Mercurial > repos > fubar > tool_factory_2

comparison getlocalrpackages.py @ 25:9fe74bd23af2 draft

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author fubar
date Mon, 02 Mar 2015 05:18:21 -0500
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24:1a4d3923aa9f 25:9fe74bd23af2
1 import os
2 import subprocess
3 import sys
4
5
6 def find_packages(prefix="package_r_"):
7 """
8 """
9 #locate env.sh | grep -i package_r_
10 #/data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/env.sh
11 #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/env.sh
12 #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh
13 #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh
14 eprefix = prefix
15 if prefix.find('/') <> -1:
16 eprefix = prefix.replace('/','\/') # for grep
17 path = '.'
18 # fails on nitesh's recent mac - locate not working
19 # cl = ['locate env.sh | grep -i %s' % eprefix,]
20 cl = ['find %s -iname "env.sh" | grep -i %s' % (path,eprefix),]
21 p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
22 out, err = p.communicate()
23 fpaths = out.split('\n')
24 fpaths = [x for x in fpaths if len(x) > 1]
25 fver = [x.split(os.path.sep)[-4:-1] for x in fpaths]
26 # >>> foo.split(os.path.sep)[-4:-1]
27 # ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
28 if len(fpaths) > 0:
29 res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)]
30 res.insert(0,['Use default (system) interpreter','system',False])
31 else:
32 res = [['Use default (system) interpreter','system',False],
33 ['**WARNING** NO package env.sh files found - is the "find" system command working? Are any interpreters installed?','system',True]]
34 if len(res) > 2:
35 res[1][2] = True # selected if more than one
36 # return a triplet - user_sees,value,selected - all unselected if False
37 return res
38
39 def testapi():
40 host_url = 'http://localhost:8080'
41 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
42 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
43 sys.path = new_path
44 from galaxy import config
45 aconfig = config.Configuration( )
46 M_A_K = aconfig.master_api_key
47 tooldeps = aconfig.tool_dependency_dir
48 gi = GalaxyInstance(url=host_url, key=M_A_K)
49
50
51 if __name__ == "__main__":
52 print find_packages()
53