concatenate tables from loop getting error - InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Question

I need to concatenate tables created from a loop. The have repeats of the names in the columns but they are telling a different story, but for some reason when running this code I get an error:

InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Here is the code:

url = 'https://www.impactfees.com/publications%20pdf/2019survey.pdf'

tables = camelot.read_pdf(url, flavor = 'stream', edge_tol = 500, pages = '4-end')

i = 0


while i in range(0,tables.n):
    table_value = tables[i].df.loc[0,4]
    header = 1
    header = tables[i].df.iloc[header]
    tables[i].df = tables[i].df.rename(columns = header)
    
    nan_v = float("NaN")
    tables[i].df.replace('',nan_v,inplace = True) 
    tables[i].df.dropna(subset = ['Jurisdiction'], inplace = True)
    tables[i].df.replace(['Jurisdiction'], nan_v, inplace = True)
    tables[i].df.dropna(subset = ['Jurisdiction'], inplace = True)

#    Tot_col = tables[i].df.columns.get_loc('Total')
#    tables[i].df = tables[i].df.iloc[:,0:Tot_col+1]
    tables[i].df['report_name'] = table_value
    tables[i].df.loc[~tables[i].df.index.duplicated(keep = 'first')]
    i = i + 1

dfs = pd.concat([table.df for table in tables])

dfs

and here is the error I am getting:

InvalidIndexError                         Traceback (most recent call last)
<ipython-input-133-2617eb5ae448> in <module>
     23     i = i + 1
     24 
---> 25 dfs = pd.concat([table.df for table in tables])
     26 
     27 

~\anaconda3\lib\site-packages\pandas\core\reshape\concat.py in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
    296     )
    297 
--> 298     return op.get_result()
    299 
    300 

~\anaconda3\lib\site-packages\pandas\core\reshape\concat.py in get_result(self)
    514                     obj_labels = obj.axes[1 - ax]
    515                     if not new_labels.equals(obj_labels):
--> 516                         indexers[ax] = obj_labels.get_indexer(new_labels)
    517 
    518                 mgrs_indexers.append((obj._mgr, indexers))

~\anaconda3\lib\site-packages\pandas\core\indexes\base.py in get_indexer(self, target, method, limit, tolerance)
   3169 
   3170         if not self.is_unique:
-> 3171             raise InvalidIndexError(
   3172                 "Reindexing only valid with uniquely valued Index objects"
   3173             )

InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Answer 1

• camelot has an issue. I had to patch utils.py to use a different user-agent
• the pages are not fully consistent, hence passing a list to rename(columns=) does not work. You need to pass a dict
• have kept two data frames - one with target rows, other with excluded rows
• there remain inconsistent columns e.g. Drain Parks

import pandas as pd
import camelot

url = 'https://www.impactfees.com/publications%20pdf/2019survey.pdf'
tables = camelot.read_pdf(url, flavor = 'stream', edge_tol = 500, pages = '4-end')

df = pd.DataFrame()
dfexc = pd.DataFrame()
for i in range(tables.n):
    dft = tables[i].df.rename(columns={i:v.replace("\n"," ") for i,v in tables[i].df.iloc[1].items() if v!=""})
    if " " in dft.columns[0]: 
        dft = dft.rename(columns={dft.columns[0]:dft.columns[0].split(" ")[0], 1:dft.columns[0].split(" ")[1]})
    m = (dft.State.str.len()!=2) | (dft.index < 2)

    dfexc = pd.concat([dfexc, tables[i].df.loc[m].assign(page=i)])
    df = pd.concat([df, dft.loc[~m].assign(page=i)])#.reset_index(drop=True)