andrewmagill

from collections import namedtuple
import pprint

## parsing user input ##

# named tuples to make things more organized?
Event = namedtuple('Event','process event')
Message = namedtuple('Message', 'sender receiver')

# raw input, ostensibly from the user

andrewmagill

services (all)

https://bisque.cyverse.org/services

data services

https://bisque.cyverse.org/data_service

data service - user

andrewmagill

The Kernel Newbie Corner

Rob Day, Linux.com

1. Your First Loadable Kernel Module - June 26, 2009
2. Your First Loadable Kernel, Part 2 - July 1, 2009
3. Loadble Kernel Modules, Coming and Going - July 8, 2009
4. Everything You Wanted to Know About Module Params- July 15, 2009
5. Building and Running a New Kernel - July 22, 2009
6. Kernel Symbols: What's Available to Your Module - July 29, 2009
7. [What's in That Loadable Module, Anyway? - Augus

andrewmagill

Design Document

Environment

VMs

• Main CMS portal
  • Public Facing portal
  • Admin portal (behind VPN)
• Main API

andrewmagill

Relationships between IDS Objects:

----------------------------

Project to Specimen

    [Contains, <specimen_id>] (alternate option: HasPart)

Specimen to Project

andrewmagill

You can query against relationships using mongodb's $elemMatch syntax. E.g.,

$ metadata-list -v -Q '{"value._relationships": {"$elemMatch": {"@id": "1539251546393416166-242ac11f-0001-012"}}}'

andrewmagill

#!/bin/bash

export PATH=$PATH:"$HOME/.aspera/connect/bin"

# get UUID and SRA number
UUID=${UUID}
SRA_NUM=${SRA}
AGAVE_FILE=${AGAVE_URL}
EXTERNAL_URL=${URL}
SRA_PATH="./SRA/"

andrewmagill

{
	"id": "demo.execute.example.com",        # id (string): Unique identifier for this system.
	"name": "Demo SGE + GSISSH demo vm",     # name (string): Common name for this system.
	"status": "UP",                          # status (string) = ['UP' or 'DOWN' or 'UNKNOWN']: The functional status of this system. Systems must be in UP status to be used.
	"type": "EXECUTION",                     # type (string) = ['EXECUTION' or 'STORAGE']: The type of this system.
	"description": "My example system using gsissh and gridftp to submit jobs used for testing.",    # description (string, optional): Verbose description of this system.
	"site": "example.com",                   # site (string, optional): The site associated with this system.
	"executionType": "HPC",                  # executionType (string) = ['HPC' or 'CONDOR' or 'CLI']: The execution paradigm used to run jobs on this system.
	"queues": [                              # queues (List[BatchQueue]): The execution paradigm used to run jobs on this system.

andrewmagill

[check] metatest 1: {"name":"metadata-test","value":"1","associationIds":["4096302858573966875-242ac11d-0001-012","4320264451024490981-242ac11d-0001-012","3705648026154823195-242ac1110-0001-012","4154082056836607515-242ac1110-0001-012","1995049352723501541-242ac1110-0001-012"]}
[check] metatest 2: {"name":"metadata-test","value":"2","associationIds":["4320264451024490981-242ac11d-0001-012","3705648026154823195-242ac1110-0001-012","4154082056836607515-242ac1110-0001-012","1995049352723501541-242ac1110-0001-012"]}
[check] metatest 3: {"name":"metadata-test","value":"3","associationIds":["3705648026154823195-242ac1110-0001-012","4154082056836607515-242ac1110-0001-012","1995049352723501541-242ac1110-0001-012"]}
[check] metatest 4: {"name":"metadata-test","value":"4","associationIds":"4320264451024490981-242ac11d-0001-012"}

### expect one match

test 1: {"associationIds": { $in: ["4096302858573966875-242ac11d-0001-012"]}}
--> {"name": "metadata-test", "value": 1}

andrewmagill

import logging
import pdb

# this config may already be done for you, if you're working on a shared project
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.DEBUG)

# you'll have to do this to get the configured logger though
logger = logging.getLogger(__name__)

# variables we'll work with