TableIO.jl

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A glue package for reading and writing tabular data. It aims to provide a uniform api for reading and writing tabular data from and to multiple sources.

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# TableIO

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A small "glue" package for reading and writing tabular data. It aims to provide a uniform api for reading and writing tabular data from and to multiple sources.
This package is "intelligent" in this sense that it automatically selects the right reading / writing methods depending on the file extension.

## Supported Formats

* CSV via <https://github.com/JuliaData/CSV.jl>
* JSON via <https://github.com/JuliaData/JSONTables.jl>
* Zipped CSV or JSON via <https://github.com/fhs/ZipFile.jl>
* JDF via <https://github.com/xiaodaigh/JDF.jl>
* Parquet via <https://github.com/JuliaIO/Parquet.jl>
* Apache Arrow via <https://github.com/JuliaData/Arrow.jl>
* Excel (xlsx) via <https://github.com/felipenoris/XLSX.jl>
* SQLite via <https://github.com/JuliaDatabases/SQLite.jl>
* PostgreSQL via <https://github.com/invenia/LibPQ.jl> - note that CSV.jl is required for PostgreSQL, too.
* Read-only: Stata (dta), SPSS (dat) and SAS (sas7bdat) via <https://github.com/queryverse/StatFiles.jl>
* HDF5 (Pandas format) via [Pandas.jl](https://github.com/JuliaPy/Pandas.jl) - requires Python with Pandas and PyTables installed on Python side.

The underlying packages are not direct dependencies of TableIO and are therefore not installed automatically with it.
This is for reduction of installation size and package load time.

For installation of the Python requirements for Pandas HDF5 use the following Julia commands:

ENV["PYTHON"] = "" # to use a separate Conda environment for Julia
    using Pkg
    Pkg.add(["PyCall", "Conda", "Pandas"])
    Pkg.build("PyCall")
    using Conda
    Conda.add("pandas")
    Conda.add("pytables")

## Installation

using Pkg
    Pkg.add("TableIO")
    using TableIO

Before using a specific format, the corresponding package needs to be installed and imported:

] add JDF
    import JDF # or using JDF

If the file format specific library is not imported and / or installed, an error message is raised.

## Reading Data

The function

read_table

reads a data source (file or database) and returns a Table.jl interface, e.g. for creating a DataFrame.

using TableIO, DataFrames

CSV Format:

using CSV
    df = DataFrame(read_table("my_data.csv"); copycols=false) # Keyword arguments can be passed to the CSV reader (CSV.jl)
    df = DataFrame(read_table("my_data.zip"); copycols=false) # zipped CSV format (assuming there is only 1 file in the archive)

JSON Format:

using Dates, JSONTables
    df = read_table("my_data.json") |> DataFrame # note that |> DataFrame(; copycols=false) gives wrong column types!
    df.my_date_col = Dates.(df.my_date_col) # Dates are imported as strings by default, need to be manually converted

df = read_table("my_data.zip", "my_data.json") |> DataFrame

Binary Formats:

using JDF
    df = DataFrame(read_table("my_data.jdf"); copycols=false) # JDF (compressed binary format)

using Parquet
    df = DataFrame(read_table("my_data.parquet"); copycols=false) # Parquet

using Arrow
    df = DataFrame(read_table("my_data.arrow"); copycols=false) # Apache Arrow

import Pandas # using gives a naming conflict
    df = DataFrame(read_table("my_data.hdf", "key"); copycols=false) # HDF5 (via Pandas)

Excel:

using XLSX
    df = DataFrame(read_table("my_data.xlsx"); copycols=false) # imports 1st sheet
    df = DataFrame(read_table("my_data.xlsx", "MyAwesomeSheet"); copycols=false) # imports named sheet

SQLite:

using SQLite
    df = DataFrame(read_table("my_data.db", "my_table"); copycols=false) # SQLite from file, table name must be given

Alternatively, SQLite database objects could be used:

using SQLite
    sqlite_db = SQLite.DB("my_data.db")
    df = DataFrame(read_table(sqlite_db, "my_table"); copycols=false) # SQLite from database connection, table name must be given

PostgreSQL:

using LibPQ, CSV # CSV is required here because `write_table!` for PostgreSQL depends on CSV
    postgres_conn = LibPQ.Connection("dbname=postgres user=postgres")
    df = DataFrame(read_table(postgres_conn, "my_table"); copycols=false) # reading from Postgres connection

StatFiles.jl integration:

using StatFiles
    df = DataFrame(read_table("my_data.dta"); copycols=false) # Stata
    df = DataFrame(read_table("my_data.sav"); copycols=false) # SPSS
    df = DataFrame(read_table("my_data.sas7bdat"); copycols=false) # SAS

For data formats supporting multiple tables inside a file, the function `list_tables` returns an alphabetically sorted list of table names.

table_names = list_tables(filename)

## Writing Data

The function

write_table!

writes a Table.jl compatible data source into a file or databse.

using TableIO, DataFrames

CSV Format:

using CSV
    write_table!("my_data.csv", df)

write_table!("my_data.zip", df) # zipped CSV. If no "inner" file name is given, the table is always stored in csv format with the same file name as the zip archive

JSON Format:

using JSONTables
    write_table!("my_data.json", df) # dictionary of arrays
    write_table!("my_data.json", df, orientation=:objecttable) # dictionary of arrays
    write_table!("my_data.json", df, orientation=:arraytable) # array of dictionaries

write_table!("my_data.zip", "my_data.json", df) # need to explicitly give a file name inside zip archive, otherwise csv format is used

Binary Formats:

using JDF
    write_table!("my_data.jdf", df) # JDF (compressed binary format)

using Parquet
    write_table!("my_data.parquet", df) # Parquet - note that Date element type is not supported yet

using Arrow
    write_table!("my_data.arrow", df) # Apache Arrow

import Pandas # using gives a naming conflict
    write_table!("my_data.hdf", "key", df) # HDF5 (via Pandas)

Excel:

write_table!("my_data.xlsx", "test_sheet_42", df) # creates sheet with defined name

SQLite:

using SQLite
    write_table!("my_data.db", "my_table", df) # SQLite from file, table must not exist

sqlite_db = SQLite.DB("my_data.db")
    write_table!(sqlite_db, "my_table", df) # SQLite from database connection

PostgreSQL:

using LibPQ, CSV
    postgres_conn = LibPQ.Connection("dbname=postgres user=postgres")
    write_table!(postgres_conn, "my_table", df) # table must exist and be compatible with the input data

StatFiles.jl integration: `write_table!` is not supported.

Additionally, it is possible to export tabular data into Julia code (`.jl` files):

write_table!("my_data.jl", "my_table", df)

To read this data, the corresponding Julia source code file can be included:

include("my_data.jl")
    @assert DataFrame(my_table) == df

## Conversions

It is possible to pass the output of `read_table` directly as input to `write_table!` for converting tabular data between different formats:

name1 = joinpath(testpath, "test.zip") # zipped CSV
    name2 = joinpath(testpath, "testx.jdf") # binary
    name3 = joinpath(testpath, "testx.xlsx") # Excel
    name4 = joinpath(testpath, "testx.db") # SQLite

write_table!(name2, read_table(name1))
    write_table!(name3, read_table(name2))
    write_table!(name4, "my_table", read_table(name3))

df_recovered = DataFrame(read_table(name4, "my_table"); copycols=false)

## PlutoUI Integration

In a [Pluto.jl](https://github.com/fonsp/Pluto.jl) notebook, TableIO can be used directly on a [PlutoUI.jl](https://github.com/fonsp/PlutoUI.jl) FilePicker output.

Example (run in a Pluto.jl notebook):

using PlutoUI, TableIO, DataFrames
    @bind f PlutoUI.FilePicker() # pick any supported file type
    df = DataFrame(read_table(f); copycols=false)

This functionality works for all supported file formats if the corresponding import packages are installed.
It is not required to import them, this is done automatically.

## Testing

The PostgreSQL component requires a running PostgreSQL database for unit tests. This database can be started using the following command:

`docker run --rm --detach --name test-libpqjl -e POSTGRES_HOST_AUTH_METHOD=trust -p 5432:5432 postgres`

## Disclaimer

If you encounter warnings like

┌ Warning: Package TableIO does not have CSV in its dependencies:
    │ - If you have TableIO checked out for development and have
    │   added CSV as a dependency but haven't updated your primary
    │   environment's manifest file, try `Pkg.resolve()`.
    │ - Otherwise you may need to report an issue with TableIO
    └ Loading CSV into TableIO from project dependency, future warnings for TableIO are suppressed.

please ignore them.

TableIO purposely has not included the libraries for the specific file formats as its own dependencies.

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