def get_ohdsi_cohort(ent: str, attr: str, phenotype: PhenotypeModel):
if len(phenotype['cohorts']) > 0:
for c in phenotype['cohorts']:
if c['name'] == ent and c['library'] == 'OHDSI' and c['funct'] == 'getCohort' and len(c['arguments']) > 0:
cohort = getCohort(c['arguments'][0])['Patients']
df = pd.DataFrame.from_records(cohort)
df['cohortStartDate'] = df['cohortStartDate'].apply(long_to_datetime)
df['cohortEndDate'] = df['cohortEndDate'].apply(long_to_datetime)
df['subject'] = df['subjectId'].astype(int)
return df
return pd.DataFrame({'nothing': []})
def get_ohdsi_cohort(ent: str, attr: str, phenotype: PhenotypeModel):
if len(phenotype['cohorts']) > 0:
for c in phenotype['cohorts']:
if c['name'] == ent and c['library'] == 'OHDSI' and c['funct'] == 'getCohort' and len(c['arguments']) > 0:
cohort = getCohort(c['arguments'][0])['Patients']
df = pd.DataFrame.from_records(cohort)
df['cohortStartDate'] = df['cohortStartDate'].apply(long_to_datetime)
df['cohortEndDate'] = df['cohortEndDate'].apply(long_to_datetime)
df['subject'] = df['subjectId'].astype(int)
return df
return pd.DataFrame({'nothing': []})
def make_fq(types, tags, fq, mapper_url, mapper_inst, mapper_key,
report_type_query, cohort_ids):
new_fq = fq
mapped_items = get_report_type_mappings(mapper_url, mapper_inst,
mapper_key)
if types and len(types) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_type_fq = 'report_type: ("' + '" OR "'.join(types) + '")'
new_fq += report_type_fq
if len(report_type_query) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_types = 'report_type: (' + report_type_query + ')'
new_fq += report_types
if len(cohort_ids) > 0:
subjects = list()
for c in cohort_ids:
patients = getCohort(c)['Patients']
subjects.extend([str(x['subjectId']) for x in patients])
del patients
if len(subjects) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
subject_fq = 'subject: (' + ' OR '.join(subjects) + ')'
new_fq += subject_fq
if len(tags) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
matched_reports = list()
for tag in tags:
try:
lookup_tag = normalize_tag(tag)
matched_reports.extend(mapped_items[lookup_tag])
except Exception as e:
traceback.print_exc(file=sys.stderr)
print("Unable to map tag %s" % tag)
if len(matched_reports) > 0:
match_report_clause = '" OR "'.join(matched_reports)
report_types = 'report_type: ("' + match_report_clause + '")'
new_fq += report_types
return new_fq
def make_fq(types, tags, fq, mapper_url, mapper_inst, mapper_key,
report_type_query, cohort_ids, job_results_filter, sources):
new_fq = fq
subjects = list()
documents = list()
if types and len(types) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_type_fq = util.solr_report_type_field + ': ("' + '" OR "'.join(
types) + '")'
new_fq += report_type_fq
if len(report_type_query) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_types = util.solr_report_type_field + ': (' + report_type_query + ')'
new_fq += report_types
if job_results_filter:
for k in job_results_filter.keys():
job_filter = job_results_filter[k]
context = job_filter.pop('context', None)
results = phenotype_results_by_context(context, job_filter)
if context.lower() == 'patient' or context.lower() == 'subject':
subjects.extend(set([str(x['subject']) for x in results]))
else:
documents.extend(set([str(x['report_id']) for x in results]))
del results
if len(cohort_ids) > 0:
for c in cohort_ids:
patients = getCohort(c)['Patients']
subjects.extend([str(x['subjectId']) for x in patients])
del patients
if len(tags) > 0:
mapped_items = get_report_type_mappings(mapper_url, mapper_inst,
mapper_key)
if len(new_fq) > 0:
new_fq += ' AND '
matched_reports = list()
for tag in tags:
try:
lookup_tag = normalize_tag(tag)
if lookup_tag in mapped_items:
matched_reports.extend(mapped_items[lookup_tag])
except Exception as e:
if util.debug_mode:
traceback.print_exc(file=sys.stderr)
print("Unable to map tag %s" % tag)
if len(matched_reports) > 0:
match_report_clause = '" OR "'.join(matched_reports)
report_types = util.solr_report_type_field + ': ("' + match_report_clause + '")'
new_fq += report_types
if len(subjects) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
subject_fq = util.solr_subject_field + ': (' + ' OR '.join(
subjects) + ')'
new_fq += subject_fq
if len(documents) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
doc_fq = util.solr_report_id_field + ': (' + ' OR '.join(
subjects) + ')'
new_fq += doc_fq
if sources and len(sources) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
sources_fq = util.solr_source_field + ': ("' + '" OR "'.join(
sources) + '")'
new_fq += sources_fq
return new_fq
def make_fq(types, tags, fq, mapper_url, mapper_inst, mapper_key, report_type_query, cohort_ids, job_results_filter,
sources):
new_fq = fq
subjects = list()
documents = list()
if sources and len(sources) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
sources_fq = util.solr_source_field + ': ("' + '" OR "'.join(sources) + '")'
new_fq += sources_fq
if types and len(types) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_type_fq = util.solr_report_type_field + ': ("' + '" OR "'.join(types) + '")'
new_fq += report_type_fq
if len(report_type_query) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
report_types = util.solr_report_type_field + ': (' + report_type_query + ')'
new_fq += report_types
if job_results_filter:
for k in job_results_filter.keys():
job_filter = job_results_filter[k]
context = job_filter.pop('context', None)
results = phenotype_results_by_context(context, job_filter)
if context.lower() == 'patient' or context.lower() == 'subject':
subjects.extend(set([str(x['subject']) for x in results]))
else:
documents.extend(set([str(x['report_id']) for x in results]))
del results
if len(cohort_ids) > 0:
for c in cohort_ids:
patients = getCohort(c)['Patients']
subjects.extend([str(x['subjectId']) for x in patients])
del patients
if len(tags) > 0:
mapped_items = get_report_type_mappings(mapper_url, mapper_inst, mapper_key)
if len(new_fq) > 0:
new_fq += ' AND '
matched_reports = list()
for tag in tags:
try:
lookup_tag = normalize_tag(tag)
if lookup_tag in mapped_items:
matched_reports.extend(mapped_items[lookup_tag])
except Exception as e:
if util.debug_mode:
traceback.print_exc(file=sys.stderr)
print("Unable to map tag %s" % tag)
if len(matched_reports) > 0:
match_report_clause = '" OR "'.join(matched_reports)
report_types = util.solr_report_type_field + ': ("' + match_report_clause + '")'
new_fq += report_types
if len(subjects) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
subject_fq = util.solr_subject_field + ': (' + ' OR '.join(subjects) + ')'
new_fq += subject_fq
if len(documents) > 0:
if len(new_fq) > 0:
new_fq += ' AND '
doc_fq = util.solr_report_id_field + ': (' + ' OR '.join(subjects) + ')'
new_fq += doc_fq
return new_fq