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Reproduce issue: schematic CLI submit does not respect -dl parameter

Open allaway opened this issue 2 years ago • 1 comments

Describe the bug Annotations are being uploaded using the SchemaLabel instead of the displayLabel:

Screen Shot 2022-05-20 at 2 22 35 PM

To Reproduce Steps to reproduce the behavior:

  1. 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 🆘

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (if applicable, please complete the following information):

  • OS: [e.g. iOS]
  • Browser [e.g. chrome, safari]
  • Version [e.g. 22]
(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

 [####################]100.00%   1/1   Done...
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...
 [####################]100.00%   1/1   Done...
    
##################################################
 Uploading file to Synapse storage 
##################################################


##################################################
 Uploading file to Synapse storage 
##################################################

Uploading [####################]100.00%   75.6kB/75.6kB (34.8kB/s) NF_Genomics_Assay_Reh_final.csv Done...
    Associated manifest file with dataset on Synapse.
 [####################]100.00%   1/1   Done...
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...
 [####################]100.00%   1/1   Done...
    No validation errors occured during validation.
File at 'NF_Genomics_Assay_Reh_final.csv' was successfully associated with dataset 'syn29660060'.

allaway avatar May 20 '22 21:05 allaway