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Dheeraj_CTM-625 #4

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Dheeraj_CTM-625 #4

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7a9c88d
Adding only the columns which are mentioned in the match criteria to …
Dec 4, 2024
d49619a
Added Prior treatment fields in Patient Match Values column
Jan 7, 2025
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50 changes: 32 additions & 18 deletions pugh-lab/plugins/trial_match_document_creator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import dateutil.parser
import datetime
from matchengine.plugin_stub import TrialMatchDocumentCreator
import ast

if TYPE_CHECKING:
from matchengine.internals.typing.matchengine_types import TrialMatch, MatchReason
Expand Down Expand Up @@ -53,23 +54,28 @@ def create_trial_matches(self, trial_match: TrialMatch) -> list:
match_doc = {}
match_doc.update(base_match_doc)
match_doc.update(reason_doc)
patient_match_values_dict = {
"genomic_alteration": reason_doc.get("genomic_alteration", ""),
"match_type": reason_doc.get("match_type", ""),
"ms_status": base_match_doc.get("ms_status", ""),
"oncotree_primary_diagnosis_name": base_match_doc.get("oncotree_primary_diagnosis_name", ""),
"age": base_match_doc.get("age", ""),
"er_status": base_match_doc.get("er_status", ""),
"her2_status": base_match_doc.get("her2_status", ""),
"pr_status": base_match_doc.get("pr_status", ""),
"true_hugo_symbol": reason_doc.get("true_hugo_symbol", ""),
"true_variant_classification": reason_doc.get("true_variant_classification", ""),
"variant_category": reason_doc.get("variant_category", ""),
"true_transcript_exon": reason_doc.get("true_transcript_exon", ""),
"true_protein_change": reason_doc.get("true_protein_change", ""),
"prior_treatment_agent": base_match_doc.get("prior_treatment_agent",""),
"oncotree_primary_diagnosis_match_value": base_match_doc.get("oncotree_primary_diagnosis_match_value", "")
}
patient_match_values_dict = {}
for reason in trial_match.match_reasons:
tv = reason.query
if reason.query_kind == "genomic":
patient_match_values_dict.update({
k: v for k, v in reason_doc.items()
if k.upper() in self._GENOMIC_COPY_FIELDS and any(k_part in k or k in k_part for k_part in tv.keys())
})
elif reason.query_kind == "clinical":
patient_match_values_dict.update({
k: v for k, v in base_match_doc.items()
if k.upper() in self._CLINICAL_COPY_FIELDS and any(k_part in k or k in k_part for k_part in tv.keys())
})
elif reason.query_kind == "prior_treatment":
query_str = reason_doc.get("query")
query_dict = ast.literal_eval(query_str)
patient_match_values_dict.update({
k: v for k, v in query_dict.items()
if k.upper() in self._PRIOR_TREATMENT_COPY_FIELDS and any(k_part in k or k in k_part for k_part in tv.keys())
})

patient_match_values_dict.update({'genomic_alteration': reason_doc.get("genomic_alteration", "")})
# Filter out key-value pairs where the value is an empty string
filtered_data = {k: v for k, v in patient_match_values_dict.items() if v != "" and v !="NA"}

Expand Down Expand Up @@ -560,4 +566,12 @@ def _get_sort_order(self, match_document: Dict) -> list:
"ER_STATUS"
}
_TRIAL_COPY_FIELDS = {'protocol_no', 'short_title', 'nickname', 'nct_id'}
_PRIOR_TREATMENT_COPY_FIELDS = {'AGENT'}
_PRIOR_TREATMENT_COPY_FIELDS = {
'AGENT',
'TREATMENT_CATEGORY',
'SUBTYPE',
'AGENT_CLASS',
'SURGERY_TYPE',
'RADIATION_TYPE',
'RADIATION_SITE'
}