def get_bundle(snapshot=None, page_num=None):
params = {'_count': 500, '_snapshot': snapshot, '_page': page_num}
#r = get(f'{server_path}/Practitioner', headers=headers, params=params)
r = get(f'{server_path}/PractitionerRole', headers=headers, params=params)
return B.Bundle(loads(r.text))
def get_bundle(snapshot=None, page_num=None):
params = {'_count': 500, '_snapshot': snapshot, '_page': page_num}
r = get(f'{server_path}/VerificationResult',
headers=headers,
params=params)
return B.Bundle(loads(r.text))
def split_bundle(
file): #split into smaller 500 entry bundles and write and post
for k in range(int(len(file.entry) / 500) + 1):
nb = B.Bundle()
nb.id = f"{file.id}-{k}"
nb.type = "batch"
nb.entry = []
for i in range(500):
try:
entry = B.BundleEntry(file.entry[k * 500 + i].as_json())
nb.entry.append(entry)
except IndexError:
break
print(k * 500 + i)
logging.info(f'posting bundle {file.id}...entries {k*500}-{k*500+i}')
post_bundle(nb)
def main(f_type, id_list, source):
f_Type = rr.r_map[source]
entries = []
if f_type == 'managing-org':
for item in get_csv(in_path,
'managing_orgs_data'): # get sample data from csv
npi = item['id']
f_id = get_f_id(f_type, npi)
logging.info(f'create resource id = {f_id}')
example = f_templ.managing_org(
item, f_id, f_type, npi) # create dict using fstring template
example = scrub_dict(example) # scrub out nulls
id_list[snakecase(f_type)].append(
(npi, f'{f_Type}/{f_id}', item['name']))
entries.append(
f_templ.entries_templ(
server_path, example, f_Type,
f_id)) # create dict using fstring template
elif f_type == 'coverage':
for state in states:
f_id = get_f_id(f_type, spinalcase(state.lower()), source)
attachment = {
'contentType':
'application/vnd.geo+json', # Mime type of the content, with charset etc.
'data': b64.geojson_b64[snakecase(
state.lower())].decode('ascii'), # Data inline, base64ed
'title':
f'GeoJSON for {state}', # Label to display in place of the data
'creation': timestamp # Date attachment was first created
}
logging.info(f'create resource id = {f_id}')
example = f_templ.coverage(
name=state,
attachment=attachment) # create dict using fstring template
id_list[snakecase(f_type)].append(
(state, f'{f_Type}/{f_id}', state))
entries.append(
f_templ.entries_templ(
server_path, example, f_Type,
f_id)) # create dict using fstring template
elif f_type == 'insuranceplan':
for item in get_csv(in_path,
'managing_orgs_data'): # get sample data from csv
npi = item['plan_id']
f_id = get_f_id(f_type, npi)
if item['is_plan'] == "TRUE":
logging.info(f'create resource id = {f_id}')
example = f_templ.insuranceplan(
item) # create dict using fstring template
example = scrub_dict(example) # scrub out nulls
id_list[snakecase(f_type)].append(
(item['plan_id'], f'{f_Type}/{f_id}', item['plan_name']))
entries.append(
f_templ.entries_templ(
server_path, example, f_Type,
f_id)) # create dict using fstring template
elif f_type == 'hie-orgaffiliation':
for entry in bundles['orgs'].entry:
z = get_zip(entry.resource.address[0].postalCode)
st = entry.resource.address[0].state
hie_list = []
if z in western_ma_zips:
hie_list.append(('wma', 'Western Massachusetts HIE'))
if st == 'RI':
hie_list.append(('ri', 'Rhode Island HIE'))
if z in hartford_zips:
hie_list.append(('hct', 'Hartford Connecticut HIE'))
for hie_item in hie_list:
prefix = f'hie-{hie_item[0]}'
parent_org = next(
po for po in bundles['managing_orgs'].entry
if po.resource.name == hie_item[1]) # get parent org
logging.info(
f'{hie_item[1]} orgaffiliation for org resource id = {entry.resource.id}'
)
example = f_templ.hie_orgaffiliation(
org=entry.resource,
parent_org=parent_org.resource,
prefix=prefix) # create dict using fstring template
oa = OA.OrganizationAffiliation(
example) # instantiate as orgaffiliation
id_list[snakecase(f_type)].append(
(oa.identifier[0].value, f'{f_Type}/{oa.id}',
oa.organization.display))
entries.append(
f_templ.entries_templ(
server_path, example, f_Type,
oa.id)) # create dict using fstring template
elif f_type == 'addin-org-role':
for n_entry in bundles['networks'].entry:
network = n_entry.resource
if network.name in addin_networks.keys():
for o_entry in bundles['orgs'].entry:
org = o_entry.resource
z = get_zip(org.address[0].postalCode)
if (org.address[0].state == addin_networks[network.name][1]
or
(addin_networks[network.name][1]
== "Greater Hartford Area" and z in hartford_zips)):
# add org-affil to orgaffil bundle
logging.info(
f'orgaffiliation for org resource id = {network.name}'
)
example = f_templ.hie_orgaffiliation(
org=org,
parent_org=network,
prefix=addin_networks[network.name]
[0]) # create dict using fstring template
oa = OA.OrganizationAffiliation(
example) # instantiate as orgaffiliation
be = B.BundleEntry(
f_templ.entries_templ(server_path, example, f_Type,
oa.id))
bundles['org_roles'].entry.append(
be
) # create lsit of classes to append to existing bundle
for oa_entry in bundles['org_roles'].entry:
logging.info(oa_entry.resource.id)
logging.info(oa_entry.resource.organization.display)
id_list[snakecase(f_type)].append(
(oa_entry.resource.id, f'{f_Type}/{oa_entry.resource.id}',
oa_entry.resource.organization.display))
elif f_type == 'addin-pract-role':
p_bundles = [
v for k, v in bundles.items()
if k in ['pract0', 'pract1', 'pract2', 'pract3']
]
for n_entry in bundles['networks'].entry:
network = n_entry.resource
if network.name in addin_networks.keys():
for p_bundle in p_bundles:
for p_entry in p_bundle.entry:
pract = p_entry.resource
z = get_zip(pract.address[0].postalCode)
if (pract.address[0].state
== addin_networks[network.name][1]
or (addin_networks[network.name][1]
== "Greater Hartford Area"
and z in hartford_zips)):
# add pract-affil to practrole bundle
# logging.info(f'practitionerrole for pract = {pract.name[0].text}, id = {pract.identifier[0].value} network = {network.name} identifier {network.identifier[0].value}')
example = f_templ.network_member_practrole(
member=pract,
network=network,
prefix=addin_networks[network.name]
[0]) # create dict using fstring template
pr = PR.PractitionerRole(
example) # instantiate as practitionerrole
be = B.BundleEntry(
f_templ.entries_templ(server_path, example,
f_Type, pr.id))
# bundles['pract_roles'].entry.append(be) # create lsit of classes to append to existing bundle
id_list[snakecase(f_type)].append(
(pr.identifier[0].value, f'{f_Type}/{pr.id}',
pr.practitioner.display))
entries.append(
f_templ.entries_templ(server_path, example,
f_Type, pr.id)
) # create dict using fstring template
elif f_type == 'endpoint':
for k, v in bundles.items():
logging.info(f'for {k} create endpoints...')
for entry in v.entry:
try:
example = f_templ.endpoint(
r=entry.resource) # create dict using fstring template
#logging.info(f'example = \n{example}')
if example:
ep = EP.Endpoint(example) # instantiate as endpoint
id_list[snakecase(f_type)].append(
(ep.id, f'{f_Type}/{ep.id}', ep.name))
entries.append(
f_templ.entries_templ(
server_path, example, f_Type,
ep.id)) # create dict using fstring template
except AttributeError:
pass
if f_type not in addins.keys():
batch_bundle = f_templ.batch_bundle_template(
f_type, entries) # create dict using fstring template
batch_json = dumps(batch_bundle, indent=3, ensure_ascii=False)
#logging.info(f'{f_type} batch_bundle as json') # as dict
fhir_file = B.Bundle(batch_bundle) # validate file
#logging.info(f'bundle looks like = {json_file}')
write_bundle(out_path, f_type, batch_json, source,
'json') # save to file
write_resource_csv(spinalcase(f_type),
resource_keys[snakecase(f_type)])
# TODO convert to xml
xml_bundle = get_xml(
convert_server, batch_json,
f_type) #use fhir server to convert bundle xml to json
write_bundle(out_path, f_type, xml_bundle, source,
'xml') #save to file
post_bundle(server_path, batch_json) #upload to fhir server
else: # append to existing bundle
batch_json = dumps(bundles[addins[f_type][1]].as_json(),
indent=3,
ensure_ascii=False) # convert to json byte
write_bundle(out_path, addins[f_type][0], batch_json,
addins[f_type][0], 'json') # save to file
# TODO convert to xml
#xml_bundle = get_xml(convert_server,batch_json,addins[f_type][0])#use fhir server to convert bundle xml to json
#write_bundle(out_path,addins[f_type][0],xml_bundle,addins[f_type][0],'xml') #save to file
# post_bundle(server_path,batch_json) #upload to fhir server
write_resource_csv(spinalcase(addins[f_type][0]),
resource_keys[snakecase(f_type)])
return
def get_bundle(in_path, in_file): # as py fhir bundle class
with open(f'{in_path}/{in_file}.json') as f:
logging.info(f'reading file = {in_file}')
return B.Bundle(load(f))