ISA-tools/isa-api

Issues

• in isatab.dump.write.py, error not caught in flatten() method

  #569 opened 3 months ago by proccaserra
  0

• mock pubmed API call in test

  #557 opened 3 months ago by proccaserra
  0

• sra_to_isatab_batch_convert from the develop branch does not work

  #568 opened 4 months ago by tbrittoborges
  0

• Add new test to catch plink related issue when serializing to TAB

  #566 opened 4 months ago by proccaserra
  1

• Upgrading to Python 3.12

  #562 opened 5 months ago by knirirr
  0

• create a repository under ISA-tools organisation for all ISA JSON-LD contexts

  #485 opened 5 months ago by proccaserra
  1

• "Performer" field missing

  #497 opened 5 months ago by proccaserra
  1

• Unable to install isatools due to PyYAML build failure

  #498 opened 5 months ago by JeremyLeland
  4

• OLS3->OLS4 update

  #506 opened 5 months ago by proccaserra
  1

• Comments[] attached to assays aren't serialized

  #511 opened 5 months ago by proccaserra
  2

• rewrite test for test_get_ontology in test_isatools_utils.py

  #528 opened 5 months ago by proccaserra
  1

• Installation Before Testing

  #544 opened 5 months ago by ptth222
  1

• Test deprecation messages

  #563 opened 5 months ago by knirirr
  0

• ISA configurations & ISA-JSON

  #559 opened 7 months ago by proccaserra
  0

• Test Data Validation Changes

  #558 opened 8 months ago by ptth222
  1

• Inconsistencies Between Code, Documentation, and Schema

  #534 opened 10 months ago by ptth222
  5

• derives_from relation on Material

  #545 opened 9 months ago by proccaserra
  0

• ISA-JSON validation error for JSON from createSimpleJSON documentation

  #480 opened 2 years ago by Hannah-Doerpholz
  2

• implement a guard in material.py

  #543 opened 10 months ago by proccaserra
  0

• refactoring needed in assay_templates.py to properly handle Ontology Source

  #542 opened 10 months ago by proccaserra
  0

• rewrite more atomic tests for Process sequence to elucidate counts of events

  #541 opened 10 months ago by proccaserra
  0

• Required Fields In Investigation XML Config

  #540 opened 10 months ago by ptth222
  0

• feature request: have a attribute (Characteristics[] or Measurement[]) on Assay Name

  #473 opened 2 years ago by proccaserra
  3

• investigation why magetab2json on MEXP31 can not complete isa.json validation following refactor

  #537 opened 10 months ago by proccaserra
  0

• documentation needed for requesting new context files for ISA

  #536 opened 10 months ago by proccaserra
  0

• in datafile.py, ensure checkum_value can not be site if checksum_type is not specified

  #535 opened 10 months ago by proccaserra
  0

• ISA Validation Configurations Too Restrictive

  #520 opened a year ago by ptth222
  5

• Characteristic values are recast as string in ISA tab

  #523 opened a year ago by terazus
  0

• ISA Tab Validation Rule Exception Messaging

  #522 opened a year ago by ptth222
  1

• copy function invoked by json2isatab converter has side effects

  #516 opened a year ago by proccaserra
  0

• Add new tests to check serialization to TAB/JSON of Quantitative Values with Units (for Characterististics. FV, PV)

  #518 opened a year ago by proccaserra
  1

• ISA converter - use of default configuration - update needed to cope with new assay definitions

  #517 opened a year ago by proccaserra
  0

• ISATAB serialization: effect of presence/absence to "Term Source REF" "Term Accession" on parsing

  #515 opened a year ago by proccaserra
  0

• Multiple Data Files of The Same Type Will Only Have 1 Name in Assay Conversion

  #509 opened a year ago by ptth222
  2

• Labeled Extract silently dropped from ISA JSON serialization if Label not declared

  #513 opened a year ago by proccaserra
  0

• create a helper function to compute checksums for all 'Data File' objects

  #512 opened a year ago by proccaserra
  0

• allow more than one identifier for ISA.Study

  #508 opened a year ago by proccaserra
  0

• Are Multiple "<entity> Name" Columns Allowed?

  #500 opened a year ago by ptth222
  3

• Unable to generate ISA-Tab files for a study and associated assays

  #503 opened a year ago by dkstayko
  0

• Different Protocol Names In Study Sequence Cause An Error

  #501 opened a year ago by ptth222
  0

• make clear that the readthedocs page is outdated

  #486 opened 2 years ago by glyg
  5

• Typo in publication name shown in README.md

  #496 opened 2 years ago by djcomlab
  0

• 0.13.0 installation error

  #487 opened 2 years ago by jundahuang9123
  4

• [TODO] Tasks for release

  #469 opened 2 years ago by terazus
  0

• Wikidata namespace(s)

  #481 opened 2 years ago by egonw
  1

• ImportError: cannot import name 'soft_unicode' from 'markupsafe'

  #476 opened 2 years ago by erlefloch
  5

• comment_schema.json is different depending on the source

  #483 opened 2 years ago by rabuono
  4

• Create a Data File Header Definition format referenceable form ISA Assay Tables.

  #475 opened 2 years ago by proccaserra
  1

• feature request: allows serialization of ISA-Tab to MS Excel

  #474 opened 2 years ago by proccaserra
  0

• pandas incompatibility (isatools bioconda distribution)

  #462 opened 2 years ago by vedina
  6