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1 import os
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2 import subprocess
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3 import sys
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4
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5
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6 def find_packages(prefix="package_r_"):
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7 """
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8 """
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9 #locate env.sh | grep -i package_r_
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10 #/data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/env.sh
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11 #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/env.sh
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12 #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh
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13 #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh
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14 eprefix = prefix
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15 if prefix.find('/') <> -1:
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16 eprefix = prefix.replace('/','\/') # for grep
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17 path = '.'
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18 # fails on nitesh's recent mac - locate not working
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19 # cl = ['locate env.sh | grep -i %s' % eprefix,]
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20 cl = ['find %s -iname "env.sh" | grep -i %s' % (path,eprefix),]
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21 p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
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22 out, err = p.communicate()
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23 fpaths = out.split('\n')
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24 fpaths = [x for x in fpaths if len(x) > 1]
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25 fver = [x.split(os.path.sep)[-4:-1] for x in fpaths]
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26 # >>> foo.split(os.path.sep)[-4:-1]
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27 # ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
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28 if len(fpaths) > 0:
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29 res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)]
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30 res.insert(0,['Use default (system) interpreter','system',False])
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31 else:
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32 res = [['Use default (system) interpreter','system',False],
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33 ['**WARNING** NO package env.sh files found - is the "find" system command working? Are any interpreters installed?','system',True]]
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34 if len(res) > 2:
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35 res[1][2] = True # selected if more than one
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36 # return a triplet - user_sees,value,selected - all unselected if False
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37 return res
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38
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39 def testapi():
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40 host_url = 'http://localhost:8080'
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41 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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42 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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43 sys.path = new_path
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44 from galaxy import config
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45 aconfig = config.Configuration( )
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46 M_A_K = aconfig.master_api_key
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47 tooldeps = aconfig.tool_dependency_dir
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48 gi = GalaxyInstance(url=host_url, key=M_A_K)
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49
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50
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51 if __name__ == "__main__":
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52 print find_packages()
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53
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