Code

Develop#29

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pnrobinson merged 31 commits intomainmonarch-initiative/oncopacket:mainfrom developmonarch-initiative/oncopacket:developCopy head branch name to clipboardNov 16, 2023

+540-344

Commits

Commits on Sep 25, 2023

• test set up to address path issue

  pnrobinson

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  803d486

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• Ignore pkl files

  

  Justin Reese

  committed
  4d9c384

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• Add lung ingest python script

  

  Justin Reese

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  6d3e855

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• Change code to always set taxonomy to Human

  

  Justin Reese

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  673636c

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• Add neoplasm disease when disease is empty, while processing mutations

  

  Justin Reese

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  426814c

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• Add arg to increase batch size when download all the things

  

  Justin Reese

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  538ea02

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• Add code to check for mutations in phenopackets (no dice)

  

  Justin Reese

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  068105a

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• Fix things so we are adding mutations to phenopackets

  

  Justin Reese

  committed
  b4ed929

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• fixing diagnosis mapper

  pnrobinson

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  9f8a8a0

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• Run tests for PRs on develop

  

  Justin Reese

  committed
  a2df42c

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• Fix tests

  

  Justin Reese

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  6b46168

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• fixing diagnosis mapper

  pnrobinson

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• adding tsv inclusion in pyproject.toml

  pnrobinson

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  80bda5e

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• Merge pull request #24 from monarch-initiative/op_diagnosis_mapper_test

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  justaddcoffee

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  e65ea47

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• Merge branch 'develop' into fix_ingest

  

  Justin Reese

  committed
  a7ba356

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• Fix test

  

  Justin Reese

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  79c6cad

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• Delete unused imports

  

  Justin Reese

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  a79f8d4

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• Fix (maybe) import of TSV for tests

  

  Justin Reese

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  08aa549

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• Merge pull request #23 from monarch-initiative/fix_ingest

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  justaddcoffee

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  2800927

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• Write out phenopackets in run_lung.py

  

  Justin Reese

  committed
  56e41f8

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• Write out phenopackets in run_lung.py

  

  Justin Reese

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  f90359c

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• Merge branch 'develop' of https://github.com/monarch-initiative/c2p into develop

  

  Justin Reese

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  7a3571a

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• adding more tsv diagnosis codes for cervical cancer

  pnrobinson

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  13d93b0

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• Fix duplicated disease entries

  

  Justin Reese

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  2deb134

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• Merge pull request #25 from monarch-initiative/more_diagnosis_codes

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  justaddcoffee

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• Do not add the disease with the same id twice.

  ielis

  committed
  5837825

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• Merge pull request #26 from monarch-initiative/fix_duplicated_disease_entries

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  ielis

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Commits on Sep 26, 2023

• Fix cache files so caches for different queries don't clobber each other

  

  Justin Reese

  committed
  25c84e1

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• Merge pull request #27 from monarch-initiative/better_cache_filename

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  justaddcoffee

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Commits on Nov 16, 2023

• mkdocs

  pnrobinson

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• documentation

  pnrobinson

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