pione 0.2.0 → 0.2.1

data/.gitignore

@@ -1,6 +1,6 @@
 *~
-~/input
-output*
+/input
+/output
 result
 html
 log.txt
@@ -14,3 +14,4 @@ nohup.out
 Gemfile.lock
 gems
 coverage
+.EosLog

data/History.txt

@@ -1,5 +1,11 @@
 # History
 
+## 0.2.1(2013/06/15)
+
+* Added basic/advaneced parameter.
+* Enabled to run rehearsal test.
+* Imporved test coverage.
+
 ## 0.2.0(2013/05/31)
 
 * Added initial package system.

data/Rakefile

@@ -82,7 +82,7 @@ end
 
 desc 'execute basic tests'
 task 'test' do
-  sh "bundle exec bacon -I lib -rsimplecov test/parser/spec_*.rb test/transformer/spec_*.rb test/model/spec_*.rb test/log/spec_*.rb test/location/spec_*.rb test/component/spec_*.rb test/util/spec_*.rb test/tuple/spec_*.rb test/uri-scheme/spec_*.rb test/agent/spec_logger.rb test/agent/spec_messenger.rb test/rule-handler/spec_action-handler.rb test/rule-handler/spec_update-criteria.rb test/tuple-space/spec_data-finder.rb test/system/spec_*.rb"
+  sh "bundle exec bacon -I lib -rsimplecov test/parser/spec_*.rb test/transformer/spec_*.rb test/model/spec_*.rb test/log/spec_*.rb test/location/spec_*.rb test/component/spec_*.rb test/util/spec_*.rb test/tuple/spec_*.rb test/uri-scheme/spec_*.rb test/agent/spec_logger.rb test/agent/spec_messenger.rb test/agent/spec_rule-provider.rb test/rule-handler/spec_action-handler.rb test/rule-handler/spec_flow-handler.rb test/rule-handler/spec_update-criteria.rb test/tuple-space/spec_data-finder.rb test/system/spec_*.rb test/command/spec_*.rb"
 end
 
 desc 'parser test'

data/bin/pione-broker

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneBroker.run
+Pione::Command::PioneBroker.run(ARGV)

data/bin/pione-clean

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneClean.run
+Pione::Command::PioneClean.run(ARGV)

data/bin/pione-client

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneClient.run
+Pione::Command::PioneClient.run(ARGV)

data/bin/pione-log

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneLog.run
+Pione::Command::PioneLog.run(ARGV)

data/bin/pione-relay

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneRelay.run
+Pione::Command::PioneRelay.run(ARGV)

data/bin/pione-relay-account-db

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneRelayAccountDB.run
+Pione::Command::PioneRelayAccountDB.run(ARGV)

data/bin/pione-relay-client-db

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneRelayClientDB.run
+Pione::Command::PioneRelayClientDB.run(ARGV)

data/bin/pione-syntax-checker

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneSyntaxChecker.run
+Pione::Command::PioneSyntaxChecker.run(ARGV)

data/bin/pione-task-worker

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneTaskWorker.run
+Pione::Command::PioneTaskWorker.run(ARGV)

data/bin/pione-tuple-space-provider

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneTupleSpaceProvider.run
+Pione::Command::PioneTupleSpaceProvider.run(ARGV)

data/bin/pione-tuple-space-receiver

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneTupleSpaceReceiver.run
+Pione::Command::PioneTupleSpaceReceiver.run(ARGV)

data/bin/pione-tuple-space-viewer

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneTupleSpaceViewer.run
+Pione::Command::PioneTupleSpaceViewer.run(ARGV)

data/bin/pione-val

@@ -2,4 +2,4 @@
 # -*- ruby -*-
 
 require 'pione'
-Pione::Command::PioneEval.run
+Pione::Command::PioneVal.run(ARGV)

data/example/CTFCorrection/CTFCorrection.pione

@@ -0,0 +1,78 @@
+Basic Param
+  $RESOLUTION := 3.80 # tiff2mrc -r
+  $CTF_DETERMINE_Cc := 0.7 # ctfDetermine -Cc
+  $CTF_DETERMINE_Cs := 2.1 # ctfDetermine -Cs
+End
+
+Advanced Param
+  $TIFF2MRC_m := 0
+  $TIFF2MRC_Offset := 0.0
+  $MRC_IMAGE_CENTER_Nx := 1000 # FIXME
+  $MRC_IMAGE_CENTER_Ny := 1000 # FIXME
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_MAX := 65535
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_HALF := 16384
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_m := 1
+  $MRC_DETERMINE_D := 50000
+  $MRC_DETERMINE_m := 128
+  $MRC_DETERMINE_CutLow := 0.025
+  $MRC_DETERMINE_CutHigh := 0.15
+  $MRC_DETERMINE_d := 3
+  $MRC_IMAGE_CTF_COMPENSATION_m := 1
+End
+
+Rule Main
+  input ('*.tif' or '*.mrc').all
+  output '*.ctf'.all
+Flow
+  rule Tiff2Mrc
+  rule Mrc2Cen
+  rule Cen2Nor
+  rule Nor2Fft
+  rule Fft2Ctfinfo
+  rule Ctfinfo2Ctf
+End
+
+Rule Tiff2Mrc
+  input '*.tif'
+  output '{$*}.mrc'
+Action
+  tiff2mrc -i {$I[1]} -o {$O[1]}.mrc -r {$RESOLUTION} -m {$TIFF2MRC_m} -Offset {$TIFF2MRC_Offset}
+End
+
+Rule Mrc2Cen
+  input '*.mrc'
+  output '{$*}.cen'
+Action
+  mrcImageCenterGet -i {$I[1]} -o {$O[1]} -Nx {$MRC_IMAGE_CENTER_Nx} -Ny {$MRC_IMAGE_CENTER_Ny}
+End
+
+Rule Cen2Nor
+  input '*.cen'
+  output '{$*}.nor'
+Action
+  mrcImageAbnormalValueRemove -i {$I[1]} -o {$O[1]} -u {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_MAX} {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_HALF} -m {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_m}
+End
+
+Rule Nor2Fft
+  input '*.nor'
+  output '{$*}.fft'
+Action
+  mrcImageFFT -i {$I[1]} -o {$O[1]}
+End
+
+Rule Fft2Ctfinfo
+  input '*.fft'
+  output '{$*}.ctfinfo'
+Action
+  ctfDetermine -i {$I[1]} -o {$O[1]} -D {$MRC_DETERMINE_D} -m {$MRC_DETERMINE_m} -CutLow {$MRC_DETERMINE_CutLow} -CutHigh {$MRC_DETERMINE_CutHigh} -d {$MRC_DETERMINE_d} -Cc {$CTF_DETERMINE_Cc} -Cs {$CTF_DETERMINE_Cs}
+End
+
+Rule Ctfinfo2Ctf
+  input '*.fft'
+  input '{$*}.ctfinfo'
+  output '{$*}.ctf'
+Action
+  mv {$I[2]} {$I[2]}.tmp2
+  grep .: {$I[2]}.tmp2 > {$I[2]}
+  mrcImageCTFCompensation -i {$I[1]} -info2 {$I[2]} -o {$O[1]} -m {$MRC_IMAGE_CTF_COMPENSATION_m}
+End

data/example/CTFCorrection/package.yml

@@ -0,0 +1 @@
+PackageName: CTFCorrection

data/example/HelloWorld/scenario/output/message.txt

@@ -0,0 +1 @@
+Hello, world!

data/example/LoopByTouch/LoopByTouch.pione

@@ -1,28 +1,20 @@
+param $N := 3
+
 Rule Main
   output '1' or '2' or '3'
 Flow
   rule Init
-  rule A
-  rule B
-  rule C
+  case $N
+  when 1
+    rule SingleLoop
+  when 2
+    rule PairLoop
+  when 3
+    rule TripletLoop
+  end
 End
 
 Rule Init
   output '1'.touch
 End
 
-Rule A
-  input '1'
-  output '2'.touch
-End
-
-Rule B
-  input '2'
-  output '3'.touch
-End
-
-Rule C
-  input '3'
-  output '1'.touch
-End
-

data/example/LoopByTouch/PairLoop.pione

@@ -0,0 +1,18 @@
+Rule PairLoop
+  input '1'
+  output '2'
+Flow
+  rule PairA
+  rule PairB
+End
+
+Rule PairA
+  input '1'
+  output '2'.touch
+End
+
+Rule PairB
+  input '2'
+  output '1'.touch
+End
+

data/example/LoopByTouch/SingleLoop.pione

@@ -0,0 +1,5 @@
+Rule SingleLoop
+  input '1'
+  output '1'.touch
+End
+

data/example/LoopByTouch/TripletLoop.pione

@@ -0,0 +1,24 @@
+Rule TripletLoop
+  input '1'
+  output '2' or '3'
+Flow
+  rule TripletA
+  rule TripletB
+  rule TripletC
+End
+
+Rule TripletA
+  input '1'
+  output '2'.touch
+End
+
+Rule TripletB
+  input '2'
+  output '3'.touch
+End
+
+Rule TripletC
+  input '3'
+  output '1'.touch
+End
+

data/example/SyntaxError/output_line_error.pione

@@ -0,0 +1,6 @@
+Rule ABC
+  input '*.a'
+  output ######
+Action
+cat {$I[1]} > {$O[1]}
+End

data/example/WorkflowPatterns/38_GeneralSynchronizingMerge/GeneralSynchronizingMerge.pione

@@ -0,0 +1,94 @@
+param $COND1 := true
+param $COND2 := not :: $COND1
+param $COND3 := true # processing is endless if $COND3 is true
+
+Rule Main
+  output 'o1'
+  output 'o2' or null
+Flow
+  rule Init
+  rule A
+  rule B
+  rule C
+  rule D
+  rule E
+  rule F
+End
+
+Rule Init
+  output 'i1'.touch
+End
+
+Rule A
+  input 'i1'
+  output 'p1' or 'p2'
+Flow
+  rule A1
+  rule A2
+End
+
+Rule A1
+  output 'p1'.touch
+  constraint $COND1
+End
+
+Rule A2
+  output 'p2'.touch
+  constraint $COND2
+End
+
+Rule B
+  input 'p1'
+  output 'p3'.touch
+End
+
+Rule C
+  input 'p2'
+  output 'p5'.touch
+End
+
+Rule D
+  input 'p3'
+  output 'p4'.touch
+End
+
+Rule E
+  input 'p4' or 'p5'
+  output 'o1'.touch
+End
+
+Rule F
+  input 'p1'
+  input 'p4'
+  output 'p1' or 'o2'
+Flow
+  rule Once
+  rule F1
+  rule F2
+End
+
+Rule Once
+  output 'once'.touch
+End
+
+Rule F1
+  input 'p1'
+  input 'once'
+  output 'p1'
+  constraint $COND3
+Flow
+  rule F1Touch
+End
+
+Rule F1Touch
+  input 'p1'
+  input 'once'
+  output 'p1'.touch
+  output 'once'.remove
+End
+
+Rule F2
+  output 'o2'.touch
+  constraint not :: $COND3
+End
+