Code

Add Testing Script#13

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Merged

rsgoncalves merged 43 commits intomainccb-hms/ontology-mapper:mainfrom task5-workflowccb-hms/ontology-mapper:task5-workflowCopy head branch name to clipboardJun 5, 2024

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Commits

Commits on Sep 20, 2021

• set up initial workflow to run UK Biobank terms through mapper

  nguyenank

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• update workflow to have correct command for calling mapper

  nguyenank

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  f3ba66e

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Commits on Oct 3, 2021

• try adding link to test repo

  nguyenank

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• add runs-on to new test job

  nguyenank

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  3bdc0fe

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• update job dependencies, enabled github authentication for private repo

  nguyenank

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  f0a43ce

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• explicitly git add file

  nguyenank

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  5181db2

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Commits on Oct 4, 2021

• update workflow to use MAPPER_SECRET token

  nguyenank

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  92bbd52

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• condense workflow to only test accessing the repository

  nguyenank

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  f98812b

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• temporarily remove dependency

  nguyenank

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  dc8a7de

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• restore full workflow

  nguyenank

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  02cbc50

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• fix nesting

  nguyenank

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  7f0d0ec

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Commits on Oct 10, 2021

• update workflow; remove unnecessary files

  nguyenank

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  066ad04

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• update workflow so repos are nested rather than side-by-side

  nguyenank

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  9b302f3

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• change reference to test repo and add debug 'ls'

  nguyenank

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  35670be

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• make moving into the tests repo a separate step

  nguyenank

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  3afdc7f

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• fix typo

  nguyenank

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  5486413

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• update paths

  nguyenank

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  aa2c0fa

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• don't use relative path for output

  nguyenank

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  dc8dd5b

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• update output file reference

  nguyenank

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  e79a3d3

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• wrap output path in quotes

  nguyenank

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  869ea95

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• add debug 'ls', refactor git add

  nguyenank

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  5a09805

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• fix summary path typo

  nguyenank

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  c4536b1

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• update to use working-directory attribute

  nguyenank

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  8f9ef88

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• correct typo in sumamry_path var name

  nguyenank

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  a217bf4

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• fix formatting on start of row

  nguyenank

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  b3e4b06

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Commits on Nov 4, 2021

• set minimum score for mapper tool to 0

  nguyenank

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Commits on Feb 7, 2022

• merge in main

  nguyenank

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  108fefe

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• update numpy version

  nguyenank

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  1fccdff

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• update testing script to run coverage error script

  nguyenank

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  7cf3a43

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• t2t.py -> text2term.py

  nguyenank

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  4843594

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• fix typo in coverage-script running

  nguyenank

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  27540e1

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• test summary.csv

  nguyenank

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  e424d44

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• adjust working directory for coverage-erro script

  nguyenank

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  20505a1

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• update output path

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  3c282d6

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• debug coverage_error script run error

  nguyenank

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  90d96b6

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• update coverage_error script to use new column names

  nguyenank

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Commits on Feb 10, 2022

• add UK Biobank EFO owl version and one error and commit message

  nguyenank

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Commits on Feb 11, 2022

• switch to coverage_one_error script

  nguyenank

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Commits on Feb 20, 2022

• test, escaping commas

  nguyenank

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• test 2, now with fixed variable names

  nguyenank

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  6f21f0b

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• test 3, with more quote marks

  nguyenank

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• add escaping, full pipeline

  nguyenank

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Commits on Jun 5, 2024

• Merge branch 'main' into task5-workflow

  rsgoncalves

  authored
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