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Implementation of annotation ID option in objects getters #108

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merged 6 commits into from
Aug 14, 2024
Merged

Implementation of annotation ID option in objects getters #108

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1870d85
get by annotation id image/dataset/project
Tom-TBT Mar 8, 2024
9b8bded
tests get from annotation
Tom-TBT Jun 1, 2024
ae119c4
Merge branch 'main' into get_from_ann
Tom-TBT Jun 6, 2024
6a18ac2
get hcs objects by annotation
Tom-TBT Jun 6, 2024
72c9e29
test of getting objects by annotation
Tom-TBT Jun 7, 2024
f190519
remove unused user_group
Tom-TBT Jun 7, 2024
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176 changes: 156 additions & 20 deletions ezomero/_gets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,6 +333,7 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,
plate: Optional[int] = None,
well: Optional[int] = None,
plate_acquisition: Optional[int] = None,
annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list of image ids based on image container

Expand All @@ -354,6 +355,9 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,
ID of Well from which to return image IDs.
plate_acquisition : int, optional
ID of Plate acquisition from which to return image IDs.
annotation : int, optional
ID of Annotation from which to return image IDs. This will return IDs
of all images linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -369,8 +373,9 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,
``ezomero.set_group`` to specify group prior to passing
the `conn` object to this function.

Only one of Project, Dataset, Plate, Well or Plate acquisition can be
specified. If none of those are specified, orphaned images are returned.
Only one of Project, Dataset, Plate, Well, Plate acquisition or Annotation
can be specified. If none of those are specified, orphaned images are
returned.

Examples
--------
Expand All @@ -381,14 +386,19 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,
# Return IDs of all images from Dataset with ID 448:

>>> ds_ims = get_image_ids(conn, dataset=448)

# Return IDs of all images annotated with Tag ID 876:

>>> tag_ims = get_image_ids(conn, annotation=876)
"""
arg_counter = 0
for arg in [project, dataset, plate, well, plate_acquisition]:

for arg in [project, dataset, plate, well, plate_acquisition, annotation]:
if arg is not None:
arg_counter += 1
if arg_counter > 1:
raise ValueError('Only one of Project/Dataset/Plate/Well'
'/PlateAcquisition can be specified')
'/PlateAcquisition/Annotation can be specified')

q = conn.getQueryService()
params = Parameters()
Expand Down Expand Up @@ -456,6 +466,16 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,
params,
conn.SERVICE_OPTS
)
elif annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM ImageAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
else:
results = q.projection(
"SELECT i.id FROM Image i"
Expand All @@ -476,13 +496,17 @@ def get_image_ids(conn: BlitzGateway, project: Optional[int] = None,

@do_across_groups
def get_project_ids(conn: BlitzGateway,
annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list with IDs for all available Projects.

Parameters
----------
conn : ``omero.gateway.BlitzGateway`` object
OMERO connection.
annotation : int, optional
ID of Annotation from which to return project IDs. This will return IDs
of all projects linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -497,19 +521,41 @@ def get_project_ids(conn: BlitzGateway,
# Return IDs of all projects accessible by current user:

>>> proj_ids = get_project_ids(conn)

# Return IDs of all projects annotated with tag id 576:

>>> proj_ids = get_project_ids(conn, annotation=576)
"""
proj_ids = []
for p in conn.listProjects():
proj_ids.append(p.getId())

q = conn.getQueryService()
params = Parameters()

if annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM ProjectAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
proj_ids = [r[0].val for r in results]
else:
proj_ids = []
for p in conn.listProjects():
proj_ids.append(p.getId())
return proj_ids


@do_across_groups
def get_dataset_ids(conn: BlitzGateway, project: Optional[int] = None,
annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list of dataset ids based on project ID.

If no project is specified, function will return orphan datasets.
If no project or annotation is specified, function will return
orphan datasets.

Parameters
----------
Expand All @@ -518,6 +564,9 @@ def get_dataset_ids(conn: BlitzGateway, project: Optional[int] = None,
project : int, optional
ID of Project from which to return dataset IDs. This will return IDs of
all datasets contained in the specified Project.
annotation : int, optional
ID of Annotation from which to return dataset IDs. This will return IDs
of all datasets linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -537,6 +586,14 @@ def get_dataset_ids(conn: BlitzGateway, project: Optional[int] = None,

>>> ds_ids = get_dataset_ids(conn, project=224)
"""
arg_counter = 0
for arg in [project, annotation]:
if arg is not None:
arg_counter += 1
if arg_counter > 1:
raise ValueError('Only one of Project/Annotation'
' can be specified')

q = conn.getQueryService()
params = Parameters()

Expand All @@ -552,6 +609,16 @@ def get_dataset_ids(conn: BlitzGateway, project: Optional[int] = None,
params,
conn.SERVICE_OPTS
)
elif annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM DatasetAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
else:
results = q.projection(
"SELECT d.id FROM Dataset d"
Expand All @@ -566,14 +633,17 @@ def get_dataset_ids(conn: BlitzGateway, project: Optional[int] = None,


@do_across_groups
def get_screen_ids(conn: BlitzGateway,
def get_screen_ids(conn: BlitzGateway, annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list with IDs for all available Screens.

Parameters
----------
conn : ``omero.gateway.BlitzGateway`` object
OMERO connection.
annotation : int, optional
ID of Annotation from which to return screen IDs. This will return IDs
of all screens linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -588,16 +658,36 @@ def get_screen_ids(conn: BlitzGateway,
# Return IDs of all screens accessible by current user:

>>> scrn_ids = get_screen_ids(conn)

# Return IDs of all screens annotated with tag id 913:

>>> proj_ids = get_screen_ids(conn, annotation=913)
"""

scrn_ids = []
for s in conn.listScreens():
scrn_ids.append(s.getId())
q = conn.getQueryService()
params = Parameters()

if annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM ScreenAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
scrn_ids = [r[0].val for r in results]
else:
scrn_ids = []
for s in conn.listScreens():
scrn_ids.append(s.getId())
return scrn_ids


@do_across_groups
def get_plate_ids(conn: BlitzGateway, screen: Optional[int] = None,
annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list of plate ids based on screen ID.

Expand All @@ -610,6 +700,9 @@ def get_plate_ids(conn: BlitzGateway, screen: Optional[int] = None,
screen : int, optional
ID of Screen from which to return plate IDs. This will return IDs of
all plates contained in the specified Screen.
annotation : int, optional
ID of Annotation from which to return plate IDs. This will return IDs
of all plates linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -629,6 +722,13 @@ def get_plate_ids(conn: BlitzGateway, screen: Optional[int] = None,

>>> pl_ids = get_plate_ids(conn, screen=224)
"""
arg_counter = 0
for arg in [screen, annotation]:
if arg is not None:
arg_counter += 1
if arg_counter > 1:
raise ValueError('Only one of Screen/Annotation'
' can be specified')

q = conn.getQueryService()
params = Parameters()
Expand All @@ -645,6 +745,16 @@ def get_plate_ids(conn: BlitzGateway, screen: Optional[int] = None,
params,
conn.SERVICE_OPTS
)
elif annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM PlateAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
else:
results = q.projection(
"SELECT p.id FROM Plate p"
Expand All @@ -660,7 +770,7 @@ def get_plate_ids(conn: BlitzGateway, screen: Optional[int] = None,

@do_across_groups
def get_well_ids(conn: BlitzGateway, screen: Optional[int] = None,
plate: Optional[int] = None,
plate: Optional[int] = None, annotation: Optional[int] = None,
across_groups: Optional[bool] = True) -> List[int]:
"""Return a list of well ids based on a container

Expand All @@ -674,6 +784,9 @@ def get_well_ids(conn: BlitzGateway, screen: Optional[int] = None,
plate : int, optional
ID of Plate from which to return well IDs. This will return IDs of
all wells belonging to the specified Plate.
annotation : int, optional
ID of Annotation from which to return well IDs. This will return IDs
of all wells linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -690,14 +803,14 @@ def get_well_ids(conn: BlitzGateway, screen: Optional[int] = None,
>>> wl_ids = get_well_ids(conn, screen=224)
"""
arg_counter = 0
for arg in [screen, plate]:
for arg in [screen, plate, annotation]:
if arg is not None:
arg_counter += 1
if arg_counter > 1:
raise ValueError('Only one of Screen/Plate'
raise ValueError('Only one of Screen/Plate/Annotation'
' can be specified')
elif arg_counter == 0:
raise ValueError('One of Screen/Plate'
raise ValueError('One of Screen/Plate/Annotation'
' must be specified')

q = conn.getQueryService()
Expand Down Expand Up @@ -727,13 +840,23 @@ def get_well_ids(conn: BlitzGateway, screen: Optional[int] = None,
params,
conn.SERVICE_OPTS
)
elif annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM WellAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
return [r[0].val for r in results]


@do_across_groups
def get_plate_acquisition_ids(
conn: BlitzGateway, screen: Optional[int] = None,
plate: Optional[int] = None,
plate: Optional[int] = None, annotation: Optional[int] = None,
across_groups: Optional[bool] = True
) -> List[int]:
"""Return a list of plate acquisition ids based on a container
Expand All @@ -750,6 +873,9 @@ def get_plate_acquisition_ids(
ID of Plate from which to return plate acquisition IDs.
This will return IDs of all plate acquisitions belonging
to the specified Plate.
annotation : int, optional
ID of Annotation from which to return run IDs. This will return IDs
of all runs linked to the specified annotation.
across_groups : bool, optional
Defines cross-group behavior of function - set to
``False`` to disable it.
Expand All @@ -766,14 +892,14 @@ def get_plate_acquisition_ids(
>>> plate_acquisition_ids = get_plate_acquisition_ids(conn, screen=224)
"""
arg_counter = 0
for arg in [screen, plate]:
for arg in [screen, plate, annotation]:
if arg is not None:
arg_counter += 1
if arg_counter > 1:
raise ValueError('Only one of Screen/Plate'
raise ValueError('Only one of Screen/Plate/Annotation'
' can be specified')
elif arg_counter == 0:
raise ValueError('One of Screen/Plate'
raise ValueError('One of Screen/Plate/Annotation'
' must be specified')

q = conn.getQueryService()
Expand Down Expand Up @@ -803,6 +929,16 @@ def get_plate_acquisition_ids(
params,
conn.SERVICE_OPTS
)
elif annotation is not None:
if not isinstance(annotation, int):
raise TypeError('Annotation ID must be integer')
params.map = {"annotation": rlong(annotation)}
results = q.projection(
"SELECT l.parent.id FROM PlateAcquisitionAnnotationLink l"
" WHERE l.child.id=:annotation",
params,
conn.SERVICE_OPTS
)
return [r[0].val for r in results]


Expand Down
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