diff apollo/ApolloOrganism.py @ 2:4be6fcac4bf2 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

--- a/apollo/ApolloOrganism.py	Tue Nov 28 12:43:22 2017 -0500
+++ b/apollo/ApolloOrganism.py	Wed Nov 29 15:39:32 2017 -0500
@@ -12,7 +12,7 @@
         self.logger = logging.getLogger(__name__)
 
     def addOrganism(self):
-        exist = self.getOrganism(self.organism_name)
+        exist = subtools.arrow_get_organism(self.organism_name)
         if not exist:
             self.logger.debug("The organism does not exist.")
             p = subtools.arrow_add_organism(self.organism_name, self.organism_dir)
@@ -29,11 +29,11 @@
 
     #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API.
     def deleteOrganism(self):
-        organism_id = self.getOrganism(self.organism_name)
+        organism_id = subtools.arrow_get_organism(self.organism_name)
         if organism_id:
             self.logger.debug("Deleting the organism %s", self.organism_name)
             subtools.arrow_delete_organism(organism_id)
-            if not self.getOrganism(self.organism_name):
+            if not subtools.arrow_get_organism(self.organism_name):
                 self.logger.debug("Organism %s has been deleted", self.organism_name)
             else:
                 self.logger.error("Organism %s cannot be deleted", self.organism_name)
@@ -42,13 +42,6 @@
             self.logger.error("Organism %s doesn't exist", self.organism_name)
             exit(-1)
 
-    #TODO: filtering by commonName doesn't work. Improve the API.
-    @staticmethod
-    def getOrganism(organism_name):
-        p = subtools.arrow_get_organism(organism_name)
-        if p:
-            return str(p)
-
     #TODO: API update_organism not working. Improve the API to enable updating directory.
     def overwriteOrganism(self):
         self.deleteOrganism()