def test_marshal_plate(self, mock_conn, owner_permissions):
row = [rlong(1), rstring("name"), rlong(1), owner_permissions, 2]
expected = {
"id": 1,
"ownerId": 1,
"name": "name",
"permsCss":
"canEdit canAnnotate canLink canDelete canChgrp isOwned",
"childCount": 2,
}
marshaled = _marshal_plate(mock_conn, row)
assert marshaled == expected
def test_marshal_plate(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring('name'), rlong(1L), owner_permissions, 2]
expected = {
'id': 1L,
'ownerId': 1L,
'name': 'name',
'permsCss':
'canEdit canAnnotate canLink canDelete isOwned canChgrp',
'childCount': 2
}
marshaled = _marshal_plate(mock_conn, row)
assert marshaled == expected
def marshal_plates(conn,
screen_id,
mapann_value,
query=False,
mapann_ns=[],
mapann_names=[],
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals plates
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param screen_id The Screen ID to filter by.
@type screen_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
plates = []
# early exit
if screen_id is None or not isinstance(screen_id, long):
return plates
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
query=query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
params.addLong("sid", screen_id)
where_clause.append('screen.id = :sid')
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
# TODO: Joining wellsample should be enough since wells are annotated
# with the same annotations as images. In the future if that changes,
# query has to be restored to:
# - count(distinct i.id) as childCount)
# - from ImageAnnotationLink ial join ial.child a join a.mapValue mv
# - join ial.parent i join i.wellSamples ws join ws.well w
# - join w.plate plate join plate.screenLinks sl join sl.parent screen
q = """
select new map(mv.value as value,
plate.id as id,
plate.name as name,
plate.details.owner.id as ownerId,
plate as plate_details_permissions,
count(distinct ws.id) as childCount)
from WellAnnotationLink wal join wal.child a join a.mapValue mv
join wal.parent w join w.wellSamples ws
join w.plate plate join plate.screenLinks sl
join sl.parent screen
where %s
group by plate.id, plate.name, mv.value
order by lower(plate.name), plate.id, mv.value
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
e = [
e[0]['id'], e[0]['name'], e[0]['ownerId'],
e[0]['plate_details_permissions'], e[0]['childCount']
]
mp = _marshal_plate(conn, e[0:5])
extra = {'extra': {'node': 'plate'}}
if mapann_value is not None:
extra['extra']['value'] = v
mp.update(extra)
plates.append(mp)
return plates
def marshal_datasets(conn,
project_id,
mapann_value,
query=False,
mapann_ns=[],
mapann_names=[],
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals plates
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param project_id The Project ID to filter by.
@type project_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
datasets = []
# early exit
if project_id is None or not isinstance(project_id, long):
return datasets
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
query=query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
params.addLong("pid", project_id)
where_clause.append('project.id = :pid')
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
dataset.id as id,
dataset.name as name,
dataset.details.owner.id as ownerId,
dataset as dataset_details_permissions,
count(distinct i.id) as childCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.datasetLinks dil
join dil.parent dataset join dataset.projectLinks pl
join pl.parent project
where %s
group by dataset.id, dataset.name, mv.value
order by lower(dataset.name), dataset.id, mv.value
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
e = [
e[0]['id'], e[0]['name'], e[0]['ownerId'],
e[0]['dataset_details_permissions'], e[0]['childCount']
]
mp = _marshal_plate(conn, e[0:5])
extra = {'extra': {'node': 'dataset'}}
if mapann_value is not None:
extra['extra']['value'] = v
mp.update(extra)
datasets.append(mp)
return datasets
}
marshaled = _marshal_dataset(mock_conn, row)
assert marshaled == expected
def test_marshal_plate(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring("name"), rlong(1L), owner_permissions, 2]
expected = {
"id": 1L,
"ownerId": 1L,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete isOwned canChgrp",
"childCount": 2,
}
marshaled = _marshal_plate(mock_conn, row)
assert marshaled == expected
def test_marshal_plate_not_owner(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring("name"), rlong(2L), owner_permissions, 2]
expected = {
"id": 1L,
"ownerId": 2L,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete",
"childCount": 2,
}
marshaled = _marshal_plate(mock_conn, row)
print marshaled
print expected
def marshal_plates(conn, screen_id,
mapann_value, query=False,
mapann_ns=[], mapann_names=[],
group_id=-1, experimenter_id=-1,
page=1, limit=settings.PAGE):
''' Marshals plates
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param screen_id The Screen ID to filter by.
@type screen_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
plates = []
# early exit
if screen_id is None or not isinstance(screen_id, long):
return plates
params, where_clause = _set_parameters(
mapann_ns=mapann_ns, mapann_names=mapann_names,
query=query, mapann_value=mapann_value,
params=None, experimenter_id=experimenter_id,
page=page, limit=limit)
params.addLong("sid", screen_id)
where_clause.append('screen.id = :sid')
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
# TODO: Joining wellsample should be enough since wells are annotated
# with the same annotations as images. In the future if that changes,
# query has to be restored to:
# - count(distinct i.id) as childCount)
# - from ImageAnnotationLink ial join ial.child a join a.mapValue mv
# - join ial.parent i join i.wellSamples ws join ws.well w
# - join w.plate plate join plate.screenLinks sl join sl.parent screen
q = """
select new map(mv.value as value,
plate.id as id,
plate.name as name,
plate.details.owner.id as ownerId,
plate as plate_details_permissions,
count(distinct ws.id) as childCount)
from WellAnnotationLink wal join wal.child a join a.mapValue mv
join wal.parent w join w.wellSamples ws
join w.plate plate join plate.screenLinks sl
join sl.parent screen
where %s
group by plate.id, plate.name, mv.value
order by lower(plate.name), plate.id, mv.value
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
e = [e[0]['id'],
e[0]['name'],
e[0]['ownerId'],
e[0]['plate_details_permissions'],
e[0]['childCount']]
mp = _marshal_plate(conn, e[0:5])
extra = {'extra': {'node': 'plate'}}
if mapann_value is not None:
extra['extra']['value'] = v
mp.update(extra)
plates.append(mp)
return plates
def marshal_datasets(conn, project_id,
mapann_value, query=False,
mapann_ns=[], mapann_names=[],
group_id=-1, experimenter_id=-1,
page=1, limit=settings.PAGE):
''' Marshals plates
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param project_id The Project ID to filter by.
@type project_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
datasets = []
# early exit
if project_id is None or not isinstance(project_id, long):
return datasets
params, where_clause = _set_parameters(
mapann_ns=mapann_ns, mapann_names=mapann_names,
query=query, mapann_value=mapann_value,
params=None, experimenter_id=experimenter_id,
page=page, limit=limit)
params.addLong("pid", project_id)
where_clause.append('project.id = :pid')
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
dataset.id as id,
dataset.name as name,
dataset.details.owner.id as ownerId,
dataset as dataset_details_permissions,
count(distinct i.id) as childCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.datasetLinks dil
join dil.parent dataset join dataset.projectLinks pl
join pl.parent project
where %s
group by dataset.id, dataset.name, mv.value
order by lower(dataset.name), dataset.id, mv.value
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
e = [e[0]['id'],
e[0]['name'],
e[0]['ownerId'],
e[0]['dataset_details_permissions'],
e[0]['childCount']]
mp = _marshal_plate(conn, e[0:5])
extra = {'extra': {'node': 'dataset'}}
if mapann_value is not None:
extra['extra']['value'] = v
mp.update(extra)
datasets.append(mp)
return datasets
def marshal_plates(conn,
screen_id,
mapann_value,
mapann_ns=[],
mapann_names=[],
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals plates
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param screen_id The Screen ID to filter by.
@type screen_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
plates = []
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
mapann_query=None,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
params.addLong("sid", screen_id)
where_clause.append('screen.id = :sid')
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(plate.id as id,
plate.name as name,
plate.details.owner.id as ownerId,
plate as plate_details_permissions,
count(distinct i.id) as childCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.wellSamples ws join ws.well w
join w.plate plate join plate.screenLinks sl join
sl.parent screen
where %s
group by plate.id, plate.name
order by lower(plate.name), plate.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
e = [
e[0]["id"], e[0]["name"], e[0]["ownerId"],
e[0]["plate_details_permissions"], e[0]["childCount"]
]
mp = _marshal_plate(conn, e[0:5])
mp.update({'extra': {'value': mapann_value, 'node': 'plate'}})
plates.append(mp)
return plates