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Update report_fhir_counts.py #5

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Update report_fhir_counts.py #5

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46 changes: 30 additions & 16 deletions smolder/summary/report_fhir_counts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from pathlib import Path
import yaml

#Can add new studies as they come available by adding their STUDY CODE to the list below:
AVAILABLE_STUDIES = [
"ABC-DS",
"BrainPower",
Expand Down Expand Up @@ -292,60 +293,73 @@ def summarize_study(fhir_client, study):
"Document References.Registered",
summary,
)
#Adding Conditions data - usually populates at the top of the file bc alphabetical order.
#I will change these once I get a list of standard codes to check for each study and then will be solidified.
#Adding Conditions data - populates at the top of the file bc alphabetical order.
#After receiving a representative list of codes, I've updated them below if other codes are required, they can be modified again.
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0001671&_summary=count",
"Conditions.Abnormal_cardiac_septum_morphology",
f"Condition?_tag={study}&code=MONDO:0005083&_summary=count",
"Conditions.psoriasis (MONDO:0005083)",
summary,
)
report_count(
fhir_client,
f"Condition?_tag={study}&code=MONDO:0002078&_summary=count",
"Conditions.heart_septal_defect",
f"Condition?_tag={study}&code=HP:000739&_summary=count",
"Conditions.Anxiety (HP:000739)",
summary,
)
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0003765&_summary=count",
"Conditions.Psoriasiform dermatitis (HP:0003765)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0001629&_summary=count",
"Conditions.ventricular_septal_defect",
f"Condition?_tag={study}&code=HP:0010535&_summary=count",
"Conditions.Sleep apnea (HP:0010535",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=MONDO:0002070&_summary=count",
"Conditions.mondo_ventricular_septal_defect",
f"Condition?_tag={study}&code=MONDO:0005296&_summary=count",
"Conditions.sleep apnea syndrome (MONDO:0005296)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0001631&_summary=count",
"Conditions.Atrial_septal_defect",
"Conditions.Atrial septal defect (HP:0001631)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0002099&_summary=count",
"Conditions.Asthma (HP:0002099)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=HP:0006695&_summary=count",
"Conditions.Atrioventricular_canal_defect",
f"Condition?_tag={study}&code=HP:0000872&_summary=count",
"Conditions.Hashimoto thyroiditis (HP:0000872)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=MONDO:0859565&_summary=count",
"Conditions.mondo_Atrioventricular_canal_defect",
f"Condition?_tag={study}&code=MONDO:0007699&_summary=count",
"Conditions.hashimoto thyroiditis (MONDO:0007699)",
summary,

)
report_count(
fhir_client,
f"Condition?_tag={study}&code=MONDO:0008608&_summary=count",
"Conditions.mondo_Down_Syndrome",
"Conditions.Down syndrome (MONDO:0008608)",
summary,

)
Expand Down