'sample_id' is hard coded in as a field in virtual_db.py

[cmatKhan]

at line 593

tfbpapi/tfbpapi/virtual_db.py

Line 593 in 21f6511

raw = list(dict.fromkeys(["sample_id"] + meta_cols + prop_raw_cols))

and 595

tfbpapi/tfbpapi/virtual_db.py

Line 595 in 21f6511

raw = list(dict.fromkeys(["sample_id"] + prop_raw_cols))

the hard coded value "sample_id" is being added to the list of fields in the construction of the sql cmd that creates a view from the config in virtual_db.py.

This should be set to the field identified by the sample_id in the config, not hard coded.

This config

repositories:
  BrentLab/callingcards:
    regulator_locus_tag:
      field: regulator_locus_tag
    regulator_symbol:
      field: regulator_symbol
    carbon_source:
      path: experimental_conditions.media.carbon_source.compound
    temperature_celsius:
      path: experimental_conditions.temperature_celsius
    dataset:
      # binding
      annotated_features:
        db_name: cc_replicate_db
        sample_id: 
          field: id
      annotated_features_combined:
        db_name: cc_combined_db
        sample_id:
          field: genome_map_id_set
      annotated_features_orig_reprocess:
        db_name: cc_replicate_repro
        sample_id:
          field: id
        carbon_source:
          field: condition
          path: media.carbon_source.compound
...

produces this error

---------------------------------------------------------------------------
BinderException                           Traceback (most recent call last)
Cell In[4], [line 3](vscode-notebook-cell:?execution_count=4&line=3)
      1 # List all registered views
      2 print("Registered views:")
----> [3](vscode-notebook-cell:?execution_count=4&line=3) for name in vdb.tables():
      4     print(f"  {name}")

File ~/code/tfbp/tfbpapi/tfbpapi/virtual_db.py:315, in VirtualDB.tables(self)
    308 def tables(self) -> list[str]:
    309     """
    310     Return sorted list of registered view names.
    311 
    312     :return: Sorted list of view names
    313 
    314     """
--> [315](https://file+.vscode-resource.vscode-cdn.net/home/chase/code/tfbp/tfbpapi/tmp/~/code/tfbp/tfbpapi/tfbpapi/virtual_db.py:315)     self._ensure_sql_views()
    316     return sorted(self._list_views())

File ~/code/tfbp/tfbpapi/tfbpapi/virtual_db.py:402, in VirtualDB._ensure_sql_views(self)
    400     return
    401 self._conn = duckdb.connect(":memory:")
--> [402](https://file+.vscode-resource.vscode-cdn.net/home/chase/code/tfbp/tfbpapi/tmp/~/code/tfbp/tfbpapi/tfbpapi/virtual_db.py:402) self._register_all_views()
    403 self._views_registered = True
...
BinderException: Binder Error: Referenced column "sample_id" not found in FROM clause!
Candidate bindings: "callingcards_enrichment", "target_symbol"

LINE 1: ...ource, 'room' AS temperature_celsius FROM (SELECT DISTINCT sample_id, regulator_locus_tag, regulator_symbol FROM __cc_...
                                                                      ^
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?d9e4bee4-09e2-4062-b482-db0939036d84) or open in a [text editor](command:workbench.action.openLargeOutput?d9e4bee4-09e2-4062-b482-db0939036d84). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

[cmatKhan]

tfbpapi/tfbpapi/virtual_db.py

Line 680 in 21f6511

config = card.get_config(config_name)

Another problem: in _resolve_metadata_fields, it does not return the metadata fields on a dataset (callingcards/annotated_features) whose metadata fields are NOT embedded (callingcards references a separate metadata parquet file)