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Same fixes for error message and read counts by stage #75

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Merged
kathrynmurie merged 3 commits into from
Jun 4, 2026
Merged

Same fixes for error message and read counts by stage #75

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c5f689f
update for better error message when optional fields are provided by …
nickjhathaway Jun 4, 2026
b5893e8
changed missing specimens/library samples into warnings instead of er…
nickjhathaway Jun 4, 2026
87e9dc6
update for pytests for new warnings;
nickjhathaway Jun 4, 2026
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121 changes: 83 additions & 38 deletions src/pmotools/pmo_builder/merge_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
from pmotools.pmo_builder.mhap_table_to_pmo import (
create_minimum_library_specimen_dict_from_mhap_table,
)
import warnings


def _convert_numpy_scalars(obj):
Expand Down Expand Up @@ -86,16 +87,17 @@ def merge_to_pmo(
specimen_names = {item["specimen_name"] for item in specimen_info}

# Check for names in library_sample_info that are not in specimen_info
# Check for names in specimen_info that are not in library_sample_info
missing_in_specimen = library_sample_names - specimen_names
missing_in_library = specimen_names - library_sample_names
for missing_lib_name in missing_in_specimen:
specimen_info.append({"specimen_name": missing_lib_name})
if missing_in_specimen:
raise ValueError(
f"library_sample_names found in the detected_microhaplotypes that don't have corresponding supplied specimen_names: {sorted(missing_in_specimen)}"
warnings.warn(
f"library_sample_names found in the detected_microhaplotypes that don't have corresponding supplied specimen_names: {sorted(missing_in_specimen)}, will be added to specimen_info with no meta"
)

# Check for names in specimen_info that are not in library_sample_info
missing_in_library = specimen_names - library_sample_names
if missing_in_library:
raise ValueError(
warnings.warn(
f"specimen_name were supplied that don't have corresponding library_sample_names in detected_microhaplotypes: {sorted(missing_in_library)}"
)

Expand Down Expand Up @@ -289,12 +291,17 @@ def _replace_names_with_IDs(
):
# SPECIMEN INFO
# replace name with project ID
any_missing_project_names = False
missing_projects = []
if project_info is not None:
missing_projects = _replace_key_with_id(
specimen_info, project_info, "project_name", "project_id"
)
else:
missing_projects = []
for spec in specimen_info:
if "project_name" not in spec:
any_missing_project_names = True
break
if not any_missing_project_names:
missing_projects = _replace_key_with_id(
specimen_info, project_info, "project_name", "project_id"
)

# LIBRARY SAMPLE INFO
# replace with sequencing_info_id, specimen_id, panel_id
Expand All @@ -307,15 +314,20 @@ def _replace_names_with_IDs(
"panel_name",
"panel_id",
)
any_missing_sequence_info_names = False
missing_sequencing = []
if sequencing_info is not None:
missing_sequencing = _replace_key_with_id(
library_sample_info,
sequencing_info,
"sequencing_info_name",
"sequencing_info_id",
)
else:
missing_sequencing = []
for lib_sample in library_sample_info:
if "sequencing_info_name" not in lib_sample:
any_missing_sequence_info_names = True
break
if not any_missing_sequence_info_names:
missing_sequencing = _replace_key_with_id(
library_sample_info,
sequencing_info,
"sequencing_info_name",
"sequencing_info_id",
)

# REP MHAPS
# replace target_name with ID
Expand All @@ -328,15 +340,21 @@ def _replace_names_with_IDs(

# DETECTED MHAPS
# Replace library_sample_name and bioinformatics_run_name
any_missing_bioinfo_run_names = False
missing_bioinfo_runs = []
if bioinfo_run_info is not None:
missing_bioinfo_runs = _replace_key_with_id(
mhap_info["detected_microhaplotypes"],
bioinfo_run_info,
"bioinformatics_run_name",
"bioinformatics_run_id",
)
else:
missing_bioinfo_runs = []
for detected in mhap_info["detected_microhaplotypes"]:
if "bioinformatics_run_name" not in detected:
any_missing_bioinfo_run_names = True
break
if not any_missing_bioinfo_run_names:
missing_bioinfo_runs = _replace_key_with_id(
mhap_info["detected_microhaplotypes"],
bioinfo_run_info,
"bioinformatics_run_name",
"bioinformatics_run_id",
)

lib_sample_lookup = _make_lookup(library_sample_info, "library_sample_name")
missing_libs = []
for detected in mhap_info["detected_microhaplotypes"]:
Expand All @@ -354,17 +372,23 @@ def _replace_names_with_IDs(
missing_read_counts_libs = []
missing_read_counts_targets = []
target_lookup = _make_lookup(panel_target_info["target_info"], "target_name")
any_read_counts_by_stage_missing_bioinfo_run_names = False
if read_counts_by_stage_info is not None:
if bioinfo_run_info is not None:
# Replace bioinformatics_run_name with bioinformatics_run_id
missing_read_counts_bioinfo_runs = _replace_key_with_id(
read_counts_by_stage_info,
bioinfo_run_info,
"bioinformatics_run_name",
"bioinformatics_run_id",
)
else:
missing_read_counts_bioinfo_runs = []
for read_counts_run in read_counts_by_stage_info:
if "bioinformatics_run_name" not in read_counts_run:
any_read_counts_by_stage_missing_bioinfo_run_names = True
break
if not any_read_counts_by_stage_missing_bioinfo_run_names:
if bioinfo_run_info is not None:
# Replace bioinformatics_run_name with bioinformatics_run_id
missing_read_counts_bioinfo_runs = _replace_key_with_id(
read_counts_by_stage_info,
bioinfo_run_info,
"bioinformatics_run_name",
"bioinformatics_run_id",
)
else:
missing_read_counts_bioinfo_runs = []

# Replace library_sample_name with library_sample_id in each run and map targets
for read_counts_run in read_counts_by_stage_info:
Expand All @@ -388,7 +412,28 @@ def _replace_names_with_IDs(
target_entry["target_id"] = target_lookup[target_name]
else:
missing_read_counts_targets.append(target_name)

merging_warnings = []
if any_missing_project_names and project_info:
merging_warnings.append(
"project_info provided but there are specimens missing project_name field"
)
if any_missing_sequence_info_names and sequencing_info:
merging_warnings.append(
"sequencing_info provided but there are library samples missing sequencing_info_name field"
)
if any_missing_bioinfo_run_names and bioinfo_run_info:
merging_warnings.append(
"bioinformatics_run_info provided but there are detected microhaplotypes missing bioinformatics_run_name field"
)
if any_read_counts_by_stage_missing_bioinfo_run_names and bioinfo_run_info:
merging_warnings.append(
"bioinformatics_run_info provided but there are read counts by stage missing bioinformatics_run_name field"
)
if merging_warnings:
warnings_text = "\n".join(merging_warnings)
raise Exception(
f"The following warnings were encountered during merging:\n{warnings_text}"
)
# If any names were missing from reference tables error
_report_missing_IDs(
missing_projects,
Expand Down
20 changes: 12 additions & 8 deletions src/pmotools/pmo_builder/read_count_by_stage_table_to_pmo.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@


def read_count_by_stage_table_to_pmo(
bioinformatics_run_name: str,
total_raw_count_table: pd.DataFrame,
bioinformatics_run_name: str | None = None,
reads_by_stage_table: pd.DataFrame | None = None,
library_sample_name_col: str = "library_sample_name",
target_name_col: str = "target_name",
Expand All @@ -19,10 +19,11 @@ def read_count_by_stage_table_to_pmo(
"""
Convert tables of read counts by stage into PMO read_counts_by_stage format.

:param bioinformatics_run_name: name for the bioinformatics run (column name or individual run name)
:type bioinformatics_run_name: str

:param total_raw_count_table: table with total raw counts per sample
:type total_raw_count_table: pd.DataFrame
:param bioinformatics_run_name: name for the bioinformatics run (column name or individual run name)
:type bioinformatics_run_name: str, optional
:param reads_by_stage_table: table of reads per sample, per locus, per stage. Can be long
format (single stage column) or wide format (multiple stage columns)
:type reads_by_stage_table: pd.DataFrame, optional
Expand Down Expand Up @@ -70,7 +71,10 @@ def read_count_by_stage_table_to_pmo(
check_additional_columns_exist(reads_by_stage_table, additional_target_cols)

# Check if bioinformatics_run_name is a column in total_raw_count_table
if bioinformatics_run_name in total_raw_count_table.columns:
if (
bioinformatics_run_name is not None
and bioinformatics_run_name in total_raw_count_table.columns
):
# Create separate entries for each unique run
output_data_list = []
unique_runs = total_raw_count_table[bioinformatics_run_name].unique()
Expand Down Expand Up @@ -292,14 +296,14 @@ def _process_reads_by_stage_table(
def _build_read_counts_by_stage_output(
library_sample_data: dict,
reads_by_stage_data: dict | None,
bioinformatics_run_name: str,
bioinformatics_run_name: str | None = None,
) -> dict:
"""
Build the final output structure for read_counts_by_stage.

:param library_sample_data: Dictionary with library sample data
:param reads_by_stage_data: Optional dictionary with reads by stage data
:param bioinformatics_run_name: Name for the bioinformatics run
:param bioinformatics_run_name: Optional name for the bioinformatics run

:return: Dictionary formatted for PMO read_counts_by_stage section
"""
Expand Down Expand Up @@ -344,8 +348,8 @@ def _build_read_counts_by_stage_output(

# Build the final output structure
output_data = {
"bioinformatics_run_name": bioinformatics_run_name,
"read_counts_by_library_sample_by_stage": read_counts_by_library_sample_by_stage,
}

if bioinformatics_run_name is not None:
output_data["bioinformatics_run_name"] = bioinformatics_run_name
return output_data
31 changes: 19 additions & 12 deletions tests/test_pmo_builder/test_merge_to_pmo.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -403,8 +403,8 @@ def test_merge_to_pmo_specimen_info_matching_names_passes(self):
output_names = {s["library_sample_name"] for s in result["library_sample_info"]}
assert output_names == expected_names

def test_merge_to_pmo_specimen_info_missing_names_raises(self):
"""Raises ValueError when specimen_info is missing names that exist in detected_microhaplotypes."""
def test_merge_to_pmo_specimen_info_missing_names_warns(self):
"""Warns (does not raise) when specimen_info is missing names that exist in detected_microhaplotypes."""
incomplete_specimen_info = [
{
"specimen_name": "samp_A",
Expand All @@ -413,20 +413,24 @@ def test_merge_to_pmo_specimen_info_missing_names_raises(self):
},
# samp_B is missing
]
with self.assertRaises(ValueError) as context:
merge_to_pmo(
with self.assertWarns(UserWarning) as context:
result = merge_to_pmo(
panel_target_info=self.for_merging_spec_info_panel_info,
mhap_info=self.for_merging_spec_info_mhap_info,
specimen_info=incomplete_specimen_info,
)
self.assertIn("samp_B", str(context.exception))

warning_message = str(context.warning)
self.assertIn("samp_B", warning_message)
self.assertIn(
"library_sample_names found in the detected_microhaplotypes that don't have corresponding supplied specimen_names",
str(context.exception),
warning_message,
)
# merge should still succeed and produce a result
self.assertIsNotNone(result)

def test_merge_to_pmo_specimen_info_extra_names_raises(self):
"""Raises ValueError when specimen_info has names not present in detected_microhaplotypes."""
def test_merge_to_pmo_specimen_info_extra_names_warns(self):
"""Warns (does not raise) when specimen_info has names not present in detected_microhaplotypes."""
excess_specimen_info = [
{
"specimen_name": "samp_A",
Expand All @@ -444,17 +448,20 @@ def test_merge_to_pmo_specimen_info_extra_names_raises(self):
"collection_date": "2022-03-01",
},
]
with self.assertRaises(ValueError) as context:
merge_to_pmo(
with self.assertWarns(UserWarning) as context:
result = merge_to_pmo(
panel_target_info=self.for_merging_spec_info_panel_info,
mhap_info=self.for_merging_spec_info_mhap_info,
specimen_info=excess_specimen_info,
)
self.assertIn("samp_C", str(context.exception))
warning_message = str(context.warning)
self.assertIn("samp_C", warning_message)
self.assertIn(
"specimen_name were supplied that don't have corresponding library_sample_names",
str(context.exception),
warning_message,
)
# merge should still succeed and produce a result
self.assertIsNotNone(result)


if __name__ == "__main__":
Expand Down
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