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Harvester updates for chemically and freeze-dried algae #440

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kyule opened this issue Apr 16, 2024 · 3 comments
Open

Harvester updates for chemically and freeze-dried algae #440

kyule opened this issue Apr 16, 2024 · 3 comments
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Back End Issue or feature concerning back end of the portal data Data cleaning is needed

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@kyule
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kyule commented Apr 16, 2024

Posting this to document the current state of the microalgae collections data:

We need to ask NEON for collector information.

We should not be traveling around the sample tree for preservative volume, preservative type, sample volume.

We should not be pulling in the taxa for freeze dried. There are none at the level of the sample itself in the API, but we need to prevent the harvester from using the field parent sample where all of the identifications are being published for freeze dried.

The algal_taxonomy tables should be used for taxonomy of the slides when sample_type="diatom" and for the chemically preserved samples otherwise.

Remarks here are actually identification remarks as far as I can tell. Perhaps we can ask NEON to change that sms field.

We need to figure out what to do in situations with multiple chemically preserved or multiple slides listed in the sample tree like this (and see attached file) -- we cannot determine which taxa go in which samples:

neon-samples (9).csv

<style> </style>
ptx_taxonomy_in.slideID WLOU.20180912.EPILITHON.1.TAXONOMY - FRACTION - A
ptx_taxonomy_in.slideID WLOU.20180912.EPILITHON.1.TAXONOMY-SLIDE-A
@kyule kyule added data Data cleaning is needed Back End Issue or feature concerning back end of the portal labels Apr 16, 2024
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kyule commented Sep 20, 2024

Freeze dried algae preparations and remarks fixed by: #567

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kyule commented Sep 21, 2024

FD determinations fixed by #569

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kyule commented Sep 25, 2024

Consider determinations aspect in the context of the subsampler.

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