diff apollo/ApolloOrganism.py @ 0:ce4f91831680 draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/apollo/ApolloOrganism.py	Fri Feb 16 10:57:13 2018 -0500
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import json
+import logging
+from util import subtools
+
+class ApolloOrganism(object):
+
+    def __init__(self, organism_name, organism_dir):
+        self.organism_name = organism_name
+        self.organism_dir = organism_dir
+        self.logger = logging.getLogger(__name__)
+
+    def addOrganism(self):
+        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)
+            if not p:
+                self.logger.error("The user is not authorized to add organism")
+                exit(-1)
+            organism = json.loads(p)
+            organism_id = organism['id']
+            self.logger.debug("A new organism %s was added to Apollo instance", p)
+            return organism_id
+        else:
+            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)
+            exit(-1)
+
+    #TODO: the JSON dictionary return by deleteOrganism still contains the deleted organism. Improve the API.
+    def deleteOrganism(self):
+        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 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)
+                exit(-1)
+        else:
+            self.logger.error("Organism %s doesn't exist", self.organism_name)
+            exit(-1)
+
+    #TODO: API update_organism not working. Improve the API to enable updating directory.
+    def overwriteOrganism(self):
+        self.deleteOrganism()
+        p = subtools.arrow_add_organism(self.organism_name, self.organism_dir)
+        if not p:
+            self.logger.error("The user is not authorized to add organism")
+            exit(-1)
+        organism = json.loads(p)
+        organism_id = organism['id']
+        self.logger.debug("A new organism %s has been added to Apollo instance", p)
+        return organism_id
+        
+    
+    
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