def _set_transport(self):
"""Plug in the appropriate transport mechanism"""
# Transport strategies differ for the different reports
if self.criteria.reportable_region:
self._transport = Distribute_client(zip_first=True)
else:
self._transport = PHINMS_client(zip_first=True)
def _set_transport(self):
"""Plug in the appropriate transport mechanism"""
# Transport strategies differ for the different reports
if self.criteria.reportable_region:
self._transport = Distribute_client(zip_first=True)
else:
self._transport = PHINMS_client(zip_first=True)
def testUnZippedUpload(self):
"Can we upload an unzipped copy"
tmpfile = tempfile.NamedTemporaryFile('w')
tmpfile.write(lorem_ipsum)
tmpfile.seek(0)
doc_id = document_store(tmpfile.name,
document_type='essence',
compress_with=None)
self.assertTrue(doc_id)
agent = PHINMS_client(zip_first=False)
self.assertFalse(agent.transfer_file(doc_id))
class GenerateReport(object):
""" Process options and generate the requested report. Optionally
persists the file to the filesystem, and uploads to the DOH sftp
server.
"""
__version__ = '0.2'
config = Config()
IGNORE_SITE = config.get('longitudinal', 'ignore_site', default='')
# Order matters, create a tuple of paired values (reportColumn,
# essenceColumn) - NB, the Diagnosis column is being bastardized.
# Previously there was an SQL function to do the subselect, but it
# ran way too slow. Now contains the foreign key to join w/ the
# diagnosis for the respective visit.
diagnosis_column_index = 7
patient_class_column_index = 11
columns = (
('Hosp', 'hospital'),
('Reg Date', 'visit_date'),
('Time', 'visit_time'),
('Sex', 'gender'),
('Age', 'age'),
('Reason For Visit', 'chief_complaint'),
('Zip Code', 'zip'),
('Diagnosis', 'visit_pk'),
('Admit Status', 'gipse_disposition'),
('Medical Record No.', 'patient_id'),
('Visit Record No.', 'visit_id'),
('Service Area', 'patient_class'),
)
assert (columns[diagnosis_column_index][1] == 'visit_pk')
assert (columns[patient_class_column_index][1] == 'patient_class')
def __init__(self,
user=None,
password=None,
report_criteria=None,
datefile=None):
"""Initialize report generation.
:param user: database user
:param password: database password
:param report_criteria: ReportCriteria defining specifics
:param datefile: useful for persistent walks through time
"""
self.user = user
self.password = password
self.criteria = report_criteria
self.database = self.criteria.database
if datefile:
assert ((self.criteria.start_date,
self.criteria.end_date) == datefile.get_date_range())
self.datePersistence = datefile
self._diags = {}
self._prepare_output_file()
self._prepare_columns()
self._set_transport()
def _prepare_columns(self):
# Don't include the patient_class column if splitting out by
# patient_class
if self.criteria.patient_class:
len_b4 = len(self.columns)
self.columns =\
self.columns[:self.patient_class_column_index] \
+ self.columns[self.patient_class_column_index + 1:]
assert (len(self.columns) + 1 == len_b4)
def _set_transport(self):
"""Plug in the appropriate transport mechanism"""
# Transport strategies differ for the different reports
if self.criteria.reportable_region:
self._transport = Distribute_client(zip_first=True)
else:
self._transport = PHINMS_client(zip_first=True)
def _generate_output_filename(self, start_date=None, end_date=None):
start_date = self.criteria.start_date if start_date is None\
else start_date
end_date = self.criteria.end_date if end_date is None else end_date
datestr = end_date.strftime('%Y%m%d')
if start_date != end_date:
datestr = '-'.join(
(start_date.strftime('%Y%m%d'), end_date.strftime('%Y%m%d')))
filename = self.criteria.report_method + '-' + datestr + '.txt'
config = Config()
tmp_dir = config.get('general', 'tmp_dir', default='/tmp')
filepath = os.path.join(tmp_dir, filename)
return filepath
def _prepare_output_file(self):
"""Open the local filesystem file for output"""
filepath = self.\
_generate_output_filename(start_date=self.criteria.start_date,
end_date=self.criteria.end_date)
# watch for oversight errors; notify if like report exists -
# unless it's size zero (from a previous failed run)
if os.path.exists(filepath) and os.path.getsize(filepath):
logging.warning("Found requested report file already "\
"exists - overwriting: '%s'"\
% filepath)
self.output = open(filepath, 'w')
self._output_filename = self.output.name
@property
def output_filename(self):
if not hasattr(self, '_output_filename'):
raise RuntimeError("prerequisite call to "\
"_prepare_output_file() "\
"didn't happen!")
return self._output_filename
def _header(self):
if self.criteria.include_vitals:
columns = [c[0] for c in self.columns]
columns += ('Measured Temperature', 'O2 Saturation',
'Self-Reported Influenza Vaccine',
'Self-Reported H1N1 Vaccine')
return '|'.join(columns)
else:
return '|'.join([c[0] for c in self.columns])
def _build_join_tables(self):
""" Scope continues to grow, build all join tables necessary
for the query. Some are only necessary with certain features
on.
"""
# Always need the list of reportable visits
self._build_visit_join_table()
if self.criteria.include_vitals:
self._build_vitals_join_table()
def _build_visit_join_table(self):
""" Helper in selection of visits for the report - this method
builds a temporary table and populates it with the visit_pks
that belong in the report. This should include all visit_pks
with the matching admit_datetime as well as any that have
received updates since the last like report was produced.
"""
# If include_vitals is on, we also need the visit_id to keep
# the joins managable. vitals don't have a patient class, so
# you can't join on the same values.
sql = "CREATE TEMPORARY TABLE reportable_pks (pk "\
"integer not null unique)"
selectCols = "fact_visit.pk"
self._getConn()
self.access.raw_query(sql)
# If we're only selecting those facilites in a region, the SQL
# is more complicated - build up the respective clauses.
joinClause = regionClause = ""
if self.criteria.reportable_region:
joinClause = "JOIN internal_reportable_region ON "\
"internal_reportable_region.dim_facility_pk = "\
"fact_visit.dim_facility_pk"
regionClause = "AND region_name = '%s'" %\
self.criteria.reportable_region
# Another HACK! One site is not even wanted by the state DOH,
# as it's being duplicated from another source, and ESSENCE
# can't help but count them twice. Remove this one site
# regardless
else:
joinClause = "JOIN internal_reportable_region ON "\
"internal_reportable_region.dim_facility_pk = "\
"fact_visit.dim_facility_pk"
regionClause = "AND region_name = '%s'" % self.IGNORE_SITE
# Limit by patient_class if requested. Note we may still end
# up with visit ids that have changed patient classes, so more
# pruning later is necessary.
pc_limit = ""
if self.criteria.patient_class:
pc_limit = "AND patient_class = '%c'" %\
self.criteria.patient_class
# Start with all visits for the requested date range
sql = "INSERT INTO reportable_pks SELECT %s FROM "\
"fact_visit %s WHERE admit_datetime BETWEEN '%s' AND "\
"'%s' %s %s" %\
(selectCols, joinClause, self.criteria.start_date,
self.criteria.end_date + timedelta(days=1),
pc_limit, regionClause)
self.access.raw_query(sql)
if self.criteria.include_updates:
# In this case, add all visits with updates since the
# last run, but no newer than the requested date (in case
# we're building reports forward from historical data)
sql = "SELECT max(processed_datetime) FROM internal_report "\
"WHERE report_method = '%s'" % self.criteria.report_method
cursor = self.access.raw_query(sql)
last_report_generated = cursor.fetchall()[0][0]
if last_report_generated is None:
last_report_generated = '2009-01-01' # our epoch
logging.debug("including updates, last_report_generated: "\
"%s", last_report_generated)
sql = "INSERT INTO reportable_pks SELECT %(sel_cols)s FROM "\
"fact_visit %(join_clause)s LEFT JOIN reportable_pks ON "\
"reportable_pks.pk = fact_visit.pk WHERE "\
"last_updated > '%(last_report)s' AND admit_datetime "\
"< '%(date)s' AND reportable_pks.pk IS NULL "\
"%(pc_limit)s %(region_clause)s" %\
{'sel_cols': selectCols,
'last_report': last_report_generated,
'date': self.criteria.end_date + timedelta(days=1),
'pc_limit': pc_limit,
'join_clause': joinClause,
'region_clause': regionClause}
self.access.raw_query(sql)
cursor = self.access.raw_query("SELECT COUNT(*) FROM "\
"reportable_pks")
logging.debug("%d visits to report on", cursor.fetchall()[0][0])
def _build_vitals_join_table(self):
"""When report is to include vitals - we use an additional
temporary table (visit_loinc_data) to hold the data for more
timely queries.
Like the rest of the report, the list of interesting visits is
limited to the rows in the reportable_pks - see
_build_join_table() for details.
"""
raise ValueError('not ported yet')
sql = """
CREATE TEMPORARY TABLE visit_loinc_data (
visit_id VARCHAR(255) not null,
patient_class CHAR(1) default null,
observation_id VARCHAR(255) not null,
observation_result VARCHAR(255) not null)
"""
self._getConn()
self.access.raw_query(sql)
sql = """
INSERT INTO visit_loinc_data (visit_id, patient_class,
observation_id, observation_result) SELECT visit.visit_id,
visit.patient_class, observation_id,
observation_result FROM visit JOIN hl7_visit ON
visit.visit_id = hl7_visit.visit_id JOIN hl7_obx ON
hl7_visit.hl7_msh_id = hl7_obx.hl7_msh_id JOIN
reportable_pks ON reportable_pks.visit_id = visit.visit_id
AND reportable_pks.patient_class = visit.patient_class
WHERE
observation_id in ('8310-5', '20564-1', '46077-4',
'29544-4')
"""
self.access.raw_query(sql)
def _select_from_essence_view(self):
"""Build up the SQL select statement to be used in gathering
the data for this report.
"""
stmt = """SELECT %s FROM essence e JOIN reportable_pks ri
ON e.visit_pk = ri.pk""" %\
(','.join(['e.' + c[1] for c in self.columns]))
return stmt
def _select_diagnosis(self):
""" Need to pull in all the diagnosis data for this report.
This is saved in an instance dictionary for use in
self._diagnosis to generate the list of diagnoses for each
respective visit.
A list of unique diagnoses ordered by rank is required.
"""
# We order descending on dx_datetime as the most recent should
# be best. Add any others as the persistence mechanism only
# saves a unique icd9 dx that has changed status.
stmt = "SELECT fact_visit_pk, rank, icd9 "\
"FROM assoc_visit_dx JOIN "\
"dim_dx ON dim_dx_pk = dim_dx.pk JOIN "\
"reportable_pks ON "\
"assoc_visit_dx.fact_visit_pk = reportable_pks.pk "\
"ORDER BY dx_datetime DESC"
cursor = self.access.raw_query(stmt)
for row in cursor.fetchall():
visit_pk = row[0]
if visit_pk in self._diags:
self._diags[visit_pk].add(row[0], row[1], row[2])
else:
self._diags[visit_pk] = \
SortedDiagnosis(row[0], row[1], row[2])
def _diagnosis(self, visit_pk):
if visit_pk in self._diags:
return [
self._diags[visit_pk].__repr__(),
]
else:
return [
'',
]
def _select_vitals(self):
""" Need to pull in all the vitals data for this report.
This is saved in an instance dictionary for use in
self._vitals_for_visit to generate the list of vitals for each
respective visit.
This is an effective NOP when self.criteria.include_vitals = False
"""
if not self.criteria.include_vitals:
return None
self._vitals = {}
stmt = """SELECT reportable_pks.visit_pk,
observation_id, observation_result
FROM visit_loinc_data JOIN reportable_pks ON
reportable_pks.visit_id = visit_loinc_data.visit_id"""
cursor = self.access.raw_query(stmt)
for row in cursor.fetchall():
visit_pk = row[0]
if visit_pk in self._vitals:
self._vitals[visit_pk].add(row[1], row[2])
else:
self._vitals[visit_pk] = \
Vitals(row[1], row[2])
def _vitals_for_visit(self, visit_pk):
"""Returns the list of vitals for the visit in question.
This is an effective NOP when self.criteria.include_vitals = False
"""
if not self.criteria.include_vitals:
return []
if visit_pk in self._vitals:
return self._vitals[visit_pk].__repr__()
else:
return Vitals().__repr__()
def _write_report(self, save_report=False):
""" Write out and potentially store the results.
Generate results via database queries and write the results to
self.output.
:param save_report: If set, persist the document and related
metadata to the mbds archive.
returns the document ID, the mbds archive key, if saved
"""
out = self.output
print >> out, self._header()
self._build_join_tables()
self._select_diagnosis()
self._select_vitals()
cursor = self.access.raw_query(self._select_from_essence_view())
for row in cursor.fetchall():
# Each row is the colums up to the diagnosis + the
# comma separated diagnosis + the rest of the columns
# and finally with vitals if configured for such
visit_pk = row[self.diagnosis_column_index] # yuck, but true
print >> out,\
'|'.join([strSansNone(column) for column in
row[:self.diagnosis_column_index]] +
self._diagnosis(visit_pk) +
[strSansNone(column) for column in
row[self.diagnosis_column_index + 1:]] +
self._vitals_for_visit(visit_pk))
# Close the file and persist to the document archive if
# requested
self.output.close()
if save_report:
metadata = {
k: v
for k, v in self.criteria._crit.items() if v is not None
}
# At this point, all documents are of 'essence' type
return document_store(document=self.output.name,
allow_duplicate_filename=True,
document_type='essence',
**metadata)
def _record_report(self, report_oid):
"""Record the details from this report generation in the db"""
if not report_oid:
return
report = Report(processed_datetime=datetime.now(),
file_path=report_oid,
report_method=self.criteria.report_method)
alchemy = AlchemyAccess(database=self.database)
alchemy.session.add(report)
alchemy.session.commit()
alchemy.disconnect()
def _transmit_report(self, report):
"""Transmit report using self._transport()"""
logging.info("initiate upload of %s", report)
self._transport.transfer_file(report)
def _transmit_differences(self, report):
"""Compute differences from yesterday's like report; transport"""
# This option really only makes sense on date range reports,
# as updates hit older data than just 'yesterday'.
if self.criteria.start_date == self.criteria.end_date:
raise ValueError("difference calculation not supported on "\
"single day reports")
# See if we can find a similar report in the archive from
# yesterday
search_criteria = {
'report_method': self.criteria.report_method,
'start_date': self.criteria.start_date - timedelta(days=1),
'end_date': self.criteria.end_date - timedelta(days=1)
}
old_doc = document_find(search_criteria, limit=1)
if old_doc is None:
logging.info("No comparable report found for difference "\
"generation")
self._transmit_report(report)
else:
target_filename = self.\
_generate_output_filename(start_date=self.criteria.start_date,
end_date=self.criteria.end_date)
# RemoveDuplicates not yet ported!!
raise ValueError("RemoveDuplicates not ported")
#from pheme.essence.remove_duplicates import RemoveDuplicates
#rd = RemoveDuplicates(new_report=report,
# old_report=old_doc,
# out=target_filename)
#rd.generate_report()
#logging.info("initiate upload of difference %s", target_filename)
#self._transport.transfer_file(target_filename)
def _getConn(self):
""" Local wrapper to get database connection
"""
if hasattr(self, 'access'):
return
self.access = DirectAccess(database=self.database,
user=self.user,
password=self.password)
def _closeConn(self):
""" Local wrapper to close database connection
"""
if hasattr(self, 'access'):
self.access.close()
def tearDown(self):
"Public interface to clean up internals"
self._closeConn()
def execute(self,
save_report=False,
transmit_report=False,
transmit_differences=False):
"""Execute the report generation
"""
logging.info("Initiate ESSENCE report generation [%s-%s] for %s",
self.criteria.start_date, self.criteria.end_date,
self.criteria.report_method)
self._getConn()
report_oid = self._write_report(save_report)
self._record_report(report_oid)
if transmit_report:
self._transmit_report(report_oid)
if transmit_differences:
self._transmit_differences(report_oid)
self._closeConn()
if hasattr(self, 'datePersistence'):
self.datePersistence.bump_date()
logging.info("Completed ESSENCE report generation [%s-%s] for %s",
self.criteria.start_date, self.criteria.end_date,
self.criteria.report_method)
class GenerateReport(object):
""" Process options and generate the requested report. Optionally
persists the file to the filesystem, and uploads to the DOH sftp
server.
"""
__version__ = '0.2'
config = Config()
IGNORE_SITE = config.get('longitudinal', 'ignore_site', default='')
# Order matters, create a tuple of paired values (reportColumn,
# essenceColumn) - NB, the Diagnosis column is being bastardized.
# Previously there was an SQL function to do the subselect, but it
# ran way too slow. Now contains the foreign key to join w/ the
# diagnosis for the respective visit.
diagnosis_column_index = 7
patient_class_column_index = 11
columns = (('Hosp', 'hospital'),
('Reg Date', 'visit_date'),
('Time', 'visit_time'),
('Sex', 'gender'),
('Age', 'age'),
('Reason For Visit', 'chief_complaint'),
('Zip Code', 'zip'),
('Diagnosis', 'visit_pk'),
('Admit Status', 'gipse_disposition'),
('Medical Record No.', 'patient_id'),
('Visit Record No.', 'visit_id'),
('Service Area', 'patient_class'),)
assert(columns[diagnosis_column_index][1] == 'visit_pk')
assert(columns[patient_class_column_index][1] == 'patient_class')
def __init__(self, user=None, password=None, report_criteria=None,
datefile=None):
"""Initialize report generation.
:param user: database user
:param password: database password
:param report_criteria: ReportCriteria defining specifics
:param datefile: useful for persistent walks through time
"""
self.user = user
self.password = password
self.criteria = report_criteria
self.database = self.criteria.database
if datefile:
assert((self.criteria.start_date, self.criteria.end_date)
== datefile.get_date_range())
self.datePersistence = datefile
self._diags = {}
self._prepare_output_file()
self._prepare_columns()
self._set_transport()
def _prepare_columns(self):
# Don't include the patient_class column if splitting out by
# patient_class
if self.criteria.patient_class:
len_b4 = len(self.columns)
self.columns =\
self.columns[:self.patient_class_column_index] \
+ self.columns[self.patient_class_column_index + 1:]
assert(len(self.columns) + 1 == len_b4)
def _set_transport(self):
"""Plug in the appropriate transport mechanism"""
# Transport strategies differ for the different reports
if self.criteria.reportable_region:
self._transport = Distribute_client(zip_first=True)
else:
self._transport = PHINMS_client(zip_first=True)
def _generate_output_filename(self, start_date=None,
end_date=None):
start_date = self.criteria.start_date if start_date is None\
else start_date
end_date = self.criteria.end_date if end_date is None else end_date
datestr = end_date.strftime('%Y%m%d')
if start_date != end_date:
datestr = '-'.join((start_date.strftime('%Y%m%d'),
end_date.strftime('%Y%m%d')))
filename = self.criteria.report_method + '-' + datestr + '.txt'
config = Config()
tmp_dir = config.get('general', 'tmp_dir', default='/tmp')
filepath = os.path.join(tmp_dir, filename)
return filepath
def _prepare_output_file(self):
"""Open the local filesystem file for output"""
filepath = self.\
_generate_output_filename(start_date=self.criteria.start_date,
end_date=self.criteria.end_date)
# watch for oversight errors; notify if like report exists -
# unless it's size zero (from a previous failed run)
if os.path.exists(filepath) and os.path.getsize(filepath):
logging.warning("Found requested report file already "\
"exists - overwriting: '%s'"\
% filepath)
self.output = open(filepath, 'w')
self._output_filename = self.output.name
@property
def output_filename(self):
if not hasattr(self, '_output_filename'):
raise RuntimeError("prerequisite call to "\
"_prepare_output_file() "\
"didn't happen!")
return self._output_filename
def _header(self):
if self.criteria.include_vitals:
columns = [c[0] for c in self.columns]
columns += ('Measured Temperature', 'O2 Saturation',
'Self-Reported Influenza Vaccine',
'Self-Reported H1N1 Vaccine')
return '|'.join(columns)
else:
return '|'.join([c[0] for c in self.columns])
def _build_join_tables(self):
""" Scope continues to grow, build all join tables necessary
for the query. Some are only necessary with certain features
on.
"""
# Always need the list of reportable visits
self._build_visit_join_table()
if self.criteria.include_vitals:
self._build_vitals_join_table()
def _build_visit_join_table(self):
""" Helper in selection of visits for the report - this method
builds a temporary table and populates it with the visit_pks
that belong in the report. This should include all visit_pks
with the matching admit_datetime as well as any that have
received updates since the last like report was produced.
"""
# If include_vitals is on, we also need the visit_id to keep
# the joins managable. vitals don't have a patient class, so
# you can't join on the same values.
sql = "CREATE TEMPORARY TABLE reportable_pks (pk "\
"integer not null unique)"
selectCols = "fact_visit.pk"
self._getConn()
self.access.raw_query(sql)
# If we're only selecting those facilites in a region, the SQL
# is more complicated - build up the respective clauses.
joinClause = regionClause = ""
if self.criteria.reportable_region:
joinClause = "JOIN internal_reportable_region ON "\
"internal_reportable_region.dim_facility_pk = "\
"fact_visit.dim_facility_pk"
regionClause = "AND region_name = '%s'" %\
self.criteria.reportable_region
# Another HACK! One site is not even wanted by the state DOH,
# as it's being duplicated from another source, and ESSENCE
# can't help but count them twice. Remove this one site
# regardless
else:
joinClause = "JOIN internal_reportable_region ON "\
"internal_reportable_region.dim_facility_pk = "\
"fact_visit.dim_facility_pk"
regionClause = "AND region_name = '%s'" % self.IGNORE_SITE
# Limit by patient_class if requested. Note we may still end
# up with visit ids that have changed patient classes, so more
# pruning later is necessary.
pc_limit = ""
if self.criteria.patient_class:
pc_limit = "AND patient_class = '%c'" %\
self.criteria.patient_class
# Start with all visits for the requested date range
sql = "INSERT INTO reportable_pks SELECT %s FROM "\
"fact_visit %s WHERE admit_datetime BETWEEN '%s' AND "\
"'%s' %s %s" %\
(selectCols, joinClause, self.criteria.start_date,
self.criteria.end_date + timedelta(days=1),
pc_limit, regionClause)
self.access.raw_query(sql)
if self.criteria.include_updates:
# In this case, add all visits with updates since the
# last run, but no newer than the requested date (in case
# we're building reports forward from historical data)
sql = "SELECT max(processed_datetime) FROM internal_report "\
"WHERE report_method = '%s'" % self.criteria.report_method
cursor = self.access.raw_query(sql)
last_report_generated = cursor.fetchall()[0][0]
if last_report_generated is None:
last_report_generated = '2009-01-01' # our epoch
logging.debug("including updates, last_report_generated: "\
"%s", last_report_generated)
sql = "INSERT INTO reportable_pks SELECT %(sel_cols)s FROM "\
"fact_visit %(join_clause)s LEFT JOIN reportable_pks ON "\
"reportable_pks.pk = fact_visit.pk WHERE "\
"last_updated > '%(last_report)s' AND admit_datetime "\
"< '%(date)s' AND reportable_pks.pk IS NULL "\
"%(pc_limit)s %(region_clause)s" %\
{'sel_cols': selectCols,
'last_report': last_report_generated,
'date': self.criteria.end_date + timedelta(days=1),
'pc_limit': pc_limit,
'join_clause': joinClause,
'region_clause': regionClause}
self.access.raw_query(sql)
cursor = self.access.raw_query("SELECT COUNT(*) FROM "\
"reportable_pks")
logging.debug("%d visits to report on", cursor.fetchall()[0][0])
def _build_vitals_join_table(self):
"""When report is to include vitals - we use an additional
temporary table (visit_loinc_data) to hold the data for more
timely queries.
Like the rest of the report, the list of interesting visits is
limited to the rows in the reportable_pks - see
_build_join_table() for details.
"""
raise ValueError('not ported yet')
sql = """
CREATE TEMPORARY TABLE visit_loinc_data (
visit_id VARCHAR(255) not null,
patient_class CHAR(1) default null,
observation_id VARCHAR(255) not null,
observation_result VARCHAR(255) not null)
"""
self._getConn()
self.access.raw_query(sql)
sql = """
INSERT INTO visit_loinc_data (visit_id, patient_class,
observation_id, observation_result) SELECT visit.visit_id,
visit.patient_class, observation_id,
observation_result FROM visit JOIN hl7_visit ON
visit.visit_id = hl7_visit.visit_id JOIN hl7_obx ON
hl7_visit.hl7_msh_id = hl7_obx.hl7_msh_id JOIN
reportable_pks ON reportable_pks.visit_id = visit.visit_id
AND reportable_pks.patient_class = visit.patient_class
WHERE
observation_id in ('8310-5', '20564-1', '46077-4',
'29544-4')
"""
self.access.raw_query(sql)
def _select_from_essence_view(self):
"""Build up the SQL select statement to be used in gathering
the data for this report.
"""
stmt = """SELECT %s FROM essence e JOIN reportable_pks ri
ON e.visit_pk = ri.pk""" %\
(','.join(['e.' + c[1] for c in self.columns]))
return stmt
def _select_diagnosis(self):
""" Need to pull in all the diagnosis data for this report.
This is saved in an instance dictionary for use in
self._diagnosis to generate the list of diagnoses for each
respective visit.
A list of unique diagnoses ordered by rank is required.
"""
# We order descending on dx_datetime as the most recent should
# be best. Add any others as the persistence mechanism only
# saves a unique icd9 dx that has changed status.
stmt = "SELECT fact_visit_pk, rank, icd9 "\
"FROM assoc_visit_dx JOIN "\
"dim_dx ON dim_dx_pk = dim_dx.pk JOIN "\
"reportable_pks ON "\
"assoc_visit_dx.fact_visit_pk = reportable_pks.pk "\
"ORDER BY dx_datetime DESC"
cursor = self.access.raw_query(stmt)
for row in cursor.fetchall():
visit_pk = row[0]
if visit_pk in self._diags:
self._diags[visit_pk].add(row[0], row[1], row[2])
else:
self._diags[visit_pk] = \
SortedDiagnosis(row[0], row[1], row[2])
def _diagnosis(self, visit_pk):
if visit_pk in self._diags:
return [self._diags[visit_pk].__repr__(), ]
else:
return ['', ]
def _select_vitals(self):
""" Need to pull in all the vitals data for this report.
This is saved in an instance dictionary for use in
self._vitals_for_visit to generate the list of vitals for each
respective visit.
This is an effective NOP when self.criteria.include_vitals = False
"""
if not self.criteria.include_vitals:
return None
self._vitals = {}
stmt = """SELECT reportable_pks.visit_pk,
observation_id, observation_result
FROM visit_loinc_data JOIN reportable_pks ON
reportable_pks.visit_id = visit_loinc_data.visit_id"""
cursor = self.access.raw_query(stmt)
for row in cursor.fetchall():
visit_pk = row[0]
if visit_pk in self._vitals:
self._vitals[visit_pk].add(row[1], row[2])
else:
self._vitals[visit_pk] = \
Vitals(row[1], row[2])
def _vitals_for_visit(self, visit_pk):
"""Returns the list of vitals for the visit in question.
This is an effective NOP when self.criteria.include_vitals = False
"""
if not self.criteria.include_vitals:
return []
if visit_pk in self._vitals:
return self._vitals[visit_pk].__repr__()
else:
return Vitals().__repr__()
def _write_report(self, save_report=False):
""" Write out and potentially store the results.
Generate results via database queries and write the results to
self.output.
:param save_report: If set, persist the document and related
metadata to the mbds archive.
returns the document ID, the mbds archive key, if saved
"""
out = self.output
print >> out, self._header()
self._build_join_tables()
self._select_diagnosis()
self._select_vitals()
cursor = self.access.raw_query(self._select_from_essence_view())
for row in cursor.fetchall():
# Each row is the colums up to the diagnosis + the
# comma separated diagnosis + the rest of the columns
# and finally with vitals if configured for such
visit_pk = row[self.diagnosis_column_index] # yuck, but true
print >> out,\
'|'.join([strSansNone(column) for column in
row[:self.diagnosis_column_index]] +
self._diagnosis(visit_pk) +
[strSansNone(column) for column in
row[self.diagnosis_column_index + 1:]] +
self._vitals_for_visit(visit_pk))
# Close the file and persist to the document archive if
# requested
self.output.close()
if save_report:
metadata = {k: v for k, v in self.criteria._crit.items() if v
is not None}
# At this point, all documents are of 'essence' type
return document_store(document=self.output.name,
allow_duplicate_filename=True,
document_type='essence', **metadata)
def _record_report(self, report_oid):
"""Record the details from this report generation in the db"""
if not report_oid:
return
report = Report(processed_datetime=datetime.now(),
file_path=report_oid,
report_method=self.criteria.report_method)
alchemy = AlchemyAccess(database=self.database)
alchemy.session.add(report)
alchemy.session.commit()
alchemy.disconnect()
def _transmit_report(self, report):
"""Transmit report using self._transport()"""
logging.info("initiate upload of %s", report)
self._transport.transfer_file(report)
def _transmit_differences(self, report):
"""Compute differences from yesterday's like report; transport"""
# This option really only makes sense on date range reports,
# as updates hit older data than just 'yesterday'.
if self.criteria.start_date == self.criteria.end_date:
raise ValueError("difference calculation not supported on "\
"single day reports")
# See if we can find a similar report in the archive from
# yesterday
search_criteria = {'report_method':
self.criteria.report_method,
'start_date': self.criteria.start_date -
timedelta(days=1), 'end_date':
self.criteria.end_date - timedelta(days=1)}
old_doc = document_find(search_criteria, limit=1)
if old_doc is None:
logging.info("No comparable report found for difference "\
"generation")
self._transmit_report(report)
else:
target_filename = self.\
_generate_output_filename(start_date=self.criteria.start_date,
end_date=self.criteria.end_date)
# RemoveDuplicates not yet ported!!
raise ValueError("RemoveDuplicates not ported")
#from pheme.essence.remove_duplicates import RemoveDuplicates
#rd = RemoveDuplicates(new_report=report,
# old_report=old_doc,
# out=target_filename)
#rd.generate_report()
#logging.info("initiate upload of difference %s", target_filename)
#self._transport.transfer_file(target_filename)
def _getConn(self):
""" Local wrapper to get database connection
"""
if hasattr(self, 'access'):
return
self.access = DirectAccess(database=self.database,
user=self.user,
password=self.password)
def _closeConn(self):
""" Local wrapper to close database connection
"""
if hasattr(self, 'access'):
self.access.close()
def tearDown(self):
"Public interface to clean up internals"
self._closeConn()
def execute(self, save_report=False, transmit_report=False,
transmit_differences=False):
"""Execute the report generation
"""
logging.info("Initiate ESSENCE report generation [%s-%s] for %s",
self.criteria.start_date,
self.criteria.end_date,
self.criteria.report_method)
self._getConn()
report_oid = self._write_report(save_report)
self._record_report(report_oid)
if transmit_report:
self._transmit_report(report_oid)
if transmit_differences:
self._transmit_differences(report_oid)
self._closeConn()
if hasattr(self, 'datePersistence'):
self.datePersistence.bump_date()
logging.info("Completed ESSENCE report generation [%s-%s] for %s",
self.criteria.start_date,
self.criteria.end_date,
self.criteria.report_method)