nerdstrike

#!/usr/bin/env python

# Find sample in warehouse, also find a study row
# Feed to npg_irods.metadata.lims.make_sample_metadata()
# Extract AVU objects and convert to JSON. They'll be turned back into AVUs later... but that's batching for you.

import json
import sqlalchemy
from npg.conf import IniData
from npg_irods.db import Config

nerdstrike

#!/usr/bin/env perl
# perl simplify_aviti_runstats.pl RunStats.json
# Emits a file in the same location with the name slim_RunStats.json

use strict;
use warnings;
use JSON;
use File::Slurp qw/read_file write_file/;

my $file_name = shift;

nerdstrike

{
   "graph" : {
      "label" : "NPG sequence pipeline job dependency graph",
      "metadata": { "description": "Perhaps we could put pipeline defaults here?" },
      "edges" : [...],
      "nodes" : [
         {
             "id" : "pipeline_start",
             "label" : "pipeline_start",
             "metadata": {

nerdstrike

import ariadne
from ariadne import QueryType, ObjectType, UnionType
import pymongo
from aiodataloader import DataLoader
from collections import defaultdict

config = {
    'host': 'IPADDRESS',
    'port': 'PORT',
    'user': 'USER',

nerdstrike

package Catalyst::Authentication::Store::ElasticSearch;

use strict;
use warnings;

use Moose;
use MooseX::NonMoose;
use Catalyst::Exception;
use Catalyst::Authentication::Store::ElasticSearch::User; # The default user storage class