Mercurial > repos > yating-l > gonramp_apollo_tools

annotate apollo/ApolloOrganism.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 4be6fcac4bf2
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1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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1 #!/usr/bin/env python
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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2
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yating-l
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3 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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4 import logging
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5 from util import subtools
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6
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7 class ApolloOrganism(object):
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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9 def __init__(self, organism_name, organism_dir):
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10 self.organism_name = organism_name
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11 self.organism_dir = organism_dir
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12 self.logger = logging.getLogger(__name__)
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13
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14 def addOrganism(self):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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15 exist = self.getOrganism(self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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16 if not exist:
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17 self.logger.debug("The organism does not exist.")
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18 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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19 if not p:
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20 self.logger.error("The user is not authorized to add organism")
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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21 exit(-1)
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22 organism = json.loads(p)
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23 organism_id = organism['id']
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24 self.logger.debug("A new organism %s was added to Apollo instance", p)
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25 return organism_id
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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26 else:
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27 self.logger.error("The organism %s is already on Apollo instance! Rerun the tool to use a different species name or choose to overwrite the organism", self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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28 exit(-1)
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30 #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API.
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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31 def deleteOrganism(self):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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32 organism_id = self.getOrganism(self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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33 if organism_id:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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34 self.logger.debug("Deleting the organism %s", self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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35 subtools.arrow_delete_organism(organism_id)
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36 if not self.getOrganism(self.organism_name):
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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37 self.logger.debug("Organism %s has been deleted", self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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38 else:
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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39 self.logger.error("Organism %s cannot be deleted", self.organism_name)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
yating-l
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40 exit(-1)
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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41 else:
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42 self.logger.error("Organism %s doesn't exist", self.organism_name)
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43 exit(-1)
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45 #TODO: filtering by commonName doesn't work. Improve the API.
1da8b9042af4 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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46 @staticmethod
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47 def getOrganism(organism_name):
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48 p = subtools.arrow_get_organism(organism_name)
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49 if p:
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50 return str(p)
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51
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52 #TODO: API update_organism not working. Improve the API to enable updating directory.
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53 def overwriteOrganism(self):
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54 self.deleteOrganism()
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55 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir)
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56 if not p:
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57 self.logger.error("The user is not authorized to add organism")
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58 exit(-1)
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59 organism = json.loads(p)
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60 organism_id = organism['id']
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61 self.logger.debug("A new organism %s has been added to Apollo instance", p)
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62 return organism_id
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63
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