Running black, and flake8, fixing flake8 errors

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+per-file-ignores =    tests/test_app.py:F841

.github/workflows/precommit.yaml

@@ -17,4 +17,4 @@ repos:
     rev: 6.1.0
     hooks:
       - id: flake8
-        args: [ --config, pyproject.toml ]
+        args: [ --config, .flake8 ]

.pre-commit-config.yaml

@@ -7,22 +7,37 @@ repos:
       - id: end-of-file-fixer
         files: '\.py$'
       - id: check-yaml
-        # Keep this unchanged for YAML files
       - id: check-added-large-files
         files: '\.py$'
 
   - repo: https://github.com/psf/black
     rev: 24.3.0
     hooks:
       - id: black
-        language_version: python3.12
+        language_version: python3.9
         files: '\.py$'
+        args:
+          - --line-length=120
+          - --exclude=staging_service/auth2Client.py
+          - --exclude=import_specifications/clients/baseclient\.py
 
   - repo: https://github.com/pycqa/flake8
     rev: 7.0.0
     hooks:
       - id: flake8
         args:
-          - --config=server/pyproject.toml
-          - --ignore=E203  # Ignore E203 directly in the pre-commit configuration
+          - --ignore=E203,W503
+          - --max-line-length=120
+          - --config=.flake8
         files: '\.py$'
+        additional_dependencies: [ flake8 ]
+
+
+#  - repo: https://github.com/astral-sh/ruff-pre-commit
+#    # Ruff version.
+#    rev: v0.4.1
+#    hooks:
+#      # Run the linter.
+#      - id: ruff
+#      # Run the formatter.
+#      - id: ruff-format

import_specifications/clients/authclient.py

@@ -5,6 +5,7 @@
 
 @author: [email protected]
 """
+
 import hashlib
 import threading as _threading
 import time as _time

import_specifications/clients/baseclient.py

@@ -54,7 +54,7 @@ def _get_token(user_id, password, auth_svc):
 
 
 def _read_inifile(
-    file=_os.environ.get("KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config")
+    file=_os.environ.get("KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config"),
 ):  # @ReservedAssignment
     # Another bandaid to read in the ~/.kbase_config file if one is present
     authdata = None
@@ -65,7 +65,14 @@ def _read_inifile(
             # strip down whatever we read to only what is legit
             authdata = {
                 x: config.get("authentication", x) if config.has_option("authentication", x) else None
-                for x in ("user_id", "token", "client_secret", "keyfile", "keyfile_passphrase", "password")
+                for x in (
+                    "user_id",
+                    "token",
+                    "client_secret",
+                    "keyfile",
+                    "keyfile_passphrase",
+                    "password",
+                )
             }
         except Exception as e:
             print("Error while reading INI file {}: {}".format(file, e))
@@ -165,15 +172,24 @@ def __init__(
             raise ValueError("Timeout value must be at least 1 second")
 
     def _call(self, url, method, params, context=None):
-        arg_hash = {"method": method, "params": params, "version": "1.1", "id": str(_random.random())[2:]}
+        arg_hash = {
+            "method": method,
+            "params": params,
+            "version": "1.1",
+            "id": str(_random.random())[2:],
+        }
         if context:
             if type(context) is not dict:
                 raise ValueError("context is not type dict as required.")
             arg_hash["context"] = context
 
         body = _json.dumps(arg_hash, cls=_JSONObjectEncoder)
         ret = _requests.post(
-            url, data=body, headers=self._headers, timeout=self.timeout, verify=not self.trust_all_ssl_certificates
+            url,
+            data=body,
+            headers=self._headers,
+            timeout=self.timeout,
+            verify=not self.trust_all_ssl_certificates,
         )
         ret.encoding = "utf-8"
         if ret.status_code == 500:
@@ -201,7 +217,9 @@ def _get_service_url(self, service_method, service_version):
             return self.url
         service, _ = service_method.split(".")
         service_status_ret = self._call(
-            self.url, "ServiceWizard.get_service_status", [{"module_name": service, "version": service_version}]
+            self.url,
+            "ServiceWizard.get_service_status",
+            [{"module_name": service, "version": service_version}],
         )
         return service_status_ret["url"]
 

import_specifications/clients/narrative_method_store_client.py

@@ -192,7 +192,10 @@ def list_methods_full_info(self, params, context=None):
            String, parameter "link" of type "url"
         """
         return self._client.call_method(
-            "NarrativeMethodStore.list_methods_full_info", [params], self._service_ver, context
+            "NarrativeMethodStore.list_methods_full_info",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def list_methods_spec(self, params, context=None):
@@ -541,7 +544,12 @@ def list_methods_spec(self, params, context=None):
            "target_property" of String, parameter "target_type_transform" of
            String, parameter "job_id_output_field" of String
         """
-        return self._client.call_method("NarrativeMethodStore.list_methods_spec", [params], self._service_ver, context)
+        return self._client.call_method(
+            "NarrativeMethodStore.list_methods_spec",
+            [params],
+            self._service_ver,
+            context,
+        )
 
     def list_method_ids_and_names(self, params, context=None):
         """
@@ -551,7 +559,10 @@ def list_method_ids_and_names(self, params, context=None):
         :returns: instance of mapping from String to String
         """
         return self._client.call_method(
-            "NarrativeMethodStore.list_method_ids_and_names", [params], self._service_ver, context
+            "NarrativeMethodStore.list_method_ids_and_names",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def list_apps(self, params, context=None):
@@ -598,7 +609,10 @@ def list_apps_full_info(self, params, context=None):
            parameter "url" of type "url"
         """
         return self._client.call_method(
-            "NarrativeMethodStore.list_apps_full_info", [params], self._service_ver, context
+            "NarrativeMethodStore.list_apps_full_info",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def list_apps_spec(self, params, context=None):
@@ -643,7 +657,12 @@ def list_app_ids_and_names(self, context=None):
         """
         :returns: instance of mapping from String to String
         """
-        return self._client.call_method("NarrativeMethodStore.list_app_ids_and_names", [], self._service_ver, context)
+        return self._client.call_method(
+            "NarrativeMethodStore.list_app_ids_and_names",
+            [],
+            self._service_ver,
+            context,
+        )
 
     def list_types(self, params, context=None):
         """
@@ -692,7 +711,10 @@ def get_method_brief_info(self, params, context=None):
            parameter "app_type" of String
         """
         return self._client.call_method(
-            "NarrativeMethodStore.get_method_brief_info", [params], self._service_ver, context
+            "NarrativeMethodStore.get_method_brief_info",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def get_method_full_info(self, params, context=None):
@@ -731,7 +753,10 @@ def get_method_full_info(self, params, context=None):
            String, parameter "link" of type "url"
         """
         return self._client.call_method(
-            "NarrativeMethodStore.get_method_full_info", [params], self._service_ver, context
+            "NarrativeMethodStore.get_method_full_info",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def get_method_spec(self, params, context=None):
@@ -1091,7 +1116,12 @@ def get_app_brief_info(self, params, context=None):
            parameter "categories" of list of String, parameter
            "loading_error" of String
         """
-        return self._client.call_method("NarrativeMethodStore.get_app_brief_info", [params], self._service_ver, context)
+        return self._client.call_method(
+            "NarrativeMethodStore.get_app_brief_info",
+            [params],
+            self._service_ver,
+            context,
+        )
 
     def get_app_full_info(self, params, context=None):
         """
@@ -1112,7 +1142,12 @@ def get_app_full_info(self, params, context=None):
            parameter "screenshots" of list of type "ScreenShot" -> structure:
            parameter "url" of type "url"
         """
-        return self._client.call_method("NarrativeMethodStore.get_app_full_info", [params], self._service_ver, context)
+        return self._client.call_method(
+            "NarrativeMethodStore.get_app_full_info",
+            [params],
+            self._service_ver,
+            context,
+        )
 
     def get_app_spec(self, params, context=None):
         """
@@ -2463,7 +2498,10 @@ def load_widget_java_script(self, params, context=None):
         :returns: instance of String
         """
         return self._client.call_method(
-            "NarrativeMethodStore.load_widget_java_script", [params], self._service_ver, context
+            "NarrativeMethodStore.load_widget_java_script",
+            [params],
+            self._service_ver,
+            context,
         )
 
     def register_repo(self, params, context=None):
@@ -2495,4 +2533,9 @@ def push_repo_to_tag(self, params, context=None):
            two values: 'beta' or 'release'.) -> structure: parameter
            "module_name" of String, parameter "tag" of String
         """
-        return self._client.call_method("NarrativeMethodStore.push_repo_to_tag", [params], self._service_ver, context)
+        return self._client.call_method(
+            "NarrativeMethodStore.push_repo_to_tag",
+            [params],
+            self._service_ver,
+            context,
+        )

import_specifications/generate_import_template.py

@@ -34,21 +34,30 @@
 def parse_args():
     parser = argparse.ArgumentParser(description="Generate a bulk import template for an app")
     parser.add_argument(
-        "app_id", help="The app ID to process, for example kb_uploadmethods/import_sra_as_reads_from_staging"
+        "app_id",
+        help="The app ID to process, for example kb_uploadmethods/import_sra_as_reads_from_staging",
     )
     parser.add_argument(
         "data_type",
-        help="The datatype corresponding to the the app. This id is shared between the "
-        + "staging service and the narrative, for example sra_reads",
+        help="The datatype corresponding to the the app."
+        + "This id is shared between the staging service and the narrative, for example sra_reads",
+    )
+    parser.add_argument(
+        "--tsv",
+        action="store_true",
+        help="Create a TSV file rather than a CSV file (the default)",
     )
-    parser.add_argument("--tsv", action="store_true", help="Create a TSV file rather than a CSV file (the default)")
     parser.add_argument(
         "--env",
         choices=["prod", "appdev", "next", "ci"],
         default="prod",
         help="The KBase environment to query, default prod",
     )
-    parser.add_argument("--print-spec", action="store_true", help="Print the input specification for the app to stderr")
+    parser.add_argument(
+        "--print-spec",
+        action="store_true",
+        help="Print the input specification for the app to stderr",
+    )
     return parser.parse_args()
 
 

scripts/prune_acls.py

@@ -3,6 +3,7 @@
 """
 Deletes ACLS from globus, and then clears out directories older than THRESHOLD (60) days
 """
+
 from __future__ import print_function  # for python 2
 
 import configparser
@@ -20,7 +21,10 @@
 current_time = time.time()
 THRESHOLD_DAYS = 60
 
-admin_acls = ["9cb619d0-4417-11e8-8e06-0a6d4e044368", "580118b2-dc53-11e6-9d02-22000a1e3b52"]
+admin_acls = [
+    "9cb619d0-4417-11e8-8e06-0a6d4e044368",
+    "580118b2-dc53-11e6-9d02-22000a1e3b52",
+]
 admin_names = ["dolsonadmin", "dolson"]
 
 config = configparser.ConfigParser()

staging_service/AutoDetectUtils.py

@@ -2,14 +2,17 @@
 This class is in charge of determining possible importers by determining the suffix of the filepath pulled in,
 and by looking up the appropriate mappings in the supported_apps_w_extensions.json file
 """
+
 from typing import Optional, Tuple, Dict
 
 
 class AutoDetectUtils:
     _MAPPINGS = None  # expects to be set by config
 
     @staticmethod
-    def determine_possible_importers(filename: str) -> Tuple[Optional[list], Dict[str, object]]:
+    def determine_possible_importers(
+        filename: str,
+    ) -> Tuple[Optional[list], Dict[str, object]]:
         """
         Given a filename, come up with a reference to all possible apps.
         :param filename: The filename to find applicable apps for

staging_service/app.py

@@ -168,11 +168,13 @@ async def write_bulk_specification(request: web.Request) -> web.json_response:
     if request.content_type != _APP_JSON:
         # There should be a way to get aiohttp to handle this but I can't find it
         return _createJSONErrorResponse(
-            f"Required content-type is {_APP_JSON}", error_class=web.HTTPUnsupportedMediaType
+            f"Required content-type is {_APP_JSON}",
+            error_class=web.HTTPUnsupportedMediaType,
         )
     if not request.content_length:
         return _createJSONErrorResponse(
-            "The content-length header is required and must be > 0", error_class=web.HTTPLengthRequired
+            "The content-length header is required and must be > 0",
+            error_class=web.HTTPLengthRequired,
         )
     # No need to check the max content length; the server already does that. See tests
     data = await request.json()
@@ -208,9 +210,9 @@ async def add_acl_concierge(request: web.Request):
     aclm = AclManager()
     result = aclm.add_acl_concierge(shared_directory=user_dir, concierge_path=concierge_path)
     result["msg"] = f"Requesting Globus Perms for the following globus dir: {concierge_path}"
-    result[
-        "link"
-    ] = f"https://app.globus.org/file-manager?destination_id={aclm.endpoint_id}&destination_path={concierge_path}"
+    result["link"] = (
+        f"https://app.globus.org/file-manager?destination_id={aclm.endpoint_id}&destination_path={concierge_path}"
+    )
     return web.json_response(result)
 
 

staging_service/auth2Client.py

@@ -4,6 +4,7 @@
 @author: [email protected]
 modified for python3 and authV2
 """
+
 import hashlib
 import time as _time