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fbergmann / harmony_scripts

Utility scripts written during HARMONY 2021
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Missing DataSet labels #7

Open luciansmith opened 3 years ago

luciansmith commented 3 years ago

The attached Copasi file generate the attached SED-ML file. In the SED-ML, we have:

    <dataSet id="ds_1_task3" label="k_off_R_G" dataReference="k_off_R_G_1_task3"/>
    <dataSet id="ds_2_task3" label="Rtot" dataReference="Rtot_1_task3"/>
    <dataSet id="ds_3_task3" label="L" dataReference="L_1_task3"/>
    <dataSet id="ds_4_task3" dataReference="_1_task3"/>
    <dataSet id="ds_5_task3" label="tot_LR" dataReference="tot_LR_1_task3"/>

where 'ds_4_task3' doesn't have a label.

Is this an issue with the Copasi file itself, or is it an issue with the generation of the SED-ML from Copasi?

Bush2016-Simplified-Carrousel-model-of-GPCR.sedml.txt Bush2016-Simplified-Carrousel-model-of-GPCR.cps.txt

luciansmith commented 3 years ago

Oh--more fundamentally, the problem is that _1_task3 has no target.

fbergmann commented 3 years ago

this is again a case, where a particle number was requested in the output, and exporting of particle numbers (and rates) is not supported. It could be added for l1v4 or as annotation i suppose.

fbergmann commented 3 years ago

i think for now i leave the items out altogether, issuing a warning. rather than having elements without labels.

luciansmith commented 3 years ago

That sounds good, though it would definitely be nice to see particle numbers in the future, eventually.