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populate metadata links file ann #152

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merged 2 commits into from
Dec 19, 2019
Merged

populate metadata links file ann #152

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0bd7e43
link file_ann to object if not linked
will-moore Aug 16, 2019
5956edc
Merge remote-tracking branch 'origin/develop' into populate_metadata_…
will-moore Dec 10, 2019
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25 changes: 23 additions & 2 deletions omero/import_scripts/Populate_Metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,14 +58,34 @@
"""


def get_original_file(conn, object_type, object_id, file_ann_id=None):
def link_file_ann(conn, object_type, object_id, file_ann_id):
"""Link File Annotation to the Object, if not already linked."""
file_ann = conn.getObject("Annotation", file_ann_id)
if file_ann is None:
sys.stderr.write("Error: File Annotation not found: %s.\n"
% file_ann_id)
sys.exit(1)
omero_object = get_object(conn, object_type, object_id)
# Check for existing links
links = list(conn.getAnnotationLinks(object_type, parent_ids=[object_id],
ann_ids=[file_ann_id]))
if len(links) == 0:
omero_object.linkAnnotation(file_ann)


def get_object(conn, object_type, object_id):
if object_type not in OBJECT_TYPES:
sys.stderr.write("Error: Invalid object type: %s.\n" % object_type)
sys.exit(1)
omero_object = conn.getObject(object_type, int(object_id))
if omero_object is None:
sys.stderr.write("Error: %s does not exist.\n" % object_type)
sys.exit(1)
return omero_object


def get_original_file(conn, object_type, object_id, file_ann_id=None):
omero_object = get_object(conn, object_type, object_id)
file_ann = None

for ann in omero_object.listAnnotations():
Expand All @@ -85,10 +105,11 @@ def get_original_file(conn, object_type, object_id, file_ann_id=None):
def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
data_type = script_params["Data_Type"]
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = int(script_params["File_Annotation"])
data_type = script_params["Data_Type"]
link_file_ann(conn, data_type, object_id, file_ann_id)
original_file = get_original_file(
conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
Expand Down