Code

Add Testing Script#13

Code

Merged

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

+76

Commits

Commits on Sep 20, 2021

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

  nguyenank

  committed
  568794c

• update workflow to have correct command for calling mapper

  nguyenank

  committed
  f3ba66e

Commits on Oct 3, 2021

• try adding link to test repo

  nguyenank

  committed
  af95902

• add runs-on to new test job

  nguyenank

  committed
  3bdc0fe

• update job dependencies, enabled github authentication for private repo

  nguyenank

  committed
  f0a43ce

• explicitly git add file

  nguyenank

  committed
  5181db2

Commits on Oct 4, 2021

• update workflow to use MAPPER_SECRET token

  nguyenank

  committed
  92bbd52

• condense workflow to only test accessing the repository

  nguyenank

  committed
  f98812b

• temporarily remove dependency

  nguyenank

  committed
  dc8a7de

• restore full workflow

  nguyenank

  committed
  02cbc50

• fix nesting

  nguyenank

  committed
  7f0d0ec

Commits on Oct 10, 2021

• update workflow; remove unnecessary files

  nguyenank

  committed
  066ad04

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

  nguyenank

  committed
  9b302f3

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

  nguyenank

  committed
  35670be

• make moving into the tests repo a separate step

  nguyenank

  committed
  3afdc7f

• fix typo

  nguyenank

  committed
  5486413

• update paths

  nguyenank

  committed
  aa2c0fa

• don't use relative path for output

  nguyenank

  committed
  dc8dd5b

• update output file reference

  nguyenank

  committed
  e79a3d3

• wrap output path in quotes

  nguyenank

  committed
  869ea95

• add debug 'ls', refactor git add

  nguyenank

  committed
  5a09805

• fix summary path typo

  nguyenank

  committed
  c4536b1

• update to use working-directory attribute

  nguyenank

  committed
  8f9ef88

• correct typo in sumamry_path var name

  nguyenank

  committed
  a217bf4

• fix formatting on start of row

  nguyenank

  committed
  b3e4b06

Commits on Nov 4, 2021

• set minimum score for mapper tool to 0

  nguyenank

  committed
  38dfcd2

Commits on Feb 7, 2022

• merge in main

  nguyenank

  committed
  108fefe

• update numpy version

  nguyenank

  committed
  1fccdff

• update testing script to run coverage error script

  nguyenank

  committed
  7cf3a43

• t2t.py -> text2term.py

  nguyenank

  committed
  4843594

• fix typo in coverage-script running

  nguyenank

  committed
  27540e1

• test summary.csv

  nguyenank

  committed
  e424d44

• adjust working directory for coverage-erro script

  nguyenank

  committed
  20505a1

• update output path

  nguyenank

  committed
  3c282d6

• debug coverage_error script run error

  nguyenank

  committed
  90d96b6

• update coverage_error script to use new column names

  nguyenank

  committed
  b36a996

Commits on Feb 10, 2022

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

  nguyenank

  committed
  ae4e50d

Commits on Feb 11, 2022

• switch to coverage_one_error script

  nguyenank

  committed
  803db57

Commits on Feb 20, 2022

• test, escaping commas

  nguyenank

  committed
  741c28b

• test 2, now with fixed variable names

  nguyenank

  committed
  6f21f0b

• test 3, with more quote marks

  nguyenank

  committed
  ea3e124

• add escaping, full pipeline

  nguyenank

  committed
  da9ddc6

Commits on Jun 5, 2024

• Merge branch 'main' into task5-workflow

  rsgoncalves

  authored
  0786f8a