sqlutilpy 0.26.0
Database query code returning numpy arrays
License: BSD
Requires Python: >=3.8
Keywords: numpy postgresql query sql sqlite array

[![Build Status](https://github.com/segasai/sqlutilpy/workflows/Testing/badge.svg)](https://github.com/segasai/sqlutilpy/actions)
[![Documentation Status](https://readthedocs.org/projects/sqlutilpy/badge/?version=latest)](http://sqlutilpy.readthedocs.io/en/latest/?badge=latest)
[![Coverage Status](https://coveralls.io/repos/github/segasai/sqlutilpy/badge.svg?branch=master)](https://coveralls.io/github/segasai/sqlutilpy?branch=master)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6867957.svg)](https://doi.org/10.5281/zenodo.6867957)

# sqlutilpy
Python module to query SQL databases and return numpy arrays, upload
tables and run join queries involving local arrays and the tables in the DB.
This module is optimized to deal efficiently with query results with millions of rows.
The module works with PostgreSQL, SQLite and DuckDB databases.

The full documentation is available [here](http://sqlutilpy.readthedocs.io/en/latest/)

Author: Sergey Koposov (Uni of Cambridge/CMU/Uni of Edinburgh)

## Installation
To install the package you just need to do pip install. 

```
pip install sqlutilpy
```
## Authentication

Throughout this readme, I will assume that if you are using PostgreSQL, then
the .pgpass file ( https://www.postgresql.org/docs/11/libpq-pgpass.html ) 
has been created with your login/password details for Postgresql. If that is not the case, many of the 
commands given below will also need user='....' and password='...' options.

## Connection information

Most of the `sqlutilpy` commands require hostname, database name.  
If you don't want to always type it, you can use standard PostgreSQL environment variables
like PGPORT, PGDATABASE, PGUSER, PGHOST for the port, database name, user name and hostname
of the connection. 


## Querying the database and retrieving the results

This command will run the query and put the columns into variables ra,dec:

```python
import sqlutilpy
ra,dec = squtilpy.get('select ra,dec from mytable', 
                 host='HOST_NAME_OF_MY_PG_SERVER', 
                 db='THE_NAME_OF_MY_DB')
```

By default `sqlutilpy.get` executes the query and returns the tuple with 
arrays. One array for each column in the query result. 
You can return the results as dictionary using `asDict` option.

## Uploading your arrays as column in a table

You can use `sqlutilpy.upload` to upload your arrays as columns in a table.

```python
x = np.arange(10)                                                   
y = x**.5                                                           
sqlutilpy.upload('mytable',(x,y),('xcol','ycol'))    
``` 
This will create a table called `mytable` with columns `xcol` and `ycol` 

## Join query involving your local data and the database table

Sometimes it is beneficial to run a join query involving your local data and the data in the database.

Imagine you have arrays `myid` and `y` and you want to extract all the 
information from `somebigtable` for objects with `id=myid`. In principle,
you could upload the arrays in the DB and run a query, but `local_join` function does that for you.

```python
myid = np.arange(10)
y = np.random.uniform(size=10)

R=sqlutilpy.local_join('''select * from mytmptable as m, 
           somebigtable as s where s.id=m.myid order by m.myid''',                                              
           'mytmptable',(myid, y),('myid','ycol'))
```

It executes a query as if your arrays were in `mytmptable`. What happens behind the scenes
is that it uploads the data to the database and runs a query against it.

## Keeping the connection open. 

Often it is beneficial to preserve an open connection to the database. You can do that if you first 
obtain the connection using `sqlutilpy.getConnection()` and then provide it directly
to `sqlutil.get()` and similar commands using `conn=` keyword:
conn = sqlutilpy.getConnection(db='mydb', user='meuser', password='something', host='hostname')
R= sqlutilpy.get('select 1', conn=conn)
R1= sqlutilpy.get('select 1', conn=conn)
```

# How to cite the software

If you use this package, please cite it through Zenodo https://doi.org/10.5281/zenodo.5160118