ruff

codebuild/deploy_eb_env.py

@@ -1,50 +1,37 @@
 """Module for deploying MetaKB EB environment."""
+
 import boto3
 import time
-elasticbeanstalk = boto3.client('elasticbeanstalk')
-servicecatalog = boto3.client('servicecatalog')
+
+elasticbeanstalk = boto3.client("elasticbeanstalk")
+servicecatalog = boto3.client("servicecatalog")
 terminate_time = 12
 eb_app_name = "Seqrepo"
 eb_env_name = "Seqrepo-staging-env"
 sc_product_id = "prod-qg2twc66t544g"
-print(f'Launching new Service Catalog Product for staging environment: '
-      f'{eb_app_name}')
-sc_product_artifacts =\
-    servicecatalog.list_provisioning_artifacts(ProductId=sc_product_id)
-for artifact in sc_product_artifacts['ProvisioningArtifactDetails']:
-    if artifact['Active']:
-        provisioning_artifact_id = artifact['Id']
+print(f"Launching new Service Catalog Product for staging environment: " f"{eb_app_name}")
+sc_product_artifacts = servicecatalog.list_provisioning_artifacts(ProductId=sc_product_id)
+for artifact in sc_product_artifacts["ProvisioningArtifactDetails"]:
+    if artifact["Active"]:
+        provisioning_artifact_id = artifact["Id"]
 try:
     eb_provisioned_product = servicecatalog.provision_product(
         ProductId=sc_product_id,
         ProvisioningArtifactId=provisioning_artifact_id,
         ProvisionedProductName=eb_env_name,
         ProvisioningParameters=[
-            {
-                'Key': 'Env',
-                'Value': eb_app_name
-            },
-            {
-                'Key': 'EnvType',
-                'Value': 'staging'
-            },
-            {
-                'Key': 'TerminateTime',
-                'Value': str(terminate_time)
-            }
-        ])
-    eb_provisioned_product_Id = \
-        eb_provisioned_product['RecordDetail']['ProvisionedProductId']
-    product_status = servicecatalog.describe_provisioned_product(
-        Id=eb_provisioned_product_Id)
-    eb_provisioned_product_status =\
-        product_status['ProvisionedProductDetail']['Status']
+            {"Key": "Env", "Value": eb_app_name},
+            {"Key": "EnvType", "Value": "staging"},
+            {"Key": "TerminateTime", "Value": str(terminate_time)},
+        ],
+    )
+    eb_provisioned_product_Id = eb_provisioned_product["RecordDetail"]["ProvisionedProductId"]
+    product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+    eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
     while eb_provisioned_product_status == "UNDER_CHANGE":
         time.sleep(10)
-        product_status = servicecatalog.describe_provisioned_product(
-            Id=eb_provisioned_product_Id)
-        eb_provisioned_product_status = \
-            product_status['ProvisionedProductDetail']['Status']
+        product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
         print(eb_provisioned_product_status)
 except Exception as e:
-    print(str(e))
+    print(str(e))

codebuild/deploy_eb_env_dev.py

@@ -1,50 +1,37 @@
 """Module for deploying MetaKB EB environment."""
+
 import boto3
 import time
-elasticbeanstalk = boto3.client('elasticbeanstalk')
-servicecatalog = boto3.client('servicecatalog')
+
+elasticbeanstalk = boto3.client("elasticbeanstalk")
+servicecatalog = boto3.client("servicecatalog")
 terminate_time = 12
 eb_app_name = "Seqrepo"
 eb_env_name = "Seqrepo-dev-env"
 sc_product_id = "prod-qg2twc66t544g"
-print(f'Launching new Service Catalog Product for staging environment: '
-      f'{eb_app_name}')
-sc_product_artifacts =\
-    servicecatalog.list_provisioning_artifacts(ProductId=sc_product_id)
-for artifact in sc_product_artifacts['ProvisioningArtifactDetails']:
-    if artifact['Active']:
-        provisioning_artifact_id = artifact['Id']
+print(f"Launching new Service Catalog Product for staging environment: " f"{eb_app_name}")
+sc_product_artifacts = servicecatalog.list_provisioning_artifacts(ProductId=sc_product_id)
+for artifact in sc_product_artifacts["ProvisioningArtifactDetails"]:
+    if artifact["Active"]:
+        provisioning_artifact_id = artifact["Id"]
 try:
     eb_provisioned_product = servicecatalog.provision_product(
         ProductId=sc_product_id,
         ProvisioningArtifactId=provisioning_artifact_id,
         ProvisionedProductName=eb_env_name,
         ProvisioningParameters=[
-            {
-                'Key': 'Env',
-                'Value': eb_app_name
-            },
-            {
-                'Key': 'EnvType',
-                'Value': 'dev'
-            },
-            {
-                'Key': 'TerminateTime',
-                'Value': str(terminate_time)
-            }
-        ])
-    eb_provisioned_product_Id = \
-        eb_provisioned_product['RecordDetail']['ProvisionedProductId']
-    product_status = servicecatalog.describe_provisioned_product(
-        Id=eb_provisioned_product_Id)
-    eb_provisioned_product_status =\
-        product_status['ProvisionedProductDetail']['Status']
+            {"Key": "Env", "Value": eb_app_name},
+            {"Key": "EnvType", "Value": "dev"},
+            {"Key": "TerminateTime", "Value": str(terminate_time)},
+        ],
+    )
+    eb_provisioned_product_Id = eb_provisioned_product["RecordDetail"]["ProvisionedProductId"]
+    product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+    eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
     while eb_provisioned_product_status == "UNDER_CHANGE":
         time.sleep(10)
-        product_status = servicecatalog.describe_provisioned_product(
-            Id=eb_provisioned_product_Id)
-        eb_provisioned_product_status = \
-            product_status['ProvisionedProductDetail']['Status']
+        product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
         print(eb_provisioned_product_status)
 except Exception as e:
     print(str(e))

codebuild/terminate_eb_env.py

@@ -1,29 +1,24 @@
 """Module for terminating MetaKB EB environment."""
+
 import boto3
 import json
 import time
-client = boto3.client('lambda')
-servicecatalog = boto3.client('servicecatalog')
+
+client = boto3.client("lambda")
+servicecatalog = boto3.client("servicecatalog")
 eb_env_name = "Seqrepo-staging-env"
 data = {"sc_provisioned_name": eb_env_name}
-client.invoke(FunctionName='igm-inf-terminate-provisioned-product',
-              Payload=json.dumps(data))
+client.invoke(FunctionName="igm-inf-terminate-provisioned-product", Payload=json.dumps(data))
 time.sleep(10)
-provisioned_product =\
-    servicecatalog.describe_provisioned_product(Name=eb_env_name)
-eb_provisioned_product_Id = \
-    provisioned_product['ProvisionedProductDetail']['Id']
-product_status = servicecatalog.describe_provisioned_product(
-    Id=eb_provisioned_product_Id)
-eb_provisioned_product_status = \
-    product_status['ProvisionedProductDetail']['Status']
+provisioned_product = servicecatalog.describe_provisioned_product(Name=eb_env_name)
+eb_provisioned_product_Id = provisioned_product["ProvisionedProductDetail"]["Id"]
+product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
 while eb_provisioned_product_status == "UNDER_CHANGE":
     time.sleep(10)
     try:
-        product_status = servicecatalog.describe_provisioned_product(
-            Id=eb_provisioned_product_Id)
-        eb_provisioned_product_status = \
-            product_status['ProvisionedProductDetail']['Status']
+        product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
     except:  # noqa: E722
         eb_provisioned_product_status = "PRODUCT NOT FOUND"
-    print(eb_provisioned_product_status)
+    print(eb_provisioned_product_status)

codebuild/terminate_eb_env_dev.py

@@ -1,29 +1,24 @@
 """Module for terminating MetaKB EB environment."""
+
 import boto3
 import json
 import time
-client = boto3.client('lambda')
-servicecatalog = boto3.client('servicecatalog')
+
+client = boto3.client("lambda")
+servicecatalog = boto3.client("servicecatalog")
 eb_env_name = "Seqrepo-dev-env"
 data = {"sc_provisioned_name": eb_env_name}
-client.invoke(FunctionName='igm-inf-terminate-provisioned-product',
-              Payload=json.dumps(data))
+client.invoke(FunctionName="igm-inf-terminate-provisioned-product", Payload=json.dumps(data))
 time.sleep(10)
-provisioned_product =\
-    servicecatalog.describe_provisioned_product(Name=eb_env_name)
-eb_provisioned_product_Id = \
-    provisioned_product['ProvisionedProductDetail']['Id']
-product_status = servicecatalog.describe_provisioned_product(
-    Id=eb_provisioned_product_Id)
-eb_provisioned_product_status = \
-    product_status['ProvisionedProductDetail']['Status']
+provisioned_product = servicecatalog.describe_provisioned_product(Name=eb_env_name)
+eb_provisioned_product_Id = provisioned_product["ProvisionedProductDetail"]["Id"]
+product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
 while eb_provisioned_product_status == "UNDER_CHANGE":
     time.sleep(10)
     try:
-        product_status = servicecatalog.describe_provisioned_product(
-            Id=eb_provisioned_product_Id)
-        eb_provisioned_product_status = \
-            product_status['ProvisionedProductDetail']['Status']
+        product_status = servicecatalog.describe_provisioned_product(Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = product_status["ProvisionedProductDetail"]["Status"]
     except:  # noqa: E722
         eb_provisioned_product_status = "PRODUCT NOT FOUND"
-    print(eb_provisioned_product_status)
+    print(eb_provisioned_product_status)

misc/load-test.py

@@ -33,7 +33,6 @@
 continuously but rather stabilize at a relatively low level on the order of tens of files.
 """
 
-
 import argparse
 import pathlib
 import random
@@ -56,12 +55,8 @@ def log(log_queue: multiprocessing.Queue, line: str):
 
 
 def lsof_count(dirname: str) -> int:
-    lsof_cmd = [
-        "bash", "-c",
-        f"lsof +D {dirname} | wc -l"]
-    lsof_p = subprocess.Popen(
-        lsof_cmd,
-        stdout=subprocess.PIPE)
+    lsof_cmd = ["bash", "-c", f"lsof +D {dirname} | wc -l"]
+    lsof_p = subprocess.Popen(lsof_cmd, stdout=subprocess.PIPE)
     (stdout, _) = lsof_p.communicate()
     stdout = stdout.decode("utf-8").strip()
     return int(stdout)
@@ -106,7 +101,8 @@ def run(self):
                     print(f"{self}: Done; processed {self.n} accessions", flush=True)
                     break
                 self.seqrepo_dataproxy.get_sequence(
-                    ac, self.query_bound_start, self.query_bound_end)
+                    ac, self.query_bound_start, self.query_bound_end
+                )
                 self.n += 1
             except queue.Empty:
                 pass
@@ -151,8 +147,13 @@ def stop(self):
 def parse_args(argv):
     ap = argparse.ArgumentParser(description=__doc__)
     ap.add_argument("-n", "--num-workers", type=int, default=1)
-    ap.add_argument("-s", "--seqrepo-path", type=pathlib.Path, required=True,
-                    help="Local SeqRepo instance to get input values from, and to monitor open file count in")
+    ap.add_argument(
+        "-s",
+        "--seqrepo-path",
+        type=pathlib.Path,
+        required=True,
+        help="Local SeqRepo instance to get input values from, and to monitor open file count in",
+    )
     ap.add_argument("-u", "--seqrepo-rest-uri", type=str, default="http://localhost:5000/seqrepo")
     ap.add_argument("-m", "--max-accessions", type=int, required=True)
     ap.add_argument("-f", "--fd-cache-size", type=int, default=0)
@@ -175,7 +176,8 @@ def main(argv):
     # log_worker.start()
 
     t_filler = multiprocessing.Process(
-        target=queue_filler_target, args=(input_queue, acs, opts.num_workers))
+        target=queue_filler_target, args=(input_queue, acs, opts.num_workers)
+    )
     t_filler.start()
 
     workers = []
@@ -213,5 +215,6 @@ def main(argv):
 
 if __name__ == "__main__":
     import coloredlogs
+
     coloredlogs.install(level="INFO")
     main(argv=sys.argv[1:])

src/seqrepo_rest_service/cli.py

@@ -10,9 +10,7 @@
 import coloredlogs
 import connexion
 from biocommons.seqrepo import SeqRepo
-from flask import Flask, redirect
-
-from . import __version__
+from flask import redirect
 
 WAIT_POLL_PERIOD = 15  # seconds between polling for SEQREPO PATH
 

src/seqrepo_rest_service/refget/routes/metadata.py

@@ -3,7 +3,12 @@
 from connexion import NoContent, request
 
 from seqrepo_rest_service.threadglobals import get_seqrepo
-from seqrepo_rest_service.utils import get_sequence_id, base64url_to_hex, problem, valid_content_types
+from seqrepo_rest_service.utils import (
+    get_sequence_id,
+    base64url_to_hex,
+    problem,
+    valid_content_types,
+)
 
 
 _logger = logging.getLogger(__name__)

src/seqrepo_rest_service/refget/routes/sequence.py

@@ -27,7 +27,7 @@ def get(id, start=None, end=None):
         start, end = int(m.group(1)), int(m.group(2)) + 1
         _logger.debug(f"Parsed `{range_header}` as ({start}, {end})")
         if start > end:
-            return problem(416, f"Range queries may specify start > end")
+            return problem(416, "Range queries may specify start > end")
 
     sr = get_seqrepo()
     seq_id = get_sequence_id(sr, id)

src/seqrepo_rest_service/refget/routes/serviceInfo.py

@@ -4,9 +4,6 @@
 import biocommons.seqrepo
 import bioutils
 
-from ... import __version__
-from ...threadglobals import get_seqrepo
-
 
 def get():
     sr = get_seqrepo()