Mercurial > repos > charles_s_test > seqsero

annotate test_bioblend.py @ 1:139f1e77d834 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
author charles_s_test
date Fri, 27 Oct 2017 17:22:36 -0400
parents 8db411fab3e1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
1 #/usr/bin/python
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
2
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
3 import sqlite3, re, os
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
4 from bioblend import galaxy
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
5
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
6 #out = open("/opt/galaxy/tools/seqserobatch/test.txt", 'w')
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
7
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
8 def get_bioblend_id():
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
9 # gi = galaxy.GalaxyInstance(url='http://galaxy.fda.gov:8080/', key='ebec9b999774b69d3f3880f0f664f56e')
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
10 gi = galaxy.GalaxyInstance(url='https://dev.galaxytrakr.org/')
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
11 job = galaxy.jobs.JobsClient(gi)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
12 j = job.get_jobs()
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
13 while j[0]['exit_code'] == 'None':
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
14 print j[0]['id'], j[0]['exit_code']
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
15 print j[0]['id'], j[0]['exit_code']
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
16
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
17 # dataset_id = galaxy.datasets.DatasetClient(gi)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
18 # output = show_stdout(dataset_id)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
19 # print output
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
20 # data = download_dataset(dataset_id, wait_for_completion=True)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
21 # print dataset_id.show_stdout()
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
22 #print gi, job
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
23
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
24 # print '"'+'tiger'+'"'
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
25 return j[0]['id']
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
26
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
27 def get_job_id(bioblend_id):
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
28 # print 'supermonkey', bioblend_id
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
29 database = '/opt/galaxy/database/universe.sqlite'
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
30 conn = sqlite3.connect(database)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
31 select = 'SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%"+bioblend_id+"%"+"'"+';'
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
32 # print select
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
33 # entries = conn.execute('SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%"+bioblend_id+"%"+"'"+';')
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
34 entries = conn.execute('SELECT job.id, job.stdout FROM job WHERE job.stdout LIKE '+"'"+"%ecbc86ac41da8f7b%"+"'"+';')
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
35 print type(entries)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
36 print entries
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
37 print select
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
38 for entry in entries:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
39 print entry
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
40 for line in entry:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
41 line = str(line)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
42 print line
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
43 # print entries
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
44
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
45 #out.write(j_join)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
46
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
47 bioblend_id = get_bioblend_id()
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
48 #print bioblend_id
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
49 #get_job_id(bioblend_id)