Merge pull request lifeomic#1 in PHI/phi_cli from feature/PHD-417-jme…

…spath-csv to master

* commit 'f82c2c4e5c0f71ea3d1c2e87d40eae74bff2477b':
  PHD-417 restored build.sh
  PHD-417 Added --jsonLine to make line per resource output and --csv to support a json to CSV conversion via a specification with the mappings of fhir jmesPath to column mapping.
  PHD-417 Updated list to dump output per bundle rather than collect them all.

lib/cmds/fhir_cmds/list.js

@@ -5,6 +5,8 @@ const querystring = require('querystring');
 const { post, getAccount } = require('../../fhir');
 const print = require('../../print');
 const url = require('url');
+const jmespath = require('jmespath');
+const fs = require('fs');
 
 exports.command = 'list <type>';
 exports.desc = 'List FHIR resources by type <type>.';
@@ -22,13 +24,29 @@ exports.builder = yargs => {
     describe: 'Number of resources to return',
     type: 'integer',
     default: 1000
+  }).option('csv', {
+    describe: 'CSV Format Configuration file in json',
+    type: 'string'
   });
 };
 
 async function search (type, query, options) {
   const account = getAccount(options);
-  const result = [];
   const limit = options.limit;
+  const csvConfigFile = options.csv;
+
+  const csvConfig = csvConfigFile != null ? JSON.parse(fs.readFileSync(csvConfigFile, 'UTF-8')) : null;
+
+  if (csvConfig && csvConfig.header) {
+    let header = '';
+    csvConfig.fieldMaps.forEach(fieldMap => {
+      if (header.length  > 0) {
+        header = header + ',';
+      }
+      header = header + fieldMap.columnName;
+    });
+    console.log(header);
+  }
 
   if (query) {
     query.pageSize = limit;
@@ -46,22 +64,57 @@ async function search (type, query, options) {
     );
 
     const data = response.data;
-    result.push(...data.entry.map(x => x.resource));
 
-    if (result.length < limit && data.link) {
+    const results = data.entry.map(x => x.resource);
+
+    if (results.length > 0) {
+      if (csvConfig) {
+        const linesResult = formatResults(results, csvConfig, options);
+        linesResult.forEach(line => {
+          console.log(line);
+        });
+      } else {
+        results.forEach(result => print(result, options));
+      }
+    }
+
+    if (results.length < limit && data.link) {
       const next = data.link.find(x => x.relation === 'next');
       if (next) {
         const parsedUrl = url.parse(next.url, true);
         query = Object.assign(query, parsedUrl.query);
       } else {
-        return result;
+        return;
       }
     } else {
-      return result;
+      return;
     }
   }
 }
 
+function formatResults (results, csvConfig, options) {
+  const lines = [];
+  results.forEach(result => {
+    const fldD = csvConfig.fieldDelimiter;
+    const valueD = csvConfig.valueDelimiter;
+    const fields = [];
+    csvConfig.fieldMaps.forEach(fieldMap => {
+      const value = jmespath.search(result, fieldMap.jpath)
+      if ( value && value.length >0 ) {
+        fields.push(valueD + value + valueD);
+      } else {
+        fields.push('');
+      }
+    });
+    let line = '';
+    fields.forEach(field => {
+      line = line + field + fldD;
+    });
+    lines.push(line.substring(0, line.length - 1));
+  });
+  return lines;
+}
+
 exports.handler = async argv => {
   if (argv.query) {
     argv.query = querystring.parse(argv.query);
@@ -77,6 +130,5 @@ exports.handler = async argv => {
     }
   }
 
-  const result = await search(argv.type, argv.query, argv);
-  print(result, argv);
+  await search(argv.type, argv.query, argv);
 };

lib/common-yargs.js

@@ -5,6 +5,9 @@ module.exports = (yargs) => {
     .option('json', {
       describe: 'List output as JSON',
       type: 'boolean'
+    }).option('jsonLine', {
+      describe: 'List output as JSON LINE Format',
+      type: 'boolean'
     }).option('account', {
       describe: 'Override the account',
       type: 'string'

lib/print.js

@@ -5,6 +5,8 @@ const yaml = require('js-yaml');
 module.exports = function (data, options) {
   if (options.json) {
     console.log(JSON.stringify(data, null, 2));
+  } else if (options.jsonLine) {
+    console.log(JSON.stringify(data, null, 0));
   } else {
     console.log(yaml.safeDump(data));
   }

package.json

@@ -29,6 +29,7 @@
     "debug": "^3.1.0",
     "get-stdin": "^6.0.0",
     "inquirer": "^5.2.0",
+    "jmespath": "^0.15.0",
     "js-yaml": "^3.13.1",
     "jsonwebtoken": "^8.2.0",
     "lodash": "^4.17.5",