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Release 0.14.2

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@terazus terazus released this 13 Feb 16:30
· 11 commits to master since this release
v0.14.2
0af0396

Enhancements and Cleanup:

ISA MODEL

  • The model.py file has been split into the model module. Each class has been split into a dedicated file.
  • Added a method from_dict() to the ISA Investigation class to let users load objects from a dictionary.
  • Added a method to_dict() to each ISA model class that let users dump ISA objects to dictionaries. (also see ISA JSONLD section)
  • Added a new GraphQL interface to ISA investigation (see below querying isa for more information)

ISA TAB

  • The isatab.py file has been split into the isatab module.
    Functions and classes have been split into three submodules: load (to read isatab files), dump (to write isafiles) and validate (to run validation rules against an isatab file). Usage remains the same.
  • The isatab validation pipeline have been reworked to allow the rules set to be extended with user custom rules. Please contact us if you would like to implement your own validation rules.

ISA JSON

  • the isajson.py file has been split into the isajson module.
    Functions and classes have been split into three files: load.py, dump.py and validate.py. Usage remains the same but there is now an alternative using dicts instead of files (see below)
  • load.py and dump.py are now wrappers. The code of the isa json serializer/deserializer has been moved to be part of the ISA model. Users can still use the old load() and dump() methods but are now able to do it directly from an investigation object. Example
from json import load
from isatools.model import Investigation

isa_json_file = 'path/to/isa.json'  # the json file path
with open(isa_json_file, 'r') as f:
    isa_json_input = load(f)  # load the dict from the file
investigation = Investigation()  # create en investigation
investigation.from_dict(isa_json_input)  # feed in the dictionary, will generated missing identifiers make inputs and outputs different
isa_json_output = investigation.to_dict()  # Dump it back to a dict
another_investigation = Investigation()  # create en investigation
another_investigation.from_dict(isa_json_output)  # feed in the dictionary
assert investigation == another_investigation  # assert equality between the created investigations.
assert investigation.to_dict() == another_investigation.to-dict()  # compare to_dict() methods

Note: identifiers may be missing from the json file and autogenerated by the ISA objects. In this case, output dictionnaries won't match which is why the investigation is being compared to another investigation.

ISA JSON-LD

SPARQL querying over ISA:

GRAPHQL querying over ISA:

MTBLS, the EMBL-EBI MetaboLights Client:

  • Refactored the MTBLS client but kept the same functions (and signature) exposed. You can now use MTBLInvestigation instead of the old functions. Example:
from isatools.net.mtbls import MTBLSInvestigation

investigation =  MTBLSInvestigation('MTBLS1')
# This creates a temp dir for the investigation that gets deleted when the object is destroyed through the automatic garbage collector. You can pass a directory if you want to persist the investigation.
investigation =  MTBLSInvestigation(mtbls_id='MTBLS1', output_directory="path/to/output/dir", output_format='tab')

# You can then run all the old function through methods with the same name and chain methods without downloading the whole investigation again.
print(investigation.get_characteristics_summary())
print(investigation.get_factor_names())

ISA SQL:

Other

Versions update:

  • Dropped python 3.6 and 3.7
  • Added compatibility for python 3.10 (production ready)
  • Added compatibility for python 3.11 (test only)
  • Bump numpy, pandas and mzml.

Cookbook

Testing:

  • The application has been further tested with CI, especially the model. Global coverage increased from 75% to 84%.
  • Build time was reduced due to mocking some network operations.

ISA-API performance profiler:

  • Added a small command line interface using cProfile to generate performance reports of different ISA features (in particular serialization and deserialization to tab and json).

Known issues:

  • There is a know performance issue with the coveralls/coverage modules on python 3.11 making the build very slow (see nedbat/coveragepy#1287). Performances for end users shouldn't be affected.

Contributors:

Assets 2