From 321cb85283dc0a182e86d0ee509cae9ced4e39cd Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Aug 2024 14:20:17 -0500
Subject: Rename module: Module contains exceptions classes.

---
 r_qtl/errors.py                 | 13 -------------
 r_qtl/exceptions.py             | 13 +++++++++++++
 r_qtl/r_qtl2.py                 |  6 +++---
 r_qtl/r_qtl2_qc.py              |  6 +++---
 scripts/process_rqtl2_bundle.py |  2 +-
 scripts/qc_on_rqtl2_bundle.py   |  4 ++--
 6 files changed, 22 insertions(+), 22 deletions(-)
 delete mode 100644 r_qtl/errors.py
 create mode 100644 r_qtl/exceptions.py

diff --git a/r_qtl/errors.py b/r_qtl/errors.py
deleted file mode 100644
index 417eb58..0000000
--- a/r_qtl/errors.py
+++ /dev/null
@@ -1,13 +0,0 @@
-"""R/qtl and R/qtl2 error types."""
-
-class RQTLError(Exception):
-    """Base class for R/qtl and R/qtl2 errors."""
-
-class InvalidFormat(RQTLError):
-    """Raised when the format of the file(s) is invalid."""
-
-class MissingFileError(InvalidFormat):
-    """
-    Raise when at least one file listed in the control file is missing from the
-    R/qtl2 bundle.
-    """
diff --git a/r_qtl/exceptions.py b/r_qtl/exceptions.py
new file mode 100644
index 0000000..9620cf4
--- /dev/null
+++ b/r_qtl/exceptions.py
@@ -0,0 +1,13 @@
+"""R/qtl and R/qtl2 error types."""
+
+class RQTLError(Exception):
+    """Base class for R/qtl and R/qtl2 errors."""
+
+class InvalidFormat(RQTLError):
+    """Raised when the format of the file(s) is invalid."""
+
+class MissingFileException(InvalidFormat):
+    """
+    Raise when at least one file listed in the control file is missing from the
+    R/qtl2 bundle.
+    """
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index c2e1148..c6282c5 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -11,7 +11,7 @@ import yaml
 
 from functional_tools import take, chain
 
-from r_qtl.errors import InvalidFormat, MissingFileError
+from r_qtl.exceptions import InvalidFormat, MissingFileException
 
 FILE_TYPES = (
     "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap",
@@ -157,7 +157,7 @@ def control_data(control_src: Union[Path, ZipFile]) -> dict:
 
     Raises
     ------
-    r_qtl.errors.InvalidFormat
+    r_qtl.exceptions.InvalidFormat
     """
     if isinstance(control_src, ZipFile):
         return __control_data_from_zipfile__(control_src)
@@ -382,7 +382,7 @@ def file_data(zfile: ZipFile,
                 zfile, member_key, cdata, process_transposed_value):
             yield row
     except KeyError as exc:
-        raise MissingFileError(*exc.args) from exc
+        raise MissingFileException(*exc.args) from exc
 
 def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
     """Load cross information where present."""
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index be1eac4..7e93d23 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -3,8 +3,8 @@ from zipfile import ZipFile
 from functools import reduce, partial
 from typing import Union, Iterator, Optional, Callable
 
-from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
+from r_qtl import exceptions as rqe
 from r_qtl.r_qtl2 import FILE_TYPES
 from r_qtl.fileerrors import MissingFile
 
@@ -59,7 +59,7 @@ def validate_bundle(zfile: ZipFile):
     """Ensure the R/qtl2 bundle is valid."""
     missing = missing_files(zfile)
     if len(missing) > 0:
-        raise rqe.MissingFileError(
+        raise rqe.MissingFileException(
                         "The following files do not exist in the bundle: " +
                         ", ".join(mfile[1] for mfile in missing))
 
@@ -111,6 +111,6 @@ def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) ->
                 if value is not None:
                     for checker in checkers:
                         yield checker(lineno=lineno, field=field, value=value)
-    except rqe.MissingFileError:
+    except rqe.MissingFileException:
         fname = cdata.get(filetype)
         yield MissingFile(filetype, fname, f"Missing '{filetype}' file '{fname}'.")
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py
index a7e169d..20cfd3b 100644
--- a/scripts/process_rqtl2_bundle.py
+++ b/scripts/process_rqtl2_bundle.py
@@ -13,9 +13,9 @@ from redis import Redis
 
 from functional_tools import take
 
-import r_qtl.errors as rqe
 import r_qtl.r_qtl2 as rqtl2
 import r_qtl.r_qtl2_qc as rqc
+import r_qtl.exceptions as rqe
 
 from uploader import jobs
 from uploader.db_utils import database_connection
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 7784c06..fc95d13 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -20,9 +20,9 @@ from uploader import jobs
 from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 
-from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
+from r_qtl import exceptions as rqe
 from r_qtl import fileerrors as rqfe
 
 from scripts.process_rqtl2_bundle import parse_job
@@ -105,7 +105,7 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals
                         __update_processed__(value)
 
         rconn.hset(fqjobid, f"{filetype}-linecount", count)
-    except rqe.MissingFileError:
+    except rqe.MissingFileException:
         fname = cdata.get(filetype)
         yield rqfe.MissingFile(filetype, fname, (
             f"The file '{fname}' does not exist in the bundle despite it being "
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