Develop Reference

Python Camelot - export files without the additional string appended to the filename

Python 3.7 with Camelot 0.7.3. Currently, Camelot exports the converted file with 'page--table-' appended to the file name - we have very specific file name requirements for our application, and I'm trying to export the file without that extra string appended to the file name. Is this possible? The documentation does not mention anything about how to get around this.

The documentation does not mention anything about how to get around this.
I'm not sure what you mean. https://camelot-py.readthedocs.io/en/master/ says:
Here’s how you can extract tables from PDF files. Check out the PDF
used in this example here.
>>> import camelot
>>> tables = camelot.read_pdf('foo.pdf')
>>> tables <TableList n=1>
>>> tables.export('foo.csv', f='csv', compress=True) # json, excel, html
Using tables.export exports all the tables in the PDF to separate files and needs to distinguish them by the filenames.
If you only need to export a specific table, use the example further down on the page:
>>> tables[0].to_csv('foo.csv') # to_json, to_excel, to_html
This passes the filename unchanged to pandas.DataFrame.to_csv, as can be seen in https://github.com/camelot-dev/camelot/blob/master/camelot/core.py#L571.

Failing to open an Excel file with Python

I'm on a Debian GNU/Linux computer, working with Python 2.7.9.
As a part of my job, I have been making python scripts that read inputs in various formats (e.g. Excel, Csv, Txt) and parse the information to more standarized files. It's not my first time opening or working with Excel files.
There's a particular file which is giving me problems, I just can't open it. When I tried with xlrd (version 0.9.3), it gave me the following error:
xlrd.open_workbook('sample.xls')
XLRDError: Unsupported format, or corrupt file: BOF not
workbook/worksheet: op=0x0009 vers=0x0002 strm=0x000a build=0 year=0
-> BIFF21
I tried to investigate the matter on my own, found a couple of answers in StackOverflow but I couldn't open it anyway. This particular answer I found may be the problem (the second explanation), but it doesn't include a workaround: https://stackoverflow.com/a/16518707/4345659
A tool that could conert the file to csv/txt would also solve the problem.
I already tried with:
xlrd
openpyxl
xlsx2csv (the shell tool)
A sample file is available here:
https://ufile.io/r4m6j
As a side note, I can open it with LibreOffice Calc and MS Excel, so I could eventually change it to csv that way. The thing is, I need to do it all with a python script.
Thanks in advance!

It seems like MS Problem. The xls file is very strange, maybe you should contact xlrd support.
But I have a crazy workaround for you: xls2ods. It works for me even though xls2csv doesn't (SiC!).
So, install catdoc first:
$sudo apt-get install catdoc
Then convert your xls file to ods and open ods using pyexcel_ods or whatever you prefer. To use pyexcel_ods install it first using pip install pyexcel_ods.
import subprocess
from pyexcel_ods import get_data
file_basename = 'sample'
returncode = subprocess.call(['xls2ods', '{}.xls'.format(file_basename)])
if returnecode > 0:
# consider to use subprocess.Popen if you need more control on stderr
exit(returncode)
data = get_data('{}.ods'.format(file_basename))
print(data)
I'm getting following output:
OrderedDict([(u'sample',
[[u'labo',
u'codfarm',
u'farmacia',
u'direccion',
u'localidad',
u'nom_medico',
u'matricula',
u'troquel',
u'producto',
u'cant_total']])])

Here is a kludge I would use:
Assuming you have LibreOffice on Debian, you could either convert all your *.xls files into *.csv using:
import os
os.system("libreoffice --headless --convert-to csv *.xls")
#or use os.call
... and then work consistently with csv.
Or you could convert only the corrupted file(s) when needed using a try/except block:
import os
try:
xlrd.open_workbook('sample.xls')
except XLRDError:
os.system("libreoffice --headless --convert-to csv sample.xls")
# mycsv = open("sample.csv", "r")
# for line in mycsv.readlines():
# ...
# ...
OBS: Keep LibreOffice closed while running the script.
Alternatively there are other tools out there to do the conversion. Here is one (which I have not tested): https://github.com/dilshod/xlsx2csv

If you are targeting windows, if you have Excel installed, and if you are familiar with Excel VBA, you will have a quick solution using the comtypes package:
http://pythonhosted.org/comtypes/
You will have direct access to Excel by its COM interfaces.

This code open an xls file and saves it as a cvs file, using the comtypes package:
import comtypes.client as cl
progId = "Excel.Application.15"
xl = cl.CreateObject(progId)
wb = xl.Workbooks.Open(r"C:\Users\aUser\Desktop\thermoList.xls")
wb.SaveAs(r"C:\Users\aUser\Desktop\thermoList.csv",FileFormat=6)
xl.DisplayAlerts = False
xl.Quit()
I could not test it with "sample.xls" which is corrupt.
Your could try with another file.
You might need to adjust the progId according to your version of Excel.

It's a file format issue. I'm not sure what file type is it but it's not Excel. I just open and saved the file with sample2.xls name and compare the types:
How are you creating this file?

If you need to get the words as a list of strings:
text_file = open("sample.xls", "r")
lines = text_file.read().replace(chr(200), '').replace(chr(0), '').replace(chr(1), '').replace(chr(5), '').replace(chr(2), '').replace(chr(3), '').replace(chr(4), '').replace(chr(6), '').replace(chr(7), '').replace(chr(8), '').replace(chr(9), '').replace(chr(10), '').replace(chr(12), '').replace(chr(15), '').replace(chr(16), '').replace(chr(17), '').replace(chr(18), '').replace(chr(49), '').replace('Arial', '')
for line in lines.split(chr(128)):
print(line)
the output:

The file you provided is corrupted, so there is no way for other responders to test it and recommend a good solution. And exception you posted confirming that.
As a solution you can try to debug some things, please see some steps below:
You mentioned you tried the xlrd library. Try to check if your xlrd module is upto date by executing this:
Python 2.7.9
>>> import xlrd
>>> xlrd.__VERSION
update to the latest official version if needed
Try to open any other *.xls file and see if it works with Python version you're using and current library.
Check module documentation it's pretty good, and there are some different things described how to use this module on various platforms( Win vs. Linux)http://xlrd.readthedocs.io/en/latest/dates.html
You always can rich out to the community (there is still a chance that you might be getting into some weird state or bug) the link is here https://github.com/python-excel/xlrd/issues
Hope that helps.

Unable to open your Excel either. Just as yadayada said, I think it is the problem of data source. If you really want to figure out the reason, I suggest you ask questions about the excel instead of python.

It's always work for me with any xls or xlsx files:
def csv_from_excel(filename_xls, filename_csv):
wb = xlrd.open_workbook(filename_xls, encoding_override='YOUR_ENCODING_HERE (f.e. "cp1251"')
sh = wb.sheet_by_index(0)
your_csv_file = open(filename_csv, 'wb')
wr = unicodecsv.writer(your_csv_file)
for rownum in xrange(sh.nrows):
wr.writerow(sh.row_values(rownum))
your_csv_file.close()
So, i don't work directly with excel file before convert them to csv. Mb it will help you

Python, openpyxl: I get the wrong value when running get_highest_column()

I am practicing with openpyxl and I'm working on an Excel file called 'test.xlsx'. The file only has 3 columns and 7 rows. The .xlsx file was created with LibreOffice.
When I run...
>>> #! python3
>>> import openpyxl
>>> wb = openpyxl.load_workbook('test.xlsx')
>>> sheet = wb.get_sheet_by_name('Sheet1')
>>> sheet.get_highest_column()
1025
The returned value should be 3.
A quick Google search suggested I run:
>>> sheet.calculate_dimension()
and got the return value:
'A1:AMK7'
This should only be 'A1:C7'.
I remember reading that LibreOffice could be part of the problem to this.
However, I can't switch to MSOffice, and I hate OpenOffice.
Is there suggestion on how I could fix this, or work around it?
Thanks!

It sounds like you're using older versions of LibreOffice and openpyxl. LibreOffice did used to set a default value of "A1:AMK7" for the dimensions but it version 5 doesn't seem to be doing that any more. openpyxl used to rely on the dimensions tag when reading files but hasn't done this for a while. Please try using openpyxl 2.3-b2

how to read a comma sep value with .txt extension into python as an array?

I am biologist and very very new to Python and before, i learnt a bit of R.
So I have a very big text file (3 GB, too big to handle in R), all values are comma seperated but the extension is .txt (I don't know if it is necessary information). what i wanted to do is to:
read it into python as an object which is equivalent of dataframe in R,
get rid of columns in the middle
reduce the size of the object
write it as txt file
take the rest to R.
If you can help me i would be very happy.
thank you

There is no real need to go into python first. Your question looks a lot like this question. The answer marked as the correct answer iteratively reads the large file, and creates a new, smaller file. Other good alternatives are using sqlite and the sqdf package, or use the ff package. This last approach works particularly well is the number of columns is small compared to the number of rows.

This will take minimal memory as it does not load the whole file at once.
import csv
with open('in.txt', 'rb') f_in, open('out.csv', 'wb') as f_out:
reader = csv.reader(f_in)
writer = csv.writer(f_out)
for row in reader:
# keep first two columns and last three columns
writer.writerow(row[:2] + row[-3:])
Note: If using Python 3 change the file modes to 'r' and 'w', respectively.

i am not familiar with r dataframe, but pandas provides helpers to read csv into pandas dataframe:
from pandas import read_csv
df = read_csv('yourfile.txt')
print df
print df['Line']
If that is not what you need you can use csv module to iterate through each line of your csv as a python list and put it into whatever data structure you want.

If you insist on using a preprocessing step, using the linux command tools is a really good and fast option. If you use Linux, these tools are already installed, under Windows you'll need to first install MinGW or Cygwin. This SO question already provides some nice pointers. In essence you use the awk tool to iteratively process the text file, creating an output text file as you go. Copying form the accepted answer of the SO question I linked:
awk -F "," '{ split ($8,array," "); sub ("\"","",array[1]); sub (NR,"",$0); sub (",","",$0); print $0 > array[1] }' file.txt
This read the file, grabs the eight column, and dumps it to a file. See the answer for more details.

Per CRAN (new features and bug fixes re: development) the new development build 3.0.0 should allow for R to use the pagefile/swap. In windows you will need to set R_MAX_MEM_SIZE to a suitably large value.

Get formula from Excel cell with python xlrd

I have to port an algorithm from an Excel sheet to python code but I have to reverse engineer the algorithm from the Excel file.
The Excel sheet is quite complicated, it contains many cells in which there are formulas that refer to other cells (that can also contains a formula or a constant).
My idea is to analyze with a python script the sheet building a sort of table of dependencies between cells, that is:
A1 depends on B4,C5,E7 formula: "=sqrt(B4)+C5*E7"
A2 depends on B5,C6 formula: "=sin(B5)*C6"
...
The xlrd python module allows to read an XLS workbook but at the moment I can access to the value of a cell, not the formula.
For example, with the following code I can get simply the value of a cell:
import xlrd
#open the .xls file
xlsname="test.xls"
book = xlrd.open_workbook(xlsname)
#build a dictionary of the names->sheets of the book
sd={}
for s in book.sheets():
sd[s.name]=s
#obtain Sheet "Foglio 1" from sheet names dictionary
sheet=sd["Foglio 1"]
#print value of the cell J141
print sheet.cell(142,9)
Anyway, It seems to have no way to get the formul from the Cell object returned by the .cell(...) method.
In documentation they say that it is possible to get a string version of the formula (in english because there is no information about function name translation stored in the Excel file). They speak about formulas (expressions) in the Name and Operand classes, anyway I cannot understand how to get the instances of these classes by the Cell class instance that must contains them.
Could you suggest a code snippet that gets the formula text from a cell?

[Dis]claimer: I'm the author/maintainer of xlrd.
The documentation references to formula text are about "name" formulas; read the section "Named references, constants, formulas, and macros" near the start of the docs. These formulas are associated sheet-wide or book-wide to a name; they are not associated with individual cells. Examples: PI maps to =22/7, SALES maps to =Mktng!$A$2:$Z$99. The name-formula decompiler was written to support inspection of the simpler and/or commonly found usages of defined names.
Formulas in general are of several kinds: cell, shared, and array (all associated with a cell, directly or indirectly), name, data validation, and conditional formatting.
Decompiling general formulas from bytecode to text is a "work-in-progress", slowly. Note that supposing it were available, you would then need to parse the text formula to extract the cell references. Parsing Excel formulas correctly is not an easy job; as with HTML, using regexes looks easy but doesn't work. It would be better to extract the references directly from the formula bytecode.
Also note that cell-based formulas can refer to names, and name formulas can refer both to cells and to other names. So it would be necessary to extract both cell and name references from both cell-based and name formulas. It may be useful to you to have info on shared formulas available; otherwise having parsed the following:
B2 =A2
B3 =A3+B2
B4 =A4+B3
B5 =A5+B4
...
B60 =A60+B59
you would need to deduce the similarity between the B3:B60 formulas yourself.
In any case, none of the above is likely to be available any time soon -- xlrd priorities lie elsewhere.

Update: I have gone and implemented a little library to do exactly what you describe: extracting the cells & dependencies from an Excel spreadsheet and converting them to python code. Code is on github, patches welcome :)
Just to add that you can always interact with excel using win32com (not very fast but it works). This does allow you to get the formula. A tutorial can be found here [cached copy] and details can be found in this chapter [cached copy].
Essentially you just do:
app.ActiveWorkbook.ActiveSheet.Cells(r,c).Formula
As for building a table of cell dependencies, a tricky thing is parsing the excel expressions. If I remember correctly the Trace code you mentioned does not always do this correctly. The best I have seen is the algorithm by E. W. Bachtal, of which a python implementation is available which works well.

So I know this is a very old post, but I found a decent way of getting the formulas from all the sheets in a workbook as well as having the newly created workbook retain all the formatting.
First step is to save a copy of your .xlsx file as .xls
-- Use the .xls as the filename in the code below
Using Python 2.7
from lxml import etree
from StringIO import StringIO
import xlsxwriter
import subprocess
from xlrd import open_workbook
from xlutils.copy import copy
from xlsxwriter.utility import xl_cell_to_rowcol
import os
file_name = '<YOUR-FILE-HERE>'
dir_path = os.path.dirname(os.path.realpath(file_name))
subprocess.call(["unzip",str(file_name+"x"),"-d","file_xml"])
xml_sheet_names = dict()
with open_workbook(file_name,formatting_info=True) as rb:
wb = copy(rb)
workbook_names_list = rb.sheet_names()
for i,name in enumerate(workbook_names_list):
xml_sheet_names[name] = "sheet"+str(i+1)
sheet_formulas = dict()
for i, k in enumerate(workbook_names_list):
xmlFile = os.path.join(dir_path,"file_xml/xl/worksheets/{}.xml".format(xml_sheet_names[k]))
with open(xmlFile) as f:
xml = f.read()
tree = etree.parse(StringIO(xml))
context = etree.iterparse(StringIO(xml))
sheet_formulas[k] = dict()
for _, elem in context:
if elem.tag.split("}")[1]=='f':
cell_key = elem.getparent().get(key="r")
cell_formula = elem.text
sheet_formulas[k][cell_key] = str("="+cell_formula)
sheet_formulas
Structure of Dictionary 'sheet_formulas'
{'Worksheet_Name': {'A1_cell_reference':'cell_formula'}}
Example results:
{u'CY16': {'A1': '=Data!B5',
'B1': '=Data!B1',
'B10': '=IFERROR(Data!B12,"")',
'B11': '=IFERROR(SUM(B9:B10),"")',

It seems that it is impossible now to do what you want with xlrd. You can have a look at this post for the detailed description of why it is so difficult to implement the functionality you need.
Note that the developping team does a great job for support at the python-excel google group.

I know this post is a little late but there's one suggestion that hasn't been covered here. Cut all the entries from the worksheet and paste using paste special (OpenOffice). This will convert the formulas to numbers so there's no need for additional programming and this is a reasonable solution for small workbooks.

Ye! With win32com it's works for me.
import win32com.client
Excel = win32com.client.Dispatch("Excel.Application")
# python -m pip install pywin32
file=r'path Excel file'
wb = Excel.Workbooks.Open(file)
sheet = wb.ActiveSheet
#Get value
val = sheet.Cells(1,1).value
# Get Formula
sheet.Cells(6,2).Formula