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Adding Support for different CSV Encodings in Import_Scripts/Populate_Metadata.py #198

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Adding Support for different CSV Encodings in Import_Scripts/Populate_Metadata.py #198

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3ccb2a5
Added support for different csv encodings in Populate_Metadata.py. Re…
JulianHn Mar 28, 2022
10f73a0
Added Test for latin-1 and cp1252 encoding in Populate_Metadata.py
JulianHn Mar 28, 2022
e21a065
Added try-except block around the get_original_file_data() code to pr…
JulianHn Jun 2, 2022
f75a8a4
Rewrote encoding test case to check all available encodings on the ma…
JulianHn Jun 2, 2022
9921b3a
Added checks for correct omero-py version, that support encodings dif…
JulianHn Jun 2, 2022
779cfd5
Change detection of omero-py version over to a method that directly
JulianHn Jun 3, 2022
3627a2a
Added skip condition to encoding test, if omero-py does not support it
JulianHn Jun 3, 2022
2490122
Keep encoding variable untouched in populate_metadata if EncSup = False
JulianHn Jun 3, 2022
dc54b13
Fixed pytest complaints except two of the "line too long" PEP8ify
JulianHn Jun 7, 2022
7f8e019
More flake8 fixes
JulianHn Jun 7, 2022
074acba
Fixed flake8 messages except for some line too longs, that are caused…
JulianHn Jun 7, 2022
a971f2f
Added try/except to catch the type-error thrown by Populate_Metadata.…
JulianHn Jun 7, 2022
b1b92a3
Added try around the string creation facility to skip test cases
JulianHn Jun 7, 2022
0d8672e
More flake8 fixes
JulianHn Jun 7, 2022
9055d76
More flake8 fixes
JulianHn Jun 7, 2022
c322eb4
Changed Caught Exception type, as omero-py upstream changed
JulianHn Jun 7, 2022
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11 changes: 9 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 @@ -107,7 +107,7 @@ def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
data_type = script_params["Data_Type"]

encoding = script_params["CSV Encoding"]
if data_type == "Image":
try:
from omero_metadata.populate import ImageWrapper # noqa: F401
Expand All @@ -120,7 +120,7 @@ def populate_metadata(client, conn, script_params):
original_file = get_original_file(
conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
data_for_preprocessing = provider.get_original_file_data(original_file)
data_for_preprocessing = provider.get_original_file_data(original_file, encoding=encoding)
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presumably this line fails if you use the wrong encoding? Or only if you use utf-8?
A try/except that returns a useful message (and/or prints it to stdout) could be helpful?

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Unfortunately no. I discovered this issue because one of our clients was using german Umlauts in their iso-8859-1 encoded CSV, which indeed raise an UnicodeDecodeError at this position. Unfortunately this does not hold true, if it would be the other way around, i.e. specifying 'iso-8859-1' on a Unicode encoded CSV. This will not return an error, but the string is non-sensical. I presume that this can lead to failures down the line in the script (e.g. when the image name is not correct due to the mis-read string), but it could also just lead to nonsensical annotations.
I'm not sure, how one would go about catching this behaviour in general.

You can see the effect for yourself with this test code:

test_str = 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZäöüÄÖÜ'

test_str.encode('latin-1').decode('utf-8')
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 52: invalid continuation byte

test.encode('utf-8').decode('latin-1')
> 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZäöüÃ\x84Ã\x96Ã\x9c'

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OK, so it's not guaranteed to fail, but if it does raise a UnicodeDecodeError that could be worth catching?

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Sure. I will try to find ways to break the other encodings as well and check what kind of errors they will give. Might not be 100% but better catching some of the errors than none.

temp_name = data_for_preprocessing.name
# 5.9.1 returns NamedTempFile where name is a string.
if isinstance(temp_name, int):
Expand Down Expand Up @@ -172,6 +172,13 @@ 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.String(
"CSV Encoding", grouping="4",
description="""Encoding of the CSV File provided. Can depend on your system locale
as well as the program used to generate the CSV File. E.g. Excel defaults to machine specific
ANSI encoding during export to CSV (i.e. cp1252 on US machines, iso-8859-1 on german machines ...).""",
default="utf-8"),

authors=["Emil Rozbicki", "OME Team"],
institutions=["Glencoe Software Inc."],
Expand Down
104 changes: 104 additions & 0 deletions test/integration/test_import_scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,3 +124,107 @@ def test_populate_metadata_for_screen(self):
assert message is not None
assert message.getValue().startswith('Table data populated')
conn.close()

def test_populate_metadata_for_cp1252(self):
sid = super(TestImportScripts, self).get_script(populate_metadata)
assert sid > 0

client, user = self.new_client_and_user()
update_service = client.getSession().getUpdateService()
plates = self.import_plates(client, plate_cols=3, plate_rows=1)
plate = plates[0]
name = plate.name.val
screen = omero.model.ScreenI()
screen.name = omero.rtypes.rstring("test_for_cp1252")
spl = omero.model.ScreenPlateLinkI()
spl.setParent(screen)
spl.setChild(plate)
spl = update_service.saveAndReturnObject(spl)
screen_id = spl.getParent().id.val
assert screen_id > 0
assert spl.getChild().id.val == plate.id.val

cvs_file = create_path("test_cp1252", ".csv")

# create a file annotation
with open(cvs_file.abspath(), 'wb+') as f:
f.write("Well,Plate, Well Type, Facility-Salt-Batch-ID\n".encode("cp1252"))
f.write(("A01,%s,Treatment,FOOL10041-101-2\n" % name).encode("cp1252"))
f.write(("A02,%s,Control,\n" % name).encode("cp1252"))
f.write(("A03,%s,Treatment,FOOL10041-101-2\n" % name).encode("cp1252"))

conn = BlitzGateway(client_obj=client)
fa = conn.createFileAnnfromLocalFile(cvs_file, mimetype="text/csv")
assert fa is not None
assert fa.id > 0
link = omero.model.ScreenAnnotationLinkI()
link.setParent(omero.model.ScreenI(screen_id, False))
link.setChild(omero.model.FileAnnotationI(fa.id, False))
link = update_service.saveAndReturnObject(link)
assert link.id.val > 0
# run the script
screen_ids = []
screen_ids.append(spl.getParent().id)

args = {
"Data_Type": omero.rtypes.rstring("Screen"),
"IDs": omero.rtypes.rlist(screen_ids),
"File_Annotation": omero.rtypes.rstring(str(fa.id)),
"CSV Encoding": omero.rtypes.rstring(str("cp1252"))
}
message = run_script(client, sid, args, "Message")
assert message is not None
assert message.getValue().startswith('Table data populated')
conn.close()

def test_populate_metadata_for_iso8859(self):
sid = super(TestImportScripts, self).get_script(populate_metadata)
assert sid > 0

client, user = self.new_client_and_user()
update_service = client.getSession().getUpdateService()
plates = self.import_plates(client, plate_cols=3, plate_rows=1)
plate = plates[0]
name = plate.name.val
screen = omero.model.ScreenI()
screen.name = omero.rtypes.rstring("test_for_iso8859")
spl = omero.model.ScreenPlateLinkI()
spl.setParent(screen)
spl.setChild(plate)
spl = update_service.saveAndReturnObject(spl)
screen_id = spl.getParent().id.val
assert screen_id > 0
assert spl.getChild().id.val == plate.id.val

cvs_file = create_path("test_iso8859", ".csv")

# create a file annotation
with open(cvs_file.abspath(), 'wb+') as f:
f.write("Well,Plate, Well Type, Facility-Salt-Batch-ID\n".encode("iso-8859-1"))
f.write(("A01,%s,Treatment,FOOL10041-101-2\n" % name).encode("iso-8859-1"))
f.write(("A02,%s,Control,\n" % name).encode("iso-8859-1"))
f.write(("A03,%s,Treatment,FOOL10041-101-2\n" % name).encode("iso-8859-1"))

conn = BlitzGateway(client_obj=client)
fa = conn.createFileAnnfromLocalFile(cvs_file, mimetype="text/csv")
assert fa is not None
assert fa.id > 0
link = omero.model.ScreenAnnotationLinkI()
link.setParent(omero.model.ScreenI(screen_id, False))
link.setChild(omero.model.FileAnnotationI(fa.id, False))
link = update_service.saveAndReturnObject(link)
assert link.id.val > 0
# run the script
screen_ids = []
screen_ids.append(spl.getParent().id)

args = {
"Data_Type": omero.rtypes.rstring("Screen"),
"IDs": omero.rtypes.rlist(screen_ids),
"File_Annotation": omero.rtypes.rstring(str(fa.id)),
"CSV Encoding": omero.rtypes.rstring(str("iso-8859-1"))
}
message = run_script(client, sid, args, "Message")
assert message is not None
assert message.getValue().startswith('Table data populated')
conn.close()