reli.clj

(defmain through-reli
  [tmp-root pail-path ts-pail-path out-path run-key country-seq]
  (let [{:keys [s-res t-res est-end] :as est-map} (forma-run-parameters run-key)
        mk-filter (fn [vcf-path ts-src]
                    (forma/filter-query (hfs-seqfile vcf-path)
                                        (:vcf-limit est-map)
                                        ts-src))]
    (assert est-map (str run-key " is not a valid run key!"))
    (workflow [tmp-root]
              vcf-step
              ([:tmp-dirs vcf-path]
                 (?- (hfs-seqfile vcf-path)
                     (<- [?a ?b]
                         ((constrained-tap
                           pail-path "vcf" s-res "00" country-seq) ?a ?b)
                         (:distinct false))))
                            rain-step
              ([:tmp-dirs rain-path]
                 (with-job-conf {"cascading.kryo.serializations" "forma.schema.TimeSeriesValue,carbonite.PrintDupSerializer:forma.schema.FireValue,carbonite.PrintDupSerializer:forma.schema.FormaValue,carbonite.PrintDupSerializer:forma.schema.NeighborValue,carbonite.PrintDupSerializer"}
                   (?- (hfs-seqfile rain-path)
                       (mk-filter vcf-path
                                  (new-adjusted-precl-tap
                                   ts-pail-path "1000" "32" t-res country-seq)))))


  (use 'forma.hadoop.jobs.scatter)
  (in-ns 'forma.hadoop.jobs.scatter)
  (through-reli "/user/hadoop/checkpoints"
                "s3n://pailbucket/master"
                "s3n://pailbucket/series"
                "s3n://formaresults/test/adjustedseries"
                "500-16"
                [:IDN])

java.lang.RuntimeException: java.lang.RuntimeException: Unable to resolve symbol: recordCompare in this context, compiling:(forma/schema.clj:56) at cascalog.Util.tryRequire(Util.java:62) at cascalog.Util.bootSimpleFn(Util.java:66) at cascalog.Util.bootFn(Util.java:73) at cascalog.ClojureCascadingBase.prepare(ClojureCascadingBase.java:47) at cascading.flow.stream.OperatorStage.prepare(OperatorStage.java:72) at cascading.flow.stream.StreamGraph.prepare(StreamGraph.java:150) at cascading.flow.hadoop.FlowMapper.run(FlowMapper.java:93) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:441) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:377) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:396) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1059) at org.apache.hadoop.mapred.Child.main(Child.java:249) Caused by: java.lang.RuntimeException: Unable to resolve symbol: recordCompare in this context, compiling:(forma/schema.clj:56) at clojure.lang.Compiler.analyze(Compiler.java:6235) at clojure.lang.Compiler.analyze(Compiler.java:6177) at clojure.lang.Compiler$VectorExpr.parse(Compiler.java:2909) at clojure.lang.Compiler.analyze(Compiler.java:6218) at clojure.lang.Compiler.analyze(Compiler.java:6177) at clojure.lang.Compiler$VectorExpr.parse(Compiler.java:2909) at clojure.lang.Compiler.analyze(Compiler.java:6218) at clojure.lang.Compiler.analyze(Compiler.java:6177) at clojure.lang.Compiler$InvokeExpr.parse(Compiler.java:3503) at clojure.lang.Compiler.analyzeSeq(Compiler.java:6411) at clojure.lang.Compiler.analyze(Compiler.java:6216) at clojure.lang.Compiler.analyze(Compiler.java:6177) at clojure.lang.Compiler$BodyExpr$Parser.parse(Compiler.java:5572) at clojure.lang.Compiler$FnMethod.parse(Compiler.java:5008) at clojure.lang.Compiler$FnExpr.parse(Compiler.java:3629) at clojure.lang.Compiler.analyzeSeq(Compiler.java:6407) at clojure.lang.Compiler.analyze(Compiler.java:6216) at clojure.lang.Compiler.eval(Compiler.java:6462) at clojure.lang.Compiler.load(Compiler.java:6902) at clojure.lang.RT.loadResourceScript(RT.java:357) at clojure.lang.RT.loadResourceScript(RT.java:348) at clojure.lang.RT.load(RT.java:427) at clojure.lang.RT.load(RT.java:398) at clojure.core$load$fn__8285.invoke(core.clj:5386) at clojure.core$load.doInvoke(core.clj:5385) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invoke(core.clj:5200) at clojure.core$load_lib.doInvoke(core.clj:5237) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invoke(core.clj:602) at clojure.core$load_libs.doInvoke(core.clj:5271) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invoke(core.clj:602) at clojure.core$require.doInvoke(core.clj:5352) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.lang.Var.invoke(Var.java:401) at cascalog.Util.tryRequire(Util.java:52) ... 13 more Caused by: java.lang.RuntimeException: Unable to resolve symbol: recordCompare in this context at clojure.lang.Util.runtimeException(Util.java:156) at clojure.lang.Compiler.resolveIn(Compiler.java:6720) at clojure.lang.Compiler.resolve(Compiler.java:6664) at clojure.lang.Compiler.analyzeSymbol(Compiler.java:6625) at clojure.lang.Compiler.analyze(Compiler.java:6198)