[BUG] Search Results Load Example Data

[singjc]

  File "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/massdash/massdash/gui.py", line 154, in main
    show_search_results_analysis.main()
  File "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/massdash/massdash/server/SearchResultsAnalysisServer.py", line 106, in main
    search_results_access_dict = self.load_search_result_entries(self.massseer_gui.file_input_settings.feature_file_entries)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/streamlit/runtime/caching/cache_utils.py", line 212, in wrapper
    return cached_func(*args, **kwargs)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/streamlit/runtime/caching/cache_utils.py", line 241, in __call__
    return self._get_or_create_cached_value(args, kwargs)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/streamlit/runtime/caching/cache_utils.py", line 267, in _get_or_create_cached_value
    return self._handle_cache_miss(cache, value_key, func_args, func_kwargs)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/streamlit/runtime/caching/cache_utils.py", line 321, in _handle_cache_miss
    computed_value = self._info.func(*func_args, **func_kwargs)
  File "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/massdash/massdash/server/SearchResultsAnalysisServer.py", line 51, in load_search_result_entries
    data_access = OSWDataAccess(entry_data['search_results_file_path'], mode='gui')
  File "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/massdash/massdash/loaders/access/OSWDataAccess.py", line 76, in __init__
    self._initializePeptideHashtable()
  File "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/massdash/massdash/loaders/access/OSWDataAccess.py", line 103, in _initializePeptideHashtable
    tmp = pd.read_sql(stmt, self.conn)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/pandas/io/sql.py", line 564, in read_sql
    return pandas_sql.read_query(
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/pandas/io/sql.py", line 2078, in read_query
    cursor = self.execute(*args)
  File "/home/justincsing/anaconda3/envs/py39/lib/python3.9/site-packages/pandas/io/sql.py", line 2030, in execute
    raise ex from exc
pandas.errors.DatabaseError: Execution failed on sql '
            SELECT MODIFIED_SEQUENCE, CHARGE, PRECURSOR_ID 
            FROM PRECURSOR
            INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
            INNER JOIN PEPTIDE ON PEPTIDE.ID = PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID': file is not a database

This seems to occur because the downloaded OSW test file is not actually an sqlite osw file

$ head /home/justincsing/Downloads/massdash_example_dataset//test.osw
{"payload":{"allShortcutsEnabled":false,"fileTree":{"test/test_data/example_dia/openswath/osw":{"items":[{"name":"test.osw","path":"test/test_data/example_dia/openswath/osw/test.osw","contentType":"file"}],"totalCount":1},"test/test_data/example_dia/openswath":{"items":[{"name":"lib","path":"test/test_data/example_dia/openswath/lib","contentType":"directory"},{"name":"osw","path":"test/test_data/example_dia/openswath/osw","contentType":"directory"},{"name":"xics","path":"test/test_data/example_dia/openswath/xics","contentType":"directory"}],"totalCount":3},"test/test_data/example_dia":{"items":[{"name":"diann","path":"test/test_data/example_dia/diann","contentType":"directory"},{"name":"dreamdia","path":"test/test_data/example_dia/dreamdia","contentType":"directory"},{"name":"openswath","path":"test/test_data/example_dia/openswath","contentType":"directory"},{"name":"raw","path":"test/test_data/example_dia/raw","contentType":"directory"}],"totalCount":4},"test/test_data":{"items":[{"name":"diann","path":"test/test_data/diann","contentType":"directory"},{"name":"example_dia","pat

$ file /home/justincsing/Downloads/massdash_example_dataset//test.osw
/home/justincsing/Downloads/massdash_example_dataset//test.osw: JSON data

Similarly for the dreamdia test example

$ file /home/justincsing/Downloads/massdash_example_dataset//test_dreamdia_report.tsv 
/home/justincsing/Downloads/massdash_example_dataset//test_dreamdia_report.tsv: JSON data