test: add unit tests for dataset 26 harmonizer

[cmungall]

Adds tests/test_harmonize_dataset26.py with 18 synthetic-data tests exercising every transformation in dataset_26.harmonize(): datetime parsing, site_id rename, depth midpoint, VWC unit conversion, location lookup, and non-numeric coercion.

Closes #19

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[claude]

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PR Review

• Read CLAUDE.md and repository context
• Read the test file (tests/test_harmonize_dataset26.py)
• Read the dataset_26 harmonizer (data/gold/expert_code/harmonize_sm/dataset_26.py)
• Analyze code quality and provide feedback

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Overall this is a well-structured test file with good coverage of the harmonizer's transformations. Here is detailed feedback:

Strengths

• Good use of @needs_pkg skip decorator to gracefully handle environments without the expert harmonizer package.
• _make_ctx, _make_payload, and _make_loc are clean helpers that keep individual tests concise.
• pytest.approx is used correctly for floating-point comparisons (depth_m, vwc, lat/lon).
• Non-numeric coercion tests (lines 283–305) are valuable edge-case coverage.

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Issues and Suggestions

1. sys.path.insert repeated in every test (lines 75, 87, 106, …)

Every single test repeats:

sys.path.insert(0, str(HARMONIZE_SM.resolve()))

This mutates global state and can accumulate duplicate entries with repeated test runs. Move it to a module-level conftest.py fixture or use a session-scoped autouse fixture. Alternatively, call it once at module import time after the needs_pkg guard check.

# At module level, after the @needs_pkg definition:
if HARMONIZE_SM.exists():
    sys.path.insert(0, str(HARMONIZE_SM.resolve()))

2. Repeated imports inside each test function

Each test re-imports from dataset_26 import harmonize and sometimes from common import DatasetResult. Python caches modules after the first import so this isn't a correctness issue, but it's verbose and unusual. Prefer importing at module level (guarded by if HARMONIZE_SM.exists()) or use a @pytest.fixture.

3. _make_ctx uses positional map_json indices, not idx (line 36)

In _make_ctx, read_ds_csv dispatches on i == idx (26) and i == ref_idx (0). But dataset_26.py accesses map_json[idx] directly at line 33:

f26 = as_list(map_json[idx]["data_payload_files"])[0]

map_json in the mock is a 2-element list (mapping[0] and mapping[1]), so map_json[26] will raise an IndexError at runtime. The mock will never reach this if the harmonizer uses ctx.dsid(26) for the identifier but uses map_json[26] for file paths.

This is a latent bug — the tests may pass only if harmonize() doesn't call as_list(map_json[idx][...]) in the path exercised by the mock. Looking at dataset_26.py line 33–34:

f26 = as_list(map_json[idx]["data_payload_files"])[0]
m26 = as_list(map_json[REF_IDX]["location_metadata_files"])[0]

These will index map_json[26] and map_json[0], crashing immediately. The synthetic mapping list in _make_ctx only has 2 entries (index 0 and 1). The tests would fail at this point unless read_ds_csv is called with idx=26 and ref_idx=0 — which it is — but the map_json[26] access would still be IndexError.

Recommendation: Either extend mapping to have 27 entries (with dummies for 1–25), or refactor _make_ctx so map_json is a dict keyed by index:

mapping = {ref_idx: {...}, idx: {...}}

This requires a small change in how harmonize() accesses map_json, or you could patch at a different level.

4. test_harmonize_datetime_correct_value comment is misleading (line 129)

The docstring says "01/15/21 in America/Denver (UTC-7 in January) -> 2021-01-15 07:00 UTC" but the test only asserts on year, month, day — not the hour. Either assert the hour (assert first_dt.hour == 7) or remove the specific UTC time from the comment so it doesn't create a false expectation.

5. test_harmonize_locations_non_empty asserts len(result.locations) == 1 (line 238)

This is a reasonable structural check, but the comment just says "non_empty". Consider renaming to test_harmonize_locations_has_one_frame for clarity.

6. set(["site_id", "latitude", "longitude"]) idiom (line 241)

Minor style: prefer the literal set syntax:

{"site_id", "latitude", "longitude"}.issubset(loc_df.columns)

7. No test for source_dataset_id in result.harmonized

dataset_26.py does not add source_dataset_id to the harmonized DataFrame (only to loc26), so this isn't missing functionality — but if the schema were to change, there's no guard. Low priority.

8. Missing test for add_loc_qc side-effect

dataset_26.py calls add_loc_qc(loc26) which adds a qc_flag column. There's no assertion that qc_flag exists in result.locations[0]. Consider:

assert "qc_flag" in result.locations[0].columns

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Summary

The most important issue is #3 (potential IndexError on map_json[26]). If the tests currently pass in CI, it's worth verifying whether harmonize() in fact hits that line or whether there's a different code path in effect. Issues #1 and #2 are code hygiene concerns worth addressing. Issues #4–#8 are minor refinements.