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created in UpdateCbioData to call an adapter\",\n+  //  version: 1,\n+  //  data_sets: comboSampleGroupDataSets,\n+  //  value_type: group.value_type,\n+\n+    // invisible\n+  //  collaborations: [],\n+  //});\n+\n+  // star the promise chain: woohoo!\n+\n+  var self = this;\n+  var deferred = Q.defer();\n+\n+  // define up here so as to be available throughout promise chain (so that\n+  // we can skip a .then block)\n+  var geneSetGroupPath;\n+  var expressionDataPath = path.join(workDir, \"data_expression.txt\");\n+  var logPath = path.join(workDir, \"*.log\");\n+  var associated_object = {\n+    collection_name: \"SampleGroups\",\n+    mongo_id: group._id,\n+  };\n+  var form_id = this.job.args.form_id;\n+\n+  Q.all([\n+      // write mongo data to files\n+\n+      // expression data to a file for use in Limma\n+      spawnCommand(getSetting(\"genomic_expression_export\"), [\n+        \"--sample_group_id\", group._id,\n+        \"--cbio\",\n+        \"--uq-sample-labels\",\n+      ], workDir, { stdoutPath: expressionDataPath }),\n+      // phenotype file for cbio importer\n+      spawnCommand(getSetting(\"clinical_export\"), [\n+        \"--sample_group_id\",\n+        this.job.args.sample_group_id,\n+        \"--form_id\",\n+        this.job.args.form_id,\n+        \"--work-dir\",\n+\n+        workDir,\n+      ], workDir),\n+    ])\n+    .then(function (spawnResults)           {\n+      console.log(\"done writing files\");\n+\n+      _.each(spawnResults, function (result) {\n+        if (result.exitCode !== 0) {\n+          throw \"Problem writing files to disk.\";\n+        }\n+      });\n+\n+      // save the file paths... order maters for spawnResults\n+      // (the order depends on the order of `spawnCommand`s in `Q.all`)\n+      var clinicalPath = spawnResults[1].stdoutPath;\n+\n+      // run CbioImporter\n+      return spawnCommand(getSetting(\"cbio_importer_path\"), [\n+        \"-c import-study\",\n+        \"-jar\",\n+        getSetting(\"cbio_core_jar_path\"),\n+        \"-s\",\n+        workDir,\n+      ], workDir );\n+    })\n+    .then(Meteor.bindEnvironment(function (cbioImportResult) {\n+      if (cbioImportResult.exitCode !== 0) {\n+        throw \"Problem running cbio importer\";\n+      }\n+      function printError (err) {\n+         if (err) {\n+           console.log(\"error creating blob:\", err);\n+         }\n+       }\n+      var meta = { form_id: form_id, cbio_import: dataSetName};\n+      console.log('importing into cbio form', form_id, dataSetName, associated_object)\n+      Blobs2.create(cbioImportResult.stdoutPath, associated_object, meta, printError);\n+\n+     deferred.resolve(cbioImportResult);\n+   }, deferred.reject))\n+    .catch(Meteor.bindEnvironment(function (reason) {\n+\n+      deferred.reject(reason);","path":"job-runner/webapp/server/classes/UpdateCbioData.js","position":150,"original_position":150,"commit_id":"509653b163b7348020e12e47d25d3caf230474b3","original_commit_id":"509653b163b7348020e12e47d25d3caf230474b3","user":{"login":"rbaertsch","id":2261899,"avatar_url":"https://avatars.githubusercontent.com/u/2261899?v=3","gravatar_id":"","url":"https://api.github.com/users/rbaertsch","html_url":"https://github.com/rbaertsch","followers_url":"https://api.github.com/users/rbaertsch/followers","following_url":"https://api.github.com/users/rbaertsch/following{/other_user}","gists_url":"https://api.github.com/users/rbaertsch/gists{/gist_id}","starred_url":"https://api.github.com/users/rbaertsch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rbaertsch/subscriptions","organizations_url":"https://api.github.com/users/rbaertsch/orgs","repos_url":"https://api.github.com/users/rbaertsch/repos","events_url":"https://api.github.com/users/rbaertsch/events{/privacy}","received_events_url":"https://api.github.com/users/rbaertsch/received_events","type":"User","site_admin":false},"body":"For WCDT, once every three months or longer. For other datasets. Once time per dataset.  A simple UI would be nice.","created_at":"2016-11-17T22:00:47Z","updated_at":"2016-11-17T22:00:47Z","html_url":"https://github.com/UCSC-MedBook/MedBook_/pull/34#discussion_r88556736","pull_request_url":"https://api.github.com/repos/UCSC-MedBook/MedBook_/pulls/34","_links":{"self":{"href":"https://api.github.com/repos/UCSC-MedBook/MedBook_/pulls/comments/88556736"},"html":{"href":"https://github.com/UCSC-MedBook/MedBook_/pull/34#discussion_r88556736"},"pull_request":{"href":"https://api.github.com/repos/UCSC-MedBook/MedBook_/pulls/34"}}},"pull_request":{"url":"https://api.github.com/repos/UCSC-MedBook/MedBook_/pulls/34","id":93417757,"html_url":"https://github.com/UCSC-MedBook/MedBook_/pull/34","diff_url":"https://github.com/UCSC-MedBook/MedBook_/pull/34.diff","patch_url":"https://github.com/UCSC-MedBook/MedBook_/pull/34.patch","issue_url":"https://api.github.com/repos/UCSC-MedBook/MedBook_/issues/34","number":34,"state":"open","locked":false,"title":"Cbioportal automatic update 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