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Expand supported link types #30

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Merged
sbesson merged 2 commits into from
May 20, 2025
Merged

Expand supported link types #30

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9910c04
Expand supported link types
DavidStirling May 7, 2025
58dac72
Add all annotation types, handle capitalisation properly
DavidStirling May 14, 2025
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24 changes: 20 additions & 4 deletions omero2pandas/upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,17 @@
"Screen": omero.model.ScreenI,
"Well": omero.model.WellI,
"Roi": omero.model.RoiI,
"BooleanAnnotation": omero.model.BooleanAnnotationI,
"CommentAnnotation": omero.model.CommentAnnotationI,
"DoubleAnnotation": omero.model.DoubleAnnotationI,
"FileAnnotation": omero.model.FileAnnotationI,
"ListAnnotation": omero.model.ListAnnotationI,
"LongAnnotation": omero.model.LongAnnotationI,
"MapAnnotation": omero.model.MapAnnotationI,
"TagAnnotation": omero.model.TagAnnotationI,
"TermAnnotation": omero.model.TermAnnotationI,
"TimestampAnnotation": omero.model.TimestampAnnotationI,
"XmlAnnotation": omero.model.XmlAnnotationI,
}


Expand Down Expand Up @@ -140,8 +151,9 @@ def generate_omero_columns_csv(csv_path, chunk_size=1000):

def create_table(source, table_name, links, conn, chunk_size):
# Create an OMERO.table and upload data
# Make type case-insensitive
links = [(t.lower().capitalize(), i) for t, i in links]
# Make type case-insensitive, handling annotation caps properly
links = [(t.lower().capitalize().replace("annotation", "Annotation"), i)
for t, i in links]
# Validate link list
working_group = None
roi_only = True
Expand All @@ -151,7 +163,8 @@ def create_table(source, table_name, links, conn, chunk_size):
f"supported as a link target")
if target_type != "Roi":
roi_only = False
target_ob = conn.getObject(target_type, target_id)
target_ob = conn.getQueryService().find(target_type, target_id,
{"omero.group": "-1"})
if target_ob is None:
raise ValueError(f"{target_type} #{target_id} not found")
target_group = target_ob.details.group.id.val
Expand Down Expand Up @@ -225,7 +238,10 @@ def create_table(source, table_name, links, conn, chunk_size):
annotation_obj.id.val, False)
link_buffer = []
for obj_type, obj_id in links:
link_obj = LINK_TYPES[obj_type]()
if "annotation" in obj_type.lower():
link_obj = omero.model.AnnotationAnnotationLinkI()
else:
link_obj = LINK_TYPES[obj_type]()
unloaded_target = OBJECT_TYPES[obj_type](obj_id, False)
link_obj.link(unloaded_target, unloaded_annotation)
link_buffer.append(link_obj)
Expand Down