def process(allPaths, lineFile, classFile, id):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": ["auto"],
"v_spans": [],
"classes": {}
}
util.add_files(obj, lineFile, classFile)
addInfo(obj, "pid", "Patient", id)
if len(allPaths) == 0:
print('warning: no path given', file=sys.stderr)
statusMap = {}
for (path, isfile) in allPaths:
if isfile:
processFile(path, id, obj, statusMap)
else:
util.process_id_directory(
path, id,
lambda file, id: processFile(file, id, obj, statusMap))
curInStart = None
curInEnd = None
curStatus = STATUS_UNKNOWN
for k in sorted(statusMap):
status = statusMap[k]
if status == curStatus:
if curInStart is None:
curInStart = k
curInEnd = k
else:
if curInStart is not None:
if curStatus == STATUS_IN:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "in_hospital"
})
elif curStatus == STATUS_PROF:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "professional"
})
curInStart = None
curStatus = status
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
addInfo(obj, "event_count", "Events", len(obj["events"]))
return obj
def process(allPaths, lineFile, classFile, id):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": [ "auto" ],
"v_spans": [],
"classes": {}
}
util.add_files(obj, lineFile, classFile)
addInfo(obj, "pid", "Patient", id)
if len(allPaths) == 0:
print('warning: no path given', file=sys.stderr)
statusMap = {}
for (path, isfile) in allPaths:
if isfile:
processFile(path, id, obj, statusMap)
else:
util.process_id_directory(path, id, lambda file, id: processFile(file, id, obj, statusMap))
curInStart = None
curInEnd = None
curStatus = STATUS_UNKNOWN
for k in sorted(statusMap):
status = statusMap[k]
if status == curStatus:
if curInStart is None:
curInStart = k
curInEnd = k
else:
if curInStart is not None:
if curStatus == STATUS_IN:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "in_hospital"
})
elif curStatus == STATUS_PROF:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "professional"
})
curInStart = None
curStatus = status
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
addInfo(obj, "event_count", "Events", len(obj["events"]))
return obj
def time():
if peek("<") or peek(">"):
c = cmp()
d = date()
return {
"<": Range(None, d),
"<=": Range(None, util.nextDay(d)),
">": Range(util.nextDay(d), None),
">=": Range(d, None)
}[c]
start = date()
if peek("-"):
char("-")
end = date()
return Range(start, util.nextDay(end))
return Range(start, util.nextDay(start))
def admissionDates(fromDate, toDate):
if fromDate == '':
if toDate == '':
return
fromDate = toDate
toDate = ''
curDate = util.toTime(fromDate)
endDate = util.toTime(toDate) if toDate != '' else curDate
while curDate <= endDate:
handleStatusEvent(curDate, STATUS_IN)
curDate = util.nextDay(curDate)
def admissionDates(fromDate, toDate):
if fromDate == '':
if toDate == '':
return
fromDate = toDate
toDate = ''
curDate = util.toTime(fromDate)
endDate = util.toTime(toDate) if toDate != '' else curDate
while curDate <= endDate:
handleStatusEvent(curDate, STATUS_IN)
curDate = util.nextDay(curDate)
def get_drugs(self, pid, obj, dict, new_dict_entries):
query = """SELECT
o.drug_exposure_id as id_row,
o.drug_exposure_start_date as date_start,
o.drug_exposure_end_date as date_end,
o.drug_concept_id as m_id,
o.drug_source_value as m_orig,
c.domain_id as m_domain,
c.concept_name as m_name,
c.vocabulary_id as m_vocab,
c.concept_code as m_num,
p.total_paid as m_cost
FROM
{schema}.drug_exposure o
LEFT JOIN {schema}.concept c ON (
c.concept_id = o.drug_concept_id
)
LEFT OUTER JOIN {schema}.drug_cost p ON (
p.drug_exposure_id = o.drug_exposure_id
)
WHERE
o.person_id = :pid
"""
for row in self._exec(query, pid=pid):
code = row['m_num']
unmapped = False
if code == 0:
code = row['m_orig']
unmapped = True
id_row = 'm' + str(row['id_row'])
d_id = row['m_id']
name = row['m_name']
vocab = row['m_vocab']
group = "Drug" if row['m_domain'] is None else row['m_domain']
desc = "{0} ({1} {2})".format(name, vocab, code)
self.add_dict(dict, new_dict_entries, group, vocab, d_id, name,
desc, code, unmapped)
date_start = self.to_time(row['date_start'])
date_end = self.to_time(
row['date_end']) if row['date_end'] else date_start
date_cur = date_start
cost = row['m_cost'] if 'm_cost' in row else None
while date_cur <= date_end:
event = self.create_event(group,
str(vocab) + str(d_id), id_row)
event['time'] = date_cur
if cost:
event['cost'] = float(cost)
cost = None
obj['events'].append(event)
date_cur = util.nextDay(date_cur)
def get_drugs(self, pid, obj, dict, new_dict_entries):
query = """SELECT
o.drug_exposure_id as id_row,
o.drug_exposure_start_date as date_start,
o.drug_exposure_end_date as date_end,
o.drug_concept_id as m_id,
o.drug_source_value as m_orig,
c.domain_id as m_domain,
c.concept_name as m_name,
c.vocabulary_id as m_vocab,
c.concept_code as m_num,
p.total_paid as m_cost
FROM
{schema}.drug_exposure o
LEFT JOIN {schema}.concept c ON (
c.concept_id = o.drug_concept_id
)
LEFT OUTER JOIN {schema}.drug_cost p ON (
p.drug_exposure_id = o.drug_exposure_id
)
WHERE
o.person_id = :pid
"""
for row in self._exec(query, pid=pid):
code = row['m_num']
unmapped = False
if code == 0:
code = row['m_orig']
unmapped = True
id_row = 'm' + str(row['id_row'])
d_id = row['m_id']
name = row['m_name']
vocab = row['m_vocab']
group = "Drug" if row['m_domain'] is None else row['m_domain']
desc = "{0} ({1} {2})".format(name, vocab, code)
self.add_dict(dict, new_dict_entries, group, vocab, d_id, name, desc, code, unmapped)
date_start = self.to_time(row['date_start'])
date_end = self.to_time(row['date_end']) if row['date_end'] else date_start
date_cur = date_start
cost = row['m_cost'] if 'm_cost' in row else None
while date_cur <= date_end:
event = self.create_event(group, str(vocab) + str(d_id), id_row)
event['time'] = date_cur
if cost:
event['cost'] = float(cost)
cost = None
obj['events'].append(event)
date_cur = util.nextDay(date_cur)
def get_diagnoses(self, pid, obj, dict, new_dict_entries):
query = """SELECT
o.condition_occurrence_id as id_row,
o.condition_start_date as date_start,
o.condition_end_date as date_end,
o.condition_concept_id as d_id,
o.condition_source_value as d_orig,
c.domain_id as d_domain,
c.concept_name as d_name,
c.vocabulary_id as d_vocab,
c.concept_code as d_num
FROM
{schema}.condition_occurrence o
LEFT JOIN {schema}.concept c ON (
c.concept_id = o.condition_concept_id
)
WHERE
o.person_id = :pid
"""
for row in self._exec(query, pid=pid):
code = row['d_num']
unmapped = False
if code == 0:
code = row['d_orig']
unmapped = True
id_row = 'c' + str(row['id_row'])
d_id = row['d_id']
name = row['d_name']
vocab = row['d_vocab']
group = "Condition" if row['d_domain'] is None else row['d_domain']
desc = "{0} ({1} {2})".format(name, vocab, code)
self.add_dict(dict, new_dict_entries, group, vocab, d_id, name,
desc, code, unmapped)
date_start = self.to_time(row['date_start'])
date_end = self.to_time(
row['date_end']) if row['date_end'] else date_start
date_cur = date_start
while date_cur <= date_end:
event = self.create_event(group,
str(vocab) + str(d_id), id_row)
event['time'] = date_cur
obj['events'].append(event)
date_cur = util.nextDay(date_cur)
def dates(fromDate, toDate):
if fromDate == '':
if toDate == '':
return
fromDate = toDate
toDate = ''
curDate = util.toTime(fromDate)
endDate = util.toTime(toDate) if toDate != '' else curDate
while curDate <= endDate:
for event in handleEvent(row, claim_id):
event['time'] = curDate
handleKey(row, "claim_amount", MODE_OPTIONAL,
lambda amount: addCost(event, amount))
obj['events'].append(event)
handleStatusEvent(curDate, curStatus)
handleKey(
row, "location_flag", MODE_OPTIONAL,
lambda flag: handleStatusEvent(
curDate, STATUS_FLAG_MAP.get(flag, STATUS_UNKNOWN)))
curDate = util.nextDay(curDate)
def dates(fromDate, toDate):
if fromDate == '':
if toDate == '':
return
fromDate = toDate
toDate = ''
curDate = util.toTime(fromDate)
endDate = util.toTime(toDate) if toDate != '' else curDate
while curDate <= endDate:
for event in handleEvent(row, claim_id):
event['time'] = curDate
handleKey(row, "claim_amount", MODE_OPTIONAL, lambda amount:
addCost(event, amount)
)
obj['events'].append(event)
handleStatusEvent(curDate, curStatus)
handleKey(row, "location_flag", MODE_OPTIONAL, lambda flag:
handleStatusEvent(curDate, STATUS_FLAG_MAP.get(flag, STATUS_UNKNOWN))
)
curDate = util.nextDay(curDate)
def get_diagnoses(self, pid, obj, dict, new_dict_entries):
query = """SELECT
o.condition_occurrence_id as id_row,
o.condition_start_date as date_start,
o.condition_end_date as date_end,
o.condition_concept_id as d_id,
o.condition_source_value as d_orig,
c.domain_id as d_domain,
c.concept_name as d_name,
c.vocabulary_id as d_vocab,
c.concept_code as d_num
FROM
{schema}.condition_occurrence o
LEFT JOIN {schema}.concept c ON (
c.concept_id = o.condition_concept_id
)
WHERE
o.person_id = :pid
"""
for row in self._exec(query, pid=pid):
code = row['d_num']
unmapped = False
if code == 0:
code = row['d_orig']
unmapped = True
id_row = 'c' + str(row['id_row'])
d_id = row['d_id']
name = row['d_name']
vocab = row['d_vocab']
group = "Condition" if row['d_domain'] is None else row['d_domain']
desc = "{0} ({1} {2})".format(name, vocab, code)
self.add_dict(dict, new_dict_entries, group, vocab, d_id, name, desc, code, unmapped)
date_start = self.to_time(row['date_start'])
date_end = self.to_time(row['date_end']) if row['date_end'] else date_start
date_cur = date_start
while date_cur <= date_end:
event = self.create_event(group, str(vocab) + str(d_id), id_row)
event['time'] = date_cur
obj['events'].append(event)
date_cur = util.nextDay(date_cur)