view test_bioblend.py @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

#/usr/bin/python

import sqlite3, re, os
from bioblend import galaxy

#out = open("/opt/galaxy/tools/seqserobatch/test.txt", 'w')

def get_bioblend_id():
#	gi = galaxy.GalaxyInstance(url='http://galaxy.fda.gov:8080/', key='ebec9b999774b69d3f3880f0f664f56e')
	gi = galaxy.GalaxyInstance(url='https://dev.galaxytrakr.org/')
	job = galaxy.jobs.JobsClient(gi)
	j = job.get_jobs()
	while j[0]['exit_code'] == 'None':
		print j[0]['id'], j[0]['exit_code']
	print j[0]['id'], j[0]['exit_code']
	
#	dataset_id = galaxy.datasets.DatasetClient(gi)
#	output = show_stdout(dataset_id)
#	print output
#	data = download_dataset(dataset_id, wait_for_completion=True)
#	print dataset_id.show_stdout()
	#print gi, job

#	print '"'+'tiger'+'"'
	return j[0]['id']

def get_job_id(bioblend_id):
#	print 'supermonkey', bioblend_id
	database = '/opt/galaxy/database/universe.sqlite'
	conn = sqlite3.connect(database)
	select = 'SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%"+bioblend_id+"%"+"'"+';'
#	print select
#	entries = conn.execute('SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%"+bioblend_id+"%"+"'"+';')
	entries = conn.execute('SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%ecbc86ac41da8f7b%"+"'"+';')
	print type(entries)
	print entries
	print select
	for entry in entries:
		print entry
		for line in entry:
			line = str(line)
			print line
#	print entries

#out.write(j_join)

bioblend_id = get_bioblend_id()
#print bioblend_id
#get_job_id(bioblend_id)