Module: WorkflowRESTClient
- Defined in:
- lib/rbbt/workflow/remote/rest/get.rb,
lib/rbbt/workflow/remote/rest/adaptor.rb
Class Method Summary collapse
Instance Method Summary collapse
- #_clean ⇒ Object
- #_run_job(cache_type = :async) ⇒ Object
- #abort ⇒ Object
- #clean ⇒ Object
- #exec_job ⇒ Object
- #get ⇒ Object
- #init_job(cache_type = nil, other_params = {}) ⇒ Object
- #load ⇒ Object
- #recursive_clean ⇒ Object
- #stream_job(task_url, task_params, stream_input, cache_type = :exec) ⇒ Object
Class Method Details
.execute_job(base_url, task, task_params, cache_type) ⇒ Object
85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 |
# File 'lib/rbbt/workflow/remote/rest/adaptor.rb', line 85 def self.execute_job(base_url, task, task_params, cache_type) self.capture_exception do task_url = URI.encode(File.join(base_url, task.to_s)) sout, sin = Misc.pipe post_thread = Thread.new(Thread.current) do |parent| bl = lambda do |rok| if Net::HTTPOK === rok _url = rok["RBBT-STREAMING-JOB-URL"] @url = File.join(task_url, File.basename(_url)) if _url rok.read_body do |c,_a, _b| sin.write c end sin.close else err = StringIO.new rok.read_body do |c,_a, _b| err.write c end text = begin reader = Zlib::GzipReader.new(err) reader.read rescue err.rewind err.read end ne = @adaptor.parse_exception text case ne when String parent.raise e.class, ne when Exception parent.raise ne else parent.raise "Error in RestClient: " << rok. end end end task_params.each do |k,v| task_params[k] = v.read if IO === v end Log.debug{ "RestClient execute: #{ task_url } - #{Misc.fingerprint task_params}" } RestClient::Request.execute(:method => :post, :url => task_url, :payload => task_params, :block_response => bl) end # It seems like now response body are now decoded by Net::HTTP after 2.1 # https://github.com/rest-client/rest-client/blob/cf3e5a115bcdb8f3344aeac0e45b44d67fac1a42/history.md decode = Gem.loaded_specs["rest-client"].version < Gem::Version.create('2.1') if decode reader = Zlib::GzipReader.new(sout) res_io = Misc.open_pipe do |sin| while c = reader.read(Misc::BLOCK_SIZE) sin.write c end sin.close @done = true end ConcurrentStream.setup(res_io, :threads => [post_thread]) do @done = true @streaming = false end else ConcurrentStream.setup(sout, :threads => [post_thread]) do @done = true @streaming = false end end end end |
Instance Method Details
#_clean ⇒ Object
231 232 233 234 235 236 237 238 239 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 231 def _clean begin _restart params = {:_update => :clean} @adaptor.clean_url(url, params) if @url rescue Exception Log.exception $! end end |
#_run_job(cache_type = :async) ⇒ Object
289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 289 def _run_job(cache_type = :async) get_streams task_url = URI.encode(File.join(base_url, task.to_s)) @adaptor.__prepare_inputs_for_restclient(inputs) task_params = inputs.merge(:_cache_type => cache_type, :jobname => base_name, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json) if cache_type == :stream or cache_type == :exec and stream_input and inputs[stream_input] io = self.stream_job(task_url, task_params, stream_input, cache_type) return io else @adaptor.execute_job(base_url, task, task_params, cache_type) end end |
#abort ⇒ Object
192 193 194 195 196 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 192 def abort return self if status == :done @adaptor.get_json(@url + '?_update=abort') if @url and @name self end |
#clean ⇒ Object
241 242 243 244 245 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 241 def clean init_job _clean self end |
#exec_job ⇒ Object
187 188 189 190 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 187 def exec_job res = _run_job(:exec) load_res res, result_type == :array ? :json : result_type end |
#get ⇒ Object
166 167 168 169 170 171 172 173 174 175 176 177 178 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 166 def get params ||= {} params = params.merge(:_format => [:string, :boolean, :tsv, :annotations,:array].include?(result_type.to_sym) ? :raw : :json ) Misc.insist 3, rand(2) + 1 do begin init_job if url.nil? @adaptor.get_raw(url, params) rescue Log.exception $! raise $! end end end |
#init_job(cache_type = nil, other_params = {}) ⇒ Object
198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 198 def init_job(cache_type = nil, other_params = {}) cache_type = :asynchronous if cache_type.nil? and not @is_exec cache_type = :exec if cache_type.nil? @last_info_time = nil @done = false get_streams @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do Misc.insist do @adaptor.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type)) end end if Open.remote? @name @url = @name @name = File.basename(@name) else @url = File.join(base_url, task.to_s, @name) end self end |
#load ⇒ Object
180 181 182 183 184 185 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 180 def load params = {} join unless done? or streaming? raise get_exception if error? or aborted? load_res get end |
#recursive_clean ⇒ Object
218 219 220 221 222 223 224 225 226 227 228 229 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 218 def recursive_clean Log.warn "Not doing recursive cleans" return begin _restart params = {:_update => :recursive_clean} @adaptor.get_raw(url, params) rescue Exception Log.exception $! end self end |
#stream_job(task_url, task_params, stream_input, cache_type = :exec) ⇒ Object
247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 |
# File 'lib/rbbt/workflow/remote/rest/get.rb', line 247 def stream_job(task_url, task_params, stream_input, cache_type = :exec) require 'rbbt/util/misc/multipart_payload' WorkflowRESTClient.capture_exception do @streaming = true Log.debug{ "RestClient stream #{Process.pid}: #{ task_url } #{stream_input} #{cache_type} - #{Misc.fingerprint task_params}" } res = RbbtMutiplartPayload.issue task_url, task_params, stream_input, nil, nil, true type = res.gets out = case type.strip when "LOCATION" @url = res.gets @url.sub!(/\?.*/,'') join WorkflowRESTClient.get_raw(@url) @done = true @streaming = false when /STREAM: (.*)/ @url = $1.strip res.callback = Proc.new do Log.medium "Done streaming result from #{@url}" @done = true @streaming = false end res when "BULK" begin res.read ensure @done = true @streaming = false end else raise "What? " + type end ConcurrentStream.setup(out, :filename => @url) out end end |