3)),l=(n(o),1e3);try{l=localStorage.getItem("collectionFuzzyCountDefault")||l}catch(e){}var r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id"),n=""+this.urlRoot+t+"/contents/"+e+"s/"+i;return"dataset_collection"==e&&(n=n+"?view=element-reference&fuzzy_count="+l),n},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i={_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_changeHideOriginals:function(e){this.hideOriginals=this.$(".hide-originals").prop("checked")},_changeName:function(e){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(e){13!==e.keyCode||this.blocking||this._clickCreate()},_getName:function(){return e.escape(this.$(".collection-name").val())},_clickMoreHelp:function(e){e.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(e){e.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(e){e.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(e,t){t=t||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(t).show().find(".alert-message").html(e)},_hideAlert:function(e){this.$(".main-help").show(),this.$(".header .alert").hide()},_cancelCreate:function(e){"function"==typeof this.oncancel&&this.oncancel.call(this)},_clickCreate:function(e){var t=this._getName();t?this.blocking||this.createList(t):this._validationWarning("name")},_setUpCommonSettings:function(e){this.hideOriginals=e.defaultHideSourceItems||!1},_renderFooter:function(t,i){var n=this,s=this.$(".footer").empty().html(this.templates.footer());return e.each(this.footerSettings,function(e,t){n.$(t).prop("checked",n[e])}),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),s},_creatorTemplates:{main:e.template(['
    ','
    ','
    '].join(""))}};t.default={CollectionCreatorMixin:i}}).call(t,i(1))},function(e,t,i){"use strict";function n(e,t){var i=/(-?[0-9\.]+)/g,n=e.toString().toLowerCase()||"",s=t.toString().toLowerCase()||"",a=String.fromCharCode(0),o=n.replace(i,a+"$1"+a).split(a),l=s.replace(i,a+"$1"+a).split(a),r=new Date(n).getTime(),d=r?new Date(s).getTime():null;if(d){if(rd)return 1}for(var c,u,h=0,f=Math.max(o.length,l.length);hu)return 1}return 0}Object.defineProperty(t,"__esModule",{value:!0}),t.default=n},function(e,t,i){"use strict";var n=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default;s.default.fn.extend({hoverhighlight:function(e,t){return e=e||"body",this.length?(a(this).each(function(){var i=a(this),n=i.data("target");n&&i.mouseover(function(i){a(n,e).css({background:t})}).mouseout(function(e){a(n).css({background:""})})}),this):this}})},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(9),l=a(o),r=i(36),d=a(r),c=i(3),u=a(c),h={defaultName:e.template("Copy of '<%- name %>'"),title:e.template((0,u.default)("Copying history")+' "<%- name %>"'),submitLabel:(0,u.default)("Copy"),errorMessage:(0,u.default)("History could not be copied."),progressive:(0,u.default)("Copying history"),activeLabel:(0,u.default)("Copy only the active, non-deleted datasets"),allLabel:(0,u.default)("Copy all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after copying this history. "),_template:e.template(["<% if( isAnon ){ %>",'
    ',"<%- anonWarning %>",(0,u.default)("You can"),' ',(0,u.default)("login here")," ",(0,u.default)("or")," ",' ',(0,u.default)("register here"),".","
    ","<% } %>","
    ",'
    ",'','","<% if( allowAll ){ %>","
    ","
    ",(0,u.default)("Choose which datasets from the original history to include:"),"
    ",'/>','',"
    ",'/>','',"<% } %>","
    "].join("")),_showAjaxIndicator:function(){var e='
     '+this.progressive+"...
    ";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(t,i,a){function o(){var e=t.$("#copy-modal-title").val();if(!e)return void t.$(".invalid-title").show();var n="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),l._showAjaxIndicator(),i.copy(!0,e,n).done(function(e){r.resolve(e)}).fail(function(t,s,a){var o={name:e,copyAllDatasets:n};d.default.ajaxErrorModal(i,t,o,l.errorMessage),r.rejectWith(r,arguments)}).done(function(){m&&t.hide()})}a=a||{};var l=this,r=n.Deferred(),c=a.nameFn||this.defaultName,h=c({name:i.get("name")}),f=a.allDatasets?"copy-all":"copy-non-deleted",p=!!e.isUndefined(a.allowAll)||a.allowAll,m=!!e.isUndefined(a.autoClose)||a.autoClose;this.modal=t;var g=a.closing_callback;return t.show(e.extend(a,{title:this.title({name:i.get("name")}),body:s(l._template({name:h,isAnon:Galaxy.user.isAnonymous(),allowAll:p,copyWhat:f,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:e.object([[(0,u.default)("Cancel"),function(){t.hide()}],[this.submitLabel,o]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&r.reject({cancelled:!0}),g&&g(e)}})),t.$("#copy-modal-title").focus().select(),t.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),o())}),r}},f=e.extend({},h,{defaultName:e.template("imported: <%- name %>"),title:e.template((0,u.default)("Importing history")+' "<%- name %>"'),submitLabel:(0,u.default)("Import"),errorMessage:(0,u.default)("History could not be imported."),progressive:(0,u.default)("Importing history"),activeLabel:(0,u.default)("Import only the active, non-deleted datasets"),allLabel:(0,u.default)("Import all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after importing this history. ")}),p=function(e,t){t=t||{};var i=window.parent.Galaxy.modal||new l.default.View({});return t.useImport?f.dialog(i,e,t):h.dialog(i,e,t)};t.default=p}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),a=n(s),o=i(2),l=n(o),r=i(4),d=function(e){return e&&e.__esModule?e:{default:e}}(r),c=l.Collection.extend({initialize:function(e,t){l.Collection.prototype.initialize.call(this,e,t),this.setOrder(t.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),Galaxy.debug("fetch options:",e),l.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(e){e=a.clone(e)||{};var t=this;e.traditional=!0,e.data=e.data||t._buildFetchData(e),Galaxy.debug("data:",e.data);var i=this._buildFetchFilters(e);return Galaxy.debug("filters:",i),a.isEmpty(i)||a.extend(e.data,this._fetchFiltersToAjaxData(i)),Galaxy.debug("data:",e.data),e},_buildFetchData:function(e){var t={};return this.order&&(t.order=this.order),a.defaults(a.pick(e,this._fetchParams),t)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(e){return a.clone(e.filters||{})},_fetchFiltersToAjaxData:function(e){var t={q:[],qv:[]};return a.each(e,function(e,i){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(i),t.qv.push(e))}),t},reset:function(e,t){return this.allFetched=!1,l.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:d.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":d.default.buildComparator("update_time",{ascending:!0}),create_time:d.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":d.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var i=this,n=i.comparators[e];if(a.isUndefined(n))throw new Error("unknown order: "+e);if(n!==i.comparator)return i.order=e,i.comparator=n,t.silent||i.trigger("changed-order",t),i}}),u=c.extend({limitPerPage:500,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=a.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?a.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(a.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=a.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=a.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t');this.$el.html(a.text(t).slideDown(e.isUndefined(i)?this.fxSpeed:i))},_hideLoadingIndicator:function(t){this.$(".loading-indicator").slideUp(e.isUndefined(t)?this.fxSpeed+200:t,function(){n(this).remove()})},_buildNewRender:function(){var e=k.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,y.default)({title:(0,C.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),n())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('
    '):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!i.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&k.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var i=k.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return k.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),k.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=k.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=n(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(t,i,n){if(!i||0!==i.status||0!==i.readyState){if(this.error(t,i,n),e.isString(t)&&e.isString(i)){var s=t,a=i;return v.default.errorModal(s,a,n)}return i&&502===i.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,i,n)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget)).fadeOut(this.fxSpeed,function(){n(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(e.first(this.viewsWhereModel({hid:t})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});S.prototype.templates=function(){var t=function(){return'
    \n            
    \n            
      \n            
      \',\n        
      '},i=x.default.wrapTemplate(['
      ','
      ','
      <%- history.name %>
      ',"
      ",'
      ','
      <%- history.nice_size %>
      ','
      ','
      ',"<% if( history.deleted && history.purged ){ %>",'
      ',(0,C.default)("This history has been purged and deleted"),"
      ","<% } else if( history.deleted ){ %>",'
      ',(0,C.default)("This history has been deleted"),"
      ","<% } else if( history.purged ){ %>",'
      ',(0,C.default)("This history has been purged"),"
      ","<% } %>","<% if( history.message ){ %>",'
      messagesmall">',"<%= history.message.text %>","
      ","<% } %>","
      ",'
      ','
      ','
      ','
      ',"
      ",'
      ','
      ','",'","
      ",'
      ',"
      ","
      ",'
      ',"
      "],"history"),n=x.default.wrapTemplate(['','",''],"pages");return e.extend(e.clone(k.prototype.templates),{el:t,controls:i,pagination:n})}(),t.default={HistoryView:S}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e){function i(t){return''+e.escape(t.slice(5))+""}function n(t){var n=e.filter(e.uniq(t.tags),function(e){return 0===e.indexOf("name:")}),s=e.sortBy(n).map(i);return'\n        
      \n            '+s.join("")+"\n        
      "}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(38),l=n(o),r=i(29),d=(n(r),i(33)),c=n(d),u=i(4),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('
      '+n+"
      ")}},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=p.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=function(t,i){var n=a(i.model);return'\n        
      \n            
      \n            \n                \n                '+(0,f.default)("Back to ")+"\n                "+e.escape(i.parentName)+'\n            \n            
      \n            
      \n                
      '+(e.escape(t.name)||e.escape(t.element_identifier))+'
      \n                
      \n                    '+n+'\n                
      \n            
      \n            
      \n            
      \n            
      \n            
      \n                \n                   \n                \n            
      \n        
      '};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:s,collectionDescription:a,CollectionView:m}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(8),o=s(a),l=i(17),r=s(l),d=i(22),c=s(d),u=i(61),h=s(u),f=i(10),p=s(f),m=i(4),g=s(m),_=i(3),v=s(_),w=r.default.DatasetListItemView,y=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='
      ';t.name&&t.help?(s+="Tool help for "+t.name+"
      ",s+=t.help):s+="Tool help is unavailable for this dataset.
      ",s+="
      ",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});y.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
      ',(0,v.default)("An error occurred setting the metadata for this dataset"),'
      ',(0,v.default)("Set it manually or retry auto-detection"),"","
      ","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
      ',(0,v.default)("This dataset has been deleted"),'
      ',(0,v.default)("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
      ',(0,v.default)("Permanently remove it from disk"),"","<% } %>","
      ","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
      ','','',"",'","
      ","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:y}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l);i(15);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'
      ',n.escape(e),"
      "].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",""+this.model,")"].join("")}});t.default={AnnotationEditor:d}}).call(t,i(2),i(1))},,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),a=i(32),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=["new","queued","running"],r=["error","deleted"],d=s.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(r)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var i in e)if((t[e[i]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),i=0;for(var n in e)i+=t[e[n]]||0;return i},numInError:function(){return this.numWithStates(r)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(l)},jobCount:function(){var e=this.states(),t=0;for(var i in e)t+=e[i];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),c=s.Collection.extend({model:d,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var e=this.models.filter(function(e){return!e.terminal()}),t=e.map(function(e){return e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(57),l=a(o),r=i(16),d=(a(r),i(8)),c=(a(d),i(37)),u=a(c),h=i(72),f=a(h),p=i(96),m=a(p),g=i(22),_=a(g),v=i(61),w=a(v),y=i(28),b=a(y),x=i(73),$=a(x),C=i(74),k=a(C),S=i(10),T=a(S),P=i(47),D=(a(P),i(4)),E=a(D),A=i(3),M=a(A);i(15);var I=l.default.HistoryView,O=I.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},I.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return I.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return I.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return I.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+(0,M.default)("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+(0,M.default)("loading...")+"")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=I.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=I.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new _.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,I.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,M.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,M.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,M.default)("Permanently delete datasets"),func:function(){if(confirm((0,M.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,M.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,M.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,M.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=b.default.createListCollection:"paired"==e?n=$.default.createPairCollection:"list:paired"==e?n=k.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=I.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(I.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",(0,M.default)("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),s("
      ").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),s("
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Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new c.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new p.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),s(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&s.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'
              Drop files here
              Type (set all): Genome (set all):
              '}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(5),d=a(r),c=i(49),u=(a(c),i(90)),h=a(u),f=i(27),p=a(f),m=i(12),g=a(m);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new p.default.View({title:(0,l.default)("Upload configuration"),container:this.$(".upload-settings"),placement:"bottom"});var s=this.app.select_genome.value(),a=this.app.select_extension.value();this.select_genome=new g.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:s,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new g.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:a,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:s,extension:a}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(s.escape(e.file_name)),this.$size.html(d.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(d.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new h.default(this).$el),this.settings.show())},_template:function(e){return'
              You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
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              "),this.model=new g,this.model.fetch({success:function(){t.render()},error:function(){console.error("Failed to fetch tours.")}})},render:function(){var e=t.template('
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              \n
              This page presents a list of interactive tours available on this Galaxy server.\nSelect any tour to get started (and remember, you can click \'End Tour\' at any time).
              \n\n
              \n    <% _.each(tourtagorder, function(tag) { %>\n    \n    <% }); %>\n
              \n\n<% _.each(tourtagorder, function(tourtagkey) { %>\n
              \n    <% var tourtag = tourtags[tourtagkey]; %>\n    
              \n        <%- tourtag.name %>\n    
              \n    
                \n    <% _.each(tourtag.tours, function(tour) { %>\n        
              • \n            >\n                <%- tour.name || tour.id %>\n            \n             - <%- tour.attributes.description || "No description given." %>\n             <% _.each(tour.attributes.tags, function(tag) { %>\n                \n                    <%- tag.charAt(0).toUpperCase() + tag.slice(1) %>\n                \n             <% }); %>\n        
                • \n    <% }); %>\n    
              \n
              \n<% }); %>'),i={};t.each(this.model.models,function(e){null===e.attributes.tags?(void 0===i.Untagged&&(i.Untagged={name:"Untagged",tours:[]}),i.Untagged.tours.push(e)):t.each(e.attributes.tags,function(t){t=t.charAt(0).toUpperCase()+t.slice(1),void 0===i[t]&&(i[t]={name:t,tours:[]}),i[t].tours.push(e)})});var r=Object.keys(i).sort();this.$el.html(e({tours:this.model.models,tourtags:i,tourtagorder:r})).on("click",".tourItem",function(t){t.preventDefault(),o(n(this).data("tour.id"))}).on("click",".tag-selector-button",function(t){var e=n(t.target),i="block",r=e.attr("tag-selector-button");e.toggleClass("btn-primary"),e.toggleClass("btn-secondary"),e.hasClass("btn-secondary")&&(i="none"),n("div[tag='"+r+"']").css({display:i})})}});e.default={ToursView:m,giveTourWithData:a,giveTourById:o,activeGalaxyTourRunner:s}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(5),s=a(o),l=i(79),u=a(l),c=t.View.extend({initialize:function(e){var i=this;this.data=[],this.data2=[],this.model=e&&e.model||new t.Model({id:s.default.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,readonly:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(e),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=n("").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("