Code

61 change code systems for data model#66

Code

Merged

aslgraefe merged 93 commits intodevelopBIH-CEI/rarelink:developfrom 61-change-code-systems-for-data-modelBIH-CEI/rarelink:61-change-code-systems-for-data-modelCopy head branch name to clipboardSep 25, 2024

+2,839-943

Commits

Commits on Sep 23, 2024

• update

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  23e2778

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• started phenopacketpipeline dev

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  c95be7f

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• update

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• added template for function

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• update

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• updated data dictionary

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• edited init for imports

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• updates

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• defined todos for phenoapcket pipeline

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• old test del

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• uncommented codesystems for test

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• edited import for resources

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• updated code systems . py with only versions

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• fixed bugs and added all column mappings

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• added todo for preproccess redcap for phenopacket pipeline function

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• typo

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• fix init

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• fixed snomed import

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• fixed snomed_ct

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• fixed smomed ct

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  5e6e8d2

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• added imports

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• fixed import

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• fix def phenopacket pipeline

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• fiox

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• typos

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• fix

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• fix

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• fix testing

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Commits on Sep 24, 2024

• updated copryright and authors

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  a26fd09

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• import rarelink cdm

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• added repetition of sections for data model

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• fixed patient status not repetitive

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• update lining fix

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• fixed gene label

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• added gene label vs

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  74a4626

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• updated mapping

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• new version phenopacket mapper

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• update pipeline

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  0adb25d

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• fix indentation

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• fixed cdm repeating elements

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• edited disease single ones

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• updated genomic diagnosis double

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• addded repeating modifiers

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• added repeating to pipeline

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• import s

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  9b5a31c

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• fix

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  fe12bef

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• fix

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• updated pipeline

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• update pipeline

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• update init

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• renamed file

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• updated import

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• updated preprocessing value sets

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  9fd52c7

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• updated name

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  2f3d7b9

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• commented out

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• added TODO in pipeliine

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• added another TODO

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Commits on Sep 25, 2024

• import phenopackets and fix

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• updated diseasses and ph features

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• uncommenteed for now

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• update zygosity function

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• added functions and import

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• updates

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• addedd class multiple_fields

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• added multiple field sclass

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  db1e469

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• added rarelink_cdm_phenopacket_mapping function

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• update

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• edits

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• edit

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• edit

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• fix

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• edot

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• edit

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• fix

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• fix

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• fixes

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• fix

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• fix

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• fix

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• clean up

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• change function

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• fix

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• changed name back

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• fix

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• fix

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• edit

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• try

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• fix

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• updates

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• added and edited 5 test patients

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• updated test data

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