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fix(data): bypass load_dataset() to fix HF Spaces streaming hang and OOM (#16)

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* fix(data): bypass load_dataset() to fix HF Spaces streaming hang and OOM

Two bugs blocked HF Spaces deployment:
1. PyArrow streaming bug (apache/arrow#45214) hangs on parquet iteration
2. load_dataset() full download OOMs on 99GB dataset

Solution:
- Pre-compute 149 case IDs in constants.py (static challenge dataset)
- Use HfFileSystem + pyarrow to download individual cases (~50MB, ~2s)
- Remove all load_dataset() calls from HF path

Fixes dropdown hang and prevents OOM crash on case selection.

* chore: remove dead code and add defensive assertion

- Remove unused create_mock_parquet_data helper function
- Remove unused Any import
- Add assertion to verify ISLES24_CASE_IDS matches ISLES24_NUM_FILES

docs/specs/08-bug-hf-spaces-dataset-loop.md CHANGED
@@ -1,166 +1,239 @@
1
- # Bug Spec: HuggingFace Spaces Dataset Loading Loop
2
 
3
- **Status:** Open
4
  **Priority:** P0 (Blocks deployment)
5
- **Branch:** `debug/hf-spaces-dataset-error`
6
  **Date:** 2025-12-08
 
7
 
8
- ## Observed Behavior
9
 
10
- Container enters infinite restart loop:
11
- 1. Application starts successfully (`Running on local URL: http://0.0.0.0:7860`)
12
- 2. Dataset download completes (`Downloading data: 100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 149/149`)
13
- 3. "Generating train split" begins processing
14
- 4. **Container restarts** (new `Application Startup` timestamp)
15
- 5. Cycle repeats indefinitely
16
 
17
- The "Select Case" dropdown **never** populates. Users see "Preparing Space" spinner forever.
 
 
 
18
 
19
- ## Environment
20
 
21
- - **Space:** `VibecoderMcSwaggins/stroke-deepisles-demo`
22
- - **Hardware:** T4-small GPU
23
- - **Base Image:** `isleschallenge/deepisles:latest`
24
- - **Dataset:** `hugging-science/isles24-stroke` (149 NIfTI files, ~2-5MB each)
25
- - **Commit:** `a2223b1`
26
-
27
- ## Timeline from Logs
28
-
29
- ```text
30
- 16:43:33 - Application Startup
31
- 16:43:33 - Initializing dataset...
32
- 16:43:33 - Downloading data: 0%
33
- 16:48:10 - Downloading data: 100% (149/149) [~5 min]
34
- 16:48:10 - Generating train split: starts
35
- 16:56:53 - Application Startup (RESTART - lost all progress)
36
- 16:56:53 - Downloading data: 0% (starts over)
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
37
  ```
38
 
39
- ## Hypotheses
 
 
40
 
41
- ### H1: Memory OOM during train split generation
42
- - Processing 149 NIfTI files into HF Dataset format
43
- - Each file loaded into memory for processing
44
- - T4-small may have limited RAM
45
- - **Evidence:** Restart happens during "Generating train split" phase
46
 
47
- ### H2: Disk space exhaustion
48
- - HF Spaces ephemeral storage limit (~50GB based on org space error)
49
- - DeepISLES base image is large
50
- - Dataset download + cache + processing temps
51
- - **Evidence:** Org space explicitly failed with "storage limit exceeded (50G)"
52
 
53
- ### H3: Gradio demo.load() timeout
54
- - `demo.load()` has internal timeout?
55
- - 7+ minutes for dataset loading exceeds limit?
56
- - **Evidence:** UI shows "Preparing Space" during load
57
 
58
- ### H4: HF Spaces health check failure
59
- - Even though port 7860 is bound, health check may require response
60
- - Long-running `demo.load()` blocks event loop?
61
- - **Evidence:** Container restarts after ~13 min total
62
 
63
- ### H5: Exception swallowed during train split
64
- - Our try/except returns `gr.Dropdown(info=f"Error: {e}")`
65
- - But Gradio shows generic "Error" not our message
66
- - Something crashes before our handler
67
 
68
- ## Code Under Suspicion
69
 
70
- ### `src/stroke_deepisles_demo/ui/app.py:34-56`
71
  ```python
72
- def initialize_case_selector() -> gr.Dropdown:
73
- try:
74
- logger.info("Initializing dataset for case selector...")
75
- case_ids = list_case_ids() # <-- This triggers full dataset load
76
-
77
- if not case_ids:
78
- return gr.Dropdown(choices=[], info="No cases found in dataset.")
79
-
80
- return gr.Dropdown(
81
- choices=case_ids,
82
- value=case_ids[0],
83
- info="Choose a case from isles24-stroke dataset",
84
- interactive=True,
85
- )
86
- except Exception as e:
87
- logger.exception("Failed to initialize dataset")
88
- return gr.Dropdown(choices=[], info=f"Error loading data: {e!s}")
89
  ```
90
 
91
- ### `src/stroke_deepisles_demo/data/loader.py`
92
- - `list_case_ids()` calls `load_isles_dataset()`
93
- - `load_isles_dataset()` calls HF `load_dataset()` (non-streaming)
94
- - Full dataset downloaded and processed into memory
 
 
 
 
 
 
 
 
 
95
 
96
- ## Potential Fixes
 
 
 
 
 
 
 
 
 
 
97
 
98
- ### Fix 1: Streaming Mode (Recommended)
99
  ```python
100
- # Instead of:
101
- ds = load_dataset("hugging-science/isles24-stroke")
102
 
103
- # Use streaming:
104
- ds = load_dataset("hugging-science/isles24-stroke", streaming=True)
105
- case_ids = [ex["case_id"] for ex in ds] # Iterate without full load
 
 
 
 
106
  ```
107
- - **Pros:** Zero disk usage, immediate start
108
- - **Cons:** Can't random access, must iterate
109
 
110
- ### Fix 2: Lazy case ID loading
111
- - Only load case IDs, not full dataset
112
- - Use HF Hub API to list files without downloading
 
 
 
 
 
 
 
 
113
 
114
- ### Fix 3: Pre-computed case ID list
115
- - Hardcode or cache the 149 case IDs
116
- - Skip dataset enumeration entirely for dropdown
 
 
 
 
 
 
 
 
 
 
 
117
 
118
- ### Fix 4: Persistent Storage
119
- - Enable HF Spaces Persistent Storage add-on
120
- - Cache survives restarts
121
- - **Cons:** Costs money, doesn't fix root cause
122
 
123
- ### Fix 5: Background thread with timeout
124
- - Run dataset load in background thread
125
- - Show "Loading..." in dropdown immediately
126
- - Update dropdown when ready (if ever)
127
 
128
- ## Investigation Needed
 
 
 
129
 
130
- 1. **Get actual error:** What exception/signal causes restart?
131
- - Need HF Spaces runtime logs (not just container logs)
132
- - Check for OOM killer, SIGKILL, etc.
133
 
134
- 2. **Measure resource usage:**
135
- - Disk usage during download/processing
136
- - Memory usage during train split generation
 
 
137
 
138
- 3. **Test streaming mode locally:**
139
- - Does `streaming=True` work with our dataset?
140
- - Can we still get case IDs?
141
 
142
- 4. **Check Gradio demo.load() behavior:**
143
- - Is there a timeout?
144
- - Does long-running load block health checks?
145
 
146
- ## Reproduction Steps
147
 
148
- 1. Go to [the demo space](https://huggingface.co/spaces/VibecoderMcSwaggins/stroke-deepisles-demo)
149
- 2. Open Logs tab
150
- 3. Watch download complete (5 min)
151
- 4. Watch "Generating train split" start
152
- 5. Observe container restart (~7-13 min mark)
153
- 6. See download start over from 0%
154
 
155
- ## Related Issues
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
156
 
157
- - Org space (`hugging-science/stroke-deepisles-demo`) failed with explicit "storage limit exceeded (50G)"
158
- - This suggests disk space IS a factor
159
- - Personal space may have same limit but hits it slower
160
 
161
- ## Next Steps
162
 
163
- 1. [ ] Get deep analysis from senior reviewer / external agent
164
- 2. [ ] Test streaming mode locally
165
- 3. [ ] Add resource monitoring/logging
166
- 4. [ ] Consider pre-computed case ID approach as quick fix
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Bug Spec: HuggingFace Spaces Dataset Loading Issues
2
 
3
+ **Status:** Root Causes Identified β†’ Comprehensive Fix Ready
4
  **Priority:** P0 (Blocks deployment)
5
+ **Branch:** `fix/pipeline-resource-leak`
6
  **Date:** 2025-12-08
7
+ **Updated:** 2025-12-08
8
 
9
+ ## Executive Summary
10
 
11
+ Two distinct bugs prevent the HuggingFace Spaces deployment from working:
 
 
 
 
 
12
 
13
+ | Bug | Symptom | Root Cause | Impact | Fix |
14
+ |-----|---------|------------|--------|-----|
15
+ | **#1** | Dropdown never populates | PyArrow streaming bug | App hangs at startup | Pre-computed case IDs |
16
+ | **#2** | OOM on case selection | `load_dataset()` downloads 99GB | App crashes on first use | HfFileSystem + pyarrow |
17
 
18
+ Both bugs stem from fundamental incompatibilities between the `datasets` library and our 99GB parquet dataset on resource-constrained HF Spaces hardware.
19
 
20
+ ---
21
+
22
+ ## Bug #1: Streaming Iteration Hang
23
+
24
+ ### Summary
25
+
26
+ The dropdown never populates because `load_dataset(..., streaming=True)` hangs indefinitely on parquet datasets. This is a **known PyArrow bug**, not a HuggingFace datasets bug.
27
+
28
+ ### The Bug Chain
29
+
30
+ 1. **Our code** calls `load_dataset("hugging-science/isles24-stroke", streaming=True)`
31
+ 2. **HF datasets** internally uses `ParquetFileFragment.to_batches()` for streaming
32
+ 3. **PyArrow** hangs when iterating batches from parquet with partial consumption
33
+ 4. **Result:** Script hangs forever, never returns case IDs
34
+
35
+ ### Upstream Issues
36
+
37
+ - **PyArrow Issue:** [apache/arrow#45214](https://github.com/apache/arrow/issues/45214) - Root cause
38
+ - **HF Datasets Issue:** [huggingface/datasets#7467](https://github.com/huggingface/datasets/issues/7467) - HF tracking
39
+ - **Status:** Open, no fix ETA
40
+ - **Maintainer:** @lhoestq (HF datasets core dev) correctly escalated to PyArrow team
41
+
42
+ ### Minimal Reproduction (Pure PyArrow, no HF)
43
+
44
+ ```python
45
+ import pyarrow.dataset as ds
46
+
47
+ file = "test-00000-of-00003.parquet"
48
+ with open(file, "rb") as f:
49
+ parquet_fragment = ds.ParquetFileFormat().make_fragment(f)
50
+ for record_batch in parquet_fragment.to_batches():
51
+ print(len(record_batch))
52
+ break # ← Partial consumption causes hang
53
+ # Script hangs here forever
54
  ```
55
 
56
+ This proves the bug is in **PyArrow's C++ layer**, not HuggingFace datasets.
57
+
58
+ ### Fix: Pre-computed Case ID List
59
 
60
+ **Why this is professional, not hacky:**
 
 
 
 
61
 
62
+ 1. **ISLES24 is a static challenge dataset** - case IDs will never change
63
+ 2. **Industry standard** - many production ML systems pre-define dataset indices
64
+ 3. **Zero startup latency** - dropdown populates instantly
65
+ 4. **No network dependency** - works offline for dropdown population
66
+ 5. **Bypasses upstream bug** - doesn't depend on PyArrow fix timeline
67
 
68
+ ---
 
 
 
69
 
70
+ ## Bug #2: Full Dataset OOM on Case Access
 
 
 
71
 
72
+ ### Summary
 
 
 
73
 
74
+ Even after fixing Bug #1, the application would crash immediately upon selecting a case. The current `get_case()` implementation calls:
75
 
 
76
  ```python
77
+ # adapter.py:213
78
+ self._hf_dataset = load_dataset(self.dataset_id, split="train")
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
79
  ```
80
 
81
+ This attempts to download the **entire 99GB dataset** into memory, which OOMs on HF Spaces.
82
+
83
+ ### Why This Wasn't Caught
84
+
85
+ The bug document initially focused on the dropdown hang (Bug #1). Bug #2 would only manifest after Bug #1 was fixed and a user actually selected a case.
86
+
87
+ ### Investigation Results
88
+
89
+ | Approach | Result | Time | Memory |
90
+ |----------|--------|------|--------|
91
+ | `load_dataset(..., streaming=True)` | **HANGS** | ∞ | N/A |
92
+ | `load_dataset(...)` (full download) | **OOMs** | ~10 min | 99GB+ |
93
+ | `HfFileSystem` + `pyarrow` (single file) | **WORKS** | 1.7s | ~50MB |
94
 
95
+ ### Dataset Structure Discovery
96
+
97
+ Critical finding: Each case is stored in a **separate parquet file**:
98
+
99
+ - **149 parquet files** named `train-00000-of-00149.parquet` through `train-00148-of-00149.parquet`
100
+ - **Each file = one case** (~600-700MB raw data per case)
101
+ - **Schema:** `subject_id`, `dwi`, `adc`, `lesion_mask` (NIfTI bytes stored as binary)
102
+
103
+ This means we can **directly access individual cases** without loading the full dataset!
104
+
105
+ ### Fix: Direct Parquet Access via HfFileSystem
106
 
 
107
  ```python
108
+ from huggingface_hub import HfFileSystem
109
+ import pyarrow.parquet as pq
110
 
111
+ fs = HfFileSystem()
112
+ fpath = f"datasets/{dataset_id}/data/train-{idx:05d}-of-00149.parquet"
113
+
114
+ with fs.open(fpath, 'rb') as f:
115
+ pf = pq.ParquetFile(f)
116
+ table = pf.read(columns=['subject_id', 'dwi', 'adc', 'lesion_mask'])
117
+ # Extract ~50MB for one case in ~2 seconds
118
  ```
 
 
119
 
120
+ **Benefits:**
121
+ - Downloads only the single case needed (~50MB vs 99GB)
122
+ - Completes in 1.7 seconds (vs hanging or OOM)
123
+ - No dependency on `datasets` library for data access
124
+ - Bypasses both PyArrow streaming bug and memory constraints
125
+
126
+ ---
127
+
128
+ ## Comprehensive Fix Implementation
129
+
130
+ ### 1. Create `constants.py` with case ID β†’ file index mapping
131
 
132
+ ```python
133
+ # src/stroke_deepisles_demo/data/constants.py
134
+
135
+ # Pre-computed case IDs for ISLES24 dataset (static challenge dataset)
136
+ # Extracted via HfFileSystem enumeration on 2025-12-08
137
+ ISLES24_CASE_IDS: tuple[str, ...] = (
138
+ "sub-stroke0001", "sub-stroke0002", ..., "sub-stroke0189"
139
+ )
140
+
141
+ # Mapping from case ID to parquet file index (0-indexed)
142
+ ISLES24_CASE_INDEX: dict[str, int] = {
143
+ case_id: idx for idx, case_id in enumerate(ISLES24_CASE_IDS)
144
+ }
145
+ ```
146
 
147
+ ### 2. Rewrite `HuggingFaceDataset.get_case()` to use HfFileSystem
 
 
 
148
 
149
+ Replace `load_dataset()` call with direct parquet access:
 
 
 
150
 
151
+ ```python
152
+ def get_case(self, case_id: str | int) -> CaseFiles:
153
+ from huggingface_hub import HfFileSystem
154
+ import pyarrow.parquet as pq
155
 
156
+ idx = self._case_index[case_id]
157
+ fpath = f"datasets/{self.dataset_id}/data/train-{idx:05d}-of-00149.parquet"
 
158
 
159
+ fs = HfFileSystem()
160
+ with fs.open(fpath, 'rb') as f:
161
+ table = pq.ParquetFile(f).read(columns=['dwi', 'adc', 'lesion_mask'])
162
+ # Extract bytes and write to temp files...
163
+ ```
164
 
165
+ ### 3. Remove all `load_dataset()` calls from HuggingFace path
 
 
166
 
167
+ The `datasets` library is completely bypassed for the HuggingFace workflow.
 
 
168
 
169
+ ---
170
 
171
+ ## All 149 Case IDs (Extracted via HfFileSystem)
 
 
 
 
 
172
 
173
+ ```
174
+ sub-stroke0001, sub-stroke0002, sub-stroke0003, sub-stroke0004, sub-stroke0005,
175
+ sub-stroke0006, sub-stroke0007, sub-stroke0008, sub-stroke0009, sub-stroke0010,
176
+ sub-stroke0011, sub-stroke0012, sub-stroke0013, sub-stroke0014, sub-stroke0015,
177
+ sub-stroke0016, sub-stroke0017, sub-stroke0019, sub-stroke0020, sub-stroke0021,
178
+ sub-stroke0022, sub-stroke0025, sub-stroke0026, sub-stroke0027, sub-stroke0028,
179
+ sub-stroke0030, sub-stroke0033, sub-stroke0036, sub-stroke0037, sub-stroke0038,
180
+ sub-stroke0040, sub-stroke0043, sub-stroke0045, sub-stroke0047, sub-stroke0048,
181
+ sub-stroke0049, sub-stroke0052, sub-stroke0053, sub-stroke0054, sub-stroke0055,
182
+ sub-stroke0057, sub-stroke0062, sub-stroke0066, sub-stroke0068, sub-stroke0070,
183
+ sub-stroke0071, sub-stroke0073, sub-stroke0074, sub-stroke0075, sub-stroke0076,
184
+ sub-stroke0077, sub-stroke0078, sub-stroke0079, sub-stroke0080, sub-stroke0081,
185
+ sub-stroke0082, sub-stroke0083, sub-stroke0084, sub-stroke0085, sub-stroke0086,
186
+ sub-stroke0087, sub-stroke0088, sub-stroke0089, sub-stroke0090, sub-stroke0091,
187
+ sub-stroke0092, sub-stroke0093, sub-stroke0094, sub-stroke0095, sub-stroke0096,
188
+ sub-stroke0097, sub-stroke0098, sub-stroke0099, sub-stroke0100, sub-stroke0101,
189
+ sub-stroke0102, sub-stroke0103, sub-stroke0104, sub-stroke0105, sub-stroke0106,
190
+ sub-stroke0107, sub-stroke0108, sub-stroke0109, sub-stroke0110, sub-stroke0111,
191
+ sub-stroke0112, sub-stroke0113, sub-stroke0114, sub-stroke0115, sub-stroke0116,
192
+ sub-stroke0117, sub-stroke0118, sub-stroke0119, sub-stroke0133, sub-stroke0134,
193
+ sub-stroke0135, sub-stroke0136, sub-stroke0137, sub-stroke0138, sub-stroke0139,
194
+ sub-stroke0140, sub-stroke0141, sub-stroke0142, sub-stroke0143, sub-stroke0144,
195
+ sub-stroke0145, sub-stroke0146, sub-stroke0147, sub-stroke0148, sub-stroke0149,
196
+ sub-stroke0150, sub-stroke0151, sub-stroke0152, sub-stroke0153, sub-stroke0154,
197
+ sub-stroke0155, sub-stroke0156, sub-stroke0157, sub-stroke0158, sub-stroke0159,
198
+ sub-stroke0161, sub-stroke0162, sub-stroke0163, sub-stroke0164, sub-stroke0165,
199
+ sub-stroke0166, sub-stroke0167, sub-stroke0168, sub-stroke0169, sub-stroke0170,
200
+ sub-stroke0171, sub-stroke0172, sub-stroke0173, sub-stroke0174, sub-stroke0175,
201
+ sub-stroke0176, sub-stroke0177, sub-stroke0178, sub-stroke0179, sub-stroke0180,
202
+ sub-stroke0181, sub-stroke0182, sub-stroke0183, sub-stroke0184, sub-stroke0185,
203
+ sub-stroke0186, sub-stroke0187, sub-stroke0188, sub-stroke0189
204
+ ```
205
 
206
+ ---
 
 
207
 
208
+ ## Environment
209
 
210
+ - **Space:** `VibecoderMcSwaggins/stroke-deepisles-demo`
211
+ - **Hardware:** T4-small GPU (limited memory)
212
+ - **Dataset:** `hugging-science/isles24-stroke` (149 parquet files, ~99GB total)
213
+ - **Dependencies:**
214
+ - `datasets @ git+https://github.com/CloseChoice/datasets.git@c1c15aa...` (fork with Nifti support)
215
+ - `pyarrow` (inherited, contains Bug #1)
216
+ - `huggingface_hub` (used for Bug #2 fix)
217
+
218
+ ---
219
+
220
+ ## References
221
+
222
+ - [PyArrow Issue #45214](https://github.com/apache/arrow/issues/45214) - Bug #1 root cause
223
+ - [PyArrow Issue #43604](https://github.com/apache/arrow/issues/43604) - Related hang issue
224
+ - [HF Datasets Issue #7467](https://github.com/huggingface/datasets/issues/7467) - HF tracking issue
225
+ - [HF Datasets Issue #7357](https://github.com/huggingface/datasets/issues/7357) - Original report
226
+
227
+ ---
228
+
229
+ ## Checklist
230
+
231
+ 1. [x] Identify Bug #1 root cause (PyArrow streaming hang)
232
+ 2. [x] Identify Bug #2 root cause (OOM on full download)
233
+ 3. [x] Extract all 149 case IDs via HfFileSystem
234
+ 4. [x] Validate direct parquet access works (1.7s per case)
235
+ 5. [x] Implement pre-computed case ID list (`constants.py`)
236
+ 6. [x] Rewrite `get_case()` to use HfFileSystem + pyarrow
237
+ 7. [x] Update tests
238
+ 8. [ ] Test on HF Spaces
239
+ 9. [ ] Monitor PyArrow issue for upstream fix
src/stroke_deepisles_demo/data/adapter.py CHANGED
@@ -7,7 +7,7 @@ import shutil
7
  import tempfile
8
  from dataclasses import dataclass, field
9
  from pathlib import Path
10
- from typing import TYPE_CHECKING, Any, Self
11
 
12
  from stroke_deepisles_demo.core.exceptions import DataLoadError
13
  from stroke_deepisles_demo.core.logging import get_logger
@@ -145,11 +145,16 @@ class HuggingFaceDataset:
145
  """Dataset adapter for HuggingFace ISLES24 dataset.
146
 
147
  Wraps the HuggingFace dataset and provides the same interface as LocalDataset.
148
- When get_case() is called, writes NIfTI bytes to temp files and returns paths.
 
 
 
 
 
149
 
150
  IMPORTANT: Use as a context manager to ensure temp files are cleaned up:
151
 
152
- with load_isles_dataset() as ds:
153
  case = ds.get_case(0)
154
  # ... process case ...
155
  # temp files automatically cleaned up
@@ -158,8 +163,8 @@ class HuggingFaceDataset:
158
  """
159
 
160
  dataset_id: str
161
- _hf_dataset: Any = field(repr=False)
162
  _case_ids: list[str] = field(default_factory=list)
 
163
  _temp_dir: Path | None = field(default=None, repr=False)
164
  _cached_cases: dict[str, CaseFiles] = field(default_factory=dict, repr=False)
165
 
@@ -182,18 +187,27 @@ class HuggingFaceDataset:
182
  def get_case(self, case_id: str | int) -> CaseFiles:
183
  """Get files for a case by ID or index.
184
 
185
- Writes NIfTI bytes to temp files on first access; returns cached paths
186
- on subsequent calls for the same case.
 
 
 
187
 
188
  Raises:
189
- DataError: If HuggingFace data is malformed or missing required fields.
 
190
  """
 
191
  if isinstance(case_id, int):
192
- idx = case_id
193
- subject_id = self._case_ids[idx]
 
 
194
  else:
195
  subject_id = case_id
196
- idx = self._case_ids.index(subject_id)
 
 
197
 
198
  # Return cached case if already materialized
199
  if subject_id in self._cached_cases:
@@ -204,17 +218,9 @@ class HuggingFaceDataset:
204
  self._temp_dir = Path(tempfile.mkdtemp(prefix="isles24_hf_"))
205
  logger.debug("Created temp directory: %s", self._temp_dir)
206
 
207
- # Lazy load full dataset on first get_case() call
208
- # This defers the expensive download until actually needed
209
- if self._hf_dataset is None:
210
- from datasets import load_dataset
211
-
212
- logger.info("Loading full dataset for case access (lazy load)...")
213
- self._hf_dataset = load_dataset(self.dataset_id, split="train")
214
- logger.info("Full dataset loaded: %d examples", len(self._hf_dataset))
215
-
216
- # Get the HuggingFace example
217
- example = self._hf_dataset[idx]
218
 
219
  # Create case subdirectory
220
  case_dir = self._temp_dir / subject_id
@@ -225,19 +231,9 @@ class HuggingFaceDataset:
225
  adc_path = case_dir / f"{subject_id}_ses-02_adc.nii.gz"
226
  mask_path = case_dir / f"{subject_id}_ses-02_lesion-msk.nii.gz"
227
 
228
- # Extract bytes with defensive error handling
229
- try:
230
- dwi_bytes = example["dwi"]["bytes"]
231
- adc_bytes = example["adc"]["bytes"]
232
- except (KeyError, TypeError) as e:
233
- raise DataLoadError(
234
- f"Malformed HuggingFace data for {subject_id}: missing 'dwi' or 'adc' bytes. "
235
- f"The dataset schema may have changed. Error: {e}"
236
- ) from e
237
-
238
  # Write the gzipped NIfTI bytes
239
- dwi_path.write_bytes(dwi_bytes)
240
- adc_path.write_bytes(adc_bytes)
241
 
242
  case_files: CaseFiles = {
243
  "dwi": dwi_path,
@@ -245,20 +241,89 @@ class HuggingFaceDataset:
245
  }
246
 
247
  # Write lesion mask if available
248
- try:
249
- mask_data = example.get("lesion_mask")
250
- if mask_data and mask_data.get("bytes"):
251
- mask_path.write_bytes(mask_data["bytes"])
252
- case_files["ground_truth"] = mask_path
253
- except (KeyError, TypeError):
254
- # Mask is optional, log and continue
255
- logger.debug("No lesion mask available for %s", subject_id)
256
 
257
  # Cache for subsequent calls
258
  self._cached_cases[subject_id] = case_files
 
 
 
 
 
 
259
 
260
  return case_files
261
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
262
  def cleanup(self) -> None:
263
  """Remove temp directory and clear cache."""
264
  if self._temp_dir and self._temp_dir.exists():
@@ -270,10 +335,11 @@ class HuggingFaceDataset:
270
 
271
  def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
272
  """
273
- Load ISLES24 dataset from HuggingFace Hub.
274
 
275
- Uses streaming mode to quickly enumerate case IDs without downloading
276
- the full dataset. Actual data is downloaded lazily when get_case() is called.
 
277
 
278
  Args:
279
  dataset_id: HuggingFace dataset identifier (e.g., "hugging-science/isles24-stroke")
@@ -281,26 +347,29 @@ def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
281
  Returns:
282
  HuggingFaceDataset providing case access
283
  """
284
- from datasets import load_dataset
285
-
286
- logger.info("Loading HuggingFace dataset: %s", dataset_id)
287
-
288
- # Use streaming to quickly get case IDs without downloading full dataset
289
- # This avoids the "Generating train split" phase that hangs on HF Spaces
290
- logger.info("Streaming dataset to enumerate case IDs...")
291
- streaming_ds = load_dataset(dataset_id, split="train", streaming=True)
292
 
293
- # Extract case IDs from streaming dataset (accesses only subject_id field,
294
- # deferring heavy binary NIfTI downloads to get_case())
295
- case_ids = []
296
- for example in streaming_ds:
297
- case_ids.append(example["subject_id"])
 
 
 
298
 
299
- logger.info("Found %d cases from HuggingFace: %s", len(case_ids), dataset_id)
 
 
 
 
300
 
301
- # Return dataset with lazy loading - full data downloaded only when get_case() called
302
  return HuggingFaceDataset(
303
  dataset_id=dataset_id,
304
- _hf_dataset=None, # Lazy load on first get_case()
305
- _case_ids=case_ids,
306
  )
 
7
  import tempfile
8
  from dataclasses import dataclass, field
9
  from pathlib import Path
10
+ from typing import TYPE_CHECKING, Self
11
 
12
  from stroke_deepisles_demo.core.exceptions import DataLoadError
13
  from stroke_deepisles_demo.core.logging import get_logger
 
145
  """Dataset adapter for HuggingFace ISLES24 dataset.
146
 
147
  Wraps the HuggingFace dataset and provides the same interface as LocalDataset.
148
+ When get_case() is called, downloads NIfTI bytes from individual parquet files
149
+ and writes them to temp files.
150
+
151
+ This implementation bypasses `load_dataset()` entirely to avoid:
152
+ 1. PyArrow streaming bug (apache/arrow#45214) that hangs on parquet iteration
153
+ 2. Memory issues from downloading the full 99GB dataset
154
 
155
  IMPORTANT: Use as a context manager to ensure temp files are cleaned up:
156
 
157
+ with build_huggingface_dataset(dataset_id) as ds:
158
  case = ds.get_case(0)
159
  # ... process case ...
160
  # temp files automatically cleaned up
 
163
  """
164
 
165
  dataset_id: str
 
166
  _case_ids: list[str] = field(default_factory=list)
167
+ _case_index: dict[str, int] = field(default_factory=dict)
168
  _temp_dir: Path | None = field(default=None, repr=False)
169
  _cached_cases: dict[str, CaseFiles] = field(default_factory=dict, repr=False)
170
 
 
187
  def get_case(self, case_id: str | int) -> CaseFiles:
188
  """Get files for a case by ID or index.
189
 
190
+ Downloads NIfTI bytes from the individual parquet file for this case
191
+ and writes to temp files. Returns cached paths on subsequent calls.
192
+
193
+ This uses HfFileSystem + pyarrow to download only the single case (~50MB)
194
+ instead of the full dataset (99GB), completing in ~2 seconds.
195
 
196
  Raises:
197
+ DataLoadError: If HuggingFace data is malformed or missing required fields.
198
+ KeyError: If case_id is not found in the dataset.
199
  """
200
+ # Resolve case_id to subject_id and file index
201
  if isinstance(case_id, int):
202
+ if case_id < 0 or case_id >= len(self._case_ids):
203
+ raise IndexError(f"Case index {case_id} out of range [0, {len(self._case_ids)})")
204
+ subject_id = self._case_ids[case_id]
205
+ file_idx = case_id
206
  else:
207
  subject_id = case_id
208
+ if subject_id not in self._case_index:
209
+ raise KeyError(f"Case ID '{subject_id}' not found in dataset")
210
+ file_idx = self._case_index[subject_id]
211
 
212
  # Return cached case if already materialized
213
  if subject_id in self._cached_cases:
 
218
  self._temp_dir = Path(tempfile.mkdtemp(prefix="isles24_hf_"))
219
  logger.debug("Created temp directory: %s", self._temp_dir)
220
 
221
+ # Download case data from individual parquet file
222
+ logger.info("Downloading case %s from HuggingFace...", subject_id)
223
+ case_data = self._download_case_from_parquet(file_idx, subject_id)
 
 
 
 
 
 
 
 
224
 
225
  # Create case subdirectory
226
  case_dir = self._temp_dir / subject_id
 
231
  adc_path = case_dir / f"{subject_id}_ses-02_adc.nii.gz"
232
  mask_path = case_dir / f"{subject_id}_ses-02_lesion-msk.nii.gz"
233
 
 
 
 
 
 
 
 
 
 
 
234
  # Write the gzipped NIfTI bytes
235
+ dwi_path.write_bytes(case_data["dwi_bytes"])
236
+ adc_path.write_bytes(case_data["adc_bytes"])
237
 
238
  case_files: CaseFiles = {
239
  "dwi": dwi_path,
 
241
  }
242
 
243
  # Write lesion mask if available
244
+ if case_data.get("mask_bytes"):
245
+ mask_path.write_bytes(case_data["mask_bytes"])
246
+ case_files["ground_truth"] = mask_path
 
 
 
 
 
247
 
248
  # Cache for subsequent calls
249
  self._cached_cases[subject_id] = case_files
250
+ logger.info(
251
+ "Case %s ready: DWI=%.1fMB, ADC=%.1fMB",
252
+ subject_id,
253
+ len(case_data["dwi_bytes"]) / 1024 / 1024,
254
+ len(case_data["adc_bytes"]) / 1024 / 1024,
255
+ )
256
 
257
  return case_files
258
 
259
+ def _download_case_from_parquet(self, file_idx: int, subject_id: str) -> dict[str, bytes]:
260
+ """Download case data directly from individual parquet file.
261
+
262
+ Uses HfFileSystem + pyarrow to read only the columns we need from
263
+ a single parquet file, avoiding the need to download the full dataset.
264
+
265
+ Args:
266
+ file_idx: Index of the parquet file (0-148)
267
+ subject_id: Expected subject ID (for validation)
268
+
269
+ Returns:
270
+ Dict with dwi_bytes, adc_bytes, and optionally mask_bytes
271
+ """
272
+ import pyarrow.parquet as pq # type: ignore[import-untyped]
273
+ from huggingface_hub import HfFileSystem
274
+
275
+ from stroke_deepisles_demo.data.constants import ISLES24_NUM_FILES
276
+
277
+ # Construct path to the specific parquet file
278
+ fpath = f"datasets/{self.dataset_id}/data/train-{file_idx:05d}-of-{ISLES24_NUM_FILES:05d}.parquet"
279
+
280
+ try:
281
+ fs = HfFileSystem()
282
+ with fs.open(fpath, "rb") as f:
283
+ pf = pq.ParquetFile(f)
284
+ # Read only the columns we need
285
+ table = pf.read(columns=["subject_id", "dwi", "adc", "lesion_mask"])
286
+ df = table.to_pandas()
287
+
288
+ if len(df) != 1:
289
+ raise DataLoadError(f"Expected 1 row in parquet file, got {len(df)}: {fpath}")
290
+
291
+ row = df.iloc[0]
292
+
293
+ # Validate subject_id matches
294
+ actual_subject_id = row["subject_id"]
295
+ if actual_subject_id != subject_id:
296
+ raise DataLoadError(
297
+ f"Subject ID mismatch: expected {subject_id}, got {actual_subject_id} in {fpath}"
298
+ )
299
+
300
+ # Extract bytes with defensive error handling
301
+ try:
302
+ dwi_bytes = row["dwi"]["bytes"]
303
+ adc_bytes = row["adc"]["bytes"]
304
+ except (KeyError, TypeError) as e:
305
+ raise DataLoadError(
306
+ f"Malformed HuggingFace data for {subject_id}: missing 'dwi' or 'adc' bytes. "
307
+ f"The dataset schema may have changed. Error: {e}"
308
+ ) from e
309
+
310
+ result: dict[str, bytes] = {
311
+ "dwi_bytes": dwi_bytes,
312
+ "adc_bytes": adc_bytes,
313
+ }
314
+
315
+ # Extract mask if available
316
+ mask_data = row.get("lesion_mask")
317
+ if mask_data is not None and isinstance(mask_data, dict) and mask_data.get("bytes"):
318
+ result["mask_bytes"] = mask_data["bytes"]
319
+
320
+ return result
321
+
322
+ except Exception as e:
323
+ if isinstance(e, DataLoadError):
324
+ raise
325
+ raise DataLoadError(f"Failed to download case {subject_id} from {fpath}: {e}") from e
326
+
327
  def cleanup(self) -> None:
328
  """Remove temp directory and clear cache."""
329
  if self._temp_dir and self._temp_dir.exists():
 
335
 
336
  def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
337
  """
338
+ Build ISLES24 dataset adapter for HuggingFace Hub.
339
 
340
+ Uses pre-computed case IDs to avoid streaming enumeration (which hangs
341
+ due to PyArrow bug apache/arrow#45214). Actual data is downloaded lazily
342
+ from individual parquet files when get_case() is called.
343
 
344
  Args:
345
  dataset_id: HuggingFace dataset identifier (e.g., "hugging-science/isles24-stroke")
 
347
  Returns:
348
  HuggingFaceDataset providing case access
349
  """
350
+ from stroke_deepisles_demo.data.constants import (
351
+ ISLES24_CASE_IDS,
352
+ ISLES24_CASE_INDEX,
353
+ ISLES24_DATASET_ID,
354
+ )
 
 
 
355
 
356
+ # Validate dataset_id matches our pre-computed constants
357
+ if dataset_id != ISLES24_DATASET_ID:
358
+ logger.warning(
359
+ "Dataset ID '%s' does not match pre-computed constants for '%s'. "
360
+ "Case IDs may be incorrect.",
361
+ dataset_id,
362
+ ISLES24_DATASET_ID,
363
+ )
364
 
365
+ logger.info(
366
+ "Building HuggingFace dataset adapter: %s (%d cases, pre-computed)",
367
+ dataset_id,
368
+ len(ISLES24_CASE_IDS),
369
+ )
370
 
 
371
  return HuggingFaceDataset(
372
  dataset_id=dataset_id,
373
+ _case_ids=list(ISLES24_CASE_IDS),
374
+ _case_index=dict(ISLES24_CASE_INDEX),
375
  )
src/stroke_deepisles_demo/data/constants.py ADDED
@@ -0,0 +1,181 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Pre-computed constants for ISLES24 dataset.
2
+
3
+ The ISLES24 challenge dataset is static (case IDs will never change).
4
+ Pre-computing these values avoids:
5
+ 1. PyArrow streaming bug (apache/arrow#45214) that hangs on parquet iteration
6
+ 2. Memory issues from downloading the full 99GB dataset
7
+
8
+ See docs/specs/08-bug-hf-spaces-dataset-loop.md for full investigation.
9
+ """
10
+
11
+ # Pre-computed case IDs for ISLES24 dataset
12
+ # Extracted via HfFileSystem enumeration on 2025-12-08
13
+ # Order matches parquet file indices (train-00000-of-00149.parquet = index 0)
14
+ ISLES24_CASE_IDS: tuple[str, ...] = (
15
+ "sub-stroke0001",
16
+ "sub-stroke0002",
17
+ "sub-stroke0003",
18
+ "sub-stroke0004",
19
+ "sub-stroke0005",
20
+ "sub-stroke0006",
21
+ "sub-stroke0007",
22
+ "sub-stroke0008",
23
+ "sub-stroke0009",
24
+ "sub-stroke0010",
25
+ "sub-stroke0011",
26
+ "sub-stroke0012",
27
+ "sub-stroke0013",
28
+ "sub-stroke0014",
29
+ "sub-stroke0015",
30
+ "sub-stroke0016",
31
+ "sub-stroke0017",
32
+ "sub-stroke0019",
33
+ "sub-stroke0020",
34
+ "sub-stroke0021",
35
+ "sub-stroke0022",
36
+ "sub-stroke0025",
37
+ "sub-stroke0026",
38
+ "sub-stroke0027",
39
+ "sub-stroke0028",
40
+ "sub-stroke0030",
41
+ "sub-stroke0033",
42
+ "sub-stroke0036",
43
+ "sub-stroke0037",
44
+ "sub-stroke0038",
45
+ "sub-stroke0040",
46
+ "sub-stroke0043",
47
+ "sub-stroke0045",
48
+ "sub-stroke0047",
49
+ "sub-stroke0048",
50
+ "sub-stroke0049",
51
+ "sub-stroke0052",
52
+ "sub-stroke0053",
53
+ "sub-stroke0054",
54
+ "sub-stroke0055",
55
+ "sub-stroke0057",
56
+ "sub-stroke0062",
57
+ "sub-stroke0066",
58
+ "sub-stroke0068",
59
+ "sub-stroke0070",
60
+ "sub-stroke0071",
61
+ "sub-stroke0073",
62
+ "sub-stroke0074",
63
+ "sub-stroke0075",
64
+ "sub-stroke0076",
65
+ "sub-stroke0077",
66
+ "sub-stroke0078",
67
+ "sub-stroke0079",
68
+ "sub-stroke0080",
69
+ "sub-stroke0081",
70
+ "sub-stroke0082",
71
+ "sub-stroke0083",
72
+ "sub-stroke0084",
73
+ "sub-stroke0085",
74
+ "sub-stroke0086",
75
+ "sub-stroke0087",
76
+ "sub-stroke0088",
77
+ "sub-stroke0089",
78
+ "sub-stroke0090",
79
+ "sub-stroke0091",
80
+ "sub-stroke0092",
81
+ "sub-stroke0093",
82
+ "sub-stroke0094",
83
+ "sub-stroke0095",
84
+ "sub-stroke0096",
85
+ "sub-stroke0097",
86
+ "sub-stroke0098",
87
+ "sub-stroke0099",
88
+ "sub-stroke0100",
89
+ "sub-stroke0101",
90
+ "sub-stroke0102",
91
+ "sub-stroke0103",
92
+ "sub-stroke0104",
93
+ "sub-stroke0105",
94
+ "sub-stroke0106",
95
+ "sub-stroke0107",
96
+ "sub-stroke0108",
97
+ "sub-stroke0109",
98
+ "sub-stroke0110",
99
+ "sub-stroke0111",
100
+ "sub-stroke0112",
101
+ "sub-stroke0113",
102
+ "sub-stroke0114",
103
+ "sub-stroke0115",
104
+ "sub-stroke0116",
105
+ "sub-stroke0117",
106
+ "sub-stroke0118",
107
+ "sub-stroke0119",
108
+ "sub-stroke0133",
109
+ "sub-stroke0134",
110
+ "sub-stroke0135",
111
+ "sub-stroke0136",
112
+ "sub-stroke0137",
113
+ "sub-stroke0138",
114
+ "sub-stroke0139",
115
+ "sub-stroke0140",
116
+ "sub-stroke0141",
117
+ "sub-stroke0142",
118
+ "sub-stroke0143",
119
+ "sub-stroke0144",
120
+ "sub-stroke0145",
121
+ "sub-stroke0146",
122
+ "sub-stroke0147",
123
+ "sub-stroke0148",
124
+ "sub-stroke0149",
125
+ "sub-stroke0150",
126
+ "sub-stroke0151",
127
+ "sub-stroke0152",
128
+ "sub-stroke0153",
129
+ "sub-stroke0154",
130
+ "sub-stroke0155",
131
+ "sub-stroke0156",
132
+ "sub-stroke0157",
133
+ "sub-stroke0158",
134
+ "sub-stroke0159",
135
+ "sub-stroke0161",
136
+ "sub-stroke0162",
137
+ "sub-stroke0163",
138
+ "sub-stroke0164",
139
+ "sub-stroke0165",
140
+ "sub-stroke0166",
141
+ "sub-stroke0167",
142
+ "sub-stroke0168",
143
+ "sub-stroke0169",
144
+ "sub-stroke0170",
145
+ "sub-stroke0171",
146
+ "sub-stroke0172",
147
+ "sub-stroke0173",
148
+ "sub-stroke0174",
149
+ "sub-stroke0175",
150
+ "sub-stroke0176",
151
+ "sub-stroke0177",
152
+ "sub-stroke0178",
153
+ "sub-stroke0179",
154
+ "sub-stroke0180",
155
+ "sub-stroke0181",
156
+ "sub-stroke0182",
157
+ "sub-stroke0183",
158
+ "sub-stroke0184",
159
+ "sub-stroke0185",
160
+ "sub-stroke0186",
161
+ "sub-stroke0187",
162
+ "sub-stroke0188",
163
+ "sub-stroke0189",
164
+ )
165
+
166
+ # Mapping from case ID to parquet file index (0-indexed)
167
+ # train-00000-of-00149.parquet contains sub-stroke0001
168
+ # train-00001-of-00149.parquet contains sub-stroke0002
169
+ # etc.
170
+ ISLES24_CASE_INDEX: dict[str, int] = {case_id: idx for idx, case_id in enumerate(ISLES24_CASE_IDS)}
171
+
172
+ # Total number of parquet files in the dataset
173
+ ISLES24_NUM_FILES: int = 149
174
+
175
+ # Sanity check: ensure constants are consistent
176
+ assert len(ISLES24_CASE_IDS) == ISLES24_NUM_FILES, (
177
+ f"ISLES24_CASE_IDS has {len(ISLES24_CASE_IDS)} entries but ISLES24_NUM_FILES is {ISLES24_NUM_FILES}"
178
+ )
179
+
180
+ # Dataset identifier on HuggingFace Hub
181
+ ISLES24_DATASET_ID: str = "hugging-science/isles24-stroke"
tests/data/test_hf_adapter.py CHANGED
@@ -1,8 +1,7 @@
1
- """Unit tests for HuggingFace dataset adapter with mocked HF dataset."""
2
 
3
  from __future__ import annotations
4
 
5
- from typing import Any
6
  from unittest.mock import MagicMock, patch
7
 
8
  import pytest
@@ -11,116 +10,122 @@ from stroke_deepisles_demo.core.exceptions import DataLoadError
11
  from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, build_huggingface_dataset
12
 
13
 
14
- def create_mock_hf_example(subject_id: str, include_mask: bool = True) -> dict[str, Any]:
15
- """Create a mock HuggingFace dataset example."""
16
- example: dict[str, Any] = {
17
- "subject_id": subject_id,
18
- "dwi": {"bytes": b"fake_dwi_nifti_data", "path": f"{subject_id}_dwi.nii.gz"},
19
- "adc": {"bytes": b"fake_adc_nifti_data", "path": f"{subject_id}_adc.nii.gz"},
20
- }
21
- if include_mask:
22
- example["lesion_mask"] = {
23
- "bytes": b"fake_mask_nifti_data",
24
- "path": f"{subject_id}_lesion-msk.nii.gz",
25
- }
26
- else:
27
- example["lesion_mask"] = None
28
- return example
29
-
30
-
31
- @pytest.fixture
32
- def mock_hf_dataset() -> MagicMock:
33
- """Create a mock HuggingFace dataset with 3 subjects."""
34
- examples = [
35
- create_mock_hf_example("sub-stroke0001"),
36
- create_mock_hf_example("sub-stroke0002"),
37
- create_mock_hf_example("sub-stroke0003", include_mask=False),
38
- ]
39
-
40
- mock_ds = MagicMock()
41
- mock_ds.__len__ = MagicMock(return_value=len(examples))
42
- mock_ds.__iter__ = MagicMock(return_value=iter(examples))
43
- mock_ds.__getitem__ = MagicMock(side_effect=lambda i: examples[i])
44
-
45
- return mock_ds
46
-
47
-
48
  class TestHuggingFaceDataset:
49
  """Tests for HuggingFaceDataset class."""
50
 
51
- def test_get_case_writes_files_to_temp_dir(self, mock_hf_dataset: MagicMock) -> None:
52
  """Test that get_case writes NIfTI bytes to temp files."""
53
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
 
 
54
  ds = HuggingFaceDataset(
55
  dataset_id="test/dataset",
56
- _hf_dataset=mock_hf_dataset,
57
  _case_ids=case_ids,
 
58
  )
59
 
60
- try:
61
- case = ds.get_case(0)
 
 
 
 
62
 
63
- assert "dwi" in case
64
- assert "adc" in case
65
- assert case["dwi"].exists()
66
- assert case["adc"].exists()
67
- assert case["dwi"].read_bytes() == b"fake_dwi_nifti_data"
68
- assert case["adc"].read_bytes() == b"fake_adc_nifti_data"
 
 
 
 
69
  finally:
70
  ds.cleanup()
71
 
72
- def test_get_case_includes_ground_truth_when_available(
73
- self, mock_hf_dataset: MagicMock
74
- ) -> None:
75
  """Test that ground truth is included when lesion_mask is present."""
76
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
 
 
77
  ds = HuggingFaceDataset(
78
  dataset_id="test/dataset",
79
- _hf_dataset=mock_hf_dataset,
80
  _case_ids=case_ids,
 
81
  )
82
 
83
  try:
84
- case = ds.get_case(0) # Has mask
85
- assert "ground_truth" in case
86
- assert case["ground_truth"].read_bytes() == b"fake_mask_nifti_data"
87
-
88
- case_no_mask = ds.get_case(2) # No mask
89
- assert "ground_truth" not in case_no_mask
 
 
 
 
 
 
 
 
 
 
 
 
 
90
  finally:
91
  ds.cleanup()
92
 
93
- def test_get_case_caches_results(self, mock_hf_dataset: MagicMock) -> None:
94
  """Test that get_case returns cached paths on subsequent calls."""
95
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
 
 
96
  ds = HuggingFaceDataset(
97
  dataset_id="test/dataset",
98
- _hf_dataset=mock_hf_dataset,
99
  _case_ids=case_ids,
 
100
  )
101
 
 
 
 
 
 
102
  try:
103
- case1 = ds.get_case(0)
104
- case2 = ds.get_case(0)
 
 
 
105
 
106
- # Same object returned (cached)
107
- assert case1 is case2
108
 
109
- # Dataset was only accessed once
110
- assert mock_hf_dataset.__getitem__.call_count == 1
111
  finally:
112
  ds.cleanup()
113
 
114
- def test_context_manager_cleans_up_temp_files(self, mock_hf_dataset: MagicMock) -> None:
115
  """Test that using context manager cleans up temp files."""
116
  case_ids = ["sub-stroke0001"]
 
 
117
  ds = HuggingFaceDataset(
118
  dataset_id="test/dataset",
119
- _hf_dataset=mock_hf_dataset,
120
  _case_ids=case_ids,
 
121
  )
122
 
123
- with ds:
 
 
 
 
 
124
  case = ds.get_case(0)
125
  temp_dir = case["dwi"].parent.parent
126
  assert temp_dir.exists()
@@ -128,60 +133,163 @@ class TestHuggingFaceDataset:
128
  # After context exit, temp dir should be gone
129
  assert not temp_dir.exists()
130
 
131
- def test_cleanup_clears_cache(self, mock_hf_dataset: MagicMock) -> None:
132
  """Test that cleanup clears the case cache."""
133
  case_ids = ["sub-stroke0001"]
 
 
134
  ds = HuggingFaceDataset(
135
  dataset_id="test/dataset",
136
- _hf_dataset=mock_hf_dataset,
137
  _case_ids=case_ids,
 
138
  )
139
 
140
- ds.get_case(0)
141
- assert len(ds._cached_cases) == 1
 
 
 
 
 
 
142
 
143
  ds.cleanup()
144
  assert len(ds._cached_cases) == 0
145
 
146
- def test_get_case_raises_data_load_error_on_malformed_data(self) -> None:
147
- """Test that get_case raises DataLoadError for malformed HF data."""
148
- # Create mock with missing 'bytes' key
149
- malformed_example = {"subject_id": "sub-stroke0001", "dwi": {}, "adc": {}}
150
- mock_ds = MagicMock()
151
- mock_ds.__len__ = MagicMock(return_value=1)
152
- mock_ds.__getitem__ = MagicMock(return_value=malformed_example)
153
 
154
  ds = HuggingFaceDataset(
155
  dataset_id="test/dataset",
156
- _hf_dataset=mock_ds,
157
- _case_ids=["sub-stroke0001"],
158
  )
159
 
 
 
 
 
 
160
  try:
161
- with pytest.raises(DataLoadError, match="Malformed HuggingFace data"):
162
- ds.get_case(0)
 
 
 
 
 
163
  finally:
164
  ds.cleanup()
165
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
166
 
167
  class TestBuildHuggingFaceDataset:
168
  """Tests for build_huggingface_dataset function."""
169
 
170
- @patch("datasets.load_dataset")
171
- def test_loads_dataset_from_hub(self, mock_load_dataset: MagicMock) -> None:
172
- """Test that build_huggingface_dataset uses streaming to enumerate case IDs."""
173
- mock_streaming_ds = MagicMock()
174
- mock_streaming_ds.__iter__ = MagicMock(
175
- return_value=iter([{"subject_id": "sub-stroke0001"}])
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
176
  )
177
- mock_load_dataset.return_value = mock_streaming_ds
178
 
179
- result = build_huggingface_dataset("test/my-dataset")
 
 
 
 
 
 
 
 
 
 
180
 
181
- # Should use streaming mode for initial case ID enumeration
182
- mock_load_dataset.assert_called_once_with("test/my-dataset", split="train", streaming=True)
183
- assert isinstance(result, HuggingFaceDataset)
184
- assert result.dataset_id == "test/my-dataset"
185
- assert result._case_ids == ["sub-stroke0001"]
186
- # Dataset should be None initially (lazy load)
187
- assert result._hf_dataset is None
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Unit tests for HuggingFace dataset adapter with mocked HF data access."""
2
 
3
  from __future__ import annotations
4
 
 
5
  from unittest.mock import MagicMock, patch
6
 
7
  import pytest
 
10
  from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, build_huggingface_dataset
11
 
12
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
13
  class TestHuggingFaceDataset:
14
  """Tests for HuggingFaceDataset class."""
15
 
16
+ def test_get_case_writes_files_to_temp_dir(self) -> None:
17
  """Test that get_case writes NIfTI bytes to temp files."""
18
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
19
+ case_index = {cid: idx for idx, cid in enumerate(case_ids)}
20
+
21
  ds = HuggingFaceDataset(
22
  dataset_id="test/dataset",
 
23
  _case_ids=case_ids,
24
+ _case_index=case_index,
25
  )
26
 
27
+ # Mock the download method
28
+ mock_data = {
29
+ "dwi_bytes": b"fake_dwi_nifti_data",
30
+ "adc_bytes": b"fake_adc_nifti_data",
31
+ "mask_bytes": b"fake_mask_nifti_data",
32
+ }
33
 
34
+ try:
35
+ with patch.object(ds, "_download_case_from_parquet", return_value=mock_data):
36
+ case = ds.get_case(0)
37
+
38
+ assert "dwi" in case
39
+ assert "adc" in case
40
+ assert case["dwi"].exists()
41
+ assert case["adc"].exists()
42
+ assert case["dwi"].read_bytes() == b"fake_dwi_nifti_data"
43
+ assert case["adc"].read_bytes() == b"fake_adc_nifti_data"
44
  finally:
45
  ds.cleanup()
46
 
47
+ def test_get_case_includes_ground_truth_when_available(self) -> None:
 
 
48
  """Test that ground truth is included when lesion_mask is present."""
49
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
50
+ case_index = {cid: idx for idx, cid in enumerate(case_ids)}
51
+
52
  ds = HuggingFaceDataset(
53
  dataset_id="test/dataset",
 
54
  _case_ids=case_ids,
55
+ _case_index=case_index,
56
  )
57
 
58
  try:
59
+ # Case with mask
60
+ mock_data_with_mask = {
61
+ "dwi_bytes": b"fake_dwi_nifti_data",
62
+ "adc_bytes": b"fake_adc_nifti_data",
63
+ "mask_bytes": b"fake_mask_nifti_data",
64
+ }
65
+ with patch.object(ds, "_download_case_from_parquet", return_value=mock_data_with_mask):
66
+ case = ds.get_case(0)
67
+ assert "ground_truth" in case
68
+ assert case["ground_truth"].read_bytes() == b"fake_mask_nifti_data"
69
+
70
+ # Case without mask
71
+ mock_data_no_mask = {
72
+ "dwi_bytes": b"fake_dwi_nifti_data",
73
+ "adc_bytes": b"fake_adc_nifti_data",
74
+ }
75
+ with patch.object(ds, "_download_case_from_parquet", return_value=mock_data_no_mask):
76
+ case_no_mask = ds.get_case(2)
77
+ assert "ground_truth" not in case_no_mask
78
  finally:
79
  ds.cleanup()
80
 
81
+ def test_get_case_caches_results(self) -> None:
82
  """Test that get_case returns cached paths on subsequent calls."""
83
  case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
84
+ case_index = {cid: idx for idx, cid in enumerate(case_ids)}
85
+
86
  ds = HuggingFaceDataset(
87
  dataset_id="test/dataset",
 
88
  _case_ids=case_ids,
89
+ _case_index=case_index,
90
  )
91
 
92
+ mock_data = {
93
+ "dwi_bytes": b"fake_dwi_nifti_data",
94
+ "adc_bytes": b"fake_adc_nifti_data",
95
+ }
96
+
97
  try:
98
+ with patch.object(
99
+ ds, "_download_case_from_parquet", return_value=mock_data
100
+ ) as mock_download:
101
+ case1 = ds.get_case(0)
102
+ case2 = ds.get_case(0)
103
 
104
+ # Same object returned (cached)
105
+ assert case1 is case2
106
 
107
+ # Download was only called once
108
+ assert mock_download.call_count == 1
109
  finally:
110
  ds.cleanup()
111
 
112
+ def test_context_manager_cleans_up_temp_files(self) -> None:
113
  """Test that using context manager cleans up temp files."""
114
  case_ids = ["sub-stroke0001"]
115
+ case_index = {"sub-stroke0001": 0}
116
+
117
  ds = HuggingFaceDataset(
118
  dataset_id="test/dataset",
 
119
  _case_ids=case_ids,
120
+ _case_index=case_index,
121
  )
122
 
123
+ mock_data = {
124
+ "dwi_bytes": b"fake_dwi_nifti_data",
125
+ "adc_bytes": b"fake_adc_nifti_data",
126
+ }
127
+
128
+ with patch.object(ds, "_download_case_from_parquet", return_value=mock_data), ds:
129
  case = ds.get_case(0)
130
  temp_dir = case["dwi"].parent.parent
131
  assert temp_dir.exists()
 
133
  # After context exit, temp dir should be gone
134
  assert not temp_dir.exists()
135
 
136
+ def test_cleanup_clears_cache(self) -> None:
137
  """Test that cleanup clears the case cache."""
138
  case_ids = ["sub-stroke0001"]
139
+ case_index = {"sub-stroke0001": 0}
140
+
141
  ds = HuggingFaceDataset(
142
  dataset_id="test/dataset",
 
143
  _case_ids=case_ids,
144
+ _case_index=case_index,
145
  )
146
 
147
+ mock_data = {
148
+ "dwi_bytes": b"fake_dwi_nifti_data",
149
+ "adc_bytes": b"fake_adc_nifti_data",
150
+ }
151
+
152
+ with patch.object(ds, "_download_case_from_parquet", return_value=mock_data):
153
+ ds.get_case(0)
154
+ assert len(ds._cached_cases) == 1
155
 
156
  ds.cleanup()
157
  assert len(ds._cached_cases) == 0
158
 
159
+ def test_get_case_by_string_id(self) -> None:
160
+ """Test that get_case works with string case IDs."""
161
+ case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
162
+ case_index = {cid: idx for idx, cid in enumerate(case_ids)}
 
 
 
163
 
164
  ds = HuggingFaceDataset(
165
  dataset_id="test/dataset",
166
+ _case_ids=case_ids,
167
+ _case_index=case_index,
168
  )
169
 
170
+ mock_data = {
171
+ "dwi_bytes": b"fake_dwi_nifti_data",
172
+ "adc_bytes": b"fake_adc_nifti_data",
173
+ }
174
+
175
  try:
176
+ with patch.object(
177
+ ds, "_download_case_from_parquet", return_value=mock_data
178
+ ) as mock_download:
179
+ case = ds.get_case("sub-stroke0002")
180
+ assert case["dwi"].exists()
181
+ # Should have been called with index 1 (second case)
182
+ mock_download.assert_called_once_with(1, "sub-stroke0002")
183
  finally:
184
  ds.cleanup()
185
 
186
+ def test_get_case_raises_key_error_for_invalid_id(self) -> None:
187
+ """Test that get_case raises KeyError for invalid case ID."""
188
+ case_ids = ["sub-stroke0001"]
189
+ case_index = {"sub-stroke0001": 0}
190
+
191
+ ds = HuggingFaceDataset(
192
+ dataset_id="test/dataset",
193
+ _case_ids=case_ids,
194
+ _case_index=case_index,
195
+ )
196
+
197
+ with pytest.raises(KeyError, match="not found in dataset"):
198
+ ds.get_case("sub-stroke9999")
199
+
200
+ def test_get_case_raises_index_error_for_out_of_range(self) -> None:
201
+ """Test that get_case raises IndexError for out of range index."""
202
+ case_ids = ["sub-stroke0001"]
203
+ case_index = {"sub-stroke0001": 0}
204
+
205
+ ds = HuggingFaceDataset(
206
+ dataset_id="test/dataset",
207
+ _case_ids=case_ids,
208
+ _case_index=case_index,
209
+ )
210
+
211
+ with pytest.raises(IndexError, match="out of range"):
212
+ ds.get_case(99)
213
+
214
 
215
  class TestBuildHuggingFaceDataset:
216
  """Tests for build_huggingface_dataset function."""
217
 
218
+ def test_uses_precomputed_case_ids(self) -> None:
219
+ """Test that build_huggingface_dataset uses pre-computed case IDs."""
220
+ result = build_huggingface_dataset("hugging-science/isles24-stroke")
221
+
222
+ assert isinstance(result, HuggingFaceDataset)
223
+ assert result.dataset_id == "hugging-science/isles24-stroke"
224
+ # Should have 149 cases from pre-computed list
225
+ assert len(result._case_ids) == 149
226
+ assert "sub-stroke0001" in result._case_ids
227
+ assert "sub-stroke0189" in result._case_ids
228
+
229
+ def test_case_index_mapping_is_correct(self) -> None:
230
+ """Test that case index mapping matches case IDs order."""
231
+ result = build_huggingface_dataset("hugging-science/isles24-stroke")
232
+
233
+ # First case should map to index 0
234
+ assert result._case_index["sub-stroke0001"] == 0
235
+ # Last case should map to index 148
236
+ assert result._case_index["sub-stroke0189"] == 148
237
+
238
+ def test_warns_for_different_dataset_id(self) -> None:
239
+ """Test that a warning is logged for non-standard dataset IDs."""
240
+ from stroke_deepisles_demo.data.adapter import logger
241
+
242
+ with patch.object(logger, "warning") as mock_warning:
243
+ build_huggingface_dataset("some-other/dataset")
244
+ mock_warning.assert_called_once()
245
+ assert "does not match pre-computed constants" in mock_warning.call_args[0][0]
246
+
247
+
248
+ class TestDownloadCaseFromParquet:
249
+ """Tests for _download_case_from_parquet method."""
250
+
251
+ def test_raises_data_load_error_on_malformed_data(self) -> None:
252
+ """Test that _download_case_from_parquet raises DataLoadError for malformed data."""
253
+ import pandas as pd # type: ignore[import-untyped]
254
+
255
+ case_ids = ["sub-stroke0001"]
256
+ case_index = {"sub-stroke0001": 0}
257
+
258
+ ds = HuggingFaceDataset(
259
+ dataset_id="test/dataset",
260
+ _case_ids=case_ids,
261
+ _case_index=case_index,
262
  )
 
263
 
264
+ # Create mock with missing 'bytes' key
265
+ mock_df = pd.DataFrame(
266
+ [
267
+ {
268
+ "subject_id": "sub-stroke0001",
269
+ "dwi": {}, # Missing 'bytes'
270
+ "adc": {},
271
+ "lesion_mask": None,
272
+ }
273
+ ]
274
+ )
275
 
276
+ mock_table = MagicMock()
277
+ mock_table.to_pandas.return_value = mock_df
278
+
279
+ mock_pf = MagicMock()
280
+ mock_pf.read.return_value = mock_table
281
+
282
+ mock_file = MagicMock()
283
+ mock_file.__enter__ = MagicMock(return_value=mock_file)
284
+ mock_file.__exit__ = MagicMock(return_value=False)
285
+
286
+ mock_fs = MagicMock()
287
+ mock_fs.open.return_value = mock_file
288
+
289
+ # Patch at the source module where they're imported, not where they're used
290
+ with (
291
+ patch("huggingface_hub.HfFileSystem", return_value=mock_fs),
292
+ patch("pyarrow.parquet.ParquetFile", return_value=mock_pf),
293
+ pytest.raises(DataLoadError, match="Malformed HuggingFace data"),
294
+ ):
295
+ ds._download_case_from_parquet(0, "sub-stroke0001")
tests/data/test_loader.py CHANGED
@@ -4,11 +4,11 @@ from __future__ import annotations
4
 
5
  import os
6
  from typing import TYPE_CHECKING
 
7
 
8
  import pytest
9
- from datasets.exceptions import DatasetNotFoundError
10
 
11
- from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, LocalDataset
12
  from stroke_deepisles_demo.data.loader import load_isles_dataset
13
 
14
  if TYPE_CHECKING:
@@ -35,10 +35,20 @@ def test_load_from_local_finds_all_cases(synthetic_isles_dir: Path) -> None:
35
  assert dataset.list_case_ids() == ["sub-stroke0001", "sub-stroke0002"]
36
 
37
 
38
- def test_load_hf_raises_on_invalid_dataset() -> None:
39
- """Test that loading a non-existent HF dataset raises DatasetNotFoundError."""
40
- with pytest.raises(DatasetNotFoundError):
41
- load_isles_dataset(source="fake/nonexistent-dataset", local_mode=False)
 
 
 
 
 
 
 
 
 
 
42
 
43
 
44
  @pytest.mark.integration
 
4
 
5
  import os
6
  from typing import TYPE_CHECKING
7
+ from unittest.mock import patch
8
 
9
  import pytest
 
10
 
11
+ from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, LocalDataset, logger
12
  from stroke_deepisles_demo.data.loader import load_isles_dataset
13
 
14
  if TYPE_CHECKING:
 
35
  assert dataset.list_case_ids() == ["sub-stroke0001", "sub-stroke0002"]
36
 
37
 
38
+ def test_load_hf_warns_on_non_standard_dataset() -> None:
39
+ """Test that loading a non-standard HF dataset logs a warning.
40
+
41
+ Note: With pre-computed case IDs, the dataset ID mismatch is only detected
42
+ at build time (warning logged), not at get_case() time. The actual 404 error
43
+ would only occur when trying to download a case that doesn't exist.
44
+ """
45
+ with patch.object(logger, "warning") as mock_warning:
46
+ ds = load_isles_dataset(source="fake/nonexistent-dataset", local_mode=False)
47
+ mock_warning.assert_called_once()
48
+ assert "does not match pre-computed constants" in mock_warning.call_args[0][0]
49
+ # Dataset is still created with pre-computed case IDs
50
+ assert isinstance(ds, HuggingFaceDataset)
51
+ assert len(ds) == 149 # Uses pre-computed list
52
 
53
 
54
  @pytest.mark.integration