Fix errors reported by new flake8 3.7.3

cron/add_manual_builds.py

@@ -6,6 +6,7 @@
 Usage:
 python add_manual_builds.py input_file builds.txt chrom_length_dir
 """
+from __future__ import print_function
 
 import os
 import sys
@@ -33,11 +34,11 @@ def add_manual_builds(input_file, build_file, chr_dir):
                 chrs = fields.pop(0).split(",")
             except Exception:
                 chrs = []
-            print>>build_file_out, build + "\t" + name + " (" + build + ")"
+            print(build + "\t" + name + " (" + build + ")", file=build_file_out)
             if chrs:  # create len file if provided chrom lens
                 chr_len_out = open(os.path.join(chr_dir, build + ".len"), 'w')
                 for chr in chrs:
-                    print>>chr_len_out, chr.replace("=", "\t")
+                    print(chr.replace("=", "\t"), file=chr_len_out)
                 chr_len_out.close()
         except Exception:
             continue

lib/galaxy/actions/library.py

@@ -126,15 +126,15 @@ def _upload_dataset(self, trans, library_id, folder_id, replace_dataset=None, **
         return output
 
     def _get_server_dir_uploaded_datasets(self, trans, params, full_dir, import_dir_desc, library_bunch, response_code, message):
-            dir_response = self._get_server_dir_files(params, full_dir, import_dir_desc)
-            files = dir_response[0]
-            if not files:
-                return dir_response
-            uploaded_datasets = []
-            for file in files:
-                name = os.path.basename(file)
-                uploaded_datasets.append(self._make_library_uploaded_dataset(trans, params, name, file, 'server_dir', library_bunch))
-            return uploaded_datasets, 200, None
+        dir_response = self._get_server_dir_files(params, full_dir, import_dir_desc)
+        files = dir_response[0]
+        if not files:
+            return dir_response
+        uploaded_datasets = []
+        for file in files:
+            name = os.path.basename(file)
+            uploaded_datasets.append(self._make_library_uploaded_dataset(trans, params, name, file, 'server_dir', library_bunch))
+        return uploaded_datasets, 200, None
 
     def _get_server_dir_files(self, params, full_dir, import_dir_desc):
         files = []

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -798,7 +798,7 @@ def validate_destination(app, destination, err_message, err_message_contents,
     valid_destination = False
     suggestion = None
 
-    if destination is 'fail' and err_message is dest_err_tool_rule_dest:  # It's a tool rule that is set to fail. It's valid
+    if destination == 'fail' and err_message is dest_err_tool_rule_dest:  # It's a tool rule that is set to fail. It's valid
         valid_destination = True
     elif app is None:
         if destination in destination_list:

lib/galaxy/jobs/runners/pulsar.py

@@ -318,9 +318,9 @@ def queue_job(self, job_wrapper):
         self.monitor_job(pulsar_job_state)
 
     def __needed_features(self, client):
-            return {
-                'remote_metadata': PulsarJobRunner.__remote_metadata(client),
-            }
+        return {
+            'remote_metadata': PulsarJobRunner.__remote_metadata(client),
+        }
 
     def __prepare_job(self, job_wrapper, job_destination):
         """Build command-line and Pulsar client for this job."""

lib/galaxy/managers/jobs.py

@@ -177,13 +177,13 @@ def replace_dataset_ids(path, key, value):
                                              d.value == json.dumps(identifier)))
                     used_ids.append(a.dataset_id)
                 elif t == 'ldda':
-                        a = aliased(model.JobToInputLibraryDatasetAssociation)
-                        conditions.append(and_(
-                            model.Job.id == a.job_id,
-                            a.name == k,
-                            a.ldda_id == v
-                        ))
-                        used_ids.append(a.ldda_id)
+                    a = aliased(model.JobToInputLibraryDatasetAssociation)
+                    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)

lib/galaxy/tools/parameters/basic.py

@@ -604,7 +604,7 @@ def visible(self):
         return True
 
     def to_param_dict_string(self, value, other_values={}):
-        if value is '':
+        if value == '':
             return 'None'
         lst = ['%s%s' % (self.user_ftp_dir, dataset) for dataset in value]
         if self.multiple:

lib/galaxy/tools/parameters/meta.py

@@ -50,7 +50,7 @@ def expand_workflow_inputs(inputs):
                 else:
                     if linked_n is None:
                         linked_n = nval
-                    elif linked_n != nval or nval is 0:
+                    elif linked_n != nval or nval == 0:
                         raise exceptions.RequestParameterInvalidException('Failed to match linked batch selections. Please select equal number of data files.')
                     linked.append(value['values'])
                     linked_keys.append((step_id, key))

lib/galaxy/util/hash_util.py

@@ -31,7 +31,7 @@ def memory_bound_hexdigest(hash_func, path=None, file=None):
 
     try:
         for block in iter(lambda: file.read(BLOCK_SIZE), b''):
-                hasher.update(block)
+            hasher.update(block)
         return hasher.hexdigest()
     finally:
         file.close()

test/api/test_workflows.py

@@ -986,19 +986,19 @@ def test_run_runtime_parameters_after_pause(self):
             assert len([x for x in content.split("\n") if x]) == 2
 
     def test_run_subworkflow_auto_labels(self):
-            history_id = self.dataset_populator.new_history()
-            test_data = """
+        history_id = self.dataset_populator.new_history()
+        test_data = """
 outer_input:
   value: 1.bed
   type: File
 """
-            job_summary = self._run_jobs(NESTED_WORKFLOW_AUTO_LABELS, test_data=test_data, history_id=history_id)
-            assert len(job_summary.jobs) == 4, "4 jobs expected, got %d jobs" % len(job_summary.jobs)
+        job_summary = self._run_jobs(NESTED_WORKFLOW_AUTO_LABELS, test_data=test_data, history_id=history_id)
+        assert len(job_summary.jobs) == 4, "4 jobs expected, got %d jobs" % len(job_summary.jobs)
 
-            content = self.dataset_populator.get_history_dataset_content(history_id)
-            self.assertEqual(
-                "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
-                content)
+        content = self.dataset_populator.get_history_dataset_content(history_id)
+        self.assertEqual(
+            "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
+            content)
 
     @skip_without_tool("cat1")
     @skip_without_tool("collection_paired_test")
@@ -3134,18 +3134,18 @@ def test_invocations_not_accessible_by_different_user_for_published_workflow(sel
             self._assert_status_code_is(usage_details_response, 403)
 
     def _invoke_paused_workflow(self, history_id):
-            workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
-            workflow_id = self.workflow_populator.create_workflow(workflow)
-            hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
-            index_map = {
-                '0': self._ds_entry(hda1),
-            }
-            invocation_id = self.__invoke_workflow(
-                history_id,
-                workflow_id,
-                index_map,
-            )
-            return workflow_id, invocation_id
+        workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
+        workflow_id = self.workflow_populator.create_workflow(workflow)
+        hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+        index_map = {
+            '0': self._ds_entry(hda1),
+        }
+        invocation_id = self.__invoke_workflow(
+            history_id,
+            workflow_id,
+            index_map,
+        )
+        return workflow_id, invocation_id
 
     def _wait_for_invocation_non_new(self, workflow_id, invocation_id):
         target_state_reached = False

test/functional/test_toolbox.py

@@ -82,7 +82,7 @@ def build_tests(app=None,
         # Create a new subclass of ToolTestCase, dynamically adding methods
         # named test_tool_XXX that run each test defined in the tool config.
         if contains and contains not in tool_id:
-                continue
+            continue
         name = name_prefix + tool_id.replace(' ', '_')
         baseclasses = (baseclass, )
         namespace = dict()

tools/maf/maf_to_bed.py

@@ -66,7 +66,7 @@ def __main__():
             for c in l:
                 spec, chrom = maf.src_split(c.src)
                 if not spec or not chrom:
-                        spec = chrom = c.src
+                    spec = chrom = c.src
                 if spec not in out_files.keys():
                     out_files[spec] = open(os.path.join(database_tmp_dir, 'primary_%s_%s_visible_bed_%s' % (output_id, spec, spec)), 'wb+')
 

tools/phenotype_association/senatag.py

@@ -139,7 +139,7 @@ def check_output(g, tagsnps):
 
     for n in tagsnps:
         for m in n.edges:
-                mysnps.append(m.name)
+            mysnps.append(m.name)
 
     mysnps = list(set(mysnps))
 

tools/stats/gsummary.py

@@ -22,7 +22,7 @@ def S3_METHODS(all="key"):
         "acosh", "asinh", "atanh", "lgamma", "gamma", "gammaCody", "digamma", "trigamma",
         "cumsum", "cumprod", "cummax", "cummin", "c"]
     Group_Ops = ["+", "-", "*", "/", "^", "%%", "%/%", "&", "|", "!", "==", "!=", "<", "<=", ">=", ">", "(", ")", "~", ","]
-    if all is "key":
+    if all == "key":
         return {'Math': Group_Math, 'Ops': Group_Ops}