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Dheeraj CTM 625 #13

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Dheeraj CTM 625 #13

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0affe71
add query clause to return data model
Oct 7, 2024
d695ff7
updated branch name for building
Oct 7, 2024
ab0629a
clean up logging messages
Oct 10, 2024
81118de
add query clause to return data model
Oct 7, 2024
a384d5c
updated branch name for building
Oct 7, 2024
7914f81
clean up logging messages
Oct 10, 2024
80cb7db
Merge remote-tracking branch 'origin/mickey-CTM-605' into mickey-CTM-605
Oct 10, 2024
0572d44
Fetching two new columns called combined_data and oncotree_primary_di…
Oct 16, 2024
1ec7ba4
Changed the combined_data column name to patient_match_values
Oct 16, 2024
c8fe4f9
Changed the combined_data column name to patient_match_values
Oct 16, 2024
0e35120
Changed the oncotree_primary_diagnosis_match_only column name to onco…
Oct 16, 2024
e7b575b
Merge pull request #15 from pughlab/mickey-CTM-605
mickey-ng Oct 16, 2024
2dce500
Merge branch 'qa_demo_1016' into Dheeraj_CTM_625
mickey-ng Oct 16, 2024
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2 changes: 1 addition & 1 deletion Dockerfile-dev
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ WORKDIR /matchminerAPI

# add github host to known hosts since it's private repo
RUN mkdir -p -m 0600 ~/.ssh && ssh-keyscan github.com >> ~/.ssh/known_hosts
RUN --mount=type=ssh pip install git+ssh://[email protected]/pughlab/pmatchengine-pugh-lab.git
RUN --mount=type=ssh pip install git+ssh://[email protected]/pughlab/pmatchengine-pugh-lab.git@mickey-CTM605-add-query

RUN pip install -r requirements.txt

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5 changes: 4 additions & 1 deletion matchminer/data_model.py
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Expand Up @@ -1720,7 +1720,10 @@ def default_temporary():
'ms_status': {'type': 'string', 'nullable': True},
'trial_step_number': {'type': 'string', 'nullable': True},
'trial_arm_number': {'type': 'string', 'nullable': True},
'match_type': {'type': 'string', 'nullable': True}
'match_type': {'type': 'string', 'nullable': True},
'patient_match_values': {'type': 'string', 'nullable': True},
'oncotree_primary_diagnosis_match_value': {'type':'string', 'nullable': True}
'query': {'type': 'json', 'nullable': True},
}

prioritizer_trial_match_schema = {
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4 changes: 1 addition & 3 deletions matchminer/message/rabbitmq_message.py
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Expand Up @@ -117,13 +117,11 @@ def process_job(self, ch, method, properties, body):
if 'user_id' in json_object:
user_id = json_object['user_id']
trial_internal_ids = json_object['trial_internal_ids']
print("Received job:", trial_internal_ids)
logging.info(f"Received job: {trial_internal_ids}")
print("running job")
try:
run_ctims_matchengine_job(trial_internal_ids)
except Exception as e:
error_msg = f"Error running job for trial internal ids {trial_internal_ids}: {str(e)}"
error_msg = f"Error running job for trial internal ids {trial_internal_ids}: {repr(e)}"
py_error_dict = {
"user_id": user_id,
"trial_internal_ids": trial_internal_ids,
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