pennbbl / bids-on-flywheel Goto Github PK

Hi folks--I ran into the error below when trying to extract a csv of project info using query-bids. I'm using Python 2.7.15rc1 on Ubuntu 18.04.02. The output below says the 5 files in my test project directory have no BIDS information, although I did run the BIDS curation gear on them. Not sure whether this is a software issue or an issue with the project data themselves--I'm happy to provide additional info if helpful.

Thanks,

Jeff

$ query-bids -proj BOLD -out BOLD.csv
Connecting to flywheel server...
Querying server...
Processing acquisitions...
100%|██████████| 1/1 [00:00<00:00, 5.53it/s]
Extracting BIDS and MR Classifier information...
100%|██████████| 5/5 [00:00<00:00, 11.79it/s]
Tidying and returning the results...
0 acquisitions could not be processed.
5 acquisitions do not have BIDS information yet.
Traceback (most recent call last):
File "/home/jeff/.local/bin/query-bids", line 11, in
sys.exit(main())
File "/home/jeff/.local/lib/python2.7/site-packages/flywheel_bids_tools/query_bids.py", line 265, in main
query_result.loc[:, drop_downs] = query_result.loc[:, drop_downs].applymap(unlist_item)
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 189, in setitem
indexer = self._get_setitem_indexer(key)
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 167, in _get_setitem_indexer
return self._convert_tuple(key, is_setter=True)
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 248, in _convert_tuple
idx = self._convert_to_indexer(k, axis=i, is_setter=is_setter)
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 1354, in _convert_to_indexer
return self._get_listlike_indexer(obj, axis, **kwargs)[1]
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 1161, in _get_listlike_indexer
raise_missing=raise_missing)
File "/home/jeff/.local/lib/python2.7/site-packages/pandas/core/indexing.py", line 1252, in _validate_read_indexer
raise KeyError("{} not in index".format(not_found))
KeyError: "['classification_Features'] not in index"

I'm trying to identify and fix metadata problems with our legacy data. When trying to upload changes using upload-bids, I get KeyErrors because the "session.label" and "subject.label" fields are not in my csv file. Example error follows.

If I manually add subject.label and session.label to both the original and modified csv files, I then get an exception regarding the info_BIDS_valid column--see the second traceback below. Not sure if this is a problem with my csv files or a code issue, but I'm attaching my modified csv file as a spreadsheet--feedback would be appreciated.

Thanks,

Jeff

##############################

Traceback #1:

$ upload-bids -orig BOLD_20190619.csv -mod BOLD_20190619_mod.csv
Traceback (most recent call last):
File "/usr/local/bin/upload-bids", line 11, in
load_entry_point('flywheel-bids-tools==0.0.11', 'console_scripts', 'upload-bids')()
File "/usr/local/lib/python2.7/site-packages/flywheel_bids_tools/upload_bids.py", line 284, in main
df_original = read_flywheel_csv(args.original)
File "/usr/local/lib/python2.7/site-packages/flywheel_bids_tools/utils.py", line 41, in read_flywheel_csv
df[col] = df[col].astype(str)
File "/usr/local/lib/python2.7/site-packages/pandas/core/frame.py", line 2927, in getitem
indexer = self.columns.get_loc(key)
File "/usr/local/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'session.label'

##############################

Traceback #2:

$ upload-bids -orig BOLD_20190619.csv -mod BOLD_20190619_mod.csv
Traceback (most recent call last):
File "/usr/local/bin/upload-bids", line 11, in
load_entry_point('flywheel-bids-tools==0.0.11', 'console_scripts', 'upload-bids')()
File "/usr/local/lib/python2.7/site-packages/flywheel_bids_tools/upload_bids.py", line 291, in main
res = validate_on_unequal_cells(unequal, df_modified)
File "/usr/local/lib/python2.7/site-packages/flywheel_bids_tools/upload_bids.py", line 165, in validate_on_unequal_cells
changed_df.columns[pair[1]]
File "/usr/local/lib/python2.7/site-packages/flywheel_bids_tools/upload_bids.py", line 147, in change_checker
raise Exception("Column {0} not recognised!".format(column))
Exception: Column info_BIDS_valid not recognised!

BOLD_20190619_mod.xlsx