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Regression
OmeroWeb.test.integration.test_tree.TestTree.test_marshal_images_share (from pytest)
Error Message
TypeError: list indices must be integers or slices, not str
Stacktrace
self = <test_tree.TestTree object at 0x7faf24ae9a60>
userA = (<omero.clients.BaseClient object at 0x7fafa495f1c0>, object #0 (::omero::model::Experimenter)
{
_id = object #1 (...nnotationLinksSeq =
{
}
_annotationLinksLoaded = False
_annotationLinksCountPerOwner =
{
}
})
shares_userA_owned = [object #0 (::omero::model::Share)
{
_id = object #1 (::omero::RLong)
{
_val = 10109
}
_detail... 2
[398] = 5
[399] = 0
[400] = 0
[401] = 0
[402] = 0
[403] = 0
}
}]
images_userA_groupA = [object #0 (::omero::model::Image)
{
_id = object #1 (::omero::RLong)
{
_val = 7378
}
_details... {
}
_name = object #55 (::omero::RString)
{
_val = Neon
}
_description = <object #14>
}]
def test_marshal_images_share(self, userA, shares_userA_owned,
images_userA_groupA):
"""
Test marshalling images for shareA
"""
conn = get_connection(userA)
share = shares_userA_owned[0]
images = images_userA_groupA
expected = expected_images(userA, images,
extraValues={'shareId': share.id.val})
> marshaled = marshal_images(conn=conn,
share_id=share.id.val)
test/integration/test_tree.py:1894:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
conn = <omeroweb.webclient.webclient_gateway.OmeroWebGateway object at 0x7fafac0ed6a0>
dataset_id = None, orphaned = False, share_id = 10109, load_pixels = False
group_id = -1, experimenter_id = -1, page = 1, date = False
thumb_version = False, limit = 200
def marshal_images(
conn,
dataset_id=None,
orphaned=False,
share_id=None,
load_pixels=False,
group_id=-1,
experimenter_id=-1,
page=1,
date=False,
thumb_version=False,
limit=settings.PAGE,
):
"""Marshals images
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param dataset_id The Dataset ID to filter by or `None` to
not filter by a specific dataset.
defaults to `None`
@type dataset_id L{long}
@param orphaned If this is to filter by orphaned data. Overridden
by dataset_id.
defaults to False
@type orphaned Boolean
@param share_id The Share ID to filter by or `None` to
not filter by a specific share.
defaults to `None`
@type share_id L{long}
@param load_pixels Whether to load the X,Y,Z dimensions
@type load_pixels Boolean
@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}
"""
images = []
params = omero.sys.ParametersI()
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
# Paging
if page is not None and page > 0:
params.page((page - 1) * limit, limit)
from_join_clauses = []
where_clause = []
if experimenter_id is not None and experimenter_id != -1:
params.addId(experimenter_id)
where_clause.append("image.details.owner.id = :id")
qs = conn.getQueryService()
extraValues = ""
if load_pixels:
extraValues = """
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeT as sizeT,
pix.sizeZ as sizeZ
"""
if date:
extraValues += """,
image.details.creationEvent.time as date,
image.acquisitionDate as acqDate
"""
q = (
"""
select new map(image.id as id,
image.archived as archived,
image.name as name,
image.details.owner.id as ownerId,
image as image_details_permissions,
image.fileset.id as filesetId %s)
"""
% extraValues
)
from_join_clauses.append("Image image")
if load_pixels:
# We use 'left outer join', since we still want images if no pixels
from_join_clauses.append("left outer join image.pixels pix")
# If this is a query to get images from a parent dataset
if dataset_id is not None:
params.add("did", rlong(dataset_id))
from_join_clauses.append("join image.datasetLinks dlink")
where_clause.append("dlink.parent.id = :did")
# If this is a query to get images with no parent datasets (orphans)
# At the moment the implementation assumes that a cross-linked
# object is not an orphan. We may need to change that so that a user
# see all the data that belongs to them that is not assigned to a container
# that they own.
elif orphaned:
orphan_where = """
not exists (
select dilink from DatasetImageLink as dilink
where dilink.child = image.id
"""
# This is what is necessary if an orphan means that it has no
# container that belongs to the image owner. This corresponds
# to marshal_orphaned as well because of the child count
# if experimenter_id is not None and experimenter_id != -1:
# orphan_where += ' and dilink.parent.details.owner.id = :id '
orphan_where += ") "
where_clause.append(orphan_where)
# Also discount any images which are part of a screen. No need to
# take owner into account on this because we don't want them in
# orphans either way
where_clause.append(
"""
not exists (
select ws from WellSample ws
where ws.image.id = image.id
)
"""
)
# If this is a query to get images in a share
if share_id is not None:
# Get the contents of the blob which contains the images in the share
# Would be nice to do this without the ShareService, preferably as part
# of the single query
image_rids = [
image_rid.getId().val
for image_rid in conn.getShareService().getContents(share_id)
if isinstance(image_rid, omero.model.ImageI)
]
# If there are no images in the share, don't bother querying
if not image_rids:
return images
params.add("iids", wrap([rlong(id) for id in image_rids]))
where_clause.append("image.id in (:iids)")
q += """
%s %s
order by lower(image.name), image.id
""" % (
" from " + " ".join(from_join_clauses),
build_clause(where_clause, "where", "and"),
)
for e in qs.projection(q, params, service_opts):
data = unwrap(e)[0]
kwargs = {}
if date:
kwargs["acqDate"] = data["acqDate"]
kwargs["date"] = data["date"]
# While marshalling the images, determine if there are any
# images mentioned in shares that are not in the results
# because they have been deleted
if share_id is not None and image_rids and data["id"] in image_rids:
> image_rids.remove(e["id"])
E TypeError: list indices must be integers or slices, not str
../../../../.venv3/lib64/python3.9/site-packages/omeroweb/webclient/tree.py:817: TypeError