diff test_bioblend.py @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_bioblend.py	Thu Oct 19 18:16:51 2017 -0400
@@ -0,0 +1,49 @@
+#/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)