Mercurial > repos > charles_s_test > seqsero

annotate test_bioblend.py @ 0:8db411fab3e1 draft

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