{"action":"created","comment":{"url":"https://api.github.com/repos/MRN-Code/quarterback/pulls/comments/89015913","pull_request_review_id":9564457,"id":89015913,"diff_hunk":"@@ -339,10 +339,59 @@ const loadFromId = (bookshelf, query, cookie) => {\n   });\n };\n \n+const generateSourceObject = (bookshelf, query) => {\n+  const parentId = query.json._topGroup._parentId;\n+  const qryStr = 'SELECT * FROM dxdba.dx_generate_source_object_f(?);';\n+\n+  return bookshelf.knex.raw(qryStr, parentId)\n+    .then(result => {\n+      const sourceObject = {};\n+\n+      Object.keys(query.json._modalities).filter(modality => { // eslint-disable-line arrow-body-style, max-len, arrow-body-style\n+        return modality !== 'Subjects' && modality !== 'Studies';\n+      }).forEach(modality => {\n+        const sources = result.rows.filter(source => { // eslint-disable-line arrow-body-style\n+          return source.filter_type === modality;\n+        }).reduce((aggregate, source) => {\n+          /* eslint-disable no-param-reassign */\n+          const cleanSource = Object.keys(source).reduce((cleaned, key) => {\n+            const value = source[key];\n+            if (typeof value === 'string') {\n+              if (value.match(/^\\d+$/)) { // numeric\n+                cleaned[key] = parseInt(value, 10);\n+              } else { // replace \" and \\n characters\n+                cleaned[key] = value.replace(/\"/g, '&quot').replace(/\\n/g, '');\n+              }\n+            } else {\n+              cleaned[key] = value;\n+            }\n+\n+            return cleaned;\n+          }, {});\n+          /* eslint-enable no-param-reassign */\n+\n+          aggregate.push(cleanSource);\n+          return aggregate;\n+        }, []);\n+\n+        sourceObject[modality] = { sources };\n+      });\n+\n+      return sourceObject;\n+    }).catch(error => {\n+      if (error.message.includes('query string argument of EXECUTE is null')) {\n+        throw boom.badRequest('invalid request id');\n+      } else {","path":"packages/steelpenny/src/lib/controllers/dataexchange/request.js","position":46,"original_position":46,"commit_id":"eff7e1255a3044f3bbf710e0e741b791710080de","original_commit_id":"eff7e1255a3044f3bbf710e0e741b791710080de","user":{"login":"swashcap","id":1858316,"avatar_url":"https://avatars.githubusercontent.com/u/1858316?v=3","gravatar_id":"","url":"https://api.github.com/users/swashcap","html_url":"https://github.com/swashcap","followers_url":"https://api.github.com/users/swashcap/followers","following_url":"https://api.github.com/users/swashcap/following{/other_user}","gists_url":"https://api.github.com/users/swashcap/gists{/gist_id}","starred_url":"https://api.github.com/users/swashcap/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swashcap/subscriptions","organizations_url":"https://api.github.com/users/swashcap/orgs","repos_url":"https://api.github.com/users/swashcap/repos","events_url":"https://api.github.com/users/swashcap/events{/privacy}","received_events_url":"https://api.github.com/users/swashcap/received_events","type":"User","site_admin":false},"body":"You can drop the `else` here as the first `throw` will cause function execution to stop.","created_at":"2016-11-21T23:50:10Z","updated_at":"2016-11-21T23:50:13Z","html_url":"https://github.com/MRN-Code/quarterback/pull/60#discussion_r89015913","pull_request_url":"https://api.github.com/repos/MRN-Code/quarterback/pulls/60","_links":{"self":{"href":"https://api.github.com/repos/MRN-Code/quarterback/pulls/comments/89015913"},"html":{"href":"https://github.com/MRN-Code/quarterback/pull/60#discussion_r89015913"},"pull_request":{"href":"https://api.github.com/repos/MRN-Code/quarterback/pulls/60"}}},"pull_request":{"url":"https://api.github.com/repos/MRN-Code/quarterback/pulls/60","id":94401022,"html_url":"https://github.com/MRN-Code/quarterback/pull/60","diff_url":"https://github.com/MRN-Code/quarterback/pull/60.diff","patch_url":"https://github.com/MRN-Code/quarterback/pull/60.patch","issue_url":"https://api.github.com/repos/MRN-Code/quarterback/issues/60","number":60,"state":"open","locked":false,"title":"Dataexchange request generate source object","user":{"login":"mstone121","id":8356789,"avatar_url":"https://avatars.githubusercontent.com/u/8356789?v=3","gravatar_id":"","url":"https://api.github.com/users/mstone121","html_url":"https://github.com/mstone121","followers_url":"https://api.github.com/users/mstone121/followers","following_url":"https://api.github.com/users/mstone121/following{/other_user}","gists_url":"https://api.github.com/users/mstone121/gists{/gist_id}","starred_url":"https://api.github.com/users/mstone121/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mstone121/subscriptions","organizations_url":"https://api.github.com/users/mstone121/orgs","repos_url":"https://api.github.com/users/mstone121/repos","events_url":"https://api.github.com/users/mstone121/events{/privacy}","received_events_url":"https://api.github.com/users/mstone121/received_events","type":"User","site_admin":false},"body":"#### Asana\r\nhttps://app.asana.com/0/inbox/52243410440448/212331776937629/212354149102203\r\n\r\n### generateSourceObject\r\nReturns the sources for the MR and Assessment modalities. \r\n\r\nRequest:\r\n```\r\n{\r\n  \"_topGroup\": {\r\n    \"_parentId\": 5845,\r\n    \"_filters\": [\r\n      {\r\n        \"_id\": \"21779\",\r\n        \"_parentId\": 9648,\r\n        \"_attributes\": [\r\n          {\r\n            \"_attributeId\": 22,\r\n            \"_parentId\": \"21779\",\r\n            \"_optionId\": \"5720\",\r\n            \"_optionLabel\": \"MCICShare\",\r\n            \"_modalityId\": 143,\r\n            \"_attributeLabel\": \"Study Name\",\r\n            \"_attributeDescription\": \"Study Name\",\r\n            \"_options\": [\r\n              \r\n            ]\r\n          }\r\n        ],\r\n        \"_statistics\": \"1\",\r\n        \"_type\": \"Studies\",\r\n        \"_modalityId\": 143\r\n      },\r\n      {\r\n        \"_id\": \"21780\",\r\n        \"_parentId\": 9648,\r\n        \"_attributes\": [\r\n          {\r\n            \"_attributeId\": 201,\r\n            \"_parentId\": \"21780\",\r\n            \"_optionId\": \"Female\",\r\n            \"_optionLabel\": \"Female\",\r\n            \"_modalityId\": 142,\r\n            \"_attributeLabel\": \"Gender\",\r\n            \"_attributeDescription\": \"Gender\",\r\n            \"_options\": [\r\n              \r\n            ]\r\n          }\r\n        ],\r\n        \"_statistics\": \"1275\",\r\n        \"_type\": \"Subjects\",\r\n        \"_modalityId\": 142\r\n      }\r\n    ],\r\n    \"_id\": 9648,\r\n    \"_children\": [\r\n      \r\n    ],\r\n    \"_type\": \"and\"\r\n  },\r\n  \"_id\": 5845,\r\n  \"_label\": \"Untitled Request\",\r\n  \"_modalities\": {\r\n    \"MR\": {\r\n      \"id\": 1,\r\n      \"label\": \"MR\",\r\n      \"count\": 1256,\r\n      \"dx_filter_order\": 1\r\n    },\r\n    \"Assessments\": {\r\n      \"id\": 112,\r\n      \"label\": \"Assessments\",\r\n      \"count\": 61,\r\n      \"dx_filter_order\": 2\r\n    },\r\n    \"Studies\": {\r\n      \"id\": 143,\r\n      \"label\": \"Studies\",\r\n      \"count\": 1,\r\n      \"dx_filter_order\": 3\r\n    },\r\n    \"Subjects\": {\r\n      \"id\": 142,\r\n      \"label\": \"Subjects\",\r\n      \"count\": 61,\r\n      \"dx_filter_order\": 4\r\n    }\r\n  },\r\n  \"_readOnly\": false\r\n}\r\n```\r\n\r\nResponse:\r\n```\r\n{\r\n   \"result\":{\r\n      \"MR\":{\r\n         \"sources\":[\r\n            {\r\n               \"data_count\":1256,\r\n               \"subject_count\":60,\r\n               \"study_id\":5720,\r\n               \"study_label\":\"MCICShare\",\r\n               \"pi_id\":\"JLAURIELLO\",\r\n               \"preapproved_message\":null,\r\n               \"approval_user\":null,\r\n               \"filter_type\":\"MR\",\r\n               \"usage_agreement_id\":1,\r\n               \"dua_label\":\"MCIC Data Sharing and Use Agreement\",\r\n               \"dua_body\":\"\\\r\n         <b>I request access to data collected by the Mind Clinical Imaging Consortium (MCIC) for the purpose of scientific investigation, teaching or the planning of clinical research studies and agree to the following terms:</b>\\\r\n         <ul>\\\r\n            <li>1. I will receive access to de-identified data and will not attempt to establish the identity of, or attempt to contact any of the MCIC participants.</li>\\\r\n            <li>2. I will not further disclose these data beyond the uses outlined in this agreement and my data use application.</li>\\\r\n            <li>3. I will require anyone on my team who utilizes these data, or anyone with whom I share these data to comply with this data use agreement.</li>\\\r\n            <li>4. I will comply with any rules and regulations imposed by my institution and its institutional review board in requesting these data.</li>\\\r\n            <li>5. I will ensure that Investigators who utilize MCIC data use appropriate administrative, physical and technical safeguards to prevent use or disclosure of the data other than as provided for by this Agreement.</li>\\\r\n            <li>6. I will report any use or disclosure of the data not provided for by this Agreement of which I become aware within 15 days of becoming aware of such use or disclosure. Reports/disclosures should be sent via email to Jody Roberts, Director of Research and Clinical Operations at MRN, jroberts@mrn.org</li>\\\r\n         </ul>\\\r\n         <b>If I publish abstracts or manuscripts using data from MCIC, I agree to the following:</b>\\\r\n         <ul>\\\r\n            <li>7. I will cite MCIC as the source of data and the DOE funding source in the publication as space allows. Ex: &quotThe imaging data and demographic information was collected and shared by [University of Iowa, University of Minnesota, University of New Mexico, Massachusetts General Hospital] the Mind Research Network supported by the Department of Energy under Award Number DE-FG02-08ER64581.&quot</li>\\\r\n            <li>8. I will cite Gollub, RL, et al “The MCIC collection: a shared repository of multi-modal, multi-site brain image data from a clinical investigation of schizophrenia” Neuroinformatics, 2013 in all reports based on these data, as appropriate.</li>\\\r\n            <li>9. I will include language similar to the following in the methods section of my manuscripts in order to accurately acknowledge data gathering by the MCIC investigators. Depending upon the length and focus of the article, it may be appropriate to include more or less than the example below, however, inclusion of some variation of the language shown below is mandatory. &quotData used in the preparation of this work were obtained from the Mind Clinical Imaging Consortium database through the Mind Research Network (www.mrn.org). The MCIC project was supported by the Department of Energy under Award Number DE-FG02-08ER64581. MCIC is the result of efforts of co-investigators from University of Iowa, University of Minnesota, University of New Mexico, Massachusetts General Hospital.</li>\\\r\n         </ul>\\\r\n         Please select &quotI Agree&quot below and complete <a target=&quot_blank&quot href=&quothttps://docs.google.com/a/mrn.org/spreadsheet/viewform?usp=drive_web&formkey=dFFLb3JBdXFpWU02OXhXT25HV1FISVE6MQ#gid=0&quot style=&quotfont-size:18px;color:blue&quot>this form</a> to finalize your request.\\\r\n         </br></br>\\\r\n         I understand that failure to abide by these guidelines will result in termination of my privileges to access MCIC data.\",\r\n               \"already_agreed\":true\r\n            }\r\n         ]\r\n      },\r\n      \"Assessments\":{\r\n         \"sources\":[\r\n            {\r\n               \"data_count\":61,\r\n               \"subject_count\":61,\r\n               \"study_id\":5720,\r\n               \"study_label\":\"MCICShare\",\r\n               \"pi_id\":\"JLAURIELLO\",\r\n               \"preapproved_message\":null,\r\n               \"approval_user\":null,\r\n               \"filter_type\":\"Assessments\",\r\n               \"usage_agreement_id\":1,\r\n               \"dua_label\":\"MCIC Data Sharing and Use Agreement\",\r\n               \"dua_body\":\"\\\r\n         <b>I request access to data collected by the Mind Clinical Imaging Consortium (MCIC) for the purpose of scientific investigation, teaching or the planning of clinical research studies and agree to the following terms:</b>\\\r\n         <ul>\\\r\n            <li>1. I will receive access to de-identified data and will not attempt to establish the identity of, or attempt to contact any of the MCIC participants.</li>\\\r\n            <li>2. I will not further disclose these data beyond the uses outlined in this agreement and my data use application.</li>\\\r\n            <li>3. I will require anyone on my team who utilizes these data, or anyone with whom I share these data to comply with this data use agreement.</li>\\\r\n            <li>4. I will comply with any rules and regulations imposed by my institution and its institutional review board in requesting these data.</li>\\\r\n            <li>5. I will ensure that Investigators who utilize MCIC data use appropriate administrative, physical and technical safeguards to prevent use or disclosure of the data other than as provided for by this Agreement.</li>\\\r\n            <li>6. I will report any use or disclosure of the data not provided for by this Agreement of which I become aware within 15 days of becoming aware of such use or disclosure. Reports/disclosures should be sent via email to Jody Roberts, Director of Research and Clinical Operations at MRN, jroberts@mrn.org</li>\\\r\n         </ul>\\\r\n         <b>If I publish abstracts or manuscripts using data from MCIC, I agree to the following:</b>\\\r\n         <ul>\\\r\n            <li>7. I will cite MCIC as the source of data and the DOE funding source in the publication as space allows. Ex: &quotThe imaging data and demographic information was collected and shared by [University of Iowa, University of Minnesota, University of New Mexico, Massachusetts General Hospital] the Mind Research Network supported by the Department of Energy under Award Number DE-FG02-08ER64581.&quot</li>\\\r\n            <li>8. I will cite Gollub, RL, et al “The MCIC collection: a shared repository of multi-modal, multi-site brain image data from a clinical investigation of schizophrenia” Neuroinformatics, 2013 in all reports based on these data, as appropriate.</li>\\\r\n            <li>9. I will include language similar to the following in the methods section of my manuscripts in order to accurately acknowledge data gathering by the MCIC investigators. Depending upon the length and focus of the article, it may be appropriate to include more or less than the example below, however, inclusion of some variation of the language shown below is mandatory. &quotData used in the preparation of this work were obtained from the Mind Clinical Imaging Consortium database through the Mind Research Network (www.mrn.org). The MCIC project was supported by the Department of Energy under Award Number DE-FG02-08ER64581. MCIC is the result of efforts of co-investigators from University of Iowa, University of Minnesota, University of New Mexico, Massachusetts General Hospital.</li>\\\r\n         </ul>\\\r\n         Please select &quotI Agree&quot below and complete <a target=&quot_blank&quot href=&quothttps://docs.google.com/a/mrn.org/spreadsheet/viewform?usp=drive_web&formkey=dFFLb3JBdXFpWU02OXhXT25HV1FISVE6MQ#gid=0&quot style=&quotfont-size:18px;color:blue&quot>this form</a> to finalize your request.\\\r\n         </br></br>\\\r\n         I understand that failure to abide by these guidelines will result in termination of my privileges to access MCIC data.\",\r\n               \"already_agreed\":true\r\n            }\r\n         ]\r\n      }\r\n   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