[Gnumed-bugs] EMR > Search all EMRs unhandled exception searching on 'thyroid'

[Busser, James]

Despite that the dialog prompts to use a regex expression, it is unclear 
whether a raw string is also intended to be handled.

I inputted

        thyroid

and triggered the following.

1) is there any idea of wanting to support (accept) such a simple string?

2) if yes, how would a regex be distinguished? Should it be single quoted?

-- Jim

(excerpt from log follows)


2011-10-31 19:20:33  DEBUG     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::get_raw_connection()
 #1410): new database connection, backend PID: 45034, readonly: False
2011-10-31 19:20:33  DEBUG     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::get_raw_connection()
 #1449): access mode [READ WRITE]
2011-10-31 19:20:33  DEBUG     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::get_connection()
 #1511): client string encoding [UTF8], isolation level [serializable], time 
zone [America/Dawson]
2011-10-31 19:20:33  ERROR     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::get_connection()
 #1535): cannot set bytea_output format
2011-10-31 19:20:39  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #153): just before switching notebook tabs
2011-10-31 19:20:39  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #161): event.GetOldSelection()=3* -> event.GetSelection()=2
2011-10-31 19:20:39  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #207): just after switching notebook tabs
2011-10-31 19:20:39  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #213): event.GetOldSelection()=3 -> event.GetSelection()=2*
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #153): just before switching notebook tabs
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #161): event.GetOldSelection()=1* -> event.GetSelection()=2
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #164): the following two should match but do not:
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #165):  event.GetOldSelection(): 1
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #166):  notebook.GetSelection(): 2
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #207): just after switching notebook tabs
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #213): event.GetOldSelection()=1 -> event.GetSelection()=2*
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #216): those two really *should* match:
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #217):  wx.Notebook.GetSelection() (before switch) : 2
2011-10-31 19:35:09  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #218):  EVT_NOTEBOOK_PAGE_CHANGED.GetOldSelection(): 1
2011-10-31 19:35:10  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #153): just before switching notebook tabs
2011-10-31 19:35:10  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #161): event.GetOldSelection()=2* -> event.GetSelection()=0
2011-10-31 19:35:10  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #207): just after switching notebook tabs
2011-10-31 19:35:10  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #213): event.GetOldSelection()=2 -> event.GetSelection()=0*
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #153): just before switching notebook tabs
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #161): event.GetOldSelection()=0* -> event.GetSelection()=2
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #164): the following two should match but do not:
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #165):  event.GetOldSelection(): 0
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changing()
 #166):  notebook.GetSelection(): 2
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #207): just after switching notebook tabs
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #213): event.GetOldSelection()=0 -> event.GetSelection()=2*
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #216): those two really *should* match:
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #217):  wx.Notebook.GetSelection() (before switch) : 2
2011-10-31 19:35:11  DEBUG     gm.ui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmHorstSpace.py::_on_notebook_page_changed()
 #218):  EVT_NOTEBOOK_PAGE_CHANGED.GetOldSelection(): 0
2011-10-31 19:35:34  ERROR     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::run_ro_queries()
 #1161): query failed: [select * from clin.v_narrative4search where narrative 
~* E'thyroid' order by pk_patient limit 1000]
2011-10-31 19:35:34  ERROR     gm.db 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py::run_ro_queries()
 #1162): PG status message: 
2011-10-31 19:35:34  DEBUG     gm.gui 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmExceptionHandlingWidgets.py::handle_uncaught_exception_wx()
 #152): unhandled exception caught:
Traceback (most recent call last):
  File "/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmGuiMain.py", 
line 2505, in __on_search_across_emrs
    gmNarrativeWidgets.search_narrative_across_emrs(parent=self)
  File 
"/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/wxpython/gmNarrativeWidgets.py",
 line 248, in search_narrative_across_emrs
    results = gmClinNarrative.search_text_across_emrs(search_term = term)
  File 
"/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/business/gmClinNarrative.py", 
line 200, in search_text_across_emrs
    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'term': 
search_term}}], get_col_idx = False)
  File "/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmPG2.py", 
line 1149, in run_ro_queries
    curs.execute(query['cmd'], args)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/psycopg2/extras.py",
 line 121, in execute
    return _cursor.execute(self, query, vars)
ProgrammingError: relation "clin.v_narrative4search" does not exist
LINE 1: select * from clin.v_narrative4search where narrative ~* E't...
                      ^

2011-10-31 19:35:34  DEBUG     gm.cfg 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmCfg2.py::get() 
#314): option [internal::debug] found in source [internal]
2011-10-31 19:35:34  DEBUG     gm.logging 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmLog2.py::log_stack_trace()
 #148): stack trace follows:
2011-10-31 19:35:34  DEBUG     gm.logging 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmLog2.py::log_stack_trace()
 #149): (locals by frame, outmost frame first)
2011-10-31 19:35:34  DEBUG     gm.logging 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmLog2.py::log_stack_trace()
 #155): >>> execution frame [<module>] in [gnumed.py] at line 549 <<<
2011-10-31 19:35:34  DEBUG     gm.logging 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmLog2.py::log_stack_trace()
 #170): _known_short_options = h?V
2011-10-31 19:35:34  DEBUG     gm.logging 
(/Users/djb/Downloads/gnumed-client.1.1.0/Gnumed/pycommon/gmLog2.py::log_stack_trace()
 #170):      no_config_files = 

(done)
-- Jim