Mercurial > repos > yating-l > gonramp_apollo_tools
comparison apollo/ApolloOrganism.py @ 2:4be6fcac4bf2 draft default tip
planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
| author | yating-l |
|---|---|
| date | Wed, 29 Nov 2017 15:39:32 -0500 |
| parents | 1da8b9042af4 |
| children |
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| 1:78af01d73add | 2:4be6fcac4bf2 |
|---|---|
| 10 self.organism_name = organism_name | 10 self.organism_name = organism_name |
| 11 self.organism_dir = organism_dir | 11 self.organism_dir = organism_dir |
| 12 self.logger = logging.getLogger(__name__) | 12 self.logger = logging.getLogger(__name__) |
| 13 | 13 |
| 14 def addOrganism(self): | 14 def addOrganism(self): |
| 15 exist = self.getOrganism(self.organism_name) | 15 exist = subtools.arrow_get_organism(self.organism_name) |
| 16 if not exist: | 16 if not exist: |
| 17 self.logger.debug("The organism does not exist.") | 17 self.logger.debug("The organism does not exist.") |
| 18 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) | 18 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) |
| 19 if not p: | 19 if not p: |
| 20 self.logger.error("The user is not authorized to add organism") | 20 self.logger.error("The user is not authorized to add organism") |
| 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) | 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) | 28 exit(-1) |
| 29 | 29 |
| 30 #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API. | 30 #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API. |
| 31 def deleteOrganism(self): | 31 def deleteOrganism(self): |
| 32 organism_id = self.getOrganism(self.organism_name) | 32 organism_id = subtools.arrow_get_organism(self.organism_name) |
| 33 if organism_id: | 33 if organism_id: |
| 34 self.logger.debug("Deleting the organism %s", self.organism_name) | 34 self.logger.debug("Deleting the organism %s", self.organism_name) |
| 35 subtools.arrow_delete_organism(organism_id) | 35 subtools.arrow_delete_organism(organism_id) |
| 36 if not self.getOrganism(self.organism_name): | 36 if not subtools.arrow_get_organism(self.organism_name): |
| 37 self.logger.debug("Organism %s has been deleted", self.organism_name) | 37 self.logger.debug("Organism %s has been deleted", self.organism_name) |
| 38 else: | 38 else: |
| 39 self.logger.error("Organism %s cannot be deleted", self.organism_name) | 39 self.logger.error("Organism %s cannot be deleted", self.organism_name) |
| 40 exit(-1) | 40 exit(-1) |
| 41 else: | 41 else: |
| 42 self.logger.error("Organism %s doesn't exist", self.organism_name) | 42 self.logger.error("Organism %s doesn't exist", self.organism_name) |
| 43 exit(-1) | 43 exit(-1) |
| 44 | |
| 45 #TODO: filtering by commonName doesn't work. Improve the API. | |
| 46 @staticmethod | |
| 47 def getOrganism(organism_name): | |
| 48 p = subtools.arrow_get_organism(organism_name) | |
| 49 if p: | |
| 50 return str(p) | |
| 51 | 44 |
| 52 #TODO: API update_organism not working. Improve the API to enable updating directory. | 45 #TODO: API update_organism not working. Improve the API to enable updating directory. |
| 53 def overwriteOrganism(self): | 46 def overwriteOrganism(self): |
| 54 self.deleteOrganism() | 47 self.deleteOrganism() |
| 55 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) | 48 p = subtools.arrow_add_organism(self.organism_name, self.organism_dir) |