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show changed precursors and revocations, not all
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@mandawilson
mandawilson committed Jan 13, 2025
1 parent e6b7f03 commit f4940a0
Showing 1 changed file with 106 additions and 43 deletions.
149 changes: 106 additions & 43 deletions scripts/validate_new_tree_and_output_rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,6 @@
# Memorial Sloan-Kettering Cancer Center
# has been advised of the possibility of such damage.

# TODO maybe only show changes to precursors/revocations?
# instead of the whole history

from collections import defaultdict
from deepdiff import DeepDiff
import argparse
Expand Down Expand Up @@ -132,46 +129,102 @@ def validate_and_display_new_internal_ids(new_internal_ids,
else:
print("\tNone")

def display_precursor_or_revocation_of_list(precursor_id,
internal_ids_to_oncotree_codes,
precursor_id_to_internal_ids,
oncotree):
precursor_code = internal_ids_to_oncotree_codes[precursor_id] if precursor_id in internal_ids_to_oncotree_codes else "unknown"
print(f"\t\t'{precursor_id}' ('{precursor_code}')'")
precursor_of_set = precursor_id_to_internal_ids[precursor_id]
for internal_id in sorted(precursor_of_set):
data = oncotree[internal_id]
pretty_label = construct_pretty_label_for_row(data[graphite.CSV_INTERNAL_ID],
data[graphite.CSV_ONCOTREE_CODE],
data[graphite.CSV_LABEL])
print(f"\t\t\t'{pretty_label}'")

# C01 + C02 + C03 -> C04
# C01, C02, and C03 become precursors to C04
# C05 -> C06 + C07 + C08
# C05 is a precursor to C06, C07, and C08
# you can have one concept be a precursor to many concepts
def validate_and_display_modified_precursors(modified_precursor_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set):
"""Displays precursors in the modified csv file. Throws an error if the
precursor is also defined as a node in the current file."""
print("\nPrecurors:")
def validate_precursors(modified_precursor_id_to_internal_ids,
internal_ids_to_oncotree_codes,
modified_internal_id_set):
"""Throws an error if the precursor is also defined as a node in the current file."""
if modified_precursor_id_to_internal_ids:
for precursor_id in sorted(modified_precursor_id_to_internal_ids.keys()):
precursor_code = internal_ids_to_oncotree_codes[precursor_id] if precursor_id in internal_ids_to_oncotree_codes else "unknown"
# are any current concepts precursors? they shouldn't be
if precursor_id in modified_internal_id_set:
print(f"Error: '{precursor_id}' ('{precursor_code}') is a precuror to '{','.join(modified_precursor_id_to_internal_ids[precursor_id])}' but '{precursor_id}' is still in this file as a current record", file=sys.stderr)
sys.exit(1)
precursor_of_set = modified_precursor_id_to_internal_ids[precursor_id]
for internal_id in precursor_of_set:
data = modified_oncotree[internal_id]
pretty_label = construct_pretty_label_for_row(data[graphite.CSV_INTERNAL_ID],
data[graphite.CSV_ONCOTREE_CODE],
data[graphite.CSV_LABEL])
print(f"\t'{precursor_id}' ('{precursor_code}') -> '{pretty_label}'")

def display_precursors_or_revocations(original_precursor_id_to_internal_ids,
modified_precursor_id_to_internal_ids,
original_oncotree,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set):
# now see if there are any changes
original_precursor_ids = set(original_precursor_id_to_internal_ids.keys())
modified_precursor_ids = set(modified_precursor_id_to_internal_ids.keys())
removed_precursors = original_precursor_ids - modified_precursor_ids
new_precursors = modified_precursor_ids - original_precursor_ids
in_both_precursors = original_precursor_ids & modified_precursor_ids
changed_precursors = set({})
if in_both_precursors:
for precursor_id in in_both_precursors:
if (original_precursor_id_to_internal_ids[precursor_id] !=
modified_precursor_id_to_internal_ids[precursor_id]):
changed_precursors.add(precursor_id)

if new_precursors or changed_precursors or removed_precursors:
if new_precursors:
print("\tNew:")
for precursor_id in sorted(new_precursors):
display_precursor_or_revocation_of_list(precursor_id,
internal_ids_to_oncotree_codes,
modified_precursor_id_to_internal_ids,
modified_oncotree)

if changed_precursors:
print("\tChanged:")
for precursor_id in sorted(changed_precursors):
original_precursor_of_set = set(original_precursor_id_to_internal_ids[precursor_id])
modified_precursor_of_set = set(modified_precursor_id_to_internal_ids[precursor_id])
print("\t\tBefore")
display_precursor_or_revocation_of_list(precursor_id,
internal_ids_to_oncotree_codes,
original_precursor_id_to_internal_ids,
original_oncotree)
print("\t\tAfter")
display_precursor_or_revocation_of_list(precursor_id,
internal_ids_to_oncotree_codes,
modified_precursor_id_to_internal_ids,
modified_oncotree)

if removed_precursors:
print("\tRemoved -- ARE YOU SURE YOU MEANT TO DO THIS?")
# TODO is this an error?
for precursor_id in sorted(removed_precursors):
display_precursor_or_revocation_of_list(precursor_id,
internal_ids_to_oncotree_codes,
original_precursor_id_to_internal_ids,
original_oncotree)
else:
print("\tNone")

# C01 + C02 + C03 -> C01
# C02 and CO3 become revocations in C01
# don't revoke anything with precursors (according to Rob's document "Oncotree History Modeling")
# a concept can only be revoked by a pre-existing concept
def validate_and_display_modified_revocations(modified_revocation_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set,
modified_precursor_id_to_internal_ids,
new_internal_ids):
print("\nRevocations:")
def validate_revocations(modified_revocation_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set,
modified_precursor_id_to_internal_ids,
new_internal_ids):
if modified_revocation_id_to_internal_ids:
for revocation_id in sorted(modified_revocation_id_to_internal_ids.keys()):
revocation_code = internal_ids_to_oncotree_codes[revocation_id] if revocation_id in internal_ids_to_oncotree_codes else "unknown"
Expand All @@ -186,13 +239,6 @@ def validate_and_display_modified_revocations(modified_revocation_id_to_internal
if internal_id in new_internal_ids:
print(f"Error: '{revocation_id}' ('{revocation_code}') revokes '{internal_id}' but '{internal_id}' is a new concept. Only a pre-existing concept can revoke something", file=sys.stderr)
sys.exit(1)
data = modified_oncotree[internal_id]
pretty_label = construct_pretty_label_for_row(data[graphite.CSV_INTERNAL_ID],
data[graphite.CSV_ONCOTREE_CODE],
data[graphite.CSV_LABEL])
print(f"\t'{revocation_id}' ('{revocation_code}') -> '{pretty_label}'")
else:
print("\tNone")

def display_possible_id_changes(removed_internal_ids,
new_internal_ids,
Expand Down Expand Up @@ -321,7 +367,9 @@ def validate_and_display_changes_for_in_both_internal_ids(in_both_internal_ids,

def validate_and_confirm_changes(original_oncotree,
modified_oncotree,
original_precursor_id_to_internal_ids,
modified_precursor_id_to_internal_ids,
original_revocation_id_to_internal_ids,
modified_revocation_id_to_internal_ids,
original_resource_uri_to_internal_ids,
modified_resource_uri_to_internal_ids,
Expand All @@ -347,16 +395,29 @@ def validate_and_confirm_changes(original_oncotree,
modified_oncotree,
oncotree_codes_to_internal_ids,
modified_resource_uri_to_internal_ids)
validate_and_display_modified_precursors(modified_precursor_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set)
validate_and_display_modified_revocations(modified_revocation_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set,
modified_precursor_id_to_internal_ids,
new_internal_ids)
validate_precursors(modified_precursor_id_to_internal_ids,
internal_ids_to_oncotree_codes,
modified_internal_id_set)
print("\nPrecursors:")
display_precursors_or_revocations(original_precursor_id_to_internal_ids,
modified_precursor_id_to_internal_ids,
original_oncotree,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set)
validate_revocations(modified_revocation_id_to_internal_ids,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set,
modified_precursor_id_to_internal_ids,
new_internal_ids)
print("\nRevocations:")
display_precursors_or_revocations(original_revocation_id_to_internal_ids,
modified_revocation_id_to_internal_ids,
original_oncotree,
modified_oncotree,
internal_ids_to_oncotree_codes,
modified_internal_id_set)
display_possible_id_changes(removed_internal_ids,
new_internal_ids,
original_oncotree,
Expand Down Expand Up @@ -631,8 +692,8 @@ def main():
# 2. read the csv data and put into various data structures to look things up later
original_oncotree, \
original_resource_uri_to_internal_ids, \
_, \
_, \
original_precursor_id_to_internal_ids, \
original_revocation_id_to_internal_ids, \
original_resource_uri_to_labels = get_oncotree_data_from_csv_file(original_file)
modified_oncotree, \
modified_resource_uri_to_internal_ids, \
Expand All @@ -657,7 +718,9 @@ def main():
# 4. say what has changed and confirm they are wanted
validate_and_confirm_changes(original_oncotree,
modified_oncotree,
original_precursor_id_to_internal_ids,
modified_precursor_id_to_internal_ids,
original_revocation_id_to_internal_ids,
modified_revocation_id_to_internal_ids,
original_resource_uri_to_internal_ids,
modified_resource_uri_to_internal_ids,
Expand Down

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