update

Author: niquola

.gitignore

@@ -1,2 +1,3 @@
 .cpcache
 .nrepl-port
+tmp

Makefile

@@ -1,5 +1,15 @@
+.PHONY: test
+
+ANTLR_URL = https://storage.googleapis.com/aidbox-public/antlr-4.7.2-complete.jar
+ANTLR_PATH  = $(shell echo "`pwd`/tmp/antlr.jar")
+ANTLR = java -Xmx500M -cp "${ANTLR_PATH}:$CLASSPATH" org.antlr.v4.Tool
+
 repl:
 	clj -A:test:nrepl -e "(-main)" -r
 
 test:
 	clj -A:test:runner
+
+gen-parser:
+	test -f ${ANTLR_PATH} || curl ${ANTLR_URL} > ${ANTLR_PATH}
+	cd parser && rm -rf *class *java && ${ANTLR} -visitor FHIRPath.g4 && env CLASSPATH="${ANTLR_PATH}:$CLASSPATH"  javac *.java

README.md

@@ -1,5 +1,6 @@
-{:paths ["src" "parser" "parser/antlr-4.7.2-complete.jar" "test"]
- :deps {exoscale/clj-yaml {:mvn/version "0.5.6"}}
+{:paths ["src" "parser" "test"]
+ :deps {clj-commons/clj-yaml           {:mvn/version "0.7.0"}
+        org.antlr/antlr4-runtime       {:mvn/version "4.7.2"}}
 
  :aliases
  {:nrepl
@@ -8,8 +9,9 @@
    {spyscope                      {:mvn/version "0.1.6"}
     org.clojure/clojure           {:mvn/version "1.10.0-RC4"}
     org.clojure/tools.nrepl       {:mvn/version "0.2.13"}
-    cider/cider-nrepl             {:mvn/version "0.19.0-SNAPSHOT"}
-    refactor-nrepl/refactor-nrepl {:mvn/version "2.4.0-SNAPSHOT"}}
+    cider/cider-nrepl             {:mvn/version "0.22.3"}
+    refactor-nrepl/refactor-nrepl {:mvn/version "2.4.0"}
+    zprint {:mvn/version "0.5.3"}}
    :jvm-opts ^:replace ["-XX:-OmitStackTraceInFastThrow"]}
 
   :test {:extra-paths ["test"]}

deps.edn

@@ -110,10 +110,11 @@
       `(fp-union ~@(proxy-super visitChildren ctx)))
 
     (visitExternalConstantTerm [^FHIRPathParser$ExternalConstantTermContext ctx]
-      (let [var (subs (.getText ctx) 1)
-            local-var (str "localvar-" var)]
-        ;; `(or (var-get ~(symbol local-var)))
-        `(get ~'**env ~(keyword var))))
+      (let [v (subs (.getText ctx) 1)
+            v (if (str/starts-with? v "\"")
+                (str/replace v #"\"" "")
+                v)]
+        `(get ~'**env ~(keyword v))))
 
     ;; (visitDateTimeLiteral [^FHIRPathParser$DateTimeLiteralContext ctx])
     ;; (visitDateTimePrecision [^FHIRPathParser$DateTimePrecisionContext ctx])
@@ -378,15 +379,13 @@
 (defn fp-substring [s & [i j]]
   (let [s (singl s)]
     (when (string? s)
-      (if (and i j)
-        (when (and (< i j) (let [l (count s)] (and (< -1 i l) (< -1 (+ i j) l))))
-          (subs s i (+ i j)))
-        (when (< i (count s))
-          (subs s i)))))
-  #_(try
-    
-    (catch Exception e
-      (assert false (pr-str e s i j)))))
+      (let [l (count s)]
+        (if (and i j)
+          (when (and (< -1 i l))
+            (subs s i (min l (+ i j))))
+          (when (< i l)
+            (subs s i)))))))
+
 (defn fp-startsWith [s ss]
   (let [s (singl s)]
     (when (string? s)
@@ -405,7 +404,7 @@
 (defn fp-replace [s ss r]
   (let [s (singl s)]
     (when (string? s)
-      (str/replace s ss r))))
+      (str/replace s (re-pattern ss) r))))
 
 (defn fp-matches [s ss]
   (let [s (singl s)]
@@ -434,21 +433,18 @@
   (let [ch (fp-children s)]
     (into ch (mapcat #(seqy (fp-descendants %)) ch))))
 
-(fp-descendants {:a [{:e 1 :d 20}] :b 2 :c 3})
+;; (fp-descendants {:a [{:e 1 :d 20}] :b 2 :c 3})
 
-(fp-descendants {:a [{:b 1 :c [{:d 1}]}]})
+;; (fp-descendants {:a [{:b 1 :c [{:d 1}]}]})
 
 (defn fp [expr data & [env]]
-  (if env
-    ((compile expr) data env)
-    ((compile expr) data)))
-
+  ((compile expr) data (assoc (or env {}) :context data)))
 
-(parse "Functions.coll1[0].a.take(10).where(use= 'ok').subs(1)")
-(parse "%var.a")
 
+;; (parse "Functions.coll1[0].a.take(10).where(use= 'ok').subs(1)")
+;; (parse "%var.a")
 
-(fp "%varo.a" {} {:varo {:a 1}})
+;; (fp "%varo.a" {} {:varo {:a 1}})
 
 ;; (type (fp "101.99" {}))
 

parser/FHIRPathBaseListener.class

@@ -100,7 +100,7 @@ tests:
   - desc: '** surround'
     expression: Functions.str.attr.replace('', 'x')
     disable: true
-    result: 'xtxexsxtx xsxtxrxixnxg'
+    result: 'xtxexsxtx xsxtxrxixnxgx'
 
   - desc: '5.6.7. matches(regex : string) : boolean'
 # If the input collection contains a single item of type string, the function will return true when the value matches the given regular expression. Regular expressions should function consistently, regardless of any culture- and locale-specific settings in the environment, should be case-sensitive, use 'single line' mode and allow Unicode characters.
@@ -123,7 +123,7 @@ tests:
     result: 'match string'
 
   - desc: '** replaceMatches 2'
-    expression: Functions.str.date.replace('\\b(?<month>\\d{1,2})/(?<day>\\d{1,2})/(?<year>\\d{2,4})\\b', '${day}-${month}-${year}')
+    expression: "Functions.str.date.replace('\\b(?<month>\\d{1,2})/(?<day>\\d{1,2})/(?<year>\\d{2,4})\\b', '${day}-${month}-${year}')"
     disable: true
     result: '30-11-1972'
 

parser/FHIRPathBaseVisitor.class

@@ -1,17 +1,12 @@
 tests:
-  - desc: '%resource (FHIR extension)'
-    expression: '%resource.n1'
-    result: [1]
   - desc: '%context'
     expression: '%context.n1'
-    result: [1]
-  - desc: '%context'
-    context:  'g1'
-    expression: '%context.n1'
-    result: [2]
+    result: 1
   - desc: '%ucum'
+    variables:
+      ucum: 'http://unitsofmeasure.org'
     expression: '%ucum'
-    result: ['http://unitsofmeasure.org']
+    result: 'http://unitsofmeasure.org'
   - expression: '%a - 1'
     variables:
       a: 5
@@ -24,5 +19,3 @@ tests:
 
 subject:
   n1: 1
-  g1:
-    n1: 2

parser/FHIRPathLexer.class

@@ -2,9 +2,8 @@
   (:require [fhirpath.core :as sut]
             [clj-yaml.core :as yaml]
             [clojure.test :refer :all]
-            [clojure.java.io :as io]))
-
-
+            [clojure.java.io :as io]
+            [clojure.string :as str]))
 
 (deftest basic-tests
 
@@ -45,10 +44,10 @@
 
 
 (defn load-case [path]
-  (yaml/parse-string (slurp (io/resource path))))
+  (yaml/parse-string (slurp (io/resource (str "fhirpath/" path)))))
 
 (defn do-test [path]
-  (let [data (load-case path)]
+  (let [data (load-case (str path))]
     (doseq [t (:tests data)]
       (println (:desc t))
       (println "EXPR=>" (:expression t))
@@ -172,15 +171,33 @@
   (is (= 4 (sut/fp "a.iif(b = 3, 4, 5 )" {:a {:b 3}})))
   (is (= 5 (sut/fp "a.iif(b = 3, 4, 5 )" {:a {:b 4}})))
 
+  (sut/fp "attr.substring(2, 1)" {:attr "abcdefg"})
+
+  (is (= "cdefg"
+         (sut/fp "attr.substring(2, 5555)" {:attr "abcdefg"})))
+  
+
+  (sut/fp "attr.replace('', 'x')", {:attr "abc"})
+
+  (sut/fp "attr.replace('\\b(?<month>\\d{1,2})/(?<day>\\d{1,2})/(?<year>\\d{2,4})\\b', '${day}-${month}-${year}')",
+          {:attr "11/30/1972"})
+
+
   (do-test "cases/6.6_math.yaml")
 
 
   (is (= 1 (sut/fp "%v.a" {} {:v {:a 1}})))
 
+  (sut/fp "%v.a" {} {:v {:a 1}})
+
 
   (do-test "cases/5.6_string_manipulation.yaml")
   (do-test "cases/5.7_tree_navigation.yaml")
   (do-test "cases/8_variables.yaml")
+  (do-test "cases/6.6_math.yaml")
+  ;; (do-test "cases/6.1_equality.yaml")
+
+  ;; (do-test "cases/6.5_boolean_logic.yaml")
 
   )