First commit for event index

[justin13601]

For #37

Summary by CodeRabbit

• New Features

  • Introduced event indexing with a new _EVENT_INDEX column in various aggregation and predicate functions.
  • Enhanced extraction and processing of subtree data with event indexing.

• Improvements

  • Enhanced data consistency by including event index columns in summary outputs.

• Tests

  • Updated end-to-end tests to include new _LAST_EVENT_INDEX fields.

[coderabbitai]

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Walkthrough

Recent updates across multiple files primarily focus on integrating an _EVENT_INDEX column for enhanced event indexing throughout various functions. These changes include adjustments in import statements, data processing logic, and output summaries to accommodate this new column. This integration enables sophisticated event tracking and processing capabilities in the aggregate.py, extract_subtree.py, predicates.py, and types.py files while ensuring that tests are updated accordingly.

Changes

Files/Groups	Change Summary
src/aces/aggregate.py, src/aces/extract_subtree.py, src/aces/predicates.py, src/aces/types.py	Added _EVENT_INDEX handling in various functions, including import adjustments and data processing logic to enhance event tracking. Defined new constants in types.py.
tests/test_e2e.py	Updated test cases to include _LAST_EVENT_INDEX fields with specific values.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant AggregateFunction as aggregate.py
    participant ExtractSubtreeFunction as extract_subtree.py
    participant PredicateFunction as predicates.py

    User->>AggregateFunction: Call aggregate_temporal_window(data)
    AggregateFunction->>AggregateFunction: Process data, use and drop _EVENT_INDEX
    User->>ExtractSubtreeFunction: Call extract_subtree(data)
    ExtractSubtreeFunction->>ExtractSubtreeFunction: Process data with _EVENT_INDEX
    User->>PredicateFunction: Call get_predicates_df()
    PredicateFunction->>PredicateFunction: Create and return dataframe with _EVENT_INDEX

Loading

Poem

In the land of data bright,
_EVENT_INDEX takes its flight,
Through code it weaves, a path so clear,
Enhancing logic, far and near.
With columns added, tests anew,
A stronger structure now in view.
🚀✨

---

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[coderabbitai]

Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between e068b97 and 2a8a66b.

Files selected for processing (5)

• src/aces/aggregate.py (27 hunks)
• src/aces/extract_subtree.py (5 hunks)
• src/aces/predicates.py (4 hunks)
• src/aces/types.py (1 hunks)
• tests/test_e2e.py (8 hunks)

Additional context used

Ruff

tests/test_e2e.py

7-7: Module level import not at top of file (E402)

---

8-8: Module level import not at top of file (E402)

---

9-9: Module level import not at top of file (E402)

---

11-11: Module level import not at top of file (E402)

---

12-12: Module level import not at top of file (E402)

---

13-13: Module level import not at top of file (E402)

src/aces/types.py

305-308: Use ternary operator end_event = self.end_event[1:] if mode == "bound_to_row" else self.end_event instead of if-else-block (SIM108)

Replace if-else-block with end_event = self.end_event[1:] if mode == "bound_to_row" else self.end_event

src/aces/aggregate.py

874-877: Use ternary operator right_inclusive = False if closed in ("left", "both") else True instead of if-else-block (SIM108)

Replace if-else-block with right_inclusive = False if closed in ("left", "both") else True

---

880-883: Use ternary operator right_inclusive = True if closed in ("right", "both") else False instead of if-else-block (SIM108)

Replace if-else-block with right_inclusive = True if closed in ("right", "both") else False

---

888-891: Use ternary operator left_inclusive = True if closed in ("left", "both") else False instead of if-else-block (SIM108)

Replace if-else-block with left_inclusive = True if closed in ("left", "both") else False

---

894-897: Use ternary operator left_inclusive = False if closed in ("right", "both") else True instead of if-else-block (SIM108)

Replace if-else-block with left_inclusive = False if closed in ("right", "both") else True

---

917-924: Combine if branches using logical or operator (SIM114)

Combine if branches

---

1013-1021: Combine if branches using logical or operator (SIM114)

Combine if branches

Additional comments not posted (9)

tests/test_e2e.py (1)

132-132: Ensure consistency of _LAST_EVENT_INDEX in test data.

The modifications to the test data to include _LAST_EVENT_INDEX fields are consistent with the changes described in the AI-generated summary. This ensures that the new event indexing logic is covered by the tests.

Also applies to: 143-143, 156-156, 167-167, 180-180, 191-191, 204-204, 215-215

src/aces/types.py (1)

16-16: Review of new types and constants for event indexing.

The introduction of EVENT_INDEX_TYPE, EVENT_INDEX_COLUMN, and LAST_EVENT_INDEX_COLUMN is consistent with the changes described in the AI-generated summary. These additions are crucial for supporting the new event indexing features across the application.
[APROVED]

Also applies to: 26-27

src/aces/extract_subtree.py (1)

11-11: Review of modifications to extract_subtree function.

The updates to the extract_subtree function to include handling of the _EVENT_INDEX column are consistent with the changes described in the AI-generated summary. These modifications are crucial for ensuring that the function correctly processes and includes this column in the input data, which is essential for the new event indexing functionality.

Also applies to: 137-137, 149-160, 248-333

src/aces/predicates.py (2)

13-14: Updated import statements to include event indexing types.

The inclusion of EVENT_INDEX_COLUMN and EVENT_INDEX_TYPE aligns with the changes outlined in the summary, ensuring the necessary types are available for handling the new _EVENT_INDEX column. This is crucial for maintaining consistency across modules that will interact with event indexes.

---

Line range hint 490-520: Introduction of _EVENT_INDEX in DataFrame output.

The addition of _EVENT_INDEX in the DataFrame output of get_predicates_df function is executed correctly. The column is computed and added in lines 642-645, ensuring every event has a unique index within its subject group. This is crucial for tracking events in sequence analysis or temporal comparisons.

However, ensure that all downstream processes that consume this DataFrame are aware of and correctly handle the new _EVENT_INDEX column.

src/aces/aggregate.py (4)

7-12: Review of imports and constants:

The import of EVENT_INDEX_COLUMN aligns with the PR's objective to handle an event index column. This addition appears necessary and correct for the functions modified in this file.

---

87-87: Ensure correct handling of _EVENT_INDEX column:

The repeated use of .drop("_EVENT_INDEX") in different configurations of the aggregate_temporal_window function is consistent with the need to remove this column post-aggregation. This change is in line with the PR's objectives and seems correctly implemented across different scenarios.

Also applies to: 102-102, 117-117, 132-132, 147-147, 162-162, 181-181, 196-196

---

314-314: Review of _EVENT_INDEX handling in aggregate_event_bound_window:

The introduction and subsequent dropping of _EVENT_index within aggregate_event_bound_window function is consistent with the handling in other functions. This ensures that the event index does not propagate beyond its necessary scope within the data pipeline.

Also applies to: 319-319, 336-336, 337-337, 353-353, 354-354, 370-370, 371-371

---

Line range hint 214-237: Complex handling of conditions and _EVENT_INDEX in boolean_expr_bound_sum:

The function boolean_expr_bound_sum has been modified to incorporate the _EVENT_index in its operations, reflecting the broader PR objectives. The handling of this column and the complex conditional logic used for boundary calculations appear correctly implemented, maintaining the integrity of the data transformation logic.

Also applies to: 512-512, 693-693, 715-715, 737-737, 759-759, 781-781, 803-803, 825-825, 847-847

[coderabbitai]

Actionable comments posted: 1

Outside diff range, codebase verification and nitpick comments (1)

src/aces/extract_subtree.py (1)

147-149: Update the example output shape.

The shape of the example output DataFrame has changed from (5, 2) to (5, 3) due to the inclusion of the _EVENT_INDEX column. Ensure that all example outputs are updated to reflect this change.

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 2a8a66b and c36b5bd.

Files selected for processing (3)

• src/aces/main.py (1 hunks)
• src/aces/extract_subtree.py (5 hunks)
• src/aces/predicates.py (5 hunks)

Additional comments not posted (7)

src/aces/__main__.py (1)

49-49: Verify the DataFrame renaming method.

The change in the rename method from using the columns keyword to directly passing a dictionary could potentially cause issues if the DataFrame does not handle this method signature as expected. Ensure that the DataFrame correctly interprets this method signature.

src/aces/extract_subtree.py (4)

11-11: Ensure consistency in column handling.

The addition of the EVENT_INDEX_COLUMN import indicates that the _EVENT_INDEX column is now being handled. Ensure that this column is consistently handled throughout the function.

---

137-137: Verify the inclusion of _EVENT_INDEX in the DataFrame.

The addition of the _EVENT_INDEX column in the example DataFrame indicates that this column is now part of the data processing. Ensure that this column is correctly handled in all relevant DataFrame operations.

---

248-250: Exclude _EVENT_INDEX from predicate_cols.

The exclusion of the _EVENT_INDEX column from predicate_cols is necessary to ensure that this column is not treated as a predicate. This change is correct and should be maintained.

---

333-333: Include _EVENT_INDEX in the summary.

The inclusion of the _EVENT_INDEX column in the summary DataFrame ensures that this column is part of the output. This change is correct and should be maintained.

src/aces/predicates.py (2)

13-14: Ensure consistency in column handling.

The addition of the EVENT_INDEX_COLUMN and EVENT_INDEX_TYPE imports indicates that the _EVENT_INDEX column is now being handled. Ensure that these constants are consistently used throughout the function.

---

490-500: Verify the inclusion of _EVENT_INDEX in the DataFrame.

The addition of the _EVENT_INDEX column in the example DataFrame indicates that this column is now part of the data processing. Ensure that this column is correctly handled in all relevant DataFrame operations.

[mmcdermott]

I would keep the "timestamp" column in these tests, and just set the pl.Config params to print wider dataframes.

[justin13601]

Actually I did this more to satistfy the pre-commit rules of lines not extending past 120 characters - should doctests still follow these rules? What's the best way to go around this?

[mmcdermott]

I think more generally here, each aggregate function should return:

1. The timestamp at the start of the window. If the window does not exist, this should be null.
2. The timestamp at the end of the window. If the window does not exist, this should be null.
3. The index of the first event inside the window. If there are no events in the window, this should be null.
4. The index of the last event inside the window. If there are no events in the window, this should be null.

Note that the distinction between "the window existing" and "events existing" is as follows:

1. A window is an interval in the patient timeline where (a) the left endpoint is <= the right endpoint and (b) either left or right endpoint can be open or closed. A window does not exist if either of these constraints are not satisfied. We can also modify this to say that "windows don't exist if they are provably empty -- e.g., [12:01, 12:01) of (3:23, 3:23)" or that "windows with equal left and right endpoints where both are open don't exist" as desired.
2. Events are in the window if they occur with a timestamp within the interval defined by the window (respecting the openness or closedness of its bounds).

[mmcdermott]

@justin13601, as we'll discuss more shortly, I'd actually suggest de-prioritizing this in favor of other things, and closing the PR for now as a result (with plans to re-visit later). Does that sound reasonable to you? If not, feel free to re-open.