Back end support for pool metrics #224
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nerdstrike
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…between use of id_product in mlwh tables
…ynamic shorten some lines for flake8
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nerdstrike
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lang_qc/db/helper/wells.py
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| well = self.get_mlwh_well_by_product_id(id_product) | ||
| if well: | ||
| product_metrics = well.pac_bio_product_metrics | ||
| if len(product_metrics) == 1: |
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One product might still have a tag and trigger demultiplexing. Let's change to a confition that chacks whether well.demultiplex_mode value contains the Instrument substring.
lang_qc/db/helper/wells.py
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| products=[ | ||
| SampleDeplexingStats( | ||
| id_product=prod.id_pac_bio_product, | ||
| tag1_name=prod.pac_bio_run.tag_identifier, |
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The product table might be not linked to the pac_bio_run table. It is fine to have either nothing or n/a, but @ces asks for a reason to be clearly displayed. I wonder whether a comment field should be added to this object.
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I suppose I should have a deliberately unlinked test case to go with this possibility.
Given that this is a data integrity problem, I wonder whether the right thing to do is to return an error to the client (say catch the exception in the controller) and render something like "data unlinked, inform NPG"? That's more immediately informative than leaving empty holes for them to guess at the significance.
| @@ -77,6 +80,44 @@ def get_mlwh_well_by_product_id( | |||
| ) | |||
| ).scalar_one_or_none() | |||
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| def get_metrics_by_well_product_id( | |||
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Other QC metrics in lang_qc/models/pacbio/qc_data.py have class methods to self-populate themselves. It might be reasonable to move this code to such class method
…o determine whether to run stats or not.
Added a check for unlinked data.
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