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