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update clinical trial

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This commit is contained in:
MuslemRahimi 2024-06-26 20:57:14 +02:00
parent 1b3abf060b
commit 6903e9acd3
1 changed files with 36 additions and 22 deletions
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58
app/cron_clinical_trial.py
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@ -12,33 +12,47 @@ import pandas as pd
import time import time
# Function to extract the string after the first 'DRUG:'
def extract_drug(string):
parts = string.split('|')
for part in parts:
if part.startswith('DRUG:'):
return part.split(': ', 1)[1].strip() # Extract the part after 'DRUG:'
return '' # Return empty string if no 'DRUG:' found
ct = ClinicalTrials() ct = ClinicalTrials()
async def get_data(company_name): async def get_data(company_name):
try: try:
get_ct_data = ct.get_study_fields(
company_name = company_name.replace('&','and')
get_ct_data = ct.get_study_fields(
search_expr=f"{company_name}", search_expr=f"{company_name}",
fields=["Study Results","Funder Type","Start Date", "Completion Date","Study Status","Study Title", 'Phases', 'Brief Summary', 'Age','Sex', 'Enrollment','Study Type','Sponsor','Study URL','NCT Number'], fields=["Study Results","Interventions","Funder Type","Start Date", "Completion Date","Study Status","Study Title", 'Phases', 'Brief Summary', 'Age','Sex', 'Enrollment','Study Type','Sponsor','Study URL','NCT Number'],
max_studies=1000, max_studies=1000,
) )
df = pd.DataFrame.from_records(get_ct_data[1:], columns=get_ct_data[0]) df = pd.DataFrame.from_records(get_ct_data[1:], columns=get_ct_data[0])
df['Completion Date'] = pd.to_datetime(df['Completion Date'],errors='coerce') df['Start Date'] = pd.to_datetime(df['Start Date'],errors='coerce')
df_sorted = df.sort_values(by='Completion Date', ascending=False) df_sorted = df.sort_values(by='Start Date', ascending=False)
# Convert 'Completion Date' back to string format
df_sorted['Completion Date'] = df_sorted['Completion Date'].apply(lambda x: x.strftime('%Y-%m-%d') if pd.notnull(x) else None)
df_sorted['Phases'] = df_sorted['Phases'].replace('PHASE2|PHASE3', 'Phase 2/3')
df_sorted['Phases'] = df_sorted['Phases'].replace('PHASE1|PHASE2', 'Phase 1/2')
df_sorted['Phases'] = df_sorted['Phases'].replace('EARLY_PHASE1', 'Phase 1')
df_sorted['Study Status'] = df_sorted['Study Status'].replace('ACTIVE_NOT_RECRUITING', 'Active') df_sorted['Start Date'] = df_sorted['Start Date'].apply(lambda x: x.strftime('%Y-%m-%d') if pd.notnull(x) else None)
df_sorted['Study Status'] = df_sorted['Study Status'].replace('NOT_YET_RECRUITING', 'Active') df_sorted['Phases'] = df_sorted['Phases'].replace('PHASE2|PHASE3', 'Phase 2/3')
df_sorted['Study Status'] = df_sorted['Study Status'].replace('UNKNOWN', '-') df_sorted['Phases'] = df_sorted['Phases'].replace('PHASE1|PHASE2', 'Phase 1/2')
df_sorted['Phases'] = df_sorted['Phases'].replace('EARLY_PHASE1', 'Phase 1')
data = df_sorted.to_dict('records') df_sorted['Study Status'] = df_sorted['Study Status'].replace('ACTIVE_NOT_RECRUITING', 'Active')
return data df_sorted['Study Status'] = df_sorted['Study Status'].replace('NOT_YET_RECRUITING', 'Active')
except Exception as e: df_sorted['Study Status'] = df_sorted['Study Status'].replace('UNKNOWN', '-')
print(f"Error fetching data for {ticker}: {e}")
return [] df_sorted['Interventions'] = df_sorted['Interventions'].apply(extract_drug)
data = df_sorted.to_dict('records')
return data
except Exception as e:
print(f"Error fetching data for {company_name}: {e}")
return []
async def save_json(symbol, data): async def save_json(symbol, data):
# Use async file writing to avoid blocking the event loop # Use async file writing to avoid blocking the event loop
@ -56,12 +70,12 @@ async def run():
cursor = con.cursor() cursor = con.cursor()
cursor.execute("PRAGMA journal_mode = wal") cursor.execute("PRAGMA journal_mode = wal")
cursor.execute("SELECT DISTINCT symbol, name FROM stocks WHERE industry = 'Biotechnology' AND symbol NOT LIKE '%.%'") cursor.execute("SELECT DISTINCT symbol, name FROM stocks WHERE (industry = 'Biotechnology' OR industry LIKE '%Drug%') AND symbol NOT LIKE '%.%'")
company_data = [{'symbol': row[0], 'name': row[1]} for row in cursor.fetchall()] company_data = [{'symbol': row[0], 'name': row[1]} for row in cursor.fetchall()]
con.close() con.close()
#test mode #test mode
#company_data = [{'symbol': 'DSGN', 'name': 'Design Therapeutics, Inc.'}] #company_data = [{'symbol': 'MRK', 'name': 'Merck & Co. Inc.'}]
print(len(company_data))
async with aiohttp.ClientSession() as session: async with aiohttp.ClientSession() as session:
tasks = [] tasks = []
for item in company_data: for item in company_data: