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kephale opened this issue Jun 23, 2017 · 1 comment
Open

Script parameters lead to unbound system variables in Clojure #5

kephale opened this issue Jun 23, 2017 · 1 comment

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@kephale
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kephale commented Jun 23, 2017

This Clojure script works:

(println "hello world")

This Clojure script works:

#@String name
#@output String output

(def output (str name "J"))

This Clojure script does not work:

#@String name

(println "hello world")

Throwing the following error:

[ERROR] Module threw exception
java.lang.NullPointerException
	at java.io.Writer.<init>(Writer.java:88)
	at java.io.PrintWriter.<init>(PrintWriter.java:113)
	at java.io.PrintWriter.<init>(PrintWriter.java:100)
	at clojure.lang.RT.errPrintWriter(RT.java:271)
	at clojure.lang.Namespace.warnOrFailOnReplace(Namespace.java:90)
	at clojure.lang.Namespace.intern(Namespace.java:72)
	at clojure.lang.Var.intern(Var.java:158)
	at clojure.lang.RT.var(RT.java:343)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.get(ClojureBindings.java:105)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.put(ClojureBindings.java:120)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:99)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:148)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at org.scijava.ui.swing.script.TextEditor.evalScript(TextEditor.java:2348)
	at org.scijava.ui.swing.script.TextEditor.access$1000(TextEditor.java:149)
	at org.scijava.ui.swing.script.TextEditor$20.execute(TextEditor.java:1939)
	at org.scijava.ui.swing.script.TextEditor$Executer$1.run(TextEditor.java:1751)
Caused by: java.lang.NullPointerException
	at java.io.Writer.<init>(Writer.java:88)
	at java.io.PrintWriter.<init>(PrintWriter.java:113)
	at java.io.PrintWriter.<init>(PrintWriter.java:100)
	at clojure.lang.RT.errPrintWriter(RT.java:271)
	at clojure.lang.Namespace.warnOrFailOnReplace(Namespace.java:90)
	at clojure.lang.Namespace.intern(Namespace.java:72)
	at clojure.lang.Var.intern(Var.java:158)
	at clojure.lang.RT.var(RT.java:343)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.get(ClojureBindings.java:105)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.put(ClojureBindings.java:120)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:99)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:148)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

Note that Clojure's println works by binding System.out to *out*, and # indicates the beginning of a reader macro in Clojure. The suspicion is that the # is slipping through and messing with the establishment of the user namespace in Clojure.
@ctrueden
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The following script works:

#@String myName
(println "hello world")

So the problem is specifically having a parameter called name here, I think.

Note the following warning which is emitted to the console for your first script:

WARNING: name already refers to: #'clojure.core/name in namespace: user, being replaced by: #'user/name

The issue is not that the clojure interpreter is receiving rogue # symbols, but merely that such variables are being injected into the bindings.

I started trying to debug by writing a Groovy script (it was an excuse to name a file clojure.groovy 😜 ):

#@ScriptService scriptService

// NB: \n avoids #@ parameter harvesting in the containing script.
script = """
\n#@String myName
(println "hello world")
"""

lang = scriptService.getLanguageByName("clojure")
println("clojure language = $lang")
engine = lang.getScriptEngine()
println("clojure engine = $engine")
//engine.put("myName", "Curtis")
engine.put("name, "Curtis")
//NB: Asking for the Bindings and putting there instead has the same effect:
//bindings = engine.getBindings(javax.script.ScriptContext.ENGINE_SCOPE)
//bindings.put("myName", "Curtis")
//bindings.put("name", "Curtis")
result = engine.eval(script)
println("result = " + result)

I was hoping to see that injecting such a variable directly into the bindings would have the same problem as the one above, but actually in that case I have different problems:

java.lang.RuntimeException: Reader tag must be a symbol
	at clojure.lang.LispReader$CtorReader.invoke(LispReader.java:1221)
	at clojure.lang.LispReader$DispatchReader.invoke(LispReader.java:684)
	at clojure.lang.LispReader.read(LispReader.java:263)
	at clojure.lang.LispReader.read(LispReader.java:196)
	at clojure.lang.LispReader.read(LispReader.java:190)
	at org.scijava.plugins.scripting.clojure.ClojureScriptEngine.eval(ClojureScriptEngine.java:86)
	at org.scijava.plugins.scripting.clojure.ClojureScriptEngine.eval(ClojureScriptEngine.java:63)
	at javax.script.ScriptEngine$eval$1.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at Script22.run(Script22.groovy:15)
	at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
	at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

Or with "name" instead of "myName":

java.lang.NullPointerException
	at java.io.Writer.<init>(Writer.java:88)
	at java.io.PrintWriter.<init>(PrintWriter.java:113)
	at java.io.PrintWriter.<init>(PrintWriter.java:100)
	at clojure.lang.RT.errPrintWriter(RT.java:271)
	at clojure.lang.Namespace.warnOrFailOnReplace(Namespace.java:90)
	at clojure.lang.Namespace.intern(Namespace.java:72)
	at clojure.lang.Var.intern(Var.java:158)
	at clojure.lang.RT.var(RT.java:343)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.get(ClojureBindings.java:105)
	at org.scijava.plugins.scripting.clojure.ClojureBindings.put(ClojureBindings.java:120)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:99)
	at javax.script.ScriptEngine$put.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
	at Script25.run(Script25.groovy:14)
	at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
	at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

I haven't looked at this code since last October (see commit history), so I basically completely forgot how anything works. And it is after midnight now, so I think I'll continue investigations some other day.

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@kephale @ctrueden