class VedisBackend(DBPlugin):
def connect(self):
path = os.path.join(self.project.outdir, DB_NAME)
self._db = Vedis(path)
def get_sample(self, sha256):
s = self._samples[sha256]
j = json.loads(s)
return Sample(self.project, j['file'], j['tags'], j['mutations'],
j.get('base_sample', None))
def put_sample(self, sample):
self._samples[sample.sha256] = sample.to_json()
# keep reference of the sample for each tag :)
for t in sample.tags:
self.put_tag(t, sample.sha256)
self._db.commit()
def put_scan(self, scan, sample=None, sha256=None):
if sha256:
h = sha256
else:
h = sample.sha256
self._scans[h] = json.dumps(scan)
self._db.commit()
def get_scan(self, sample=None, sha256=None):
if sha256:
h = sha256
else:
h = sample.sha256
res = self._scans[h]
if res:
return json.loads(res)
return None
def put_tag(self, tag, sha256):
t = self._db.Set('tag_' + tag)
t.add(sha256)
def get_tagged_samples(self, tag):
return self._db.Set('tag_' + tag)
@property
def _samples(self):
return self._db.Hash('samples')
@property
def _scans(self):
return self._db.Hash('scans')
@property
def all_samples(self):
# no way to use a generator with vedis
# still ok for small analyses, we'll need to
# support other DBs to reduce memory usage
for s in self._samples.keys():
yield self.get_sample(s)
class VedisBackend(DBPlugin):
def connect(self):
path = os.path.join(self.project.outdir, DB_NAME)
self._db = Vedis(path)
def get_sample(self, sha256):
s = self._samples[sha256]
j = json.loads(s)
bs = j.get('base_sample', None)
if bs is not None:
bs = self.get_sample(bs)
#watch out for recursion!
return Sample(self.project, j['file'], j['tags'], j['mutations'], bs)
@commit_on_success
def put_sample(self, sample):
self._samples[sample.sha256] = sample.to_json()
# keep reference of the sample for each tag :)
for t in sample.tags:
self.put_tag(t, sample.sha256)
@commit_on_success
def put_tag(self, tag, sha256):
t = self._db.Set('tag_' + tag)
t.add(sha256)
def get_tagged_samples(self, tag):
if isinstance(tag, basestring):
tag = [
tag,
]
for t in tag:
for s in self._db.Set('tag_' + t):
yield self.get_sample(s)
@property
def _samples(self):
return self._db.Hash('samples')
@property
def _scans(self):
return self._db.Hash('scans')
def _pending_scans(self, scanner):
return self._db.Set('{}_pending'.format(scanner))
def _done_scans(self, scanner):
return self._db.Set('{}_done'.format(scanner))
def get_pending_scans(self, scanner):
pending = self._pending_scans(scanner)
if len(pending) == 0:
return []
scans = []
for p in pending:
d = self._get_scan(p)
scans.append(
Scan(scanner=scanner,
uuid=d['uuid'],
sample=d['sample'],
scan_id=d['scan_id'],
scan_results=d['scan_results']))
return scans
@property
def all_samples(self):
# TODO: fix this
for s in self._samples.keys():
yield self.get_sample(s)
@commit_on_success
def _put_scan_results(self, scan_result):
self._scanresults[res.uuid] = scan_result
# "update" the set of scanresults for a given scan
@staticmethod
def res_to_dict(scan):
return {
'label': scan.label,
'sample': scan.sample.sha256,
'av': scan.av,
'extra': scan.extra
}
def _get_scan(self, uuid):
return self._db.Hash(uuid)
def _get_scan_result(self, scan):
return self._db.Set(scan.uuid + '_results')
def _res_by_sample(self, sample):
return self._db.Set(scan.sample.sha + '_results')
def _res_by_av(self, av):
return self._db.Set(av + '_results')
def _scan_by_sample(self, sample):
return self._db.Set(sample.sha256 + '_scans')
@commit_on_success
def put_scan(self, scan):
scanner = scan.scanner.short_name
if scan.pending:
# add to pending Set
self._pending_scans(scanner).add(scan.uuid)
else:
self._pending_scans(scanner).remove(scan.uuid)
self._put_scan_results(scan.scan_results)
self._done_scan(scanner).add(scan.uuid)
self._scan_by_sample(scan.sample).add(scan.uuid)
for res in scan.scan_results:
self._results(res.uuid).update(**res.to_dict())
# add its reference to sets for quick querying
self._res_by_sample(scan.sample).add(res.uuid)
self._res_by_av(res.av).add(res.uuid)
self._get_scan(scan.uuid).update(**scan.to_dict())
l.debug("Scan %s stored in database", scan)
def get_scan_results(self, av):
pass
def close(self):
self._db.close()
