Check uniqueness of input paths and obs_ids in merge tool

docs/changes/2611.feature.rst

@@ -0,0 +1,6 @@
+The ``ctapipe-merge`` tool now checks for duplicated input files and
+raises an error in that case.
+
+The ``HDF5Merger`` class, and thus also the ``ctapipe-merge`` tool,
+now checks for duplicated obs_ids during merging, to prevent
+invalid output files.

src/ctapipe/conftest.py

@@ -592,6 +592,14 @@ def proton_train_clf(model_tmp_path, energy_regressor_path):
         ],
         raises=True,
     )
+
+    # modify obs_ids by adding a constant, this enables merging gamma and proton files
+    # which is used in the merge tool tests.
+    with tables.open_file(outpath, mode="r+") as f:
+        for table in f.walk_nodes("/", "Table"):
+            if "obs_id" in table.colnames:
+                obs_id = table.col("obs_id")
+                table.modify_column(colname="obs_id", column=obs_id + 1_000_000_000)
     return outpath
 
 

src/ctapipe/io/hdf5merger.py

@@ -188,6 +188,8 @@ def __init__(self, output_path=None, **kwargs):
         self.data_model_version = None
         self.subarray = None
         self.meta = None
+        self._merged_obs_ids = set()
+
         # output file existed, so read subarray and data model version to make sure
         # any file given matches what we already have
         if appending:
@@ -202,6 +204,9 @@ def __init__(self, output_path=None, **kwargs):
             )
             self.required_nodes = _get_required_nodes(self.h5file)
 
+            # this will update _merged_obs_ids from existing input file
+            self._check_obs_ids(self.h5file)
+
     def __call__(self, other: str | Path | tables.File):
         """
         Append file ``other`` to the output file
@@ -267,7 +272,32 @@ def _check_can_merge(self, other):
                     f"Required node {node_path} not found in {other.filename}"
                 )
 
+    def _check_obs_ids(self, other):
+        keys = [
+            "/configuration/observation/observation_block",
+            "/dl1/event/subarray/trigger",
+        ]
+
+        for key in keys:
+            if key in other.root:
+                obs_ids = other.root[key].col("obs_id")
+                break
+        else:
+            raise CannotMerge(
+                f"Input file {other.filename} is missing keys required to"
+                f" check for duplicated obs_ids. Tried: {keys}"
+            )
+
+        duplicated = self._merged_obs_ids.intersection(obs_ids)
+        if len(duplicated) > 0:
+            msg = f"Input file {other.filename} contains obs_ids already included in output file: {duplicated}"
+            raise CannotMerge(msg)
+
+        self._merged_obs_ids.update(obs_ids)
+
     def _append(self, other):
+        self._check_obs_ids(other)
+
         # Configuration
         self._append_subarray(other)
 

src/ctapipe/io/tests/test_merge.py

@@ -68,7 +68,7 @@ def test_simple(tmp_path, gamma_train_clf, proton_train_clf):
         merger(proton_train_clf)
 
     subarray = SubarrayDescription.from_hdf(gamma_train_clf)
-    assert subarray == SubarrayDescription.from_hdf(output), "Subarays do not match"
+    assert subarray == SubarrayDescription.from_hdf(output), "Subarrays do not match"
 
     tel_groups = [
         "/dl1/event/telescope/parameters",
@@ -164,3 +164,28 @@ def test_muon(tmp_path, dl1_muon_output_file):
     n_input = len(input_table)
     assert len(table) == n_input
     assert_table_equal(table, input_table)
+
+
+def test_duplicated_obs_ids(tmp_path, dl2_shower_geometry_file):
+    from ctapipe.io.hdf5merger import CannotMerge, HDF5Merger
+
+    output = tmp_path / "invalid.dl1.h5"
+
+    # check for fresh file
+    with HDF5Merger(output) as merger:
+        merger(dl2_shower_geometry_file)
+
+        with pytest.raises(
+            CannotMerge, match="Input file .* contains obs_ids already included"
+        ):
+            merger(dl2_shower_geometry_file)
+
+    # check for appending
+    with HDF5Merger(output, overwrite=True) as merger:
+        merger(dl2_shower_geometry_file)
+
+    with HDF5Merger(output, append=True) as merger:
+        with pytest.raises(
+            CannotMerge, match="Input file .* contains obs_ids already included"
+        ):
+            merger(dl2_shower_geometry_file)

src/ctapipe/tools/merge.py

@@ -3,6 +3,7 @@
 """
 import sys
 from argparse import ArgumentParser
+from collections import Counter
 from pathlib import Path
 
 from tqdm.auto import tqdm
@@ -161,6 +162,13 @@ def setup(self):
             )
             sys.exit(1)
 
+        counts = Counter(self.input_files)
+        duplicated = [p for p, c in counts.items() if c > 1]
+        if len(duplicated) > 0:
+            raise ToolConfigurationError(
+                f"Same file given multiple times. Duplicated files are: {duplicated}"
+            )
+
         self.merger = self.enter_context(HDF5Merger(parent=self))
         if self.merger.output_path in self.input_files:
             raise ToolConfigurationError(

src/ctapipe/tools/tests/test_merge.py

@@ -5,11 +5,12 @@
 from pathlib import Path
 
 import numpy as np
+import pytest
 import tables
 from astropy.table import vstack
 from astropy.utils.diff import report_diff_values
 
-from ctapipe.core import run_tool
+from ctapipe.core import ToolConfigurationError, run_tool
 from ctapipe.io import TableLoader
 from ctapipe.io.astropy_helpers import read_table
 from ctapipe.io.tests.test_astropy_helpers import assert_table_equal
@@ -176,7 +177,6 @@ def test_muon(tmp_path, dl1_muon_output_file):
         argv=[
             f"--output={output}",
             str(dl1_muon_output_file),
-            str(dl1_muon_output_file),
         ],
         raises=True,
     )
@@ -185,6 +185,24 @@ def test_muon(tmp_path, dl1_muon_output_file):
     input_table = read_table(dl1_muon_output_file, "/dl1/event/telescope/muon/tel_001")
 
     n_input = len(input_table)
-    assert len(table) == 2 * n_input
-    assert_table_equal(table[:n_input], input_table)
-    assert_table_equal(table[n_input:], input_table)
+    assert len(table) == n_input
+    assert_table_equal(table, input_table)
+
+
+def test_duplicated(tmp_path, dl1_file, dl1_proton_file):
+    from ctapipe.tools.merge import MergeTool
+
+    output = tmp_path / "invalid.dl1.h5"
+    with pytest.raises(ToolConfigurationError, match="Same file given multiple times"):
+        run_tool(
+            MergeTool(),
+            argv=[
+                str(dl1_file),
+                str(dl1_proton_file),
+                str(dl1_file),
+                f"--output={output}",
+                "--overwrite",
+            ],
+            cwd=tmp_path,
+            raises=True,
+        )