Search code examples
pythonpandasparse-error

Jupiter Notebook Pandas read_csv Parse Error

I try to Write a Dashboard using Python in Anaconda Jupiter Notebook. As first I want to read in CSV files from a online source and this is where the Problem begins :D

Everything is written correctly but i have a Parse Error:

  ParserError                               Traceback (most recent call last)
<ipython-input-96-112ac527c079> in <module>
----> 1 confirmed_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")
      2 death_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")
      3 recovered_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv")

~/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in parser_f(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, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    700                     skip_blank_lines=skip_blank_lines)
    701 
--> 702         return _read(filepath_or_buffer, kwds)
    703 
    704     parser_f.__name__ = name

~/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
    433 
    434     try:
--> 435         data = parser.read(nrows)
    436     finally:
    437         parser.close()

~/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in read(self, nrows)
   1137     def read(self, nrows=None):
   1138         nrows = _validate_integer('nrows', nrows)
-> 1139         ret = self._engine.read(nrows)
   1140 
   1141         # May alter columns / col_dict

~/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in read(self, nrows)
   1993     def read(self, nrows=None):
   1994         try:
-> 1995             data = self._reader.read(nrows)
   1996         except StopIteration:
   1997             if self._first_chunk:

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

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

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

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

pandas/_libs/parsers.pyx in pandas._libs.parsers.raise_parser_error()

ParserError: Error tokenizing data. C error: Expected 1 fields in line 32, saw 2

My code is Following:

#import packages and data

import pandas as pd
import numpy as np

confirmed_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")
death_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")
recovered_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv")

confirmed_df.head()

I try to look at the Dataframe header for confirmed_df and got a list of Links and stuff i don't know where i comes from?!

looks like this:

Printscreen

Can anybody help?

BR

Ben

Solution

  • Please try by fetching contect as raw data from git repository:

    #In the latest version of pandas (0.19.2) you can directly pass the url
confirmed_df = pd.read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")
death_df = pd.read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")
recovered_df = pd.read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv")

    or by fetching content through web:

    import pandas as pd
import io
import requests
url="https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
s=requests.get(url).content
confirmed_df=pd.read_csv(io.StringIO(s.decode('utf-8')))
#death_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")
#recovered_df = pd.read_csv("https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv")

print(confirmed_df.head())