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Hotfix/fix combine multiple pmos #57

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Merged
nickjhathaway merged 3 commits into from
Nov 22, 2025
Merged

Hotfix/fix combine multiple pmos #57

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38b7b52
was still using old fields;
nickjhathaway Nov 19, 2025
8d3943c
fix for having the same specimen in different files when combining;
nickjhathaway Nov 19, 2025
040633e
added more tests for properly throwing dup library_sample_names and s…
nickjhathaway Nov 21, 2025
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59 changes: 44 additions & 15 deletions src/pmotools/pmo_engine/pmo_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,13 +158,11 @@ def combine_multiple_pmos(pmos: list[dict]):
new_index = len(pmo_out["panel_info"])
# update target indexes to make sure reaction points to the right target indexes
for reaction in panel_copy["reactions"]:
for target_id_reaction in range(
len(reaction["target_id_reactions"])
):
reaction["target_id_reactions"][
for target_id_reaction in range(len(reaction["panel_targets"])):
reaction["panel_targets"][
target_id_reaction
] = target_info_old_index_key[pmo_index][
reaction["target_id_reactions"][target_id_reaction]
reaction["panel_targets"][target_id_reaction]
]
pmo_out["panel_info"].append(panel_copy)
panel_info_out_index_key[panel_copy["panel_name"]] = new_index
Expand Down Expand Up @@ -227,10 +225,12 @@ def combine_multiple_pmos(pmos: list[dict]):
# update project_id
pmo_out["specimen_info"] = copy.deepcopy(pmos[0]["specimen_info"])
specimen_names = []
specimen_index_key = {}
duplicate_specimen_names = []
for specimen in pmo_out["specimen_info"]:
if specimen["specimen_name"] in specimen_names:
duplicate_specimen_names.append(specimen["specimen_name"])
specimen_index_key[specimen["specimen_name"]] = len(specimen_names)
specimen_names.append(specimen["specimen_name"])

# key1 pmo_index, key2 old_index, val new_index
Expand All @@ -239,23 +239,52 @@ def combine_multiple_pmos(pmos: list[dict]):
for specimen_info_index, specimen_info in enumerate(pmo["specimen_info"]):
# checkin for duplicates
if specimen_info["specimen_name"] in specimen_names:
duplicate_specimen_names.append(specimen_info["specimen_name"])
specimen_names.append(specimen_info["specimen_name"])
new_index = len(pmo_out["specimen_info"])
# update project_id
specimen_info_copy = copy.deepcopy(specimen_info)
specimen_info_copy["project_id"] = project_info_old_index_key[
pmo_index
][specimen_info_copy["project_id"]]
pmo_out["specimen_info"].append(specimen_info_copy)
specimen_info_old_index_key[pmo_index][specimen_info_index] = new_index
# if specimen is exactly the same, then no issues
# @todo allow merging of info and as long as the meta present in both are the same then it should be fine
if (
specimen_info
!= pmo_out["specimen_info"][
specimen_index_key[specimen_info["specimen_name"]]
]
):
duplicate_specimen_names.append(specimen_info["specimen_name"])
specimen_info_old_index_key[pmo_index][
specimen_info_index
] = specimen_index_key[specimen_info["specimen_name"]]
else:
# update key for the already present id
specimen_info_old_index_key[pmo_index][
specimen_info_index
] = specimen_index_key[specimen_info["specimen_name"]]
else:
specimen_index_key[specimen_info["specimen_name"]] = len(
specimen_names
)
specimen_names.append(specimen_info["specimen_name"])
new_index = len(pmo_out["specimen_info"])
# update project_id
specimen_info_copy = copy.deepcopy(specimen_info)
specimen_info_copy["project_id"] = project_info_old_index_key[
pmo_index
][specimen_info_copy["project_id"]]
pmo_out["specimen_info"].append(specimen_info_copy)
specimen_info_old_index_key[pmo_index][
specimen_info_index
] = new_index

## library_sample_info
pmo_out["library_sample_info"] = copy.deepcopy(pmos[0]["library_sample_info"])
# key1 pmo_index, key2 old_index, val new_index
library_sample_info_old_index_key = defaultdict(dict)
duplicate_library_sample_names = []
library_sample_names = []
# have to add the library_sample_names already added in the first PMO
for library_sample in pmo_out["library_sample_info"]:
if library_sample["library_sample_name"] in library_sample_names:
duplicate_library_sample_names.append(
library_sample["library_sample_name"]
)
library_sample_names.append(library_sample["library_sample_name"])
for pmo_index, pmo in enumerate(pmos[1:], start=1):
for library_sample_info_index, library_sample_info in enumerate(
pmo["library_sample_info"]
Expand Down
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