Add autopep8 script to help rebasing branches after #4440.

Fixes a few more PEP8 issues as part of the autopep8'ing as well.

.ci/autopep8.sh

@@ -0,0 +1,2 @@
+exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -s -d ',' - )
+autopep8 -i -r --exclude $exclude --select E11,E101,E127,E201,E202,E22,E301,E302,E303,E304,E306,E711,W291,W292,W293,W391 ./lib/ ./test/

lib/galaxy/actions/admin.py

@@ -13,6 +13,7 @@ class AdminActions(object):
     """
     Mixin for controllers that provide administrative functionality.
     """
+
     def _create_quota(self, params, decode_id=None):
         if params.amount.lower() in ('unlimited', 'none', 'no limit'):
             create_amount = None

lib/galaxy/app.py

@@ -44,6 +44,7 @@ app = None
 
 class UniverseApplication(object, config.ConfiguresGalaxyMixin):
     """Encapsulates the state of a Universe application"""
+
     def __init__(self, **kwargs):
         if not log.handlers:
             # Paste didn't handle it, so we need a temporary basic log

lib/galaxy/datatypes/dataproviders/base.py

@@ -291,6 +291,7 @@ class MultiSourceDataProvider(DataProvider):
 
     An iterator over iterators.
     """
+
     def __init__(self, source_list, **kwargs):
         """
         :param source_list: an iterator of iterables

lib/galaxy/datatypes/dataproviders/chunk.py

@@ -74,6 +74,7 @@ class Base64ChunkDataProvider(ChunkDataProvider):
     """
     Data provider that yields chunks of base64 encoded data from its file.
     """
+
     def encode(self, chunk):
         """
         Return chunks encoded in base 64.

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -44,6 +44,7 @@ class DatasetDataProvider(base.DataProvider):
     and conv. methods for using dataset metadata to set up and control how
     the data is provided.
     """
+
     def __init__(self, dataset, **kwargs):
         """
         :param dataset: the Galaxy dataset whose file will be the source
@@ -164,6 +165,7 @@ class ConvertedDatasetDataProvider(DatasetDataProvider):
     Class that uses the file contents of a dataset after conversion to a different
     format.
     """
+
     def __init__(self, dataset, **kwargs):
         raise NotImplementedError('Abstract class')
         self.original_dataset = dataset
@@ -185,6 +187,7 @@ class DatasetColumnarDataProvider(column.ColumnarDataProvider):
     dataset's metadata to buuild settings for the ColumnarDataProvider it's
     inherited from.
     """
+
     def __init__(self, dataset, **kwargs):
         """
         All kwargs are inherited from ColumnarDataProvider.
@@ -208,6 +211,7 @@ class DatasetDictDataProvider(column.DictDataProvider):
     dataset's metadata to buuild settings for the DictDataProvider it's
     inherited from.
     """
+
     def __init__(self, dataset, **kwargs):
         """
         All kwargs are inherited from DictDataProvider.
@@ -575,6 +579,7 @@ class DatasetSubprocessDataProvider(external.SubprocessDataProvider):
     for the process).
     """
     # TODO: below should be a subclass of this and not RegexSubprocess
+
     def __init__(self, dataset, *args, **kwargs):
         """
         :param args: the list of strings used to build commands.
@@ -690,6 +695,7 @@ class BcftoolsDataProvider(line.RegexLineDataProvider):
 
     This can be piped through other providers (column, map, genome region, etc.).
     """
+
     def __init__(self, dataset, **kwargs):
         # TODO: as samtools
         raise NotImplementedError()
@@ -702,6 +708,7 @@ class BGzipTabixDataProvider(base.DataProvider):
 
     This can be piped through other providers (column, map, genome region, etc.).
     """
+
     def __init__(self, dataset, **kwargs):
         # TODO: as samtools - need more info on output format
         raise NotImplementedError()

lib/galaxy/datatypes/dataproviders/exceptions.py

@@ -7,6 +7,7 @@ class InvalidDataProviderSource(TypeError):
     """
     Raised when a unusable source is passed to a provider.
     """
+
     def __init__(self, source=None, msg=''):
         msg = msg or 'Invalid source for provider: %s' % (source)
         super(InvalidDataProviderSource, self).__init__(msg)
@@ -25,6 +26,7 @@ class NoProviderAvailable(TypeError):
 
     Meant to be used within a class that builds dataproviders (e.g. a Datatype)
     """
+
     def __init__(self, factory_source, format_requested=None, msg=''):
         self.factory_source = factory_source
         self.format_requested = format_requested

lib/galaxy/datatypes/dataproviders/external.py

@@ -31,6 +31,7 @@ class SubprocessDataProvider(base.DataProvider):
     subprocess as its data source.
     """
     # TODO: need better ways of checking returncode, stderr for errors and raising
+
     def __init__(self, *args, **kwargs):
         """
         :param args: the list of strings used to build commands.
@@ -80,6 +81,7 @@ class RegexSubprocessDataProvider(line.RegexLineDataProvider):
     RegexLineDataProvider that uses a SubprocessDataProvider as its data source.
     """
     # this is a conv. class and not really all that necc...
+
     def __init__(self, *args, **kwargs):
         # using subprocess as proxy data source in filtered line prov.
         subproc_provider = SubprocessDataProvider(*args)
@@ -135,6 +137,7 @@ class GzipDataProvider(base.DataProvider):
 
     This can be piped through other providers (column, map, genome region, etc.).
     """
+
     def __init__(self, source, **kwargs):
         unzipped = gzip.GzipFile(source, 'rb')
         super(GzipDataProvider, self).__init__(unzipped, **kwargs)
@@ -148,6 +151,7 @@ class TempfileDataProvider(base.DataProvider):
     it to be used as a source where a file_name is needed (e.g. as a parameter
     to a command line tool: samtools view -t <this_provider.source.file_name>)
     """
+
     def __init__(self, source, **kwargs):
         # TODO:
         raise NotImplementedError()

lib/galaxy/datatypes/dataproviders/hierarchy.py

@@ -23,6 +23,7 @@ class HierarchalDataProvider(line.BlockDataProvider):
 
     e.g. XML, HTML, GFF3, Phylogenetic
     """
+
     def __init__(self, source, **kwargs):
         # TODO: (and defer to better (than I can write) parsers for each subtype)
         super(HierarchalDataProvider, self).__init__(source, **kwargs)

lib/galaxy/datatypes/dataproviders/line.py

@@ -139,6 +139,7 @@ class BlockDataProvider(base.LimitedOffsetDataProvider):
     e.g. Fasta, GenBank, MAF, hg log
     Note: mem intensive (gathers list of lines before output)
     """
+
     def __init__(self, source, new_block_delim_fn=None, block_filter_fn=None, **kwargs):
         """
         :param new_block_delim_fn: T/F function to determine whether a given line

lib/galaxy/datatypes/genetics.py

@@ -320,7 +320,6 @@ class Rgenetics(Html):
         return 'text/html'
 
     def set_meta(self, dataset, **kwd):
-
         """
         for lped/pbed eg
 
@@ -617,10 +616,10 @@ class RexpBase(Html):
             del useConc[i]  # get rid of concordance
             del useCols[i]  # and usecols entry
         for i, conc in enumerate(useConc):  # these are all unique columns for the design matrix
-                ccounts = sorted((conc.get(code, 0), code) for code in conc.keys())  # decorate
-                cc = [(x[1], x[0]) for x in ccounts]  # list of code count tuples
-                codeDetails = (head[useCols[i]], cc)  # ('foo',[('a',3),('b',11),..])
-                listCol.append(codeDetails)
+            ccounts = sorted((conc.get(code, 0), code) for code in conc.keys())  # decorate
+            cc = [(x[1], x[0]) for x in ccounts]  # list of code count tuples
+            codeDetails = (head[useCols[i]], cc)  # ('foo',[('a',3),('b',11),..])
+            listCol.append(codeDetails)
         if len(listCol) > 0:
             res = listCol
             # metadata.pheCols becomes [('bar;22,zot;113','foo'), ...]
@@ -706,7 +705,6 @@ class RexpBase(Html):
             dataset.metadata = copy_from.metadata
 
     def set_meta(self, dataset, **kwd):
-
         """
         NOTE we apply the tabular machinary to the phenodata extracted
         from a BioC eSet or affybatch.

lib/galaxy/datatypes/graph.py

@@ -106,6 +106,7 @@ class XGMMLGraphDataProvider(dataproviders.hierarchy.XMLDataProvider):
         'edges': contains objects of the form:
             { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> }
     """
+
     def __iter__(self):
         # use simple graph to store nodes and links, later providing them as a dict
         #   essentially this is a form of aggregation
@@ -139,6 +140,7 @@ class SIFGraphDataProvider(dataproviders.column.ColumnarDataProvider):
         'edges': contains objects of the form:
             { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> }
     """
+
     def __iter__(self):
         # use simple graph to store nodes and links, later providing them as a dict
         #   essentially this is a form of aggregation

lib/galaxy/datatypes/molecules.py

@@ -754,7 +754,7 @@ class CML(GenericXml):
                     if line.lstrip().startswith('<?xml version="1.0"?>') or \
                        line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
                        line.lstrip().startswith('</cml>'):
-                            continue
+                        continue
                     lines.append(line)
                     if line.lstrip().startswith('</molecule>'):
                         yield lines

lib/galaxy/datatypes/mothur.py

@@ -904,6 +904,7 @@ class SffFlow(Tabular):
           GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ...
           GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ...
     """
+
     def __init__(self, **kwd):
         super(SffFlow, self).__init__(**kwd)
 

lib/galaxy/datatypes/neo4j.py

@@ -20,6 +20,7 @@ class Neo4j(Html):
     derived from html - composite datatype elements
     stored in extra files path
     """
+
     def generate_primary_file(self, dataset=None):
         """
         This is called only at upload to write the html file

lib/galaxy/datatypes/text.py

@@ -487,6 +487,7 @@ class SnpSiftDbNSFP(Text):
     ## Create tabix index
     tabix -s 1 -b 2 -e 2 dbNSFP2.3.txt.gz
     """
+
     def __init__(self, **kwd):
         Text.__init__(self, **kwd)
         self.add_composite_file('%s.gz', description='dbNSFP bgzip', substitute_name_with_metadata='reference_name', is_binary=True)

lib/galaxy/datatypes/util/gff_util.py

@@ -16,6 +16,7 @@ class GFFInterval(GenomicInterval):
     A GFF interval, including attributes. If file is strictly a GFF file,
     only attribute is 'group.'
     """
+
     def __init__(self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4,
                  strand_col=6, score_col=5, default_strand='.', fix_strand=False):
         # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this,
@@ -52,6 +53,7 @@ class GFFFeature(GFFInterval):
     """
     A GFF feature, which can include multiple intervals.
     """
+
     def __init__(self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4,
                  strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=[],
                  raw_size=0):

lib/galaxy/jobs/__init__.py

@@ -55,6 +55,7 @@ class JobDestination(Bunch):
     """
     Provides details about where a job runs
     """
+
     def __init__(self, **kwds):
         self['id'] = None
         self['url'] = None
@@ -87,6 +88,7 @@ class JobToolConfiguration(Bunch):
     A JobToolConfiguration will have the required attribute 'id' and optional
     attributes 'handler', 'destination', and 'params'
     """
+
     def __init__(self, **kwds):
         self['handler'] = None
         self['destination'] = None
@@ -723,6 +725,7 @@ class JobWrapper(object, HasResourceParameters):
     Wraps a 'model.Job' with convenience methods for running processes and
     state management.
     """
+
     def __init__(self, job, queue, use_persisted_destination=False):
         self.job_id = job.id
         self.session_id = job.session_id
@@ -2101,6 +2104,7 @@ class NoopQueue(object):
     """
     Implements the JobQueue / JobStopQueue interface but does nothing
     """
+
     def put(self, *args, **kwargs):
         return
 
@@ -2116,6 +2120,7 @@ class ParallelismInfo(object):
     Stores the information (if any) for running multiple instances of the tool in parallel
     on the same set of inputs.
     """
+
     def __init__(self, tag):
         self.method = tag.get('method')
         if isinstance(tag, dict):

lib/galaxy/jobs/deferred/__init__.py

@@ -151,6 +151,7 @@ class DeferredJobQueue(object):
 
 class FakeTrans(object):
     """A fake trans for calling the external set metadata tool"""
+
     def __init__(self, app, history=None, user=None):
         class Dummy(object):
             def __init__(self):

lib/galaxy/jobs/handler.py

@@ -27,6 +27,7 @@ class JobHandler(object):
     """
     Handle the preparation, running, tracking, and finishing of jobs
     """
+
     def __init__(self, app):
         self.app = app
         # The dispatcher launches the underlying job runners
@@ -109,11 +110,11 @@ class JobHandlerQueue(object):
                        model.Job.states.QUEUED,
                        model.Job.states.RUNNING)
         if self.app.config.user_activation_on:
-                jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                    .outerjoin(model.User) \
-                    .filter(model.Job.state.in_(in_list) &
-                            (model.Job.handler == self.app.config.server_name) &
-                            or_((model.Job.user_id == null()), (model.User.active == true()))).all()
+            jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
+                .outerjoin(model.User) \
+                .filter(model.Job.state.in_(in_list) &
+                        (model.Job.handler == self.app.config.server_name) &
+                        or_((model.Job.user_id == null()), (model.User.active == true()))).all()
         else:
             jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
                 .filter(model.Job.state.in_(in_list) &

lib/galaxy/jobs/manager.py

@@ -16,6 +16,7 @@ class JobManager(object):
     TODO: Currently the app accesses "job_queue" and "job_stop_queue" directly.
           This should be decoupled.
     """
+
     def __init__(self, app):
         self.app = app
         if self.app.is_job_handler():

lib/galaxy/jobs/runners/godocker.py

@@ -21,6 +21,7 @@ class Godocker(object):
     """
     API parameters
     """
+
     def __init__(self, server, login, apikey, noCert):
         self.token = None
         self.server = server

lib/galaxy/jobs/runners/util/drmaa/__init__.py

@@ -11,6 +11,7 @@ class DrmaaSessionFactory(object):
     """
     Abstraction used to production DrmaaSession wrappers.
     """
+
     def __init__(self):
         self.session_constructor = Session
 

lib/galaxy/jobs/transfer_manager.py

@@ -19,6 +19,7 @@ class TransferManager(object):
     """
     Manage simple data transfers from URLs to temporary locations.
     """
+
     def __init__(self, app):
         self.app = app
         self.sa_session = app.model.context.current

lib/galaxy/managers/deletable.py

@@ -18,6 +18,7 @@ class DeletableManagerMixin(object):
     that they are no longer needed, should not be displayed, or may be actually
     removed by an admin/script.
     """
+
     def delete(self, item, flush=True, **kwargs):
         """
         Mark as deleted and return.
@@ -72,6 +73,7 @@ class PurgableManagerMixin(DeletableManagerMixin):
     purging is often removal of some additional, non-db resource (e.g. a dataset's
     file).
     """
+
     def purge(self, item, flush=True, **kwargs):
         """
         Mark as purged and return.

lib/galaxy/model/__init__.py

@@ -3304,6 +3304,7 @@ class DatasetCollection(object, Dictifiable, UsesAnnotations):
 class DatasetCollectionInstance(object, HasName):
     """
     """
+
     def __init__(
         self,
         collection=None,

lib/galaxy/model/item_attrs.py

@@ -21,6 +21,7 @@ class UsesItemRatings:
         (2) item-rating association table has a column with a foreign key referencing
         item table that contains the item's id.
     """
+
     def get_ave_item_rating_data(self, db_session, item, webapp_model=None):
         """ Returns the average rating for an item."""
         if webapp_model is None:
@@ -96,6 +97,7 @@ class UsesItemRatings:
 
 class UsesAnnotations:
     """ Mixin for getting and setting item annotations. """
+
     def get_item_annotation_str(self, db_session, user, item):
         """ Returns a user's annotation string for an item. """
         annotation_obj = self.get_item_annotation_obj(db_session, user, item)

lib/galaxy/model/metadata.py

@@ -37,6 +37,7 @@ class Statement(object):
     statements.  This is how we shove the metadata element spec into
     the class.
     """
+
     def __init__(self, target):
         self.target = target
 
@@ -61,6 +62,7 @@ class MetadataCollection(object):
     handles processing the metadata elements when they are set and
     retrieved, returning default values in cases when metadata is not set.
     """
+
     def __init__(self, parent):
         self.parent = parent
         # initialize dict if needed
@@ -205,6 +207,7 @@ class MetadataSpecCollection(odict):
     list.  append() is also implemented for simplicity and does not
     "append".
     """
+
     def __init__(self, dict=None):
         odict.__init__(self, dict=None)
 
@@ -309,6 +312,7 @@ class MetadataElementSpec(object):
     Defines a metadata element and adds it to the metadata_spec (which
     is a MetadataSpecCollection) of datatype.
     """
+
     def __init__(self, datatype, name=None, desc=None,
                  param=MetadataParameter, default=None, no_value=None,
                  visible=True, set_in_upload=False, **kwargs):

lib/galaxy/model/orm/logging_connection_proxy.py

@@ -58,6 +58,7 @@ class TraceLoggerProxy(ConnectionProxy):
     """
     Logs SQL statements using a metlog client
     """
+
     def __init__(self, trace_logger):
         self.trace_logger = trace_logger
 

lib/galaxy/model/search.py

@@ -79,6 +79,7 @@ class ViewField(object):
         its chain of parents to find out which library it belongs to
 
     """
+
     def __init__(self, name, sqlalchemy_field=None, handler=None, post_filter=None, id_decode=False):
         self.name = name
         self.sqlalchemy_field = sqlalchemy_field
@@ -603,6 +604,7 @@ class GalaxyQuery(object):
     """
     This class represents a data structure of a compiled GQL query
     """
+
     def __init__(self, field_list, table_name, conditional):
         self.field_list = field_list
         self.table_name = table_name
@@ -614,6 +616,7 @@ class GalaxyQueryComparison(object):
     This class represents the data structure of the comparison arguments of a
     compiled GQL query (ie where name='Untitled History')
     """
+
     def __init__(self, left, operator, right):
         self.left = left
         self.operator = operator
@@ -625,6 +628,7 @@ class GalaxyQueryAnd(object):
     This class represents the data structure of the comparison arguments of a
     compiled GQL query (ie where name='Untitled History')
     """
+
     def __init__(self, left, right):
         self.left = left
         self.operator = 'and'
@@ -669,6 +673,7 @@ class GalaxySearchEngine(object):
     """
     Primary class for searching. Parses GQL (Galaxy Query Language) queries and returns a 'SearchQuery' class
     """
+
     def __init__(self):
         self.parser = parsley.makeGrammar(gqlGrammar, {
             're': re,

lib/galaxy/objectstore/__init__.py

@@ -749,6 +749,7 @@ def build_object_store_from_config(config, fsmon=False, config_xml=None):
 
 def local_extra_dirs(func):
     """Non-local plugin decorator using local directories for the extra_dirs (job_work and temp)."""
+
     def wraps(self, *args, **kwargs):
         if kwargs.get('base_dir', None) is None:
             return func(self, *args, **kwargs)

lib/galaxy/objectstore/azure_blob.py

@@ -35,6 +35,7 @@ class AzureBlobObjectStore(ObjectStore):
     cache exists that is used as an intermediate location for files between
     Galaxy and Azure.
     """
+
     def __init__(self, config, config_xml):
         if BlockBlobService is None:
             raise Exception(NO_BLOBSERVICE_ERROR_MESSAGE)

lib/galaxy/objectstore/pithos.py

@@ -75,6 +75,7 @@ class PithosObjectStore(ObjectStore):
     Object store that stores objects as items in a Pithos+ container.
     Cache is ignored for the time being.
     """
+
     def __init__(self, config, config_xml):
         if KamakiClient is None:
             raise Exception(NO_KAMAKI_ERROR_MESSAGE)

lib/galaxy/objectstore/rods.py

@@ -33,6 +33,7 @@ class IRODSObjectStore(DiskObjectStore):
     """
     Galaxy object store based on iRODS
     """
+
     def __init__(self, config, file_path=None, extra_dirs=None):
         super(IRODSObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs)
         assert irods is not None, IRODS_IMPORT_MESSAGE

lib/galaxy/objectstore/s3.py

@@ -47,6 +47,7 @@ class S3ObjectStore(ObjectStore):
     cache exists that is used as an intermediate location for files between
     Galaxy and S3.
     """
+
     def __init__(self, config, config_xml):
         if boto is None:
             raise Exception(NO_BOTO_ERROR_MESSAGE)

lib/galaxy/queue_worker.py

@@ -103,7 +103,7 @@ def _get_new_toolbox(app):
     from galaxy import tools
     from galaxy.tools.special_tools import load_lib_tools
     if hasattr(app, 'tool_shed_repository_cache'):
-                app.tool_shed_repository_cache.rebuild()
+        app.tool_shed_repository_cache.rebuild()
     tool_configs = app.config.tool_configs
     if app.config.migrated_tools_config not in tool_configs:
         tool_configs.append(app.config.migrated_tools_config)
@@ -196,6 +196,7 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
     handler, will have one of these used for dispatching so called 'control'
     tasks.
     """
+
     def __init__(self, app, queue=None, task_mapping=control_message_to_task, connection=None):
         super(GalaxyQueueWorker, self).__init__()
         log.info("Initializing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))

lib/galaxy/quota/__init__.py

@@ -10,6 +10,7 @@ log = logging.getLogger(__name__)
 
 class NoQuotaAgent(object):
     """Base quota agent, always returns no quota"""
+
     def __init__(self, model):
         self.model = model
         self.sa_session = model.context
@@ -42,6 +43,7 @@ class NoQuotaAgent(object):
 
 class QuotaAgent(NoQuotaAgent):
     """Class that handles galaxy quotas"""
+
     def get_quota(self, user, nice_size=False):
         """
         Calculated like so:

lib/galaxy/security/__init__.py

@@ -223,9 +223,9 @@ class GalaxyRBACAgent(RBACAgent):
         """
         roles = []
         for item_permission in item.actions:
-                permission_action = self.get_action(item_permission.action)
-                if permission_action == action:
-                    roles.append(item_permission.role)
+            permission_action = self.get_action(item_permission.action)
+            if permission_action == action:
+                roles.append(item_permission.role)
         return roles
 
     def get_valid_roles(self, trans, item, query=None, page=None, page_limit=None, is_library_access=False):

lib/galaxy/tools/__init__.py

@@ -325,6 +325,7 @@ class DefaultToolState(object):
     Keeps track of the state of a users interaction with a tool between
     requests.
     """
+
     def __init__(self):
         self.page = 0
         self.rerun_remap_job_id = None
@@ -2396,12 +2397,12 @@ class MergeCollectionTool(DatabaseOperationTool):
         identifiers_map = {}
         for input_num, input_list in enumerate(input_lists):
             for dce in input_list.collection.elements:
-                    element_identifier = dce.element_identifier
-                    if element_identifier not in identifiers_map:
-                        identifiers_map[element_identifier] = []
-                    elif dupl_actions == "fail":
-                        raise Exception("Duplicate collection element identifiers found for [%s]" % element_identifier)
-                    identifiers_map[element_identifier].append(input_num)
+                element_identifier = dce.element_identifier
+                if element_identifier not in identifiers_map:
+                    identifiers_map[element_identifier] = []
+                elif dupl_actions == "fail":
+                    raise Exception("Duplicate collection element identifiers found for [%s]" % element_identifier)
+                identifiers_map[element_identifier].append(input_num)
 
         for copy, input_list in enumerate(input_lists):
             for dce in input_list.collection.elements:

lib/galaxy/tools/actions/__init__.py

@@ -24,6 +24,7 @@ class ToolExecutionCache(object):
     """ An object mean to cache calculation caused by repeatedly evaluting
     the same tool by the same user with slightly different parameters.
     """
+
     def __init__(self, trans):
         self.trans = trans
         self.current_user_roles = trans.get_current_user_roles()
@@ -34,6 +35,7 @@ class ToolAction(object):
     The actions to be taken when a tool is run (after parameters have
     been converted and validated).
     """
+
     def execute(self, tool, trans, incoming={}, set_output_hid=True):
         raise TypeError("Abstract method")
 

lib/galaxy/tools/deps/__init__.py

@@ -69,6 +69,7 @@ class DependencyManager(object):
     and should each contain a file 'env.sh' which can be sourced to make the
     dependency available in the current shell environment.
     """
+
     def __init__(self, default_base_path, conf_file=None, app_config={}):
         """
         Create a new dependency manager looking for packages under the paths listed

lib/galaxy/tools/deps/brew_exts.py

@@ -547,7 +547,7 @@ def which(file):
     # http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python
     for path in os.environ["PATH"].split(":"):
         if os.path.exists(path + "/" + file):
-                return path + "/" + file
+            return path + "/" + file
 
     return None
 

lib/galaxy/tools/deps/mulled/mulled_search.py

@@ -26,6 +26,7 @@ class QuaySearch():
     """
     Tool to search within a quay organization for a given software name.
     """
+
     def __init__(self, organization):
         self.index = None
         self.organization = organization

lib/galaxy/tools/deps/requirements.py

@@ -20,6 +20,7 @@ class ToolRequirement(object):
     run (for example, a program, package, or library).  Requirements can
     optionally assert a specific version.
     """
+
     def __init__(self, name=None, type=None, version=None, specs=[]):
         self.name = name
         self.type = type
@@ -94,6 +95,7 @@ class ToolRequirements(object):
     """
     Represents all requirements (packages, env vars) needed to run a tool.
     """
+
     def __init__(self, tool_requirements=None):
         if tool_requirements:
             if not isinstance(tool_requirements, list):

lib/galaxy/tools/deps/resolvers/modules.py

@@ -80,6 +80,7 @@ class DirectoryModuleChecker(object):
 
     Searches the paths listed in modulepath to for a file or directory matching the module name.
     If the version=True, searches for files named module/version."""
+
     def __init__(self, module_dependency_resolver, modulepath, prefetch):
         self.module_dependency_resolver = module_dependency_resolver
         self.directories = modulepath.split(pathsep)
@@ -109,6 +110,7 @@ class AvailModuleChecker(object):
     module names into module and version on '/' and discarding a postfix matching default_indicator
     (by default '(default)'. Matching is done using the module and
     (if version=True) the module version."""
+
     def __init__(self, module_dependency_resolver, modulepath, prefetch, default_indicator=DEFAULT_INDICATOR):
         self.module_dependency_resolver = module_dependency_resolver
         self.modulepath = modulepath

lib/galaxy/tools/imp_exp/__init__.py

@@ -22,6 +22,7 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
         Class provides support for performing jobs that import a history from
         an archive.
     """
+
     def __init__(self, app, job_id):
         self.app = app
         self.job_id = job_id
@@ -217,8 +218,8 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
                     """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by
                         the encoded object. This only works because HDAs are created above. """
                     if obj_dct.get('__HistoryDatasetAssociation__', False):
-                            return self.sa_session.query(model.HistoryDatasetAssociation) \
-                                .filter_by(history=new_history, hid=obj_dct['hid']).first()
+                        return self.sa_session.query(model.HistoryDatasetAssociation) \
+                            .filter_by(history=new_history, hid=obj_dct['hid']).first()
                     return obj_dct
                 jobs_attrs = loads(jobs_attr_str, object_hook=as_hda)
 
@@ -249,6 +250,7 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
 
                     class HistoryDatasetAssociationIDEncoder(json.JSONEncoder):
                         """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """
+
                         def default(self, obj):
                             """ Encode an HDA, default encoding for everything else. """
                             if isinstance(obj, model.HistoryDatasetAssociation):
@@ -309,6 +311,7 @@ class JobExportHistoryArchiveWrapper(object, UsesAnnotations):
     Class provides support for performing jobs that export a history to an
     archive.
     """
+
     def __init__(self, job_id):
         self.job_id = job_id
 
@@ -358,6 +361,7 @@ class JobExportHistoryArchiveWrapper(object, UsesAnnotations):
 
         class HistoryDatasetAssociationEncoder(json.JSONEncoder):
             """ Custom JSONEncoder for a HistoryDatasetAssociation. """
+
             def default(self, obj):
                 """ Encode an HDA, default encoding for everything else. """
                 if isinstance(obj, trans.app.model.HistoryDatasetAssociation):

lib/galaxy/tools/parameters/basic.py

@@ -251,6 +251,7 @@ class TextToolParameter(ToolParameter):
     >>> sorted( p.to_dict( trans ).items() )
     [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -455,6 +456,7 @@ class BooleanToolParameter(ToolParameter):
     >>> print p.to_param_dict_string( False )
     _falsevalue
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -506,6 +508,7 @@ class FileToolParameter(ToolParameter):
     >>> sorted( p.to_dict( trans ).items() )
     [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -562,6 +565,7 @@ class FTPFileToolParameter(ToolParameter):
     >>> sorted( p.to_dict( trans ).items() )
     [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -634,6 +638,7 @@ class HiddenToolParameter(ToolParameter):
     >>> sorted( p.to_dict( trans ).items() )
     [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -668,6 +673,7 @@ class ColorToolParameter(ToolParameter):
         ...
     ValueError: Failed to convert 'None' to RGB.
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -699,6 +705,7 @@ class BaseURLToolParameter(HiddenToolParameter):
     >>> sorted( p.to_dict( trans ).items() )
     [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super(BaseURLToolParameter, self).__init__(tool, input_source)
@@ -755,6 +762,7 @@ class SelectToolParameter(ToolParameter):
     >>> print p.to_param_dict_string( ["y", "z"] )
     y,z
     """
+
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
@@ -946,6 +954,7 @@ class GenomeBuildParameter(SelectToolParameter):
     >>> [ i for i in o if i[ 1 ] == 'hg18' ]
     [('Human Mar. 2006 (NCBI36/hg18) (hg18)', 'hg18', False)]
     """
+
     def __init__(self, *args, **kwds):
         super(GenomeBuildParameter, self).__init__(*args, **kwds)
         if self.tool:
@@ -1013,6 +1022,7 @@ class ColumnListParameter(SelectToolParameter):
     >>> print clp.name
     numerical_column
     """
+
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         SelectToolParameter.__init__(self, tool, input_source)
@@ -1195,6 +1205,7 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     >>> assert d[ 'options' ][ 1 ][ 'name' ] == 'Option 5'
     >>> assert d[ 'options' ][ 1 ][ 'value' ] == 'option5'
     """
+
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
 
@@ -1965,6 +1976,7 @@ class HiddenDataToolParameter(HiddenToolParameter, DataToolParameter):
     Hidden parameter that behaves as a DataToolParameter. As with all hidden
     parameters, this is a HACK.
     """
+
     def __init__(self, tool, elem):
         DataToolParameter.__init__(self, tool, elem)
         self.value = "None"

lib/galaxy/tools/parameters/dynamic_options.py

@@ -57,6 +57,7 @@ class StaticValueFilter(Filter):
         keep: Keep columns matching value (True)
               Discard columns matching value (False)
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.value = elem.get("value", None)
@@ -100,6 +101,7 @@ class DataMetaFilter(Filter):
         - separator: When multiple split by this (,)
 
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.ref_name = elem.get("ref", None)
@@ -196,6 +198,7 @@ class ParamValueFilter(Filter):
         - ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter
 
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.ref_name = elem.get("ref", None)
@@ -238,6 +241,7 @@ class UniqueValueFilter(Filter):
     Required Attributes:
         column: column in options to compare with
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         column = elem.get("column", None)
@@ -268,6 +272,7 @@ class MultipleSplitterFilter(Filter):
     Optional Attributes:
         separator: Split column by this (,)
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.separator = elem.get("separator", ",")
@@ -296,6 +301,7 @@ class AttributeValueSplitterFilter(Filter):
         pair_separator: Split column by this (,)
         name_val_separator: Split name-value pair by this ( whitespace )
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.pair_separator = elem.get("pair_separator", ",")
@@ -331,6 +337,7 @@ class AdditionalValueFilter(Filter):
         name: Display name to appear in select list (value)
         index: Index of option list to add value (APPEND)
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.value = elem.get("value", None)
@@ -375,6 +382,7 @@ class RemoveValueFilter(Filter):
         key: metadata key to compare to
 
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.value = elem.get("value", None)
@@ -424,6 +432,7 @@ class SortByColumnFilter(Filter):
     Required Attributes:
         column: column to sort by
     """
+
     def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         column = elem.get("column", None)
@@ -455,6 +464,7 @@ filter_types = dict(data_meta=DataMetaFilter,
 
 class DynamicOptions(object):
     """Handles dynamically generated SelectToolParameter options"""
+
     def __init__(self, elem, tool_param):
         def load_from_parameter(from_parameter, transform_lines=None):
             obj = self.tool_param

lib/galaxy/tools/parameters/validation.py

@@ -233,6 +233,7 @@ class DatasetOkValidator(Validator):
 
 class DatasetEmptyValidator(Validator):
     """Validator that checks if a dataset has a positive file size."""
+
     def __init__(self, message=None):
         self.message = message
 
@@ -250,6 +251,7 @@ class DatasetEmptyValidator(Validator):
 
 class DatasetExtraFilesPathEmptyValidator(Validator):
     """Validator that checks if a dataset's extra_files_path exists and is not empty."""
+
     def __init__(self, message=None):
         self.message = message
 

lib/galaxy/tools/parser/interface.py

@@ -196,6 +196,7 @@ class PagesSource(object):
     Pages are deprecated so ideally this outer list will always
     be exactly a singleton.
     """
+
     def __init__(self, page_sources):
         self.page_sources = page_sources
 
@@ -298,6 +299,7 @@ class ToolStdioRegex(object):
     attribute that contains "output" and/or "error", and a "level"
     attribute that contains "warning" or "fatal".
     """
+
     def __init__(self):
         self.match = ""
         self.stdout_match = False
@@ -312,6 +314,7 @@ class ToolStdioExitCode(object):
     This is a container for the <stdio> element's <exit_code> subelement.
     The exit_code element has a range of exit codes and the error level.
     """
+
     def __init__(self):
         self.range_start = float("-inf")
         self.range_end = float("inf")

lib/galaxy/tools/wrappers.py

@@ -49,6 +49,7 @@ class RawObjectWrapper(ToolParameterValueWrapper):
     """
     Wraps an object so that __str__ returns module_name:class_name.
     """
+
     def __init__(self, obj):
         self.obj = obj
 
@@ -71,6 +72,7 @@ class InputValueWrapper(ToolParameterValueWrapper):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.
     """
+
     def __init__(self, input, value, other_values={}):
         self.input = input
         self.value = value
@@ -124,6 +126,7 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
         Provide access to any field by name or index for this particular value.
         Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected).
         """
+
         def __init__(self, input, value, other_values, path_rewriter):
             self._input = input
             self._value = value
@@ -181,6 +184,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         according to the metadata spec. Methods implemented to match behavior
         of a Metadata Collection.
         """
+
         def __init__(self, metadata):
             self.metadata = metadata
 
@@ -314,6 +318,7 @@ class HasDatasets:
 class DatasetListWrapper(list, ToolParameterValueWrapper, HasDatasets):
     """
     """
+
     def __init__(self, job_working_directory, datasets, dataset_paths=[], **kwargs):
         if not isinstance(datasets, list):
             datasets = [datasets]

lib/galaxy/util/__init__.py

@@ -407,18 +407,18 @@ def pretty_print_time_interval(time=False, precise=False):
 
     if precise:
         if day_diff == 0:
-                if second_diff < 10:
-                    return "just now"
-                if second_diff < 60:
-                    return str(second_diff) + " seconds ago"
-                if second_diff < 120:
-                    return "a minute ago"
-                if second_diff < 3600:
-                    return str(second_diff / 60) + " minutes ago"
-                if second_diff < 7200:
-                    return "an hour ago"
-                if second_diff < 86400:
-                    return str(second_diff / 3600) + " hours ago"
+            if second_diff < 10:
+                return "just now"
+            if second_diff < 60:
+                return str(second_diff) + " seconds ago"
+            if second_diff < 120:
+                return "a minute ago"
+            if second_diff < 3600:
+                return str(second_diff / 60) + " minutes ago"
+            if second_diff < 7200:
+                return "an hour ago"
+            if second_diff < 86400:
+                return str(second_diff / 3600) + " hours ago"
         if day_diff == 1:
             return "yesterday"
         if day_diff < 7:
@@ -599,7 +599,7 @@ def which(file):
     # http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python
     for path in os.environ["PATH"].split(":"):
         if os.path.exists(path + "/" + file):
-                return path + "/" + file
+            return path + "/" + file
 
     return None
 
@@ -721,7 +721,7 @@ class Params(object):
                     key not in self.NEVER_SANITIZE and
                     True not in [key.endswith("|%s" % nonsanitize_parameter) for
                                  nonsanitize_parameter in self.NEVER_SANITIZE]):
-                        self.__dict__[key] = sanitize_param(value)
+                    self.__dict__[key] = sanitize_param(value)
                 else:
                     self.__dict__[key] = value
         else:

lib/galaxy/util/bunch.py

@@ -5,6 +5,7 @@ class Bunch(object):
     Often we want to just collect a bunch of stuff together, naming each item of
     the bunch; a dictionary's OK for that, but a small do-nothing class is even handier, and prettier to use.
     """
+
     def __init__(self, **kwds):
         self.__dict__.update(kwds)
 

lib/galaxy/util/heartbeat.py

@@ -33,6 +33,7 @@ class Heartbeat(threading.Thread):
     """
     Thread that periodically dumps the state of all threads to a file
     """
+
     def __init__(self, config, name="Heartbeat Thread", period=20, fname="heartbeat.log"):
         threading.Thread.__init__(self, name=name)
         self.config = config

lib/galaxy/util/odict.py

@@ -14,6 +14,7 @@ class odict(UserDict):
     added. Calling keys(), values(), items(), etc. will return results in this
     order.
     """
+
     def __init__(self, dict=None):
         item = dict
         self._keys = []

lib/galaxy/util/pastescript/loadwsgi.py

@@ -723,6 +723,7 @@ class FuncLoader(_Loader):
     Dot notation is supported in both the module and function name, e.g.:
         use = call:my.module.path:object.method
     """
+
     def __init__(self, spec):
         self.spec = spec
         if ':' not in spec:

lib/galaxy/util/simplegraph.py

@@ -10,6 +10,7 @@ class SimpleGraphNode(object):
     """
     Node representation.
     """
+
     def __init__(self, index, **data):
         """
         :param index: index of this node in some parent list
@@ -26,6 +27,7 @@ class SimpleGraphEdge(object):
     """
     Edge representation.
     """
+
     def __init__(self, source_index, target_index, **data):
         """
         :param source_index: index of the edge's source node in some parent list
@@ -53,6 +55,7 @@ class SimpleGraph(object):
     These graphs are not specifically directed but since source and targets on the
     edges are listed - it could easily be used that way.
     """
+
     def __init__(self, nodes=None, edges=None):
         # use an odict so that edge indeces actually match the final node list indeces
         self.nodes = nodes or odict()

lib/galaxy/util/sleeper.py

@@ -6,6 +6,7 @@ class Sleeper(object):
     Provides a 'sleep' method that sleeps for a number of seconds *unless*
     the notify method is called (from a different thread).
     """
+
     def __init__(self):
         self.condition = threading.Condition()
 

lib/galaxy/util/ucsc.py

@@ -9,6 +9,7 @@ class UCSCLimitException(Exception):
 
 class UCSCOutWrapper(object):
     """File-like object that throws an exception if it encounters the UCSC limit error lines"""
+
     def __init__(self, other):
         self.other = iter(other)
         # Need one line of lookahead to be sure we are hitting the limit message

lib/galaxy/visualization/data_providers/genome.py

@@ -1270,6 +1270,7 @@ class BigWigDataProvider (BBIDataProvider):
     Provides data from BigWig files; position data is reported in 1-based
     coordinate system, i.e. wiggle format.
     """
+
     def _get_dataset(self):
         if self.converted_dataset is not None:
             f = open(self.converted_dataset.file_name)

lib/galaxy/visualization/data_providers/phyloviz/baseparser.py

@@ -3,6 +3,7 @@ import json
 
 class Node(object):
     """Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree"""
+
     def __init__(self, nodeName, **kwargs):
         """Creates a node and adds in the typical annotations"""
         self.name, self.id = nodeName, kwargs.get("id", 0)

lib/galaxy/visualization/genomes.py

@@ -75,6 +75,7 @@ class Genome(object):
     """
     Encapsulates information about a known genome/dbkey.
     """
+
     def __init__(self, key, description, len_file=None, twobit_file=None):
         self.key = key
         self.description = description

lib/galaxy/visualization/plugins/config_parser.py

@@ -452,6 +452,7 @@ class ParamModifierParser(ParamParser):
     (normal) param (e.g. 'hda_ldda' can equal 'hda' or 'ldda' and control
     whether a visualizations 'dataset_id' param is for an HDA or LDDA).
     """
+
     def parse(self, element):
         # modifies is required
         modifies = element.get('modifies')

lib/galaxy/visualization/plugins/plugin.py

@@ -329,6 +329,7 @@ class StaticFileVisualizationPlugin(VisualizationPlugin):
     """
     # TODO: these are not embeddable by their nature - update config
     # TODO: should do render/render_saved here since most of the calc done there is unneeded in this case
+
     def _render(self, render_vars, trans=None, embedded=None, **kwargs):
         """
         Render the static file simply by reading and returning it.

lib/galaxy/visualization/plugins/utils.py

@@ -15,6 +15,7 @@ class OpenObject(dict):
     KeyError).
     JSON-serializable.
     """
+
     def __getitem__(self, key):
         if key not in self:
             return None

lib/galaxy/web/form_builder.py

@@ -49,6 +49,7 @@ class TextField(BaseField):
     >>> print TextField( "bins", size=4, value="default" ).get_html()
     <input type="text" name="bins" size="4" value="default">
     """
+
     def __init__(self, name, size=None, value=None, **kwds):
         super(TextField, self).__init__(name, value, **kwds)
         self.size = int(size or 10)
@@ -76,6 +77,7 @@ class PasswordField(BaseField):
     >>> print PasswordField( "bins", size=4, value="default" ).get_html()
     <input type="password" name="bins" size="4" value="default">
     """
+
     def __init__(self, name, size=None, value=None, **kwds):
         super(PasswordField, self).__init__(name, value, **kwds)
         self.name = name
@@ -213,6 +215,7 @@ class HiddenField(BaseField):
     >>> print HiddenField( "foo", 100 ).get_html()
     <input type="hidden" name="foo" value="100">
     """
+
     def __init__(self, name, value=None, **kwds):
         super(HiddenField, self).__init__(name, value, **kwds)
         self.name = name
@@ -265,6 +268,7 @@ class SelectField(BaseField):
     <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div>
     <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div>
     """
+
     def __init__(self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None, field_id=None, value=None, selectlist=None, **kwds):
         super(SelectField, self).__init__(name, value, **kwds)
         self.name = name

lib/galaxy/web/framework/base.py

@@ -52,6 +52,7 @@ class WebApplication(object):
     complicated encoding of arguments in the PATH_INFO can be performed
     with routes.
     """
+
     def __init__(self):
         """
         Create a new web application object. To actually connect some
@@ -263,6 +264,7 @@ class WSGIEnvironmentProperty(object):
     associated object (provides property style access to keys in the WSGI
     environment)
     """
+
     def __init__(self, key, default=''):
         self.key = key
         self.default = default
@@ -278,6 +280,7 @@ class LazyProperty(object):
     Property that replaces itself with a calculated value the first time
     it is used.
     """
+
     def __init__(self, func):
         self.func = func
 
@@ -299,6 +302,7 @@ class DefaultWebTransaction(object):
     TODO: Provide hooks to allow application specific state to be included
           in here.
     """
+
     def __init__(self, environ):
         self.environ = environ
         self.request = Request(environ)
@@ -343,6 +347,7 @@ class Request(webob.Request):
     """
     Encapsulates an HTTP request.
     """
+
     def __init__(self, environ):
         """
         Create a new request wrapping the WSGI environment `environ`
@@ -406,6 +411,7 @@ class Response(object):
     Describes an HTTP response. Currently very simple since the actual body
     of the request is handled separately.
     """
+
     def __init__(self):
         """
         Create a new Response defaulting to HTML content and "200 OK" status

lib/galaxy/web/framework/formbuilder.py

@@ -12,6 +12,7 @@ class FormBuilder(object):
     """
     Simple class describing an HTML form
     """
+
     def __init__(self, action="", title="", name="form", submit_text="submit", use_panels=False):
         self.title = title
         self.name = name
@@ -42,6 +43,7 @@ class FormInput(object):
     """
     Simple class describing a form input element
     """
+
     def __init__(self, type, name, label, value=None, error=None, help=None, use_label=True, extra_attributes={}, **kwargs):
         self.type = type
         self.name = name
@@ -70,6 +72,7 @@ class DatalistInput(FormInput):
 
 class SelectInput(FormInput):
     """ A select form input. """
+
     def __init__(self, name, label, value=None, options=[], error=None, help=None, use_label=True):
         FormInput.__init__(self, "select", name, label, value=value, error=error, help=help, use_label=use_label)
         self.options = options
@@ -80,6 +83,7 @@ class FormData(object):
     Class for passing data about a form to a template, very rudimentary, could
     be combined with the tool form handling to build something more general.
     """
+
     def __init__(self):
         # TODO: galaxy's two Bunchs are defined differently. Is this right?
         self.values = bunch.Bunch()

lib/galaxy/web/framework/helpers/grids.py

@@ -529,12 +529,14 @@ class GridColumn(object):
 
 class ReverseSortColumn(GridColumn):
     """ Column that reverses sorting; this is useful when the natural sort is descending. """
+
     def sort(self, trans, query, ascending, column_name=None):
         return GridColumn.sort(self, trans, query, (not ascending), column_name=column_name)
 
 
 class TextColumn(GridColumn):
     """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """
+
     def filter(self, trans, user, query, column_filter):
         """ Modify query to filter using free text, case independence. """
         if column_filter == "All":
@@ -615,6 +617,7 @@ class IntegerColumn(TextColumn):
     JobIdColumn column in the SpecifiedDateListGrid class in the jobs controller of
     the reports webapp for an example.
     """
+
     def get_single_filter(self, user, a_filter):
         model_class_key_field = getattr(self.model_class, self.key)
         assert int(a_filter), "The search entry must be an integer"
@@ -627,6 +630,7 @@ class IntegerColumn(TextColumn):
 
 class CommunityRatingColumn(GridColumn, UsesItemRatings):
     """ Column that displays community ratings for an item. """
+
     def get_value(self, trans, grid, item):
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model)
         return trans.fill_template("tool_shed_rating.mako",
@@ -667,6 +671,7 @@ class CommunityRatingColumn(GridColumn, UsesItemRatings):
 
 class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
     """ Column that displays and filters item owner's annotations. """
+
     def __init__(self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None):
         GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
         self.sortable = False
@@ -695,6 +700,7 @@ class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
 
 class CommunityTagsColumn(TextColumn):
     """ Column that supports community tags. """
+
     def __init__(self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None):
         GridColumn.__init__(self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False)
         self.model_tag_association_class = model_tag_association_class
@@ -714,24 +720,25 @@ class CommunityTagsColumn(TextColumn):
         return query
 
     def get_filter(self, trans, user, column_filter):
-            # Parse filter to extract multiple tags.
-            if isinstance(column_filter, list):
-                # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
-                column_filter = ",".join(column_filter)
-            raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8"))
-            clause_list = []
-            for name, value in raw_tags:
-                if name:
-                    # Filter by all tags.
-                    clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%")))
-                    if value:
-                        # Filter by all values.
-                        clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%")))
-            return and_(*clause_list)
+        # Parse filter to extract multiple tags.
+        if isinstance(column_filter, list):
+            # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
+            column_filter = ",".join(column_filter)
+        raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8"))
+        clause_list = []
+        for name, value in raw_tags:
+            if name:
+                # Filter by all tags.
+                clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%")))
+                if value:
+                    # Filter by all values.
+                    clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%")))
+        return and_(*clause_list)
 
 
 class IndividualTagsColumn(CommunityTagsColumn):
     """ Column that supports individual tags. """
+
     def get_value(self, trans, grid, item):
         return trans.fill_template("/tagging_common.mako",
                                    tag_type="individual",
@@ -744,24 +751,25 @@ class IndividualTagsColumn(CommunityTagsColumn):
                                    use_toggle_link=True)
 
     def get_filter(self, trans, user, column_filter):
-            # Parse filter to extract multiple tags.
-            if isinstance(column_filter, list):
-                # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
-                column_filter = ",".join(column_filter)
-            raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8"))
-            clause_list = []
-            for name, value in raw_tags:
-                if name:
-                    # Filter by individual's tag names.
-                    clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%"), self.model_tag_association_class.user == user)))
-                    if value:
-                        # Filter by individual's tag values.
-                        clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%"), self.model_tag_association_class.user == user)))
-            return and_(*clause_list)
+        # Parse filter to extract multiple tags.
+        if isinstance(column_filter, list):
+            # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
+            column_filter = ",".join(column_filter)
+        raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8"))
+        clause_list = []
+        for name, value in raw_tags:
+            if name:
+                # Filter by individual's tag names.
+                clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_tname).like("%" + name.lower() + "%"), self.model_tag_association_class.user == user)))
+                if value:
+                    # Filter by individual's tag values.
+                    clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_value).like("%" + value.lower() + "%"), self.model_tag_association_class.user == user)))
+        return and_(*clause_list)
 
 
 class MulticolFilterColumn(TextColumn):
     """ Column that performs multicolumn filtering. """
+
     def __init__(self, col_name, cols_to_filter, key, visible, filterable="default"):
         GridColumn.__init__(self, col_name, key=key, visible=visible, filterable=filterable)
         self.cols_to_filter = cols_to_filter
@@ -788,6 +796,7 @@ class MulticolFilterColumn(TextColumn):
 
 class OwnerColumn(TextColumn):
     """ Column that lists item's owner. """
+
     def get_value(self, trans, grid, item):
         return item.user.username
 
@@ -802,6 +811,7 @@ class OwnerColumn(TextColumn):
 
 class PublicURLColumn(TextColumn):
     """ Column displays item's public URL based on username and slug. """
+
     def get_link(self, trans, grid, item):
         if item.user.username and item.slug:
             return dict(action='display_by_username_and_slug', username=item.user.username, slug=item.slug)
@@ -815,6 +825,7 @@ class PublicURLColumn(TextColumn):
 
 class DeletedColumn(GridColumn):
     """ Column that tracks and filters for items with deleted attribute. """
+
     def get_accepted_filters(self):
         """ Returns a list of accepted filters for this column. """
         accepted_filter_labels_and_vals = {"active" : "False", "deleted" : "True", "all": "All"}
@@ -840,6 +851,7 @@ class StateColumn(GridColumn):
     IMPORTANT NOTE: self.model_class must have a states Bunch or dict if
     this column type is used in the grid.
     """
+
     def get_value(self, trans, grid, item):
         return item.state
 
@@ -863,6 +875,7 @@ class StateColumn(GridColumn):
 
 class SharingStatusColumn(GridColumn):
     """ Grid column to indicate sharing status. """
+
     def get_value(self, trans, grid, item):
         # Delete items cannot be shared.
         if item.deleted:
@@ -953,6 +966,7 @@ class GridOperation(object):
 
 class DisplayByUsernameAndSlugGridOperation(GridOperation):
     """ Operation to display an item by username and slug. """
+
     def get_url_args(self, item):
         return {'action' : 'display_by_username_and_slug', 'username' : item.user.username, 'slug' : item.slug}
 

lib/galaxy/web/framework/middleware/request_id.py

@@ -6,6 +6,7 @@ class RequestIDMiddleware(object):
     A WSGI middleware that creates a unique ID for the request and
     puts it in the environment
     """
+
     def __init__(self, app, global_conf=None):
         self.app = app
 

lib/galaxy/web/framework/middleware/sentry.py

@@ -24,6 +24,7 @@ class Sentry(object):
     A WSGI middleware which will attempt to capture any
     uncaught exceptions and send them to Sentry.
     """
+
     def __init__(self, application, dsn):
         assert Client is not None, RAVEN_IMPORT_MESSAGE
         self.application = application

lib/galaxy/web/framework/middleware/translogger.py

@@ -74,13 +74,13 @@ class TransLogger(object):
         if bytes is None:
             bytes = '-'
         if time.daylight:
-                offset = time.altzone / 60 / 60 * -100
+            offset = time.altzone / 60 / 60 * -100
         else:
-                offset = time.timezone / 60 / 60 * -100
+            offset = time.timezone / 60 / 60 * -100
         if offset >= 0:
-                offset = "+%0.4d" % (offset)
+            offset = "+%0.4d" % (offset)
         elif offset < 0:
-                offset = "%0.4d" % (offset)
+            offset = "%0.4d" % (offset)
         d = {
             'REMOTE_ADDR': environ.get('REMOTE_ADDR') or '-',
             'REMOTE_USER': environ.get('REMOTE_USER') or '-',

lib/galaxy/web/framework/middleware/xforwardedhost.py

@@ -3,6 +3,7 @@ class XForwardedHostMiddleware(object):
     A WSGI middleware that changes the HTTP host header in the WSGI environ
     based on the X-Forwarded-Host header IF found
     """
+
     def __init__(self, app, global_conf=None):
         self.app = app
 

lib/galaxy/web/framework/webapp.py

@@ -70,6 +70,7 @@ class WebApplication(base.WebApplication):
         * builds mako template lookups.
         * generates GalaxyWebTransactions.
     """
+
     def __init__(self, galaxy_app, session_cookie='galaxysession', name=None):
         self.name = name
         base.WebApplication.__init__(self)

lib/galaxy/webapps/galaxy/api/provenance.py

@@ -13,6 +13,7 @@ log = logging.getLogger(__name__)
 class BaseProvenanceController(BaseAPIController):
     """
     """
+
     def __init__(self, app):
         super(BaseProvenanceController, self).__init__(app)
         self.hda_manager = managers.hdas.HDAManager(app)

lib/galaxy/webapps/galaxy/api/remote_files.py

@@ -70,13 +70,13 @@ class RemoteFilesAPIController(BaseAPIController):
             if base_dir is None:
                 raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow usage of import directory.')
             if format == 'jstree':
-                    disable = kwd.get('disable', 'folders')
-                    try:
-                        importdir_jstree = self.__create_jstree(base_dir, disable)
-                        response = importdir_jstree.jsonData()
-                    except Exception as exception:
-                        log.debug(str(exception))
-                        raise exceptions.InternalServerError('Could not create tree representation of the given folder: ' + str(base_dir))
+                disable = kwd.get('disable', 'folders')
+                try:
+                    importdir_jstree = self.__create_jstree(base_dir, disable)
+                    response = importdir_jstree.jsonData()
+                except Exception as exception:
+                    log.debug(str(exception))
+                    raise exceptions.InternalServerError('Could not create tree representation of the given folder: ' + str(base_dir))
             elif format == 'ajax':
                 raise exceptions.NotImplemented('Not implemented yet. Sorry.')
             else:

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -787,9 +787,9 @@ class AdminToolshed(AdminGalaxy):
                         message = 'All selected tool dependencies are already installed.'
                         status = 'error'
                 else:
-                        message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
-                        message += ' and restart your Galaxy server to install tool dependencies.'
-                        status = 'error'
+                    message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
+                    message += ' and restart your Galaxy server to install tool dependencies.'
+                    status = 'error'
         installed_tool_dependencies_select_field = \
             tool_dependency_util.build_tool_dependencies_select_field(trans.app,
                                                                       tool_shed_repository=tool_shed_repository,
@@ -856,10 +856,10 @@ class AdminToolshed(AdminGalaxy):
                         kwd['message'] = 'All selected tool dependencies are already installed.'
                         kwd['status'] = 'error'
                 else:
-                        message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
-                        message += ' and restart your Galaxy server to install tool dependencies.'
-                        kwd['message'] = message
-                        kwd['status'] = 'error'
+                    message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
+                    message += ' and restart your Galaxy server to install tool dependencies.'
+                    kwd['message'] = message
+                    kwd['status'] = 'error'
         # Redirect if no tool dependencies are in the process of being installed.
         if tool_shed_repository.tool_dependencies_being_installed:
             return self.tool_dependency_grid(trans, **kwd)

lib/galaxy/webapps/galaxy/controllers/requests_common.py

@@ -1620,13 +1620,13 @@ class RequestsCommon(BaseUIController, UsesFormDefinitionsMixin):
                             workflow_dict['mappings'][int(k[len(kwd_tag):])] = {'ds_tag': v}
             field_values = {}
             for field_index, field in enumerate(request.type.sample_form.fields):
-                    field_name = field['name']
-                    input_value = params.get('sample_%i_field_%i' % (index, field_index), '')
-                    if field['type'] == CheckboxField.__name__:
-                        field_value = CheckboxField.is_checked(input_value)
-                    else:
-                        field_value = util.restore_text(input_value)
-                    field_values[field_name] = field_value
+                field_name = field['name']
+                input_value = params.get('sample_%i_field_%i' % (index, field_index), '')
+                if field['type'] == CheckboxField.__name__:
+                    field_value = CheckboxField.is_checked(input_value)
+                else:
+                    field_value = util.restore_text(input_value)
+                field_values[field_name] = field_value
             library_select_field, folder_select_field = self.__build_library_and_folder_select_fields(trans=trans,
                                                                                                       user=request.user,
                                                                                                       sample_index=index,

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -24,6 +24,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
     """
     Controller class that maps to the url root of Galaxy (i.e. '/').
     """
+
     def __init__(self, app):
         super(RootController, self).__init__(app)
         self.history_manager = managers.histories.HistoryManager(app)

lib/galaxy/webapps/galaxy/controllers/userskeys.py

@@ -66,12 +66,12 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
         for user in trans.sa_session.query(trans.app.model.User) \
                                     .filter(trans.app.model.User.table.c.deleted == false()) \
                                     .order_by(trans.app.model.User.table.c.email):
-                uid = int(user.id)
-                userkey = ""
-                for api_user in trans.sa_session.query(trans.app.model.APIKeys) \
-                        .filter(trans.app.model.APIKeys.user_id == uid):
-                    userkey = api_user.key
-                users.append({'uid': uid, 'email': user.email, 'key': userkey})
+            uid = int(user.id)
+            userkey = ""
+            for api_user in trans.sa_session.query(trans.app.model.APIKeys) \
+                    .filter(trans.app.model.APIKeys.user_id == uid):
+                userkey = api_user.key
+            users.append({'uid': uid, 'email': user.email, 'key': userkey})
         return trans.fill_template('webapps/galaxy/user/list_users.mako',
                                    cntrller=cntrller,
                                    users=users,

lib/galaxy/webapps/reports/app.py

@@ -11,6 +11,7 @@ log = logging.getLogger(__name__)
 
 class UniverseApplication(object):
     """Encapsulates the state of a Universe application"""
+
     def __init__(self, **kwargs):
         log.debug("python path is: %s", ", ".join(sys.path))
         self.name = "reports"

lib/galaxy/webapps/tool_shed/util/ratings_util.py

@@ -7,6 +7,7 @@ log = logging.getLogger(__name__)
 
 class ItemRatings(UsesItemRatings):
     """Overrides rate_item method since we also allow for comments"""
+
     def rate_item(self, trans, user, item, rating, comment=''):
         """ Rate an item. Return type is <item_class>RatingAssociation. """
         item_rating = self.get_user_item_rating(trans.sa_session, user, item, webapp_model=trans.model)

lib/galaxy/workflow/extract.py

@@ -163,6 +163,7 @@ class FakeJob(object):
     Fake job object for datasets that have no creating_job_associations,
     they will be treated as "input" datasets.
     """
+
     def __init__(self, dataset):
         self.is_fake = True
         self.id = "fake_%s" % dataset.id

lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py

@@ -112,14 +112,14 @@ class InstalledRepositoryGrid(grids.Grid):
 
     class DeletedColumn(grids.DeletedColumn):
 
-            def get_accepted_filters(self):
-                """ Returns a list of accepted filters for this column. """
-                accepted_filter_labels_and_vals = {"Active": "False", "Deactivated or uninstalled": "True", "All": "All"}
-                accepted_filters = []
-                for label, val in accepted_filter_labels_and_vals.items():
-                    args = {self.key: val}
-                    accepted_filters.append(grids.GridColumnFilter(label, args))
-                return accepted_filters
+        def get_accepted_filters(self):
+            """ Returns a list of accepted filters for this column. """
+            accepted_filter_labels_and_vals = {"Active": "False", "Deactivated or uninstalled": "True", "All": "All"}
+            accepted_filters = []
+            for label, val in accepted_filter_labels_and_vals.items():
+                args = {self.key: val}
+                accepted_filters.append(grids.GridColumnFilter(label, args))
+            return accepted_filters
 
     # Grid definition
     title = "Installed tool shed repositories"

test/casperjs/casperjs_runner.py

@@ -345,6 +345,7 @@ class Test_01_User(CasperJSTestCase):
     """Tests for the Galaxy user centered functionality:
     registration, login, etc.
     """
+
     def test_10_registration(self):
         """User registration tests:
         register new user, logout, attempt bad registrations.
@@ -369,6 +370,7 @@ class Test_01_User(CasperJSTestCase):
 class Test_02_Tools(CasperJSTestCase):
     """(Minimal) casperjs tests for tools.
     """
+
     def test_10_upload(self):
         """Tests uploading files
         """
@@ -378,6 +380,7 @@ class Test_02_Tools(CasperJSTestCase):
 class Test_03_HistoryPanel(CasperJSTestCase):
     """Tests for History fetching, rendering, and modeling.
     """
+
     def test_00_history_panel(self):
         """Test history panel basics (controls, structure, refresh, history options menu, etc.).
         """
@@ -397,6 +400,7 @@ class Test_03_HistoryPanel(CasperJSTestCase):
 class Test_04_HDAs(CasperJSTestCase):
     """Tests for HistoryDatasetAssociation fetching, rendering, and modeling.
     """
+
     def test_00_HDA_states(self):
         """Test structure rendering of HDAs in all the possible HDA states
         """
@@ -406,6 +410,7 @@ class Test_04_HDAs(CasperJSTestCase):
 class Test_05_API(CasperJSTestCase):
     """Tests for API functionality and security.
     """
+
     def test_00_history_api(self):
         """Test history API.
         """

test/galaxy_selenium/driver_factory.py

@@ -76,7 +76,7 @@ def _which(file):
     # http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python
     for path in os.environ["PATH"].split(":"):
         if os.path.exists(path + "/" + file):
-                return path + "/" + file
+            return path + "/" + file
 
     return None
 

test/shed_functional/functional/test_0060_workflows.py

@@ -19,6 +19,7 @@ workflow_repository_long_description = "Long description of the workflow for tes
 
 class TestToolShedWorkflowFeatures(ShedTwillTestCase):
     '''Test valid and invalid workflows.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)

test/shed_functional/functional/test_0400_repository_component_reviews.py

@@ -37,6 +37,7 @@ repository_long_description = 'Long description of Galaxy filtering tool for tes
 
 class TestRepositoryComponentReviews(ShedTwillTestCase):
     '''Test repository component review features.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         """

test/shed_functional/functional/test_0410_repository_component_review_access_control.py

@@ -17,6 +17,7 @@ repository_long_description = 'Long description of Galaxy filtering tool for tes
 
 class TestRepositoryComponentReviews(ShedTwillTestCase):
     '''Test repository component review features.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         """

test/shed_functional/functional/test_0420_citable_urls_for_repositories.py

@@ -26,6 +26,7 @@ first_changeset_hash = ''
 
 class TestRepositoryCitableURLs(ShedTwillTestCase):
     '''Test repository citable url features.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         """

test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py

@@ -12,6 +12,7 @@ log = logging.getLogger(__name__)
 
 class ToolWithToolDependencies(ShedTwillTestCase):
     '''Test installing a repository with tool dependencies.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)

test/shed_functional/functional/test_1060_install_repository_with_workflow.py

@@ -20,6 +20,7 @@ workflow_repository_long_description = "Long description of the workflow for tes
 
 class ToolWithRepositoryDependencies(ShedTwillTestCase):
     '''Test installing a repository with repository dependencies.'''
+
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)

test/shed_functional/functional/test_1070_invalid_tool.py

@@ -9,6 +9,7 @@ category_description = 'Test 1070 for a repository with an invalid tool.'
 
 class TestFreebayesRepository(ShedTwillTestCase):
     '''Test repository with multiple revisions with invalid tools.'''
+
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)

tools/data_source/upload.py

@@ -346,39 +346,39 @@ def add_file(dataset, registry, json_file, output_path):
 
 
 def add_composite_file(dataset, json_file, output_path, files_path):
-        if dataset.composite_files:
-            os.mkdir(files_path)
-            for name, value in dataset.composite_files.items():
-                value = util.bunch.Bunch(**value)
-                if dataset.composite_file_paths[value.name] is None and not value.optional:
-                    file_err('A required composite data file was not provided (%s)' % name, dataset, json_file)
-                    break
-                elif dataset.composite_file_paths[value.name] is not None:
-                    dp = dataset.composite_file_paths[value.name]['path']
-                    isurl = dp.find('://') != -1  # todo fixme
-                    if isurl:
-                        try:
-                            temp_name, dataset.is_multi_byte = sniff.stream_to_file(urlopen(dp), prefix='url_paste')
-                        except Exception as e:
-                            file_err('Unable to fetch %s\n%s' % (dp, str(e)), dataset, json_file)
-                            return
-                        dataset.path = temp_name
-                        dp = temp_name
-                    if not value.is_binary:
-                        tmpdir = output_adjacent_tmpdir(output_path)
-                        tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
-                        if dataset.composite_file_paths[value.name].get('space_to_tab', value.space_to_tab):
-                            sniff.convert_newlines_sep2tabs(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
-                        else:
-                            sniff.convert_newlines(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
-                    shutil.move(dp, os.path.join(files_path, name))
-        # Move the dataset to its "real" path
-        shutil.move(dataset.primary_file, output_path)
-        # Write the job info
-        info = dict(type='dataset',
-                    dataset_id=dataset.dataset_id,
-                    stdout='uploaded %s file' % dataset.file_type)
-        json_file.write(dumps(info) + "\n")
+    if dataset.composite_files:
+        os.mkdir(files_path)
+        for name, value in dataset.composite_files.items():
+            value = util.bunch.Bunch(**value)
+            if dataset.composite_file_paths[value.name] is None and not value.optional:
+                file_err('A required composite data file was not provided (%s)' % name, dataset, json_file)
+                break
+            elif dataset.composite_file_paths[value.name] is not None:
+                dp = dataset.composite_file_paths[value.name]['path']
+                isurl = dp.find('://') != -1  # todo fixme
+                if isurl:
+                    try:
+                        temp_name, dataset.is_multi_byte = sniff.stream_to_file(urlopen(dp), prefix='url_paste')
+                    except Exception as e:
+                        file_err('Unable to fetch %s\n%s' % (dp, str(e)), dataset, json_file)
+                        return
+                    dataset.path = temp_name
+                    dp = temp_name
+                if not value.is_binary:
+                    tmpdir = output_adjacent_tmpdir(output_path)
+                    tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
+                    if dataset.composite_file_paths[value.name].get('space_to_tab', value.space_to_tab):
+                        sniff.convert_newlines_sep2tabs(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
+                    else:
+                        sniff.convert_newlines(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
+                shutil.move(dp, os.path.join(files_path, name))
+    # Move the dataset to its "real" path
+    shutil.move(dataset.primary_file, output_path)
+    # Write the job info
+    info = dict(type='dataset',
+                dataset_id=dataset.dataset_id,
+                stdout='uploaded %s file' % dataset.file_type)
+    json_file.write(dumps(info) + "\n")
 
 
 def output_adjacent_tmpdir(output_path):