Potential issue with edge filtering during GConstruct

Ran into this error during CI:

https://github.com/awslabs/graphstorm/actions/runs/15907555054/job/44866847860?pr=1288
```
[2025-06-26T16:53:30.453Z] =================================== FAILURES ===================================
[2025-06-26T16:53:30.453Z] _____________________________ test_parse_edge_data _____________________________
[2025-06-26T16:53:30.453Z] def test_parse_edge_data():
[2025-06-26T16:53:30.453Z] np.random.seed(1)
[2025-06-26T16:53:30.453Z] with tempfile.TemporaryDirectory() as tmpdirname:
[2025-06-26T16:53:30.453Z] str_src_ids = np.array([str(i) for i in range(10)])
[2025-06-26T16:53:30.453Z] str_dst_ids = np.array([str(i) for i in range(15)])
[2025-06-26T16:53:30.453Z] node_id_map = {"src": IdMap(str_src_ids),
[2025-06-26T16:53:30.453Z] "dst": IdMap(str_dst_ids)}
[2025-06-26T16:53:30.453Z]
[2025-06-26T16:53:30.453Z] src_ids = np.array([str(random.randint(0, 20)) for _ in range(15)])
[2025-06-26T16:53:30.453Z] dst_ids = np.array([str(random.randint(0, 25)) for _ in range(15)])
[2025-06-26T16:53:30.453Z] feat = np.random.rand(15, 10)
[2025-06-26T16:53:30.453Z] data = {
[2025-06-26T16:53:30.453Z] "src_id": src_ids,
[2025-06-26T16:53:30.453Z] "dst_id": dst_ids,
[2025-06-26T16:53:30.453Z] "feat": feat,
[2025-06-26T16:53:30.453Z] }
[2025-06-26T16:53:30.453Z]
[2025-06-26T16:53:30.453Z] feat_ops = [Noop("feat", "feat", None)]
[2025-06-26T16:53:30.453Z] label_ops = [
[2025-06-26T16:53:30.453Z] LinkPredictionProcessor(None, None, [0.7,0.1,0.2], None)]
[2025-06-26T16:53:30.453Z] data_file = os.path.join(tmpdirname, "data.parquet")
[2025-06-26T16:53:30.453Z] write_data_parquet(data, data_file)
[2025-06-26T16:53:30.453Z]
[2025-06-26T16:53:30.453Z] conf = {
[2025-06-26T16:53:30.453Z] "source_id_col": "src_id",
[2025-06-26T16:53:30.453Z] "dest_id_col": "dst_id",
[2025-06-26T16:53:30.453Z] "relation": ("src", "rel", "dst"),
[2025-06-26T16:53:30.453Z] "features": [
[2025-06-26T16:53:30.453Z] {"feature_col": "feat", "feature_name": "feat", "feature_dim": [10]}
[2025-06-26T16:53:30.453Z] ]
[2025-06-26T16:53:30.453Z] }
[2025-06-26T16:53:30.453Z] keys = ["src_id", "dst_id", "feat"]
[2025-06-26T16:53:30.453Z] src_ids, dst_ids, feat_data, _ = \
[2025-06-26T16:53:30.453Z] > parse_edge_data(data_file, feat_ops, label_ops, node_id_map,
[2025-06-26T16:53:30.453Z] partial(read_data_parquet, data_fields=keys),
[2025-06-26T16:53:30.453Z] conf, skip_nonexist_edges=True)
[2025-06-26T16:53:30.453Z] tests/unit-tests/gconstruct/test_construct_graph.py:2031:
[2025-06-26T16:53:30.453Z] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
[2025-06-26T16:53:30.453Z] python/graphstorm/gconstruct/construct_graph.py:211: in parse_edge_data
[2025-06-26T16:53:30.453Z] feat_data = {key: feat[dst_exist_locs] \
[2025-06-26T16:53:30.453Z] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
[2025-06-26T16:53:30.453Z] .0 =
[2025-06-26T16:53:30.453Z] > feat_data = {key: feat[dst_exist_locs] \
[2025-06-26T16:53:30.453Z] for key, feat in feat_data.items()}
[2025-06-26T16:53:30.453Z] E IndexError: arrays used as indices must be of integer (or boolean) type
[2025-06-26T16:53:30.453Z] python/graphstorm/gconstruct/construct_graph.py:211: IndexError
[2025-06-26T16:53:30.453Z] ------------------------------ Captured log call -------------------------------
[2025-06-26T16:53:30.453Z] WARNING root:id_map.py:299 source nodes of src do not exist. Skip 10 edges
[2025-06-26T16:53:30.453Z] WARNING root:id_map.py:314 dest nodes of dst do not exist. Skip 5 edges
[2025-06-26T16:53:30.453Z] =============================== warnings summary ===============================
[2025-06-26T16:53:30.453Z] ../usr/local/lib/python3.10/dist-packages/torchdata/datapipes/__init__.py:18
[2025-06-26T16:53:30.453Z] /usr/local/lib/python3.10/dist-packages/torchdata/datapipes/__init__.py:18: UserWarning:
[2025-06-26T16:53:30.453Z] ################################################################################
[2025-06-26T16:53:30.453Z] WARNING!
[2025-06-26T16:53:30.453Z] The 'datapipes', 'dataloader2' modules are deprecated and will be removed in a
[2025-06-26T16:53:30.453Z] future torchdata release! Please see https://github.com/pytorch/data/issues/1196
[2025-06-26T16:53:30.453Z] to learn more and leave feedback.
[2025-06-26T16:53:30.453Z] ################################################################################
[2025-06-26T16:53:30.453Z]
[2025-06-26T16:53:30.453Z] deprecation_warning()
[2025-06-26T16:53:30.453Z] tests/unit-tests/test_gsf.py:681
[2025-06-26T16:53:30.453Z] /graphstorm/tests/unit-tests/test_gsf.py:681: DeprecationWarning: invalid escape sequence '\g'
[2025-06-26T16:53:30.453Z] graph_name = "\graph_name"
[2025-06-26T16:53:30.453Z] tests/unit-tests/gconstruct/test_construct_graph.py::test_process_features_fp16
[2025-06-26T16:53:30.453Z] /graphstorm/python/graphstorm/gconstruct/utils.py:633: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. (Triggered internally at ../torch/csrc/utils/tensor_new.cpp:274.)
[2025-06-26T16:53:30.453Z] arr = th.tensor(self._arr)
[2025-06-26T16:53:30.453Z] tests/unit-tests/gconstruct/test_construct_graph.py::test_label
[2025-06-26T16:53:30.453Z] /graphstorm/python/graphstorm/gconstruct/transform.py:1932: RuntimeWarning: invalid value encountered in cast
[2025-06-26T16:53:30.453Z] res[self.label_name] = np.int32(label)
[2025-06-26T16:53:30.453Z] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
[2025-06-26T16:53:30.453Z] =========================== short test summary info ============================
[2025-06-26T16:53:30.453Z] FAILED tests/unit-tests/gconstruct/test_construct_graph.py::test_parse_edge_data
[2025-06-26T16:53:30.453Z] !!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
[2025-06-26T16:53:30.453Z] =================== 1 failed, 24 passed, 4 warnings in 9.92s ===================
[2025-06-26T16:53:31.344Z] Exit code: 1
```

Potential cause (from GenAI analysis)

The problem is in how the feature data is being indexed in `parse_edge_data` after filtering out non-existent edges.

In `map_node_ids`, when `skip_nonexist_edges=True`, it returns `src_exist_locs` and `dst_exist_locs` to indicate which edges should be kept. However, in `parse_edge_data`, the code is trying to apply these filters sequentially:

```python
if src_exist_locs is not None:
feat_data = {key: feat[src_exist_locs] \
for key, feat in feat_data.items()}
if dst_exist_locs is not None:
feat_data = {key: feat[dst_exist_locs] \
for key, feat in feat_data.items()}
```

The issue is that after applying `src_exist_locs`, the feature data is already filtered, but then it tries to apply `dst_exist_locs` which still contains indices based on the original unfiltered data. This causes the indexing error because `dst_exist_locs` contains indices that are now out of bounds.

Start in python/graphstorm/gconstruct/construct_graph.py at parse_edge_data and reproduce the failure with tests/unit-tests/gconstruct/test_construct_graph.py::test_parse_edge_data. Check how source and destination existence locations are applied to feature data. Done means the test passes when both endpoints contain missing IDs and the retained feature rows match the retained edges.

Written by the indexing model from the issue text.