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Add more opts support for getObjects('Annotation') #489

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c86f8e2
Start to add more opts support for getObjects('Annotation')
will-moore Nov 24, 2025
16dc35a
Merge remote-tracking branch 'origin/master' into getObjects_Annotations
will-moore Jun 30, 2026
4d6c32e
Support parent_type and parent_ids for getObjects('Annotation')
will-moore Jun 30, 2026
559eb61
Support ns for getObjects('Annotation')
will-moore Jun 30, 2026
4c1ee1d
load File for FileAnnotations
will-moore Jul 1, 2026
b0e6410
Always try to load annotation.File
will-moore Jul 1, 2026
367e22e
Remove special handling of 'rating' annotation
will-moore Jul 2, 2026
97c30cc
Fix docstring
will-moore Jul 30, 2026
9a2ce90
raise AttributeError for invalid ann_type
will-moore Jul 30, 2026
513ce54
Use conn.getObject('TagAnnotation'...) to load Tags
will-moore Jul 30, 2026
2ce949c
Add XmlAnnotationWrapper to KNOWN_WRAPPERS
will-moore Jul 30, 2026
d16cce3
getObject('Annotation') parent_type case insensitive
will-moore Jul 31, 2026
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203 changes: 53 additions & 150 deletions src/omero/gateway/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3377,7 +3377,7 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None,
wrapper = KNOWN_WRAPPERS.get(obj_type.lower(), None)
if wrapper is None:
raise KeyError(
"obj_type of %s not supported by getOjbects(). "
"obj_type of %s not supported by getObjects(). "
"E.g. use 'Image' etc" % obj_type)
else:
raise AttributeError(
Expand Down Expand Up @@ -5134,6 +5134,7 @@ class AnnotationWrapper (BlitzObjectWrapper):
# E.g. DoubleAnnotationI : DoubleAnnotationWrapper
registry = {}
OMERO_TYPE = None
OMERO_CLASS = "Annotation"

def __init__(self, *args, **kwargs):
"""
Expand Down Expand Up @@ -5164,13 +5165,49 @@ def _getQueryString(cls, opts=None):
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
parent_type: (optional) "Project", "Dataset", "Image" etc
parent_ids: (optional) list of IDs for the parent type
ns: (optional) namespace string to filter by
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from Annotation obj "

query, clauses, params = super(
AnnotationWrapper, cls)._getQueryString(opts)
if opts is None:
opts = {}

fetch_file = ""
if cls.OMERO_CLASS in ("Annotation", "FileAnnotation"):
fetch_file = "left outer join fetch obj.file as file"

query = (f"select obj from {cls.OMERO_CLASS} obj "
f"{fetch_file} "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()

# We want to make parent_type case-insensitive...
if 'parent_type' in opts:
# Title case works for most objects...

@sbesson sbesson Jul 31, 2026

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Can we move this utility to a separate utility method for transforming lower-case strings into case-sensitive object types with associated unit tests ?

I see a few places in the gateway that can use it. There might be use cases elsewhere in OMERO.py.

obj_type = opts['parent_type'].title()
# Handle special cases for certain annotatable object types
for otype in ["ExperimenterGroup", "LightPath", "LightSource",
"OriginalFile", "PlaneInfo", "PlateAcquisition"]:
if obj_type == otype.title():
obj_type = otype
ids_clause = ""
if 'parent_ids' in opts:

@sbesson sbesson Jul 31, 2026

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What is the real-world use case associated with specifying parent_type but no parent_ids?
I think it should be easy to enforce that parent_ids must be supplied if parent_type is specified. And that can always be relaxed later on if there is a real need.

ids_clause = f"and link.parent.id in (:parent_ids)"
params.add("parent_ids", rlist([rlong(i) for i in opts['parent_ids']]))

clause = f"""exists (from {obj_type}AnnotationLink as link
where link.child.id = obj.id {ids_clause})"""
clauses.append(clause)

if 'ns' in opts:
clauses.append("obj.ns=:ns")
params.add("ns", rstring(opts['ns']))

return (query, clauses, params)

@classmethod
def _register(cls, regklass):
Expand Down Expand Up @@ -5315,29 +5352,14 @@ class FileAnnotationWrapper (AnnotationWrapper, OmeroRestrictionWrapper):
"""

OMERO_TYPE = FileAnnotationI
OMERO_CLASS = "FileAnnotation"

def __init__(self, *args, **kwargs):
super(FileAnnotationWrapper, self).__init__(*args, **kwargs)
self._file = None

_attrs = ('file|OriginalFileWrapper',)

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("FileAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from FileAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent join fetch obj.file")
return query, [], omero.sys.ParametersI()

def getValue(self):
""" Not implemented """
pass
Expand Down Expand Up @@ -5519,22 +5541,7 @@ class TimestampAnnotationWrapper (AnnotationWrapper):
"""

OMERO_TYPE = TimestampAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("TimestampAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from TimestampAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "TimestampAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5574,22 +5581,7 @@ class BooleanAnnotationWrapper (AnnotationWrapper):
"""

OMERO_TYPE = BooleanAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("BooleanAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from BooleanAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "BooleanAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5617,10 +5609,11 @@ def setValue(self, val):

class TagAnnotationWrapper (AnnotationWrapper):
"""
omero_model_BooleanAnnotationI class wrapper extends AnnotationWrapper.
omero_model_TagAnnotationI class wrapper extends AnnotationWrapper.
"""

OMERO_TYPE = TagAnnotationI
OMERO_CLASS = "TagAnnotation"

def countTagsInTagset(self):
# temp solution waiting for #5785
Expand Down Expand Up @@ -5667,22 +5660,6 @@ def listParents(self, withlinks=True):
self._conn, l.parent, l))
return rv

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("TagAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from TagAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()

def getValue(self):
"""
Gets the value of the Tag
Expand Down Expand Up @@ -5714,22 +5691,7 @@ class CommentAnnotationWrapper (AnnotationWrapper):
"""

OMERO_TYPE = CommentAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("CommentAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from CommentAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "CommentAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5760,22 +5722,7 @@ class LongAnnotationWrapper (AnnotationWrapper):
omero_model_LongAnnotationI class wrapper extends AnnotationWrapper.
"""
OMERO_TYPE = LongAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("LongAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from LongAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "LongAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5807,22 +5754,7 @@ class DoubleAnnotationWrapper (AnnotationWrapper):
omero_model_DoubleAnnotationI class wrapper extends AnnotationWrapper.
"""
OMERO_TYPE = DoubleAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("DoubleAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from DoubleAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "DoubleAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5855,22 +5787,7 @@ class TermAnnotationWrapper (AnnotationWrapper):
only in 4.2+
"""
OMERO_TYPE = TermAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("TermAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""
query = ("select obj from TermAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "TermAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -5902,6 +5819,7 @@ class XmlAnnotationWrapper (CommentAnnotationWrapper):
omero_model_XmlAnnotationI class wrapper extends CommentAnnotationWrapper.
"""
OMERO_TYPE = XmlAnnotationI
OMERO_CLASS = "XmlAnnotation"

AnnotationWrapper._register(XmlAnnotationWrapper)

Expand All @@ -5914,23 +5832,7 @@ class MapAnnotationWrapper (AnnotationWrapper):
omero_model_MapAnnotationI class wrapper.
"""
OMERO_TYPE = MapAnnotationI

@classmethod
def _getQueryString(cls, opts=None):
"""
Used for building queries in generic methods such as
getObjects("MapAnnotation").
Returns a tuple of (query, clauses, params).

:param opts: Dictionary of optional parameters.
NB: No options supported for this class.
:return: Tuple of string, list, ParametersI
"""

query = ("select obj from MapAnnotation obj "
"join fetch obj.details.owner as owner "
"join fetch obj.details.creationEvent")
return query, [], omero.sys.ParametersI()
OMERO_CLASS = "MapAnnotation"

def getValue(self):
"""
Expand Down Expand Up @@ -11139,6 +11041,7 @@ def refreshWrappers():
"termannotation": TermAnnotationWrapper,
"timestampannotation": TimestampAnnotationWrapper,
"mapannotation": MapAnnotationWrapper,
"xmlannotation": XmlAnnotationWrapper,
# allows for getObjects("Annotation", ids)
"annotation": AnnotationWrapper._wrap})

Expand Down