Mercurial > repos > yating-l > jbrowsehubtoapollo

annotate util/Reader.py @ 0:bc00f5c4c59e draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git
author yating-l
date Tue, 17 Oct 2017 17:28:05 -0400
parents
children 2ae1e96a8380
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0
bc00f5c4c59e planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git
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1 import json
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2 import re
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3 import logging
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4 import codecs
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5 from apollo.ApolloUser import ApolloUser
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6 from util import santitizer
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7
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8 class Reader(object):
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9
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10 def __init__(self, input_json_file):
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11 self.inputFile = input_json_file
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12 self.args = self.loadJson()
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13
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14
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15 def loadJson(self):
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16 try:
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17 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
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18 return json.load(data_file)
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19 except IOError:
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20 print "Cannot find JSON file\n"
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21 exit(1)
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22
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23 def getJBrowseHubDir(self):
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24 try:
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25 return self.args["jbrowse_hub"]
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26 except KeyError:
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27 print ("jbrowse_hub is not defined in the input file!")
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28 exit(1)
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29
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30 def getToolDir(self):
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31 try:
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32 return self.args["tool_directory"]
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33 except KeyError:
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34 print ("tool_directory is not defined in the input file!")
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35 exit(1)
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36
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37 def getExtFilesPath(self):
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38 try:
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39 return self.args["extra_files_path"]
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40 except KeyError:
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41 print ("extra_files_path is not defined in the input file!")
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42 exit(1)
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43
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44 def getUserEmail(self):
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45 try:
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46 return self.args["user_email"]
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47 except KeyError:
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48 print ("user_email is not defined in the input file!")
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49 exit(1)
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50
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51 def getDebugMode(self):
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52 try:
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53 return self.args["debug_mode"]
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54 except KeyError:
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55 print ("debug_mode is not defined in the input file!")
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56 exit(1)
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57
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58 def getApolloHost(self):
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59 apollo_host = self.args.get("apollo_host")
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60 return apollo_host
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61
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62
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63 def getSpeciesName(self):
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64 species_name = santitizer.sanitize_name_input(self.args["species_name"])
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65 return species_name
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66
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67 def getGenomeName(self):
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68 jbrowse_hub = self.getJBrowseHubDir()
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69 with open(jbrowse_hub, 'r') as f:
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70 html = f.read()
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71 m = re.search('The new Organism "(.+?)" is created on Apollo', html)
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72 if m:
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73 genome_name = m.group(1)
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74 else:
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75 print("Cannot find genome name in the jbrowse hub file!")
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76 exit(1)
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77 return genome_name
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78
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79
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80 def getApolloUser(self):
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81 user_info = self.args.get("apollo_user")
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82 if not user_info:
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83 firstname = "demo"
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84 lastname = "user"
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85 password = "gonramp"
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86 user_email = self.getUserEmail()
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87 else:
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88 firstname = user_info['firstname']
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89 lastname = user_info['lastname']
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90 user_email = user_info['user_email']
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91 password = user_info['password']
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92 apollo_user = ApolloUser(user_email, firstname, lastname, password)
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93 return apollo_user
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94
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95