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excel – Python Pandas – Read csv file containing multiple tables

Posted by: admin March 9, 2020 Leave a comment

Questions:

I have a single .csv file containing multiple tables.

Using Pandas, what would be the best strategy to get two DataFrame inventory and HPBladeSystemRack from this one file ?

The input .csv looks like this:

Inventory       
System Name            IP Address    System Status
dg-enc05                             Normal
dg-enc05_vc_domain                   Unknown
dg-enc05-oa1           172.20.0.213  Normal

HP BladeSystem Rack         
System Name               Rack Name   Enclosure Name
dg-enc05                  BU40  
dg-enc05-oa1              BU40        dg-enc05
dg-enc05-oa2              BU40        dg-enc05

The best I’ve come up with so far is to convert this .csv file into Excel workbook (xlxs), split the tables into sheets and use:

inventory = read_excel('path_to_file.csv', 'sheet1', skiprow=1)
HPBladeSystemRack = read_excel('path_to_file.csv', 'sheet2', skiprow=2)

However:

  • This approach requires xlrd module.
  • Those log files have to be analyzed in real time, so that it would be way better to find a way to analyze them as they come from the logs.
  • The real logs have far more tables than those two.
How to&Answers:

If you know the table names beforehand, then something like this:

df = pd.read_csv("jahmyst2.csv", header=None, names=range(3))
table_names = ["Inventory", "HP BladeSystem Rack", "Network Interface"]
groups = df[0].isin(table_names).cumsum()
tables = {g.iloc[0,0]: g.iloc[1:] for k,g in df.groupby(groups)}

should work to produce a dictionary with keys as the table names and values as the subtables.

>>> list(tables)
['HP BladeSystem Rack', 'Inventory']
>>> for k,v in tables.items():
...     print("table:", k)
...     print(v)
...     print()
...     
table: HP BladeSystem Rack
              0          1               2
6   System Name  Rack Name  Enclosure Name
7      dg-enc05       BU40             NaN
8  dg-enc05-oa1       BU40        dg-enc05
9  dg-enc05-oa2       BU40        dg-enc05

table: Inventory
                    0             1              2
1         System Name    IP Address  System Status
2            dg-enc05           NaN         Normal
3  dg-enc05_vc_domain           NaN        Unknown
4        dg-enc05-oa1  172.20.0.213         Normal

Once you’ve got that, you can set the column names to the first rows, etc.

Answer:

I assume you know the names of the tables you want to parse out of the csv file. If so, you could retrieve the index positions of each, and select the relevant slices accordingly. As a sketch, this could look like:

df = pd.read_csv('path_to_file')    
index_positions = []
for table in table_names:
    index_positions.append(df[df['col_with_table_names']==table].index.tolist()[0])

## Include end of table for last slice, omit for iteration below
index_positions.append(df.index.tolist()[-1])

tables = {}
for position in index_positions[:-1]:
    table_no = index_position.index(position)
    tables[table_names[table_no] = df.loc[position:index_positions[table_no+10]]

There are certainly more elegant solutions but this should give you a dictionary with the table names as keys and the corresponding tables as values.

Answer:

Pandas doesn’t seem to be ready to do this easily, so I ended up doing my own split_csv function. It only requires table names and will output .csv files named after each table.

import csv
from os.path import dirname # gets parent folder in a path
from os.path import join # concatenate paths

table_names = ["Inventory", "HP BladeSystem Rack", "Network Interface"]

def split_csv(csv_path, table_names):
    tables_infos = detect_tables_from_csv(csv_path, table_names)
    for table_info in tables_infos:
        split_csv_by_indexes(csv_path, table_info)

def split_csv_by_indexes(csv_path, table_info):
    title, start_index, end_index = table_info
    print title, start_index, end_index
    dir_ = dirname(csv_path)
    output_path = join(dir_, title) + ".csv"
    with open(output_path, 'w') as output_file, open(csv_path, 'rb') as input_file:
        writer = csv.writer(output_file)
        reader = csv.reader(input_file)
        for i, line in enumerate(reader):
            if i < start_index:
                continue
            if i > end_index:
                break
            writer.writerow(line)

def detect_tables_from_csv(csv_path, table_names):
    output = []
    with open(csv_path, 'rb') as csv_file:
        reader = csv.reader(csv_file)
        for idx, row in enumerate(reader):
            for col in row:
                match = [title for title in table_names if title in col]
                if match:
                    match = match[0] # get the first matching element
                    try:
                        end_index = idx - 1
                        start_index
                    except NameError:
                        start_index = 0
                    else:
                        output.append((previous_match, start_index, end_index))
                    print "Found new table", col
                    start_index = idx
                    previous_match = match
                    match = False

        end_index = idx  # last 'end_index' set to EOF
        output.append((previous_match, start_index, end_index))
        return output


if __name__ == '__main__':
    csv_path = 'switch_records.csv'
    try:
        split_csv(csv_path, table_names)
    except IOError as e:
        print "This file doesn't exist. Aborting."
        print e
        exit(1)