
(displayDuplicateRuleIds graphics2d)


(mkNSaveDishNet RKB tinyDish)

(savePNet pnet1 tinyDish.json)
(savePNet pnet3 tinySubnet.json)
(savePNet pnet5 tinyPathnet.json)

(jsonTest graphics2d)
(dnetTest graphics2d pnet1)
(pnetTest graphics2d pnet3)

(loadg2dlib graphics2d ../../PLALib/G2D/garudaIO.lsp)

(displayUnreachable RKB graphics2d)

(g2dexe graphics2d (apply  exportUniprot "graph2" "g2uniprot.txt"))

(g2dexe graphics2d (define jkb (getAttr (fetch (getAttr (fetch "graph2") "kbname")) "jkb")))
	
(g2dexe graphics2d (invoke java.lang.System.err "println" (invoke (apply graph2Xs "graph2" "bprot2hugo") "toString")))
	
(g2dexe graphics2d (invoke java.lang.System.err "println" (getAttr jkb "componentInfoSpec")))

*** what is going on
(show control)
(show requests)
(show wait4s)
(show log)
(show summary)

(reset control)
(reset wait4s)
(graphics2d OK)

(show notes qval occmap RKB)
(createDefBasicUOps RKB JSONU/locs.json LOCATIONOPS)
(createDefBasicUOps RKB JSONU/basicOps.json PROTEINOPS)
(createDefBasicUJKB JSONU RKB PROTEINOPS CHEMICALOPS GENEOPS)

(g2dexe graphics2d (apply initJKB "RKB") )
(g2dexe graphics2d (apply loadbasicjkb "RKB" "JSONU"))
(g2dexe graphics2d  (apply fixNids "RKB"))


(createDefBasicJKB JSONB RKB  PROTEINOPS CHEMICALOPS GENEOPS)
(g2dexe graphics2d (apply initJKB "RKB"))
(g2dexe graphics2d  (apply loadjkb "RKB" "JSONB"))
(g2dexe graphics2d  (apply fixNids "RKB"))


(g2dexe graphics2d (apply displayJRuleEvidence "graph2" "001.EgfR.irt.Egf"))


**** debugging 
*** dot verbosity 
(g2dexe graphics2d (supdate "g2d.graph.Dot" "dotDebug" (boolean true)))
(g2dexe graphics2d (supdate "g2d.graph.Dot" "dotDebug" (boolean false)))

**** turn on IOP/g2d VERBOSITY
 (g2dexe graphics2d (supdate "g2d.util.ActorMsg" "VERBOSE" (boolean true)))
 (g2dexe graphics2d (supdate "g2d.Main" "DEBUG" (boolean true)))

**** turn off IOP/g2d VERBOSITY
 (g2dexe graphics2d (supdate "g2d.util.ActorMsg" "VERBOSE" (boolean false)))
 (g2dexe graphics2d (supdate "g2d.Main" "DEBUG" (boolean false)))

**** saving LoLa input  (by turning on loladebug)
(g2dexe graphics2d (seq (define lolaDebug (boolean true)) (invoke java.lang.System.err "println" (concat "lolaDebug = " lolaDebug))))

**** by turning off loladebug
(g2dexe graphics2d (seq (define lolaDebug (boolean false)) (invoke java.lang.System.err "println" (concat "lolaDebug = " lolaDebug))))


**** exporting json

(g2dexe graphics2d (invoke java.lang.System.err "println" (apply exportJSON "RKB"  "JSON")))
(g2dexe graphics2d (invoke java.lang.System.err "println" (apply exportJSONgraph "graph2" "description" "JSON" "g2")))



**** testing
(g2dexe graphics2d (invoke java.lang.System.err "println" (apply printArr (getAttr (fetch "RKB") "occ-labs"))))

(g2dexe graphics2d (invoke java.lang.System.err "println" (lookup (getAttr (fetch "RKB") "jkb") "rulemap" )))

(g2dexe graphics2d (invoke java.lang.System.err "println" (lookup(invoke (lookup (getAttr (fetch "RKB") "jkb") "rulemap") "get" "001.EgfR.irt.Egf") "uname")))


**** geting the exploration history  -- replace ? by the xpnet id
(show note history tval xnet xpnet?)

**** showing bits
(show notes gval graph1)
(show note selections gval graph2)
(show entry gval graph1)
(show val gval graph1)

**** saving something
(save rasDish-net1.txt C entry tval pnet pnet1)
(save EgfDish.txt C entry gval graph5)

**** save all entries in eset.txt
(save eset.txt C eset)

**** save net of type <nettype> with id <pname> in <filename>
(save <filename> C entry tval <nettype> <pname>)

