Merge pull request #10751 from nsoranzo/py36_again

Upgrade syntax using `pyupgrade --py36-plus`

lib/galaxy/config/__init__.py

@@ -871,7 +871,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self._set_alt_paths('file_path', self._in_data_dir('files'))  # this is called BEFORE guessing id/uuid
         ID, UUID = 'id', 'uuid'
         if self.is_set('object_store_store_by'):
-            assert self.object_store_store_by in [ID, UUID], "Invalid value for object_store_store_by [{}]".format(self.object_store_store_by)
+            assert self.object_store_store_by in [ID, UUID], f"Invalid value for object_store_store_by [{self.object_store_store_by}]"
         elif os.path.basename(self.file_path) == 'objects':
             self.object_store_store_by = UUID
         else:

lib/galaxy/dependencies/__init__.py

@@ -90,7 +90,7 @@ class ConditionalDependencies:
                     if 'type' in store.attrib:
                         self.object_stores.append(store.attrib['type'])
             else:
-                with open(object_store_conf_path, "r") as f:
+                with open(object_store_conf_path) as f:
                     job_conf_dict = yaml.safe_load(f)
 
                 def collect_types(from_dict):
@@ -147,7 +147,7 @@ class ConditionalDependencies:
             "file_sources_config_file",
             join(dirname(self.config_file), 'file_sources_conf.yml'))
         if exists(file_sources_conf_yml):
-            with open(file_sources_conf_yml, "r") as f:
+            with open(file_sources_conf_yml) as f:
                 file_sources_conf = yaml.safe_load(f)
         else:
             file_sources_conf = []

lib/galaxy/jobs/__init__.py

@@ -1942,7 +1942,7 @@ class JobWrapper(HasResourceParameters):
     def get_output_path(self, dataset):
         if getattr(dataset, "fake_dataset_association", False):
             return dataset.file_name
-        assert dataset.id is not None, "{} needs to be flushed to find output path".format(dataset)
+        assert dataset.id is not None, f"{dataset} needs to be flushed to find output path"
         if self.output_paths is None:
             self.compute_outputs()
         for (hda, dataset_path) in self.output_hdas_and_paths.values():

lib/galaxy/tool_util/cwl/runnable.py

@@ -16,7 +16,7 @@ def get_outputs(path):
         return [CwlWorkflowOutput(label) for label in workflow.output_labels]
 
 
-class CwlWorkflowOutput(object):
+class CwlWorkflowOutput:
 
     def __init__(self, label):
         self._label = label
@@ -25,7 +25,7 @@ class CwlWorkflowOutput(object):
         return self._label
 
 
-class ToolOutput(object):
+class ToolOutput:
 
     def __init__(self, tool_output):
         self._tool_output = tool_output

lib/galaxy/tool_util/verify/interactor.py

@@ -845,7 +845,7 @@ class DictClientTestConfig:
         if tool_id in self._tools:
             tool_test_config = self._tools[tool_id]
         if tool_test_config is None:
-            tool_id = "%s/%s" % (tool_id, tool_version)
+            tool_id = f"{tool_id}/{tool_version}"
             if tool_id in self._tools:
                 tool_version_test_config = self._tools[tool_id]
         else:

lib/galaxy/tool_util/verify/script.py

@@ -107,22 +107,22 @@ class Results:
     def info_message(self):
         messages = []
         passed_tests = self._tests_with_status('success')
-        messages.append("Passed tool tests ({0}): {1}".format(
+        messages.append("Passed tool tests ({}): {}".format(
             len(passed_tests),
             [t["id"] for t in passed_tests]
         ))
         failed_tests = self._tests_with_status('failure')
-        messages.append("Failed tool tests ({0}): {1}".format(
+        messages.append("Failed tool tests ({}): {}".format(
             len(failed_tests),
             [t["id"] for t in failed_tests]
         ))
         skiped_tests = self._tests_with_status('skip')
-        messages.append("Skipped tool tests ({0}): {1}".format(
+        messages.append("Skipped tool tests ({}): {}".format(
             len(skiped_tests),
             [t["id"] for t in skiped_tests]
         ))
         errored_tests = self._tests_with_status('error')
-        messages.append("Errored tool tests ({0}): {1}".format(
+        messages.append("Errored tool tests ({}): {}".format(
             len(errored_tests),
             [t["id"] for t in errored_tests]
         ))
@@ -198,7 +198,7 @@ def test_tools(
             if log:
                 log.info("Report written to '%s'", os.path.abspath(results.test_json))
                 log.info(results.info_message())
-                log.info("Total tool test time: {0}".format(dt.datetime.now() - tool_test_start))
+                log.info("Total tool test time: {}".format(dt.datetime.now() - tool_test_start))
             if history_created and not no_history_cleanup:
                 galaxy_interactor.delete_history(test_history)
 
@@ -337,7 +337,7 @@ def main(argv=None):
     client_test_config_path = args.client_test_config
     if client_test_config_path is not None:
         log.debug(f"Reading client config path {client_test_config_path}")
-        with open(client_test_config_path, "r") as f:
+        with open(client_test_config_path) as f:
             client_test_config = yaml.full_load(f)
     else:
         client_test_config = {}
@@ -417,7 +417,7 @@ def setup_global_logger(name, log_file=None, verbose=False):
         log_file = temp.name
     file_handler = logging.FileHandler(log_file)
     logger.addHandler(file_handler)
-    logger.info("Storing log file in: {0}".format(log_file))
+    logger.info(f"Storing log file in: {log_file}")
     return logger
 
 

lib/galaxy/tools/__init__.py

@@ -2494,7 +2494,7 @@ class ExpressionTool(Tool):
                 continue
             if val.output_type == "data":
 
-                with open(out_data[key].file_name, "r") as f:
+                with open(out_data[key].file_name) as f:
                     src = json.load(f)
                 assert isinstance(src, dict), f"Expected dataset 'src' to be a dictionary - actual type is {type(src)}"
                 dataset_id = src["id"]

lib/galaxy/tools/actions/__init__.py

@@ -517,7 +517,7 @@ class DefaultToolAction:
                         completed_job=completed_job,
                         **element_kwds
                     )
-                    log.info("Handled collection output named {} for tool {} {}".format(name, tool.id, handle_output_timer))
+                    log.info(f"Handled collection output named {name} for tool {tool.id} {handle_output_timer}")
                 else:
                     handle_output(name, output)
                     log.info(f"Handled output named {name} for tool {tool.id} {handle_output_timer}")

lib/galaxy/tools/data_fetch.py

@@ -384,7 +384,7 @@ def _has_src_to_path(upload_config, item, is_dataset=False):
         try:
             path = sniff.stream_url_to_file(url, file_sources=get_file_sources(upload_config.working_directory))
         except Exception as e:
-            raise Exception("Failed to fetch url %s. %s" % (url, str(e)))
+            raise Exception("Failed to fetch url {}. {}".format(url, str(e)))
 
         if not is_dataset:
             # Actual target dataset will validate and put results in dict

lib/galaxy/tools/parameters/dynamic_options.py

@@ -165,7 +165,7 @@ class DataMetaFilter(Filter):
             if isinstance(m, list):
                 meta_value |= set(m)
             elif isinstance(m, dict):
-                meta_value |= set(["%s,%s" % (k, v) for k, v in m.items()])
+                meta_value |= {f"{k},{v}" for k, v in m.items()}
             elif isinstance(m, str) and os.path.isfile(m):
                 with open(m) as fh:
                     for line in fh:
@@ -679,7 +679,7 @@ class DynamicOptions:
                 else:
                     # Pass just the first megabyte to parse_file_fields.
                     log.warning("Attempting to load options from large file, reading just first megabyte")
-                    with open(path, 'r') as fh:
+                    with open(path) as fh:
                         contents = fh.read(1048576)
                     options += self.parse_file_fields(StringIO(contents))
         elif self.tool_data_table:

lib/galaxy/tools/toolbox/watcher.py

@@ -90,7 +90,7 @@ class ToolConfWatcher:
     def shutdown(self):
         if self._active:
             self._active = False
-            if self.thread.isAlive():
+            if self.thread.is_alive():
                 self.exit.set()
                 self.thread.join()
             self.thread = None

lib/galaxy/util/checkers.py

@@ -28,7 +28,7 @@ def check_html(name, file_path=True):
     """
     # Handles files if file_path is True or text if file_path is False
     if file_path:
-        temp = open(name, "r", encoding='utf-8')
+        temp = open(name, encoding='utf-8')
     else:
         temp = StringIO(util.unicodify(name))
     try:

lib/galaxy/web/framework/base.py

@@ -20,11 +20,6 @@ from paste.response import HeaderDict
 
 from galaxy.util import smart_str
 
-try:
-    file_types = (file, io.IOBase)
-except NameError:
-    file_types = (io.IOBase, )
-
 log = logging.getLogger(__name__)
 
 #: time of the most recent server startup
@@ -237,7 +232,7 @@ class WebApplication:
             start_response(trans.response.wsgi_status(),
                            trans.response.wsgi_headeritems())
             return body
-        elif isinstance(body, file_types):
+        elif isinstance(body, io.IOBase):
             # Stream the file back to the browser
             return send_file(start_response, trans, body)
         else:
@@ -344,7 +339,7 @@ def _read_lines(self):
     # Adapt `self.__file = None` to Python name mangling of class-private attributes.
     # We need to patch the original FieldStorage class attribute, not the cgi_FieldStorage
     # class.
-    setattr(self, '_FieldStorage__file', None)
+    self._FieldStorage__file = None
     if self.outerboundary:
         self.read_lines_to_outerboundary()
     else:
@@ -464,7 +459,7 @@ class Response:
         """
         result = self.headers.headeritems()
         # Add cookie to header
-        for name, crumb in self.cookies.items():
+        for crumb in self.cookies.values():
             header, value = str(crumb).split(': ', 1)
             result.append((header, value))
         return result

lib/galaxy/webapps/base/webapp.py

@@ -284,7 +284,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                 if key.startswith(acr):
                     self.set_cors_allow(name=key[len(acr):], value=value)
         else:
-            resp_name = 'Access-Control-Allow-{}'.format(name)
+            resp_name = f'Access-Control-Allow-{name}'
             if value is None:
                 value = self.request.headers.get(acr + name, None)
             if value:

packages/app/galaxy/project_galaxy_app.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-app"

packages/auth/galaxy/project_galaxy_auth.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-auth"

packages/data/galaxy/project_galaxy_data.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-data"

packages/job_execution/galaxy/project_galaxy_job_execution.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-job-execution"

packages/job_metrics/galaxy/project_galaxy_job_metrics.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-job-metrics"

packages/objectstore/galaxy/project_galaxy_objectstore.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-objectstore"

packages/selenium/galaxy/project_galaxy_selenium.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-selenium"

packages/test_api/galaxy/project_galaxy_test_api.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-test-api"

packages/test_base/galaxy/project_galaxy_test_base.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-test-base"

packages/test_driver/galaxy/project_galaxy_test_driver.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-test-driver"

packages/test_selenium/galaxy/project_galaxy_test_selenium.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-test-selenium"

packages/tool_util/galaxy/project_galaxy_tool_util.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '21.1.0.dev3'
 
 PROJECT_NAME = "galaxy-tool-util"

packages/util/galaxy/project_galaxy_util.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.2.dev0'
 
 PROJECT_NAME = "galaxy-util"

packages/web_framework/galaxy/project_galaxy_web_framework.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 __version__ = '20.9.1.dev0'
 
 PROJECT_NAME = "galaxy-web-framework"

scripts/release-diff.py

@@ -115,7 +115,7 @@ def load_at_time(path, revision=None):
             ["git", "show", f"{revision}:{path}"], stderr=subprocess.STDOUT
         )
     else:
-        with open(path, "r") as handle:
+        with open(path) as handle:
             return handle.read()
 
 

test/integration/test_kubernetes_staging.py

@@ -15,6 +15,9 @@ import os
 import random
 import string
 import tempfile
+import time
+
+import yaml
 
 from galaxy.jobs.runners.util.pykube_util import (
     Job,
@@ -146,8 +149,8 @@ class KubernetesStagingContainerIntegrationTestCase(CancelsJob, BaseKubernetesSt
 
     @property
     def instance_id(self):
-        import yaml
-        config = yaml.load(open(self.job_config_file))
+        with open(self.job_config_file) as fh:
+            config = yaml.safe_load(fh)
         return config["execution"]["environments"]["pulsar_k8s_environment"]["k8s_galaxy_instance_id"]
 
     @skip_without_tool("cat_data_and_sleep")
@@ -161,7 +164,6 @@ class KubernetesStagingContainerIntegrationTestCase(CancelsJob, BaseKubernetesSt
             delete_response = self.dataset_populator.cancel_job(job_id)
             assert delete_response.json() is True
 
-            import time
             time.sleep(5)
 
             assert self._active_kubernetes_jobs == 0

test/unit/app/tools/test_data_fetch.py

@@ -246,5 +246,5 @@ class ExecuteContext:
     @property
     def galaxy_json(self):
         assert os.path.exists(self.galaxy_json_path)
-        with open(self.galaxy_json_path, "r") as f:
+        with open(self.galaxy_json_path) as f:
             return json.load(f)

test/unit/tool_util/test_verify_script.py

@@ -178,7 +178,7 @@ def test_results():
     results.write()
     message = results.info_message()
 
-    with open(f.name, "r") as f:
+    with open(f.name) as f:
         report_obj = json.load(f)
     assert "tests" in report_obj
     assert len(report_obj["tests"]) == 1
@@ -193,7 +193,7 @@ def test_results():
     results.write()
     message = results.info_message()
 
-    with open(f.name, "r") as f:
+    with open(f.name) as f:
         report_obj = json.load(f)
     assert len(report_obj["tests"]) == 2
     assert report_obj["results"]["skips"] == 1
@@ -245,7 +245,7 @@ def assert_results_not_written(results):
 
 def assert_results_written(results):
     assert os.stat(results.test_json).st_size > 0
-    with open(results.test_json, "r") as f:
+    with open(results.test_json) as f:
         json.load(f)