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Clean up annotation unique ID logic #98

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Merged
erickmartins merged 1 commit into from
Apr 15, 2025
Merged

Clean up annotation unique ID logic #98

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58 changes: 12 additions & 46 deletions src/generate_xml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,6 @@
import shutil
import copy

ann_count = 0


def create_proj_and_ref(**kwargs) -> Tuple[Project, ProjectRef]:
proj = Project(**kwargs)
Expand Down Expand Up @@ -365,7 +363,6 @@ def create_filepath_annotations(id: str, conn: BlitzGateway,
proj: Optional[str] = None,
) -> Tuple[List[XMLAnnotation],
List[AnnotationRef]]:
global ann_count
ns = 'openmicroscopy.org/cli/transfer'
anns = []
anrefs = []
Expand All @@ -389,12 +386,8 @@ def create_filepath_annotations(id: str, conn: BlitzGateway,
common_root = Path(common_root) / proj / ds
path = os.path.join(common_root, 'mock_folder')
xml = create_path_xml(path)
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)
else:
if simple:
Expand All @@ -405,78 +398,53 @@ def create_filepath_annotations(id: str, conn: BlitzGateway,
filename = Path(f).name
f = Path(common_root) / proj / ds / filename
xml = create_path_xml(str(f))
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)
else:
f = f'pixel_images/{clean_id}.tiff'
if simple:
f = f'{clean_id}.tiff'
f = Path(common_root) / proj / ds / f
xml = create_path_xml(str(f))
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)
xml = create_path_xml(str(f))
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)

elif fp_type == "Annotation":
filename = str(Path(filename).name)
f = f'file_annotations/{clean_id}/{filename}'
xml = create_path_xml(str(f))
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)
elif fp_type == "Plate":
xml = create_path_xml(plate_path)
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
anns.append(an)
ann_count += 1
anref = AnnotationRef(id=an.id)
anrefs.append(anref)
return anns, anrefs


def create_figure_annotations(id: str) -> Tuple[XMLAnnotation,
AnnotationRef]:
ns = id
global ann_count
clean_id = int(ns.split(":")[-1])
f = f'figures/Figure_{clean_id}.json'
xml = create_path_xml(str(f))
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
ann_count += 1
return (an, anref)
an, anref = create_xml_and_ref(namespace=ns, value=xml)
return an, anref


def create_provenance_metadata(conn: BlitzGateway, img_id: int,
hostname: str,
metadata: Union[List[str], None], plate: bool
) -> Union[Tuple[MapAnnotation, AnnotationRef],
Tuple[None, None]]:
global ann_count
if not metadata:
return None, None
software = "omero-cli-transfer"
Expand Down Expand Up @@ -511,10 +479,7 @@ def create_provenance_metadata(conn: BlitzGateway, img_id: int,
if "db_id" in metadata:
md_dict['database_id'] = db_id
xml = create_metadata_xml(md_dict)
an, anref = create_xml_and_ref(id=ann_count,
namespace=ns,
value=xml)
ann_count += 1
an, anref = create_xml_and_ref(namespace=ns, value=xml)
return an, anref


Expand Down Expand Up @@ -984,8 +949,9 @@ def populate_xml(datatype: str, id: int, filepath: str, conn: BlitzGateway,
hostname: str, barchive: bool, simple: bool, figure: bool,
metadata: List[str]) -> Tuple[OME, dict]:
ome = OME()
global ann_count
ann_count = uuid4().int >> 64
# Create a throw-away annotation so we can reset the auto-id-numbering to a
# very high random value.
CommentAnnotation(id=uuid4().int >> 64, value="")
obj = conn.getObject(datatype, id)
if datatype == 'Project':
populate_project(obj, ome, conn, hostname, metadata, simple)
Expand Down