Use context manager for file handling in codebase

[wjbmattingly]

Current Behavior

Many Python files currently uses direct open() which requires manually closing each file.

Proposed Change

Replace direct open() calls with Python's context manager (with statement) to ensure proper file handling and automatic cleanup.

Rationale

1. Performance remains the same
2. with ensures proper file handling and automatically closes the file when done, even if an exception occurs
3. Prevents potential resource leaks from unclosed file handles

Code Changes

# Before
fh = open('nohup.out')
while not finished:
    lines = fh.readlines()
    # ... rest of the while loop ...

# After
with open('nohup.out') as fh:
    while not finished:
        lines = fh.readlines()
        # ... rest of the while loop ...

Implementation Notes

• This is a best practice change that implements the context manager protocol
• No functional changes to the core logic
• Improves resource management and exception handling

Files Affected

1. ./pipeline/storage/cache/filesystem.py
2. ./pipeline/storage/marklogic/ml_lexer.py
3. ./pipeline/storage/idmap/filesystem.py
4. ./pipeline/storage/idmap/redis.py
5. ./pipeline/sources/internal/library/mapper.py
6. ./pipeline/sources/internal/library/loader.py
7. ./pipeline/sources/internal/ipch/loader.py
8. ./pipeline/sources/internal/final/mapper.py
9. ./pipeline/sources/external/ror/loader.py
10. ./pipeline/sources/external/geonames/loader.py
11. ./pipeline/sources/external/viaf/loader.py
12. ./pipeline/sources/external/viaf/index_loader.py
13. ./pipeline/sources/external/lc/mapper.py
14. ./pipeline/sources/external/lc/loader.py
15. ./pipeline/sources/external/dnb/mapper.py
16. ./pipeline/sources/external/dnb/loader.py
17. ./pipeline/sources/external/wikidata/loader.py
18. ./pipeline/sources/external/wikidata/index_loader.py
19. ./pipeline/sources/external/getty/harvester.py
20. ./pipeline/sources/external/getty/fetcher.py
21. ./pipeline/process/validator.py
22. ./pipeline/process/update_manager.py
23. ./pipeline/process/reference_manager.py
24. ./pipeline/process/base/mapper.py
25. ./experiments/test-gemini-results.py
26. ./experiments/gemini-places.py
27. ./scripts/storage/make_test_dataset.py
28. ./scripts/storage/populate-timestamps.py
29. ./scripts/storage/watch-mlcp.py
30. ./scripts/storage/manage-data.py
31. ./scripts/storage/google-sames-diffs.py
32. ./scripts/storage/make-wd-differents.py
33. ./scripts/storage/merge-metatypes.py
34. ./scripts/runs/run-reconcile.py
35. ./scripts/runs/run-merge.py
36. ./scripts/runs/run-export.py

Tasks

• Identify files that need updating
• Update each file in a separate branch
• Use this opportunity to remove unnecessary files
• Test the pipeline to make sure the pipeline continues to run as expected