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Fix rule and check.#524

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ptth222 wants to merge 98 commits intoISA-tools:developISA-tools/isa-api:developfrom ptth222:ontology-source-check-fixptth222/isa-api:ontology-source-check-fixCopy head branch name to clipboard

+25,582-1,109

Commits

Commits on Nov 6, 2023

• should fix issue 511

  proccaserra

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  c9859d4

Commits on Nov 10, 2023

• corrections, test passing (new test)

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  195cf71

• minor edit

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  34f9291

Commits on Nov 12, 2023

• fixes issue ISA-tools#512

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  2f489f5

• fixes issue ISA-tools#512

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  034291f

Commits on Nov 15, 2023

• adding a test to check if comments on assay declaration are properly serialized in isatab2json conversion

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  818332d

• fixes issue ISA-tools#506 - updating to ols4

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  324bcd4

Commits on Nov 20, 2023

• minor fix to test

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  1ec71db

Commits on Jan 30, 2024

• Fix rule and check.

  Show description for 1e88823
  ptth222

  committed
  1e88823

Commits on Feb 4, 2024

• several fixes related to TAB and JSON serialization but resolution incomplete, WIP

  proccaserra

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  2bf8347

Commits on Feb 8, 2024

• fixing outstanding roundtrip issues object , documenting in notebook

  proccaserra

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  a9a75ea

Commits on Feb 11, 2024

• minor revisions

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  8a6870c

• Merge branch 'develop' into issue-511

  proccaserra

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  2d692db

• Merge branch 'develop' into issue-511

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  e108bb9

Commits on Feb 12, 2024

• refactoring

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  3fe7b5f

• fixing linting

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  4f2d76d

• removed unnecessary condition

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  03d6e8b

• add name to process

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  79f9a8e

• minor change

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  d5edfd5

• refactor convert value

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  1b4e937

• reformat arrays, TODO: move to constant.py

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  8694f53

• fixing assay import

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  30969df

• fixing constructor

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  5d03523

• removing print statement

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  07ae789

Commits on Feb 14, 2024

• linting

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  b1d770c

• full test coverage for pubmed.py

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  3e70aa1

Commits on Feb 19, 2024

• refactoring & moving arrays defining valid ISA-Tab fields from isatab writer to constant.py

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  9707b82

• reworking Comments on class and adding line at end of file

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  52b0f6b

• setting default value to Comment to empty strings rather than None, linting

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  9f13021

• linting

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  290ac60

• linting & adding a todo

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  c478357

• linting & end of file empty line

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  7756895

• linting

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  88f43cb

• linting

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  b9d185b

• linting

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  d1529ce

• linting

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  04c5ade

• adding docstrings, linting, and adding 2 functions to deal with checksum

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  b330257

• linting

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  07dcdc3

• linting

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  4ad3fbe

• refactoring ISA-TAB field headers to constants.py, fixing import, linting

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  6b250e0

• linting

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  ab93449

• refactor defautls ISA-Tab fields to constants.py, linting

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  2d2464b

• refactor defautls ISA-Tab fields to constants.py, linting

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  57fc39e

• refactor defautls ISA-Tab fields to constants.py, linting

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  ef1af3f

• linting

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  e293d79

• linting

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  6faedb6

• linting

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  35fda9c

• linting

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  8ee180f

• linting and docstring

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  c435846

• linting

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  fd62efe

• linting and docstring

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  080dbf3

• linting and docstring

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  cd1103e

• linting and docstring

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  c2b5dad

• linting and docstring

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  97e9b1c

• linting and docstring

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  ed5325d

• linting

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  fca2799

• adding missing import for OntologySource

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  b38dc2b

• linting and minor corrections such variable renaming

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  e06c22e

• adding new tests to augment coverage or refining existing ones

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  0955a5e

• linting

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  7407f05

• minor corrections to functions invoked in tests

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  6a548d1

Commits on Feb 21, 2024

• simplifying statement to if c.category:

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  23e02a8

• correction to protocol type in chain definition

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  c536f20

• removing superfluous test following refactor

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  f9254c0

• removing needless indentation

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  1615bf3

• removing json validation from test to avoid time out but issue-537

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  9b2479b

• reinstating indentation for test when using with and context

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  691c447

• uncommented tear down and changing process_sequence count in test (check is needed)

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  68322f6

Commits on Feb 23, 2024

• removing commented code

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  bb85e75

• using format() instead of + for consistency

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  f5eb964

• use assertion

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  d16568c

• minor edit

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  8f80615

• simplifying test, reverting

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  156c9de

• adding empty line at end of file

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  e8eebc7

• removing Array Design REF from _LABELS_ASSAY_NODES to keep tests from test_isatab.py unchanged, added a TODO for reform tests

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  7c41650

• implementing a guard on c.category to reduce indentation

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  aac5dc3

• reset old value following the change to constants.py

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  a3badef

• deleting commented old code

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  dfad022

• reactivating test which was timing out, fixes issue ISA-tools#537

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  a7f2836

• moving import statement, removing commented code

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  8bebd8f

• fixing docstrings

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  1844b15

• typo in docstring, issue 542 created for a refactoring

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  0bef66d

• linting

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  c259347

• linting

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  82a200b

• adding raises error type to docstring

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  dc650b1

• overwrite

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  f9fcaa5

• adding docstrings

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  1ee43e7

• removing commented code

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  1aa9ac1

• simplifying test in if statement

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  044f3a0

• nothing

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  b0a2172

• fix to file extension check

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  dd83f75

• removing unused import, add eof line

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  701b2ae

• linting

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  9c8f559

• more linting

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  62b3e4f

• removing print statement

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  5b936f0

• linting

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  f175d94

• fixing formatting;

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  dbfa307

Commits on Mar 1, 2024

• Merge branch 'issue-511' into ontology-source-check-fix

  terazus

  authored
  9a5fb86