reformatted with black and isort

Author: reece

src/seqrepo_rest_service/__main__.py

@@ -1,3 +1,4 @@
 if __name__ == "__main__":
     from .cli import main
+
     main()

src/seqrepo_rest_service/cli.py

@@ -9,15 +9,13 @@
 import pathlib
 import time
 
-from biocommons.seqrepo import SeqRepo
 import coloredlogs
 import connexion
+from biocommons.seqrepo import SeqRepo
 from flask import Flask, redirect
 
 from . import __version__
 
-
-
 WAIT_POLL_PERIOD = 15  # seconds between polling for SEQREPO PATH
 
 

src/seqrepo_rest_service/refget/routes/metadata.py

@@ -3,8 +3,8 @@
 from connexion import NoContent, request
 
 from ...threadglobals import get_seqrepo
-from ...utils import get_sequence_id, base64url_to_hex, problem, valid_content_types
-
+from ...utils import (base64url_to_hex, get_sequence_id, problem,
+                      valid_content_types)
 
 _logger = logging.getLogger(__name__)
 
@@ -14,7 +14,7 @@ def get(id):
     if accept_header and accept_header not in valid_content_types:
         _logger.warn(f"{accept_header} not valid")
         return problem(406, "Invalid Accept header")
-    
+
     sr = get_seqrepo()
     seq_id = get_sequence_id(sr, id)
     if not seq_id:
@@ -30,10 +30,7 @@ def get(id):
         "md5": md5_id,
         "trunc512": base64url_to_hex(seq_id),
         "length": seqinfo["len"],
-        "aliases": [
-            {"naming_authority": a["namespace"], "alias": a["alias"]}
-            for a in aliases
-            ]
-        }
+        "aliases": [{"naming_authority": a["namespace"], "alias": a["alias"]} for a in aliases],
+    }
 
     return {"metadata": md}, 200

src/seqrepo_rest_service/refget/routes/sequence.py

@@ -6,7 +6,6 @@
 from ...threadglobals import get_seqrepo
 from ...utils import get_sequence_id, problem, valid_content_types
 
-
 _logger = logging.getLogger(__name__)
 
 range_re = re.compile("^bytes=(\d+)-(\d+)$")
@@ -16,7 +15,7 @@ def get(id, start=None, end=None):
     accept_header = request.headers.get("Accept", None)
     if accept_header and accept_header not in valid_content_types:
         return problem(406, "Invalid Accept header")
-    
+
     range_header = request.headers.get("Range", None)
     if range_header:
         _logger.debug(f"Received header `Range: {range_header}`")
@@ -29,13 +28,13 @@ def get(id, start=None, end=None):
         _logger.debug(f"Parsed `{range_header}` as ({start}, {end})")
         if start > end:
             return problem(416, f"Range queries may specify start > end")
-        
+
     sr = get_seqrepo()
     seq_id = get_sequence_id(sr, id)
     if not seq_id:
         return NoContent, 404
     seqinfo = sr.sequences.fetch_seqinfo(seq_id)
-   
+
     if start is not None and end is not None:
         if start >= seqinfo["len"]:
             return problem(416, "Invalid coordinates: start > sequence length")
@@ -45,11 +44,12 @@ def get(id, start=None, end=None):
         if start > end:
             return problem(501, "Invalid coordinates: start > end")
         if not (0 <= start <= end <= seqinfo["len"]) and not range_header:
-            return problem(416, "Invalid coordinates: must obey 0 <= start <= end <= sequence_length")
+            return problem(
+                416, "Invalid coordinates: must obey 0 <= start <= end <= sequence_length"
+            )
 
     try:
         status = 206 if ((start or end) and range_header) else 200
         return sr.sequences.fetch(seq_id, start, end), status
     except KeyError:
         return NoContent, 404
-    

src/seqrepo_rest_service/refget/routes/serviceInfo.py

@@ -1,27 +1,25 @@
-from ... import __version__
-
-from ...threadglobals import get_seqrepo
-
-import biocommons.seqrepo 
+import biocommons.seqrepo
 import bioutils
 
+from ... import __version__
+from ...threadglobals import get_seqrepo
 
 
 def get():
     sr = get_seqrepo()
-    
+
     return {
         "service": {
             "algorithms": ["md5", "trunc512"],
-            "circular_supported" : False,
+            "circular_supported": False,
             "subsequence_limit": None,
             "supported_api_versions": ["1.0"],
         },
         "x-config": {
             "seqrepo-rest-service": {
                 "version": __version__,
                 "url": "https://github.com/biocommons/seqrepo-rest-service/",
-                },
+            },
             "seqrepo": {
                 "version": biocommons.seqrepo.__version__,
                 "root": sr._root_dir,
@@ -31,5 +29,5 @@ def get():
                 "version": bioutils.__version__,
                 "url": "https://github.com/biocommons/bioutils/",
             },
-        }
+        },
     }

src/seqrepo_rest_service/seqrepo/routes/metadata.py

@@ -5,7 +5,6 @@
 from ...threadglobals import get_seqrepo
 from ...utils import get_sequence_ids, problem
 
-
 _logger = logging.getLogger(__name__)
 
 
@@ -27,6 +26,6 @@ def get(alias):
         "aliases": [f"{a['namespace']}:{a['alias']}" for a in aliases],
         "alphabet": seqinfo["alpha"],
         "length": seqinfo["len"],
-        }
+    }
 
     return md, 200

src/seqrepo_rest_service/seqrepo/routes/ping.py

@@ -1,14 +1,13 @@
-from ...threadglobals import get_seqrepo
-
-import biocommons.seqrepo 
+import biocommons.seqrepo
 import bioutils
-
 from pkg_resources import get_distribution
 
+from ...threadglobals import get_seqrepo
+
 
 def get():
     sr = get_seqrepo()
-    
+
     return {
         "version": get_distribution("seqrepo-rest-service").version,
         "url": "https://github.com/biocommons/seqrepo-rest-service/",
@@ -22,5 +21,5 @@ def get():
                 "version": bioutils.__version__,
                 "url": "https://github.com/biocommons/bioutils/",
             },
-        }
+        },
     }

src/seqrepo_rest_service/seqrepo/routes/sequence.py

@@ -6,7 +6,6 @@
 from ...threadglobals import get_seqrepo
 from ...utils import get_sequence_ids, problem
 
-
 _logger = logging.getLogger(__name__)
 
 

src/seqrepo_rest_service/threadglobals.py

@@ -14,13 +14,11 @@
 def get_seqrepo():
     seqrepo_dir = current_app.config["seqrepo_dir"]
     _logger.info(f"Opening {seqrepo_dir=}")
-    return _get_or_create(
-        "seqrepo",
-        lambda: SeqRepo(root_dir=seqrepo_dir))
+    return _get_or_create("seqrepo", lambda: SeqRepo(root_dir=seqrepo_dir))
 
 
 def _get_or_create(k, f):
-    k = '_' + k
+    k = "_" + k
     o = getattr(g, k, None)
     if o is None:
         o = f()

src/seqrepo_rest_service/utils.py

@@ -1,14 +1,12 @@
+import logging
+import re
 from base64 import urlsafe_b64decode, urlsafe_b64encode
 from binascii import hexlify, unhexlify
 from http.client import responses as http_responses
-import logging
-import re
 
 import connexion
-
 from bioutils.accessions import infer_namespaces
 
-
 _logger = logging.getLogger(__name__)
 
 
@@ -19,35 +17,37 @@
     "application/json",
     "text/plain",
     "*/*",
-    ]
+]
 
 
 def hex_to_base64url(s):
     return urlsafe_b64encode(unhexlify(s)).decode("ascii")
 
+
 def base64url_to_hex(s):
     return hexlify(urlsafe_b64decode(s)).decode("ascii")
 
+
 def get_sequence_id(sr, query):
     """determine sequence_ids after guessing form of query
 
     The query may be:
       * A fully-qualified sequence alias (e.g., VMC:0123 or refseq:NM_01234.5)
       * A digest or digest prefix from VMC, TRUNC512, or MD5
       * A sequence accession (without namespace)
- 
+
     Returns None if not found; seq_id if only one match; raises
-    RuntimeError for ambiguous matches. 
+    RuntimeError for ambiguous matches.
 
     """
-    
+
     seq_ids = get_sequence_ids(sr, query)
     if len(seq_ids) == 0:
         _logger.warning(f"No sequence found for {query}")
         return None
     if len(seq_ids) > 1:
         raise RuntimeError(f"Multiple distinct sequences found for {query}")
-    return seq_ids.pop()        # exactly 1 id found
+    return seq_ids.pop()  # exactly 1 id found
 
 
 def get_sequence_ids(sr, query):
@@ -57,7 +57,7 @@ def get_sequence_ids(sr, query):
       * A fully-qualified sequence alias (e.g., VMC:0123 or refseq:NM_01234.5)
       * A digest or digest prefix from VMC, TRUNC512, or MD5
       * A sequence accession (without namespace)
- 
+
     The first match will be returned.
     """
 
@@ -74,10 +74,10 @@ def problem(status, message):
     return connexion.problem(status=status, title=http_responses[status], detail=message)
 
 
-
 ############################################################################
 # INTERNAL
 
+
 def _generate_nsa_options(query):
     """
     >>> _generate_nsa_options("NM_000551.3")
@@ -103,7 +103,7 @@ def _generate_nsa_options(query):
     if namespaces:
         nsa_options = [(ns, query) for ns in namespaces]
         return nsa_options
-    
+
     # if hex, try md5 and TRUNC512
     if re.match(r"^(?:[0-9A-Fa-f]{8,})$", query):
         nsa_options = [("MD5", query + "%")]