style: make black, flake8 and isort happy

Smeds · Smeds · commit 408ba7cd4178 · 2025-02-26T16:59:05.000-05:00
diff --git a/planemo/database/postgres_singularity.py b/planemo/database/postgres_singularity.py
@@ -3,21 +3,13 @@
 import os
 import subprocess
 import time
+from tempfile import mkdtemp
 
-from galaxy.tool_util.deps import (
-    singularity_util,
-)
 from galaxy.util.commands import execute
 
+from planemo.io import info
 from .interface import DatabaseSource
-from tempfile import mkdtemp
-from planemo.io import (
-    info,
-)
-from .postgres import (
-    ExecutesPostgresSqlMixin,
-)
-
+from .postgres import ExecutesPostgresSqlMixin
 
 DEFAULT_CONTAINER_NAME = "planemopostgres"
 DEFAULT_POSTGRES_DATABASE_NAME = "galaxy"
@@ -27,43 +19,53 @@
 DEFAULT_DOCKERIMAGE = "postgres:14.2-alpine3.15"
 DEFAULT_SIF_NAME = "postgres_14_2-alpine3_15.sif"
 
-DEFAULT_CONNECTION_STRING = f"postgresql://{DEFAULT_POSTGRES_USER}:{DEFAULT_POSTGRES_PASSWORD}@localhost:{DEFAULT_POSTGRES_PORT_EXPOSE}/{DEFAULT_POSTGRES_DATABASE_NAME}"   
+DEFAULT_CONNECTION_STRING = f"postgresql://{DEFAULT_POSTGRES_USER}:{DEFAULT_POSTGRES_PASSWORD}@localhost:{DEFAULT_POSTGRES_PORT_EXPOSE}/{DEFAULT_POSTGRES_DATABASE_NAME}"
 
 
 def start_postgres_singularity(
-    singularity_path, container_instance_name, database_location, databasename=DEFAULT_POSTGRES_DATABASE_NAME, user=DEFAULT_POSTGRES_USER, password=DEFAULT_POSTGRES_PASSWORD, **kwds
+    singularity_path,
+    container_instance_name,
+    database_location,
+    databasename=DEFAULT_POSTGRES_DATABASE_NAME,
+    user=DEFAULT_POSTGRES_USER,
+    password=DEFAULT_POSTGRES_PASSWORD,
+    **kwds,
 ):
     info(f"Postgres database stored at: {database_location}")
-    pgdata_path = os.path.join(database_location, 'pgdata')
-    pgrun_path = os.path.join(database_location, 'pgrun')
+    pgdata_path = os.path.join(database_location, "pgdata")
+    pgrun_path = os.path.join(database_location, "pgrun")
 
     if not os.path.exists(pgdata_path):
         os.makedirs(pgdata_path)
     if not os.path.exists(pgrun_path):
         os.makedirs(pgrun_path)
 
-    version_file = os.path.join(pgdata_path, 'PG_VERSION')
+    version_file = os.path.join(pgdata_path, "PG_VERSION")
     if not os.path.exists(version_file):
         # Run container for a short while to initialize the database
         # The database will not be initilizaed during a
-        # 'singularity instance start' command
+        # "singularity instance start" command
         init_database_command = [
             singularity_path,
-            'run',
-            '-B', f'{pgdata_path}:/var/lib/postgresql/data',
-            '-B', f'{pgrun_path}:/var/run/postgresql',
-            '-e',
-            '-C',
-            '--env', f'POSTGRES_DB={databasename}',
-            '--env', f'POSTGRES_USER={user}',
-            '--env', f'POSTGRES_PASSWORD={password}',
-            '--env', 'POSTGRES_INITDB_ARGS=\'--encoding=UTF-8\'',
+            "run",
+            "-B",
+            f"{pgdata_path}:/var/lib/postgresql/data",
+            "-B",
+            f"{pgrun_path}:/var/run/postgresql",
+            "-e",
+            "-C",
+            "--env",
+            f"POSTGRES_DB={databasename}",
+            "--env",
+            f"POSTGRES_USER={user}",
+            "--env",
+            f"POSTGRES_PASSWORD={password}",
+            "--env",
+            "POSTGRES_INITDB_ARGS='--encoding=UTF-8'",
             f"docker://{DEFAULT_DOCKERIMAGE}",
         ]
         info(f"Initilizing postgres database in folder: {pgdata_path}")
-        process = subprocess.Popen(init_database_command,
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE)
+        process = subprocess.Popen(init_database_command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         # Give the container time to initialize the database
         for _ in range(10):
             if os.path.exists(version_file):
@@ -80,12 +82,14 @@ def start_postgres_singularity(
     # when starting a instance of the container.
     run_command = [
         singularity_path,
-        'instance',
-        'start',
-        '-B', f'{pgdata_path}:/var/lib/postgresql/data',
-        '-B', f'{pgrun_path}:/var/run/postgresql',
-        '-e',
-        '-C',
+        "instance",
+        "start",
+        "-B",
+        f"{pgdata_path}:/var/lib/postgresql/data",
+        "-B",
+        f"{pgrun_path}:/var/run/postgresql",
+        "-e",
+        "-C",
         f"docker://{DEFAULT_DOCKERIMAGE}",
         container_instance_name,
     ]
@@ -112,20 +116,22 @@ def __init__(self, **kwds):
         self.database_password = DEFAULT_POSTGRES_PASSWORD
         self.database_host = "localhost"  # TODO: Make docker host
         self.database_port = DEFAULT_POSTGRES_PORT_EXPOSE
-        if 'postgres_storage_location' in kwds and kwds['postgres_storage_location'] is not None:
-            self.database_location = kwds['postgres_storage_location']
+        if "postgres_storage_location" in kwds and kwds["postgres_storage_location"] is not None:
+            self.database_location = kwds["postgres_storage_location"]
         else:
-            self.database_location = os.path.join(mkdtemp(suffix='_planemo_postgres_db'))
-        self.container_instance_name = f'{DEFAULT_CONTAINER_NAME}-{int(time.time()*1000000)}'
+            self.database_location = os.path.join(mkdtemp(suffix="_planemo_postgres_db"))
+        self.container_instance_name = f"{DEFAULT_CONTAINER_NAME} - {int(time.time()*1000000)}"
         self._kwds = kwds
 
     def __enter__(self):
-        start_postgres_singularity(singularity_path=self.singularity_path,
-                                   database_location=self.database_location,
-                                   user=self.database_user,
-                                   password=self.database_password,
-                                   container_instance_name=self.container_instance_name,
-                                   **self._kwds)
+        start_postgres_singularity(
+            singularity_path=self.singularity_path,
+            database_location=self.database_location,
+            user=self.database_user,
+            password=self.database_password,
+            container_instance_name=self.container_instance_name,
+            **self._kwds,
+        )
 
     def __exit__(self, exc_type, exc_value, traceback):
         stop_postgress_singularity(self.container_instance_name)
diff --git a/planemo/engine/factory.py b/planemo/engine/factory.py
@@ -26,7 +26,7 @@ def build_engine(ctx, **kwds):
     """Build an engine from the supplied planemo configuration."""
     engine_type_str = kwds.get("engine", "galaxy")
     if engine_type_str == "galaxy":
-        if 'database_type' in kwds and kwds['database_type'] == 'postgres_singularity':
+        if "database_type" in kwds and kwds["database_type"] == "postgres_singularity":
             engine_type = LocalManagedGalaxyEngineWithSingularityDB
         else:
             engine_type = LocalManagedGalaxyEngine
diff --git a/planemo/engine/galaxy.py b/planemo/engine/galaxy.py
@@ -12,6 +12,7 @@
 from galaxy.tool_util.verify import interactor
 
 from planemo import io
+from planemo.database.postgres_singularity import SingularityPostgresDatabaseSource
 from planemo.galaxy.activity import (
     execute,
     execute_rerun,
@@ -26,7 +27,6 @@
     Rerunnable,
     RunnableType,
 )
-from planemo.database.postgres_singularity import SingularityPostgresDatabaseSource
 from .interface import BaseEngine
 
 if TYPE_CHECKING:
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -33,8 +33,8 @@
 
 from planemo import git
 from planemo.config import OptionSource
-from planemo.deps import ensure_dependency_resolvers_conf_configured
 from planemo.database import postgres_singularity
+from planemo.deps import ensure_dependency_resolvers_conf_configured
 from planemo.docker import docker_host_args
 from planemo.galaxy.workflows import (
     get_toolshed_url_for_tool_id,
@@ -1136,7 +1136,7 @@ def default_use_path_paste(self):
 
 
 def _database_connection(database_location, **kwds):
-    if 'database_type' in kwds and kwds['database_type'] == 'postgres_singularity':
+    if "database_type" in kwds and kwds["database_type"] == "postgres_singularity":
         default_connection = postgres_singularity.DEFAULT_CONNECTION_STRING
     else:
         default_connection = DATABASE_LOCATION_TEMPLATE % database_location
