def handle_resource(resource_type):
if resource_type == 'metadata':
return redirect("/static/doc/metadata")
if resource_type in [
'callsets', 'variantsets', 'readgroupsets', 'referencesets',
'variant'
]:
if request.method == 'GET':
return ga4gh.api.ga_handle_search(request, resource_type)
elif resource_type in [
'variantset', 'genomes', 'files', 'runs', 'genomes'
]:
if request.method == 'GET':
return basespace.api.bs_handle_search(request, resource_type)
elif resource_type in RESOURCES:
if request.method == 'GET':
return ttam.api.ttam_handle_search(request, resource_type)
else:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == 'GET':
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def read_history(resource_type, resource_id, version):
if resource_type is not None and resource_type not in RESOURCES:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
return fhir_api.handle_history(fhir_request, resource_type, resource_id, version)
def launch_app(client_id):
# TODO refactor this. No DRY!!!
user = request.session.user
app = (App.query.filter_by(user_id=user.email,
client_id=client_id).first())
if app is None:
return NOT_FOUND
if request.method == 'GET':
# prompt user to select a patient to launch
# TODO make this more readable
patients = [{
'id':
pt.resource_id,
'desc':
json.loads(pt.data).get('text',
{}).get('div', 'No description available')
} for pt in Resource.query.filter_by(owner_id=user.email,
resource_type='Patient').all()]
if len(patients) > 0:
return render_template('launch_context.html',
cont_url=request.url,
resources=json.dumps({'Patient': patients}))
else:
selected_pt = None
else:
selected_pt = request.form['Patient']
ctx = Context()
if selected_pt is not None:
ctx.context = json.dumps({'Patient': selected_pt})
db.session.add(ctx)
db.session.commit()
# launch!
launch_args = {'launch': ctx.id, 'iss': get_api_base()}
return redirect('%s?%s' % (app.launch_uri, urlencode(launch_args)))
def handle_resources(resource_type, resource_id):
if resource_type in [
'callsets', 'variantsets', 'readgroupsets', 'referencesets',
'variant'
]:
if request.method == 'GET':
return ga4gh.api.ga_handle_read(request, resource_type,
resource_id)
elif resource_type in [
'variantset', 'genomes', 'files', 'runs', 'genomes'
]:
if request.method == 'GET':
return basespace.api.bs_handle_read(request, resource_type,
resource_id)
elif resource_type in RESOURCES:
if request.method == 'GET':
return ttam.api.ttam_handle_read(request, resource_type,
resource_id)
else:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request, is_resource=False)
if request.method == 'GET':
return fhir_api.handle_read(fhir_request, resource_type, resource_id)
elif request.method == 'PUT':
return fhir_api.handle_update(fhir_request, resource_type, resource_id)
else:
return fhir_api.handle_delete(fhir_request, resource_type, resource_id)
def launch_app(client_id):
# TODO refactor this. No DRY!!!
user = request.session.user
app = App.query.filter_by(user_id=user.email, client_id=client_id).first()
if app is None:
return NOT_FOUND
if request.method == "GET":
# prompt user to select a patient to launch
# TODO make this more readable
patients = [
{"id": pt.resource_id, "desc": json.loads(pt.data).get("text", {}).get("div", "No description available")}
for pt in Resource.query.filter_by(owner_id=user.email, resource_type="Patient").all()
]
if len(patients) > 0:
return render_template(
"launch_context.html", cont_url=request.url, resources=json.dumps({"Patient": patients})
)
else:
selected_pt = None
else:
selected_pt = request.form["Patient"]
ctx = Context()
if selected_pt is not None:
ctx.context = json.dumps({"Patient": selected_pt})
db.session.add(ctx)
db.session.commit()
# launch!
launch_args = {"launch": ctx.id, "iss": get_api_base()}
return redirect("%s?%s" % (app.launch_uri, urlencode(launch_args)))
def handle_resources(resource_type, resource_id):
if resource_type in ['callsets', 'variantsets', 'readgroupsets', 'referencesets', 'variant']:
if request.method == 'GET':
return ga4gh.api.ga_handle_read(request, resource_type, resource_id)
elif resource_type in ['variantset', 'genomes', 'files', 'runs', 'genomes']:
if request.method == 'GET':
return basespace.api.bs_handle_read(request, resource_type, resource_id)
elif resource_type in RESOURCES:
if request.method == 'GET':
return ttam.api.ttam_handle_read(request, resource_type, resource_id)
else:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request, is_resource=False)
if request.method == 'GET':
return fhir_api.handle_read(fhir_request,
resource_type,
resource_id)
elif request.method == 'PUT':
return fhir_api.handle_update(fhir_request,
resource_type,
resource_id)
else:
return fhir_api.handle_delete(fhir_request,
resource_type,
resource_id)
def read_history(resource_type, resource_id, version):
if resource_type is not None and resource_type not in RESOURCES:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
return fhir_api.handle_history(fhir_request, resource_type, resource_id,
version)
def handle_resource(resource_type):
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == 'GET':
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def handle_resource(resource_type):
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == "GET":
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def handle_resources(resource_type, resource_id):
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request, is_resource=False)
if request.method == 'GET':
return fhir_api.handle_read(fhir_request, resource_type, resource_id)
elif request.method == 'PUT':
return fhir_api.handle_update(fhir_request, resource_type, resource_id)
else:
return fhir_api.handle_delete(fhir_request, resource_type, resource_id)
def handle_resources(resource_type, resource_id):
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request, is_resource=False)
if request.method == "GET":
return fhir_api.handle_read(fhir_request, resource_type, resource_id)
elif request.method == "PUT":
return fhir_api.handle_update(fhir_request, resource_type, resource_id)
else:
return fhir_api.handle_delete(fhir_request, resource_type, resource_id)
def handle_resource(resource_type):
if resource_type in ['callsets', 'variantsets', 'readgroupsets', 'referencesets', 'variant']:
if request.method == 'GET':
return ga4gh.api.ga_handle_search(request, resource_type)
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == 'GET':
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def handle_resource(resource_type):
if resource_type in [
'callsets', 'variantsets', 'readgroupsets', 'referencesets',
'variant'
]:
if request.method == 'GET':
return ga4gh.api.ga_handle_search(request, resource_type)
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == 'GET':
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def handle_resources_policy(resource_type, resource_id):
if resource_type not in RESOURCES:
return fhir_error.inform_not_found()
request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request, is_resource=False)
if request.method == 'GET':
return fhir_api.handle_read(fhir_request,
resource_type,
resource_id)
elif request.method == 'PUT' or request.method == 'POST':
return fhir_api.handle_add_policy(fhir_request,
resource_type,
resource_id)
else:
return fhir_api.handle_delete_policy(fhir_request,
resource_type,
resource_id)
def index_reference(index, element, owner_id, g):
'''
index a reference
'''
if 'display' in element:
index['text'] = '::%s::' % (element['display'], )
if 'reference' in element:
reference_url = element['reference']
reference = REFERENCE_RE.match(reference_url)
index['referenced_url'] = reference_url
if reference.group('extern_base') is None or reference.group(
'extern_base') == get_api_base():
# reference is internal reference, we want to link the reference to a Resource
index['referenced'] = Resource.query.filter_by(
resource_type=reference.group('resource_type'),
resource_id=reference.group('resource_id'),
owner_id=owner_id,
visible=True).first()
return index
def launch_app(client_id):
# TODO refactor this. No DRY!!!
user = request.session.user
app = (App.query
.filter_by(user_id=user.email, client_id=client_id)
.first())
if app is None:
return NOT_FOUND
if request.method == 'GET':
# prompt user to select a patient to launch
# TODO make this more readable
patients = [{'id': pt.resource_id, 'desc': json.loads(pt.data).get('text', {}).get('div', 'No description available')}
for pt in Resource
.query
.filter_by(
owner_id=user.email,
resource_type='Patient')
.all()]
if len(patients) > 0:
return render_template(
'launch_context.html',
cont_url=request.url,
resources=json.dumps({'Patient': patients}))
else:
selected_pt = None
else:
selected_pt = request.form['Patient']
ctx = Context()
if selected_pt is not None:
ctx.context = json.dumps({'Patient': selected_pt})
db.session.add(ctx)
db.session.commit()
# launch!
launch_args = {
'launch': ctx.id,
'iss': get_api_base()
}
return redirect('%s?%s'% (
app.launch_uri,
urlencode(launch_args)))
def __init__(self,
query,
request,
version_specific=False,
ttam_resource=None):
self.api_base = get_api_base()
self.request_url = request.url
self.data_format = request.format
self.version_specific = version_specific
self.update_time = datetime.now().isoformat()
self.resources = query.\
limit(request.count).\
offset(request.offset).all()
self.resource_count = query.count()
#print self.resource_count
if ttam_resource is not None:
# 23andMe resource(s) are being requested here.
# We need to figure out the paging properties for 23andme resources.
# We preserve determinism here by lining all internal resources before
# 23andMe resources (
# think about it like this ...---, with '.' being internal, and '-' being 23andMe.
# Here we have three internal resources and 3 23andMe resources.
# So a 4-offset is the same as a 0-offset of 23andMe resources,
# and a 1-offset is also a 0-offset of 23andMe. And so forth).
num_resources = len(self.resources)
ttam_offset = (request.offset - self.resource_count
if request.offset >= self.resource_count else 0)
ttam_limit = request.count - num_resources
ttam_resources, ttam_count = ttam.get_many(ttam_resource,
request.args,
ttam_offset, ttam_limit)
self.resource_count += ttam_count
if num_resources < request.count:
self.resources.extend(ttam_resources)
self.next_url = (request.get_next_url() if len(self.resources) +
request.offset < self.resource_count else None)
self.prev_url = (request.get_prev_url()
if request.offset - request.count >= 0 else None)
def __init__(self, request, is_resource=True):
self.args = request.args
self.format = self.args.get('_format', 'xml')
self.api_base = get_api_base()
self.url = request.url
self.base_url = request.base_url
self.authorizer = request.authorizer
# paging params
self.count = int(self.args.get('_count', PAGE_SIZE))
self.offset = int(self.args.get('_offset', 0))
if request.method in ('POST', 'PUT'):
# regardless of format of uploaded data
# we process it as a json object (technically a Python Dict)
if self.format == 'xml':
dataroot = etree.fromstring(request.data)
# tag of an etree element = {whatever xmlns value is}[element name]
# we only care about `element name` here
resource_type = dataroot.tag.split('}')[-1]
self.data = xml_to_json(dataroot, resource_type)
else:
self.data = json.loads(request.data)
def __init__(self, request, is_resource=True):
self.args = request.args
self.format = self.args.get('_format', 'xml')
self.api_base = get_api_base()
self.url = request.url
self.base_url = request.base_url
self.authorizer = request.authorizer
# paging params
self.count = int(self.args.get('_count', PAGE_SIZE))
self.offset = int(self.args.get('_offset', 0))
if request.method in ('POST', 'PUT'):
# regardless of format of uploaded data
# we process it as a json object (technically a Python Dict)
if self.format == 'xml':
dataroot = etree.fromstring(request.data)
# tag of an etree element = {whatever xmlns value is}[element name]
# we only care about `element name` here
resource_type = dataroot.tag.split('}')[-1]
self.data = xml_to_json(dataroot, resource_type)
else:
self.data = json.loads(request.data)
def __init__(self, query, request, version_specific=False, ttam_resource=None):
self.api_base = get_api_base()
self.request_url = request.url
self.data_format = request.format
self.version_specific = version_specific
self.update_time = datetime.now().isoformat()
self.resources = query.\
limit(request.count).\
offset(request.offset).all()
self.resource_count = query.count()
if ttam_resource is not None:
# 23andMe resource(s) are being requested here.
# We need to figure out the paging properties for 23andme resources.
# We preserve determinism here by lining all internal resources before
# 23andMe resources (
# think about it like this ...---, with '.' being internal, and '-' being 23andMe.
# Here we have three internal resources and 3 23andMe resources.
# So a 4-offset is the same as a 0-offset of 23andMe resources,
# and a 1-offset is also a 0-offset of 23andMe. And so forth).
num_resources = len(self.resources)
ttam_offset = (request.offset - self.resource_count
if request.offset >= self.resource_count
else 0)
ttam_limit = request.count - num_resources
ttam_resources, ttam_count = ttam.get_many(ttam_resource, request.args, ttam_offset, ttam_limit)
self.resource_count += ttam_count
if num_resources < request.count:
self.resources.extend(ttam_resources)
self.next_url = (request.get_next_url()
if len(self.resources) + request.offset < self.resource_count
else None)
self.prev_url = (request.get_prev_url()
if request.offset - request.count >= 0
else None)
def handle_resource(resource_type):
if resource_type == 'metadata':
return redirect("/static/doc/metadata")
if resource_type in ['callsets', 'variantsets', 'readgroupsets', 'referencesets', 'variant']:
if request.method == 'GET':
return ga4gh.api.ga_handle_search(request, resource_type)
elif resource_type in ['variantset', 'genomes', 'files', 'runs', 'genomes']:
if request.method == 'GET':
return basespace.api.bs_handle_search(request, resource_type)
elif resource_type in RESOURCES:
if request.method == 'GET':
return ttam.api.ttam_handle_search(request, resource_type)
else:
return fhir_error.inform_not_found()
g.api_base = request.api_base = util.get_api_base()
fhir_request = fhir_api.FHIRRequest(request)
if request.method == 'GET':
return fhir_api.handle_search(fhir_request, resource_type)
else:
return fhir_api.handle_create(fhir_request, resource_type)
def index_reference(index, element, owner_id, g):
'''
index a reference
'''
if 'display' in element:
index['text'] = '::%s::' % (element['display'],)
if 'reference' in element:
reference_url = element['reference']
reference = REFERENCE_RE.match(reference_url)
index['referenced_url'] = reference_url
if reference.group('extern_base') is None or reference.group('extern_base') == get_api_base():
# reference is internal reference, we want to link the reference to a Resource
index['referenced'] = Resource.query.filter_by(resource_type=reference.group('resource_type'),
resource_id=reference.group('resource_id'),
owner_id=owner_id,
visible=True).first()
return index
