Roman Valls Guimera brainstorm

## tasks.py
#!/usr/bin/env python

import subprocess
from celery.task import task

# Task overlapping:
# lvm_create --> archive --> transfer(delayed?) --> (verify) --> lvm_destroy
#                basecalling --> fastq transfer (8h ?)
#   Without LVM:
#   archive     --> transfer --> verify

## logbook_mailhandler.py
#!/usr/bin/env python
# Small logbook snippet addressing some confusion on record injection

import logbook

handler = logbook.MailHandler("test@example.com", ['recipient@example.com'],
                              format_string=u'''Subject: [BCBB] {record.extra[run]} \n\n {record.message}''', level='INFO', bubble = True)

log = logbook.Logger("mailtest.log")

## add_final_a_index.py
#!/usr/bin/env python

import csv
import sys
import os

ss_reader = csv.DictReader(open(sys.argv[1], 'rU'))
ss_writer = csv.DictWriter(open(os.path.splitext(sys.argv[1])[0]+"_a.csv", 'w'), ss_reader.fieldnames)

ss_writer.writerow(dict((fn,fn) for fn in ss_reader.fieldnames))

## tarit_hiseq2000.sh
#!/bin/sh
# Generates a TAR archive while computing MD5 checksum for each file.
# From VeriTAR: http://www.g-loaded.eu/2007/12/01/veritar-verify-checksums-of-files-within-a-tar-archive/

DATASET_PATH=`readlink -f $1`
DATASET=`basename $DATASET_PATH`
EXCLUDE_FILES="--exclude .DS_Store --exclude .AppleDouble"

echo "Creating TAR + MD5 for dataset: $DATASET"
tar -cvpf $DATASET.tar $DATASET_PATH $EXCLUDE_FILES \

## dotfilter_symlinker.py
#!/bin/env python

import os
import logging
import glob
import random
from collections import *

fters = defaultdict(set)
all = set(["%04d.filter" % x for x in range(1, 70)])

## quick_delivery.sh
#!/bin/sh

DATASET="
SRC=""
DST=""

if [ -d ${SRC}${DATASET} ]; then
    echo "Copying ${SRC}${DATASET} into $DST..."
    chown -R $USER:uppmax ${SRC}${DATASET}
    rsync -a ${SRC}${DATASET} ${DST}

## slack_backup.py
import os
import time
import json
import gzip
import datetime
import requests
import cPickle as pickle
from datetime import datetime

slack_token = "<SLACK_TOKEN>"

## timelapse.py
#!/usr/bin/env python
import flickrapi
import datetime
import os
import shutil
import subprocess

api_key = 'SETME!!!'
api_secret = 'SETME!!!'

## svg_ipython.svg

      
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                IPython SVG and pyveplot broken graph
              
          
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## pouta-docker-machine.sh
#!/bin/bash

# To use an Openstack cloud you need to authenticate against keystone, which
# returns a **Token** and **Service Catalog**.  The catalog contains the
# endpoint for all services the user/tenant has access to - including nova,
# glance, keystone, swift.
#
# *NOTE*: Using the 2.0 *auth api* does not mean that compute api is 2.0.  We
# will use the 1.1 *compute api*
export OS_AUTH_URL=https://pouta.csc.fi:5001/v2.0
	#!/usr/bin/env python

	import subprocess
	from celery.task import task

	# Task overlapping:
	# lvm_create --> archive --> transfer(delayed?) --> (verify) --> lvm_destroy
	# basecalling --> fastq transfer (8h ?)
	# Without LVM:
	# archive --> transfer --> verify
	#!/usr/bin/env python
	# Small logbook snippet addressing some confusion on record injection

	import logbook

	handler = logbook.MailHandler("test@example.com", ['recipient@example.com'],
	format_string=u'''Subject: [BCBB] {record.extra[run]} \n\n {record.message}''', level='INFO', bubble = True)

	log = logbook.Logger("mailtest.log")
	#!/usr/bin/env python

	import csv
	import sys
	import os

	ss_reader = csv.DictReader(open(sys.argv[1], 'rU'))
	ss_writer = csv.DictWriter(open(os.path.splitext(sys.argv[1])[0]+"_a.csv", 'w'), ss_reader.fieldnames)

	ss_writer.writerow(dict((fn,fn) for fn in ss_reader.fieldnames))
	#!/bin/sh
	# Generates a TAR archive while computing MD5 checksum for each file.
	# From VeriTAR: http://www.g-loaded.eu/2007/12/01/veritar-verify-checksums-of-files-within-a-tar-archive/

	DATASET_PATH=`readlink -f $1`
	DATASET=`basename $DATASET_PATH`
	EXCLUDE_FILES="--exclude .DS_Store --exclude .AppleDouble"

	echo "Creating TAR + MD5 for dataset: $DATASET"
	tar -cvpf $DATASET.tar $DATASET_PATH $EXCLUDE_FILES \
	#!/bin/env python

	import os
	import logging
	import glob
	import random
	from collections import *

	fters = defaultdict(set)
	all = set(["%04d.filter" % x for x in range(1, 70)])
	#!/bin/sh

	DATASET="
	SRC=""
	DST=""

	if [ -d ${SRC}${DATASET} ]; then
	echo "Copying ${SRC}${DATASET} into $DST..."
	chown -R $USER:uppmax ${SRC}${DATASET}
	rsync -a ${SRC}${DATASET} ${DST}
	import os
	import time
	import json
	import gzip
	import datetime
	import requests
	import cPickle as pickle
	from datetime import datetime

	slack_token = "<SLACK_TOKEN>"
	#!/usr/bin/env python
	import flickrapi
	import datetime
	import os
	import shutil
	import subprocess

	api_key = 'SETME!!!'
	api_secret = 'SETME!!!'
	#!/bin/bash

	# To use an Openstack cloud you need to authenticate against keystone, which
	# returns a Token and Service Catalog. The catalog contains the
	# endpoint for all services the user/tenant has access to - including nova,
	# glance, keystone, swift.
	#
	# NOTE: Using the 2.0 auth api does not mean that compute api is 2.0. We
	# will use the 1.1 compute api
	export OS_AUTH_URL=https://pouta.csc.fi:5001/v2.0