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comparison util/add_datatype.py @ 0:0bca8a6364a7 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 17:21:18 -0500
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-1:000000000000 0:0bca8a6364a7
1 #!/usr/bin/python
2
3 """
4 This script copy the huba datatype into your galaxy:
5 - Add under <registration>, the datatype_conf
6 - Add huba.xml under display_application/ucsc/
7 - Add hubAssembly.py inside lib/galaxy/datatypes
8 Place yourself in the folder of the python script, and launch it
9 - Based on the fact datatypes_conf
10 """
11
12 import argparse
13 import os
14 import shutil
15 import sys
16 import xml.etree.ElementTree as ET
17
18
19 def main(argv):
20 # Command Line parsing init
21 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
22
23 parser.add_argument('-g', '--galaxy_root', help='Galaxy root folder', required=True)
24
25 # Get the args passed in parameter
26 args = parser.parse_args()
27
28 galaxy_root_path = args.galaxy_root
29
30 add_datatype_conf(galaxy_root_path)
31 add_huba_xml(galaxy_root_path)
32 add_hubAssembly(galaxy_root_path)
33
34
35 def add_datatype_conf(galaxy_root_path):
36 print "======= Add datatype ======="
37 datatype_conf_path = os.path.join(galaxy_root_path, 'config/datatypes_conf.xml')
38 # TODO: Not relative to this python file but based on a parameter galaxy_root
39 # TODO: Check if datatypes_conf.xml, if not create it by copying datatypes_conf.xml.sample
40 # TODO: For debug only
41 # tree = ET.parse('../test-data/add_datatype/datatypes_conf.xml.sample')
42 # TODO: UnComment for prod
43 tree = ET.parse(datatype_conf_path)
44 root = tree.getroot()
45 print root.tag
46 registration = root[0]
47 print registration.attrib
48
49 huba_datatype = ET.parse('../trackHub/datatypes_conf.xml').getroot()
50 # TODO: Verify the datatype is not already existing, else do not add / write. And in another version, check it
51 registration.append(huba_datatype)
52 tree.write(datatype_conf_path)
53 print "datatype added in %s" % datatype_conf_path
54 return
55
56
57 def add_huba_xml(galaxy_root_path):
58 print "======= Add hub xml ======="
59 displayApp_ucsc_path = os.path.join(galaxy_root_path, "display_applications/ucsc/")
60 shutil.copy("../trackHub/huba.xml", displayApp_ucsc_path)
61 print "Content of %s now: %s" % (displayApp_ucsc_path, os.listdir(displayApp_ucsc_path))
62 return
63
64
65 def add_hubAssembly(galaxy_root_path):
66 print "======= Add hubAssembly ======="
67 datatype_lib_path = os.path.join(galaxy_root_path, "lib/galaxy/datatypes/")
68 shutil.copy("../trackHub/hubAssembly.py", datatype_lib_path)
69 print "Content of %s now: %s" % (datatype_lib_path, os.listdir(datatype_lib_path))
70 return
71
72
73 if __name__ == "__main__":
74 main(sys.argv)