cool-seq-tool 0.14.4__tar.gz → 0.14.5__tar.gz

cool_seq_tool-0.14.5/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @GenomicMedLab/cool-seq-tool-maintainers

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.4
+Version: 0.14.5
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -2,6 +2,7 @@
 
 import logging
 
+from ga4gh.core.models import Extension
 from ga4gh.vrs.models import SequenceLocation, SequenceReference
 from pydantic import ConfigDict, Field, StrictInt, StrictStr, model_validator
 
@@ -65,9 +66,6 @@ class TxSegment(BaseModelForbidExtra):
     genomic_location: SequenceLocation = Field(
         ..., description="The genomic position of a transcript segment."
     )
-    is_exonic: bool = Field(
-        default=True, description="If the position occurs on an exon"
-    )
 
     @model_validator(mode="before")
     def check_seg_pos(cls, values: dict) -> dict:  # noqa: N805
@@ -99,8 +97,8 @@ class TxSegment(BaseModelForbidExtra):
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                     },
                     "end": 154192135,
+                    "extensions": [{"name": "is_exonic", "value": True}],
                 },
-                "is_exonic": True,
             }
         }
     )
@@ -157,8 +155,8 @@ class GenomicTxSeg(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "end": 154192135,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
                 "errors": [],
             }
@@ -224,8 +222,8 @@ class GenomicTxSegService(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "end": 154192135,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
                 "seg_end": {
                     "exon_ord": 7,
@@ -237,8 +235,8 @@ class GenomicTxSegService(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "start": 154170399,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
             }
         }
@@ -730,7 +728,12 @@ class ExonGenomicCoordsMapper:
         ), None
 
     def _get_vrs_seq_loc(
-        self, genomic_ac: str, genomic_pos: int, is_seg_start: bool, strand: Strand
+        self,
+        genomic_ac: str,
+        genomic_pos: int,
+        is_seg_start: bool,
+        strand: Strand,
+        is_exonic: bool = True,
     ) -> tuple[SequenceLocation | None, str | None]:
         """Create VRS Sequence Location for genomic position where transcript segment
         occurs
@@ -740,6 +743,8 @@ class ExonGenomicCoordsMapper:
         :param is_seg_start: ``True`` if ``genomic_pos`` is where the transcript segment
             starts. ``False`` if ``genomic_pos`` is where the transcript segment ends.
         :param strand: Strand
+        :param is_exonic: A boolean indicating if the genomic breakpoint occurs
+            on an exon. By default, this is set to ``True``.
         :return: Tuple containing VRS location (if successful) and error message (if
             unable to get GA4GH identifier for ``genomic_ac``).
         """
@@ -759,6 +764,7 @@ class ExonGenomicCoordsMapper:
             ),
             start=genomic_pos if use_start else None,
             end=genomic_pos if not use_start else None,
+            extensions=[Extension(name="is_exonic", value=is_exonic)],
         ), None
 
     async def _genomic_to_tx_segment(
@@ -947,7 +953,7 @@ class ExonGenomicCoordsMapper:
         )
 
         genomic_location, err_msg = self._get_vrs_seq_loc(
-            genomic_ac, genomic_pos, is_seg_start, strand
+            genomic_ac, genomic_pos, is_seg_start, strand, is_exonic
         )
         if err_msg:
             return GenomicTxSeg(errors=[err_msg])
@@ -961,7 +967,6 @@ class ExonGenomicCoordsMapper:
                 exon_ord=exon_num,
                 offset=offset,
                 genomic_location=genomic_location,
-                is_exonic=is_exonic,
             ),
         )
 

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/src/cool_seq_tool/resources/status.py

@@ -3,6 +3,7 @@
 import logging
 from collections import namedtuple
 from pathlib import Path
+from urllib.parse import urlparse
 
 from agct._core import ChainfileError
 from asyncpg import InvalidCatalogNameError, UndefinedTableError
@@ -11,7 +12,7 @@ from biocommons.seqrepo import SeqRepo
 from cool_seq_tool.handlers.seqrepo_access import SEQREPO_ROOT_DIR, SeqRepoAccess
 from cool_seq_tool.mappers.liftover import LiftOver
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
-from cool_seq_tool.sources.uta_database import UTA_DB_URL, UtaDatabase
+from cool_seq_tool.sources.uta_database import UTA_DB_URL, ParseResult, UtaDatabase
 
 _logger = logging.getLogger(__name__)
 
@@ -119,14 +120,20 @@ async def check_status(
     else:
         status["liftover"] = True
 
+    parsed_result = ParseResult(urlparse(db_url))
+    sanitized_url = parsed_result.sanitized_url
     try:
         await UtaDatabase.create(db_url)
+    except ValueError:
+        _logger.exception("Database URL is not valid")
     except (OSError, InvalidCatalogNameError, UndefinedTableError):
-        _logger.exception("Encountered error instantiating UTA at URI %s", UTA_DB_URL)
+        _logger.exception(
+            "Encountered error instantiating UTA at URI %s", sanitized_url
+        )
     except Exception as e:
         _logger.critical(
             "Encountered unexpected error instantiating UTA from URI %s: %s",
-            UTA_DB_URL,
+            sanitized_url,
             e,
         )
     else:

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/src/cool_seq_tool/sources/uta_database.py

@@ -5,7 +5,7 @@ import logging
 from os import environ
 from typing import Any, Literal, TypeVar
 from urllib.parse import ParseResult as UrlLibParseResult
-from urllib.parse import quote, unquote, urlparse
+from urllib.parse import unquote, urlparse, urlunparse
 
 import asyncpg
 import boto3
@@ -101,8 +101,7 @@ class UtaDatabase:
         """
         self.schema = None
         self._connection_pool = None
-        original_pwd = db_url.split("//")[-1].split("@")[0].split(":")[-1]
-        self.db_url = db_url.replace(original_pwd, quote(original_pwd))
+        self.db_url = db_url
         self.args = self._get_conn_args()
 
     def _get_conn_args(self) -> DbConnectionArgs:
@@ -954,3 +953,28 @@ class ParseResult(UrlLibParseResult):
         """Create schema property."""
         path_elems = self.path.split("/")
         return path_elems[2] if len(path_elems) > 2 else None
+
+    @property
+    def sanitized_url(self) -> str:
+        """Sanitized DB URL with the password masked"""
+        netloc = ""
+        if self.username:
+            netloc += self.username
+            if self.password is not None and self.password != "":
+                netloc += ":***"
+            netloc += "@"
+        if self.hostname:
+            netloc += f"{self.hostname}"
+        if self.port:
+            netloc += f":{self.port}"
+
+        return urlunparse(
+            (
+                self.scheme,
+                netloc,
+                self.path,
+                self.params,
+                self.query,
+                self.fragment,
+            )
+        )

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.4
+Version: 0.14.5
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/src/cool_seq_tool.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@ CITATION.cff
 LICENSE
 README.md
 pyproject.toml
+.github/CODEOWNERS
 .github/ISSUE_TEMPLATE/bug-report.yaml
 .github/ISSUE_TEMPLATE/feature-request.yaml
 .github/workflows/checks.yaml

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/tests/mappers/test_exon_genomic_coords.py

@@ -183,8 +183,8 @@ def tpm3_exon1():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "end": 154192135,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
-            "is_exonic": True,
         },
     }
     return GenomicTxSeg(**params)
@@ -208,8 +208,8 @@ def tpm3_exon8():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "start": 154170399,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
-            "is_exonic": True,
         },
     }
     return GenomicTxSeg(**params)
@@ -294,8 +294,8 @@ def mane_braf():
                     "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
                 },
                 "end": 140801559,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
-            "is_exonic": True,
         },
         "seg_end": {
             "exon_ord": 14,
@@ -307,8 +307,8 @@ def mane_braf():
                     "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
                 },
                 "start": 140753336,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
-            "is_exonic": True,
         },
     }
     return GenomicTxSegService(**params)
@@ -332,6 +332,7 @@ def wee1_exon2_exon11():
                     "refgetAccession": "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1",
                 },
                 "start": 9576092,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
         "seg_end": {
@@ -344,6 +345,7 @@ def wee1_exon2_exon11():
                     "refgetAccession": "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1",
                 },
                 "end": 9588449,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
     }
@@ -368,6 +370,7 @@ def mane_wee1_exon2_exon11():
                     "refgetAccession": "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1",
                 },
                 "start": 9576092,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
         "seg_end": {
@@ -380,6 +383,7 @@ def mane_wee1_exon2_exon11():
                     "refgetAccession": "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1",
                 },
                 "end": 9588449,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
     }
@@ -404,6 +408,7 @@ def ntrk1_exon10_exon17():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "start": 156874570,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
         "seg_end": {
@@ -416,6 +421,7 @@ def ntrk1_exon10_exon17():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "end": 156881850,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
         },
     }
@@ -441,8 +447,8 @@ def zbtb10_exon3_end():
                     "refgetAccession": "SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs",
                 },
                 "end": 80514010,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -466,8 +472,8 @@ def zbtb10_exon5_start():
                     "refgetAccession": "SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs",
                 },
                 "start": 80518580,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -493,8 +499,8 @@ def tpm3_exon6_end():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "start": 154171410,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -518,8 +524,8 @@ def tpm3_exon5_start():
                     "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 },
                 "end": 154173080,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -545,8 +551,8 @@ def gusbp3_exon2_end():
                     "refgetAccession": "SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI",
                 },
                 "start": 69680764,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -570,8 +576,8 @@ def eln_grch38_intronic():
                     "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
                 },
                 "start": 74028173,
+                "extensions": [{"name": "is_exonic", "value": True}],
             },
-            "is_exonic": True,
         },
         "seg_end": {
             "exon_ord": 7,
@@ -583,8 +589,8 @@ def eln_grch38_intronic():
                     "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
                 },
                 "end": 74043599,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
     }
     return GenomicTxSegService(**params)
@@ -608,8 +614,8 @@ def gusbp3_exon5_start():
                     "refgetAccession": "SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI",
                 },
                 "end": 69645878,
+                "extensions": [{"name": "is_exonic", "value": False}],
             },
-            "is_exonic": False,
         },
         "seg_end": None,
     }
@@ -660,7 +666,10 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
                 assert (
                     actual_seg.genomic_location.end == expected_seg.genomic_location.end
                 )
-                assert actual_seg.is_exonic == expected_seg.is_exonic
+                assert (
+                    actual_seg.genomic_location.extensions
+                    == expected_seg.genomic_location.extensions
+                )
 
         assert actual.errors == expected.errors
     else:
@@ -728,7 +737,10 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
                 actual_seg.genomic_location.start == expected_seg.genomic_location.start
             )
             assert actual_seg.genomic_location.end == expected_seg.genomic_location.end
-            assert actual_seg.is_exonic == expected_seg.is_exonic
+            assert (
+                actual_seg.genomic_location.extensions
+                == expected_seg.genomic_location.extensions
+            )
 
         assert actual.errors == expected.errors
     else:

{cool_seq_tool-0.14.4 → cool_seq_tool-0.14.5}/tests/sources/test_uta_database.py

@@ -1,11 +1,14 @@
 """Test UTA data source."""
 
+from urllib.parse import urlparse
+
 import pytest
 
 from cool_seq_tool.schemas import Strand
 from cool_seq_tool.sources.uta_database import (
     GenomicTxData,
     GenomicTxMetadata,
+    ParseResult,
     TxExonAlnData,
 )
 
@@ -360,3 +363,98 @@ async def test_get_mane_transcripts_from_genomic_pos(test_db):
     # invalid ac
     resp = await test_db.get_transcripts_from_genomic_pos("NC_000007.14232", 140753336)
     assert resp == []
+
+
+@pytest.mark.parametrize(
+    ("raw_url", "expected"),
+    [
+        # Username + password
+        (
+            "postgresql://user:pass@localhost:5432/dbname",
+            {
+                "scheme": "postgresql",
+                "username": "user",
+                "password": "pass",
+                "hostname": "localhost",
+                "port": 5432,
+                "database": "dbname",
+                "sanitized_url": "postgresql://user:***@localhost:5432/dbname",
+            },
+        ),
+        # Username with null password
+        (
+            "postgresql://user@localhost/dbname",
+            {
+                "scheme": "postgresql",
+                "username": "user",
+                "password": None,
+                "hostname": "localhost",
+                "port": None,
+                "database": "dbname",
+                "sanitized_url": "postgresql://user@localhost/dbname",
+            },
+        ),
+        # Password is "0"
+        (
+            "postgresql://user:0@localhost/dbname",
+            {
+                "scheme": "postgresql",
+                "username": "user",
+                "password": "0",
+                "hostname": "localhost",
+                "port": None,
+                "database": "dbname",
+                "sanitized_url": "postgresql://user:***@localhost/dbname",
+            },
+        ),
+        # Empty password
+        (
+            "postgresql://user:@localhost/dbname",
+            {
+                "scheme": "postgresql",
+                "username": "user",
+                "password": "",
+                "hostname": "localhost",
+                "port": None,
+                "database": "dbname",
+                "sanitized_url": "postgresql://user@localhost/dbname",
+            },
+        ),
+        # No username
+        (
+            "postgresql://localhost:5432/dbname",
+            {
+                "scheme": "postgresql",
+                "username": None,
+                "password": None,
+                "hostname": "localhost",
+                "port": 5432,
+                "database": "dbname",
+                "sanitized_url": "postgresql://localhost:5432/dbname",
+            },
+        ),
+        # With query params
+        (
+            "postgresql://user:secret@localhost/dbname?query#fragment",
+            {
+                "scheme": "postgresql",
+                "username": "user",
+                "password": "secret",
+                "hostname": "localhost",
+                "port": None,
+                "database": "dbname",
+                "sanitized_url": "postgresql://user:***@localhost/dbname?query#fragment",
+            },
+        ),
+    ],
+)
+async def test_parsed_url(raw_url, expected):
+    parsed_result = ParseResult(urlparse(raw_url))
+
+    assert parsed_result.scheme == expected["scheme"]
+    assert parsed_result.username == expected["username"]
+    assert parsed_result.password == expected["password"]
+    assert parsed_result.hostname == expected["hostname"]
+    assert parsed_result.port == expected["port"]
+    assert parsed_result.database == expected["database"]
+    assert parsed_result.sanitized_url == expected["sanitized_url"]