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Fix #13 #14

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Jul 18, 2024
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Fix #13 #14

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355 changes: 177 additions & 178 deletions omero_tagsearch/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -283,198 +283,197 @@ def tag_image_search(request, conn=None, **kwargs):
import time

start = time.time()
if request.method == "GET":

selected_tags = [int(x) for x in request.GET.getlist("selectedTags")]
excluded_tags = [int(x) for x in request.GET.getlist("excludedTags")]
operation = request.GET.get("operation")
selected_tags = [int(x) for x in request.GET.getlist("selectedTags")]
excluded_tags = [int(x) for x in request.GET.getlist("excludedTags")]
operation = request.GET.get("operation")

# validate experimenter is in the active group
active_group = (
request.session.get("active_group")
or conn.getEventContext().groupId
# validate experimenter is in the active group
active_group = (
request.session.get("active_group")
or conn.getEventContext().groupId
)
service_opts = conn.SERVICE_OPTS.copy()
service_opts.setOmeroGroup(active_group)

def get_annotated_obj(obj_type, in_ids, excl_ids):
# Get the images that match
params = Parameters()
params.map = {}
params.map["in_ids"] = rlist([rlong(o) for o in set(in_ids)])

hql = ("select link.parent.id from %sAnnotationLink link "
"where link.child.id in (:in_ids) " % (obj_type))
if len(excl_ids) > 0:
params.map["ex_ids"] = rlist([rlong(o) for o in set(excl_ids)])
hql += (" and link.parent.id not in "
"(select link.parent.id from %sAnnotationLink link "
"where link.child.id in (:ex_ids)) " % (obj_type))

hql += "group by link.parent.id"
if operation == "AND":
hql += f" having count (distinct link.child) = {len(in_ids)}"

qs = conn.getQueryService()
return [x[0].getValue() for x in qs.projection(hql,
params,
service_opts)]

context = {}
html_response = ""
remaining = set([])

manager = {"containers": {}}
preview = False
count_d = {}
if selected_tags:
image_ids = get_annotated_obj("Image", selected_tags,
excluded_tags)
count_d["image"] = len(image_ids)

dataset_ids = get_annotated_obj("Dataset", selected_tags,
excluded_tags)
count_d["dataset"] = len(dataset_ids)

project_ids = get_annotated_obj("Project", selected_tags,
excluded_tags)
count_d["project"] = len(project_ids)

screen_ids = get_annotated_obj("Screen", selected_tags,
excluded_tags)
count_d["screen"] = len(screen_ids)

plate_ids = get_annotated_obj("Plate", selected_tags,
excluded_tags)
count_d["plate"] = len(plate_ids)

well_ids = get_annotated_obj("Well", selected_tags,
excluded_tags)
count_d["well"] = len(well_ids)

acquisition_ids = get_annotated_obj("PlateAcquisition",
selected_tags, excluded_tags)
count_d["acquisition"] = len(acquisition_ids)

if image_ids:
images = conn.getObjects("Image", ids=image_ids)
manager["containers"]["image"] = list(images)

if dataset_ids:
datasets = conn.getObjects("Dataset", ids=dataset_ids)
manager["containers"]["dataset"] = list(datasets)

if project_ids:
projects = conn.getObjects("Project", ids=project_ids)
manager["containers"]["project"] = list(projects)

if screen_ids:
screens = conn.getObjects("Screen", ids=screen_ids)
manager["containers"]["screen"] = list(screens)

if plate_ids:
plates = conn.getObjects("Plate", ids=plate_ids)
manager["containers"]["plate"] = list(plates)

if well_ids:
wells = []
for w in conn.getObjects("Well", ids=well_ids):
w.name = f"{w.getParent().name} - {w.getWellPos()}"
wells.append(w)
manager["containers"]["well"] = wells

if acquisition_ids:
acquisitions = conn.getObjects(
"PlateAcquisition", ids=acquisition_ids
)
manager["containers"]["acquisition"] = list(acquisitions)

manager["c_size"] = sum(count_d.values())
if manager["c_size"] > 0:
preview = True

context["manager"] = manager

html_response = render_to_string(
"omero_tagsearch/search_details.html", context
)
service_opts = conn.SERVICE_OPTS.copy()
service_opts.setOmeroGroup(active_group)

def get_annotated_obj(obj_type, in_ids, excl_ids):
middle = time.time()

def get_objects_annotations(obj_type, oids):
# Get the images that match
params = Parameters()
params.map = {}
params.map["in_ids"] = rlist([rlong(o) for o in set(in_ids)])

hql = ("select link.parent.id from %sAnnotationLink link "
"where link.child.id in (:in_ids) " % (obj_type))
if len(excl_ids) > 0:
params.map["ex_ids"] = rlist([rlong(o) for o in set(excl_ids)])
hql += (" and link.parent.id not in "
"(select link.parent.id from %sAnnotationLink link "
"where link.child.id in (:ex_ids)) " % (obj_type))

hql += "group by link.parent.id"
hql = (
"select distinct link.child.id " +
"from %sAnnotationLink link " % obj_type
)
if operation == "AND":
hql += f" having count (distinct link.child) = {len(in_ids)}"
hql += "where link.parent.id in (:oids)"
params.map["oids"] = rlist([rlong(o) for o in oids])

qs = conn.getQueryService()
return [x[0].getValue() for x in qs.projection(hql,
params,
service_opts)]

context = {}
html_response = ""
remaining = set([])

manager = {"containers": {}}
preview = False
count_d = {}
if selected_tags:
image_ids = get_annotated_obj("Image", selected_tags,
excluded_tags)
count_d["image"] = len(image_ids)

dataset_ids = get_annotated_obj("Dataset", selected_tags,
excluded_tags)
count_d["dataset"] = len(dataset_ids)

project_ids = get_annotated_obj("Project", selected_tags,
excluded_tags)
count_d["project"] = len(project_ids)

screen_ids = get_annotated_obj("Screen", selected_tags,
excluded_tags)
count_d["screen"] = len(screen_ids)

plate_ids = get_annotated_obj("Plate", selected_tags,
excluded_tags)
count_d["plate"] = len(plate_ids)

well_ids = get_annotated_obj("Well", selected_tags,
excluded_tags)
count_d["well"] = len(well_ids)

acquisition_ids = get_annotated_obj("PlateAcquisition",
selected_tags, excluded_tags)
count_d["acquisition"] = len(acquisition_ids)

return [
result[0].val for result in qs.projection(hql,
params,
service_opts)
]

# Calculate remaining possible tag navigations
# TODO Compare subquery to pass-in performance
# sub_hql = """
# SELECT link.parent.id
# FROM ImageAnnotationLink link
# WHERE link.child.id IN (:oids)
# GROUP BY link.parent.id
# HAVING count (link.parent) = %s
# """ % len(selected_tags)
# hql = """
# SELECT DISTINCT link.child.id
# FROM ImageAnnotationLink link
# WHERE link.parent.id IN (%s)
# """ % sub_hql

if operation == "AND":
if image_ids:
images = conn.getObjects("Image", ids=image_ids)
manager["containers"]["image"] = list(images)

remaining.update(get_objects_annotations("Image",
image_ids))
if dataset_ids:
datasets = conn.getObjects("Dataset", ids=dataset_ids)
manager["containers"]["dataset"] = list(datasets)

remaining.update(get_objects_annotations("Dataset",
dataset_ids))
if project_ids:
projects = conn.getObjects("Project", ids=project_ids)
manager["containers"]["project"] = list(projects)

if screen_ids:
screens = conn.getObjects("Screen", ids=screen_ids)
manager["containers"]["screen"] = list(screens)

if plate_ids:
plates = conn.getObjects("Plate", ids=plate_ids)
manager["containers"]["plate"] = list(plates)

remaining.update(get_objects_annotations("Project",
project_ids))
if well_ids:
wells = []
for w in conn.getObjects("Well", ids=well_ids):
w.name = f"{w.getParent().name} - {w.getWellPos()}"
wells.append(w)
manager["containers"]["well"] = wells

remaining.update(get_objects_annotations("Well",
well_ids))
if acquisition_ids:
acquisitions = conn.getObjects(
"PlateAcquisition", ids=acquisition_ids
)
manager["containers"]["acquisition"] = list(acquisitions)

manager["c_size"] = sum(count_d.values())
if manager["c_size"] > 0:
preview = True

context["manager"] = manager

html_response = render_to_string(
"omero_tagsearch/search_details.html", context
)

middle = time.time()

def get_objects_annotations(obj_type, oids):
# Get the images that match
params = Parameters()
params.map = {}
hql = (
"select distinct link.child.id " +
"from %sAnnotationLink link " % obj_type
)
if operation == "AND":
hql += "where link.parent.id in (:oids)"
params.map["oids"] = rlist([rlong(o) for o in oids])

qs = conn.getQueryService()
return [
result[0].val for result in qs.projection(hql,
params,
service_opts)
]

# Calculate remaining possible tag navigations
# TODO Compare subquery to pass-in performance
# sub_hql = """
# SELECT link.parent.id
# FROM ImageAnnotationLink link
# WHERE link.child.id IN (:oids)
# GROUP BY link.parent.id
# HAVING count (link.parent) = %s
# """ % len(selected_tags)
# hql = """
# SELECT DISTINCT link.child.id
# FROM ImageAnnotationLink link
# WHERE link.parent.id IN (%s)
# """ % sub_hql

if operation == "AND":
if image_ids:
remaining.update(get_objects_annotations("Image",
image_ids))
if dataset_ids:
remaining.update(get_objects_annotations("Dataset",
dataset_ids))
if project_ids:
remaining.update(get_objects_annotations("Project",
project_ids))
if well_ids:
remaining.update(get_objects_annotations("Well",
well_ids))
if acquisition_ids:
remaining.update(
get_objects_annotations("PlateAcquisition",
acquisition_ids))
if plate_ids:
remaining.update(get_objects_annotations("Plate",
plate_ids))
if screen_ids:
remaining.update(get_objects_annotations("Screen",
screen_ids))

end = time.time()
logger.info(
"Tag Query Times. Preview: %ss, Remaining: %ss, Total:%ss"
% ((middle - start), (end - middle), (end - start))
)
remaining.update(
get_objects_annotations("PlateAcquisition",
acquisition_ids))
if plate_ids:
remaining.update(get_objects_annotations("Plate",
plate_ids))
if screen_ids:
remaining.update(get_objects_annotations("Screen",
screen_ids))

# Return the navigation data and the html preview for display
# return {"navdata": list(remaining), "html": html_response}
return HttpResponse(
json.dumps(
{
"navdata": list(remaining),
"preview": preview,
"count": count_d,
"html": html_response,
}
),
content_type="application/json",
end = time.time()
logger.info(
"Tag Query Times. Preview: %ss, Remaining: %ss, Total:%ss"
% ((middle - start), (end - middle), (end - start))
)

# Return the navigation data and the html preview for display
# return {"navdata": list(remaining), "html": html_response}
return HttpResponse(
json.dumps(
{
"navdata": list(remaining),
"preview": preview,
"count": count_d,
"html": html_response,
}
),
content_type="application/json",
)