def code_details_with_site(code, code_system_uri, site):
# from code details fetching
# fromCode_details = db.code_details(code, code_system)
req_fromcode_oid = '''
select c.oid,cs.code_system,cs.uri,cs.version,c.code,c.designation
from mappings m
inner join codes c on (c.oid=m.code)
inner join code_systems cs on (c.code_system=cs.oid)
inner join sites s on (s.oid=m.site)
where c.code_system=(select oid from code_systems
where uri=:uri)
and s.site=:site
and c.code=:code
'''
with wcursor(True) as cursor:
fromcodedetails = cursor.execute(req_fromcode_oid, {
'uri': code_system_uri,
'code': code,
'site': site
}).fetchall()
if not len(fromcodedetails):
return "no such code: {}@{}".format(code, code_system_uri), 404
keys = [
"id", h.CODE_SYSTEM, h.CODE_SYSTEM_URI, h.CODE_SYSTEM_VERSION, h.CODE,
h.DESIGNATION
]
code_details = h.dictFromKeyValues(keys, fromcodedetails[0])
code_details['site'] = site
return code_details
def delete_mapping(site=None, concept=None):
log.warning('XXXXXXXX deleting mapping {}@{}'.format(concept, site))
assert (site is not None) or (concept is not None)
d = {'site': site, 'concept': concept}
where = ' and '.join([
f"{k}=(select oid from {k}s where {k}=:{k})" for k, v in d.items()
if v is not None
])
request = f"delete from mappings where {where}"
with wcursor(False) as cursor:
try:
d = h.dictFromKeyValues([h.SITE, h.CONCEPT], [site, concept])
log_execute(request, d)
cursor.execute(request, d)
ans = {'modified_mappings': cursor.rowcount}
log.warning(ans)
# delete_code_for_concept(cursor, site=site, concept=concept)
req = f'''
delete from codes
where oid in (select m.code from mappings m where {where})
'''
cursor.execute(req, {'site': site, 'concept': concept})
except Exception as e:
log.error("!!!! error deleting the mapping")
log.error(e)
log.error(request)
log.error(d)
db.rollback()
raise e
commit_and_rebuild()
return ans
def build_all_code_systems():
with wcursor(readonly=True) as cursor:
values = cursor.execute(
"select uri, code_system, version from code_systems").fetchall()
return [
h.dictFromKeyValues(
[h.CODE_SYSTEM_URI, h.CODE_SYSTEM, h.CODE_SYSTEM_VERSION], v)
for v in values
]
def build_all_codes():
global codes
with wcursor(True) as cursor:
cursor.execute(
'SELECT code, code_systems.code_system, designation, uri from {}'.
format(mkjoin('codes', 'code_systems', 'code_system', 'oid')))
ans = cursor.fetchall()
codes = [
h.dictFromKeyValues(
[h.CODE, h.CODE_SYSTEM, h.DESIGNATION, h.CODE_SYSTEM_URI], e)
for e in ans
]
def list_all_codes(site=''):
ans = query_perhaps_condition(condition='where s.site=?',
query='''
select c.code, cs.code_system, cs.uri, c.designation
from mappings m
inner join codes c on (m.code=c.oid)
inner join code_systems cs on (c.code_system=cs.oid)
inner join sites s on (m.site=s.oid)
{}
''')(site)
return [
h.dictFromKeyValues(
[h.CODE, h.CODE_SYSTEM, h.CODE_SYSTEM_URI, h.DESIGNATION], e)
for e in ans
]
def build_all_mappings():
global mappings
query = '''
select concepts.concept,cs.code_system,cs.uri,c.code,c.designation,s.site
from mappings m
inner join codes c on (m.code = c.oid)
inner join concepts on (m.concept = concepts.oid)
inner join sites s on (m.site = s.oid)
inner join code_systems cs on (c.code_system = cs.oid);
'''
columns = [
h.CONCEPT, h.CODE_SYSTEM, h.CODE_SYSTEM_URI, h.CODE, h.DESIGNATION,
h.SITE
]
with wcursor(True) as cursor:
mappings = [
h.dictFromKeyValues(columns, e)
for e in cursor.execute(query).fetchall()
]
def list_all_code_systems():
keys = [h.CODE_SYSTEM_URI, h.CODE_SYSTEM, h.CODE_SYSTEM_VERSION]
with wcursor(True) as cursor:
values = cursor.execute(
"select uri, code_system, version from code_systems").fetchall()
return [h.dictFromKeyValues(keys, v) for v in values]
def build_all_equivalences():
global equivalences
keys = list_column('equivalences', 'equivalence')
values = list_column('equivalences', 'definition')
equivalences = h.dictFromKeyValues(keys, values)