Problem:
import tabula as tb
import pandas as pd
other = "https://github.com/chezou/tabula-py/raw/master/tests/resources/data.pdf"
dfs = tb.read_pdf(other, stream=True) #this works
file="D:\Favorites\1. Programming\Projects\cell penetrating peptide supplemental.pdf"
tables = tb.read_pdf(file, pages = "all", multiple_tables = True)
tables
output:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-29-c598474e8fa3> in <module>
6
7 file="D:\Favorites\1. Programming\Projects\cell penetrating peptide supplemental.pdf"
----> 8 tables = tb.read_pdf(file, pages = "all", multiple_tables = True)
9 tables
~\anaconda3\lib\site-packages\tabula\io.py in read_pdf(input_path, output_format, encoding, java_options, pandas_options, multiple_tables, user_agent, **kwargs)
312
313 if not os.path.exists(path):
--> 314 raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
315
316 if os.path.getsize(path) == 0:
FileNotFoundError: [Errno 2] No such file or directory: 'D:\\Favorites\x01. Programming\\Projects\\cell penetrating peptide supplemental.pdf'
It seems like everyone else who had this issue didn't get it resolved.
The first advice I followed was to check that the file actually exists.
file=r"D:\Favorites\1. Programming\Projects\cell penetrating peptide supplemental.pdf"
print( os.path.isfile(file))
print(os.path.exists(file))
print(os.path.getsize(file) == 0)
output:
True
True
False
??????? why is it raising an error that it should only raise if print(os.path.exists(file)) is False?
I tried a file from the internet and it worked perfectly. The file I'm trying to read doesn't have a URL. I can't view it from my browser. I only have the option to download it. Otherwise i'd just try feeding its URL into the function.
UPDATE: I tried the suggested solution
import tabula as tb
import pandas as pd
tables = tb.read_pdf(r"D:\Favorites\1. Programming\Projects\cell penetrating peptide supplemental.pdf", pages = "all", multiple_tables = True)
tables
and got this:
Got stderr: Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font PKLNYU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 4 (33) in font PKLNYU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 3 (34) in font PKLNYU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (35) in font PKLNYU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (36) in font PKLNYU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font FLAXFE+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (33) in font FLAXFE+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (34) in font FLAXFE+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font BPOUDD+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 4 (33) in font BPOUDD+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 3 (34) in font BPOUDD+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (35) in font BPOUDD+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (36) in font BPOUDD+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font DCUQIG+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (33) in font DCUQIG+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font DREOWG+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (33) in font DREOWG+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font EWGNLJ+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (33) in font EWGNLJ+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (34) in font EWGNLJ+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font PUHGFM+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (33) in font PUHGFM+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (34) in font PUHGFM+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font UHIZXI+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 4 (33) in font UHIZXI+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 3 (34) in font UHIZXI+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (35) in font UHIZXI+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 2 (36) in font UHIZXI+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDFont <init>
WARNING: Invalid ToUnicode CMap in font UCENHU+CambriaMath
Jun 28, 2020 11:17:13 AM org.apache.pdfbox.pdmodel.font.PDSimpleFont toUnicode
WARNING: No Unicode mapping for 1 (33) in font UCENHU+CambriaMath
The problem is that tabula-py has a localize_file function that is called in read_pdf. localize_file will invoke os.path.expanduser to expand the path. For example, in Unix-like systems, "~" is an alias for the user home directory. Thus os.path.expanduser will do the following expansion in Mac OS X
>>> os.path.expanduser("~/Documents")
'/Users/username/Documents'
Unfortunately, this function has another effect: it treats \ as an escape symbol for ANSI escape codes since it invokes os.fspath inside the function. so if you run
>>> os.path.expanduser("\125")
'U'
>>> os.fspath("\125")
'U'
In your case, \1 in the path has been escaped to \x01 so Windows cannot find such a directory. In order to keep your path unchanged, pass it as a raw string, i.e. put an r before it like this
>>> os.path.expanduser(r"\125")
'\\125'
references:
tabula's read_pdf line 311 localize_file is invoked
tabula's localize_file line 72 os.path.expanduser is invoked