eparse 0.7.3

Excel spreadsheet crawler and table parser for data discovery, extraction, and querying

eparse

Description

Excel spreadsheet crawler and table parser for data extraction and querying.

Features

• Command-line interface

• Recursive Excel file discovery

• Sub-tabular data extraction (logical tables)

• SQLite and PostgreSQL database interfaces

• CLI query tool

• Summary data metrics

Installation

To install eparse, you can use pip and the latest version on PyPI:

$ pip install eparse

Or you can clone this repo and install from source:

$ git clone https://github.com/ChrisPappalardo/eparse.git
$ cd eparse
$ pip install .

If you plan to use the postgres interface, you also need to install the postgres package psycopg2. Instructions can be found here. This package is optional, and you can use the other interfaces such as the SQLite3 interface without having to install psycopg2.

The easiest way to install the psycopg2 package for your particular environment may be to install the pre-compiled binary driver as follows:

$ pip install psycopg2-binary

If you see an error while trying to use a postgres endpoint such as postgres://user:pass@host:port/my_db that mentions the postgres driver is missing, then you know you haven’t properly installed (and compiled) psycopg2.

Usage

eparse can be used as either a python library or from the command-line. You can view supported CLI commands and usage with --help as follows:

$ eparse --help
Usage: eparse [OPTIONS] COMMAND [ARGS]...

excel parser

Options:
-i, --input TEXT   input source
-o, --output TEXT  output destination
-f, --file TEXT    file(s) or dir(s) to target
-d, --debug        use debug mode
-l, --loose        find tables loosely
-r, --recursive    find files recursively
-t, --truncate     truncate dataframe output
-v, --verbose      increase output verbosity
--help             Show this message and exit.

Commands:
migrate  migrate eparse table
parse    parse table(s) found in sheet for target(s)
query    query eparse output
scan     scan for excel files in target

You can also use eparse from python like so:

from eparse.core import get_df_from_file

print([table for table in get_df_from_file('myfile.xlsx')])
102   Date  Principal Repayment   Date  Principal Repayment
103  44834        700757.679004  44926        430013.148303
104  44926         71957.776108  45016        100576.127808
105  45016         147578.19262  45107        898008.340095
106  45107         32801.363072  45199         841656.13896
...

Scan

To scan one or more directories for Excel files with descriptive information, you can use the scan command like so:

$ eparse -v -f <path_to_files> scan

Increase the verbosity with additional flags, such as -vvv, for more descriptive information about the file(s), including sheet names.

Parse

Excel files can be parsed as follows:

$ eparse -v -f <path_to_files> parse

This mode will list each table found in each Excel file to the command-line. This mode is useful for initial discovery for parseable data.

eparse uses a simple algorithm for identifying tables. Table “corners” are identified as cells that contain empty cells above and to the right (or sheet boundaries). A densely or sparsely populated 2x2 table must follow in order for data to be extracted in relation to that cell. eparse will automatically adjust for rowspan labels and empty table corners and the dense vs. sparse criterion can be controlled with the --loose flag.

eparse was written to accomodate various types of output formats and endpoints, including null:///, stdout:///, sqlite3:///db_name, and postgres://user:password@host:port/db_name.

null

This mode is useful for validating files and generating descriptive info, and is the default. The command above with -v is an example of this mode, which lists out the tables found.

stdout

This mode is good for viewing data extracted from Excel files in the console. For example, you could view all tables found in Sheet1 with the following command:

$ eparse -f <path_to_files> -o stdout:/// parse -s "Sheet1"

eparse uses pandas to handle table data. You can view larger tables without truncation using the -t flag as follows:

$ eparse -t -f <path_to_files> -o stdout:/// parse -s "Sheet1"

Data in table format is useful for human viewing, but a serialized form is better for data interfacing. Serialize your output with the -z flag as follows:

$ eparse -t -f <path_to_files> -o stdout:/// parse -z

Each cell of extracted table data is serialized as follows:

• row - 0-indexed table row number

• column - 0-indexed table column number

• value - the value of the cell as a str

• type - the implied python type of the data found

• c_header - the column header

• r_header - the row header

• excel_RC - the RC reference from the spreadsheet (e.g. B10)

• sheet - the name of the sheet

• f_name - the name of the file

sqlite3

eparse uses the peewee package for ORM and database integration. The interfaces module contains an ExcelParse model that provides data persistence and a common interface.

To create a SQLite3 database with your parsed Excel data, use the following command:

$ mkdir .files
$ eparse -f <path_to_files> -o sqlite3:/// parse -z

This command will automatically generate a unique database filename using the uuid python package in the .files/ sub-directory of the working directory. You may need to create this directory before running this command, as shown.

You can also specify a path and filename of your choosing, like so:

$ mkdir .files
$ eparse -f <path_to_files> -o sqlite3:///path/filename.db parse -z

postgres

eparse also supports postgresql integrations. As mentioned above, you will need psycopg2 installed for postgresql integrations to work. The eparse BaseDatabaseInterface abstracts the implementation details, so you would use this interface the same way you use the others, with the exception of the endpoint.

To use a postgresql database as the source and/or destination of your data, you would supply an --input and/or --output endpoint to the tool as follows:

$ eparse -o postgres://user:password@host:port/db_name ...

Where details like user, host, port are provided to you by your db administrator. eparse will create the necessary table(s) and indexes for you when inserting data into the database.

Query

Once you have stored parsed data, you can begin to query it using the peewee ORM. This can be done with the tool or directly with the database.

For example, query distinct column header names from a generated SQLite3 database as follows:

$ eparse -i sqlite3:///.files/<db_file> -o stdout:/// query -m get_c_header
               c_header  Total Rows  Data Types  Distinct Values
  0             ABC-col         150           2               76
  1             DEF-col        3981           3               15
  2             GHI-col          20           1                2
  ..                ...         ...         ...              ...

This command will give descriptive information of each distinct c_header found, including total rows, unique data types, and distinct values.

You can also get raw un-truncated data as follows:

$ eparse -t -i sqlite3:///.files/<db_file> -o stdout:/// query

Filtering data on content is easy. Use the --filter option as follows:

$ eparse -i sqlite3:///.files/<db_file> -o stdout:/// query --filter f_name "somefile.xlsx"

The above command will filter all rows from an Excel file named somefile.xlsx. You can use any of the following django-style filters:

• __eq equals X

• __lt less than X

• __lte less than or equal to X

• __gt greater than X

• __gte greater than or equal to X

• __ne not equal to X

• __in X is in

• __is is X

• __like like expression, such as %somestr%, case sensitive

• __ilike like expression, such as %somestr%, case insensitive

• __regexp regular expression matching such as ^.*?foo.*?$

Filters are applied to the ORM fields like so:

• --filter row__gte 4 all extracted table rows >= 5

• --filter f_name__ilike "%foo%" all data from filenames with foo

• --filter value__ne 100 all data with values other than 100

Queried data can even be stored into a new database for creating curated data subsets, as follows:

$ eparse -i sqlite3:///.files/<db_file> \
         -o sqlite3:///.files/<subq_db_file> \
         query --filter f_name "somefile.xlsx"

Since database files the tool generates when using sqlite3:/// are SQLite native, you can also use SQLite database client tools and execute raw SQL like so:

$ sudo apt-get install -y sqlite3-tools
$ sqlite3 .files/<db_file>
SQLite version 3.37.2 2022-01-06 13:25:41
Enter ".help" for usage hints.
sqlite> .schema
CREATE TABLE IF NOT EXISTS "excelparse" ("id" INTEGER NOT NULL PRIMARY KEY, "row" INTEGER NOT NULL, "column" INTEGER NOT NULL, "value" VARCHAR(255) NOT NULL, "type" VARCHAR(255) NOT NULL, "c_header" VARCHAR(255) NOT NULL, "r_header" VARCHAR(255) NOT NULL, "excel_RC" VARCHAR(255) NOT NULL, "name" VARCHAR(255) NOT NULL, "sheet" VARCHAR(255) NOT NULL, "f_name" VARCHAR(255) NOT NULL);
sqlite> .header on
sqlite> SELECT * FROM excelparse LIMIT 1;
id|row|column|value|type|c_header|r_header|excel_RC|name|sheet|f_name
1|0|0|ABC|<class 'str'>|SomeCol|SomeRow|B2|MyTable|Sheet1|myfile.xlsm

Migrate

eparse wouldn’t be a solid tool without the ability to migrate your eparse databases for future code changes. You can apply migrations that ship with future versions of eparse as follows:

$ eparse -i sqlite3:///.files/<db_file> migrate -m <migration>
applied <migration>

It is up to you to determine the migrations you need based on the eparse version you are upgrading from and to. Migrations can be found in eparse/migrations.py

Unstructured

If you would like to use eparse to partition xls[x] files alongside unstructured, you can do so with our contributed partition and partition_xlsx modules. Simply import the partition function from eparse.contrib.unstructured.partition and use it instead of partition from unstructured.partition.auto like so:

from eparse.contrib.unstructured.partition import partition

elements = partition(filename='some_file.xlsx', eparse_mode='...')

Valid eparse_mode settings are available in eparse.contrib.unstructured.xlsx._eparse_modes.

Contributing

As an open-source project, contributions are always welcome. Please see Contributing for more information.

License

eparse is licensed under the MIT License. See the LICENSE file for more details.

Contact

Thanks for your support of eparse. Feel free to contact me at [e-mail] or connect with me on Github.

History

0.7.3 (2023-08-23)

• Updated partition and partition_xlsx for latest unstructured

0.7.2 (2023-08-22)

• Relaxed unstructured dependency requirement for compatibility

0.7.1 (2023-08-20)

• Added unstructured contrib to core package

• Uopdaed README with instructions

0.7.0 (2023-08-18)

• Added html conversion functions and an html data interface

• Added get_table_digest to core

0.6.3 (2023-06-30)

• Updated get_df_from_file to accept filename or io object

0.6.1 (2023-06-22)

• Added get_df_from_file helper function

• Added contrib with unstructured partition handler

0.5.0 (2023-06-14)

• Optimized database interfaces

0.4.0 (2023-06-14)

• Added postgresql interface

0.3.0 (2023-06-14)

• Added inteface classes

• Added migrations

0.2.0 (2023-06-12)

• Added migrate command

• Added 0.1.2 to 0.2.0 migration

0.1.2 (2023-06-07)

• Updated README

0.1.1 (2023-06-06)

• Updated requirements

• Updated README

0.1.0 (2023-06-06)

• First release on PyPI.