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Add Auto header detection to Populate_Metadata.py #232

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Add Auto header detection to Populate_Metadata.py #232

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6214991
Added auto header detection
muhanadz Mar 26, 2024
98fb078
Merge branch 'ome:develop' into auto_header
muhanadz Jul 17, 2026
e190baa
fix regression issues
muhanadz Jul 17, 2026
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26 changes: 24 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 @@ -34,8 +34,12 @@

try:
# Hopefully this will import
# https://github.com/ome/omero-metadata/blob/v0.3.1/src/populate_metadata.py
# Automatic header detection requires omero-metadata >= 0.11.0.

@sbesson sbesson Aug 4, 2026

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Given the modern Python requirements (Python 3.10+), I wonder if we want to start using importlib.metadata for introspecting the package version and packaging for checking a minimal version

>>> from importlib.metadata import version
>>> from packaging.version import Version
>>> version('omero_metadata')
'0.13.0'
>>> Version(version('omero_metadata')) >= Version('0.11')
True
>>> Version(version('omero_metadata')) >= Version('0.14')
False
>>>

from omero_metadata.populate import ParsingContext
try:
from omero_metadata.cli import MetadataControl
except ImportError:
MetadataControl = None
OBJECT_TYPES = (
'Plate',
'Screen',
Expand All @@ -47,6 +51,7 @@

except ImportError:
from omero.util.populate_metadata import ParsingContext
MetadataControl = None
OBJECT_TYPES = (
'Plate',
'Screen',
Expand Down Expand Up @@ -107,6 +112,7 @@ def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
data_type = script_params["Data_Type"]
allow_nan = script_params["Allow_NaN"]

if data_type == "Image":
try:
Expand All @@ -129,7 +135,19 @@ def populate_metadata(client, conn, script_params):
return "Please upgrade omero-py to 5.9.1 or later"
objecti = getattr(omero.model, data_type + 'I')
omero_object = objecti(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
if MetadataControl is not None and \
hasattr(MetadataControl, "detect_headers"):
header_type = None
with open(temp_name, 'rt', encoding='utf-8-sig') as csv_file:
first_row = csv_file.readline()
if "# header" not in first_row:
header_type = MetadataControl.detect_headers(
temp_name, keep_default_na=allow_nan)
ctx = ParsingContext(
client, omero_object, "", column_types=header_type,
allow_nan=allow_nan)
else:
ctx = ParsingContext(client, omero_object, "")

try:
if hasattr(ctx, "parse_from_handle"):
Expand Down Expand Up @@ -172,6 +190,10 @@ def run_script():
"File_Annotation", grouping="3",
description="File Annotation ID containing metadata to populate. "
"Note this is not the same as the File ID."),
scripts.Bool(
"Allow_NaN", grouping="3",
description="Allow Numeric NaN values in the table.",
default=True),

authors=["Emil Rozbicki", "OME Team"],
institutions=["Glencoe Software Inc."],
Expand Down
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