def fetch_patientlist():
if request.method == 'POST':
session['patientlist'] = request.form["get-list"]
app.logger.info(f'session["patientlist"]= {session["patientlist"]}')
requests_object = fetch(session['patientlist']) # requests object
write_out(app.root_path, "test-argo-pl-group.json",
dumps(requests_object.json(), indent=4))
write_out(app.root_path, "test-argo-pl-group.yml",
yaml(requests_object.json()))
py_group = pyfhir(requests_object.json(), Type="Group")
app.logger.info(f'group id = {py_group.id}')
session['md_string'] = md_template(
'fetch_patientlist.md',
base_name=session['base_name'],
url_string=requests_object.url,
count=requests_object.json()['quantity'])
session["use_case"] = "endpoint"
my_string = '''## After Fetching the List of User Facing lists, a Patient list is selected using a simple Fetch operation: <br>Click on the blue buttons below to continue...'''
return render_template('group_details.html',
my_intro=my_string,
title="Fetch Patient List",
current_time=datetime.datetime.now(),
ht_offset=425,
seq_ht=425,
my_string=session['md_string'],
pyfhir=py_group)
def remove_containers(self):
delete_targets = getattr(self.args, "delete_targets")
if len(delete_targets) < 1:
raise ValueError("you must supply at least one container id or name to delete")
force = getattr(self.args, "force")
for d in delete_targets:
con = self.client.containers.get(d)
con.remove(force)
write_out(con["id"])
def display_all_image_info(self):
col_fmt = "{0:40}{1:12}{2:14}{3:18}{4:14}"
write_out(
col_fmt.format("REPOSITORY", "TAG", "IMAGE ID", "CREATED", "SIZE"))
for i in self.client.images.list():
for r in i["repoTags"]:
rsplit = r.rindex(":")
name = r[0:rsplit - 1]
tag = r[rsplit + 1:]
write_out(
col_fmt.format(name, tag, i["id"][:12],
stringTimeToHuman(i["created"]),
convert_size(i["size"])))
def bundle_to_file(dict_bundle, type='bundle'):
write_out(app.root_path, f"test-argo-pl-{type}.json",
dumps(dict_bundle, indent=4))
write_out(app.root_path, f"test-argo-pl-{type}.yml",
y_dump(dict_bundle, sort_keys=False))
def fwd():
'''
reassemble message bundle:
new bundle id, timestamp
new messageheader.id and sender and source and destination
if "intermed-no-change" is checked then add provenance for MH
elif "intermed-change" is checked then add provenance for MH and and sender Org and remove coverage
use prov template as dicts with variable
add static text for forwarding messages
'''
now = datetime.datetime.utcnow()
fhir_now = FD.FHIRDate(f'{str(now.isoformat())}Z')
#get existing bundle and modify
app.logger.info(f'****** see what is in session = {session}')
f_name = session['f_names'][-1]
app.logger.info(
f'line nnnn f_name list = {session["f_names"]} f_name item = {f_name}')
data = read_in(in_path=app.root_path,
f_name=f_name) # most recent saved bundle
#data = cache.get('notification_bundle')
#app.logger.info(f'data = {data}')
#convert to r4models
b = pyfhir(loads(data))
b.id = str(uuid.uuid1())
b.timestamp = fhir_now
mh = b.entry[0].resource
mh.id = str(uuid.uuid1())
b.entry[0].fullUrl = uuid.UUID(mh.id).urn
mh.sender.reference = "urn:uuid:4f7c997a-d6a4-11ea-814c-b5baa7182d44" # hardcoded for now
mh.sender.display = "Da Vinci Intermediary" # hardcoded for now
mh.source.name = "Da Vinci Intermediary Source Application"
mh.source.endpoint = "https://example.org/Endpoints/P999"
mh.source.contact.system = 'phone'
mh.source.contact.value = '+1-800-555-5555'
session['resource_list'][0] = f'MessageHeader/{mh.id}'
################### ADD Provenance ################################SHOULD BE REMOVED NOT NEEDED ANYMORE
app.logger.info(
f'************intermed is {request.form["intermed"]}*************')
provenance = get_prov(
target=f'MessageHeader/{mh.id}',
author=mh.author.reference,
org=mh.responsible.reference,
sender=mh.sender.reference,
activity=request.form['intermed'],
now=now,
)
prov_entry = B.BundleEntry()
prov_entry.fullUrl = uuid.UUID(provenance.id).urn
prov_entry.resource = provenance
b.entry.insert(1, prov_entry)
session['resource_list'].insert(1, f'Provenance/{provenance.id}')
################### ADD new sender Org ################################
sender = getattr(fhirtemplates, 'sender') # hardcode org for now
org = pyfhir(sender) #convert to fhirclient model
add_profile(org)
org_entry = B.BundleEntry()
org_entry.fullUrl = uuid.UUID(org.id).urn
org_entry.resource = org
b.entry.append(org_entry)
session['resource_list'].append(f'Organization/{org.id}')
################### Remove Coverage and Referenced Org ################################SHOULD BE REMOVED NOT NEEDED ANYMORE
if request.form[
'intermed'] == 'amend': # example for intermediary as sender with change in content
try:
coverage_index = next((index for (index, r) in enumerate(b.entry)
if r.resource.resource_type == 'Coverage'))
except StopIteration:
pass
else:
coverage = b.entry.pop(coverage_index).resource
session['resource_list'].pop(coverage_index)
payor_url = coverage.payor[0].reference
try:
payor_index = next((index for (index, r) in enumerate(b.entry)
if r.fullUrl == payor_url))
except StopIteration:
pass
else:
b.entry.pop(payor_index)
session['resource_list'].pop(payor_index)
# writing to ig examples file and running the IG Build:
notification_bundle = dumps(b.as_json(), indent=2)
#app.logger.info(f'notification_bundle = {message_bundles[0]}')
f_name = f'davinci-notification-bundle-{b.id}.json'
write_out(app.root_path, f_name, notification_bundle)
app.logger.info(
f'writing example notification bundle to {app.root_path}/test_output/{f_name}'
)
session['f_names'].append(
f_name) # keep track of f_names for session to delete later
session.modified = True
app.logger.info(f'****** see what is in session = {session}***')
return render_template(
'sub_template5.html',
title="Forwarding Notification Bundle Prep",
endpoint_urls=alerts_servers,
endpoint='$process-message',
notification_bundle=notification_bundle,
b_id=b.id,
forwarding=True,
)
def mb():
'''
fetch encounter ids - 1 for single bundle, multiple for batching using a transaction bundle
create messageheader, coverage, orgs 1 and 2
fetch graph of resources as list
create bundle
'''
################### Assemble Bundle ################################
app.logger.info(f'****** line 492 see what is in session = {session}***')
#app.logger.info(f'****** line 465 see what is in cache = {cache.get("encounters")}***')
#encounters = cache.get("encounters") # get resources from cache
session['resource_list'] = []
message_bundles = []
now = datetime.datetime.utcnow()
is_message_bundle = len(session['my_encounters']) < 2
cache_notif_bundle = cache.get("notification_bundle")
################
#for loop over encounters if encounter length >1 then create transaction bundle
if not is_message_bundle and cache_notif_bundle: #if cached use it instead
for b in loads(cache_notif_bundle)["entry"]:
session['resource_list'].append(
f'{b["resource"]["resourceType"]}/{b["resource"]["id"]}')
for r in b["resource"]["entry"]:
session['resource_list'].append(
f'{r["resource"]["resourceType"]}/{r["resource"]["id"]}')
return render_template(
'sub_template5.html',
my_string=
'Getting Resources ready for Tansaction Bundle of Da Vinci Notification Message Bundle...',
title="Notification Bundle Prep",
endpoint_urls=alerts_servers,
endpoint='transaction',
notification_bundle=cache_notif_bundle,
b_id=loads(cache_notif_bundle)["id"],
)
else:
#################
for r_id, ver in session['my_encounters']: #encounters:
encounter = fetch('Encounter', _id=r_id, ver=ver) #as dict
encounter = pyfhir(
r_dict=encounter) # convert encounter to pyfhir instance
add_profile(encounter) # add profile if not already there
resources = [encounter]
# create messageheader
mh = getattr(fhirtemplates, 'messageheader') # resources as dict
mh = pyfhir(mh) #convert to fhirclient
mh.id = str(uuid.uuid1())
mh.focus[0].reference = f"Encounter/{encounter.id}"
if encounter.status == "in-progress" and encounter.class_fhir.code == "EMER":
mh.eventCoding.code = 'notification-admit'
mh.eventCoding.display = 'Notification Admit'
elif encounter.status == "in-progress" and encounter.class_fhir.code == "IMP":
mh.eventCoding.code = 'notification-transfer'
mh.eventCoding.display = 'Notification Transfer'
mh.meta.profile[1] = profile_list['MessageHeader_transfer']
elif encounter.status == "finished":
mh.eventCoding.code = 'notification-discharge'
mh.eventCoding.display = 'Notification Discharge'
mh.meta.profile[1] = profile_list['MessageHeader_discharge']
# TODO add discharge subtypes and handle other statuses
mh.focus[
0].display = f'{mh.eventCoding.display}({encounter.type[0].text})'
# mh.destination[0].name = list(alerts_servers.keys())[0]
# mh.destination[0].endpoint = list(alerts_servers.values())[0]
# TODO make a selection for the destination
mh.sender.reference = encounter.serviceProvider.reference
mh.sender.display = encounter.serviceProvider.display
mh.author.reference = encounter.participant[0].individual.reference
mh.author.display = encounter.participant[0].individual.display
mh.responsible.reference = encounter.serviceProvider.reference
mh.responsible.display = encounter.serviceProvider.display
resources.insert(0, mh)
for i in get_ids: # [{Type:Type, args=(args)}]
Type = i['Type']
args = i['args']
is_req = i['is_req']
my_id = get_r_id(encounter, *args)
app.logger.info(f'******my_id = {my_id}')
resource = fetch(Type, _id=my_id, ver=None)
append_resource(resource,
resources,
Type=Type,
id=my_id,
is_req=is_req)
resource = search(
'Condition',
patient=get_r_id(encounter, 'subject', 'reference'),
encounter=encounter.id,
) # fetch condition
append_resource(resource, resources, Type='Condition')
resource = search(
'Coverage',
patient=get_r_id(encounter, 'subject', 'reference'),
) # fetch coverage
coverage = pyfhir(r_dict=resource)
append_resource(resource, resources, Type='Coverage')
if coverage:
my_id = get_r_id(coverage, 'payor', 'reference')
resource = fetch(
'Organization',
_id=my_id,
) # fetch coverage
append_resource(resource,
resources,
Type='Organization',
id=my_id)
# assume sender = author i.e. no separate sender initially save for intermediary
# sender = getattr(fhirtemplates,'sender') # hardcode org for now
# resource = pyfhir(sender) #convert to fhirclient model
# add_profile(resource)
# resources.append(resource)
message_bundles.append(bundler(
resources, 'message', validate_me)) # returns as json string!
session['resource_list'] = session['resource_list'] + [
f'{r.resource_type}/{r.id}' for r in resources
]
################### End Assemble Bundle ################################
# endfor loop over encounters, if encounter length > 1 then create transaction Bundles
# writing to ig examples file and running the IG Build:
#f_name = f'davinci_notification_bundle_{now.strftime("%Y%m%d%H%M%S.%f")}.json'
if is_message_bundle:
my_string = "Getting Resources ready for Da Vinci Notification Message Bundle..."
app.logger.info(f' type my_string = {type(my_string)}')
notification_bundle = message_bundles[0]
endpoint = '$process-message'
else:
'''
if message_bundles length > 2 then bundle as transaction.
loop through message bundles and convert back to pyfhir object and save to array
then bundle again in a transaction and get a transaction as json string back. (modify the function to do this too)
'''
pyfhir_messages = [pyfhir(loads(b)) for b in message_bundles]
notification_bundle = bundler(pyfhir_messages, 'transaction',
validate_me)
my_string = 'Getting Resources ready for Tansaction Bundle of Da Vinci Notification Message Bundle...'
endpoint = 'transaction'
cache.set('notification_bundle', notification_bundle)
b_id = loads(notification_bundle)["id"]
f_name = f'davinci-notification-bundle-{b_id}.json'
write_out(app.root_path, f_name, notification_bundle)
app.logger.info(
f'writing example notification bundle to {app.root_path}/test_output/{f_name}'
)
session['f_names'].append(
f_name) # keep track of f_names for session to delete later
session.modified = True
app.logger.info(f'****** see what is in session = {session}***')
#app.logger.info(f'notification_bundle = {message_bundles[0]}')
#cache.set('notification_bundle', notification_bundle, timeout=60*15 )
#app.logger.info(f'****** line 574 see what is in cache = {cache.get("notification_bundle")}***')
return render_template(
'sub_template5.html',
my_string=my_string,
title="Notification Bundle Prep",
endpoint_urls=alerts_servers,
endpoint=endpoint,
notification_bundle=notification_bundle,
b_id=loads(notification_bundle)["id"],
)