Example5 - AIDA AIF

[angelosalatino]

Dear authors, I am bumping into an issue while running the Example5 - AIDA AIF notebook. In particular, I am running everything on Binder. I managed to get to the section "Let's make a file that has one entity per row".

When I run:

entities = pd.read_csv("sample_data/aida/results/HC00001DO.entities.labels.tsv", delimiter='\t')
entities

I get the following error. Can you help me debugging this?

---------------------------------------------------------------------------
EmptyDataError                            Traceback (most recent call last)
<ipython-input-20-ba39b3192728> in <module>
----> 1 entities = pd.read_csv("sample_data/aida/results/HC00001DO.entities.labels.tsv", delimiter='\t')
      2 entities

/srv/conda/envs/notebook/lib/python3.7/site-packages/pandas/io/parsers.py in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    684     )
    685 
--> 686     return _read(filepath_or_buffer, kwds)
    687 
    688 

/srv/conda/envs/notebook/lib/python3.7/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
    450 
    451     # Create the parser.
--> 452     parser = TextFileReader(fp_or_buf, **kwds)
    453 
    454     if chunksize or iterator:

/srv/conda/envs/notebook/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds)
    944             self.options["has_index_names"] = kwds["has_index_names"]
    945 
--> 946         self._make_engine(self.engine)
    947 
    948     def close(self):

/srv/conda/envs/notebook/lib/python3.7/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
   1176     def _make_engine(self, engine="c"):
   1177         if engine == "c":
-> 1178             self._engine = CParserWrapper(self.f, **self.options)
   1179         else:
   1180             if engine == "python":

/srv/conda/envs/notebook/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds)
   2006         kwds["usecols"] = self.usecols
   2007 
-> 2008         self._reader = parsers.TextReader(src, **kwds)
   2009         self.unnamed_cols = self._reader.unnamed_cols
   2010 

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()

EmptyDataError: No columns to parse from file

[angelosalatino]

@szeke @dgarijo @filievski

[dgarijo]

Hi Angelo, Let me check if I need to update the binder notebook. Last time I checked this notebook was running successfully

El mié., 14 oct. 2020 4:48 a. m., Angelo Antonio Salatino < notifications@github.com> escribió:

@szeke https://github.com/szeke @dgarijo https://github.com/dgarijo @filievski https://github.com/filievski

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[dgarijo]

@angelosalatino, for some reason, the Binder notebook was pointing to the dev branch, which may not be fully stable. Please use the following binder notebook, which is the same but uses the master branch:

https://mybinder.org/v2/gh/usc-isi-i2/kgtk/master?filepath=examples%2FExample5%20-%20AIDA%20AIF.ipynb

I have run this successfully end to end just now, so I think it will work for you as well.

I will update the readme file with the right link

[dgarijo]

FYI, I also ran it with Docker successfully, which takes less time (if you have Docker installed and 4.9 GB to spare :)

docker run -it -p 8888:8888 uscisii2/kgtk:latest /bin/bash -c "jupyter notebook --ip='*' --port=8888 --no-browser"

And go to kgtk/examples/ and select the notebook

[angelosalatino]

Hi @dgarijo, I can now confirm that everything works fine.

Cheers