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Draft attempt at ingestion using mapping file #24

Merged
merged 21 commits into from
May 29, 2024
Merged

Draft attempt at ingestion using mapping file #24

merged 21 commits into from
May 29, 2024

Commits on May 13, 2024

  1. Draft attempt at ingestion using mapping file 

    - Reads data into class then back out again, probably not very efficient.
- Not tested with multiple rows of input data
- Can't cope with multiple columns trying to set the same variable (need logic in mapping file for this)
    @pipliggins
    pipliggins committed May 13, 2024
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  2. Ignore duplicate keys if values are the same

    @pipliggins
    pipliggins committed May 13, 2024
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  3. Improve single row 1:1 test without output comparison

    @pipliggins
    pipliggins committed May 13, 2024
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Commits on May 14, 2024

  1. Multiple rows of encounter can be read in & out

    @pipliggins
    pipliggins committed May 14, 2024
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  2. Draft one-to-many conversion for observation

    @pipliggins
    pipliggins committed May 14, 2024
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Commits on May 15, 2024

  1. Update overwritten cleanup() func in remaining classes

    @pipliggins
    pipliggins committed May 15, 2024
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  2. Start condensing ingestion code

    @pipliggins
    pipliggins committed May 15, 2024
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  3. Create generic data conversion function for users

    @pipliggins
    pipliggins committed May 15, 2024
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  4. Remove load_data functions

    @pipliggins
    pipliggins committed May 15, 2024
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  5. Make fhirflat installable

    @pipliggins
    pipliggins committed May 15, 2024
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  6. Allow mappings from google sheets

    @pipliggins
    pipliggins committed May 15, 2024
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  7. Update test workflow for package

    @pipliggins
    pipliggins committed May 15, 2024
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Commits on May 17, 2024

  1. Allow lists to be created during ingestion. 

    Backbone elements converted to full FHIR to be written out as *_dense.
Add ID to Encounter resource
    @pipliggins
    pipliggins committed May 17, 2024
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Commits on May 20, 2024

  1. Improve references

    @pipliggins
    pipliggins committed May 20, 2024
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  2. Add race extension

    @pipliggins
    pipliggins committed May 20, 2024
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  3. Misc fixes, add presenceAbsence and prespecifiedQuery extensions

    @pipliggins
    pipliggins committed May 20, 2024
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Commits on May 22, 2024

  1. Misc updates, now passes private checks on dengue data subset

    @pipliggins
    pipliggins committed May 22, 2024
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  2. Fix some typehinting errors

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    pipliggins committed May 22, 2024
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  3. Update init file

    @pipliggins
    pipliggins committed May 22, 2024
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  4. Update some relative imports and fix different types test warning

    @pipliggins
    pipliggins committed May 22, 2024
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Commits on May 23, 2024

  1. Fix more types

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    pipliggins committed May 23, 2024
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