[ARVADOS] updated: 67f17818338153fc6f7b0c65f51e97bbb16f0cc7
git at public.curoverse.com
git at public.curoverse.com
Tue May 13 13:14:44 EDT 2014
Summary of changes:
sdk/cli/bin/arv-run-pipeline-instance | 46 ++++++++++++++++++++++-------------
sdk/ruby/lib/arvados.rb | 7 +++---
2 files changed, 33 insertions(+), 20 deletions(-)
via 67f17818338153fc6f7b0c65f51e97bbb16f0cc7 (commit)
from d0b6bb76a0a7478794faebd3e1e5ab94b717596d (commit)
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commit 67f17818338153fc6f7b0c65f51e97bbb16f0cc7
Author: Tom Clegg <tom at curoverse.com>
Date: Tue May 13 13:13:58 2014 -0400
2673: Move auth to headers, avoid combining request body with GET method.
diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index b86b217..e552d77 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -226,10 +226,10 @@ class PipelineInstance
:parameters => {
:uuid => uuid
},
- :body => {
- :api_token => ENV['ARVADOS_API_TOKEN']
- },
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
debuglog "Failed to get pipeline_instance: #{j[:errors] rescue nil}", 0
@@ -242,10 +242,12 @@ class PipelineInstance
def self.create(attributes)
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
:body => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:pipeline_instance => attributes
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
abort "Failed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
@@ -259,10 +261,12 @@ class PipelineInstance
:uuid => @pi[:uuid]
},
:body => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:pipeline_instance => @attributes_to_update.to_json
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
debuglog "Failed to save pipeline_instance: #{j[:errors] rescue nil}", 0
@@ -291,20 +295,24 @@ class JobCache
@cache ||= {}
result = $client.execute(:api_method => $arvados.jobs.get,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:uuid => uuid
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
@cache[uuid] = JSON.parse result.body, :symbolize_names => true
end
def self.where(conditions)
result = $client.execute(:api_method => $arvados.jobs.list,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:limit => 10000,
:where => conditions.to_json
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
list = JSON.parse result.body, :symbolize_names => true
if list and list[:items].is_a? Array
list[:items]
@@ -315,11 +323,13 @@ class JobCache
def self.create(job, create_params)
@cache ||= {}
result = $client.execute(:api_method => $arvados.jobs.create,
- :parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
+ :body => {
:job => job.to_json
}.merge(create_params),
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
j = JSON.parse result.body, :symbolize_names => true
if j.is_a? Hash and j[:uuid]
@cache[j[:uuid]] = j
@@ -348,10 +358,12 @@ class WhRunPipelineInstance
else
result = $client.execute(:api_method => $arvados.pipeline_templates.get,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:uuid => template
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
@template = JSON.parse result.body, :symbolize_names => true
if !@template[:uuid]
abort "#{$0}: fatal: failed to retrieve pipeline template #{template} #{@template[:errors].inspect rescue nil}"
diff --git a/sdk/ruby/lib/arvados.rb b/sdk/ruby/lib/arvados.rb
index 567423f..429777e 100644
--- a/sdk/ruby/lib/arvados.rb
+++ b/sdk/ruby/lib/arvados.rb
@@ -210,8 +210,6 @@ class Arvados
end
def self.api_exec(method, parameters={})
api_method = arvados_api.send(api_models_sym).send(method.name.to_sym)
- parameters = parameters.
- merge(:api_token => arvados.config['ARVADOS_API_TOKEN'])
parameters.each do |k,v|
parameters[k] = v.to_json if v.is_a? Array or v.is_a? Hash
end
@@ -230,7 +228,10 @@ class Arvados
execute(:api_method => api_method,
:authenticated => false,
:parameters => parameters,
- :body => body)
+ :body => body,
+ :headers => {
+ authorization: 'OAuth2 '+arvados.config['ARVADOS_API_TOKEN']
+ })
resp = JSON.parse result.body, :symbolize_names => true
if resp[:errors]
raise Arvados::TransactionFailedError.new(resp[:errors])
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