pyfsdb 0.9.4

A python implementation of the flat-file streaming database

Objective

A python implementation of the FSDB flat-file streaming database.

Installation

Using pip:

pip3 install pyfsdb

Or manually:

git clone [e-mail]:gawseed/pyfsdb.git
cd pyfsdb
python3 setup.py build
python3 setup.py install

Example Usage

The FSDB file format contains headers and footers that supplement the data within a file. The most common separator is tab-separated, but can wrap CSVs and other datatypes (see the FSDB documentation for full details). The file also contains footers that trace all the piped commands that were used to create a file, thus documenting the history of its creation within the metadata in the file.

Example pyfsdb code for reading a file

Reading in row by row:

import pyfsdb
db = pyfsdb.Fsdb("myfile.fsdb")
print(db.column_names)
for row in db:
    print(row)

Example FSDB file

#fsdb -F t col1 two andthree
1	key1	42.0
2	key2	123.0

Example writing to an FSDB formatted file.

import pyfsdb
db = pyfsdb.Fsdb(out_file="myfile.fsdb")
db.out_column_names=('one', 'two')
db.append([4, 'hello world'])
db.close()

Read below for further usage details.

Installation

pip3 install pyfsdb

Additional Usage Details

The real power of the FSDB comes from the build up of tool-suites that all interchange FSDB formatted files. This allows chaining multiple commands together to achieve a goal. Though the original base set of tools are in perl, you don't need to know perl for most of them.

Let's create a ./mydemo command:

import sys, pyfsdb

db = pyfsdb.Fsdb(file_handle=sys.stdin, out_file_handle=sys.stdout)
value_column = db.get_column_number('value')

for row in db:     # reads a row from the input stream
    row[value_column] = float(row[value_column]) * 2
    db.append(row) # sends the row to the output stream

db.close()

And then feed it this file:

#fsdb -F t col1 value
1	42.0
2	123.0

We can run it thus'ly:

# cat test.fsdb | ./mydemo
#fsdb -F t col1 value
1	84.0
2	246.0
#   | ./test.py

Or chain it together with multiple FSDB commands:

# cat test.fsdb | ./mydemo | dbcolstats valueq
cat test.fsdb | PYTHONPATH=pyfsdb python3 ./test.py | dbcolstats value | dbcol mean stddev sum min max | dbfilealter -R C
#fsdb -R C mean stddev sum min max
mean: 165
stddev: 114.55
sum: 330
min: 84
max: 246

#   | ./test.py
#   | dbcolstats value
#   | dbcol mean stddev sum min max
#   | dbfilealter -R C

See also

The FSDB website and manual page for the original perl module:

https://www.isi.edu/~johnh/SOFTWARE/FSDB/