(require 'asdf)
(setq *load-verbose* t)
(setq *compile-verbose* t)
(push (truename "./jss") asdf::*central-registry*)
(push (truename "./owl") asdf::*central-registry*)
(push (truename "./bug") asdf::*central-registry*)
(push (truename "./patches") asdf::*central-registry*)
(push (truename "./server") asdf::*central-registry*)
(defparameter *pellet-dir* (namestring (truename "./extlib")))

(eval-when (:compile-toplevel :load-toplevel :execute)
  (asdf::oos 'asdf::load-op 'jss)
  (asdf::oos 'asdf::load-op 'owl)
  (asdf::oos 'asdf::load-op 'bug)
;  (asdf::oos 'asdf::load-op 'patches)
)

(dolist (m '("(setq *default-kb* (owl-load-combined)); generate and load ijr904+ecocyc compounds owl"
	  "(generate-sames-by-name) ; based on this, generate sameIndividual statements for same named compounds not otherwise mapped"
	  "(setq *default-kb* (owl-load-combined :recreate t)); reload including this mapping"
	  "(describe-entity \"bug:casEntry\"); describe a class"
	  "(length (collect-sames)) ; how many compounds have been mapped from one to the other database"
	     "(do-some-queries) ; show some sparql queries and results"
	 "(load \"biopax/proto/pathways-with-compounds.lisp\") show how to query pathways that a compound participates in"))
  (princ m) (terpri))

(defun load-combined ()
  (setq *default-kb* 
	(load-kb-jena 
	 (concatenate 
	  'string "file://"  
	  (namestring (truename "bug:combined.owl"))))))

(defun do-some-queries ()
  (let ((*print-case* :downcase))
    (loop for (desc query use-reasoner) in *sample-queries*
       do (format t "~&~a~%---- Query (lisp) ----" desc)
       (pprint `(sparql ',(eval-uri-reader-macro query) :use-reasoner ,use-reasoner))
       (format t "~&~%---- Query (sparql) ----~%")
       (princ (sparql-stringify query))
       (format t "~%~a~%" "---- Result ----")
       (pprint (sparql query :use-reasoner use-reasoner))
       (format t "~%~a~%" "================================================================")
       )))				

(defparameter *sample-queries*
  '(("What small molecules are associated with KEGG id C00645?"
     (:select (?mol) () 
      (?mol !bug:classifiedByKEGG ?kegg) 
      (?kegg !bug:hasID "C00645"))
     t)
    ("What small molecules have the chemical formula c6h15o9p, and what are their names, cas, kegg ids?"
     (:select (?name ?cas ?kegg ) (:distinct t)
      (?formula !bug:hasFormula "c6h15o9p")
      (?mol !bug:hasChemicalFormula ?formula)
      (?mol !bug:hasName ?name)
      (:optional (?mol !bug:definedByCAS ?casf) (?casf !bug:hasID ?cas))
      (:optional (?mol !bug:classifiedByKEGG ?keggf) (?keggf !bug:hasID ?kegg)) )
     t
     )
    ("Which pairs (only show 10) of molecules have the same name? don't use reasoner here - it has a bug"
     (:select (?mol1 ?mol2 ?name)
      (:limit 10)
      (?mol1 !bug:hasName ?name)
      (?mol2 !bug:hasName ?name)
      (:filter (not (equal ?mol1 ?mol2))))
     nil)
    ("What molecules have 3 letter names(only show 10)?"
     (:select (?mol ?name) (:limit 10)
      (?mol !bug:hasName ?name)
      (:filter (regex ?name "^...$")))
     t
     )
    ("What molecules have 3 letter names (but only show 1 if something else is sameAs?
Exercise: Why does ADP show up twice? Hint: Used the function (describe-entity uri)."
     (:select (?mol ?name) ()
      (?mol !bug:hasName ?name)
      (:filter (and (is-canonical ?mol) 
		    (regex ?name "^...$")))) t)
    ("Which pairs of small molecules are considered to be the same?"
     (:select (?mol1 ?mol2) ()
      (?mol1 !rdf:type !bug:smallMolecule)
      (?mol2 !owl:sameAs ?mol1)
      (:filter (and (is-canonical ?mol1) (not (equal ?mol1 ?mol2)))))
     :jena)
    ))