Error on launch: "java.lang.IllegalArgumentException: Key must be integer"

[martinodb]

Hello. I'm trying to use CSNePS, but I'm getting error messages on launch. I've tried snepsgui.sh, sneps.sh and also "lein run", with the same result. The error message is as follows:

$ ./csneps.sh 
java.lang.IllegalArgumentException: Key must be integer
 at clojure.lang.APersistentVector.assoc (APersistentVector.java:345)
    clojure.lang.APersistentVector.assoc (APersistentVector.java:18)
    clojure.lang.RT.assoc (RT.java:792)
    clojure.core$assoc__4371.invokeStatic (core.clj:191)
    clojure.core$update_in.invokeStatic (core.clj:5950)
    clojure.core$update_in.doInvoke (core.clj:5939)
    clojure.lang.RestFn.applyTo (RestFn.java:146)
    clojure.core$apply.invokeStatic (core.clj:652)
    clojure.core$update_in.invokeStatic (core.clj:5949)
    clojure.core$update_in.doInvoke (core.clj:5939)
    clojure.lang.RestFn.invoke (RestFn.java:467)
    cider_nrepl.plugin$middleware.invokeStatic (plugin.clj:54)
    cider_nrepl.plugin$middleware.invoke (plugin.clj:17)
    clojure.lang.Var.invoke (Var.java:379)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:750)
    leiningen.core.project$apply_middleware.invoke (project.clj:743)
    clojure.core.protocols$fn__6755.invokeStatic (protocols.clj:167)
    clojure.core.protocols/fn (protocols.clj:124)
    clojure.core.protocols$fn__6710$G__6705__6719.invoke (protocols.clj:19)
    clojure.core.protocols$seq_reduce.invokeStatic (protocols.clj:31)
    clojure.core.protocols$fn__6738.invokeStatic (protocols.clj:75)
    clojure.core.protocols/fn (protocols.clj:75)
    clojure.core.protocols$fn__6684$G__6679__6697.invoke (protocols.clj:13)
    clojure.core$reduce.invokeStatic (core.clj:6545)
    clojure.core$reduce.invoke (core.clj:6527)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:745)
    leiningen.core.project$apply_middleware.invoke (project.clj:743)
    leiningen.core.project$activate_middleware.invokeStatic (project.clj:777)
    leiningen.core.project$activate_middleware.invoke (project.clj:773)
    leiningen.core.project$init_project.invokeStatic (project.clj:902)
    leiningen.core.project$init_project.invoke (project.clj:892)
    leiningen.core.project$read.invokeStatic (project.clj:973)
    leiningen.core.project$read.invoke (project.clj:970)
    leiningen.core.project$read.invokeStatic (project.clj:974)
    leiningen.core.project$read.invoke (project.clj:970)
    leiningen.core.main$_main$fn__5998.invoke (main.clj:397)
    leiningen.core.main$_main.invokeStatic (main.clj:394)
    leiningen.core.main$_main.doInvoke (main.clj:391)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.lang.Var.invoke (Var.java:379)
    clojure.lang.AFn.applyToHelper (AFn.java:154)
    clojure.lang.Var.applyTo (Var.java:700)
    clojure.core$apply.invokeStatic (core.clj:646)
    clojure.main$main_opt.invokeStatic (main.clj:314)
    clojure.main$main_opt.invoke (main.clj:310)
    clojure.main$main.invokeStatic (main.clj:421)
    clojure.main$main.doInvoke (main.clj:384)
    clojure.lang.RestFn.invoke (RestFn.java:436)
    clojure.lang.Var.invoke (Var.java:388)
    clojure.lang.AFn.applyToHelper (AFn.java:160)
    clojure.lang.Var.applyTo (Var.java:700)
    clojure.main.main (main.java:37)

I'm using the latest unmodified git cloned version:

 git log
commit cfa25695fd2117a1ab71e99219b94cef49692de4
Author: Daniel R. Schlegel <drschleg@buffalo.edu>
Date:   Sat Jan 20 16:42:55 2018 -0500

    Missing channels built in cases where semtypes weren't subtypes, but were compatible, at build time.

Thanks in advance!

[digitalneoplasm]

Hmm, that actually looks like it could be a Leiningen issue - which version of it are you using? My environment is:

$ lein --version Leiningen 2.8.1 on Java 9.0.1 Java HotSpot(TM) 64-Bit Server VM

I did just notice there was an issue compiling some of the Java files on Java 9, and have pushed an update for that to my current dev branch:

https://github.com/SNePS/CSNePS/tree/semtype-objectlang

so you might try that branch too.

[martinodb]

Hey, thanks for the quick reply.

OK, this is interesting. My Leiningen version was 2.7.1 (just to clarify, I checked it was working well with some other Clojure projects, only had problems with CSNePS AFAIK), so I upgraded and now it's 2.8.1. In another project's repo, I can do a "lein --version" to check:

 $ lein --version
Leiningen 2.8.1 on Java 1.8.0_171 OpenJDK 64-Bit Server VM

(Yes, the Java version is outdated, but I updated it and still no luck. More below.)

Now when I run "lein --version" in the SNePS repo, I don't get those errors, but instead I get the following:

 lein --version
Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.

I've just checked that it happens both branches, that is in master and in semtype-objectlang.

$ lein --version
Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.
$ git branch
* master
  semtype-objectlang
$ git checkout semtype-objectlang 
M   csneps.sh
M   csnepsgui.sh
Switched to branch 'semtype-objectlang'
Your branch is up-to-date with «origin/semtype-objectlang».
 $ lein --version
Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.

Here's a desciption in the Leiningen FAQ. I guess it shouldn't happen:

https://github.com/technomancy/leiningen/blob/master/doc/FAQ.md

So, I updateted from Java 8 to Java 10, which should support Java 9 programs, then I upgraded Leiningen again, and tried it in my own Clojure projects to check that it works:

$ lein --version
Leiningen 2.8.1 on Java 10.0.1 Java HotSpot(TM) 64-Bit Server VM

I get the same result I got right after upgrading Leiningen without upgrading Java (that is, no more "Key must be integer" error, but a new warning about "insecure HTTP"):

$ lein --version
Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.Tried to use insecure HTTP repository without TLS.
This is almost certainly a mistake; however in rare cases where it's
intentional please see `lein help faq` for details.

Also checked in both branches (master and semtype-objectlang).

I'm a bit lost here. So what should I try next?

Cheers.

[digitalneoplasm]

Ah! Yes, this is something Leiningen has started doing in the name of security. Add these three lines to the beginning of the project.clj file:

(require 'cemerick.pomegranate.aether) (cemerick.pomegranate.aether/register-wagon-factory! "http" #(org.apache.maven.wagon.providers.http.HttpWagon.))

This will allow it to use plain http repositories, instead of requiring https. I believe one of the libraries I'm using refers to some artifact that is only on one of these repositories which for some reason does not use https. At some point I plan to go through and re-evaluate which of these external libraries I really want to be using... Some which are deeply integrated (like JUNG) haven't been updated in many years now.

Let me know if that does or doesn't fix it up :)

[martinodb]

OK, so now the "insecure HTTP" is gone, but we are back to the "Key must be integer" error:

$ lein --version
java.lang.IllegalArgumentException: Key must be integer
 at clojure.lang.APersistentVector.assoc (APersistentVector.java:345)
    clojure.lang.APersistentVector.assoc (APersistentVector.java:18)
    clojure.lang.RT.assoc (RT.java:792)
    clojure.core$assoc__4371.invokeStatic (core.clj:191)
    clojure.core$update_in.invokeStatic (core.clj:5950)
    clojure.core$update_in.doInvoke (core.clj:5939)
    clojure.lang.RestFn.applyTo (RestFn.java:146)
    clojure.core$apply.invokeStatic (core.clj:652)
    clojure.core$update_in.invokeStatic (core.clj:5949)
    clojure.core$update_in.doInvoke (core.clj:5939)
    clojure.lang.RestFn.invoke (RestFn.java:467)
    cider_nrepl.plugin$middleware.invokeStatic (plugin.clj:54)
    cider_nrepl.plugin$middleware.invoke (plugin.clj:17)
    clojure.lang.Var.invoke (Var.java:379)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:801)
    leiningen.core.project$apply_middleware.invoke (project.clj:794)
    clojure.core.protocols$fn__6755.invokeStatic (protocols.clj:167)
    clojure.core.protocols/fn (protocols.clj:124)
    clojure.core.protocols$fn__6710$G__6705__6719.invoke (protocols.clj:19)
    clojure.core.protocols$seq_reduce.invokeStatic (protocols.clj:31)
    clojure.core.protocols$fn__6738.invokeStatic (protocols.clj:75)
    clojure.core.protocols/fn (protocols.clj:75)
    clojure.core.protocols$fn__6684$G__6679__6697.invoke (protocols.clj:13)
    clojure.core$reduce.invokeStatic (core.clj:6545)
    clojure.core$reduce.invoke (core.clj:6527)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:796)
    leiningen.core.project$apply_middleware.invoke (project.clj:794)
    leiningen.core.project$activate_middleware.invokeStatic (project.clj:828)
    leiningen.core.project$activate_middleware.invoke (project.clj:824)
    leiningen.core.project$init_project.invokeStatic (project.clj:952)
    leiningen.core.project$init_project.invoke (project.clj:942)
    leiningen.core.project$read.invokeStatic (project.clj:1023)
    leiningen.core.project$read.invoke (project.clj:1020)
    leiningen.core.project$read.invokeStatic (project.clj:1024)
    leiningen.core.project$read.invoke (project.clj:1020)
    leiningen.core.main$_main$fn__4734.invoke (main.clj:416)
    leiningen.core.main$_main.invokeStatic (main.clj:411)
    leiningen.core.main$_main.doInvoke (main.clj:408)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.lang.Var.invoke (Var.java:379)
    clojure.lang.AFn.applyToHelper (AFn.java:154)
    clojure.lang.Var.applyTo (Var.java:700)
    clojure.core$apply.invokeStatic (core.clj:646)
    clojure.main$main_opt.invokeStatic (main.clj:314)
    clojure.main$main_opt.invoke (main.clj:310)
    clojure.main$main.invokeStatic (main.clj:421)
    clojure.main$main.doInvoke (main.clj:384)
    clojure.lang.RestFn.invoke (RestFn.java:436)
    clojure.lang.Var.invoke (Var.java:388)
    clojure.lang.AFn.applyToHelper (AFn.java:160)
    clojure.lang.Var.applyTo (Var.java:700)
    clojure.main.main (main.java:37)

As usual, I checked again that Leiningen is working, in another Clojure project:

 $ lein --version
Leiningen 2.8.1 on Java 10.0.1 Java HotSpot(TM) 64-Bit Server VM

Just to clarify, I copy-pasted the code you posted at the beginning of the project.clj file, so that now it starts like this:

(require 'cemerick.pomegranate.aether)
(cemerick.pomegranate.aether/register-wagon-factory!
"http" #(org.apache.maven.wagon.providers.http.HttpWagon.))

(defproject Sneps3-Clojure "1.0.0-SNAPSHOT"

I did this small change in both branches of my forked version of CSNePS. I tested the change on both branches. Same result.

[martinodb]

UPDATE: I found the problem! I had to remove, in my "~/.lein/profiles.clj", these two lines related to CIDER:

[cider/cider-nrepl "0.15.1"]
[refactor-nrepl "2.3.1"]

It's no big deal because I'm not using CIDER anyway. Still it would be interesting if you can confirm the issue. Maybe I can try with more recent versions of those two.

This is my "profiles.clj" once corrected:

{:user
  {:plugins [
     ;; [cider/cider-nrepl "0.15.1"]
     ;; [refactor-nrepl "2.3.1"]
     [lein-ns-dep-graph "0.2.0-SNAPSHOT"]]}
   :dependencies [
     [alembic "0.3.2"]
     [org.clojure/tools.nrepl "0.2.12"]]}

{:dev {:source-paths ["dev" "src" "test"]
         :dependencies [[org.clojure/tools.namespace "0.2.11"]]}}

Oh, one more thing, I only got it to work in the branch semtype-objectlang, not in master.

$ git branch         
* master
  semtype-objectlang
$ ./csnepsgui.sh 
Compiling 3 source files to /home/(...)/SNEPS/CSNePS-forked/CSNePS/target/classes
/home/(...)/SNEPS/CSNePS-forked/CSNePS/src/jvm/edu/buffalo/cse/sneps3/gui/ComparableTreeNode.java:23: error: no suitable method found for sort(Vector<TreeNode>)
        Collections.sort(this.children);
                   ^
    method Collections.<T#1>sort(List<T#1>) is not applicable
      (inference variable T#1 has incompatible bounds
        equality constraints: TreeNode
        upper bounds: Comparable<? super T#1>)
    method Collections.<T#2>sort(List<T#2>,Comparator<? super T#2>) is not applicable
      (cannot infer type-variable(s) T#2
        (actual and formal argument lists differ in length))
  where T#1,T#2 are type-variables:
    T#1 extends Comparable<? super T#1> declared in method <T#1>sort(List<T#1>)
    T#2 extends Object declared in method <T#2>sort(List<T#2>,Comparator<? super T#2>)
Note: /home/martin/Documentos/programming/ontology/SNEPS/CSNePS-forked/CSNePS/src/jvm/edu/buffalo/cse/sneps3/gui/JungGraphPanel.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
1 error
Compilation of Java sources(lein javac) failed.

$ git checkout semtype-objectlang 
M   csneps.sh
M   csnepsgui.sh
Switched to branch 'semtype-objectlang'
Your branch is up-to-date with 'origin/semtype-objectlang'.

$ git branch
  master
* semtype-objectlang

$ ./csnepsgui.sh 
Compiling 4 source files to /home/(...)/SNEPS/CSNePS-forked/CSNePS/target/classes
Note: /home/(...)/SNEPS/CSNePS-forked/CSNePS/src/jvm/edu/buffalo/cse/sneps3/gui/JungGraphPanel.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Knowledge Base cleared. Contexts, slots, caseframes, and semantic types reinitialized.
ba7d5881-a55f-4a76-a5b3-d85646897506

BTW, after loading the demo in snepsgui, there's a null pointer exception, but the GUI seems to still work normally. I don't know if that's expected at this stage, otherwise I can open another issue if you like.

caseframe: MinMax
    type: :Proposition
    slots:  min3
        max3

class java.lang.Exception
class java.lang.Exception
Exception The set of fillers, #{b a}, is too few for the minimum restriction (3) on the slot min3.  csneps.util/error (util.clj:202)

class java.lang.Exception
class java.lang.Exception
Exception The set of fillers, #{4 3 1 2}, is too many for the maximum restriction (3) on the slot max3.  csneps.util/error (util.clj:202)

class java.lang.NullPointerException
class java.lang.NullPointerException
NullPointerException   edu.buffalo.cse.sneps3.gui.dataaccess.Model.getDownCableset (Model.java:346)

Cheers :)

[jobez]

is there any fix to this? i would love to be able to explore this project with cider x emacs but am getting the same java.lang.IllegalArgumentException: Key must be integer

edit: an easy enough workaround to those having difficulty of 'jacking-in' with cider is to run the lein repl :headless :host localhost and just run cider-connect