Narrow Overly Broad Exception Handlers

[kunal-10-cloud]

Problem Statement

The codebase contains four locations that catch the overly broad except Exception clause. This anti-pattern masks real bugs by silently swallowing unexpected errors, making debugging significantly more difficult.

Affected Locations:

File	Line	Context	Current Behavior
malariagen_data/anoph/base.py	137	Filesystem initialization	Catches all exceptions from _init_filesystem()
malariagen_data/anoph/base.py	146	Config file loading	Catches all exceptions from json.load()
malariagen_data/anoph/sample_metadata.py	1867	Pandas query evaluation	Catches all exceptions from data.eval()
malariagen_data/anoph/map_params.py	45	Basemap provider initialization	Catches all exceptions from provider functions

Impact

Debuggability Issues

When unexpected errors occur:

• Real bugs are silently caught and re-raised generically, losing critical stack trace context
• Hours spent debugging because the true root cause is masked
• Difficult to distinguish between expected and unexpected failures

Example Scenario

If a typo or logic error occurs inside _init_filesystem() (e.g., a NameError or AttributeError):

• Current behavior: silently caught, wrapped in generic IOError
• Correct behavior: should propagate, revealing the actual bug

Current Anti-Pattern

try:
    self._fs, self._base_path = _init_filesystem(self._url, **storage_options)
except Exception as exc:  # ← Catches EVERYTHING
    raise IOError(...) from exc

Solution Approach

Replace each bare except Exception with a specific tuple of exception types that the wrapped code is actually designed to raise.

Expected Exceptions by Location:

1. base.py:137 → (OSError, ImportError)

   • OSError: filesystem/connection/auth failures
   • ImportError: missing auth modules

2. base.py:146 → (OSError, json.JSONDecodeError)

   • OSError: file read failures
   • JSONDecodeError: malformed JSON in config

3. sample_metadata.py:1867 → (KeyError, NameError, SyntaxError, TypeError, AttributeError)

   • All expected errors from pandas DataFrame.eval()

4. map_params.py:45 → (ImportError, ModuleNotFoundError, AttributeError)

   • Import failures and missing provider attributes

Benefits

• Prevents Silent Failures — Unexpected errors bubble up immediately with full context
• Improves Debuggability — Stack traces show real root causes, not generic wrappers
• Explicit Intent — Exception types clearly document what errors are expected at each location
• Zero Behavior Change — Expected errors handled identically, only unintended exceptions propagate
• Minimal Code Diff — 4 lines changed, no logic alterations

[kunal-10-cloud]

Hi @jonbrenas i have made a PR(#1226) for this issue, please review it once whenever you are available and let me know if any changes are required