Adding ISA-JSON support as input file.#88

Merged

bedroesb merged 63 commits intousegalaxy-eu:masterfrom ELIXIR-Belgium:dev

Dec 18, 2023

+16,576-66

Commits on Sep 22, 2023

Initial push of the ISA JSON parser app
Kevin De Pelseneer
committed
Updated isa_study.py:
Kevin De Pelseneer
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Update test file.
Kevin De Pelseneer
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Add method to dump object in a pandas DataFrame and renamed to Ena Object and Ena study
Kevin De Pelseneer
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Update EnaStudy:
Kevin De Pelseneer
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Commits on Sep 24, 2023

Add other Classes
Kevin De Pelseneer
committed

Commits on Sep 25, 2023

Replaced test ISA Json by one without pooled samples
Kevin De Pelseneer
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Commits on Sep 26, 2023

Add additional objects
Kevin De Pelseneer
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Updated validation
Kevin De Pelseneer
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Implementation of the Ena Samples functionality
Kevin De Pelseneer
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remove init file
Kevin De Pelseneer
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Add documentation
Kevin De Pelseneer
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Commits on Sep 27, 2023

- Implement Submission wrapper object
Kevin De Pelseneer
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Add Test Class for Ena Study
Kevin De Pelseneer
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Renamed read-isa-json folder
Kevin De Pelseneer
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Add init file to the tests folder
Kevin De Pelseneer
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Fix failing tests
Kevin De Pelseneer
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Rename test file to accomodate other class objects
Kevin De Pelseneer
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Add test for reading an ISA JSON and producing studies
Kevin De Pelseneer
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Delete read_isa_json folder and move example script
Kevin De Pelseneer
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Worked on parsing experiment data for ENA submissions
Kevin De Pelseneer
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Commits on Sep 28, 2023

Implement exporting to dataframe
Kevin De Pelseneer
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Change alias prefix of experiments to the samples url. Makes more sense?
Kevin De Pelseneer
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Get sample alias out of the list
Kevin De Pelseneer
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Implementation of Ena Runs
Kevin De Pelseneer
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Implement Submission
Kevin De Pelseneer
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Commits on Sep 29, 2023

Cleaning up classes
Kevin De Pelseneer
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Implement Characteristic class for Ena Sample
Kevin De Pelseneer
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Clean up example script
Kevin De Pelseneer
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Move clip_off_prefix to the common ena_std_lib module.
Kevin De Pelseneer
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Annotation of the classes and modules
Kevin De Pelseneer
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Remove unused imports
Kevin De Pelseneer
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Commits on Oct 3, 2023

Fix typo
Kevin De Pelseneer
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Commits on Oct 11, 2023

Implementation of assay streams for ena runs
Kevin De Pelseneer
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Rearranged EnaSubmission
Kevin De Pelseneer
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Commits on Oct 12, 2023

Prefix is fetched from custom metadata
Kevin De Pelseneer
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Commits on Oct 13, 2023

Sanitize samples + fix sample_alias in experiments
Kevin De Pelseneer
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clean up
Kevin De Pelseneer
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Replace simple dictionary validation by extensive JSON schema validation
Kevin De Pelseneer
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Replace script by jupyter notebook
Kevin De Pelseneer
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Commits on Oct 20, 2023

Restructure isa json support (#1 )
bedroesb
authored
specify pytest version
bedroesb
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Upload simple test case ISA JSON
Kevin De Pelseneer
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Fix simple test case
Kevin De Pelseneer
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Fix experiment alias in runs table
Kevin De Pelseneer
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Commits on Nov 8, 2023

Make run alias the process id instead of sample id for sequencing data with paired library layout
Kevin De Pelseneer
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Fixed typo in example data
Kevin De Pelseneer
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Adapt get_parameter_values for multi-output process
Kevin De Pelseneer
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Move get_parameter_values and fetch_parameters to shared ena_std_lib
Kevin De Pelseneer
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Implementation of ParameterValues for samples
Kevin De Pelseneer
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Commits on Nov 9, 2023

Replace NaN in dataframes by empty string
Kevin De Pelseneer
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Remove example python notebook
kdp-cloud
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Commits on Nov 16, 2023

Commits on Nov 20, 2023

Commits on Dec 15, 2023

doc
bedroesb
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add isa_json
bedroesb
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Commits on Dec 18, 2023