def __init__(self):
self.logger = logging.getLogger(self.__module__ + '.' + self.__class__.__name__)
self.logger.addHandler(logging.NullHandler())
# An instance of the DieseaseMeta class (composition).
self._disease_meta = DiseaseMeta()
# A flag to mark whether DiseaseMeta is dirty or not
self._dm_dirty = False
self._id = None
self._tags = []
self._links = {}
self._version = None
self._d = { "study": None,
"tags": [] }
for propname, spec in VisitAttribute.__dict.iteritems():
t = spec[0]
x = property(VisitAttribute._bindRead(propname), VisitAttribute._bindWrite(propname, t))
setattr(self.__class__, propname, x)
class VisitAttribute(Base):
namespace = "ihmp"
__dict = {
'comment': [ str, None ],
'survey_id': [ str, None ],
'study': [ str, None ],
# These are the disease metadata fields
'disease_comment': [ "DiseaseMeta.comment", None ],
'disease_name': [ "DiseaseMeta.name", None ],
'disease_description': [ "DiseaseMeta.description", None ],
'disease_ontology_id': [ "DiseaseMeta.disease_ontology_id", None ],
'disease_mesh_id': [ "DiseaseMeta.mesh_id", None ],
'disease_nci_id': [ "DiseaseMeta.nci_id", None ],
'disease_umls_concept_id': [ "DiseaseMeta.umls_concept_id", None ],
'disease_study_status': [ "DiseaseMeta.study_disease_status", None ],
# These are the clinical patient fields
'age' : [ int , "clinical_patient" ],
'height' : [ float , "clinical_patient" ],
'weight' : [ float , "clinical_patient" ],
'weight_diff' : [ str , "clinical_patient" ],
'bmi' : [ float , "clinical_patient" ],
'hbi' : [ bool , "clinical_patient" ],
'hbi_total' : [ float , "clinical_patient" ],
'sccai' : [ bool , "clinical_patient" ],
'sccai_total' : [ float , "clinical_patient" ],
'fast_gluc' : [ int , "clinical_patient" ],
'thirtym_gluc' : [ int , "clinical_patient" ],
'sixtym_gluc' : [ int , "clinical_patient" ],
# These are the hrt fields
'prior': [ bool, "hrt" ],
'current': [ bool, "hrt" ],
'duration': [ str, "hrt" ],
# These are the health assessment fields
'self_assess' : [ bool , "health_assessment" ],
'self_condition' : [ str , "health_assessment" ],
'abdominal_pain' : [ bool , "health_assessment" ],
'acute_dis' : [ str , "health_assessment" ],
'arthralgia' : [ bool , "health_assessment" ],
'bowel_day' : [ int , "health_assessment" ],
'bowel_night' : [ int , "health_assessment" ],
'cancer' : [ str , "health_assessment" ],
'cancer_mtc' : [ bool , "health_assessment" ],
'chest_pain' : [ bool , "health_assessment" ],
'claudication' : [ bool , "health_assessment" ],
'chronic_dis' : [ str , "health_assessment" ],
'diarrhea' : [ bool , "health_assessment" ],
'dyspnea' : [ bool , "health_assessment" ],
'ery_nodosum' : [ bool , "health_assessment" ],
'fever' : [ str , "health_assessment" ],
'leg_edema' : [ bool , "health_assessment" ],
'neurologic' : [ bool , "health_assessment" ],
'pregnant' : [ bool , "health_assessment" ],
'preg_plans' : [ bool , "health_assessment" ],
'pyo_gangrenosum' : [ bool , "health_assessment" ],
'rash' : [ bool , "health_assessment" ],
'stool_blood' : [ bool , "health_assessment" ],
'stool_soft' : [ int , "health_assessment" ],
'surgery' : [ str , "health_assessment" ],
'urgency_def' : [ str , "health_assessment" ],
'uveitis' : [ bool , "health_assessment" ],
'weight_change' : [ str , "health_assessment" ],
'diag_other' : [ str , "health_assessment" ],
'hosp' : [ bool , "health_assessment" ],
'work_missed' : [ int , "health_assessment" ],
# These are the medications fields
'new_meds' : [ bool, "medications" ],
'stopped_meds' : [ bool, "medications" ],
'abx' : [ bool, "medications" ],
'chemo' : [ bool, "medications" ],
'immunosupp' : [ bool, "medications" ],
# These are the tests fields
'colonoscopy': [ bool, "tests" ],
'oral_contrast': [ bool, "tests" ],
# These are the psych fields
'psychiatric' : [ bool, "psych" ],
'upset' : [ int , "psych" ],
'control' : [ int , "psych" ],
'stress' : [ int , "psych" ],
'stress_def' : [ str , "psych" ],
'confident' : [ int , "psych" ],
'going_your_way' : [ int , "psych" ],
'coping' : [ int , "psych" ],
'irritation' : [ int , "psych" ],
'on_top' : [ int , "psych" ],
'anger' : [ int , "psych" ],
'difficulties' : [ int , "psych" ],
# These are the exercise fields
'vig_activity_days' : [ int, "exercise" ],
'vig_activity_hours' : [ int, "exercise" ],
'vig_activity_minutes' : [ int, "exercise" ],
'mod_activity_days' : [ int, "exercise" ],
'mod_activity_hours' : [ int, "exercise" ],
'mod_activity_minutes' : [ int, "exercise" ],
'walking_days' : [ int, "exercise" ],
'walking_hours' : [ int, "exercise" ],
'walking_minutes' : [ int, "exercise" ],
'activity_30d' : [ str, "exercise" ],
'activity_3m' : [ str, "exercise" ],
'activity_change_30d' : [ str, "exercise" ],
'activity_change_3m' : [ str, "exercise" ],
# These are the dietary log fields
'alcohol' : [ bool , "dietary_log" ],
'beans' : [ bool , "dietary_log" ],
'biscuit' : [ bool , "dietary_log" ],
'bread' : [ str , "dietary_log" ],
'bread_spread' : [ str , "dietary_log" ],
'breadrolls' : [ bool , "dietary_log" ],
'cheese' : [ bool , "dietary_log" ],
'cereal' : [ bool , "dietary_log" ],
'cereal_type' : [ str , "dietary_log" ],
'chips_crisps' : [ bool , "dietary_log" ],
'dairy' : [ bool , "dietary_log" ],
'diet_drinks' : [ bool , "dietary_log" ],
'eggs' : [ bool , "dietary_log" ],
'fish' : [ bool , "dietary_log" ],
'fish_white' : [ bool , "dietary_log" ],
'fish_oil' : [ bool , "dietary_log" ],
'fish_count' : [ int , "dietary_log" ],
'fruit' : [ bool , "dietary_log" ],
'fruit_count' : [ int , "dietary_log" ],
'grains' : [ bool , "dietary_log" ],
'ice_cream' : [ bool , "dietary_log" ],
'juice' : [ bool , "dietary_log" ],
'meat' : [ bool , "dietary_log" ],
'meat_red' : [ bool , "dietary_log" ],
'meat_white' : [ bool , "dietary_log" ],
'meat_product' : [ bool , "dietary_log" ],
'milk' : [ str , "dietary_log" ],
'pastry' : [ bool , "dietary_log" ],
'poultry' : [ bool , "dietary_log" ],
'probiotic' : [ bool , "dietary_log" ],
'salt' : [ str , "dietary_log" ],
'shellfish' : [ bool , "dietary_log" ],
'soda' : [ bool , "dietary_log" ],
'starch' : [ bool , "dietary_log" ],
'starch_type' : [ bool , "dietary_log" ],
'sugar' : [ str , "dietary_log" ],
'sugar_drinks' : [ bool , "dietary_log" ],
'sweets' : [ bool , "dietary_log" ],
'sweets_count' : [ int , "dietary_log" ],
'veg' : [ bool , "dietary_log" ],
'veg_green' : [ bool , "dietary_log" ],
'veg_root' : [ bool , "dietary_log" ],
'veg_raw' : [ bool , "dietary_log" ],
'water' : [ bool , "dietary_log" ],
'yogurt' : [ bool , "dietary_log" ],
# These are the dietary log "today" fields
'breakfast_tod': [ str, "dietary_log_today" ],
'breakfast_food': [ str, "dietary_log_today" ],
'breakfast_amt': [ str, "dietary_log_today" ],
'lunch_tod': [ str, "dietary_log_today" ],
'lunch_food': [ str, "dietary_log_today" ],
'lunch_amt': [ str, "dietary_log_today" ],
'dinner_tod': [ str, "dietary_log_today" ],
'dinner_food': [ str, "dietary_log_today" ],
'dinner_amt': [ str, "dietary_log_today" ],
'other_food_intake': [ str, "dietary_log_today" ]
}
@staticmethod
def _getx(self, propname, *args):
if propname in self.__dict:
propType = self.__dict[propname][0]
if type(propType) == str and propType.startswith("DiseaseMeta."):
dm_name = propType.replace("DiseaseMeta.", "", 1)
value = getattr(self._disease_meta, dm_name)
elif propname in self._d:
value = self._d[propname]
else:
value = None
else:
raise AttributeError("Unknown attribute %s" % propname)
return value
@staticmethod
def _setx(self, value, n):
self._d[n] = value
@staticmethod
def _bindRead(name):
def getXXXX(self, *args):
return VisitAttribute._getx(self, name, *args)
getXXXX.__name__ = name
return getXXXX
@staticmethod
def _bindWrite(name, t):
def setXXXX(self, val):
func = VisitAttribute._setx
if t == str:
func = enforce_string(func)
elif t == int:
func = enforce_int(func)
elif t == float:
func = enforce_float(func)
elif t == list:
func = enforce_list(func)
elif t == bool:
func = enforce_bool(func)
elif t == dict:
func = enforce_dict(func)
func(self, val, name)
setXXXX.__name__ = name
return setXXXX
def __init__(self):
self.logger = logging.getLogger(self.__module__ + '.' + self.__class__.__name__)
self.logger.addHandler(logging.NullHandler())
# An instance of the DieseaseMeta class (composition).
self._disease_meta = DiseaseMeta()
# A flag to mark whether DiseaseMeta is dirty or not
self._dm_dirty = False
self._id = None
self._tags = []
self._links = {}
self._version = None
self._d = { "study": None,
"tags": [] }
for propname, spec in VisitAttribute.__dict.iteritems():
t = spec[0]
x = property(VisitAttribute._bindRead(propname), VisitAttribute._bindWrite(propname, t))
setattr(self.__class__, propname, x)
def __setattr__(self, name, value):
if name == "_d":
self.__dict__[name] = value
return
if name not in VisitAttribute.__dict:
super(VisitAttribute, self).__setattr__(name, value)
#raise AttributeError("Tsk tsk")
else:
nameType = self.__dict[name][0]
if type(nameType) == str and nameType.startswith("DiseaseMeta."):
dm_name = nameType.replace("DiseaseMeta.", "", 1)
self.logger.debug("Setting DiseaseMeta {} property.".format(dm_name))
setattr(self._disease_meta, dm_name, value)
self.logger.debug("Setting flag that DiseaseMeta is dirty.")
self._dm_dirty = True
else:
func = getattr(self.__class__, name)
func.__set__(self, value)
@staticmethod
def required_fields():
return ("study", "tags")
@staticmethod
def load_visit_attr(attrib_data):
"""
Takes the provided JSON string and converts it to a
VisitAttribute object.
Args:
attrib_data (str): The JSON string to convert
Returns:
Returns a VisitAttribute instance.
"""
module_logger.info("Creating a template " + __name__ + ".")
attrib = VisitAttribute()
module_logger.debug("Filling in " + __name__ + " details.")
attrib._set_id(attrib_data['id'])
attrib._links = attrib_data['linkage']
attrib._version = attrib_data['ver']
# Required fields
attrib.comment = attrib_data['meta']['comment']
attrib.study = attrib_data['meta']['study']
attrib.survey_id = attrib_data['meta']['survey_id']
attrib.tags = attrib_data['meta']['tags']
module_logger.debug("Returning loaded " + __name__ + ".")
return attrib
@staticmethod
def load(attrib_id):
"""
Loads the data for the node from OSDF to this object. If the provided
ID does not exist, then an error message is generated.
Args:
attrib_id (str): The OSDF ID for the document to load.
Returns:
A VisitAttribute object with all the available OSDF data loaded
into it.
"""
module_logger.debug("In load. Specified ID: %s" % attrib_id)
session = iHMPSession.get_session()
module_logger.info("Got iHMP session.")
data = session.get_osdf().get_node(attrib_id)
attrib = VisitAttribute.load_visit_attr(data)
return attrib
def validate(self):
"""
Validates the current object's data against the schema in the OSDF instance.
Args:
None
Returns:
A list of strings, where each string is a validation error that the
OSDF instance identified.
"""
self.logger.debug("In validate.")
document = self._get_raw_doc()
session = iHMPSession.get_session()
self.logger.info("Got iHMP session.")
(valid, error_message) = session.get_osdf().validate_node(document)
problems = []
if not valid:
self.logger.info("Validation did not succeed for " + __name__ + ".")
problems.append(error_message)
if 'associated_with' not in self._links.keys():
problems.append("Must add an 'associated_with' link to a visit.")
self.logger.debug("Number of validation problems: %s." % len(problems))
return problems
def is_valid(self):
"""
Validates the current object's data/JSON against the current schema
in the OSDF instance for the specific object. However, unlike
validate(), this method does not provide exact error messages,
it states if the validation was successful or not.
Args:
None
Returns:
True if the data validates, False if the current state of
fields in the instance does not validate with OSDF.
"""
self.logger.debug("In is_valid.")
document = self._get_raw_doc()
session = iHMPSession.get_session()
self.logger.info("Got iHMP session.")
(valid, error_message) = session.get_osdf().validate_node(document)
if 'associated_with' not in self._links.keys():
self.logger.error("Must have an 'associated_with' linkage.")
valid = False
self.logger.debug("Valid? %s" % str(valid))
return valid
def _get_raw_doc(self):
self.logger.debug("In _get_raw_doc.")
doc = {
'acl': {
'read': [ 'all' ],
'write': [ VisitAttribute.namespace ]
},
'linkage': self.links,
'ns': VisitAttribute.namespace,
'node_type': 'visit_attr',
'meta': {
'tags': self.tags,
'comment': self.comment,
'survey_id': self.survey_id,
'study': self.study,
'subtype': self.study
}
}
# Go through each of the properties, and add it to the document
# if it contains data
for propname, spec in VisitAttribute.__dict.iteritems():
# Don't encode 'special' properties that are delegated, such
# as the DiseaseMeta fields...
if spec[1] is None:
continue
value = getattr(self, propname)
if value is not None:
self.logger.debug("Value found for {} property.".format(propname))
section = spec[1]
# Set the section to a dictionary if it doesn't exist yet
if section not in doc['meta']:
doc['meta'][section] = {}
# Handle special cases
if propname == "sixtym_gluc":
propname = "60m_gluc"
elif propname == "thirtym_gluc":
propname = "30m_gluc"
if propname == "vig_activity_days":
if "vig_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['vig_activity'] = {}
doc['meta']['exercise']['vig_activity']['days'] = value
elif propname == "vig_activity_hours":
if "vig_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['vig_activity'] = {}
doc['meta']['exercise']['vig_activity']['hours'] = value
elif propname == "vig_activity_minutes":
if "vig_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['vig_activity'] = {}
doc['meta']['exercise']['vig_activity']['minutes'] = value
elif propname == "mod_activity_days":
if "mod_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['mod_activity'] = {}
doc['meta']['exercise']['mod_activity']['days'] = value
elif propname == "mod_activity_hours":
if "mod_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['mod_activity'] = {}
doc['meta']['exercise']['mod_activity']['hours'] = value
elif propname == "mod_activity_minutes":
if "mod_activity" not in doc['meta']['exercise']:
doc['meta']['exercise']['mod_activity'] = {}
doc['meta']['exercise']['mod_activity']['minutes'] = value
elif propname == "walking_days":
if "walking" not in doc['meta']['exercise']:
doc['meta']['exercise']['walking'] = {}
doc['meta']['exercise']['walking']['days'] = value
elif propname == "walking_hours":
if "walking" not in doc['meta']['exercise']:
doc['meta']['exercise']['walking'] = {}
doc['meta']['exercise']['walking']['hours'] = value
elif propname == "walking_minutes":
if "walking" not in doc['meta']['exercise']:
doc['meta']['exercise']['walking'] = {}
doc['meta']['exercise']['walking']['minutes'] = value
# dietary log "today"
elif propname == "breakfast_tod":
if "breakfast" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['breakfast'] = {}
doc['meta']['dietary_log_today']['breakfast']['tod'] = value
elif propname == "breakfast_food":
if "breakfast" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['breakfast'] = {}
doc['meta']['dietary_log_today']['breakfast']['food'] = value
elif propname == "breakfast_amt":
if "breakfast" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['breakfast'] = {}
doc['meta']['dietary_log_today']['breakfast']['amt'] = value
elif propname == "lunch_tod":
if "lunch" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['lunch'] = {}
doc['meta']['dietary_log_today']['lunch']['tod'] = value
elif propname == "lunch_food":
if "lunch" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['lunch'] = {}
doc['meta']['dietary_log_today']['lunch']['food'] = value
elif propname == "lunch_amt":
if "lunch" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['lunch'] = {}
doc['meta']['dietary_log_today']['lunch']['amt'] = value
elif propname == "dinner_tod":
if "dinner" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['dinner'] = {}
doc['meta']['dietary_log_today']['dinner']['tod'] = value
elif propname == "dinner_food":
if "dinner" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['dinner'] = {}
doc['meta']['dietary_log_today']['dinner']['food'] = value
elif propname == "dinner_amt":
if "dinner" not in doc['meta']['dietary_log_today']:
doc['meta']['dietary_log_today']['dinner'] = {}
doc['meta']['dietary_log_today']['dinner']['amt'] = value
else:
doc['meta'][section][propname] = value
# If we've configured fields in the DiseaseMeta class, fill the disease
# portion of the document, which is delegated to the DiseaseMeta class.
if self._dm_dirty:
doc['meta']['disease_meta'] = self._disease_meta._get_raw_doc()
if self._id is not None:
self.logger.debug(__name__ + " object has the OSDF id set.")
doc['id'] = self._id
if self._version is not None:
self.logger.debug(__name__ + " object has the OSDF version set.")
doc['ver'] = self._version
return doc
@staticmethod
def search(query = "\"visit_attr\"[node_type]"):
"""
Searches OSDF for VisitAttribute nodes. Any criteria the user wishes to
add is provided by the user in the query language specifications
provided in the OSDF documentation. A general format is (including the
quotes and brackets):
"search criteria"[field to search]
If there are any results, they are returned as SampleAttribute instances,
otherwise an empty list will be returned.
Args:
query (str): The query for the OSDF framework. Defaults to the
SampleAttribute node type.
Returns:
Returns an array of VisitAttribute objects. It returns an empty
list if there are no results.
"""
module_logger.debug("In search.")
session = iHMPSession.get_session()
module_logger.info("Got iHMP session.")
if query != '"visit_attr"[node_type]':
query = '({}) && "visit_attr"[node_type]'.format(query)
module_logger.debug("Submitting OQL query: {}".format(query))
attrib_data = session.get_osdf().oql_query(VisitAttribute.namespace, query)
all_results = attrib_data['results']
result_list = list()
if len(all_results) > 0:
for result in all_results:
attrib_result = VisitAttribute.load_visit_attr(result)
result_list.append(attrib_result)
return result_list
def save(self):
"""
Saves the data to OSDF. The JSON form of the object is not valid, then
the data is not saved. If the instance was saved previously, then the
node ID is assigned the alphanumeric assigned by the OSDF instance. If
not saved previously, then the node ID is 'None', and upon a successful
save, will be defined as the alphanumeric ID from OSDF. In addition,
the document's version is updated when a successful save operation is
completed.
Args:
None
Returns;
True if successful, False otherwise.
"""
self.logger.debug("In save.")
if not self.is_valid():
self.logger.error("Cannot save, data is invalid.")
return False
session = iHMPSession.get_session()
self.logger.info("Got iHMP session.")
success = False
if self._id is None:
# The document has not yet been saved
data = self._get_raw_doc()
self.logger.info("Got the raw JSON document.")
try:
self.logger.info("Attempting to save a new node.")
node_id = session.get_osdf().insert_node(data)
self.logger.info("Save for VisitAttribute %s successful." % node_id)
self.logger.info("Setting ID for VisitAttribute %s." % node_id)
self._set_id(node_id)
self._version = 1
success = True
except Exception as e:
self.logger.error("An error occurred while saving. " +
"Reason: %s" % e)
else:
data = self._get_raw_doc()
try:
self.logger.info("Attempting to update ID: %s." % self.id)
session.get_osdf().edit_node(data)
self.logger.info("Update for %s successful." % self.id)
success = True
except Exception as e:
msg = "An error occurred while updating " + \
"VisitAttribute %s. Reason: %s" % (self.id, e)
self.logger.error(msg)
return success
