Mercurial > repos > yating-l > gonramp_apollo_tools

annotate util/Reader.py @ 0:1da8b9042af4 draft

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Mon, 27 Nov 2017 14:47:03 -0500
parents
children
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0
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
parents:
diff changeset
1 import json
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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2 import re
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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3 import logging
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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4 import codecs
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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5 import socket
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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6 from apollo.ApolloUser import ApolloUser
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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7 from util import santitizer
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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8
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yating-l
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9 class Reader(object):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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10
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11 def __init__(self, input_json_file):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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12 self.inputFile = input_json_file
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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13 self.args = self.loadJson()
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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14
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15
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16 def loadJson(self):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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17 try:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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18 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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19 return json.load(data_file)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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20 except IOError:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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21 print "Cannot find JSON file\n"
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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22 exit(1)
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23
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24 def getJBrowseHubDir(self):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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25 try:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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26 return self.args["jbrowse_hub"]
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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27 except KeyError:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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28 print ("jbrowse_hub is not defined in the input file!")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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29 exit(1)
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30
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31 def getToolDir(self):
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32 try:
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33 return self.args["tool_directory"]
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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34 except KeyError:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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35 print ("tool_directory is not defined in the input file!")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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36 exit(1)
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37
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38 def getExtFilesPath(self):
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39 try:
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yating-l
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40 return self.args["extra_files_path"]
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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41 except KeyError:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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42 print ("extra_files_path is not defined in the input file!")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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43 exit(1)
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44
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45 def getUserEmail(self):
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46 try:
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47 return self.args["user_email"]
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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48 except KeyError:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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49 print ("user_email is not defined in the input file!")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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50 exit(1)
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51
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52 def getDebugMode(self):
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53 try:
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54 return self.args["debug_mode"]
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55 except KeyError:
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56 print ("debug_mode is not defined in the input file!")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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57 exit(1)
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58
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59 def getPortNum(self):
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60 try:
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61 return self.args["port"]
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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62 except KeyError:
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63 print ("port is not defined in the input file!")
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64 exit(1)
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65
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66 def getApolloHost(self):
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67 #apollo_host = self.args.get("apollo_host")
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68 hostname = socket.gethostname()
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69 ip = socket.gethostbyname(hostname)
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70 protocol = socket.getprotobyname(hostname)
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71 apollo_host = str(protocol) + str(ip)
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72 return apollo_host
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73
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74
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75 def getSpeciesName(self):
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76 species_name = santitizer.sanitize_name_input(self.args["species_name"])
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77 return species_name
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78
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79 def getAction(self):
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80 action = self.args.get("action")
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81 return action
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82
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83 def getAdminUser(self):
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84 apollo_admin = self.args.get("apollo_admin")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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85 return apollo_admin
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86
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87
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88 def getOperationList(self):
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89 l = self.args.get("operations")
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90 return l
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91
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92