Adding ISA-JSON support as input file. #88
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added 30 commits
September 22, 2023 15:05
- Initiate IsaStudy directly from isa JSON file - Add typing system - Add Dict validation before creating the IsaStudy object
…ject and Ena study
- Add study alias - Add std module for common functions - Add docstrings
- Add runs and experiments to Study object
* start with nan fix * instrument_model * update templates * updating xml templates * version bump * not everything mandatory * some improvements * unicode problem * encode with utf-8 * add updated templates * update minimal example * update templates * update readme * move structure * update more paths * start with integration * get example working
…a with paired library layout
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@bgruening hey! This feature would allow the tool to parse ISA-JSON making a connection between FAIRDOM-SEEK and ENA. (also possible other platform that export ISA-JSON). The parser creates datatables that can be used by the existing parts of the ENA upload tool. This is a BETA feature though... maybe it will disappear when repositories will except ISA-JSON themselves. Any opinions? |
bgruening
approved these changes
Dec 16, 2023
ena_upload/_version.py
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| @@ -1 +1 @@ | |||
| __version__ = "0.6.3" | |||
| __version__ = "0.6.4" | |||
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That probably justifies a larger version bump.
ena_upload/ena_upload.py
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| @@ -857,6 +876,24 @@ def main(): | |||
| schema_dataframe[schema] = xl_sheet | |||
| path = os.path.dirname(os.path.abspath(xlsx)) | |||
| schema_tables[schema] = f"{path}/ENA_template_{schema}.tsv" | |||
| elif isa_json_file: | |||
| # Read json file | |||
| isa_json = json.load(open(isa_json_file)) | |||
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the file handle is here kept open, maybe use a with open statement?
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@bgruening thanks for spotting! Yes quite a big one @kdp-cloud wrote a nice piece of code, and now all the rest looks very janky 😄 |
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This pull request will add ISA JSON support as input file. This JSON file is generated from FAIRDOM-SEEK. Since an ISA JSON can hold many assay streams, we introduce a new parameter,
isa_assay_streamtogether with theisa_jsonparameter.