SNPITDBClient

class snappl.dbclient.SNPITDBClient(url=None, username=None, password=None, passwordfile=None, **kwargs)[source]

Bases: rkAuthClient

A client for communcating with the Roman SNPIT internal database.

To use: instantiate. (See __init__ docstring.)

For the most part, most people will just pass this on as an argument to snappl library calls.

To use it directly, call one of the two methods “post” or “send”. Both take two arguments; the first is the relative URL to the base URL you passed to the constructor. (So, if the base url is “https://snpit-server.domain.org”, and you want to conatncat “https://snpit-server.domain.org/foo”, you would just pass “foo” as the URL to post or send.) The second argument is a dictionary that will be pased to the server as POST data. (See the documentation on the web API to figure out what you can send here.)

“post” will return a requests.Response object. “send” is what you call when you expect a JSON response; it will return you the parsed python object from the server (which will be a dictionary or a list).

Create a SNPITDBClient.

Parameters:

  • url (string) – The base URL of the roman snpit internal db. If not given, will use the config value system.db.url

  • username (string) – Username on the roman snpit internal db web api. If not given, will use the config value system.db.username

  • password (string) – Password on the roman snpit internal db web api. If not given, will first try using the config value system.db.password; if that is None, or if that is not in the config file, will read the passowrd as the first line in the file given in the config value system.db.passwordfile

  • retries (int, default 5) – When calling send or post, if the request to the server doesn’t return a HTTP 200, try again at most this many times.

  • maxtimeout (float, default 30.) – If retries are taking a very long time, don’t keep retrying if this much time has passed.

  • retrysleep (float, default 0.2) – After the first failed attempt to contact the server, sleep this many seconds before retrying.

  • sleepfac (float, default 2) – Multiply the sleep time by this much after each retry.

  • sleepfuzz (bool, default True) – Randomly adjust the sleep time by 10% of itself (Gaussian, sort of) so that if lots of processes are running, they will (hopefully) dsync.

  • verify (bool, default True) – Verify SSL certs? Sometimes for tests when you’re using a test web server with a self-signed cert you may need to set this to fale.

Attributes Summary

default_dbclient

Methods Summary

get([set_default, use_default])

Create a SNPITDBClient

Attributes Documentation

default_dbclient = None

Methods Documentation

classmethod get(set_default=True, use_default=True, **kwargs)[source]

Create a SNPITDBClient

All arguments are optional. Will pull the url, and username from config options system.db.url and system.db.username respectively. If system.db.password is null, will read the password from the file system.db.passwordfile, otherwise will use the password in system.db.password. (NOTE: you should leave system.db.password as null, as config files are usually global and are often committed to github archives!)

Parameters:

  • set_default (bool, default True) – If use_default is True and a SNPITDBClient has already been created, then just use that one. Otherwise, save the newly created SNPITDBClient as the default.

  • use_default (bool, default True) – If a SNPITDBClient has already been created, just return that. If this is False, or one doesn’t already exist, make a new one. WARNING : thought required about how this might interact with multiprocessing and/or multithreading. It may be safe, but you might want to make sure to always make a new dbclient with each new process.

  • url (string) – The base URL of the roman snpit internal db. If not given, will use the config value system.db.url

  • username (string) – Username on the roman snpit internal db web api. If not given, will use the config value system.db.username

  • password (string) – Password on the roman snpit internal db web api. If not given, will first try using the config value system.db.password; if that is None, or if that is not in the config file, will read the passowrd as the first line in the file given in the config value system.db.passwordfile

  • retries (int, default 5) – When calling send or post, if the request to the server doesn’t return a HTTP 200, try again at most this many times.

  • maxtimeout (float, default 30.) – If retries are taking a very long time, don’t keep retrying if this much time has passed.

  • retrysleep (float, default 0.2) – After the first failed attempt to contact the server, sleep this many seconds before retrying.

  • sleepfac (float, default 2) – Multiply the sleep time by this much after each retry.

  • sleepfuzz (bool, default True) – Randomly adjust the sleep time by 10% of itself (Gaussian, sort of) so that if lots of processes are running, they will (hopefully) dsync.

  • verify (bool, default True) – Verify SSL certs? Sometimes for tests when you’re using a test web server with a self-signed cert you may need to set this to fale.