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fix datetime writing #106

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merged 3 commits into from
Aug 25, 2021
Merged

fix datetime writing #106

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f49f24b
fix for newer xmlschema
tlambert03 Aug 25, 2021
6a219c9
fix encode dates
tlambert03 Aug 25, 2021
ed3e683
Merge branch 'master' into fixdates
tlambert03 Aug 25, 2021
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7 changes: 4 additions & 3 deletions src/ome_types/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
from xml.etree import ElementTree

import xmlschema
from elementpath.datatypes import DateTime10
from xmlschema import ElementData, XMLSchemaParseError
from xmlschema.converters import XMLSchemaConverter
from xmlschema.documents import XMLSchemaValueError
Expand Down Expand Up @@ -189,7 +188,9 @@ def element_encode(
tag = xsd_element.qualified_name
if not isinstance(obj, OMEType):
if isinstance(obj, datetime):
return ElementData(tag, DateTime10.fromdatetime(obj), None, {})
return ElementData(
tag, obj.isoformat().replace("+00:00", "Z"), None, {}
)
elif isinstance(obj, ElementTree.Element):
# ElementData can't represent mixed content, so we'll leave this
# element empty and fix it up after encoding is complete.
Expand Down Expand Up @@ -241,7 +242,7 @@ def element_encode(
elif isinstance(value, Enum):
value = value.value
elif isinstance(value, datetime):
value = DateTime10.fromdatetime(value)
value = value.isoformat().replace("+00:00", "Z")
attributes[name] = value
elif name == "Value" and xsd_element.local_name in {"BinData", "UUID", "M"}:
text = value
Expand Down
44 changes: 44 additions & 0 deletions testing/data/OverViewScan.ome.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
<?xml version="1.0"?>
<ome:OME xmlns:ome="http://www.openmicroscopy.org/Schemas/OME/2016-06"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
<ome:Plate ID="Plate:1" WellOriginX="0" WellOriginY="0">
<ome:PlateAcquisition ID="PlateAcquisition:1"
StartTime="2016-03-11T10:23:44.925154Z"/>
</ome:Plate>
<ome:Experimenter ID="Experimenter:M1SRH" UserName="M1SRH"/>
<ome:Instrument ID="Instrument:0">
<ome:Microscope Manufacturer="Zeiss" Model="" SerialNumber=""/>
<ome:Filament ID="LightSource:1" Type="Other"/>
<ome:Detector ID="Detector:506m_Intern" Model="Axiocam506m"/>
<ome:Objective ID="Objective:1"/>
</ome:Instrument>
<ome:Image ID="Image:0" Name="TR1">
<ome:AcquisitionDate>2016-03-11T10:23:44.925154Z</ome:AcquisitionDate>
<ome:ObjectiveSettings ID="Objective:1" Medium="Air"
RefractiveIndex="1.000293"/>
<ome:Pixels ID="Pixels:1-0" DimensionOrder="XYZCT" SignificantBits="14"
Type="uint16" SizeX="7398" SizeY="3212" SizeZ="1" SizeC="1"
SizeT="1" PhysicalSizeX="4.5743626119409"
PhysicalSizeXUnit="µm" PhysicalSizeY="4.5743626119409"
PhysicalSizeYUnit="µm">
<ome:Channel ID="Channel:0-0" Name="DAPI"
AcquisitionMode="WideField"
IlluminationType="Epifluorescence"
ExcitationWavelength="353"
ExcitationWavelengthUnit="nm" EmissionWavelength="465"
EmissionWavelengthUnit="nm" Fluor="DAPI">
<ome:DetectorSettings ID="Detector:506m_Intern"
Binning="Other"/>
</ome:Channel>
<ome:TiffData IFD="1"/>
</ome:Pixels>
</ome:Image>
<ome:StructuredAnnotations>
<ome:XMLAnnotation
ID="urn:lsid:allencell.org:Annotation:AcquisitionSoftware">
<ome:Description>ZEN 2 (blue edition)2.3.64.0</ome:Description>
<ome:Value/>
</ome:XMLAnnotation>
</ome:StructuredAnnotations>
</ome:OME>