def load (self, context):
if self.uid == -1:
return
# Is it already loaded? Convenience check for client calls
# don't need to verify loads from the cache.
if context.config.use_cache:
try:
if self.journal_title:
# Already loaded
return
except AttributeError:
# Note already loaded, so continue
pass
cursor = context.get_cursor()
cursor.execute("""
SELECT journal_title, abbreviation, issn, nlm_id
FROM medline_journals
WHERE uid = %s
""", self.uid)
fields = [d[0] for d in cursor.description]
desc = dtuple.TupleDescriptor([[f] for f in fields])
rows = cursor.fetchall()
for row in rows:
row = dtuple.DatabaseTuple(desc, row)
for k, v in row.items():
self.set(k, v)
if context.config.use_cache:
context.cache_set('%s:%s' % (self.ALT_CACHE_KEY, self.issn), self)
def load(self, context):
if self.uid == -1:
return
# Is it already loaded? Convenience check for client calls
# don't need to verify loads from the cache.
if context.config.use_cache:
try:
if getattr(self, self.CACHE_CHECK_KEY):
# Already loaded
return
except AttributeError:
# Note already loaded, so continue
pass
cursor = context.get_cursor()
cursor.execute(
"""
SELECT reference, comments
FROM human_studies
WHERE uid = %s
""",
self.uid,
)
fields = [d[0] for d in cursor.description]
desc = dtuple.TupleDescriptor([[f] for f in fields])
row = cursor.fetchone()
row = dtuple.DatabaseTuple(desc, row)
self.reference = row["reference"]
self.comments = row["comments"]
if context.config.use_cache:
context.cache_set("%s:%s" % (self.CACHE_KEY, self.uid), self)
def load_from_issn (self, context, issn):
if not issn:
return
if context.config.use_cache:
j = context.cache_get('%s:%s' % (self.ALT_CACHE_KEY, issn))
if j \
and j.journal_title:
for att in ('uid', 'journal_title', 'abbreviation',
'issn', 'eissn', 'iso_abbr', 'nlm_id'):
self.set(att, getattr(j, att))
return
cursor = context.get_cursor()
cursor.execute("""
SELECT uid, journal_title, abbreviation, nlm_id
FROM medline_journals
WHERE issn = %s
""", issn)
fields = [d[0] for d in cursor.description]
desc = dtuple.TupleDescriptor([[f] for f in fields])
rows = cursor.fetchall()
if rows:
row = rows[0]
row = dtuple.DatabaseTuple(desc, row)
for k, v in row.items():
self.set(k, v)
self.issn = issn
if context.config.use_cache:
context.cache_set('%s:%s' % (self.CACHE_KEY, self.uid), self)
context.cache_set('%s:%s' % (self.ALT_CACHE_KEY, self.issn), self)
def save(self, context):
cursor = context.get_cursor()
try:
if self.uid == -1:
cursor.execute(
"""
INSERT INTO human_studies
(reference, comments)
VALUES (%s, %s)
""",
(self.reference, self.comments),
)
self.uid = self.get_new_uid(context)
context.logger.info("HumanStudy created with uid %s", self.uid)
else:
cursor.execute(
"""
UPDATE human_studies
SET reference = %s, comments = %s
WHERE uid = %s
""",
(self.reference, self.comments, self.uid),
)
context.logger.info("HumanStudy %s updates", self.uid)
except:
print traceback.print_exc()
raise Error, "Duplicate reference"
if context.config.use_cache:
context.cache_set("%s:%s" % (self.CACHE_KEY, self.uid), self)
def save(self, context):
cursor = context.get_cursor()
try:
if self.uid == -1:
cursor.execute(
"""
INSERT INTO human_studies
(reference, comments)
VALUES (%s, %s)
""", (self.reference, self.comments))
self.uid = self.get_new_uid(context)
context.logger.info('HumanStudy created with uid %s', self.uid)
else:
cursor.execute(
"""
UPDATE human_studies
SET reference = %s, comments = %s
WHERE uid = %s
""", (self.reference, self.comments, self.uid))
context.logger.info('HumanStudy %s updates', self.uid)
except:
print traceback.print_exc()
raise Error, 'Duplicate reference'
if context.config.use_cache:
context.cache_set('%s:%s' % (self.CACHE_KEY, self.uid), self)
def load(self, context):
if self.uid == -1:
return
# Is it already loaded? Convenience check for client calls
# don't need to verify loads from the cache.
if context.config.use_cache:
try:
if getattr(self, self.CACHE_CHECK_KEY):
# Already loaded
return
except AttributeError:
# Note already loaded, so continue
pass
cursor = context.get_cursor()
cursor.execute(
"""
SELECT reference, comments
FROM human_studies
WHERE uid = %s
""", self.uid)
fields = [d[0] for d in cursor.description]
desc = dtuple.TupleDescriptor([[f] for f in fields])
row = cursor.fetchone()
row = dtuple.DatabaseTuple(desc, row)
self.reference = row['reference']
self.comments = row['comments']
if context.config.use_cache:
context.cache_set('%s:%s' % (self.CACHE_KEY, self.uid), self)
def save (self, context, update_all=False):
# NOTE: For now, do not allow creation of arbitrary concepts
if self.uid == -1:
return
cursor = context.get_cursor()
# NOTE: For now, only allow update of preferred_name
cursor.execute("""
UPDATE umls_concepts
SET preferred_name = %s
WHERE umls_concept_id = %s
""", (self.term, self.uid))
if context.config.use_cache:
context.cache_set('%s:%s' % (self.CACHE_KEY, self.uid), self)
def save(self, context, update_all=False):
# NOTE: For now, do not allow creation of arbitrary concepts
if self.uid == -1:
return
cursor = context.get_cursor()
# NOTE: For now, only allow update of preferred_name
cursor.execute(
"""
UPDATE umls_concepts
SET preferred_name = %s
WHERE umls_concept_id = %s
""", (self.term, self.uid))
if context.config.use_cache:
context.cache_set('%s:%s' % (self.CACHE_KEY, self.uid), self)
