Mercurial > repos > sanbi-uwc > build_ctb_explorer

annotate build_ctb_explorer.py @ 1:0819302402d3 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
author sanbi-uwc
date Fri, 10 Jun 2016 05:01:56 -0400
parents e80a66932a1e
children 4af7d0144c82
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e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
sanbi-uwc
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1 #!/usr/bin/env python
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
sanbi-uwc
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2 from __future__ import print_function
1
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e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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4 import argparse
1
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
sanbi-uwc
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5 import datetime
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e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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6 import glob
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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7 import shutil
1
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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8
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9 import os
0
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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11 try:
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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12 from urllib.parse import urlparse
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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13 except ImportError:
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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14 from urlparse import urlparse
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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15 import logging
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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17 log = logging.getLogger(__name__)
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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19
1
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20 def copy_output_file_to_dataset(dir_name, input_dir, dt_type=None):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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21 """
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
sanbi-uwc
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22 Copy the datasets file to the news dataset cbt_browser
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
sanbi-uwc
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23 :param dir_name: the target output directory for the ctb_explorer dataset
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
sanbi-uwc
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24 :param input_dir: the input files
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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25 :param dt_type: the type of input dataset (neo4jdb, jbrowse - default to None)
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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26 :return: boolean
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
sanbi-uwc
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27 """
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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28 dt_loc = input_dir.rpartition('/')[2].replace(".dat", "_files")
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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29 if dt_type:
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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30 if dt_type == "neo4jdb":
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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31 src_files = glob.glob(os.path.dirname(input_dir) + '/{}/{}'.format(dt_loc, dt_type) + "/*" )
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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32 else:
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33 src_files = glob.glob(os.path.dirname(input_dir) + '/{}'.format(dt_loc) + "/*" )
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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34 else:
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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35 return False
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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36 for file_name in src_files:
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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37 if os.path.isfile(file_name):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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38 shutil.copy2(file_name, dir_name)
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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39 elif os.path.isdir(file_name):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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40 # create the parent dir before copytree
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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41 os.chdir(dir_name)
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42 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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43 return True
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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44
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45
0
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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46 class BuildCtbExplorerRunner(object):
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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47 def __init__(self, args=None):
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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48 """
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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49 Initializes an object to run CtbRunner in Galaxy.
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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50 """
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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51 # Check whether the options are specified and saves them into the object
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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52 self.args = args
1
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53 self.output_neo4jdb = args.output_neo4jdb
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54 self.output_jbrowser = args.output_jbrowser
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55 self.input_neo4jdb = args.input_neo4jdb
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56 self.input_jbrowser = args.input_jbrowser
0
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57
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58 def build_ctb_explorer(self):
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59 """
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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60 :rtype: boolean
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61 """
1
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62 if copy_output_file_to_dataset(self.output_neo4jdb, self.input_neo4jdb, dt_type="neo4jdb") and \
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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63 copy_output_file_to_dataset(self.output_jbrowser, self.input_jbrowser, dt_type="jbrowser"):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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64 print("CTB Report run time: %s" % str(datetime.date.today()))
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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65 print("Neo4jDB - Input: %s" % str(self.args.input_neo4jdb))
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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66 print("JBrowser - Input: %s" % str(self.args.input_jbrowser))
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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67 else:
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68 return False
0
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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69 return True
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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70
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71
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72 def main():
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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73 parser = argparse.ArgumentParser(description="Tool used to build a combat-tb explorer dataset")
1
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74 parser.add_argument('--output_neo4jdb')
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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75 parser.add_argument('--output_jbrowser')
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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76 parser.add_argument('--input_neo4jdb')
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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77 parser.add_argument('--input_jbrowser')
0
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78 args = parser.parse_args()
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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79
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80 ctb_explorer_runner = BuildCtbExplorerRunner(args)
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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81
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82 # make the output directory (neo4j)
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83 if not os.path.exists(args.output_neo4jdb):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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84 os.makedirs(args.output_neo4jdb)
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85
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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86 # make the output directory (jbrowser)
1
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87 if not os.path.exists(args.output_jbrowser):
0819302402d3 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit ea7fb439a8f9fbb055af51db4aa3dd3469f273b0
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88 os.makedirs(args.output_jbrowser)
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89
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90 status = ctb_explorer_runner.build_ctb_explorer()
e80a66932a1e planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/build_ctb_explorer commit a955714f2385d7b35f795cf1442a15492ecacb8f
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91
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92 if status is None:
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93 exit(1)
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94
1
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95 if __name__ == "__main__": main()