lint

interactive_tests.py

@@ -219,6 +219,7 @@
 
 
 from refget import fasta_file_to_seqcol
+
 fasta_file_to_seqcol("demo_fasta/demo0.fa")
 fasta_file_to_seqcol("/home/nsheff/sandbox/HG002.alt.pat.f1_v2.unmasked.fa.gz")
 
@@ -235,28 +236,33 @@
 sha512t24u_digest_bytes("test")
 
 
-var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
+var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
 
 import random
 import timeit
 import string
+
 strs = []
 for i in range(1000):
-    strs.append(''.join(random.choices(string.ascii_uppercase + string.digits, k=1000)))
+    strs.append("".join(random.choices(string.ascii_uppercase + string.digits, k=1000)))
+
 
 # Define the functions to benchmark
 def benchmark_sha512t24u_digest():
     for var in strs:
         sha512t24u_digest(var)
 
+
 def benchmark_gc_count_checksum():
     for var in strs:
         gc_count.checksum_from_str(var).sha512
 
+
 def benchmark_gc_sha512_only():
     for var in strs:
         gc_count.sha512t24u_digest(var)
 
+
 # Benchmark the functions
 time_sha512t24u_digest = timeit.timeit(benchmark_sha512t24u_digest, number=1000)
 time_gc_count_checksum = timeit.timeit(benchmark_gc_count_checksum, number=1000)
@@ -265,4 +271,3 @@ def benchmark_gc_sha512_only():
 print(f"sha512t24u_digest: {time_sha512t24u_digest} seconds")
 print(f"gc_count.checksum_from_str().sha512: {time_gc_count_checksum} seconds")
 print(f"gc_count.sha512t24u_digest: {time_gc_512_only} seconds")
-

refget/agents.py

@@ -59,7 +59,7 @@ def load_json(source):
     :return: The loaded JSON as a dictionary.
     """
     if os.path.isfile(source):
-        with open(source, 'r', encoding='utf-8') as file:
+        with open(source, "r", encoding="utf-8") as file:
             return json.load(file)
     else:
         try:
@@ -71,22 +71,25 @@ def load_json(source):
             raise e
 
 
-
 class SeqColAgent(object):
     def __init__(self, engine, inherent_attrs=None):
         self.engine = engine
         self.inherent_attrs = inherent_attrs
 
-    def get(self, digest: str, return_format: str = "level2", attribute: str = None, itemwise_limit: int = None) -> SequenceCollection:
+    def get(
+        self,
+        digest: str,
+        return_format: str = "level2",
+        attribute: str = None,
+        itemwise_limit: int = None,
+    ) -> SequenceCollection:
         with Session(self.engine) as session:
-            statement = select(SequenceCollection).where(
-                SequenceCollection.digest == digest
-            )
+            statement = select(SequenceCollection).where(SequenceCollection.digest == digest)
             results = session.exec(statement)
             seqcol = results.one_or_none()
             if not seqcol:
                 raise ValueError(f"SequenceCollection with digest '{digest}' not found")
-            if attribute:  
+            if attribute:
                 return getattr(seqcol, attribute).value
             elif return_format == "level2":
                 return seqcol.level2()
@@ -176,7 +179,10 @@ def list_by_offset(self, limit=50, offset=0):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"pagination": { "page": int(offset/limit), "page_size": limit, "total": count}, "results": seqcols}
+            return {
+                "pagination": {"page": int(offset / limit), "page_size": limit, "total": count},
+                "results": seqcols,
+            }
 
     def list(self, page_size=100, cursor=None):
         with Session(self.engine) as session:
@@ -189,9 +195,7 @@ def list(self, page_size=100, cursor=None):
                 )
             else:
                 list_stmt = (
-                    select(SequenceCollection)
-                    .limit(page_size)
-                    .order_by(SequenceCollection.digest)
+                    select(SequenceCollection).limit(page_size).order_by(SequenceCollection.digest)
                 )
             cnt_stmt = select(func.count(SequenceCollection.digest))
             cnt_res = session.exec(cnt_stmt)
@@ -270,9 +274,7 @@ def add_from_fasta_pep(self, pep: peppy.Project, fa_root):
         for s in pep.samples:
             file_path = os.path.join(fa_root, s.fasta)
             print(f"Fasta to be loaded: Name: {s.sample_name} File path: {file_path}")
-            pangenome_obj[s.sample_name] = self.parent.seqcol.add_from_fasta_file(
-                file_path
-            )
+            pangenome_obj[s.sample_name] = self.parent.seqcol.add_from_fasta_file(file_path)
 
         p = build_pangenome_model(pangenome_obj)
         return self.add(p)
@@ -285,7 +287,11 @@ def list_by_offset(self, limit=50, offset=0):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"pagination": { "page": int(offset/limit), "page_size": limit, "total": count}, "results": seqcols}
+            return {
+                "pagination": {"page": int(offset / limit), "page_size": limit, "total": count},
+                "results": seqcols,
+            }
+
 
 class AttributeAgent(object):
     def __init__(self, engine):
@@ -312,16 +318,17 @@ def list(self, attribute_type, offset=0, limit=50):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
+            return {
+                "pagination": {"page": offset * limit, "page_size": limit, "total": count},
+                "results": seqcols,
+            }
 
     def search(self, attribute_type, digest, offset=0, limit=50):
         Attribute = ATTR_TYPE_MAP[attribute_type]
         with Session(self.engine) as session:
             list_stmt = (
                 select(SequenceCollection)
-                .where(
-                    getattr(SequenceCollection, f"{attribute_type}_digest") == digest
-                )
+                .where(getattr(SequenceCollection, f"{attribute_type}_digest") == digest)
                 .offset(offset)
                 .limit(limit)
             )
@@ -332,7 +339,10 @@ def search(self, attribute_type, digest, offset=0, limit=50):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
+            return {
+                "pagination": {"page": offset * limit, "page_size": limit, "total": count},
+                "results": seqcols,
+            }
 
 
 class RefgetDBAgent(object):
@@ -341,7 +351,6 @@ class RefgetDBAgent(object):
     """
 
     def __init__(
-<<<<<<< HEAD
         self,
         engine: Optional[SqlalchemyDatabaseEngine] = None,
         postgres_str: Optional[str] = None,
@@ -358,7 +367,7 @@ def __init__(
                 POSTGRES_DB = os.getenv("POSTGRES_DB")
                 POSTGRES_USER = os.getenv("POSTGRES_USER")
                 POSTGRES_PASSWORD = os.getenv("POSTGRES_PASSWORD")
-                schema=f'{SCHEMA_FILEPATH}/seqcol.json',
+                schema = (f"{SCHEMA_FILEPATH}/seqcol.json",)
                 postgres_str = URL.create(
                     "postgresql",
                     username=POSTGRES_USER,
@@ -392,7 +401,9 @@ def __init__(
                 self.inherent_attrs = self.schema_dict["ga4gh"]["inherent"]
             except KeyError:
                 self.inherent_attrs = inherent_attrs
-                _LOGGER.warning(f"No 'inherent' attributes found in schema; using defaults: {inherent_attrs}")
+                _LOGGER.warning(
+                    f"No 'inherent' attributes found in schema; using defaults: {inherent_attrs}"
+                )
         else:
             _LOGGER.warning("No schema provided; using defaults")
             self.schema_dict = None
@@ -449,6 +460,6 @@ def truncate(self):
             result = session.exec(statement)
             statement = delete(SortedSequencesAttr)
             result = session.exec(statement)
-            
+
             session.commit()
             return result1.rowcount

refget/clients.py

@@ -3,10 +3,12 @@
 
 _LOGGER = logging.getLogger(__name__)
 
+
 class SequencesClient(object):
     """
     A client for interacting with a refget sequences API.
     """
+
     def __init__(self, seq_urls=["https://www.ebi.ac.uk/ena/cram/sequence/"]):
         self.seq_urls = seq_urls
 
@@ -84,17 +86,17 @@ def list_collections(self, page=None, page_size=None, attribute=None, attribute_
         """
         params = {}
         if page is not None:
-            params['page'] = page
+            params["page"] = page
         if page_size is not None:
-            params['page_size'] = page_size
+            params["page_size"] = page_size
 
         if attribute and attribute_digest:
             endpoint = f"/list/collections/{attribute}/{attribute_digest}"
         else:
             endpoint = "/list/collections"
 
         return _try_urls(self.seqcol_api_urls, endpoint, params=params)
-    
+
     def list_attributes(self, attribute, page=None, page_size=None):
         """
         Lists all available values for a given attribute with optional paging support.
@@ -103,40 +105,43 @@ def list_attributes(self, attribute, page=None, page_size=None):
             attribute (str): The attribute to list values for.
             page (int, optional): The page number to retrieve. Defaults to None.
             page_size (int, optional): The number of items per page. Defaults to None.
-            
+
         Returns:
             dict: The JSON response containing the list of available values for the attribute.
         """
         params = {}
         if page is not None:
-            params['page'] = page
+            params["page"] = page
         if page_size is not None:
-            params['page_size'] = page_size
+            params["page_size"] = page_size
 
         endpoint = f"/list/attributes/{attribute}"
         return _try_urls(self.seqcol_api_urls, endpoint, params=params)
 
 
 class RefGetClient(SequencesClient, SeqColClient):
     """
-    A client for interacting with a refget API, for either 
+    A client for interacting with a refget API, for either
     sequences or sequence collections, or both.
     """
 
-    def __init__(self,
-                 seq_api_urls=["https://www.ebi.ac.uk/ena/cram/sequence"],
-                 seqcol_api_urls=["https://seqcolapi.databio.org"]):
+    def __init__(
+        self,
+        seq_api_urls=["https://www.ebi.ac.uk/ena/cram/sequence"],
+        seqcol_api_urls=["https://seqcolapi.databio.org"],
+    ):
         if seq_api_urls:
             SequencesClient.__init__(self, seq_api_urls)
         if seqcol_api_urls:
             SeqColClient.__init__(self, seqcol_api_urls)
 
     def __repr__(self):
         return f"<RefGetClient(seq_api_urls={self.seq_api_urls}, seqcol_api_urls={self.seqcol_api_urls})>"
-    
+
 
 # Utilities
 
+
 def _wrap_response(response):
     """
     Wraps a response in a try/except block to catch any exceptions.
@@ -152,7 +157,8 @@ def _wrap_response(response):
         return response.json()
     except requests.exceptions.RequestException as e:
         raise RuntimeError(f"An error occurred: {e}")
-
+
+
 def _try_urls(urls, endpoint, params=None):
     """
     Tries the list of URLs in succession until a successful response is received.
@@ -173,8 +179,12 @@ def _try_urls(urls, endpoint, params=None):
             result = _wrap_response(response)
             _LOGGER.info(f"Successful response from {base_url}")
             return result
-        except (requests.exceptions.ConnectionError, requests.exceptions.Timeout, requests.exceptions.RequestException) as e:
+        except (
+            requests.exceptions.ConnectionError,
+            requests.exceptions.Timeout,
+            requests.exceptions.RequestException,
+        ) as e:
             _LOGGER.debug(f"Error from {base_url}: {e}")
             errors.append(f"Error from {base_url}: {e}")
     error_message = "All URLs failed:\n" + "\n".join(errors)
-    raise ConnectionError(error_message)
+    raise ConnectionError(error_message)

refget/const.py

@@ -57,6 +57,7 @@ def _schema_path(name):
 GTARS_INSTALLED = False
 try:
     from gtars.digests import digest_fasta, sha512t24u_digest
+
     GTARS_INSTALLED = True
 except ImportError:
     GTARS_INSTALLED = False

refget/hash_functions.py

@@ -7,6 +7,7 @@
 import binascii
 from typing import Union
 
+
 def trunc512_digest(seq, offset=24):
     digest = hashlib.sha512(seq.encode("utf-8")).digest()
     hex_digest = binascii.hexlify(digest[:offset])
@@ -39,15 +40,13 @@ def trunc512_to_ga4gh(trunc512):
     return _ga4gh_format(digest, digest_length)
 
 
-
 # def trunc512_digest(seq, offset=24) -> str:
 #     """Deprecated GA4GH digest function"""
 #     digest = hashlib.sha512(seq.encode()).digest()
 #     hex_digest = binascii.hexlify(digest[:offset])
 #     return hex_digest.decode()
 
 
-
 # def sha512t24u_digest_bytes(seq: Union[str, bytes], offset: int = 24) -> str:
 #     """GA4GH digest function"""
 #     if isinstance(seq, str):
@@ -56,6 +55,7 @@ def trunc512_to_ga4gh(trunc512):
 #     tdigest_b64us = base64.urlsafe_b64encode(digest[:offset])
 #     return tdigest_b64us.decode("ascii")
 
+
 def py_sha512t24u_digest(seq: Union[str, bytes], offset: int = 24) -> str:
     """GA4GH digest function in python"""
     if isinstance(seq, str):
@@ -64,16 +64,20 @@ def py_sha512t24u_digest(seq: Union[str, bytes], offset: int = 24) -> str:
     tdigest_b64us = base64.urlsafe_b64encode(digest[:offset])
     return tdigest_b64us.decode("ascii")
 
+
 def md5(seq):
     return hashlib.md5(seq.encode()).hexdigest()
 
+
 from .const import GTARS_INSTALLED
 
 if GTARS_INSTALLED:
     from gtars.digests import sha512t24u_digest as gtars_sha512t24u_digest
+
     sha512t24u_digest = gtars_sha512t24u_digest
 else:
+
     def gtars_sha512t24u_digest(seq):
         raise Exception("gtars is not installed")
-    
+
     sha512t24u_digest = py_sha512t24u_digest