def self.create(attributes)
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
:body_object => {
- :pipeline_instance => attributes.to_json
+ :pipeline_instance => attributes
},
:authenticated => false,
:headers => {
:uuid => @pi[:uuid]
},
:body_object => {
- :pipeline_instance => @attributes_to_update.to_json
+ :pipeline_instance => @attributes_to_update
},
:authenticated => false,
:headers => {
def [](x)
@pi[x]
end
+
+ def log_stderr(msg)
+ $arv.log.create log: {
+ event_type: 'stderr',
+ object_uuid: self[:uuid],
+ owner_uuid: self[:owner_uuid],
+ properties: {"text" => msg},
+ }
+ end
+
protected
def initialize(j)
@attributes_to_update = {}
end
msg += "Job submission was: #{body.to_json}"
- $client.execute(:api_method => $arvados.logs.create,
- :body_object => {
- :log => {
- :object_uuid => pipeline[:uuid],
- :event_type => 'stderr',
- :owner_uuid => pipeline[:owner_uuid],
- :properties => {"text" => msg}
- }
- },
- :authenticated => false,
- :headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
- })
+ pipeline.log_stderr(msg)
nil
end
end
if template.match /[^-0-9a-z]/
# Doesn't look like a uuid -- use it as a filename.
@template = JSON.parse File.read(template), :symbolize_names => true
- if !@template[:components]
- abort ("#{$0}: Template loaded from #{template} " +
- "does not have a \"components\" key")
- end
else
result = $client.execute(:api_method => $arvados.pipeline_templates.get,
:parameters => {
end
end
+ if not @template[:components].is_a?(Hash)
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Template missing \"components\" hash"
+ end
@components = @template[:components].dup
+ bad_components = @components.each_pair.select do |cname, cspec|
+ not cspec.is_a?(Hash)
+ end
+ if bad_components.any?
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components not specified with hashes: #{bad_components.map(&:first).join(', ')}"
+ end
+
+ bad_components = @components.each_pair.select do |cname, cspec|
+ not cspec[:script_parameters].is_a?(Hash)
+ end
+ if bad_components.any?
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components missing \"script_parameters\" hashes: #{bad_components.map(&:first).join(', ')}"
+ end
+
errors = []
@components.each do |componentname, component|
component[:script_parameters].each do |parametername, parameter|
end
def setup_instance
- if $options[:submit]
- @instance ||= PipelineInstance.
- create(:components => @components,
- :pipeline_template_uuid => @template[:uuid],
- :state => 'New')
+ if @instance
+ @instance[:properties][:run_options] ||= {}
+ if @options[:no_reuse]
+ # override properties of existing instance
+ @instance[:properties][:run_options][:enable_job_reuse] = false
+ else
+ # Default to "enable reuse" if not specified. (This code path
+ # can go away when old clients go away.)
+ if @instance[:properties][:run_options][:enable_job_reuse].nil?
+ @instance[:properties][:run_options][:enable_job_reuse] = true
+ end
+ end
else
- @instance ||= PipelineInstance.
- create(:components => @components,
- :pipeline_template_uuid => @template[:uuid],
- :state => 'RunningOnClient')
+ @instance = PipelineInstance.
+ create(components: @components,
+ properties: {
+ run_options: {
+ enable_job_reuse: !@options[:no_reuse]
+ }
+ },
+ pipeline_template_uuid: @template[:uuid],
+ state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
end
self
end
# dealing with new API servers.
:minimum_script_version => c[:minimum_script_version],
:exclude_script_versions => c[:exclude_minimum_script_versions],
- :find_or_create => !(@options[:no_reuse] || c[:nondeterministic]),
+ :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
+ !c[:nondeterministic]),
:filters => c[:filters]
})
if job
end
end
end
+
+ def abort(msg)
+ if @instance
+ if ["New", "Ready", "RunningOnClient",
+ "RunningOnServer"].include?(@instance[:state])
+ @instance[:state] = "Failed"
+ @instance.save
+ end
+ @instance.log_stderr(msg)
+ end
+ Kernel::abort(msg)
+ end
end
runner = WhRunPipelineInstance.new($options)