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DSTU2libs.py
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import json, requests, sqlite3, os, argparse, itertools
def DSTU2fixEntity(conn,entity,args):
entity,successful=fixEntity(conn,entity,args)
return entity,successful
def fixEntity(conn,entity,args):
c=conn.cursor()
resourceType=entity.get('resourceType')
successful="success"
if(resourceType=="Patient"):
pass
elif(resourceType=="Observation"):
if(entity.get('effectiveDateTime')==None):
print("Cannot import this file, needs effectiveDateTime")
successful="removeFile"
pass
reference=entity.get('subject').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['subject']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="Medication"):
print("we don't handle medications")
successful="removeFile"
# if(entity.get('product')!=None):
# # We have a product, and it may have ingrediants
# if(entity.get('product').get('ingredient')!=None):
# for ingredient in entity.get('product').get('ingredient'):
# if(ingredient.get('item')!=None):
# reference=ingredient.get('item').get('reference').split('/')
# referenceType=reference[-2]
# referenceID=reference[-1]
# c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
# result=c.fetchone()
# if(result):
# referenceID=result[2]
# ingredient['item']['reference']="{}/{}".format(referenceType,referenceID)
# else:
# successful="notSuccess"
# break
elif(resourceType=="Condition"):
if(entity.get('patient')!=None):
reference=entity.get('patient').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['patient']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
if(entity.get('asserter')!=None):
reference=entity.get('asserter').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['asserter']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="Encounter"):
if(entity.get('patient')!=None):
reference=entity.get('patient').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['patient']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
if(entity.get('indication')!=None):
for indication in entity.get('indication'):
reference=indication.get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
indication['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
break
elif(resourceType=="Procedure"):
if(entity.get('performedDateTime')==None):
print("Cannot import this file, needs performedDateTime")
successful="removeFile"
pass
reference=entity.get('subject').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['subject']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="MedicationStatement"):
if(entity.get('patient')!=None):
reference=entity.get('patient').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['patient']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="Practitioner"):
if(entity.get('practitionerRole'!=None)):
print("need to implement")
if(entity.get('qualification'!=None)):
print("need to convert qualification")
elif(resourceType=="MedicationOrder"):
if(entity.get('dateWritten')==None):
print("Cannot import this file, needs dateWritten")
successful="removeFile"
pass
if(entity.get('dateEnded')==None):
entity['dateEnded']=entity.get('dateWritten')
if(entity.get('patient')!=None):
reference=entity.get('patient').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['patient']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
if(entity.get('prescriber')!=None):
reference=entity.get('prescriber').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['prescriber']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
if(entity.get('medicationReference')!=None):
reference=entity.get('medicationReference').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['medicationReference']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="Device"):
print("we don't allow posting of Devices currently")
successful="removeFile"
# if(entity.get('patient')!=None):
# reference=entity.get('patient').get('reference').split('/')
# referenceType=reference[-2]
# referenceID=reference[-1]
# c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
# result=c.fetchone()
# if(result):
# referenceID=result[2]
# entity['patient']['reference']="{}/{}".format(referenceType,referenceID)
# else:
# successful="notSuccess"
# if(entity.get('owner')!=None):
# print("need to implement owner in Device")
# successful="removeFile"
# pass
# if(entity.get('location')!=None):
# print("need to implement location in Device")
# successful="removeFile"
# pass
elif(resourceType=="DeviceUseStatement"):
if(entity.get('whenUsed')==None):
print("Cannot import this file, needs whenUsed")
successful="removeFile"
pass
reference=entity.get('subject').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['subject']['reference']="{}/{}".format(referenceType,referenceID)
entity['contained'][0]['patient']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
elif(resourceType=="DocumentReference"):
if(entity.get('subject')!=None):
reference=entity.get('subject').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['subject']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
if(entity.get('author')!=None):
for author in entity.get('author'):
reference=author.get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
author['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
break
if(args.pull_files):
if(entity.get('content')!=None):
# TODO: We can convert any files to base64 and properly submit it. Just need to set the base64 to the attachment.data field
for content in entity.get('content'):
if(content.get('attachment')!=None):
if(content['attachment'].get('contentType')=='application/pdf'):
print("{}{}".format(args.originalserver,content['attachment'].get('url')))
response=requests.get("{}{}".format(args.originalserver,content['attachment'].get('url')))
filename=content['attachment'].get('url').split("/")
print(filename)
with open(filename[2], 'wb') as f:
f.write(response.content)
elif(resourceType=="Organization"):
if(entity.get('partOf')!=None):
reference=entity.get('partOf').get('reference').split('/')
referenceType=reference[-2]
referenceID=reference[-1]
c.execute("SELECT * from IDMap WHERE oldID='{}' AND resourceType='{}';".format(referenceID,referenceType))
result=c.fetchone()
if(result):
referenceID=result[2]
entity['partOf']['reference']="{}/{}".format(referenceType,referenceID)
else:
successful="notSuccess"
else:
print("we don't know how to handle {} files yet".format(resourceType))
successful="removeFile"
pass
return entity,successful