ISA-tools/isa-api

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ISA tools API

Stars: 48
Forks: 42
Open beginner issues: 0
Indexed issues: 42

Dominant language: Python
License: No license data
Last GitHub push: Jul 23, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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42 open issues indexed

design descriptor section parsing issue if n>128 Open

ISA-tools/isa-api#622 · 1 assignee · Opened May 22, 2026
update context_url in json2jsonld.py Open

bug

ISA-tools/isa-api#613 · 1 assignee · Opened Feb 10, 2026
unused variables in json2jsonld.py code Open

clean-up

ISA-tools/isa-api#610 · 2 assignees · Opened Feb 6, 2026
ISA-TAB writer and column order for 'Normalisation Name', 'Data Transformation Name', 'Derived Data File' Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ISA-tools/isa-api#602 · Opened Nov 10, 2025
if Ontology Name evaluates to a Number by Pandas, ISA parsing fails Open

enhancement

ISA-tools/isa-api#587 · 1 assignee · Opened Oct 16, 2025
AttributeError 'pkgutil' again Python 3.13 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ISA-tools/isa-api#581 · Opened Jul 21, 2025
ISA configurations & ISA-JSON Open

discussion required documentation enhancement

ISA-tools/isa-api#559 · 1 assignee · Opened Apr 29, 2024
Test Data Validation Changes Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ISA-tools/isa-api#558 · 1 comment · Opened Mar 29, 2024
implement a guard in material.py Open

enhancement

ISA-tools/isa-api#543 · 1 assignee · Opened Feb 23, 2024
refactoring needed in assay_templates.py to properly handle Ontology Source Open

enhancement

ISA-tools/isa-api#542 · 1 assignee · Opened Feb 23, 2024
rewrite more atomic tests for Process sequence to elucidate counts of events Open

ISA-tools/isa-api#541 · 1 assignee · Opened Feb 23, 2024
investigation why magetab2json on MEXP31 can not complete isa.json validation following refactor Open

bug

ISA-tools/isa-api#537 · 1 assignee · Opened Feb 21, 2024
documentation needed for requesting new context files for ISA Open

documentation

ISA-tools/isa-api#536 · 1 assignee · Opened Feb 19, 2024
in datafile.py, ensure checkum_value can not be set if checksum_type is not specified Open

enhancement

ISA-tools/isa-api#535 · 1 assignee · Opened Feb 19, 2024
Inconsistencies Between Code, Documentation, and Schema Open

ISA-tools/isa-api#534 · 5 comments · 2 assignees · Opened Feb 16, 2024
ISA Tab Validation Rule Exception Messaging Open

ISA-tools/isa-api#522 · 1 comment · 2 assignees · Opened Jan 23, 2024
Add new tests to check serialization to TAB/JSON of Quantitative Values with Units (for Characterististics. FV, PV) Open

documentation enhancement

ISA-tools/isa-api#518 · 1 comment · 1 assignee · Opened Jan 8, 2024
ISA converter - use of default configuration - update needed to cope with new assay definitions Open

blocker bug documentation

ISA-tools/isa-api#517 · 1 assignee · Opened Jan 8, 2024
copy function invoked by json2isatab converter has side effects Open

documentation enhancement

ISA-tools/isa-api#516 · 1 assignee · Opened Dec 18, 2023
ISATAB serialization: effect of presence/absence to "Term Source REF" "Term Accession" on parsing Open

documentation

ISA-tools/isa-api#515 · 1 assignee · Opened Dec 18, 2023
Labeled Extract silently dropped from ISA JSON serialization if Label not declared Open

bug

ISA-tools/isa-api#513 · 1 assignee · Opened Nov 10, 2023
create a helper function to compute checksums for all 'Data File' objects Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ISA-tools/isa-api#512 · Opened Nov 2, 2023
Multiple Data Files of The Same Type Will Only Have 1 Name in Assay Conversion Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

ISA-tools/isa-api#509 · 2 comments · Opened Nov 1, 2023
allow more than one identifier for ISA.Study Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ISA-tools/isa-api#508 · Opened Oct 31, 2023
Different Protocol Names In Study Sequence Cause An Error Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

ISA-tools/isa-api#501 · Opened Aug 28, 2023
Are Multiple "<entity> Name" Columns Allowed? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ISA-tools/isa-api#500 · 3 comments · Opened Aug 28, 2023
make clear that the readthedocs page is outdated Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

ISA-tools/isa-api#486 · 5 comments · Opened Dec 21, 2022
ISA-JSON validation error for JSON from createSimpleJSON documentation Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ISA-tools/isa-api#480 · 2 comments · Opened Nov 28, 2022
ImportError: cannot import name 'soft_unicode' from 'markupsafe' Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

ISA-tools/isa-api#476 · 5 comments · Opened Nov 9, 2022
Create a Data File Header Definition format referenceable form ISA Assay Tables. Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

ISA-tools/isa-api#475 · 1 comment · Opened Nov 8, 2022
feature request: allows serialization of ISA-Tab to MS Excel Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

ISA-tools/isa-api#474 · Opened Nov 8, 2022
feature request: have a attribute (Characteristics[] or Measurement[]) on Assay Name Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

ISA-tools/isa-api#473 · 3 comments · Opened Nov 8, 2022
Refactor isatab deprecated functions for galaxy Open

clean-up

ISA-tools/isa-api#461 · 2 assignees · Opened Sep 21, 2022
review open branches Open

high priority

ISA-tools/isa-api#442 · 1 assignee · Opened Feb 22, 2022
Organise requirements by alphabetic order Open

ISA-tools/isa-api#439 · 1 assignee · Opened Feb 18, 2022
isatab.validate does not return a failure of rule 1003 during validation Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

ISA-tools/isa-api#437 · Opened Feb 11, 2022
checking for duplicate characteristics throws a warning unduly Open

ISA-tools/isa-api#411 · 1 assignee · Opened Aug 6, 2021
Using ISA-API render more flexible /easier to create custom "configuration file" ? Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

ISA-tools/isa-api#393 · 1 comment · Opened Mar 24, 2021
Add support for "Image Data File" Open

enhancement new feature

ISA-tools/isa-api#375 · 1 comment · 1 assignee · Opened Nov 20, 2020
Add Code Contributor Guidelines (covering coding style and process + examples) Open

doc low priority

ISA-tools/isa-api#316 · 1 comment · 1 assignee · Opened Aug 13, 2018
Add function to remove protocols declared but not used Open

enhancement low priority new feature

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ISA-tools/isa-api#279 · Opened Nov 22, 2017
sra2isa conversion: add support for SRA Pool/Pool_Member representation Open

bug convert low priority

ISA-tools/isa-api#153 · 1 assignee · Opened Oct 13, 2016

ISA-tools/isa-api

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