Medable · davideaquaro · Nov 10, 2022 · Nov 2, 2022 · Nov 4, 2022 · Nov 10, 2022
diff --git a/packages/mdctl-axon-tools/__tests__/MIG-85/MIG-85.test.js b/packages/mdctl-axon-tools/__tests__/MIG-85/MIG-85.test.js
@@ -5,8 +5,7 @@ jest.mock('@medable/mdctl-api-driver/lib/cortex.object', () => ({ Object: class
 jest.mock('../../lib/mappings')
 
 const fs = require('fs'),
-      StudyManifestTools = require('../../lib/StudyManifestTools'),
-      study = require('../../../mdctl-cli/tasks/study')
+      StudyManifestTools = require('../../lib/StudyManifestTools')
 
 describe('MIG-85 - Test partial migrations in StudyManifestTools', () => {
 
@@ -104,6 +103,13 @@ describe('MIG-85 - Test partial migrations in StudyManifestTools', () => {
                   toArray: () => entities.filter(e => e.object === 'c_task')
                 })
               })
+
8000
            },
+            object: {
+              find: () => ({
+                paths: () => ({
+                  toArray: () => [{ uniqueKey: 'c_key' }]
+                })
+              })
             }
           }
         }
@@ -227,6 +233,7 @@ describe('MIG-85 - Test partial migrations in StudyManifestTools', () => {
           ingestTransform = fs.readFileSync(`${__dirname}/../../packageScripts/ingestTransform.js`).toString()
 
     jest.spyOn(StudyManifestTools.prototype, 'getOrgObjectInfo').mockImplementation(() => dummyReferences)
+    jest.spyOn(StudyManifestTools.prototype, 'getOrgAndReferences').mockImplementation(() => ({ org, dummyReferences }))
     jest.spyOn(StudyManifestTools.prototype, 'validateReferences').mockImplementation(() => entities)
     jest.spyOn(StudyManifestTools.prototype, 'createManifest').mockImplementation(() => manifest)
     jest.spyOn(StudyManifestTools.prototype, 'getObjectIDsArray').mockImplementation(() => entities.filter(o => o.object === 'c_task'))

diff --git a/packages/mdctl-axon-tools/lib/StudyManifestTools.js b/packages/mdctl-axon-tools/lib/StudyManifestTools.js
@@ -691,7 +691,7 @@ class StudyManifestTools {
     // eslint-disable-next-line no-restricted-syntax
        for await (const key of manifestKeys) {
       // Determine whether queriying by c_study or c_key
-      const property = (study) ? 'c_study' : 'c_key',
+      const property = (study) ? 'c_study' : first((await org.objects.object.find({ name: key }).paths('uniqueKey').toArray()).map(({ uniqueKey }) => uniqueKey)),
             // Use the study ID or the entities inside the "includes" array in the manifest
             values = (study) ? [study._id] : manifestObject[key].includes
 
@@ -710,7 +710,7 @@ class StudyManifestTools {
         case 'ec__document_template': {
           // Get the eConsents ID's from the study or the manifest
           // econsent template properties are namespaced ec__, rather than c_
-          const ecProp = property === 'c_study' ? 'ec__study' : 'ec__key'
+          const ecProp = property === 'c_study' ? 'ec__study' : property
           ids = (await this.getObjectIDsArray(org, key, ecProp, values)).map(v => v._id)
           // Load the manifest for the current ID's and their dependencies
           objectAndDependencies = await this.getConsentManifestEntities(org, ids, orgReferenceProps)
@@ -730,8 +730,12 @@ class StudyManifestTools {
           objectAndDependencies = await this.getGroupManifestEntities(org, ids, orgReferenceProps)
           break
         }
-        case 'c_site':
-        case 'c_anchor_date_template': {
+        // Altough c_fault has reference to c_study it will not be included in the below list since that reference is not used
+        // If we included it c_fault will not get exported in a full study export
+        case 'c_anchor_date_template':
+        case 'c_participant_schedule':
+        case 'c_patient_flag':
+        case 'c_site': {
           pluralName = this.mapObjectNameToPlural(key)
           // These objects seem not to have dependencies so we'll load them directly
           objectAndDependencies = await this.getExportObjects(org, pluralName, { [property]: { $in: values } }, orgReferenceProps)
@@ -744,8 +748,9 @@ class StudyManifestTools {
           } catch (e) {
             pluralName = key
           }
-          // Export the entire entity (no 'where' filter) if present
-          objectAndDependencies = await this.getExportObjects(org, pluralName, null, orgReferenceProps)
+          const where = property !== 'c_study' ? { [property]: { $in: values } } : null
+          // Allow to export individual instances (if specified) or all of them
+          objectAndDependencies = await this.getExportObjects(org, pluralName, where, orgReferenceProps)
           break
         }
       }

diff --git a/packages/mdctl-cli/tasks/study.js b/packages/mdctl-cli/tasks/study.js
@@ -85,7 +85,7 @@ class Study extends Task {
     try {
       let manifestJSON
       if (manifestObj) {
-        manifestJSON = this.validateManifest(manifestObj)
+        manifestJSON = this.validateManifest(manifestObj, studyTools.getAvailableObjectNames())
       }
       const { manifest } = await studyTools.getStudyManifest(manifestJSON)
 
@@ -196,7 +196,7 @@ class Study extends Task {
 
   }
 
-  validateManifest(manifestObject) {
+  validateManifest(manifestObject, validKeys) {
     let manifestJSON
     try {
       manifestJSON = JSON.parse(manifestObject)
@@ -214,13 +214,16 @@ class Study extends Task {
       }
     }
     /*
-      Ignore any keys passed in other than Assignments and eConsents.
-      In future this will be removed but for now we will only support those 2 objects together
+      We are allowing to export only "parent" objects, i.e. objects
+      that have dependencies
     */
-    manifestJSON = _.pick(manifestJSON, ['c_task', 'ec__document_template', 'object'])
+    manifestJSON = _.pick(manifestJSON, ['object', ...validKeys])
     if (_.isEqual(manifestJSON, { object: 'manifest' })) {
-      // This means that the manifest passed does not contain Assignments or eConsents
-      throw Fault.create('kInvalidArgument', { reason: 'No Assignments or eConsents to export' })
+      // This means that the manifest passed does not contain any object to export
+      throw Fault.create('kInvalidArgument', { reason: 'Nothing to export' })
+    }
+    if (!manifestJSON.object || manifestJSON.object !== 'manifest') {
+      throw Fault.create('kInvalidArgument', { reason: 'Invalid manifest. Please make sure it contains the right key/value ("object": "manifest")' })
     }
     return manifestJSON
   }

diff --git a/packages/mdctl-cli/test/tasks/study.js b/packages/mdctl-cli/test/tasks/study.js
@@ -1,12 +1,15 @@
 // eslint-disable-next-line import/no-extraneous-dependencies
 const { assert, expect } = require('chai'),
+      { StudyManifestTools } = require('@medable/mdctl-axon-tools'),
       Study = require('../../tasks/study')
 
-let study
+let study,
+    studyManifest
 
 describe('MIG-85 - Test partial migrations in study.js module', () => {
   before(() => {
     study = new Study()
+    studyManifest = new StudyManifestTools()
   })
 
   it('Test validateManifest function - Invalid file path', () => {
@@ -45,10 +48,34 @@ describe('MIG-85 - Test partial migrations in study.js module', () => {
       .equal(res.reason, 'The manifest is not a valid JSON')
   })
 
+  it('Test validateManifest function - Invalid manifest', () => {
+    const manifest = `{
+            "c_group_task": {
+              "includes": [
+                "key-002"
+              ]
+            }
+          }`
+
+    let res
+    try {
+      res = study.validateManifest(manifest, studyManifest.getAvailableObjectNames())
+    } catch (err) {
+      res = err
+    }
+
+    assert
+      .equal(res.errCode, 'mdctl.invalidArgument.unspecified')
+    assert
+      .equal(res.code, 'kInvalidArgument')
+    assert
+      .equal(res.reason, 'Invalid manifest. Please make sure it contains the right key/value ("object": "manifest")')
+  })
+
   it('Test validateManifest function - No entities to export', () => {
     const manifest = `{
       "object": "manifest",
-      "c_group": {
+      "c_step": {
         "includes": [
           "key-014"
         ]
@@ -62,7 +89,7 @@ describe('MIG-85 - Test partial migrations in study.js module', () => {
    
     let res
     try {
-      res = study.validateManifest(manifest)
+      res = study.validateManifest(manifest, studyManifest.getAvailableObjectNames())
     } catch (err) {
       res = err
     }
@@ -72,11 +99,11 @@ describe('MIG-85 - Test partial migrations in study.js module', () => {
     assert
       .equal(res.code, 'kInvalidArgument')
     assert
-      .equal(res.reason, 'No Assignments or eConsents to export')
+      .equal(res.reason, 'Nothing to export')
 
   })
 
-  it('Test validateManifest function - Removed entities other than Assignments and eConsents', () => {
+  it('Test validateManifest function - Removed not allowed entities', () => {
     const manifest = `{
             "object": "manifest",
             "c_task": {
@@ -90,7 +117,7 @@ describe('MIG-85 - Test partial migrations in study.js module', () => {
               ]
             }
           }`,
-          res = study.validateManifest(manifest)
+          res = study.validateManifest(manifest, studyManifest.getAvailableObjectNames())
 
     expect(res)
       .to.deep.equal({