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Store the original variant description as the source of the submission #561

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merged 4 commits into from
Oct 5, 2021

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loeswerkman
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Added the source column to the VOG table.

  • Column will be added and filled automatically for new variants.
  • Column will be added for existing variants, and filled automatically where its value can be established

Closes #560
Related to #550

@loeswerkman loeswerkman requested a review from ifokkema October 5, 2021 08:59
@loeswerkman loeswerkman self-assigned this Oct 5, 2021
@loeswerkman loeswerkman changed the base branch from master to release/3.5 October 5, 2021 08:59
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@ifokkema ifokkema left a comment

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A few changes are needed; please see my comments (by accident in Dutch, but oh well). Could you take care of the needed changes?
Additionally, to actually test the code written in inc-upgrade.php and to be able to use this new field, you'll have to increase the version of the code to 3.5-pre-03 as well. You can do this in inc-init.php. Please make that change as well and add it to this branch.
Thanks!

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// Get the ID by its column suffix and give this as the source.
$sID = $_DB->query(
'SELECT id FROM ' . TABLE_GENOME_BUILDS .
'WHERE column_suffix = ?', array($sColumnSuffix))->fetchColumn();
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Not sure how this is possible, but there is another space missing. I thought we tested this code - this should have caused a query error. Anyway, I'll fix it.

- SQL is prettier and easier to read when aligned.
- Since I already forgot an implementation detail, better document it.
@ifokkema ifokkema merged commit 53e22a7 into release/3.5 Oct 5, 2021
@ifokkema ifokkema deleted the gb/sourceVariant branch October 5, 2021 13:13
@ifokkema ifokkema changed the title Gb/source variant Store the original variant description as the source of the submission Oct 5, 2021
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Store genome build or transcript on which the variant was found.
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