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Parametrise disease name #2712

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abhidg opened this issue May 31, 2022 · 4 comments
Closed

Parametrise disease name #2712

abhidg opened this issue May 31, 2022 · 4 comments
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P0: Critical path blocker Blocking testing or the launch critical path, drop everything to investigate & fix
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@abhidg
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abhidg commented May 31, 2022

Parametrise disease name (which is currently set to covid-19) to make it easy to start up new line list instances.

@abhidg abhidg added the P0: Critical path blocker Blocking testing or the launch critical path, drop everything to investigate & fix label May 31, 2022
@abhidg abhidg added this to the Agnes milestone May 31, 2022
@jim-sheldon
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jim-sheldon commented May 31, 2022

This is related to globaldothealth/monkeypox#21. It might be better to work with the script in the Monkeypox repo, since that is almost certainly closer to a Minimum Viable Product.

Which parts of the system does this issue relate to? Depending on how much code needs modification to satisfy the requirements of this issue, it might make more sense to break this into multiple issues.

@abhidg
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abhidg commented May 31, 2022

Both products need parametrization:

  1. One is a transformed dataset from a private Google spreadsheet, with a corresponding map. This dataset should also ideally be behind a ToS/privacy policy and require authentication to access (it's not right now, but there are no substantial differences in the privacy requirements between this and product 2). It'll also have associated map viz. There will be no support for adding additional sources, this product would only be for first N cases (let's say 10000 but could be higher depending on curator availability), this is Turnkey epidemic system monkeypox#21

  2. Product corresponding to this repo, which supports multiple sources and more complex data schemas. The dataset from 1, can be bulk uploaded / inserted as was the case when the COVID-19 line list transitioned.

It's worthwhile to parametrize disease in this repo as well, since we might soon have to support restricted sources / more complex schemas, if not for the current monkeypox outbreak, but for the next pathogen. Partners may also want to try the full-fledged version for something other than COVID-19.

@iamleeg iamleeg modified the milestones: Agnes, Oberon Jun 1, 2022
@iamleeg iamleeg self-assigned this Jun 10, 2022
@iamleeg
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iamleeg commented Jun 10, 2022

Note that it's not just about parameterising the disease name! Other details are also disease specific, e.g. date validation; names of VoCs; perhaps more.

iamleeg added a commit that referenced this issue Jun 13, 2022
If you set the env GDH_URL, we use that

(R users can set this in .Renvironment, apparently)

Otherwise build from the disease/environment you specify.
iamleeg added a commit that referenced this issue Jun 13, 2022
iamleeg added a commit that referenced this issue Jun 13, 2022
iamleeg added a commit that referenced this issue Jun 14, 2022
If you set the env GDH_URL, we use that

(R users can set this in .Renvironment, apparently)

Otherwise build from the disease/environment you specify.
iamleeg added a commit that referenced this issue Jun 14, 2022
iamleeg added a commit that referenced this issue Jun 14, 2022
iamleeg added a commit that referenced this issue Jun 14, 2022
iamleeg added a commit that referenced this issue Jun 14, 2022
iamleeg added a commit that referenced this issue Jun 15, 2022
iamleeg added a commit that referenced this issue Jun 15, 2022
@iamleeg
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iamleeg commented Jun 15, 2022

Calling this done, with the following work covered by other issues:

  1. the database setup script, default database names, data-service model, and OpenAPI schema are all still coupled to the COVID-19 case schema. Issues Implement reusable data service #2714, Configure data export for monkeypox schema #2715, Set up Monkeypox database #2704, and Custom field creator for curator portal #2725 relate to supporting a different database with a different schema.
  2. Terms of Use have some specific citations and statements about the COVID-19 data: these need rewriting anyway (Updated TOU #2675) so we can work out how to load the new terms of use when we have them.

@iamleeg iamleeg closed this as completed Jun 15, 2022
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