cleaned up commit

README.rst

@@ -1,4 +1,3 @@
-
 Apollo API Library
 ==================
 

apollo/organisms/__init__.py

@@ -70,7 +70,6 @@ def update_organism(self, organism_id, common_name, directory, blatdb=None, spec
         """
         Update an organism
 
-        :param no_reload_sequences:
 
         :type organism_id: str
         :param organism_id: Organism ID Number
@@ -93,6 +92,9 @@ def update_organism(self, organism_id, common_name, directory, blatdb=None, spec
         :type public: bool
         :param public: User's email
 
+        :type no_reload_sequences: bool
+        :param no_reload_sequences:
+
         :rtype: dict
         :return: a dictionary with information about the updated organism
         """

bootstrap_apollo.sh

@@ -3,12 +3,13 @@
 export GALAXY_SHARED_DIR=`pwd`/apollo_shared_dir
 mkdir -p "$GALAXY_SHARED_DIR"
 
-docker run --memory=4g -d -it -p 8888:8080 -v `pwd`/apollo_shared_dir/:`pwd`/apollo_shared_dir/ quay.io/gmod/apollo:latest
+#docker run --memory=4g -d -it -p 8888:8080 -v `pwd`/apollo_shared_dir/:`pwd`/apollo_shared_dir/ quay.io/gmod/apollo:latest
 
 echo "[BOOTSTRAP] Waiting while Apollo starts up..."
 # Wait for apollo to be online
 for ((i=0;i<30;i++))
 do
+    echo $i
     APOLLO_UP=$(arrow users get_users 2> /dev/null | head -1 | grep '^\[$' -q; echo "$?")
 	if [[ $APOLLO_UP -eq 0 ]]; then
 		break

test-data/arrow.yml

@@ -1,5 +1,5 @@
 __default: local
 local:
-    url: "http://localhost:8888"
-    username: "[email protected]"
-    password: "password"
+    url: "http://localhost:8080/apollo"
+    username: "[email protected]"
+    password: "demo"

test/organism_test.py

@@ -95,8 +95,6 @@ def test_delete_organism(self):
         time.sleep(3)
 
         org_info = wa.organisms.show_organism('temp_org')
-        print "DELETE WITH ID"
-        print json.dumps(org_info)
 
         wa.organisms.delete_organism(org_info['id'])
 
@@ -165,16 +163,12 @@ def test_update_organism(self):
         other_org_info = wa.organisms.show_organism('test_organism')
 
         org_info = wa.organisms.show_organism('temp_org')
-        print "BBBBB"
-        print json.dumps(org_info)
 
         wa.organisms.update_organism(org_info['id'], 'temp_org', other_org_info['directory'], species='updatedspecies', genus='updatedgenus', blatdb=other_org_info['directory'] + "/seq/genome.2bit", public=False, no_reload_sequences=True)
         # Returns useless stuff
 
         time.sleep(3)
         org_info = wa.organisms.show_organism('temp_org')
-        print "CCCCC"
-        print json.dumps(org_info)
 
         assert org_info['species'] == 'updatedspecies'
         assert org_info['genus'] == 'updatedgenus'

test/remote_test.py

@@ -15,18 +15,11 @@ def test_delete_organism(self):
         time.sleep(3)
 
         org_info = wa.organisms.show_organism('temp_org')
-        orgs = wa.organisms.get_organisms()
-
-        print "AAAAA"
-        print json.dumps(org_info)
-        print "org count"
-        print str(len(orgs))
+        # orgs = wa.organisms.get_organisms()
 
         wa.remote.delete_organism(org_info['id'])
 
         time.sleep(3)
-        print "B org count"
-        print str(len(orgs))
 
         orgs = wa.organisms.get_organisms()