def _call_fut(self, *args, **kw):
from occams_forms.renderers import apply_data
return apply_data(*args, **kw)
def form(context, request):
"""
XXX: Cannot merge into single view
because of the way patient forms are handled
"""
db_session = request.db_session
patient = context.__parent__.__parent__
schema = context.schema
(is_phi, ) = (db_session.query(
db_session.query(models.patient_schema_table).filter_by(
schema_id=schema.id).exists()).one())
if not is_phi:
previous_url = request.current_route_path(
_route_name='studies.patient_forms')
show_metadata = True
# We cannot determine which study this form will be applied to
# so just use any version from active studies
available_schemata = (db_session.query(datastore.Schema).join(
models.study_schema_table).join(models.Study).filter(
datastore.Schema.name == context.schema.name).filter(
datastore.Schema.publish_date != sa.null()).filter(
datastore.Schema.retract_date == sa.null()))
allowed_versions = sorted(
set(s.publish_date for s in available_schemata))
else:
previous_url = request.current_route_path(
_route_name='studies.patient')
show_metadata = False
allowed_versions = None
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(
db_session,
context.schema,
entity=context,
show_metadata=show_metadata,
transition=transition,
allowed_versions=allowed_versions,
)
form = Form(request.POST, data=entity_data(context))
if request.method == 'POST':
if not request.has_permission('edit', context):
raise HTTPForbidden()
if form.validate():
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, context, form.data, upload_dir)
db_session.flush()
request.session.flash(
_(u'Changes saved to: %s' % context.schema.title), 'success')
return HTTPFound(location=previous_url)
return {
'phi':
get_phi_entities(patient, request),
'patient':
view_json(patient, request),
'form':
render_form(form,
disabled=not request.has_permission('edit'),
cancel_url=previous_url,
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form'
}),
}
def _call_fut(self, *args, **kw):
from occams_forms.renderers import apply_data
return apply_data(*args, **kw)
def terminate_ajax(context, request):
db_session = request.db_session
try:
entity = (
db_session.query(datastore.Entity)
.join(datastore.Entity.schema)
.filter(datastore.Schema.name.in_(
# Only search for forms being used as temrination forms
db_session.query(datastore.Schema.name)
.join(models.Study.termination_schema)
.subquery()))
.join(datastore.Context)
.filter_by(external='enrollment', key=context.id)
.one())
except orm.exc.MultipleResultsFound:
raise Exception('Should only have one...')
except orm.exc.NoResultFound:
schema = context.study.termination_schema
entity = datastore.Entity(schema=schema)
# XXX: This is really bad form as we're applying
# side-effects to a GET request, but there is no time
# to make this look prety...
# If you remove this line you will be creating random termination
# entries...
context.entities.add(entity)
else:
schema = entity.schema
if not entity.state:
entity.state = (
db_session.query(datastore.State)
.filter_by(name='pending-entry')
.one())
if 'termination_date' not in schema.attributes:
msg = 'There is no "termination_date" configured on: {}'
log.warn(msg.format(schema.name))
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(
db_session, schema,
entity=entity, transition=transition, show_metadata=False)
form = Form(request.POST, data=entity_data(entity))
def validate_termination_date(form, field):
if not (field.data >= context.latest_consent_date):
raise wtforms.ValidationError(request.localizer.translate(
_(u'Termination must be on or after latest consent (${date})'),
mapping={'date': context.latest_consent_date}
))
# Inject a validator into the termination form so that we
# ensure that the termination date provided is valid
form.termination_date.validators.append(validate_termination_date)
if request.method == 'POST':
check_csrf_token(request)
if form.validate():
if not entity.id:
# changing termination version *should* not be
# allowed, just assign the schema that's already being used
context.entities.add(entity)
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, entity, form.data, upload_dir)
context.termination_date = form.termination_date.data
db_session.flush()
return HTTPOk(json=view_json(context, request))
else:
return HTTPBadRequest(json={'errors': wtferrors(form)})
return render_form(
form,
cancel_url=request.current_route_path(_route_name='studies.patient'),
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form',
'data-bind': 'formentry: {}, submit: $root.terminateEnrollment'
}
)
def apply_direct_mappings(task):
# get all the direct mappings for processing
mappings = (
Session.query(models.Mapping)
.filter_by(type=u'direct').all()
)
default_state = (
Session.query(datastore.State)
.filter_by(name='pending-entry')
.one()
)
redis = app.redis
total_mappings = len(mappings)
count = 0
mappings_id = six.text_type(str(uuid.uuid4()))
redis.hmset(mappings_id, {
'count': count,
'total': total_mappings
})
for mapping in mappings:
source_schema_name = mapping.logic['source_schema']
source_schema_publish_date = mapping.logic['source_schema_publish_date']
source_variable = mapping.logic['source_variable']
target_schema_name = mapping.logic['target_schema']
target_schema_publish_date = mapping.logic['target_schema_publish_date']
target_variable = mapping.logic['target_variable']
# get records that have a matching schema for source schema
records = (
Session.query(models.SiteData)
.filter(
models.SiteData.data['form_name'].astext == source_schema_name
)
.filter(
models.SiteData.data['form_publish_date'].astext == source_schema_publish_date
).all()
)
for record in records:
pid = record.data['pid']
collect_date = record.data['collect_date']
patient = (
Session.query(studies.Patient)
.filter_by(pid=pid)
.one()
)
target_schema = (
Session.query(datastore.Schema)
.filter_by(name=target_schema_name)
.filter_by(publish_date=target_schema_publish_date)
).one()
# if the target schema already exists we want to add data
# to the schema rather than creating a new entity
entity_exists = False
for item in patient.entities:
if item.schema.name == target_schema_name and \
item.schema.publish_date.isoformat() == \
target_schema_publish_date:
entity = item
entity_exists = True
break
if not entity_exists:
entity = datastore.Entity(
schema=target_schema,
collect_date=collect_date,
state=default_state
)
patient.entities.add(entity)
if mapping.logic['choices_mapping']:
# add handling if there is no value to map
source_key = record.data.get(source_variable)
payload = {target_variable: source_key}
upload_dir = tempfile.mkdtemp()
apply_data(Session, entity, payload, upload_dir)
shutil.rmtree(upload_dir)
else:
# non-choices processing
source_key = record.data.get(source_variable)
payload = {target_variable: source_key}
upload_dir = tempfile.mkdtemp()
apply_data(Session, entity, payload, upload_dir)
shutil.rmtree(upload_dir)
redis.hincrby(mappings_id, 'count')
data = redis.hgetall(mappings_id)
# redis-py returns everything as string, so we need to clean it
for key in ('count', 'total'):
data[key] = int(data[key])
redis.publish('direct', json.dumps(data))
def populate_project(
db_session,
project_name,
consolidated_frame,
pid_column=DEFAULT_PID_COLUMN,
visit_column=DEFAULT_VISIT_COLUMN,
collect_date_column=DEFAULT_COLLECT_DATE_COLUMN,
):
"""
Processes a final dataframe (i.e. a frame after mappings have been applied)
and creates entities for the target project.
:param db_session: Current database transaction session
:type db_session: sqlalchemy.orm.session.Session
:param project_name: study where entities will be applied
:type project_name: str
:param consolidated_frame: dataframe populated with mapped variables
:type consolidated_frame: pandas.DataFrame
:returns: none
"""
site = db_session.query(studies.Site).filter_by(name=project_name).one()
project = (db_session.query(
studies.Study).filter_by(name=project_name).one())
default_state = (db_session.query(
datastore.State).filter_by(name='pending-entry').one())
for index, row in consolidated_frame.iterrows():
pid = row['pid']
try:
patient = (db_session.query(
studies.Patient).filter_by(pid=pid).one())
except orm.exc.NoResultFound:
patient = studies.Patient(site=site, pid=pid)
db_session.add(patient)
db_session.flush()
for schema in project.schemata:
payload = {}
for attribute in schema.iterleafs():
column_name = '_'.join(
[project.name, schema.name, attribute.name])
if column_name not in row:
continue
value = row[column_name]
if isinstance(value, numbers.Number) and math.isnan(value):
continue
payload[attribute.name] = value
# Avoid creating empty records
if not payload:
continue
calculated_collect_date_column = '_'.join(
[project.name, schema.name, collect_date_column])
collect_date = row[calculated_collect_date_column]
entity = datastore.Entity(schema=schema,
collect_date=collect_date,
state=default_state)
patient.entities.add(entity)
upload_dir = tempfile.mkdtemp()
apply_data(db_session, entity, payload, upload_dir)
shutil.rmtree(upload_dir)
db_session.flush()
def form(context, request):
"""
XXX: Cannot merge into single view
because of the way patient forms are handled
"""
db_session = request.db_session
patient = context.__parent__.__parent__
schema = context.schema
(is_phi,) = (
db_session.query(
db_session.query(models.patient_schema_table)
.filter_by(schema_id=schema.id)
.exists())
.one())
if not is_phi:
previous_url = request.current_route_path(
_route_name='studies.patient_forms')
show_metadata = True
# We cannot determine which study this form will be applied to
# so just use any version from active studies
available_schemata = (
db_session.query(datastore.Schema)
.join(models.study_schema_table)
.join(models.Study)
.filter(datastore.Schema.name == context.schema.name)
.filter(datastore.Schema.publish_date != sa.null())
.filter(datastore.Schema.retract_date == sa.null()))
allowed_versions = sorted(set(
s.publish_date for s in available_schemata))
else:
previous_url = request.current_route_path(
_route_name='studies.patient')
show_metadata = False
allowed_versions = None
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(
db_session,
context.schema,
entity=context,
show_metadata=show_metadata,
transition=transition,
allowed_versions=allowed_versions,
)
form = Form(request.POST, data=entity_data(context))
if request.method == 'POST':
if not request.has_permission('edit', context):
raise HTTPForbidden()
if form.validate():
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, context, form.data, upload_dir)
db_session.flush()
request.session.flash(
_(u'Changes saved to: %s' % context.schema.title), 'success')
return HTTPFound(location=previous_url)
return {
'phi': get_phi_entities(patient, request),
'patient': view_json(patient, request),
'form': render_form(
form,
disabled=not request.has_permission('edit'),
cancel_url=previous_url,
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form'
}
),
}
def populate_project(
db_session,
project_name,
consolidated_frame,
pid_column=DEFAULT_PID_COLUMN,
visit_column=DEFAULT_VISIT_COLUMN,
collect_date_column=DEFAULT_COLLECT_DATE_COLUMN,
):
"""
Processes a final dataframe (i.e. a frame after mappings have been applied)
and creates entities for the target project.
:param db_session: Current database transaction session
:type db_session: sqlalchemy.orm.session.Session
:param project_name: study where entities will be applied
:type project_name: str
:param consolidated_frame: dataframe populated with mapped variables
:type consolidated_frame: pandas.DataFrame
:returns: none
"""
site = db_session.query(studies.Site).filter_by(name=project_name).one()
project = (
db_session.query(studies.Study)
.filter_by(name=project_name)
.one()
)
default_state = (
db_session.query(datastore.State)
.filter_by(name='pending-entry')
.one()
)
for index, row in consolidated_frame.iterrows():
pid = row['pid']
try:
patient = (
db_session.query(studies.Patient)
.filter_by(pid=pid)
.one()
)
except orm.exc.NoResultFound:
patient = studies.Patient(site=site, pid=pid)
db_session.add(patient)
db_session.flush()
for schema in project.schemata:
payload = {}
for attribute in schema.iterleafs():
column_name = '_'.join([
project.name, schema.name, attribute.name
])
if column_name not in row:
continue
value = row[column_name]
if isinstance(value, numbers.Number) and math.isnan(value):
continue
payload[attribute.name] = value
# Avoid creating empty records
if not payload:
continue
calculated_collect_date_column = '_'.join([
project.name, schema.name, collect_date_column
])
collect_date = row[calculated_collect_date_column]
entity = datastore.Entity(
schema=schema,
collect_date=collect_date,
state=default_state
)
patient.entities.add(entity)
upload_dir = tempfile.mkdtemp()
apply_data(db_session, entity, payload, upload_dir)
shutil.rmtree(upload_dir)
db_session.flush()
def form(context, request):
"""
XXX: Cannot merge into single view
because of the way patient forms are handled
"""
db_session = request.db_session
visit = context.__parent__.__parent__
allowed_schemata = (db_session.query(datastore.Schema).join(
models.study_schema_table).join(models.Study).join(
models.Cycle).filter(
datastore.Schema.name == context.schema.name).filter(
models.Cycle.id.in_([cycle.id for cycle in visit.cycles])))
allowed_versions = [s.publish_date for s in allowed_schemata]
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(
db_session,
context.schema,
entity=context,
show_metadata=True,
transition=transition,
allowed_versions=allowed_versions,
)
form = Form(request.POST, data=entity_data(context))
if request.method == 'POST':
if not request.has_permission('edit', context):
raise HTTPForbidden()
if form.validate():
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, context, form.data, upload_dir)
db_session.flush()
request.session.flash(
_(u'Changes saved for: ${form}',
mapping={'form': context.schema.title}), 'success')
return HTTPFound(location=request.current_route_path(
_route_name='studies.visit'))
return {
'visit':
view_json(visit, request),
'form':
render_form(
form,
disabled=not request.has_permission('edit'),
cancel_url=request.current_route_path(_route_name='studies.visit'),
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form'
}),
}
def terminate_ajax(context, request):
db_session = request.db_session
try:
entity = (
db_session.query(datastore.Entity).join(
datastore.Entity.schema).filter(
datastore.Schema.name.in_(
# Only search for forms being used as temrination forms
db_session.query(datastore.Schema.name).join(
models.Study.termination_schema
).subquery())).join(datastore.Context).filter_by(
external='enrollment', key=context.id).one())
except orm.exc.MultipleResultsFound:
raise Exception('Should only have one...')
except orm.exc.NoResultFound:
schema = context.study.termination_schema
entity = datastore.Entity(schema=schema)
# XXX: This is really bad form as we're applying
# side-effects to a GET request, but there is no time
# to make this look prety...
# If you remove this line you will be creating random termination
# entries...
context.entities.add(entity)
context.patient.entities.add(entity)
else:
schema = entity.schema
if not entity.state:
entity.state = (db_session.query(
datastore.State).filter_by(name='pending-entry').one())
if 'termination_date' not in schema.attributes:
msg = 'There is no "termination_date" configured on: {}'
log.warn(msg.format(schema.name))
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(db_session,
schema,
entity=entity,
transition=transition,
show_metadata=False)
form = Form(request.POST, data=entity_data(entity))
def validate_termination_date(form, field):
if not (field.data >= context.latest_consent_date):
raise wtforms.ValidationError(
request.localizer.translate(_(
u'Termination must be on or after latest consent (${date})'
),
mapping={
'date':
context.latest_consent_date
}))
# Inject a validator into the termination form so that we
# ensure that the termination date provided is valid
form.termination_date.validators.append(validate_termination_date)
if request.method == 'POST':
check_csrf_token(request)
if form.validate():
if not entity.id:
# changing termination version *should* not be
# allowed, just assign the schema that's already being used
context.entities.add(entity)
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, entity, form.data, upload_dir)
context.termination_date = form.termination_date.data
db_session.flush()
return HTTPOk(json=view_json(context, request))
else:
return HTTPBadRequest(json={'errors': wtferrors(form)})
return render_form(
form,
cancel_url=request.current_route_path(_route_name='studies.patient'),
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form',
'data-bind': 'formentry: {}, submit: $root.terminateEnrollment'
})
def form(context, request):
"""
XXX: Cannot merge into single view
because of the way patient forms are handled
"""
db_session = request.db_session
visit = context.__parent__.__parent__
allowed_schemata = (
db_session.query(datastore.Schema)
.join(models.study_schema_table)
.join(models.Study)
.join(models.Cycle)
.filter(models.Cycle.id.in_([cycle.id for cycle in visit.cycles])))
allowed_versions = [s.publish_date for s in allowed_schemata]
if request.has_permission('retract'):
transition = modes.ALL
elif request.has_permission('transition'):
transition = modes.AVAILABLE
else:
transition = modes.AUTO
Form = make_form(
db_session,
context.schema,
entity=context,
show_metadata=True,
transition=transition,
allowed_versions=allowed_versions,
)
form = Form(request.POST, data=entity_data(context))
if request.method == 'POST':
if not request.has_permission('edit', context):
raise HTTPForbidden()
if form.validate():
upload_dir = request.registry.settings['studies.blob.dir']
apply_data(db_session, context, form.data, upload_dir)
db_session.flush()
request.session.flash(
_(u'Changes saved for: ${form}', mapping={
'form': context.schema.title}),
'success')
return HTTPFound(location=request.current_route_path(
_route_name='studies.visit'))
return {
'visit': view_json(visit, request),
'form': render_form(
form,
disabled=not request.has_permission('edit'),
cancel_url=request.current_route_path(_route_name='studies.visit'),
attr={
'method': 'POST',
'action': request.current_route_path(),
'role': 'form'
}
),
}