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Escape n3 triples to deal with multiline issues #24

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merged 1 commit into from
Dec 4, 2024

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joshmoore
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@andrawaag has been running into issues with various parsers due to the newlines in literals:

http://www.openmicroscopy.org/rdf/2016-06/ome_core/Value      """<SegmentDefinition>
          <Name>example</Name>
          ...
        </SegmentDefinition>""" .

Based on:

<http://www.openmicroscopy.org/rdf/2016-06/ome_core/Value>      """<ChannelThresholds>\n          <RoiName>012</RoiName>\n 

If this is not sufficient, then we may need to create a Graph object very frequently and use the .serialize() method.

@joshmoore
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Merging for release in the 0.5.x line for testing during https://www.denbi.de/de-nbi-events/1678-biohackathon-germany-3

If it needs reverting, we can do that quickly (and/or put it behind an option)

@joshmoore joshmoore merged commit 9473b99 into German-BioImaging:main Dec 4, 2024
@joshmoore joshmoore deleted the escaping branch December 4, 2024 10:36
@joshmoore
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joshmoore commented Dec 6, 2024

A heads up that this apparently is failing for graphDB on the micro symbol

image

_:N601882e7d0f24751893771b77ef8b624     http://www.openmicroscopy.org/rdf/2016-06/ome_core/Symbol     "\xb5m"

@andrawaag
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I am not sure if this issue is related. That microsymbol is not part of a multiline triple, but a proper triple where graphDB is complaining about the escape sequencing.
The quick (and dirty) fix where "\xb5m" is changed into "xb5m"

seem to have "solved" it

@joshmoore
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That's fine. I think it more points to what's being used for escaping. I out then together in #28 since I think we'll need graphDB in the testing mix.

Cc @CFGrote

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