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Update isa json based on response #37

Merged
merged 25 commits into from
Jun 21, 2024
Merged

Update isa json based on response #37

merged 25 commits into from
Jun 21, 2024

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kdp-cloud
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  • New pydantic Model for the reponse of a target repository.
  • Adds basic functionality to update the ISA JSON file with accessions, based on the response from target repositories.
  • Simplification of the ISA JSON model
  • Implementation of MyPy Type checking

Fixes issue #21

@kdp-cloud
Add response model as a pydantic class
5e0431d
@kdp-cloud
Move models to separate folder
5e7c8df
@kdp-cloud
typo
3a0683a
@kdp-cloud
Add test for reducing ISA JSON for BioSamples
973cb32
@kdp-cloud
Modify for BioSamples
c8a52be
@kdp-cloud
typo
7973c8c
@kdp-cloud
First version of submit_to_biosamples
8795a2e
@kdp-cloud
Add class methods to create a RepositoryResponse from JSON
d6f11f4
@kdp-cloud
Add example repo responses
04a70e1
@kdp-cloud
Get rid of deprecation warnings
53a3571
@kdp-cloud
Add field validator to check for duplicate keys
4623037
@kdp-cloud
Add functionality that updates the ISA-JSON
373ff06
@kdp-cloud
Add test for add accessions to an ISA-JSON that has no accession char…
6b8472a 
…acteristics category
@kdp-cloud
Ignore __init__.py
687a70c
@kdp-cloud
Add functionality if Accession characteristics categories are present
144ccb6
@kdp-cloud
Update accession characteristic if the value is of type OntologyAnnot…
4851fb7 
…ation
@kdp-cloud
Implementing mypy type checking and conforming the current code to mypy
2d3c14c
@kdp-cloud
Linting
306feba
@kdp-cloud
Add type checking to workflow
3820640
@kdp-cloud
whoops!
f62c90b
@kdp-cloud
pass flag to install the Library stubs
dc68dbf
@kdp-cloud
Pass non-interactive flag
30e698b
@kdp-cloud
stricter type annotations
2c3199b
@kdp-cloud kdp-cloud requested a review from bedroesb June 6, 2024 11:36
@kdp-cloud kdp-cloud self-assigned this Jun 6, 2024
@kdp-cloud kdp-cloud linked an issue Jun 6, 2024 that may be closed by this pull request
Receipt reader / Applying accessions to ISA object in memory #21
Closed
@kdp-cloud kdp-cloud marked this pull request as ready for review June 6, 2024 11:52
apriltuesday
apriltuesday approved these changes Jun 20, 2024
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Nice work!

mars-cli/mars_lib/models/repository_response.py Outdated Show resolved Hide resolved
@kdp-cloud
Convert OS env variable to str
dac38e3 
Makes pyright happy!
@kdp-cloud kdp-cloud merged commit f3c745a into main Jun 21, 2024
16 checks passed
@kdp-cloud kdp-cloud deleted the update_isa_json_based_on_response branch June 21, 2024 15:13
@kdp-cloud kdp-cloud removed the request for review from bedroesb June 26, 2024 09:49
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@apriltuesday apriltuesday apriltuesday approved these changes

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Receipt reader / Applying accessions to ISA object in memory
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