Open dlogan opened 10 years ago
See also the email between Carolina, Anne and Lee on November 8, 2013 regarding this very same issue.
This one is pretty clear:
The measurements XML file has an XML element,
The user supplied the ImageIndex XML file, here in the proper subfolder: https://imageweb.broadinstitute.org/imaging/docs/People/David/Forum/Columbus%20index%20files/
When I run this, I get the error below. I told the user to remove the space character in "Alexa 488" and replace it with an underscore. Hopefully that fixes it.
Traceback (most recent call last):
File "cpa.py", line 522, in <module>
app = CPAnalyst(redirect=False)
File "/usr/local/lib/wxPython-unicode-2.8.12.1/lib/python2.7/site-packages/wx-2.8-mac-unicode/wx/_core.py", line 7981, in __init__
self._BootstrapApp()
File "/usr/local/lib/wxPython-unicode-2.8.12.1/lib/python2.7/site-packages/wx-2.8-mac-unicode/wx/_core.py", line 7555, in _BootstrapApp
return _core_.PyApp__BootstrapApp(*args, **kwargs)
File "cpa.py", line 440, in OnInit
if not show_load_dialog():
File "/Users/dlogan/github/CellProfiler-Analyst/cpa/guiutils.py", line 809, in show_load_dialog
load_columbus(filename)
File "/Users/dlogan/github/CellProfiler-Analyst/cpa/parseperkinelmer.py", line 115, in load_columbus
create_per_image_table(plates, channels, imagesets, image_dir)
File "/Users/dlogan/github/CellProfiler-Analyst/cpa/parseperkinelmer.py", line 268, in create_per_image_table
%(', '.join(col+' '+typ for col, typ in col_defs)))
File "/Users/dlogan/github/CellProfiler-Analyst/cpa/dbconnect.py", line 64, in fn
return f(db, *args, **kwargs)
File "/Users/dlogan/github/CellProfiler-Analyst/cpa/dbconnect.py", line 512, in execute
'\nSecond exception was: %s'%(connID, query, e, e2))
dbconnect.DBException: ERROR: Database query failed for connection "MainThread" and failed to reconnect
Query was: "CREATE TABLE per_image (ImageNumber INTEGER, Plate TEXT, Well VARCHAR(3), FieldID INTEGER, PlaneID INTEGER, TimepointID INTEGER, PlateColumns TEXT, PlateRows TEXT, Name TEXT, MeasurementStartTime TEXT, PlateTypeName TEXT, MeasurementID TEXT, Image_File_DAPI TEXT, Image_File_Alexa 488 TEXT, Image_Path_DAPI TEXT, Image_Path_Alexa 488 TEXT)"
First exception was: near "488": syntax error
Second exception was: ERROR: Database query failed for connection "MainThread"
Query was: "CREATE TABLE per_image (ImageNumber INTEGER, Plate TEXT, Well VARCHAR(3), FieldID INTEGER, PlaneID INTEGER, TimepointID INTEGER, PlateColumns TEXT, PlateRows TEXT, Name TEXT, MeasurementStartTime TEXT, PlateTypeName TEXT, MeasurementID TEXT, Image_File_DAPI TEXT, Image_File_Alexa 488 TEXT, Image_Path_DAPI TEXT, Image_Path_Alexa 488 TEXT)"
Exception was: near "488": syntax error
Fortunately, spaces in names are expressly forbidden in CP 2.1.
That is a very good thing! ... though here CPA is reading in Columbus XML files not supplied by CP (afaik). So unfortunately we can't force an input standard in this odd case :/
This came from a Forum user who also works with Carolina at SciLife I believe (Jordi). This is the Forum issue: http://www.cellprofiler.org/forum/viewtopic.php?f=12&t=3378#p10082
When I load the provided MeasurementIndex.ColumbusIDX.xml file into CPA instead of the properties file, I get this error below, indicating to me that the path is not being parsed properly:
Attachments: http://cellprofiler.org/issues/uploaded/6JJvDo/MeasurementIndex.ColumbusIDX.xml