Mercurial > repos > yating-l > gonramp_apollo_tools
comparison apollo/ApolloOrganism.py @ 0:ce4f91831680 draft default tip
planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
| author | yating-l |
|---|---|
| date | Fri, 16 Feb 2018 10:57:13 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:ce4f91831680 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import json | |
| 4 import logging | |
| 5 from util import subtools | |
| 6 | |
| 7 class ApolloOrganism(object): | |
| 8 | |
| 9 def __init__(self, organism_name, organism_dir): | |
| 10 self.organism_name = organism_name | |
| 11 self.organism_dir = organism_dir | |
| 12 self.logger = logging.getLogger(__name__) | |
| 13 | |
| 14 def addOrganism(self): | |
| 15 exist = subtools.arrow_get_organism(self.organism_name) | |
| 16 if not exist: | |
| 17 self.logger.debug("The organism does not exist.") | |
| 18 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) | |
| 19 if not p: | |
| 20 self.logger.error("The user is not authorized to add organism") | |
| 21 exit(-1) | |
| 22 organism = json.loads(p) | |
| 23 organism_id = organism['id'] | |
| 24 self.logger.debug("A new organism %s was added to Apollo instance", p) | |
| 25 return organism_id | |
| 26 else: | |
| 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) | |
| 28 exit(-1) | |
| 29 | |
| 30 #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API. | |
| 31 def deleteOrganism(self): | |
| 32 organism_id = subtools.arrow_get_organism(self.organism_name) | |
| 33 if organism_id: | |
| 34 self.logger.debug("Deleting the organism %s", self.organism_name) | |
| 35 subtools.arrow_delete_organism(organism_id) | |
| 36 if not subtools.arrow_get_organism(self.organism_name): | |
| 37 self.logger.debug("Organism %s has been deleted", self.organism_name) | |
| 38 else: | |
| 39 self.logger.error("Organism %s cannot be deleted", self.organism_name) | |
| 40 exit(-1) | |
| 41 else: | |
| 42 self.logger.error("Organism %s doesn't exist", self.organism_name) | |
| 43 exit(-1) | |
| 44 | |
| 45 #TODO: API update_organism not working. Improve the API to enable updating directory. | |
| 46 def overwriteOrganism(self): | |
| 47 self.deleteOrganism() | |
| 48 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) | |
| 49 if not p: | |
| 50 self.logger.error("The user is not authorized to add organism") | |
| 51 exit(-1) | |
| 52 organism = json.loads(p) | |
| 53 organism_id = organism['id'] | |
| 54 self.logger.debug("A new organism %s has been added to Apollo instance", p) | |
| 55 return organism_id | |
| 56 | |
| 57 | |
| 58 |