working upsert logic based on upsert plugin.

Refresh token is broken again.

frontend/src/app/models/fasten/resource_fhir.ts

@@ -1,7 +0,0 @@
-export class ResourceFhir {
-  user_id?: string
-  source_id: string
-  source_resource_type: string
-  source_resource_id: string
-  payload: any
-}

frontend/src/app/models/fasten/source.spec.ts

@@ -1,7 +0,0 @@
-import { Source } from './source';
-
-describe('Source', () => {
-  it('should create an instance', () => {
-    expect(new Source()).toBeTruthy();
-  });
-});

frontend/src/app/models/fasten/source.ts

@@ -1,26 +0,0 @@
-export class Source {
-  id?: string
-  user_id?: number
-  source_type: string
-  patient_id: string
-
-  oauth_authorization_endpoint: string
-  oauth_token_endpoint: string
-  oauth_registration_endpoint: string
-  oauth_introspection_endpoint: string
-  oauth_userinfo_endpoint: string
-  oauth_token_endpoint_auth_methods_supported: string
-
-  api_endpoint_base_url:   string
-  client_id:             string
-  redirect_uri:          string
-  scopes:               string //space seperated string
-  access_token:          string
-  refresh_token:         string
-  id_token:              string
-  expires_at:            number
-  code_challenge:        string
-  code_verifier:         string
-
-  confidential: boolean
-}

frontend/src/app/workers/source-sync.worker.ts

@@ -19,6 +19,10 @@ export class SourceSyncWorker implements DoWork<string, string> {
 
           const db = NewRepositiory(sourceSyncMessage.userIdentifier, sourceSyncMessage.encryptionKey)
           const client = NewClient(sourceSyncMessage.source.source_type, sourceSyncMessage.source)
+          //TODO: validate the FHIR version from the datasource matches the client
+          // if the source token has been refreshed, we need to store it in the DB.
+          // await db.CreateSource()
+
           console.log("!!!!!!!!!!!!!!STARTING WORKER SYNC!!!!!!!!!", sourceSyncMessage)
           return client.SyncAll(db)
             .then((resp) => {

frontend/src/lib/database/interface.ts

@@ -9,6 +9,8 @@ export interface IDatabaseDocument {
   _id?: string
   _rev?: string
   doc_type: string
+  updated_at?: string
+
   populateId(): void
   base64Id(): string
 }

frontend/src/lib/database/plugins/upsert.ts

@@ -0,0 +1,86 @@
+export class PouchdbUpsert {
+  public static upsert(db, docId, diffFun, cb?) {
+    var promise = PouchdbUpsert.upsertInner(db, docId, diffFun);
+    if (typeof cb !== 'function') {
+      return promise;
+    }
+    promise.then(function(resp) {
+      cb(null, resp);
+    }, cb);
+  };
+
+  public static putIfNotExists(db, docId, doc, cb?) {
+    if (typeof docId !== 'string') {
+      cb = doc;
+      doc = docId;
+      docId = doc._id;
+    }
+
+    var diffFun = function(existingDoc) {
+      if (existingDoc._rev) {
+        return false; // do nothing
+      }
+      return doc;
+    };
+
+    var promise = PouchdbUpsert.upsertInner(db, docId, diffFun);
+    if (typeof cb !== 'function') {
+      return promise;
+    }
+    promise.then(function(resp) {
+      cb(null, resp);
+    }, cb);
+  };
+
+  ///////////////////////////////////////////////////////////////////////////////////////
+  // private methods
+  ///////////////////////////////////////////////////////////////////////////////////////
+  // this is essentially the "update sugar" function from daleharvey/pouchdb#1388
+  // the diffFun tells us what delta to apply to the doc.  it either returns
+  // the doc, or false if it doesn't need to do an update after all
+  private static upsertInner(db, docId, diffFun) {
+    if (typeof docId !== 'string') {
+      return Promise.reject(new Error('doc id is required'));
+    }
+
+    return db.get(docId).catch(function (err) {
+      /* istanbul ignore next */
+      if (err.status !== 404) {
+        throw err;
+      }
+      return {};
+    }).then(function (doc) {
+      // the user might change the _rev, so save it for posterity
+      var docRev = doc._rev;
+      var newDoc = diffFun(doc);
+
+      if (!newDoc) {
+        // if the diffFun returns falsy, we short-circuit as
+        // an optimization
+        return { updated: false, rev: docRev, id: docId };
+      }
+
+      // users aren't allowed to modify these values,
+      // so reset them here
+      newDoc._id = docId;
+      newDoc._rev = docRev;
+      return PouchdbUpsert.tryAndPut(db, newDoc, diffFun);
+    });
+  }
+
+  private static tryAndPut(db, doc, diffFun) {
+    return db.put(doc).then((res) => {
+      return {
+        updated: true,
+        rev: res.rev,
+        id: doc._id
+      };
+    }, (err) => {
+      /* istanbul ignore next */
+      if (err.status !== 409) {
+        throw err;
+      }
+      return this.upsertInner(db, doc._id, diffFun);
+    });
+  }
+}

frontend/src/lib/database/pouchdb_repository.ts

@@ -8,8 +8,11 @@ import {Base64} from '../utils/base64';
 // PouchDB & plugins
 import * as PouchDB from 'pouchdb/dist/pouchdb';
 import * as PouchCrypto from 'crypto-pouch';
+import {PouchdbUpsert} from './plugins/upsert';
 PouchDB.plugin(PouchCrypto);
 
+
+
 // !!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!
 // most pouchdb plugins seem to fail when used in a webworker.
 // !!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!
@@ -19,6 +22,15 @@ PouchDB.plugin(PouchCrypto);
 // PouchDB.plugin(find);
 // PouchDB.debug.enable('pouchdb:find')
 
+// import * as rawUpsert from 'pouchdb-upsert';
+// const upsert: PouchDB.Plugin = (rawUpsert as any);
+// PouchDB.plugin(upsert);
+
+// import {PouchdbUpsert} from './plugins/upsert';
+// const upsert = new PouchdbUpsert()
+// console.log("typeof PouchdbUpsert",typeof upsert, upsert)
+// PouchDB.plugin(upsert.default)
+
 // YOU MUST USE globalThis not window or self.
 // YOU MUST NOT USE console.* as its not available in a webworker context
 
@@ -85,7 +97,7 @@ export class PouchdbRepository implements IDatabaseRepository {
   // Source
 
   public async CreateSource(source: Source): Promise<string> {
-    return this.createDocument(source);
+    return this.upsertDocument(source);
   }
 
   public async GetSource(source_id: string): Promise<Source> {
@@ -145,11 +157,11 @@ export class PouchdbRepository implements IDatabaseRepository {
   // Resource
 
   public async CreateResource(resource: ResourceFhir): Promise<string> {
-    return this.createDocument(resource);
+    return this.upsertDocument(resource);
   }
 
   public async CreateResources(resources: ResourceFhir[]): Promise<string[]> {
-    return this.createBulk(resources);
+    return this.upsertBulk(resources);
   }
 
   public async GetResource(resource_id: string): Promise<ResourceFhir> {
@@ -214,30 +226,80 @@ export class PouchdbRepository implements IDatabaseRepository {
     // }
   }
 
-  // create a new document. Returns a promise of the generated id.
-  protected createDocument(doc: IDatabaseDocument) : Promise<string> {
+
+  // update/insert a new document. Returns a promise of the generated id.
+  protected upsertDocument(newDoc: IDatabaseDocument) : Promise<string> {
     // make sure we always "populate" the ID for every document before submitting
-    doc.populateId()
+    newDoc.populateId()
 
     // NOTE: All friends are given the key-prefix of "friend:". This way, when we go
     // to query for friends, we can limit the scope to keys with in this key-space.
 
     return this.GetDB()
-      .then((db) => db.put(doc))
+      .then((db) => {
+        return PouchdbUpsert.upsert(db, newDoc._id, (existingDoc: IDatabaseDocument) => {
+          //diffFunc - function that takes the existing doc as input and returns an updated doc.
+          // If this diffFunc returns falsey, then the update won't be performed (as an optimization).
+          // If the document does not already exist, then {} will be the input to diffFunc.
+
+          const isExistingEmpty = Object.keys(existingDoc).length === 0
+          if(isExistingEmpty){
+            //always return new doc (and set update_at if not already set)
+            //if this is a ResourceFhir doc, see if theres a updatedDate already
+            if(newDoc.doc_type == DocType.ResourceFhir){
+              newDoc.updated_at = newDoc.updated_at || (newDoc as any).meta?.updated_at
+            }
+            newDoc.updated_at = newDoc.updated_at || (new Date().toISOString())
+            return newDoc
+          }
+
+          if(newDoc.doc_type == DocType.ResourceFhir){
+
+            //for resourceFhir docs, we only care about comparing the resource_raw content
+            const existingContent = JSON.stringify((existingDoc as ResourceFhir).resource_raw)
+            const newContent = JSON.stringify((newDoc as ResourceFhir).resource_raw)
+            if(existingContent == newContent){
+              return false //do not update
+            } else {
+              //theres a difference. Set the updated_at date if possible, otherwise use the current date
+              (newDoc as ResourceFhir).updated_at = (newDoc as any).meta?.updated_at || (new Date().toISOString())
+              return newDoc
+            }
+
+          } else if(newDoc.doc_type == DocType.Source){
+            delete existingDoc._rev
+            const existingContent = JSON.stringify(existingDoc)
+            const newContent = JSON.stringify(newDoc)
+            if(existingContent == newContent){
+              return false //do not update, content is the same for source object
+            } else {
+              //theres a difference. Set the updated_at date
+              (newDoc as Source).updated_at = (new Date().toISOString())
+              return { ...existingDoc, ...newDoc };
+            }
+
+
+          } else {
+            throw new Error("unknown doc_type, cannot diff for upsert: " + newDoc.doc_type)
+          }
+        })
+
+      })
       .then(( result ): string => {
           return( result.id );
         }
       );
   }
 
-  // create multiple documents, returns a list of generated ids
-  protected createBulk(docs: IDatabaseDocument[]): Promise<string[]> {
+  protected upsertBulk(docs: IDatabaseDocument[]): Promise<string[]> {
     return this.GetDB()
       .then((db) => {
-        return db.bulkDocs(docs.map((doc) => { doc.populateId(); return doc }))
-      })
-      .then((results): string[] => {
-        return results.map((result) => result.id)
+
+        return Promise.all(docs.map((doc) => {
+          doc.populateId();
+          return this.upsertDocument(doc)
+        }))
+
       })
   }
 
@@ -271,6 +333,44 @@ export class PouchdbRepository implements IDatabaseRepository {
       })
   }
 
+  //DEPRECATED
+  /**
+   * create multiple documents, returns a list of generated ids
+   * @deprecated
+   * @param docs
+   * @protected
+   */
+  protected createBulk(docs: IDatabaseDocument[]): Promise<string[]> {
+    return this.GetDB()
+      .then((db) => {
+        return db.bulkDocs(docs.map((doc) => { doc.populateId(); return doc }))
+      })
+      .then((results): string[] => {
+        return results.map((result) => result.id)
+      })
+  }
+
+  /**
+   * create a new document. Returns a promise of the generated id.
+   * @deprecated
+   * @param doc
+   * @protected
+   */
+  protected createDocument(doc: IDatabaseDocument) : Promise<string> {
+    // make sure we always "populate" the ID for every document before submitting
+    doc.populateId()
+
+    // NOTE: All friends are given the key-prefix of "friend:". This way, when we go
+    // to query for friends, we can limit the scope to keys with in this key-space.
+
+    return this.GetDB()
+      .then((db) => db.put(doc))
+      .then(( result ): string => {
+          return( result.id );
+        }
+      );
+  }
+
   ///////////////////////////////////////////////////////////////////////////////////////
   // Sync private/protected methods
   ///////////////////////////////////////////////////////////////////////////////////////

frontend/src/lib/models/database/resource_fhir.ts

@@ -6,9 +6,8 @@ export class ResourceFhir {
   _id?: string
   _rev?: string
   doc_type: DocType = DocType.ResourceFhir
+  updated_at?: string
 
-  created_at?: Date
-  updated_at?: Date
   source_id: string = ""
   source_resource_type: string = ""
   source_resource_id: string = ""

frontend/src/lib/models/database/source.ts

@@ -7,8 +7,9 @@ export class Source extends LighthouseSourceMetadata{
   _id?: string
   _rev?: string
   doc_type: string
-  source_type: SourceType
+  updated_at?: string
 
+  source_type: SourceType
   patient: string
   access_token:          string
   refresh_token?:         string