{"action":"created","issue":{"url":"https://api.github.com/repos/hail-is/hail/issues/1368","repository_url":"https://api.github.com/repos/hail-is/hail","labels_url":"https://api.github.com/repos/hail-is/hail/issues/1368/labels{/name}","comments_url":"https://api.github.com/repos/hail-is/hail/issues/1368/comments","events_url":"https://api.github.com/repos/hail-is/hail/issues/1368/events","html_url":"https://github.com/hail-is/hail/issues/1368","id":206307726,"number":1368,"title":"VariantDataset globals property not working","user":{"login":"jigold","id":1693348,"avatar_url":"https://avatars.githubusercontent.com/u/1693348?v=3","gravatar_id":"","url":"https://api.github.com/users/jigold","html_url":"https://github.com/jigold","followers_url":"https://api.github.com/users/jigold/followers","following_url":"https://api.github.com/users/jigold/following{/other_user}","gists_url":"https://api.github.com/users/jigold/gists{/gist_id}","starred_url":"https://api.github.com/users/jigold/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jigold/subscriptions","organizations_url":"https://api.github.com/users/jigold/orgs","repos_url":"https://api.github.com/users/jigold/repos","events_url":"https://api.github.com/users/jigold/events{/privacy}","received_events_url":"https://api.github.com/users/jigold/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-02-08T20:00:33Z","updated_at":"2017-02-08T21:08:14Z","closed_at":null,"body":"Issue came up on doctest branch.\r\n\r\nReproducible example:\r\n```\r\nassoc_vds = hc.import_vcf('src/test/resources/sample.vcf')\r\n  .split_multi()\r\n  .variant_qc()\r\n  .annotate_samples_expr('sa.culprit = gs.filter(g => v == Variant(\"20\", 13753124, \"A\", \"C\")).map(g => g.gt).collect()[0]')\r\n  .annotate_samples_expr('sa.pheno = rnorm(1,1) * sa.culprit')\r\n  .annotate_samples_expr('sa.cov1 = rnorm(0,1)')\r\n  .annotate_samples_expr('sa.cov2 = rnorm(0,1)')\r\n  .linreg('sa.pheno', ['sa.cov1', 'sa.cov2']).annotate_variants_expr('va.useInKinship = va.qc.AF > 0.05')\r\n\r\nkinship_vds = assoc_vds.filter_variants_expr('va.useInKinship')\r\nlmm_vds = assoc_vds.lmmreg(kinship_vds, 'sa.pheno', ['sa.cov1', 'sa.cov2'])\r\n\r\nlmm_vds.globals\r\n```\r\n\r\nError message:\r\n```\r\nFailed example:\r\n    lmm_vds.globals\r\nException raised:\r\n    Traceback (most recent call last):\r\n      File \"//anaconda/lib/python2.7/doctest.py\", line 1315, in __run\r\n        compileflags, 1) in test.globs\r\n      File \"<doctest default[1]>\", line 1, in <module>\r\n        lmm_vds.globals\r\n      File \"/Users/jigold/hail/python/hail/dataset.py\", line 1958, in globals\r\n        self._globals = self.global_schema._convert_to_py(self._jvds.globalAnnotation())\r\n      File \"/Users/jigold/hail/python/hail/type.py\", line 423, in _convert_to_py\r\n        d[f.name] = f.typ._convert_to_py(annotation.get(i))\r\n      File \"/Users/jigold/hail/python/hail/type.py\", line 423, in _convert_to_py\r\n        d[f.name] = f.typ._convert_to_py(annotation.get(i))\r\n      File \"/Users/jigold/hail/python/hail/type.py\", line 243, in _convert_to_py\r\n        lst = env.jutils.iterableToArrayList(annotation)\r\n      File \"/Users/jigold/spark-2.0.2-bin-hadoop2.7/python/lib/py4j-0.10.3-src.zip/py4j/java_gateway.py\", line 1133, in __call__\r\n        answer, self.gateway_client, self.target_id, self.name)\r\n      File \"/Users/jigold/spark-2.0.2-bin-hadoop2.7/python/pyspark/sql/utils.py\", line 63, in deco\r\n        return f(*a, **kw)\r\n      File \"/Users/jigold/spark-2.0.2-bin-hadoop2.7/python/lib/py4j-0.10.3-src.zip/py4j/protocol.py\", line 323, in get_return_value\r\n        format(target_id, \".\", name, value))\r\n    Py4JError: An error occurred while calling o155.iterableToArrayList. Trace:\r\n    py4j.Py4JException: Method iterableToArrayList([class [D]) does not exist\r\n        at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:318)\r\n        at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:326)\r\n        at py4j.Gateway.invoke(Gateway.java:272)\r\n        at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)\r\n        at py4j.commands.CallCommand.execute(CallCommand.java:79)\r\n        at py4j.GatewayConnection.run(GatewayConnection.java:214)\r\n        at java.lang.Thread.run(Thread.java:745)\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/hail-is/hail/issues/comments/278462009","html_url":"https://github.com/hail-is/hail/issues/1368#issuecomment-278462009","issue_url":"https://api.github.com/repos/hail-is/hail/issues/1368","id":278462009,"user":{"login":"johnc1231","id":13773586,"avatar_url":"https://avatars.githubusercontent.com/u/13773586?v=3","gravatar_id":"","url":"https://api.github.com/users/johnc1231","html_url":"https://github.com/johnc1231","followers_url":"https://api.github.com/users/johnc1231/followers","following_url":"https://api.github.com/users/johnc1231/following{/other_user}","gists_url":"https://api.github.com/users/johnc1231/gists{/gist_id}","starred_url":"https://api.github.com/users/johnc1231/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johnc1231/subscriptions","organizations_url":"https://api.github.com/users/johnc1231/orgs","repos_url":"https://api.github.com/users/johnc1231/repos","events_url":"https://api.github.com/users/johnc1231/events{/privacy}","received_events_url":"https://api.github.com/users/johnc1231/received_events","type":"User","site_admin":false},"created_at":"2017-02-08T21:08:14Z","updated_at":"2017-02-08T21:08:14Z","body":"Worked on this a little bit, seems to me that specifically lmmreg creates a global annotation that doesn't agree with signature. Pretty sure I've fixed it, but I'd like to ask one of you guys about it first."}}
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