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Reproduce issue: schematic CLI submit does not respect -dl parameter
Describe the bug Annotations are being uploaded using the SchemaLabel instead of the displayLabel:
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To Reproduce Steps to reproduce the behavior:
-
schematic model --config ./schematic_config.yml submit -mp NF_Genomics_Assay_Reh_final.csv -vc GenomicsAssayTemplate -d syn29660060 --use_display_label -hb -rr
Expected behavior Final annotations should be camelCase not PascalCase
Priority (select one)
- [x] Minor ⬇️
- [ ] Major 📢
- [ ] Critical 🆘
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(data_curator_env) ➜ testing schematic model --config ./schematic_config.yml submit -mp NF_Genomics_Assay_Reh_final.csv -vc GenomicsAssayTemplate -d syn29660060 --use_display_label -hb -rr
Starting schematic...
The (model > input > location) argument with value 'NF.jsonld' is being read from the config file.
The (model > input > file_type) argument with value 'local' is being read from the config file.
UPGRADE AVAILABLE
A more recent version of the Synapse Client (2.6.0) is available. Your version (2.5.1) can be upgraded by typing:
pip install --upgrade synapseclient
Python Synapse Client version 2.6.0 release notes
https://python-docs.synapse.org/build/html/news.html
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Downloading [####################]100.00% 35.7MB/35.7MB (9.6MB/s) SYNAPSE_TABLE_QUERY_95417761.csv.synapse_download_95417761 Done...
/opt/miniconda3/envs/data_curator_env/lib/python3.9/site-packages/synapseclient/table.py:1968: DtypeWarning: Columns (56) have mixed types.Specify dtype option on import or set low_memory=False.
return _csv_to_pandas_df(self.filepath,
JSON schema successfully generated from schema.org schema!
JSON schema file log stored as /Users/rallaway/Downloads/62ab417dc1b64041806f120bb6061b6c/schematic/log.json
Great Expetations suite will not be utilized.
Uploading [####################]100.00% 75.6kB/75.6kB (45.4kB/s) table.csv Done...
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Uploading file to Synapse storage
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Uploading file to Synapse storage
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Uploading [####################]100.00% 75.6kB/75.6kB (34.8kB/s) NF_Genomics_Assay_Reh_final.csv Done...
Associated manifest file with dataset on Synapse.
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Downloading [####################]100.00% 176.7kB/176.7kB (778.8kB/s) SYNAPSE_TABLE_QUERY_95417772.csv Done...
Uploading [####################]100.00% 152.1kB/152.1kB (83.8kB/s) table.csv Done...
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No validation errors occured during validation.
File at 'NF_Genomics_Assay_Reh_final.csv' was successfully associated with dataset 'syn29660060'.