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Fix #55 suppress_output for create_or_update_organism.py and delete_organism.py, version bump to 4.2.9 #57

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Fix #55 suppress_output for create_or_update_organism.py and delete_organism.py, version bump to 4.2.9 #57

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3c9b6ba
bump version to 4.2.6
Aug 25, 2020
d5301e5
disabled return_all for add_organism
Aug 25, 2020
49f9a0b
4.3.7 version bump and suppress_output
Aug 26, 2020
9105a6e
add suppress_output for delete_organism
Aug 26, 2020
b176afd
swap suppress_output true like expected
Aug 26, 2020
c05f9c0
bioconda updated apollo package, retesting
Aug 26, 2020
8e9f84d
replaced expected org metadata output
Aug 26, 2020
90a7b58
removed suppress_output from remote add
Aug 26, 2020
aadcce4
bump to 4.2.8 and suppress output in update
Sep 4, 2020
11a1cee
4.2.9 bump for update fix
Sep 7, 2020
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10 changes: 7 additions & 3 deletions tools/apollo/create_or_update_organism.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,8 @@ def zip_data_dir(dataset_data_dir, tar):
species=args.species,
public=args.public,
blatdb=blat_db,
no_reload_sequences=args.no_reload_sequences
no_reload_sequences=args.no_reload_sequences,
suppress_output=True
)
time.sleep(2)

Expand Down Expand Up @@ -219,7 +220,8 @@ def zip_data_dir(dataset_data_dir, tar):
genus=args.genus,
species=args.species,
public=args.public,
metadata=None
metadata=None,
suppress_output=True
)

# Must sleep before we're ready to handle
Expand All @@ -239,5 +241,7 @@ def zip_data_dir(dataset_data_dir, tar):
res = wa.groups.update_organism_permissions(group['name'], org_cn,
administrate=False, write=True, read=True,
export=True)
# Get expected metadata for organism since AllOrganism output is suppressed from add_organism
data = wa.organisms.show_organism(org_cn)

print(json.dumps(data, indent=2))
print(json.dumps([data], indent=2))
3 changes: 2 additions & 1 deletion tools/apollo/delete_organism.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,4 +55,5 @@ def IsRemote():
if IsRemote():
print(wa.remote.delete_organism(org['commonName']))
else:
print(wa.organisms.delete_organism(org['id']))
wa.organisms.delete_organism(org['id'], suppress_output=True)
print(org)
4 changes: 2 additions & 2 deletions tools/apollo/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
<?xml version="1.0"?>
<macros>
<token name="@WRAPPER_VERSION@">4.2.5</token>
<token name="@WRAPPER_VERSION@">4.2.9</token>

<xml name="requirements">
<requirements>
<requirement type="package" version="4.2.5">apollo</requirement>
<requirement type="package" version="4.2.9">apollo</requirement>
<yield/>
</requirements>
</xml>
Expand Down