def test_get_date_time(self):
"""Tests that only a full date-time string is valid"""
assert getDateTime("2015-12-01 00:00:00") is not None
assert getDateTime("2015-12-01 23:59:59") is not None
with pytest.raises(ValueError):
getDateTime("12345")
with pytest.raises(ValueError):
getDateTime("invalid")
with pytest.raises(ValueError):
getDateTime("2015-12-01")
def test_get_date_time(self):
""" Tests that only a full date-time string is valid """
assert getDateTime("2015-12-01 00:00:00") is not None
assert getDateTime("2015-12-01 23:59:59") is not None
with pytest.raises(ValueError):
getDateTime("12345")
with pytest.raises(ValueError):
getDateTime("invalid")
with pytest.raises(ValueError):
getDateTime("2015-12-01")
def search(
self,
query,
onlyTypes,
fields,
searchGroup,
ownedBy,
useAcquisitionDate,
date=None,
rawQuery=False,
):
# If rawQuery, the raw lucene query is used in search.byFullText()
# and fields is ignored.
# If fields contains 'annotation', we really want to search files too
# docs.openmicroscopy.org/latest/omero/developers/Modules/Search.html
fields = set(fields)
if "annotation" in fields or "file" in fields:
fields = fields.union(
("file.name", "file.path", "file.format", "file.contents"))
fields.discard("file") # Not supported
fields = list(fields)
if "plates" in onlyTypes:
onlyTypes.append("plateacquisitions")
created = None
self.moreResults = False
batchSize = 500
if len(onlyTypes) == 1:
batchSize = 1000
if date is not None:
p = str(date).split("_")
if len(p) > 1:
try:
d1 = getDateTime(p[0] + " 00:00:00")
d2 = getDateTime(p[1] + " 23:59:59")
created = [
rtime(
long(
time.mktime(d1.timetuple()) +
1e-6 * d1.microsecond) * 1000),
rtime(
long(
time.mktime(d2.timetuple()) +
1e-6 * d2.microsecond) * 1000),
]
except ValueError:
# User entered an invalid date format - Ignore
pass
else:
msg = "date should be start_end, e.g. 2015-12-01_2016-01-01"
raise ValueError(msg)
def doSearch(searchType):
""" E.g. searchType is 'images' """
objType = searchType[0:-1] # remove 's'
obj_list = list(
self.conn.searchObjects(
[objType],
query,
created,
fields=fields,
batchSize=batchSize,
searchGroup=searchGroup,
ownedBy=ownedBy,
useAcquisitionDate=useAcquisitionDate,
rawQuery=rawQuery,
), )
return obj_list
self.containers = {}
resultCount = 0
self.searchError = None
self.iids = []
try:
for dt in onlyTypes:
dt = str(dt)
if dt in [
"projects",
"datasets",
"images",
"screens",
"plateacquisitions",
"plates",
"wells",
]:
self.containers[dt] = doSearch(dt)
if dt == "wells":
for well in self.containers[dt]:
well.name = "%s - %s" % (
well.listParents()[0].name,
well.getWellPos(),
)
if dt == "images":
self.iids = [i.id for i in self.containers[dt]]
# If we get a full page of results, we know there are more
if len(self.containers[dt]) == batchSize:
self.moreResults = True
resultCount += len(self.containers[dt])
except Exception as x:
logger.info("Search Exception: %s" % x.message)
if isinstance(x, omero.ServerError):
# Only show message to user if we can be helpful
if "TooManyClauses" in x.message:
self.searchError = (
"Please try to narrow down your query. The wildcard"
" matched too many terms.")
elif ":" in query:
self.searchError = (
"There was an error parsing your query."
" Colons ':' are reserved for searches of"
" key-value annotations in the form: 'key:value'.")
self.c_size = resultCount